From 2c81b6059b6c821cd5b1822d3c80ccc956e0b57e Mon Sep 17 00:00:00 2001 From: jgart Date: Sun, 15 Aug 2021 01:45:36 -0400 Subject: [PATCH 001/171] Set default, type, and help method for engine in argparse Fixes --engine cli option not showing up --- repo2docker/__main__.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/repo2docker/__main__.py b/repo2docker/__main__.py index 1dd49ebe9..ebe3ab965 100644 --- a/repo2docker/__main__.py +++ b/repo2docker/__main__.py @@ -217,7 +217,12 @@ def get_argparser(): "--cache-from", action="append", default=[], help=Repo2Docker.cache_from.help ) - argparser.add_argument("--engine", help="Name of the container engine") + argparser.add_argument( + "--engine", + type=str, + default="docker", + help=Repo2Docker.engine.help, + ) return argparser From e9ad8fdb417ef00e0febbd8bda422b8c98b764d3 Mon Sep 17 00:00:00 2001 From: Min RK Date: Mon, 24 Oct 2022 14:30:08 +0200 Subject: [PATCH 002/171] run submodule test over https avoids assertion with file-based submodules --- tests/conftest.py | 21 +++++++++++++-------- tests/unit/contentproviders/test_git.py | 4 ++-- 2 files changed, 15 insertions(+), 10 deletions(-) diff --git a/tests/conftest.py b/tests/conftest.py index 46860ab2f..5ea3f9dc1 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -121,7 +121,7 @@ def repo_with_content(git_repo): yield git_repo, sha1 -@pytest.fixture() +@pytest.fixture def repo_with_submodule(): """Create a git repository with a git submodule in a non-master branch. @@ -134,15 +134,13 @@ def repo_with_submodule(): the submodule yet. """ - with TemporaryDirectory() as git_a_dir, TemporaryDirectory() as git_b_dir: + submodule_repo = "https://github.com/binderhub-ci-repos/requirements" + submod_sha1_b = "20c4fe55a9b2c5011d228545e821b1c7b1723652" + + with TemporaryDirectory() as git_a_dir: # create "parent" repository subprocess.check_call(["git", "init"], cwd=git_a_dir) _add_content_to_git(git_a_dir) - # create repository with 2 commits that will be the submodule - subprocess.check_call(["git", "init"], cwd=git_b_dir) - _add_content_to_git(git_b_dir) - submod_sha1_b = _get_sha1(git_b_dir) - _add_content_to_git(git_b_dir) # create a new branch in the parent without any submodule subprocess.check_call( @@ -153,7 +151,14 @@ def repo_with_submodule(): ["git", "checkout", "-b", "branch-with-submod"], cwd=git_a_dir ) subprocess.check_call( - ["git", "submodule", "add", git_b_dir, "submod"], cwd=git_a_dir + [ + "git", + "submodule", + "add", + submodule_repo, + "submod", + ], + cwd=git_a_dir, ) # checkout the first commit for the submod, not the latest subprocess.check_call( diff --git a/tests/unit/contentproviders/test_git.py b/tests/unit/contentproviders/test_git.py index 3957a95f3..65779bf6d 100644 --- a/tests/unit/contentproviders/test_git.py +++ b/tests/unit/contentproviders/test_git.py @@ -33,7 +33,7 @@ def test_submodule_clone(repo_with_submodule): pass assert os.path.exists(os.path.join(clone_dir2, "test")) - assert not os.path.exists(os.path.join(submod_dir, "test")) + assert not os.path.exists(os.path.join(submod_dir, "requirements.txt")) with TemporaryDirectory() as clone_dir: submod_dir = os.path.join(clone_dir, "submod") # set by fixture @@ -42,7 +42,7 @@ def test_submodule_clone(repo_with_submodule): for _ in git_content.fetch(spec, clone_dir): pass assert os.path.exists(os.path.join(clone_dir, "test")) - assert os.path.exists(os.path.join(submod_dir, "test")) + assert os.path.exists(os.path.join(submod_dir, "requirements.txt")) # get current sha1 of submodule cmd = ["git", "rev-parse", "HEAD"] From 0b53691786c54d3b48e65993bee6f87db090f562 Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Thu, 20 Oct 2022 18:41:17 +0200 Subject: [PATCH 003/171] refactor: rename docs/doc-requirements.txt to docs/requirements.txt --- .gitpod.yml | 2 +- docs/{doc-requirements.txt => requirements.txt} | 0 docs/source/contributing/contributing.md | 4 ++-- docs/source/contributing/tasks.md | 12 ------------ readthedocs.yml | 2 +- 5 files changed, 4 insertions(+), 16 deletions(-) rename docs/{doc-requirements.txt => requirements.txt} (100%) diff --git a/.gitpod.yml b/.gitpod.yml index f89636401..157da39ef 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -1,7 +1,7 @@ tasks: - init: | pip3 install sphinx-autobuild - pip3 install -r docs/doc-requirements.txt + pip3 install -r docs/requirements.txt pip3 install -e. command: | sphinx-autobuild docs/source/ docs/build/html/ diff --git a/docs/doc-requirements.txt b/docs/requirements.txt similarity index 100% rename from docs/doc-requirements.txt rename to docs/requirements.txt diff --git a/docs/source/contributing/contributing.md b/docs/source/contributing/contributing.md index 96859a6b1..98075dd78 100644 --- a/docs/source/contributing/contributing.md +++ b/docs/source/contributing/contributing.md @@ -126,7 +126,7 @@ python3 -m venv . source bin/activate pip3 install -e . pip3 install -r dev-requirements.txt -pip3 install -r docs/doc-requirements.txt +pip3 install -r docs/requirements.txt pip3 install black ``` @@ -187,7 +187,7 @@ Then you are good to go! If you only changed the documentation, you can also build the documentation locally using `sphinx` . ```bash -pip install -r docs/doc-requirements.txt +pip install -r docs/requirements.txt cd docs/ make html diff --git a/docs/source/contributing/tasks.md b/docs/source/contributing/tasks.md index b6602e0d0..3fe47585c 100644 --- a/docs/source/contributing/tasks.md +++ b/docs/source/contributing/tasks.md @@ -155,18 +155,6 @@ release on the [GitHub repository releases page](https://github.com/jupyterhub/r That's it! -## Keeping the Pipfile and requirements files up to date - -We now have both a `dev-requirements.txt` and a `Pifile` for repo2docker, as -such it is important to keep these in sync/up-to-date. - -Both files use `pip identifiers` so if you are updating for example the Sphinx version -in the `doc-requirements.txt` (currently `Sphinx = ">=1.4,!=1.5.4"`) you can use the -same syntax to update the Pipfile and viceversa. - -At the moment this has to be done manually so please make sure to update both -files accordingly. - # Uncommon tasks ## Compare generated Dockerfiles between repo2docker versions diff --git a/readthedocs.yml b/readthedocs.yml index 4fae81d64..4409431ea 100644 --- a/readthedocs.yml +++ b/readthedocs.yml @@ -3,4 +3,4 @@ type: sphinx python: version: 3 setup_py_install: true -requirements_file: docs/doc-requirements.txt +requirements_file: docs/requirements.txt From b4a1b50984608ef9a381da362b13f2f39732de0b Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Thu, 20 Oct 2022 18:51:17 +0200 Subject: [PATCH 004/171] Update .gitignore --- .gitignore | 180 +++++++++++++++++++++++++++++++++++++++++++++++++---- 1 file changed, 168 insertions(+), 12 deletions(-) diff --git a/.gitignore b/.gitignore index 31b06b9a6..1f6672428 100644 --- a/.gitignore +++ b/.gitignore @@ -1,23 +1,15 @@ +# Manually added parts to .gitignore +# ---------------------------------- +# .#* -dist -build *.tar.gz -*.egg-info *.py[co] -__pycache__ -MANIFEST .DS_Store -.cache -.pytest_cache -.coverage -htmlcov repo2docker/s2i ^bin/ -lib/ -lib64/ share/ include/ @@ -31,7 +23,171 @@ tests/dockerfile/legacy/root.frozen.yml generated/ test_file_text.txt - \.vscode/ tests/dockerfile_diff.sh + + +# Python .gitignore from https://github.com/github/gitignore/blob/HEAD/Python.gitignore +# ------------------------------------------------------------------------------------- +# +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class + +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ +cover/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +.pybuilder/ +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# poetry +# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control +#poetry.lock + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +#pdm.lock +# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it +# in version control. +# https://pdm.fming.dev/#use-with-ide +.pdm.toml + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ +venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ + +# PyCharm +# JetBrains specific template is maintained in a separate JetBrains.gitignore that can +# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore +# and can be added to the global gitignore or merged into this file. For a more nuclear +# option (not recommended) you can uncomment the following to ignore the entire idea folder. +#.idea/ From 9559cf2517a5bb85a897c12eedd916a486b69f67 Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Thu, 20 Oct 2022 18:51:32 +0200 Subject: [PATCH 005/171] docs: add devenv and linkcheck --- .gitpod.yml | 6 ++-- docs/Makefile | 38 +++++++++++++++------ docs/make.bat | 43 +++++++++++++++++------- docs/requirements.txt | 1 + docs/source/contributing/contributing.md | 6 ++-- 5 files changed, 65 insertions(+), 29 deletions(-) diff --git a/.gitpod.yml b/.gitpod.yml index 157da39ef..717449570 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -2,9 +2,9 @@ tasks: - init: | pip3 install sphinx-autobuild pip3 install -r docs/requirements.txt - pip3 install -e. + pip3 install -e . command: | - sphinx-autobuild docs/source/ docs/build/html/ + sphinx-autobuild docs/source/ docs/_build/html/ name: Sphinx preview ports: -- port: 8000 + - port: 8000 diff --git a/docs/Makefile b/docs/Makefile index d82ce5f94..c1a96d05b 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -1,20 +1,38 @@ -# Minimal makefile for Sphinx documentation -# +# Makefile for Sphinx documentation generated by sphinx-quickstart +# ---------------------------------------------------------------------------- -# You can set these variables from the command line. -SPHINXOPTS = -W -SPHINXBUILD = python3 -msphinx -SPHINXPROJ = repo2docker +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build SOURCEDIR = source -BUILDDIR = build +BUILDDIR = _build # Put it first so that "make" without argument is like "make help". help: - @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) .PHONY: help Makefile # Catch-all target: route all unknown targets to Sphinx using the new -# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). +# "make mode" option. %: Makefile - @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) + + +# Manually added commands +# ---------------------------------------------------------------------------- + +# For local development: +# - builds and rebuilds html on changes to source +# - starts a livereload enabled webserver and opens up a browser +devenv: + sphinx-autobuild -b html --open-browser "$(SOURCEDIR)" "$(BUILDDIR)/html" $(SPHINXOPTS) + +# For local development and CI: +# - verifies that links are valid +linkcheck: + $(SPHINXBUILD) -b linkcheck "$(SOURCEDIR)" "$(BUILDDIR)/linkcheck" $(SPHINXOPTS) + @echo + @echo "Link check complete; look for any errors in the above output " \ + "or in $(BUILDDIR)/linkcheck/output.txt." diff --git a/docs/make.bat b/docs/make.bat index e097ad9c1..b7a7c83c6 100644 --- a/docs/make.bat +++ b/docs/make.bat @@ -5,32 +5,51 @@ pushd %~dp0 REM Command file for Sphinx documentation if "%SPHINXBUILD%" == "" ( - set SPHINXBUILD=python -msphinx + set SPHINXBUILD=sphinx-build ) set SOURCEDIR=source -set BUILDDIR=build -set SPHINXPROJ=repo2docker +set BUILDDIR=_build if "%1" == "" goto help +if "%1" == "devenv" goto devenv +if "%1" == "linkcheck" goto linkcheck +goto default + +:default %SPHINXBUILD% >NUL 2>NUL if errorlevel 9009 ( echo. - echo.The Sphinx module was not found. Make sure you have Sphinx installed, - echo.then set the SPHINXBUILD environment variable to point to the full - echo.path of the 'sphinx-build' executable. Alternatively you may add the - echo.Sphinx directory to PATH. + echo.The 'sphinx-build' command was not found. Open and read README.md! + exit /b 1 +) +%SPHINXBUILD% -M %1 "%SOURCEDIR%" "%BUILDDIR%" %SPHINXOPTS% +goto end + + +:help +%SPHINXBUILD% -M help "%SOURCEDIR%" "%BUILDDIR%" %SPHINXOPTS% +goto end + + +:devenv +sphinx-autobuild >NUL 2>NUL +if errorlevel 9009 ( echo. - echo.If you don't have Sphinx installed, grab it from - echo.http://sphinx-doc.org/ + echo.The 'sphinx-autobuild' command was not found. Open and read README.md! exit /b 1 ) +sphinx-autobuild -b html --open-browser "%SOURCEDIR%" "%BUILDDIR%/html" %SPHINXOPTS% +goto end + -%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% +:linkcheck +%SPHINXBUILD% -b linkcheck "%SOURCEDIR%" "%BUILDDIR%/linkcheck" %SPHINXOPTS% +echo. +echo.Link check complete; look for any errors in the above output +echo.or in "%BUILDDIR%/linkcheck/output.txt". goto end -:help -%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% :end popd diff --git a/docs/requirements.txt b/docs/requirements.txt index e9ab5d3af..e67e8e066 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -2,3 +2,4 @@ sphinx==4.0.2 sphinxcontrib-autoprogram==0.1.7 pydata-sphinx-theme==0.6.3 myst-parser==0.15.2 +sphinx-autobuild diff --git a/docs/source/contributing/contributing.md b/docs/source/contributing/contributing.md index 98075dd78..f4f2f0a1f 100644 --- a/docs/source/contributing/contributing.md +++ b/docs/source/contributing/contributing.md @@ -184,13 +184,11 @@ Then you are good to go! ## Building the documentation locally -If you only changed the documentation, you can also build the documentation locally using `sphinx` . +You can build and inspect the result of documentation changes locally. ```bash pip install -r docs/requirements.txt cd docs/ -make html +make devenv ``` - -Then open the file `docs/build/html/index.html` in your browser. From 85919afa991aa6e9cb4f383f2adeaaf28f29326f Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Thu, 20 Oct 2022 19:00:32 +0200 Subject: [PATCH 006/171] docs: update and relax pinned requirements --- docs/requirements.txt | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index e67e8e066..5aa039db9 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,5 +1,4 @@ -sphinx==4.0.2 -sphinxcontrib-autoprogram==0.1.7 -pydata-sphinx-theme==0.6.3 -myst-parser==0.15.2 +myst-parser>=0.18 +pydata-sphinx-theme>=0.11 sphinx-autobuild +sphinxcontrib-autoprogram>=0.1.7 From 8b9b05b32c3832be00e5573b73b834a1c9daa84c Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Thu, 20 Oct 2022 19:00:50 +0200 Subject: [PATCH 007/171] docs: update readthedocs config --- .readthedocs.yaml | 19 +++++++++++++++++++ docs/source/conf.py | 6 +++++- docs/source/contributing/contributing.md | 1 + readthedocs.yml | 6 ------ 4 files changed, 25 insertions(+), 7 deletions(-) create mode 100644 .readthedocs.yaml delete mode 100644 readthedocs.yml diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 000000000..dde32e62f --- /dev/null +++ b/.readthedocs.yaml @@ -0,0 +1,19 @@ +# Configuration on how ReadTheDocs (RTD) builds our documentation +# ref: https://readthedocs.org/projects/repo2docker-service/ +# ref: https://docs.readthedocs.io/en/stable/config-file/v2.html +# +version: 2 + +sphinx: + configuration: docs/source/conf.py + +build: + os: ubuntu-22.04 + tools: + python: "3.10" + +python: + install: + - requirements: docs/requirements.txt + - method: pip + path: . diff --git a/docs/source/conf.py b/docs/source/conf.py index f9ea70a92..2847bc7cb 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -3,7 +3,11 @@ # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. -extensions = ["sphinx.ext.extlinks", "sphinxcontrib.autoprogram", "myst_parser"] +extensions = [ + "myst_parser", + "sphinx.ext.extlinks", + "sphinxcontrib.autoprogram", +] extlinks = { "issue": ("https://github.com/jupyterhub/repo2docker/issues/%s", "Issue #"), diff --git a/docs/source/contributing/contributing.md b/docs/source/contributing/contributing.md index f4f2f0a1f..23c248706 100644 --- a/docs/source/contributing/contributing.md +++ b/docs/source/contributing/contributing.md @@ -187,6 +187,7 @@ Then you are good to go! You can build and inspect the result of documentation changes locally. ```bash +pip install -e . pip install -r docs/requirements.txt cd docs/ diff --git a/readthedocs.yml b/readthedocs.yml deleted file mode 100644 index 4409431ea..000000000 --- a/readthedocs.yml +++ /dev/null @@ -1,6 +0,0 @@ -name: repo2docker -type: sphinx -python: - version: 3 - setup_py_install: true -requirements_file: docs/requirements.txt From 7ea7454049a3ba8e585f4afc60bf5a21c5646b2a Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Sat, 22 Oct 2022 12:36:52 +0200 Subject: [PATCH 008/171] docs: update conf.py --- docs/source/conf.py | 187 +++++++++++--------------------------------- 1 file changed, 44 insertions(+), 143 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 2847bc7cb..ade178ef8 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -1,42 +1,48 @@ -# -- General configuration ------------------------------------------------ +# Configuration file for Sphinx to build our documentation to HTML. +# +# Configuration reference: https://www.sphinx-doc.org/en/master/usage/configuration.html +# +import datetime -# Add any Sphinx extension module names here, as strings. They can be -# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom -# ones. + +# -- Project information ----------------------------------------------------- +# ref: https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information +# +project = "BinderHub" +copyright = f"{datetime.date.today().year}, Project Jupyter Contributors" +author = "Project Jupyter Contributors" + + +# -- General Sphinx configuration --------------------------------------------------- +# ref: https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration +# extensions = [ "myst_parser", "sphinx.ext.extlinks", "sphinxcontrib.autoprogram", ] - +root_doc = "index" +source_suffix = [".md", ".rst"] +default_role = "literal" +exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] +templates_path = ["_templates"] extlinks = { "issue": ("https://github.com/jupyterhub/repo2docker/issues/%s", "Issue #"), "pr": ("https://github.com/jupyterhub/repo2docker/pull/%s", "PR #"), "user": ("https://github.com/%s", "@"), } -# Add any paths that contain templates here, relative to this directory. -templates_path = ["_templates"] - -def setup(app): - app.add_css_file("custom.css") # may also be a URL - - -# The suffix(es) of source filenames. -# You can specify multiple suffix as a list of string: +# -- General MyST configuration ----------------------------------------------------- +# ref: https://myst-parser.readthedocs.io/en/latest/configuration.html # -# source_suffix = ['.rst', '.md'] -source_suffix = [".rst", ".md"] - -# The root toctree document. -root_doc = master_doc = "index" +myst_enable_extensions = [ + "colon_fence", +] -# General information about the project. -project = "repo2docker" -copyright = "2019, Project Jupyter" -author = "Project Jupyter" +# -- Referenceable variables -------------------------------------------------- +# # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. @@ -59,130 +65,25 @@ def setup(app): default_python=default_python ) -# The language for content autogenerated by Sphinx. Refer to documentation -# for a list of supported languages. -# -# This is also used if you do content translation via gettext catalogs. -# Usually you set "language" from the command line for these cases. -language = None - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -# This patterns also effect to html_static_path and html_extra_path -exclude_patterns = [] - -# The name of the Pygments (syntax highlighting) style to use. -pygments_style = "sphinx" - -# If true, `todo` and `todoList` produce output, else they produce nothing. -todo_include_todos = False - -# MyST configuration - -myst_enable_extensions = [ - "colon_fence", -] - -# -- Options for HTML output ---------------------------------------------- - -# The theme to use for HTML and HTML Help pages. See the documentation for -# a list of builtin themes. +# -- Options for HTML output ------------------------------------------------- +# ref: https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output # -html_theme = "pydata_sphinx_theme" html_logo = "_static/images/logo.png" html_favicon = "_static/images/favicon.ico" - -# Theme options are theme-specific and customize the look and feel of a theme -# further. For a list of options available for each theme, see the -# documentation. -# -# html_theme_options = {} - -# Add any paths that contain custom static files (such as style sheets) here, -# relative to this directory. They are copied after the builtin static files, -# so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ["_static"] -html_sidebars = {} - -# -- Options for HTMLHelp output ------------------------------------------ - -# Output file base name for HTML help builder. -htmlhelp_basename = "repo2dockerdoc" +html_css_files = ["custom.css"] - -# -- Options for LaTeX output --------------------------------------------- - -latex_elements = { - # The paper size ('letterpaper' or 'a4paper'). - # - # 'papersize': 'letterpaper', - # The font size ('10pt', '11pt' or '12pt'). - # - # 'pointsize': '10pt', - # Additional stuff for the LaTeX preamble. - # - # 'preamble': '', - # Latex figure (float) alignment - # - # 'figure_align': 'htbp', +# pydata_sphinx_theme reference: https://pydata-sphinx-theme.readthedocs.io/en/latest/ +html_theme = "pydata_sphinx_theme" +html_theme_options = { + "use_edit_page_button": True, + "github_url": "https://github.com/jupyterhub/repo2docker", + "twitter_url": "https://twitter.com/mybinderteam", +} +html_context = { + "github_user": "jupyterhub", + "github_repo": "repo2docker", + "github_version": "main", + "doc_path": "docs/source", } - -# Grouping the document tree into LaTeX files. List of tuples -# (source start file, target name, title, -# author, documentclass [howto, manual, or own class]). -latex_documents = [ - ( - master_doc, - "repo2docker.tex", - "repo2docker Documentation", - "Project Jupyter", - "manual", - ) -] - - -# -- Options for manual page output --------------------------------------- - -# One entry per manual page. List of tuples -# (source start file, name, description, authors, manual section). -man_pages = [(master_doc, "repo2docker", "repo2docker Documentation", [author], 1)] - - -# -- Options for Texinfo output ------------------------------------------- - -# Grouping the document tree into Texinfo files. List of tuples -# (source start file, target name, title, author, -# dir menu entry, description, category) -texinfo_documents = [ - ( - master_doc, - "repo2docker", - "repo2docker Documentation", - author, - "repo2docker", - "One line description of project.", - "Miscellaneous", - ) -] - - -# -- Options for Epub output ---------------------------------------------- - -# Bibliographic Dublin Core info. -epub_title = project -epub_author = author -epub_publisher = author -epub_copyright = copyright - -# The unique identifier of the text. This can be a ISBN number -# or the project homepage. -# -# epub_identifier = '' - -# A unique identification for the text. -# -# epub_uid = '' - -# A list of files that should not be packed into the epub file. -epub_exclude_files = ["search.html"] From 7ffeae734abd18de127e9f2ad1b1814c754422f7 Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Sat, 22 Oct 2022 12:39:40 +0200 Subject: [PATCH 009/171] docs: add copybutton, opengraph, rediraffe --- docs/requirements.txt | 3 +++ docs/source/conf.py | 43 +++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 46 insertions(+) diff --git a/docs/requirements.txt b/docs/requirements.txt index 5aa039db9..5c38c561a 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,4 +1,7 @@ myst-parser>=0.18 pydata-sphinx-theme>=0.11 sphinx-autobuild +sphinx-copybutton sphinxcontrib-autoprogram>=0.1.7 +sphinxext-opengraph +sphinxext-rediraffe diff --git a/docs/source/conf.py b/docs/source/conf.py index ade178ef8..fc2aec098 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -18,8 +18,11 @@ # extensions = [ "myst_parser", + "sphinx_copybutton", "sphinx.ext.extlinks", "sphinxcontrib.autoprogram", + "sphinxext.opengraph", + "sphinxext.rediraffe", ] root_doc = "index" source_suffix = [".md", ".rst"] @@ -87,3 +90,43 @@ "github_version": "main", "doc_path": "docs/source", } + + +# -- Options for linkcheck builder ------------------------------------------- +# ref: https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-the-linkcheck-builder +# +linkcheck_ignore = [ + r"(.*)github\.com(.*)#", # javascript based anchors + r"(.*)/#%21(.*)/(.*)", # /#!forum/jupyter - encoded anchor edge case + r"https://github.com/[^/]*$", # too many github usernames / searches in changelog + "https://github.com/jupyterhub/repo2docker/pull/", # too many PRs in changelog + "https://github.com/jupyterhub/repo2docker/compare/", # too many comparisons in changelog +] +linkcheck_anchors_ignore = [ + "/#!", + "/#%21", +] + + +# -- Options for the opengraph extension ------------------------------------- +# ref: https://github.com/wpilibsuite/sphinxext-opengraph#options +# +# This extension help others provide better thumbnails and link descriptions +# when they link to this documentation from other websites, such as +# https://discourse.jupyter.org. +# +# ogp_site_url is set automatically by RTD +ogp_image = "_static/images/logo.png" +ogp_use_first_image = True + + +# -- Options for the rediraffe extension ------------------------------------- +# ref: https://github.com/wpilibsuite/sphinxext-rediraffe#readme +# +# This extensions help us relocated content without breaking links. If a +# document is moved internally, we should configure a redirect like below. +# +rediraffe_branch = "main" +rediraffe_redirects = { + # "old-file": "new-folder/new-file-name", +} From 59a9663fbdb98eab2f88dc71d7de45388af1ea76 Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Sat, 22 Oct 2022 12:45:00 +0200 Subject: [PATCH 010/171] docs: fix link warnings --- docs/source/changelog.rst | 16 ++++++++-------- docs/source/contributing/contributing.md | 4 +++- 2 files changed, 11 insertions(+), 9 deletions(-) diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst index b34506d1e..23a4ed9d6 100644 --- a/docs/source/changelog.rst +++ b/docs/source/changelog.rst @@ -5,7 +5,7 @@ Changelog Version 2022.10.0 ================= -`Full changelog `_ +`Full changelog `__ New features ------------ @@ -61,7 +61,7 @@ Other merged PRs Version 2022.02.0 ================= -`Full changelog `_ +`Full changelog `__ New features ------------ @@ -77,7 +77,7 @@ New features - Set labels when building image from Dockerfile :pr:`1097` by :user:`TimoRoth` - jupyterlab 3.1.17 :pr:`1092` by :user:`minrk` - Bump JupyterLab to 3.1.11 :pr:`1081` by :user:`choldgraf` -- Bootstrap base env with micromamba :pr:`1062` by :user:`wolfv ` +- Bootstrap base env with micromamba :pr:`1062` by :user:`wolfv` - Default UI to JupyterLab :pr:`1035` by :user:`SylvainCorlay` API changes @@ -111,7 +111,7 @@ Other merged PRs Version 2021.08.0 ================= -`Full changelog `_ +`Full changelog `__ The repo2docker container image has moved to `quay.io/jupyterhub/repo2docker `_ @@ -157,14 +157,14 @@ Other merged PRs Version 2021.03.0 ================= -`Full changelog `_ +`Full changelog `__ New features ------------ - freeze with mamba, add 3.9 :pr:`1017` by :user:`minrk` - Add GH workflow to push releases to PYPi and introduce CalVer :pr:`1004` by :user:`betatim` -- Add entrypoint script which automatically propagates *_PROXY env vars… :pr:`1003` ([@g-braeunlich](https://github.com/g-braeunlich)) +- Add entrypoint script which automatically propagates \*_PROXY env vars… :pr:`1003` ([@g-braeunlich](https://github.com/g-braeunlich)) - Update to JupyterLab 3.0 :pr:`996` by :user:`jtpio` - Fetch available Julia versions from hosted json :pr:`994` by :user:`tomyun` - Add a contentprovider for Software Heritage persistent ID (SWHID) :pr:`988` by :user:`douardda` @@ -178,7 +178,7 @@ Bug fixes --------- - fix dataverse regression introduced in last release :pr:`1011` by :user:`MridulS` -- buildpacks.r: dont use apt-key directly to respect *_proxy env vars :pr:`1019` ([@g-braeunlich](https://github.com/g-braeunlich)) +- buildpacks.r: dont use apt-key directly to respect \*_proxy env vars :pr:`1019` ([@g-braeunlich](https://github.com/g-braeunlich)) Other merged PRs ---------------- @@ -193,7 +193,7 @@ Other merged PRs Version 2021.01.0 ================= -`Full changelog `_ +`Full changelog `__ New features ------------ diff --git a/docs/source/contributing/contributing.md b/docs/source/contributing/contributing.md index 23c248706..7d101dfe6 100644 --- a/docs/source/contributing/contributing.md +++ b/docs/source/contributing/contributing.md @@ -60,7 +60,7 @@ This outlines the process for getting changes to the repo2docker project merged. Getting consensus with the community is a great way to save time later. 3. Make edits in [your fork](https://help.github.com/en/articles/fork-a-repo) of the [repo2docker repository](https://github.com/jupyterhub/repo2docker). 4. Make a [pull request](https://help.github.com/en/articles/about-pull-requests). -Read the [next section](#guidelines-to-getting-a-pull-request-merged) for guidelines for both reviewers and contributors on merging a PR. +Read the [next section](guidelines-to-getting-a-pull-request-merged) for guidelines for both reviewers and contributors on merging a PR. 6. Wait for a community member to merge your changes. Remember that **someone else must merge your pull request**. That goes for new contributors and long term maintainers alike. @@ -68,6 +68,8 @@ Read the [next section](#guidelines-to-getting-a-pull-request-merged) for guidel that `main` is always in a deployable state. 7. (optional) Deploy a new version of repo2docker to mybinder.org by [following these steps](http://mybinder-sre.readthedocs.io/en/latest/deployment/how.html) +(guidelines-to-getting-a-pull-request-merged)= + ## Guidelines to getting a Pull Request merged These are not hard rules to be enforced by 🚓 but they are suggestions written by the repo2docker maintainers to help complete your contribution as smoothly as possible for both you and for them. From 2dba862d5b5ef7cc851f3f37406b635a0814841f Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Tue, 25 Oct 2022 19:43:20 +0200 Subject: [PATCH 011/171] Apply suggestions from code review Co-authored-by: Simon Li --- docs/source/conf.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index fc2aec098..11c156cfe 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -8,7 +8,7 @@ # -- Project information ----------------------------------------------------- # ref: https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information # -project = "BinderHub" +project = "repo2docker" copyright = f"{datetime.date.today().year}, Project Jupyter Contributors" author = "Project Jupyter Contributors" @@ -82,7 +82,6 @@ html_theme_options = { "use_edit_page_button": True, "github_url": "https://github.com/jupyterhub/repo2docker", - "twitter_url": "https://twitter.com/mybinderteam", } html_context = { "github_user": "jupyterhub", From 5f5e3bbbb4e941ffef08ee55cc55d31fe5aa56e8 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 31 Oct 2022 08:56:57 +0000 Subject: [PATCH 012/171] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- repo2docker/__main__.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/repo2docker/__main__.py b/repo2docker/__main__.py index ebe3ab965..87fd9ddaf 100644 --- a/repo2docker/__main__.py +++ b/repo2docker/__main__.py @@ -218,9 +218,9 @@ def get_argparser(): ) argparser.add_argument( - "--engine", - type=str, - default="docker", + "--engine", + type=str, + default="docker", help=Repo2Docker.engine.help, ) From 6826d72aa2e5474e625e989df7264512d600061a Mon Sep 17 00:00:00 2001 From: Min RK Date: Fri, 26 Jun 2020 12:38:25 +0200 Subject: [PATCH 013/171] allow user to specify a single port with default command Allows specifying `-p9999` or `-p5555:9999` without also needing to override the default command app retrieves port arguments from length-1 port mapping for default command, instead of requiring random port OR overriding the whole command --- repo2docker/__main__.py | 2 +- repo2docker/app.py | 33 +++++++++++++++++++++------------ repo2docker/utils.py | 11 ++++++++--- 3 files changed, 30 insertions(+), 16 deletions(-) diff --git a/repo2docker/__main__.py b/repo2docker/__main__.py index 2f9887ff9..1b52b1aee 100644 --- a/repo2docker/__main__.py +++ b/repo2docker/__main__.py @@ -354,7 +354,7 @@ def make_r2d(argv=None): ) sys.exit(1) - if args.ports and not r2d.run_cmd: + if args.ports and len(args.ports) > 1 and not r2d.run_cmd: print( "To publish user defined port mapping, user must specify " "the command to run in the container" diff --git a/repo2docker/app.py b/repo2docker/app.py index d9a114a40..4625ac3fb 100755 --- a/repo2docker/app.py +++ b/repo2docker/app.py @@ -595,8 +595,24 @@ def start_container(self): self.hostname = host_name if not self.run_cmd: - port = str(self._get_free_port()) - self.port = port + if len(self.ports) == 1: + # single port mapping specified + # retrieve container and host port from dict + # {'8888/tcp': ('hostname', 'port')} + # or + # {'8888/tcp': 'port'} + container_port_proto, host_port = next(iter(self.ports.items())) + if isinstance(host_port, tuple): + # (hostname, port) tuple or string port + host_name, host_port = host_port + self.hostname = host_name + host_port = int(host_port) + container_port = int(container_port_proto.split("/", 1)[0]) + else: + # no port specified, pick a random one + container_port = host_port = str(self._get_free_port()) + self.ports = {"%s/tcp" % container_port: host_port} + self.port = host_port # To use the option --NotebookApp.custom_display_url # make sure the base-notebook image is updated: # docker pull jupyter/base-notebook @@ -606,20 +622,13 @@ def start_container(self): "--ip", "0.0.0.0", "--port", - port, - "--NotebookApp.custom_display_url=http://{}:{}".format(host_name, port), + container_port, + f"--NotebookApp.custom_display_url=http://{host_name}:{host_port}" "--NotebookApp.default_url=/lab", ] - ports = {"%s/tcp" % port: port} else: # run_cmd given by user, if port is also given then pass it on run_cmd = self.run_cmd - if self.ports: - ports = self.ports - else: - ports = {} - # store ports on self so they can be retrieved in tests - self.ports = ports container_volumes = {} if self.volumes: @@ -634,7 +643,7 @@ def start_container(self): run_kwargs = dict( publish_all_ports=self.all_ports, - ports=ports, + ports=self.ports, command=run_cmd, volumes=container_volumes, environment=self.environment, diff --git a/repo2docker/utils.py b/repo2docker/utils.py index ef61814ba..e8833bd84 100644 --- a/repo2docker/utils.py +++ b/repo2docker/utils.py @@ -139,10 +139,10 @@ def check_port(port): raise ValueError( 'Port specification "{}" has ' "an invalid port.".format(mapping) ) - if p > 65535: + if not 0 < p <= 65535: raise ValueError( 'Port specification "{}" specifies ' - "a port above 65535.".format(mapping) + "a port outside 1-65535.".format(mapping) ) return port @@ -168,7 +168,12 @@ def check_port_string(p): return ports for mapping in port_mappings: - parts = mapping.split(":") + if ":" in mapping: + parts = mapping.split(":") + else: + # single port '8888' specified, + # treat as '8888:8888' + parts = [mapping, mapping] *host, container_port = parts # just a port From b314ba90cd1060c2fe81cbb80fe18378af733383 Mon Sep 17 00:00:00 2001 From: Min RK Date: Mon, 29 Jun 2020 09:03:14 +0200 Subject: [PATCH 014/171] test new port argument possibilities --- tests/unit/test_args.py | 5 ----- tests/unit/test_ports.py | 16 +++++++++++++++- 2 files changed, 15 insertions(+), 6 deletions(-) diff --git a/tests/unit/test_args.py b/tests/unit/test_args.py index 5e8c2484a..e5fd2c1ab 100644 --- a/tests/unit/test_args.py +++ b/tests/unit/test_args.py @@ -3,7 +3,6 @@ """ import os import pytest -import logging from repo2docker.__main__ import make_r2d from repo2docker import __version__ @@ -71,10 +70,6 @@ def test_run_required(): with pytest.raises(SystemExit): make_r2d(["--no-run", "-p", "8000:8000", "."]) - # Can't publish any ports while running if we don't specify a command explicitly - with pytest.raises(SystemExit): - make_r2d(["-p", "8000:8000", "."]) - def test_clean(): """ diff --git a/tests/unit/test_ports.py b/tests/unit/test_ports.py index edb71424a..445e6c4c0 100644 --- a/tests/unit/test_ports.py +++ b/tests/unit/test_ports.py @@ -13,6 +13,7 @@ import pytest from repo2docker.app import Repo2Docker +from repo2docker.__main__ import make_r2d def read_port_mapping_response( @@ -95,7 +96,7 @@ def _cleanup(): else: break else: - pytest.fail("Never succeded in talking to %s" % url) + pytest.fail("Never succeeded in talking to %s" % url) assert "Directory listing" in r.text @@ -113,3 +114,16 @@ def test_port_mapping(request, tmpdir, host, protocol): """Test a port mapping""" port = str(random.randint(50000, 51000)) read_port_mapping_response(request, tmpdir, host=host, port=port, protocol=protocol) + + +@pytest.mark.parametrize( + "port_str, port_dict", + [ + ("8000", {"8000/tcp": "8000"}), + ("8000:9000", {"9000/tcp": "8000"}), + ("127.0.0.1:8000:9000", {"9000/tcp": ("127.0.0.1", "8000")}), + ], +) +def test_port_args(port_str, port_dict): + app = make_r2d(["-p", port_str, "."]) + assert app.ports == port_dict From b3234b54f0bcbc3e12347b14b3b549f2e72d58d8 Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Mon, 31 Oct 2022 11:43:36 +0100 Subject: [PATCH 015/171] Refactor to f-strings to comply with pyupgrade --- repo2docker/app.py | 2 +- tests/unit/test_ports.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/repo2docker/app.py b/repo2docker/app.py index 4625ac3fb..e11f36b6c 100755 --- a/repo2docker/app.py +++ b/repo2docker/app.py @@ -611,7 +611,7 @@ def start_container(self): else: # no port specified, pick a random one container_port = host_port = str(self._get_free_port()) - self.ports = {"%s/tcp" % container_port: host_port} + self.ports = {f"{container_port}/tcp": host_port} self.port = host_port # To use the option --NotebookApp.custom_display_url # make sure the base-notebook image is updated: diff --git a/tests/unit/test_ports.py b/tests/unit/test_ports.py index 445e6c4c0..09944e873 100644 --- a/tests/unit/test_ports.py +++ b/tests/unit/test_ports.py @@ -96,7 +96,7 @@ def _cleanup(): else: break else: - pytest.fail("Never succeeded in talking to %s" % url) + pytest.fail(f"Never succeeded in talking to {url}") assert "Directory listing" in r.text From 803a1c223b5d5799d3a90f4cb2adcb6003a50c8b Mon Sep 17 00:00:00 2001 From: Nicholas Bollweg Date: Mon, 19 Oct 2020 08:54:07 -0400 Subject: [PATCH 016/171] ensure existence/permissions on custom target dir, if doesn't exist, repo copy slash --- repo2docker/buildpacks/base.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/repo2docker/buildpacks/base.py b/repo2docker/buildpacks/base.py index 2a5536b04..50fd939cb 100644 --- a/repo2docker/buildpacks/base.py +++ b/repo2docker/buildpacks/base.py @@ -105,7 +105,9 @@ # Allow target path repo is cloned to be configurable ARG REPO_DIR=${HOME} -ENV REPO_DIR ${REPO_DIR} +RUN [ ! -d ${REPO_DIR} ] \ + && mkdir -p ${REPO_DIR} \ + && chown -R ${NB_USER}:${NB_USER} ${REPO_DIR} WORKDIR ${REPO_DIR} RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR} @@ -144,7 +146,7 @@ USER root # Copy stuff. -COPY --chown={{ user }}:{{ user }} src/ ${REPO_DIR} +COPY --chown={{ user }}:{{ user }} src/ ${REPO_DIR}/ # Run assemble scripts! These will actually turn the specification # in the repository into an image. From df733fc81bfedd235650e597b0834859e930cfd6 Mon Sep 17 00:00:00 2001 From: Nicholas Bollweg Date: Mon, 19 Oct 2020 09:20:41 -0400 Subject: [PATCH 017/171] normalize ENV syntax, combine more layers --- repo2docker/buildpacks/base.py | 34 ++++++++++++++++++++-------------- 1 file changed, 20 insertions(+), 14 deletions(-) diff --git a/repo2docker/buildpacks/base.py b/repo2docker/buildpacks/base.py index 50fd939cb..28eaada34 100644 --- a/repo2docker/buildpacks/base.py +++ b/repo2docker/buildpacks/base.py @@ -27,18 +27,18 @@ RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \ locale-gen -ENV LC_ALL en_US.UTF-8 -ENV LANG en_US.UTF-8 -ENV LANGUAGE en_US.UTF-8 +ENV LC_ALL=en_US.UTF-8 \ + LANG=en_US.UTF-8 \ + LANGUAGE=en_US.UTF-8 # Use bash as default shell, rather than sh -ENV SHELL /bin/bash +ENV SHELL=/bin/bash # Set up user ARG NB_USER ARG NB_UID -ENV USER ${NB_USER} -ENV HOME /home/${NB_USER} +ENV USER=${NB_USER} \ + HOME=/home/${NB_USER} RUN groupadd \ --gid ${NB_UID} \ @@ -81,13 +81,13 @@ {% if build_env -%} # Environment variables required for build {% for item in build_env -%} -ENV {{item[0]}} {{item[1]}} +ENV {{item[0]}}={{item[1]}} {% endfor -%} {% endif -%} {% if path -%} # Special case PATH -ENV PATH {{ ':'.join(path) }}:${PATH} +ENV PATH={{ ':'.join(path) }}:${PATH} {% endif -%} {% if build_script_files -%} @@ -105,9 +105,15 @@ # Allow target path repo is cloned to be configurable ARG REPO_DIR=${HOME} -RUN [ ! -d ${REPO_DIR} ] \ - && mkdir -p ${REPO_DIR} \ - && chown -R ${NB_USER}:${NB_USER} ${REPO_DIR} +ENV REPO_DIR=${REPO_DIR} +RUN if [ ! -d "${REPO_DIR}" ] \ + ; then \ + mkdir -p "${REPO_DIR}" \ + && chown -R ${NB_USER}:${NB_USER} "${REPO_DIR}" \ + ; else \ + echo "${REPO_DIR} already exists..." \ + ; fi + WORKDIR ${REPO_DIR} RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR} @@ -119,12 +125,12 @@ # # The XDG standard suggests ~/.local/bin as the path for local user-specific # installs. See https://specifications.freedesktop.org/basedir-spec/basedir-spec-latest.html -ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH} +ENV PATH=${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH} {% if env -%} # The rest of the environment {% for item in env -%} -ENV {{item[0]}} {{item[1]}} +ENV {{item[0]}}={{item[1]}} {% endfor -%} {% endif -%} @@ -175,7 +181,7 @@ # Add start script {% if start_script is not none -%} RUN chmod +x "{{ start_script }}" -ENV R2D_ENTRYPOINT "{{ start_script }}" +ENV R2D_ENTRYPOINT="{{ start_script }}" {% endif -%} # Add entrypoint From 23e195f3631a0479b4137b78889002df357323b6 Mon Sep 17 00:00:00 2001 From: Nicholas Bollweg Date: Mon, 19 Oct 2020 10:31:19 -0400 Subject: [PATCH 018/171] add path check in conda/repo-dir, more docs in conftest.py --- .../conda/r3.6-target-repo-dir-flag/verify.py | 10 ++++++++++ tests/conftest.py | 18 +++++++++++++----- 2 files changed, 23 insertions(+), 5 deletions(-) diff --git a/tests/conda/r3.6-target-repo-dir-flag/verify.py b/tests/conda/r3.6-target-repo-dir-flag/verify.py index 706dc41a9..d284c28a6 100755 --- a/tests/conda/r3.6-target-repo-dir-flag/verify.py +++ b/tests/conda/r3.6-target-repo-dir-flag/verify.py @@ -1,6 +1,7 @@ #!/usr/bin/env python import sys import os +from glob import glob # conda should still be in /srv/conda # and Python should still be in $NB_PYTHON_PREFIX @@ -15,3 +16,12 @@ # Repo should be writable assert os.access("/srv/repo", os.W_OK) + +# All files in repo dir should be readable and writeable +for path in glob("/src/repo/**/*", recursive=True): + assert os.access(path, os.R_OK) + assert os.access(path, os.W_OK) + +# Should be able to make a new file +with open("/srv/repo/writeable", "w") as fp: + fp.write("writeable") diff --git a/tests/conftest.py b/tests/conftest.py index 5ea3f9dc1..550eb359e 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,11 +1,19 @@ """ Custom test collector for our integration tests. -Each directory that has a script named 'verify' is considered -a test. jupyter-repo2docker is run on that directory, -and then ./verify is run inside the built container. It should -return a non-zero exit code for the test to be considered a -success. + +Test lifecycle: +- Find all directories that contain `verify` or `*.repos.yaml` +- If `verify` is found: + - Run `jupyter-repo2docker` on the test directory. + - Extra arguments may be added as YAML list of strings in `extra-args.yaml`. + - Run `./verify` inside the built container. + - It should return a non-zero exit code for the test to be considered a + successful. +- If a `*.repos.yaml` is found: + - For each entry of the form `{name, url, ref, verify}` + - Run `jupyter-repo2docker` with the `url` and `ref` + - Run the `verify` inside the built container """ import os From 2f13af8a29935bd2c567062a055c2d9a186e3f29 Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Mon, 31 Oct 2022 10:58:30 +0100 Subject: [PATCH 019/171] Apply suggestions from code review --- repo2docker/buildpacks/base.py | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/repo2docker/buildpacks/base.py b/repo2docker/buildpacks/base.py index 28eaada34..57ed2f353 100644 --- a/repo2docker/buildpacks/base.py +++ b/repo2docker/buildpacks/base.py @@ -106,13 +106,10 @@ # Allow target path repo is cloned to be configurable ARG REPO_DIR=${HOME} ENV REPO_DIR=${REPO_DIR} -RUN if [ ! -d "${REPO_DIR}" ] \ - ; then \ - mkdir -p "${REPO_DIR}" \ - && chown -R ${NB_USER}:${NB_USER} "${REPO_DIR}" \ - ; else \ - echo "${REPO_DIR} already exists..." \ - ; fi +# Create a folder and grant the user permissions if it doesn't exist +RUN if [ ! -d "${REPO_DIR}" ]; then \ + /usr/bin/install -o ${NB_USER} -g ${NB_USER} -d "${REPO_DIR}"; \ + fi WORKDIR ${REPO_DIR} RUN chown ${NB_USER}:${NB_USER} ${REPO_DIR} From 55a9cd81f8b06b2208727433f9fa73120459d045 Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Sun, 23 Oct 2022 12:19:15 +0200 Subject: [PATCH 020/171] Create wheels with the build package --- .github/workflows/release.yml | 9 +++++---- .github/workflows/test.yml | 2 +- dev-requirements.txt | 2 +- 3 files changed, 7 insertions(+), 6 deletions(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index e5d5ba16f..e298f9bd1 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -34,14 +34,15 @@ jobs: with: python-version: "3.9" - - name: Install dependencies + - name: install build requirements run: | - pip install -r dev-requirements.txt + pip install build pip freeze - - name: Build distribution archives + - name: build release run: | - python setup.py sdist bdist_wheel + python -m build --sdist --wheel . + ls -l dist # This step is only run when a new tag is pushed # all previous steps always run in order to exercise them diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 4dfca1ce3..40ddffb80 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -116,7 +116,7 @@ jobs: - name: Install repo2docker run: | - python setup.py bdist_wheel + python -m build --wheel . pip install dist/*.whl # add for mercurial tests diff --git a/dev-requirements.txt b/dev-requirements.txt index 57592762f..245b425e5 100644 --- a/dev-requirements.txt +++ b/dev-requirements.txt @@ -1,3 +1,4 @@ +build codecov conda-lock pre-commit @@ -5,4 +6,3 @@ pytest-cov pytest>=4.6 pyyaml requests_mock -wheel From 224633af93c2d471d69666115a7d4d3cdaf7c59f Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Sun, 23 Oct 2022 12:19:55 +0200 Subject: [PATCH 021/171] ci: upload built wheels as an artifact for ease of inspection --- .github/workflows/release.yml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index e298f9bd1..4f158f6f7 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -44,6 +44,13 @@ jobs: python -m build --sdist --wheel . ls -l dist + # ref: https://github.com/actions/upload-artifact#readme + - uses: actions/upload-artifact@v3 + with: + name: repo2docker_service-${{ github.sha }} + path: "dist/*" + if-no-files-found: error + # This step is only run when a new tag is pushed # all previous steps always run in order to exercise them - name: Publish distribution to PyPI From f3284bfcd1ac44351391f6a72c0a11e4a7039a0c Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Mon, 31 Oct 2022 13:48:33 +0100 Subject: [PATCH 022/171] Apply suggestions from code review --- .github/workflows/release.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 4f158f6f7..6f1b274ef 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -47,7 +47,7 @@ jobs: # ref: https://github.com/actions/upload-artifact#readme - uses: actions/upload-artifact@v3 with: - name: repo2docker_service-${{ github.sha }} + name: repo2docker-${{ github.sha }} path: "dist/*" if-no-files-found: error From 8a28264b972c14a1d78251cddbef6930eefdefd9 Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Sun, 23 Oct 2022 13:05:32 +0200 Subject: [PATCH 023/171] ci: stop running pre-commit in gha, rely on pre-commit.ci --- .github/workflows/test.yml | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 40ddffb80..91ff90cb2 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -39,7 +39,7 @@ env: GIT_AUTHOR_NAME: CI User jobs: - pre-commit: + populate-pip-cache: runs-on: ubuntu-22.04 strategy: @@ -65,12 +65,21 @@ jobs: - name: Install dependencies run: | pip install -r dev-requirements.txt + + # add for mercurial tests + pip install mercurial hg-evolve + pip freeze - - run: pre-commit run --all-files + - name: Install repo2docker + run: | + python -m build --wheel . + pip install dist/*.whl + + pip freeze test: - needs: pre-commit + needs: populate-pip-cache runs-on: ubuntu-${{ matrix.ubuntu_version }} strategy: From ea1fbcd440dce6d6fce1e5521bebabe98316b84b Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Mon, 31 Oct 2022 13:59:58 +0100 Subject: [PATCH 024/171] ci: stop populating pip cache in a pre-requisite test job --- .github/workflows/test.yml | 46 -------------------------------------- 1 file changed, 46 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 91ff90cb2..62c20c13a 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -39,47 +39,7 @@ env: GIT_AUTHOR_NAME: CI User jobs: - populate-pip-cache: - runs-on: ubuntu-22.04 - - strategy: - fail-fast: false - matrix: - python_version: ["3.9"] - - steps: - - uses: actions/checkout@v3 - - uses: actions/setup-python@v4 - with: - python-version: "${{ matrix.python_version }}" - - # There will almost never be a cache hit on the cache key when this job is - # run, as it is the first of all jobs in this workflow. The subsequent - # jobs in this workflow can rely on this cache though. - - name: Save pip's install cache on job completion - uses: actions/cache@v3 - with: - path: ~/.cache/pip - key: "${{ github.run_id }}-${{ matrix.python_version }}" - - - name: Install dependencies - run: | - pip install -r dev-requirements.txt - - # add for mercurial tests - pip install mercurial hg-evolve - - pip freeze - - - name: Install repo2docker - run: | - python -m build --wheel . - pip install dist/*.whl - - pip freeze - test: - needs: populate-pip-cache runs-on: ubuntu-${{ matrix.ubuntu_version }} strategy: @@ -112,12 +72,6 @@ jobs: with: python-version: "${{ matrix.python_version }}" - - name: Restore pip's install cache from previous job - uses: actions/cache@v3 - with: - path: ~/.cache/pip - key: "${{ github.run_id }}-${{ matrix.python_version }}" - - name: Install dependencies run: | pip install -r dev-requirements.txt From 9a80e95600d7c4df6c8641c4533a3376ada1068a Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Mon, 31 Oct 2022 12:51:00 +0100 Subject: [PATCH 025/171] pipfile: pass --clear flag, and do it separetely to not be ignored Maybe --clear flag works as part of `pipenv install` now, but code inspection indicates to me it still don't. This resolves the issue with the pipenv versions we currently use in tests at least. --- repo2docker/buildpacks/pipfile/__init__.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/repo2docker/buildpacks/pipfile/__init__.py b/repo2docker/buildpacks/pipfile/__init__.py index a5117ff56..959c8b72d 100644 --- a/repo2docker/buildpacks/pipfile/__init__.py +++ b/repo2docker/buildpacks/pipfile/__init__.py @@ -154,7 +154,8 @@ def get_assemble_scripts(self): "${NB_USER}", """(cd {working_directory} && \\ PATH="${{KERNEL_PYTHON_PREFIX}}/bin:$PATH" \\ - pipenv install {install_option} --system --dev \\ + pipenv install {install_option} --system --dev && \\ + pipenv --clear \\ )""".format( working_directory=working_directory, install_option="--ignore-pipfile" From 38f5aceb45a8f3df1f6d68f619c7904cb047fd6f Mon Sep 17 00:00:00 2001 From: Min RK Date: Wed, 26 Jan 2022 15:49:49 +0100 Subject: [PATCH 026/171] Add check-tmp step to local repo tests - check-tmp checks disk usage in a collection of directories, and fails if they exceed a certain size, reporting on contents - re-use images and skip build stage in verify/check-tmp tests. Should save some time, even though the build cache would have been used. This way, we don't even check. --- tests/check-tmp | 86 +++++++++++++++++++++++++++++++++++++++++++++++ tests/conftest.py | 46 +++++++++++++++++++++---- 2 files changed, 125 insertions(+), 7 deletions(-) create mode 100755 tests/check-tmp diff --git a/tests/check-tmp b/tests/check-tmp new file mode 100755 index 000000000..3c63489fb --- /dev/null +++ b/tests/check-tmp @@ -0,0 +1,86 @@ +#!/usr/bin/env python3 +""" +Script to check for leftover files + +Checks a collection of temporary or cache directories, +to ensure we aren't wasting image size by forgetting cleanup steps. + +This script is run in every local repo image we test +""" + +import os +import sys +from subprocess import check_output +from textwrap import indent + +# directories larger than this are considered a failure +# a few little files here aren't a problem +THRESHOLD = 1 # in MB + +MB = 1024 * 1024 + +# the paths to check +# all of these locations +# should be cleaned up +# missing is okay +PATHS = [ + "/tmp/", + "~/", + "~/.cache/", + # not running with read permissions on root + # "/root/", +] + + +def du(path): + """Return disk usage in megabytes of a path""" + # -ks: get total size, reported in kilobytes + out = check_output(["du", "-Hks", path]) + return int(out.split(None, 1)[0]) / 1024 + + +def check_dir_size(path): + """Check the size of a directory + + Returns: + + True: directory size is below THRESHOLD or is missing + False: directory is larger than THRESHOLD + """ + path = os.path.expanduser(path) + + if not os.path.exists(path): + print(f"{path}: missing OK") + return True + + size_mb = du(path) + print(f"{path}: {size_mb:.1f} MB", end=" ") + if size_mb <= THRESHOLD: + print("OK") + return True + else: + print("FAIL") + # check size of files one-level deep (du only reports dirs) + for name in os.listdir(path): + subpath = os.path.join(path, name) + if os.path.isfile(subpath): + file_sz = os.stat(subpath).st_size / MB + if file_sz > 0.1: + print(f" {file_sz:.1f}M {subpath}") + # get report on all subdirs that are at least 100k + print( + indent( + check_output(["du", "-Hh", "-t", "100000", path]).decode("utf8"), " " + ) + ) + return False + + +def main(): + results = [check_dir_size(path) for path in PATHS] + if not all(results): + sys.exit(1) + + +if __name__ == "__main__": + main() diff --git a/tests/conftest.py b/tests/conftest.py index 550eb359e..c9bd11d93 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -22,14 +22,17 @@ import requests import subprocess import time - from tempfile import TemporaryDirectory + +import escapism import pytest import yaml from repo2docker.__main__ import make_r2d +TESTS_DIR = os.path.abspath(os.path.dirname(__file__)) + def pytest_collect_file(parent, path): if path.basename == "verify": @@ -38,12 +41,18 @@ def pytest_collect_file(parent, path): return RemoteRepoList.from_parent(parent, fspath=path) -def make_test_func(args): +def make_test_func(args, skip_build=False): """Generate a test function that runs repo2docker""" def test(): app = make_r2d(args) app.initialize() + if skip_build: + + def build_noop(): + print("Skipping build") + + app.skip_build = build_noop if app.run_cmd: # verify test, run it app.start() @@ -184,14 +193,14 @@ def repo_with_submodule(): class Repo2DockerTest(pytest.Function): """A pytest.Item for running repo2docker""" - def __init__(self, name, parent, args=None): + def __init__(self, name, parent, args=None, skip_build=False): self.args = args self.save_cwd = os.getcwd() - f = parent.obj = make_test_func(args) + f = parent.obj = make_test_func(args, skip_build=skip_build) super().__init__(name, parent, callobj=f) def reportinfo(self): - return self.parent.fspath, None, "" + return (self.parent.fspath, None, "") def repr_failure(self, excinfo): err = excinfo.value @@ -217,11 +226,34 @@ def collect(self): extra_args = yaml.safe_load(f) args += extra_args + print(self.fspath.basename, self.fspath.dirname, str(self.fspath)) + # re-use image name for multiple tests of the same image + # so we don't run through the build twice + rel_repo_dir = os.path.relpath(self.fspath.dirname, TESTS_DIR) + image_name = f"r2d-tests-{escapism.escape(rel_repo_dir, escape_char='-').lower()}-{int(time.time())}" + args.append(f"--image-name={image_name}") args.append(self.fspath.dirname) - yield Repo2DockerTest.from_parent(self, name="build", args=args) + + yield Repo2DockerTest.from_parent( + self, + name=self.fspath.basename, + args=args + ["./verify"], + skip_build=True, + ) + + # mount the tests dir as a volume + check_tmp_args = ( + args[:-1] + + ["--volume", f"{TESTS_DIR}:/io/tests"] + + [args[-1], "/io/tests/check-tmp"] + ) + yield Repo2DockerTest.from_parent( - self, name=self.fspath.basename, args=args + ["./verify"] + self, + name="check-tmp", + args=check_tmp_args, + skip_build=True, ) From 2da784ca215cd158a22f6d4a84c98e888ce7337c Mon Sep 17 00:00:00 2001 From: Min RK Date: Wed, 26 Jan 2022 16:35:37 +0100 Subject: [PATCH 027/171] check-tmp needs to run on Python 3.5 --- tests/check-tmp | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/check-tmp b/tests/check-tmp index 3c63489fb..d76572838 100755 --- a/tests/check-tmp +++ b/tests/check-tmp @@ -50,11 +50,11 @@ def check_dir_size(path): path = os.path.expanduser(path) if not os.path.exists(path): - print(f"{path}: missing OK") + print("{path}: missing OK".format(**locals())) return True size_mb = du(path) - print(f"{path}: {size_mb:.1f} MB", end=" ") + print("{path}: {size_mb:.1f} MB".format(**locals()), end=" ") if size_mb <= THRESHOLD: print("OK") return True @@ -66,7 +66,7 @@ def check_dir_size(path): if os.path.isfile(subpath): file_sz = os.stat(subpath).st_size / MB if file_sz > 0.1: - print(f" {file_sz:.1f}M {subpath}") + print(" {file_sz:.1f}M {subpath}".format(**locals())) # get report on all subdirs that are at least 100k print( indent( From 6b0291551dba56ca5b3522ab170ebb2aa124cc04 Mon Sep 17 00:00:00 2001 From: Min RK Date: Wed, 26 Jan 2022 16:47:40 +0100 Subject: [PATCH 028/171] Make sure we delete /tmp/shiny.deb revealed by check-tmp --- repo2docker/buildpacks/_r_base.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/repo2docker/buildpacks/_r_base.py b/repo2docker/buildpacks/_r_base.py index 09ec90d64..c73273793 100644 --- a/repo2docker/buildpacks/_r_base.py +++ b/repo2docker/buildpacks/_r_base.py @@ -33,7 +33,7 @@ def rstudio_base_scripts(r_version): echo '{shiny_sha256sum} /tmp/shiny.deb' | sha256sum -c - && \ apt-get update > /dev/null && \ apt install -y --no-install-recommends /tmp/rstudio.deb /tmp/shiny.deb && \ - rm /tmp/rstudio.deb && \ + rm /tmp/*.deb && \ apt-get -qq purge && \ apt-get -qq clean && \ rm -rf /var/lib/apt/lists/* From bd02e2e997cf1bcf6a20d798891cf1d4de371c18 Mon Sep 17 00:00:00 2001 From: Min RK Date: Thu, 27 Jan 2022 10:09:45 +0100 Subject: [PATCH 029/171] run check-tmp as root - avoids permission errors - lets us check /root/ where we've left files in the past --- tests/check-tmp | 8 +++++--- tests/conftest.py | 13 ++++++++++--- 2 files changed, 15 insertions(+), 6 deletions(-) diff --git a/tests/check-tmp b/tests/check-tmp index d76572838..6437c4371 100755 --- a/tests/check-tmp +++ b/tests/check-tmp @@ -25,10 +25,12 @@ MB = 1024 * 1024 # missing is okay PATHS = [ "/tmp/", + # check whole home? + # this shouldn't be empty, but for our tests (so far) it should be very small + # This is the easiest way to ensure we aren't leaving any unexpected files + # without knowing ahead of time where all possible caches might be (.npm, .cache, etc.) "~/", - "~/.cache/", - # not running with read permissions on root - # "/root/", + "/root/", ] diff --git a/tests/conftest.py b/tests/conftest.py index c9bd11d93..19c0ca6ec 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -41,12 +41,14 @@ def pytest_collect_file(parent, path): return RemoteRepoList.from_parent(parent, fspath=path) -def make_test_func(args, skip_build=False): +def make_test_func(args, skip_build=False, extra_run_kwargs=None): """Generate a test function that runs repo2docker""" def test(): app = make_r2d(args) app.initialize() + if extra_run_kwargs: + app.extra_run_kwargs.update(extra_run_kwargs) if skip_build: def build_noop(): @@ -193,10 +195,14 @@ def repo_with_submodule(): class Repo2DockerTest(pytest.Function): """A pytest.Item for running repo2docker""" - def __init__(self, name, parent, args=None, skip_build=False): + def __init__( + self, name, parent, args=None, skip_build=False, extra_run_kwargs=None + ): self.args = args self.save_cwd = os.getcwd() - f = parent.obj = make_test_func(args, skip_build=skip_build) + f = parent.obj = make_test_func( + args, skip_build=skip_build, extra_run_kwargs=extra_run_kwargs + ) super().__init__(name, parent, callobj=f) def reportinfo(self): @@ -254,6 +260,7 @@ def collect(self): name="check-tmp", args=check_tmp_args, skip_build=True, + extra_run_kwargs={"user": "root"}, ) From 757799516da67482e343ee64bdf536955eb91a71 Mon Sep 17 00:00:00 2001 From: Min RK Date: Thu, 27 Jan 2022 10:54:11 +0100 Subject: [PATCH 030/171] ensure some cache files are cleaned up --- repo2docker/buildpacks/pipfile/__init__.py | 5 ++++- tests/venv/postBuild/postBuild | 3 ++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/repo2docker/buildpacks/pipfile/__init__.py b/repo2docker/buildpacks/pipfile/__init__.py index 959c8b72d..202140990 100644 --- a/repo2docker/buildpacks/pipfile/__init__.py +++ b/repo2docker/buildpacks/pipfile/__init__.py @@ -88,7 +88,10 @@ def get_preassemble_scripts(self): scripts = super().get_preassemble_scripts() # install pipenv to install dependencies within Pipfile.lock or Pipfile scripts.append( - ("${NB_USER}", "${KERNEL_PYTHON_PREFIX}/bin/pip install pipenv==2018.11.26") + ( + "${NB_USER}", + "${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir pipenv==2018.11.26", + ) ) return scripts diff --git a/tests/venv/postBuild/postBuild b/tests/venv/postBuild/postBuild index c1e89e8a3..4f301be50 100755 --- a/tests/venv/postBuild/postBuild +++ b/tests/venv/postBuild/postBuild @@ -1,3 +1,4 @@ #!/bin/bash jupyter nbextension enable --py --sys-prefix ipyleaflet -npm install --global configurable-http-proxy \ No newline at end of file +npm install --global configurable-http-proxy +npm cache clean --force From e7c93b0fc8bcb89efae203b3432e49a00be522d4 Mon Sep 17 00:00:00 2001 From: Min RK Date: Tue, 1 Feb 2022 14:51:13 +0100 Subject: [PATCH 031/171] update pipenv to 2022.1.8 pipenv 2018 doesn't actually clear its cache when asked to 2021.5.29 is the last to support 2.7, 3.5 --- repo2docker/buildpacks/pipfile/__init__.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/repo2docker/buildpacks/pipfile/__init__.py b/repo2docker/buildpacks/pipfile/__init__.py index 202140990..e928d01ec 100644 --- a/repo2docker/buildpacks/pipfile/__init__.py +++ b/repo2docker/buildpacks/pipfile/__init__.py @@ -11,6 +11,7 @@ import toml +from ...semver import parse_version as V from ..conda import CondaBuildPack VERSION_PAT = re.compile(r"\d+(\.\d+)*") @@ -87,10 +88,15 @@ def get_preassemble_scripts(self): """scripts to run prior to staging the repo contents""" scripts = super().get_preassemble_scripts() # install pipenv to install dependencies within Pipfile.lock or Pipfile + if V(self.python_version) < V("3.6"): + # last pipenv version to support 2.7, 3.5 + pipenv_version = "2021.5.29" + else: + pipenv_version = "2022.1.8" scripts.append( ( "${NB_USER}", - "${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir pipenv==2018.11.26", + f"${{KERNEL_PYTHON_PREFIX}}/bin/pip install --no-cache-dir pipenv=={pipenv_version}", ) ) return scripts From 89f2b61db6eb26e2b56686d9e07357e77ee282c9 Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Mon, 31 Oct 2022 19:26:55 +0100 Subject: [PATCH 032/171] ci: use non-deprecated codecov uploader --- .github/workflows/test.yml | 4 +--- dev-requirements.txt | 1 - 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 62c20c13a..4995d238c 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -91,6 +91,4 @@ jobs: run: | pytest --verbose --color=yes --durations=10 --cov=repo2docker tests/${{ matrix.repo_type }} - - name: Submit codecov report - run: | - codecov + - uses: codecov/codecov-action@v3 diff --git a/dev-requirements.txt b/dev-requirements.txt index 245b425e5..6553a6743 100644 --- a/dev-requirements.txt +++ b/dev-requirements.txt @@ -1,5 +1,4 @@ build -codecov conda-lock pre-commit pytest-cov From ce44f98c9a68efc958de7ac4d4d966dd8ec79b3b Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Sun, 23 Oct 2022 17:57:07 +0200 Subject: [PATCH 033/171] pre-commit: enable pyupgrade --- .pre-commit-config.yaml | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index aaf7a3305..42d13f19e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -9,13 +9,17 @@ # - Register git hooks: pre-commit install --install-hooks # repos: - # # Autoformat: Python code, syntax patterns are modernized - # - repo: https://github.com/asottile/pyupgrade - # rev: v3.0.0 - # hooks: - # - id: pyupgrade - # args: - # - --py38-plus + # Autoformat: Python code, syntax patterns are modernized + - repo: https://github.com/asottile/pyupgrade + rev: v3.2.0 + hooks: + - id: pyupgrade + args: + - --py36-plus + # check-tmp is a Python based test script run in created environments + # that can be at least Python 3.5 even though we require Python 3.6 for + # repo2docker itself. + exclude: check-tmp # Autoformat: Python code - repo: https://github.com/psf/black From 5a93542321d755330fe70bc2d5393928dbce372a Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Sun, 23 Oct 2022 16:09:11 +0000 Subject: [PATCH 034/171] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- repo2docker/__main__.py | 2 +- repo2docker/_version.py | 16 +++---- repo2docker/app.py | 4 +- repo2docker/buildpacks/base.py | 9 ++-- repo2docker/buildpacks/conda/__init__.py | 4 +- repo2docker/buildpacks/docker.py | 3 +- repo2docker/buildpacks/legacy/__init__.py | 2 +- repo2docker/buildpacks/python/__init__.py | 6 +-- repo2docker/buildpacks/r.py | 4 +- repo2docker/contentproviders/dataverse.py | 7 ++- repo2docker/contentproviders/doi.py | 18 +++---- repo2docker/contentproviders/figshare.py | 5 +- repo2docker/contentproviders/git.py | 19 ++++---- repo2docker/contentproviders/hydroshare.py | 6 +-- repo2docker/contentproviders/mercurial.py | 10 ++-- repo2docker/contentproviders/swhid.py | 16 +++---- repo2docker/contentproviders/zenodo.py | 7 +-- repo2docker/engine.py | 2 +- tests/conftest.py | 2 +- tests/memlimit/dockerfile/postBuild | 2 +- tests/memlimit/non-dockerfile/postBuild | 2 +- tests/unit/contentproviders/test_dataverse.py | 6 +-- tests/unit/contentproviders/test_doi.py | 2 +- tests/unit/contentproviders/test_figshare.py | 24 ++++------ .../unit/contentproviders/test_hydroshare.py | 6 +-- tests/unit/contentproviders/test_swhid.py | 14 +++--- tests/unit/contentproviders/test_zenodo.py | 28 +++++------ tests/unit/test_args.py | 2 +- tests/unit/test_connect_url.py | 4 +- tests/unit/test_env.py | 4 +- tests/unit/test_ports.py | 4 +- tests/unit/test_r.py | 7 +-- tests/unit/test_users.py | 4 +- tests/unit/test_utils.py | 2 +- tests/unit/test_volumes.py | 6 +-- versioneer.py | 47 +++++++++---------- 36 files changed, 139 insertions(+), 167 deletions(-) diff --git a/repo2docker/__main__.py b/repo2docker/__main__.py index 1b52b1aee..c3e7ef7e5 100644 --- a/repo2docker/__main__.py +++ b/repo2docker/__main__.py @@ -52,7 +52,7 @@ def __call__(self, parser, namespace, values, option_string=None): # key pass using current value, or don't pass if "=" not in values: try: - value_to_append = "{}={}".format(values, os.environ[values]) + value_to_append = f"{values}={os.environ[values]}" except KeyError: # no local def, so don't pass return diff --git a/repo2docker/_version.py b/repo2docker/_version.py index 442840369..aca7b127e 100644 --- a/repo2docker/_version.py +++ b/repo2docker/_version.py @@ -84,7 +84,7 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env= stderr=(subprocess.PIPE if hide_stderr else None), ) break - except EnvironmentError: + except OSError: e = sys.exc_info()[1] if e.errno == errno.ENOENT: continue @@ -94,7 +94,7 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env= return None, None else: if verbose: - print("unable to find command, tried %s" % (commands,)) + print(f"unable to find command, tried {commands}") return None, None stdout = p.communicate()[0].strip() if sys.version_info[0] >= 3: @@ -147,7 +147,7 @@ def git_get_keywords(versionfile_abs): # _version.py. keywords = {} try: - f = open(versionfile_abs, "r") + f = open(versionfile_abs) for line in f.readlines(): if line.strip().startswith("git_refnames ="): mo = re.search(r'=\s*"(.*)"', line) @@ -162,7 +162,7 @@ def git_get_keywords(versionfile_abs): if mo: keywords["date"] = mo.group(1) f.close() - except EnvironmentError: + except OSError: pass return keywords @@ -186,11 +186,11 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): if verbose: print("keywords are unexpanded, not using") raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = set([r.strip() for r in refnames.strip("()").split(",")]) + refs = {r.strip() for r in refnames.strip("()").split(",")} # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of # just "foo-1.0". If we see a "tag: " prefix, prefer those. TAG = "tag: " - tags = set([r[len(TAG) :] for r in refs if r.startswith(TAG)]) + tags = {r[len(TAG) :] for r in refs if r.startswith(TAG)} if not tags: # Either we're using git < 1.8.3, or there really are no tags. We use # a heuristic: assume all version tags have a digit. The old git %d @@ -199,7 +199,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): # between branches and tags. By ignoring refnames without digits, we # filter out many common branch names like "release" and # "stabilization", as well as "HEAD" and "master". - tags = set([r for r in refs if re.search(r"\d", r)]) + tags = {r for r in refs if re.search(r"\d", r)} if verbose: print("discarding '%s', no digits" % ",".join(refs - tags)) if verbose: @@ -302,7 +302,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): if verbose: fmt = "tag '%s' doesn't start with prefix '%s'" print(fmt % (full_tag, tag_prefix)) - pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % ( + pieces["error"] = "tag '{}' doesn't start with prefix '{}'".format( full_tag, tag_prefix, ) diff --git a/repo2docker/app.py b/repo2docker/app.py index e11f36b6c..718b12b29 100755 --- a/repo2docker/app.py +++ b/repo2docker/app.py @@ -568,7 +568,7 @@ def push_image(self): ) last_emit_time = time.time() self.log.info( - "Successfully pushed {}".format(self.output_image_spec), + f"Successfully pushed {self.output_image_spec}", extra=dict(phase=R2dState.PUSHING), ) @@ -767,7 +767,7 @@ def build(self): self.subdir, extra=dict(phase=R2dState.FAILED), ) - raise FileNotFoundError("Could not find {}".format(checkout_path)) + raise FileNotFoundError(f"Could not find {checkout_path}") with chdir(checkout_path): for BP in self.buildpacks: diff --git a/repo2docker/buildpacks/base.py b/repo2docker/buildpacks/base.py index 57ed2f353..16476e9d8 100644 --- a/repo2docker/buildpacks/base.py +++ b/repo2docker/buildpacks/base.py @@ -462,7 +462,7 @@ def render(self, build_args=None): last_user = "root" for user, script in self.get_build_scripts(): if last_user != user: - build_script_directives.append("USER {}".format(user)) + build_script_directives.append(f"USER {user}") last_user = user build_script_directives.append( "RUN {}".format(textwrap.dedent(script.strip("\n"))) @@ -472,7 +472,7 @@ def render(self, build_args=None): last_user = "root" for user, script in self.get_assemble_scripts(): if last_user != user: - assemble_script_directives.append("USER {}".format(user)) + assemble_script_directives.append(f"USER {user}") last_user = user assemble_script_directives.append( "RUN {}".format(textwrap.dedent(script.strip("\n"))) @@ -482,7 +482,7 @@ def render(self, build_args=None): last_user = "root" for user, script in self.get_preassemble_scripts(): if last_user != user: - preassemble_script_directives.append("USER {}".format(user)) + preassemble_script_directives.append(f"USER {user}") last_user = user preassemble_script_directives.append( "RUN {}".format(textwrap.dedent(script.strip("\n"))) @@ -616,8 +616,7 @@ def _filter_tar(tar): build_kwargs.update(extra_build_kwargs) - for line in client.build(**build_kwargs): - yield line + yield from client.build(**build_kwargs) class BaseImage(BuildPack): diff --git a/repo2docker/buildpacks/conda/__init__.py b/repo2docker/buildpacks/conda/__init__.py index 4408ad8ed..662e70bfe 100644 --- a/repo2docker/buildpacks/conda/__init__.py +++ b/repo2docker/buildpacks/conda/__init__.py @@ -377,7 +377,7 @@ def get_env_scripts(self): r""" echo auth-none=1 >> /etc/rstudio/rserver.conf && \ echo auth-minimum-user-id=0 >> /etc/rstudio/rserver.conf && \ - echo "rsession-which-r={0}/bin/R" >> /etc/rstudio/rserver.conf && \ + echo "rsession-which-r={}/bin/R" >> /etc/rstudio/rserver.conf && \ echo www-frame-origin=same >> /etc/rstudio/rserver.conf """.format( env_prefix @@ -387,7 +387,7 @@ def get_env_scripts(self): "${NB_USER}", # Register the jupyter kernel r""" - R --quiet -e "IRkernel::installspec(prefix='{0}')" + R --quiet -e "IRkernel::installspec(prefix='{}')" """.format( env_prefix ), diff --git a/repo2docker/buildpacks/docker.py b/repo2docker/buildpacks/docker.py index 5f0c2fb33..e0ccfc95c 100644 --- a/repo2docker/buildpacks/docker.py +++ b/repo2docker/buildpacks/docker.py @@ -57,5 +57,4 @@ def build( build_kwargs.update(extra_build_kwargs) - for line in client.build(**build_kwargs): - yield line + yield from client.build(**build_kwargs) diff --git a/repo2docker/buildpacks/legacy/__init__.py b/repo2docker/buildpacks/legacy/__init__.py index 7f5d004f6..a1b91e026 100644 --- a/repo2docker/buildpacks/legacy/__init__.py +++ b/repo2docker/buildpacks/legacy/__init__.py @@ -20,7 +20,7 @@ def detect(self): """Check if current repo should be built with the Legacy BuildPack.""" log = logging.getLogger("repo2docker") try: - with open("Dockerfile", "r") as f: + with open("Dockerfile") as f: for line in f: if line.startswith("FROM"): if "andrewosh/binder-base" in line.split("#")[0].lower(): diff --git a/repo2docker/buildpacks/python/__init__.py b/repo2docker/buildpacks/python/__init__.py index 7ea2a8264..0c12f91b8 100644 --- a/repo2docker/buildpacks/python/__init__.py +++ b/repo2docker/buildpacks/python/__init__.py @@ -67,7 +67,7 @@ def _get_pip_scripts(self): scripts.append( ( "${NB_USER}", - '{} install --no-cache-dir -r "{}"'.format(pip, requirements_file), + f'{pip} install --no-cache-dir -r "{requirements_file}"', ) ) return scripts @@ -126,9 +126,7 @@ def get_assemble_scripts(self): # setup.py exists *and* binder dir is not used if not self.binder_dir and os.path.exists(setup_py): - assemble_scripts.append( - ("${NB_USER}", "{} install --no-cache-dir .".format(pip)) - ) + assemble_scripts.append(("${NB_USER}", f"{pip} install --no-cache-dir .")) return assemble_scripts def detect(self): diff --git a/repo2docker/buildpacks/r.py b/repo2docker/buildpacks/r.py index eaf44b2b5..9009a4d87 100644 --- a/repo2docker/buildpacks/r.py +++ b/repo2docker/buildpacks/r.py @@ -139,7 +139,7 @@ def detect(self): self._checkpoint_date = datetime.date.today() - datetime.timedelta( days=2 ) - self._runtime = "r-{}".format(str(self._checkpoint_date)) + self._runtime = f"r-{str(self._checkpoint_date)}" return True def get_env(self): @@ -223,7 +223,7 @@ def get_mran_snapshot_url(self, snapshot_date, max_days_prior=7): for i in range(max_days_prior): try_date = snapshot_date - datetime.timedelta(days=i) # Fall back to MRAN if packagemanager.rstudio.com doesn't have it - url = "https://mran.microsoft.com/snapshot/{}".format(try_date.isoformat()) + url = f"https://mran.microsoft.com/snapshot/{try_date.isoformat()}" r = requests.head(url) if r.ok: return url diff --git a/repo2docker/contentproviders/dataverse.py b/repo2docker/contentproviders/dataverse.py index a1c57caa9..c308c2d09 100644 --- a/repo2docker/contentproviders/dataverse.py +++ b/repo2docker/contentproviders/dataverse.py @@ -20,7 +20,7 @@ class Dataverse(DoiProvider): def __init__(self): data_file = os.path.join(os.path.dirname(__file__), "dataverse.json") - with open(data_file, "r") as fp: + with open(data_file) as fp: self.hosts = json.load(fp)["installations"] super().__init__() @@ -97,7 +97,7 @@ def fetch(self, spec, output_dir, yield_output=False): record_id = spec["record"] host = spec["host"] - yield "Fetching Dataverse record {}.\n".format(record_id) + yield f"Fetching Dataverse record {record_id}.\n" url = "{}/api/datasets/:persistentId?persistentId={}".format( host["url"], record_id ) @@ -114,8 +114,7 @@ def fetch(self, spec, output_dir, yield_output=False): file_ref = {"download": file_url, "filename": filename} fetch_map = {key: key for key in file_ref.keys()} - for line in self.fetch_file(file_ref, fetch_map, output_dir): - yield line + yield from self.fetch_file(file_ref, fetch_map, output_dir) new_subdirs = os.listdir(output_dir) # if there is only one new subdirectory move its contents diff --git a/repo2docker/contentproviders/doi.py b/repo2docker/contentproviders/doi.py index c1941ba83..01d048ec7 100644 --- a/repo2docker/contentproviders/doi.py +++ b/repo2docker/contentproviders/doi.py @@ -23,7 +23,7 @@ def __init__(self): self.session = Session() self.session.headers.update( { - "user-agent": "repo2docker {}".format(__version__), + "user-agent": f"repo2docker {__version__}", } ) @@ -38,7 +38,7 @@ def _urlopen(self, req, headers=None): if not isinstance(req, request.Request): req = request.Request(req) - req.add_header("User-Agent", "repo2docker {}".format(__version__)) + req.add_header("User-Agent", f"repo2docker {__version__}") if headers is not None: for key, value in headers.items(): req.add_header(key, value) @@ -52,7 +52,7 @@ def doi2url(self, doi): doi = normalize_doi(doi) try: - resp = self._request("https://doi.org/{}".format(doi)) + resp = self._request(f"https://doi.org/{doi}") resp.raise_for_status() # If the DOI doesn't resolve, just return URL except HTTPError: @@ -67,26 +67,26 @@ def fetch_file(self, file_ref, host, output_dir, unzip=False): # file related to a record file_url = deep_get(file_ref, host["download"]) fname = deep_get(file_ref, host["filename"]) - logging.debug("Downloading file {} as {}\n".format(file_url, fname)) + logging.debug(f"Downloading file {file_url} as {fname}\n") - yield "Requesting {}\n".format(file_url) + yield f"Requesting {file_url}\n" resp = self._request(file_url, stream=True) resp.raise_for_status() if path.dirname(fname): sub_dir = path.join(output_dir, path.dirname(fname)) if not path.exists(sub_dir): - yield "Creating {}\n".format(sub_dir) + yield f"Creating {sub_dir}\n" makedirs(sub_dir, exist_ok=True) dst_fname = path.join(output_dir, fname) with open(dst_fname, "wb") as dst: - yield "Fetching {}\n".format(fname) + yield f"Fetching {fname}\n" for chunk in resp.iter_content(chunk_size=None): dst.write(chunk) if unzip and is_zipfile(dst_fname): - yield "Extracting {}\n".format(fname) + yield f"Extracting {fname}\n" zfile = ZipFile(dst_fname) zfile.extractall(path=output_dir) zfile.close() @@ -106,4 +106,4 @@ def fetch_file(self, file_ref, host, output_dir, unzip=False): copytree(path.join(output_dir, d), output_dir) shutil.rmtree(path.join(output_dir, d)) - yield "Fetched files: {}\n".format(os.listdir(output_dir)) + yield f"Fetched files: {os.listdir(output_dir)}\n" diff --git a/repo2docker/contentproviders/figshare.py b/repo2docker/contentproviders/figshare.py index 4b1517fc9..5d27684d1 100644 --- a/repo2docker/contentproviders/figshare.py +++ b/repo2docker/contentproviders/figshare.py @@ -91,10 +91,9 @@ def fetch(self, spec, output_dir, yield_output=False): only_one_file = len(files) == 1 for file_ref in files: unzip = file_ref["name"].endswith(".zip") and only_one_file - for line in self.fetch_file(file_ref, host, output_dir, unzip): - yield line + yield from self.fetch_file(file_ref, host, output_dir, unzip) @property def content_id(self): """The Figshare article ID""" - return "{}.v{}".format(self.article_id, self.article_version) + return f"{self.article_id}.v{self.article_version}" diff --git a/repo2docker/contentproviders/git.py b/repo2docker/contentproviders/git.py index 345298c76..9e5fb48e7 100644 --- a/repo2docker/contentproviders/git.py +++ b/repo2docker/contentproviders/git.py @@ -29,13 +29,12 @@ def fetch(self, spec, output_dir, yield_output=False): # this prevents HEAD's submodules to be cloned if ref doesn't have them cmd.extend(["--no-checkout"]) cmd.extend([repo, output_dir]) - for line in execute_cmd(cmd, capture=yield_output): - yield line + yield from execute_cmd(cmd, capture=yield_output) except subprocess.CalledProcessError as e: - msg = "Failed to clone repository from {repo}".format(repo=repo) + msg = f"Failed to clone repository from {repo}" if ref != "HEAD": - msg += " (ref {ref})".format(ref=ref) + msg += f" (ref {ref})" msg += "." raise ContentProviderException(msg) from e @@ -54,23 +53,21 @@ def fetch(self, spec, output_dir, yield_output=False): "specifying `--ref`." ) else: - msg = "Failed to check out ref {}".format(ref) + msg = f"Failed to check out ref {ref}" raise ValueError(msg) # We don't need to explicitly checkout things as the reset will # take care of that. If the hash is resolved above, we should be # able to reset to it - for line in execute_cmd( + yield from execute_cmd( ["git", "reset", "--hard", hash], cwd=output_dir, capture=yield_output - ): - yield line + ) # ensure that git submodules are initialised and updated - for line in execute_cmd( + yield from execute_cmd( ["git", "submodule", "update", "--init", "--recursive"], cwd=output_dir, capture=yield_output, - ): - yield line + ) cmd = ["git", "rev-parse", "HEAD"] sha1 = subprocess.Popen(cmd, stdout=subprocess.PIPE, cwd=output_dir) diff --git a/repo2docker/contentproviders/hydroshare.py b/repo2docker/contentproviders/hydroshare.py index 1cb8b6975..3378129ab 100755 --- a/repo2docker/contentproviders/hydroshare.py +++ b/repo2docker/contentproviders/hydroshare.py @@ -61,7 +61,7 @@ def fetch(self, spec, output_dir, yield_output=False, timeout=120): bag_url = "{}{}".format(host["django_irods"], resource_id) - yield "Downloading {}.\n".format(bag_url) + yield f"Downloading {bag_url}.\n" # bag downloads are prepared on demand and may need some time conn = self.urlopen(bag_url) @@ -82,7 +82,7 @@ def fetch(self, spec, output_dir, yield_output=False, timeout=120): time.sleep(wait_time) conn = self.urlopen(bag_url) if conn.status_code != 200: - msg = "Failed to download bag. status code {}.\n".format(conn.status_code) + msg = f"Failed to download bag. status code {conn.status_code}.\n" yield msg raise ContentProviderException(msg) # Bag creation seems to need a small time buffer after it says it's ready. @@ -102,4 +102,4 @@ def fetch(self, spec, output_dir, yield_output=False, timeout=120): @property def content_id(self): """The HydroShare resource ID""" - return "{}.v{}".format(self.resource_id, self.version) + return f"{self.resource_id}.v{self.version}" diff --git a/repo2docker/contentproviders/mercurial.py b/repo2docker/contentproviders/mercurial.py index 60d5f2fd8..e29584f29 100644 --- a/repo2docker/contentproviders/mercurial.py +++ b/repo2docker/contentproviders/mercurial.py @@ -41,8 +41,7 @@ def fetch(self, spec, output_dir, yield_output=False): # don't update so the clone will include an empty working # directory, the given ref will be updated out later cmd.extend(["--noupdate"]) - for line in execute_cmd(cmd, capture=yield_output): - yield line + yield from execute_cmd(cmd, capture=yield_output) except subprocess.CalledProcessError as error: msg = f"Failed to clone repository from {repo}" @@ -54,17 +53,16 @@ def fetch(self, spec, output_dir, yield_output=False): # check out the specific ref given by the user if ref is not None: try: - for line in execute_cmd( + yield from execute_cmd( ["hg", "update", "--clean", ref] + args_enabling_topic, cwd=output_dir, capture=yield_output, - ): - yield line + ) except subprocess.CalledProcessError: self.log.error( "Failed to update to ref %s", ref, extra=dict(phase=R2dState.FAILED) ) - raise ValueError("Failed to update to ref {}".format(ref)) + raise ValueError(f"Failed to update to ref {ref}") cmd = ["hg", "identify", "-i"] + args_enabling_topic sha1 = subprocess.Popen(cmd, stdout=subprocess.PIPE, cwd=output_dir) diff --git a/repo2docker/contentproviders/swhid.py b/repo2docker/contentproviders/swhid.py index e20501770..2a964e70f 100644 --- a/repo2docker/contentproviders/swhid.py +++ b/repo2docker/contentproviders/swhid.py @@ -34,12 +34,12 @@ def __init__(self): self.session = requests.Session() self.session.headers.update( { - "user-agent": "repo2docker {}".format(__version__), + "user-agent": f"repo2docker {__version__}", } ) def set_auth_token(self, token): - header = {"Authorization": "Bearer {}".format(token)} + header = {"Authorization": f"Bearer {token}"} self.session.headers.update(header) def _request(self, url, method="GET"): @@ -72,8 +72,8 @@ def detect(self, swhid, ref=None, extra_args=None): return {"swhid": swhid, "swhid_obj": swhid_dict} def fetch_directory(self, dir_hash, output_dir): - url = "{}/vault/directory/{}/".format(self.base_url, dir_hash) - yield "Fetching directory {} from {}\n".format(dir_hash, url) + url = f"{self.base_url}/vault/directory/{dir_hash}/" + yield f"Fetching directory {dir_hash} from {url}\n" resp = self._request(url, "POST") receipt = resp.json() status = receipt["status"] @@ -92,7 +92,7 @@ def fetch_directory(self, dir_hash, output_dir): # move its content one level up copytree(path.join(output_dir, dir_hash), output_dir) shutil.rmtree(path.join(output_dir, dir_hash)) - yield "Fetched files: {}\n".format(os.listdir(output_dir)) + yield f"Fetched files: {os.listdir(output_dir)}\n" def fetch(self, spec, output_dir, yield_output=False): swhid = spec["swhid"] @@ -101,12 +101,12 @@ def fetch(self, spec, output_dir, yield_output=False): if swhid_obj["type"] == "rev": # need to get the directory for this revision sha1git = swhid_obj["hash"] - url = "{}/revision/{}/".format(self.base_url, sha1git) - yield "Fetching revision {} from {}\n".format(sha1git, url) + url = f"{self.base_url}/revision/{sha1git}/" + yield f"Fetching revision {sha1git} from {url}\n" resp = self._request(url) assert resp.ok, (resp.content, self.session.headers) directory = resp.json()["directory"] - self.swhid = "swh:1:dir:{}".format(directory) + self.swhid = f"swh:1:dir:{directory}" yield from self.fetch_directory(directory, output_dir) elif swhid_obj["type"] == "dir": self.swhid = swhid diff --git a/repo2docker/contentproviders/zenodo.py b/repo2docker/contentproviders/zenodo.py index 7a5d09325..a58e295f8 100644 --- a/repo2docker/contentproviders/zenodo.py +++ b/repo2docker/contentproviders/zenodo.py @@ -66,7 +66,7 @@ def fetch(self, spec, output_dir, yield_output=False): record_id = spec["record"] host = spec["host"] - yield "Fetching Zenodo record {}.\n".format(record_id) + yield f"Fetching Zenodo record {record_id}.\n" resp = self.urlopen( "{}{}".format(host["api"], record_id), headers={"accept": "application/json"}, @@ -77,10 +77,7 @@ def fetch(self, spec, output_dir, yield_output=False): files = deep_get(record, host["filepath"]) only_one_file = len(files) == 1 for file_ref in files: - for line in self.fetch_file( - file_ref, host, output_dir, unzip=only_one_file - ): - yield line + yield from self.fetch_file(file_ref, host, output_dir, unzip=only_one_file) @property def content_id(self): diff --git a/repo2docker/engine.py b/repo2docker/engine.py index 9b5e92eb2..459b2be83 100644 --- a/repo2docker/engine.py +++ b/repo2docker/engine.py @@ -131,7 +131,7 @@ def config(self): return self._config def __repr__(self): - return "Image(tags={},config={})".format(self.tags, self.config) + return f"Image(tags={self.tags},config={self.config})" class ContainerEngine(LoggingConfigurable): diff --git a/tests/conftest.py b/tests/conftest.py index 19c0ca6ec..eda58223f 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -212,7 +212,7 @@ def repr_failure(self, excinfo): err = excinfo.value if isinstance(err, SystemExit): cmd = "jupyter-repo2docker %s" % " ".join(map(pipes.quote, self.args)) - return "%s | exited with status=%s" % (cmd, err.code) + return f"{cmd} | exited with status={err.code}" else: return super().repr_failure(excinfo) diff --git a/tests/memlimit/dockerfile/postBuild b/tests/memlimit/dockerfile/postBuild index af9f9a3b4..4fe5360f2 100755 --- a/tests/memlimit/dockerfile/postBuild +++ b/tests/memlimit/dockerfile/postBuild @@ -20,7 +20,7 @@ with open("mem_allocate_mb") as f: mem_allocate_mb = int(f.read().strip()) size = 1024 * 1024 * mem_allocate_mb -print("trying to allocate {}MB".format(mem_allocate_mb)) +print(f"trying to allocate {mem_allocate_mb}MB") ret = libc.malloc(size) diff --git a/tests/memlimit/non-dockerfile/postBuild b/tests/memlimit/non-dockerfile/postBuild index af9f9a3b4..4fe5360f2 100755 --- a/tests/memlimit/non-dockerfile/postBuild +++ b/tests/memlimit/non-dockerfile/postBuild @@ -20,7 +20,7 @@ with open("mem_allocate_mb") as f: mem_allocate_mb = int(f.read().strip()) size = 1024 * 1024 * mem_allocate_mb -print("trying to allocate {}MB".format(mem_allocate_mb)) +print(f"trying to allocate {mem_allocate_mb}MB") ret = libc.malloc(size) diff --git a/tests/unit/contentproviders/test_dataverse.py b/tests/unit/contentproviders/test_dataverse.py index 3d912a7b9..63a584716 100644 --- a/tests/unit/contentproviders/test_dataverse.py +++ b/tests/unit/contentproviders/test_dataverse.py @@ -12,8 +12,8 @@ test_dv = Dataverse() -harvard_dv = next((_ for _ in test_dv.hosts if _["name"] == "Harvard Dataverse")) -cimmyt_dv = next((_ for _ in test_dv.hosts if _["name"] == "CIMMYT Research Data")) +harvard_dv = next(_ for _ in test_dv.hosts if _["name"] == "Harvard Dataverse") +cimmyt_dv = next(_ for _ in test_dv.hosts if _["name"] == "CIMMYT Research Data") test_hosts = [ ( [ @@ -153,7 +153,7 @@ def mock_filecontent(req, context): for l in dv.fetch(spec, d): output.append(l) unpacked_files = set(os.listdir(d)) - expected = set(["directory", "some-file.txt"]) + expected = {"directory", "some-file.txt"} assert expected == unpacked_files assert os.path.isfile( os.path.join(d, "directory", "subdirectory", "the-other-file.txt") diff --git a/tests/unit/contentproviders/test_doi.py b/tests/unit/contentproviders/test_doi.py index dbe391604..ed2dcb736 100644 --- a/tests/unit/contentproviders/test_doi.py +++ b/tests/unit/contentproviders/test_doi.py @@ -27,7 +27,7 @@ def test_url_headers(requests_mock): result = doi.urlopen("https://mybinder.org", headers=headers) assert "test1" in result.request.headers assert "Test2" in result.request.headers - assert result.request.headers["User-Agent"] == "repo2docker {}".format(__version__) + assert result.request.headers["User-Agent"] == f"repo2docker {__version__}" def test_unresolving_doi(): diff --git a/tests/unit/contentproviders/test_figshare.py b/tests/unit/contentproviders/test_figshare.py index 7d29fbcbc..3de67e985 100644 --- a/tests/unit/contentproviders/test_figshare.py +++ b/tests/unit/contentproviders/test_figshare.py @@ -113,8 +113,8 @@ def test_detect_not_figshare(): def figshare_archive(prefix="a_directory"): with NamedTemporaryFile(suffix=".zip") as zfile: with ZipFile(zfile.name, mode="w") as zip: - zip.writestr("{}/some-file.txt".format(prefix), "some content") - zip.writestr("{}/some-other-file.txt".format(prefix), "some more content") + zip.writestr(f"{prefix}/some-file.txt", "some content") + zip.writestr(f"{prefix}/some-other-file.txt", "some more content") yield zfile.name @@ -127,7 +127,7 @@ def test_fetch_zip(requests_mock): { "name": "afake.zip", "is_link_only": False, - "download_url": "file://{}".format(fig_path), + "download_url": f"file://{fig_path}", } ] } @@ -135,9 +135,7 @@ def test_fetch_zip(requests_mock): "https://api.figshare.com/v2/articles/123456/versions/42", json=mock_response, ) - requests_mock.get( - "file://{}".format(fig_path), content=open(fig_path, "rb").read() - ) + requests_mock.get(f"file://{fig_path}", content=open(fig_path, "rb").read()) # with patch.object(Figshare, "urlopen", new=mock_urlopen): with TemporaryDirectory() as d: @@ -146,7 +144,7 @@ def test_fetch_zip(requests_mock): output.append(l) unpacked_files = set(os.listdir(d)) - expected = set(["some-other-file.txt", "some-file.txt"]) + expected = {"some-other-file.txt", "some-file.txt"} assert expected == unpacked_files @@ -157,12 +155,12 @@ def test_fetch_data(requests_mock): "files": [ { "name": "afake.file", - "download_url": "file://{}".format(a_path), + "download_url": f"file://{a_path}", "is_link_only": False, }, { "name": "bfake.data", - "download_url": "file://{}".format(b_path), + "download_url": f"file://{b_path}", "is_link_only": False, }, {"name": "cfake.link", "is_link_only": True}, @@ -173,12 +171,8 @@ def test_fetch_data(requests_mock): "https://api.figshare.com/v2/articles/123456/versions/42", json=mock_response, ) - requests_mock.get( - "file://{}".format(a_path), content=open(a_path, "rb").read() - ) - requests_mock.get( - "file://{}".format(b_path), content=open(b_path, "rb").read() - ) + requests_mock.get(f"file://{a_path}", content=open(a_path, "rb").read()) + requests_mock.get(f"file://{b_path}", content=open(b_path, "rb").read()) with TemporaryDirectory() as d: output = [] diff --git a/tests/unit/contentproviders/test_hydroshare.py b/tests/unit/contentproviders/test_hydroshare.py index da80905fb..b0211c52f 100755 --- a/tests/unit/contentproviders/test_hydroshare.py +++ b/tests/unit/contentproviders/test_hydroshare.py @@ -103,8 +103,8 @@ def test_detect_hydroshare(requests_mock): def hydroshare_archive(prefix="b8f6eae9d89241cf8b5904033460af61/data/contents"): with NamedTemporaryFile(suffix=".zip") as zfile: with ZipFile(zfile.name, mode="w") as zip: - zip.writestr("{}/some-file.txt".format(prefix), "some content") - zip.writestr("{}/some-other-file.txt".format(prefix), "some more content") + zip.writestr(f"{prefix}/some-file.txt", "some content") + zip.writestr(f"{prefix}/some-other-file.txt", "some more content") yield zfile @@ -149,7 +149,7 @@ def test_fetch_bag(): output.append(l) unpacked_files = set(os.listdir(d)) - expected = set(["some-other-file.txt", "some-file.txt"]) + expected = {"some-other-file.txt", "some-file.txt"} assert expected == unpacked_files diff --git a/tests/unit/contentproviders/test_swhid.py b/tests/unit/contentproviders/test_swhid.py index 953218e3c..48c1fa31e 100644 --- a/tests/unit/contentproviders/test_swhid.py +++ b/tests/unit/contentproviders/test_swhid.py @@ -99,7 +99,7 @@ def mocked_provider(tmpdir, dirhash, tarfile_buf): adapter.register_uri( "GET", - "mock://api/1/revision/{}/".format(NULLID), + f"mock://api/1/revision/{NULLID}/", json={ "author": {"fullname": "John Doe "}, "directory": dirhash, @@ -107,25 +107,25 @@ def mocked_provider(tmpdir, dirhash, tarfile_buf): ) adapter.register_uri( "POST", - "mock://api/1/vault/directory/{}/".format(dirhash), + f"mock://api/1/vault/directory/{dirhash}/", json={ - "fetch_url": "mock://api/1/vault/directory/{}/raw/".format(dirhash), + "fetch_url": f"mock://api/1/vault/directory/{dirhash}/raw/", "status": "new", }, ) adapter.register_uri( "GET", - "mock://api/1/vault/directory/{}/".format(dirhash), + f"mock://api/1/vault/directory/{dirhash}/", [ { "json": { - "fetch_url": "mock://api/1/vault/directory/{}/raw/".format(dirhash), + "fetch_url": f"mock://api/1/vault/directory/{dirhash}/raw/", "status": "pending", } }, { "json": { - "fetch_url": "mock://api/1/vault/directory/{}/raw/".format(dirhash), + "fetch_url": f"mock://api/1/vault/directory/{dirhash}/raw/", "status": "done", } }, @@ -133,7 +133,7 @@ def mocked_provider(tmpdir, dirhash, tarfile_buf): ) adapter.register_uri( "GET", - "mock://api/1/vault/directory/{}/raw/".format(dirhash), + f"mock://api/1/vault/directory/{dirhash}/raw/", content=tarfile_buf, ) return provider diff --git a/tests/unit/contentproviders/test_zenodo.py b/tests/unit/contentproviders/test_zenodo.py index c46cf8d94..88e143c60 100644 --- a/tests/unit/contentproviders/test_zenodo.py +++ b/tests/unit/contentproviders/test_zenodo.py @@ -82,8 +82,8 @@ def test_detect_zenodo(test_input, expected, requests_mock): def zenodo_archive(prefix="a_directory"): with NamedTemporaryFile(suffix=".zip") as zfile: with ZipFile(zfile.name, mode="w") as zip: - zip.writestr("{}/some-file.txt".format(prefix), "some content") - zip.writestr("{}/some-other-file.txt".format(prefix), "some more content") + zip.writestr(f"{prefix}/some-file.txt", "some content") + zip.writestr(f"{prefix}/some-other-file.txt", "some more content") yield zfile.name @@ -96,15 +96,13 @@ def test_fetch_software_from_github_archive(requests_mock): "files": [ { "filename": "some_dir/afake.zip", - "links": {"download": "file://{}".format(zen_path)}, + "links": {"download": f"file://{zen_path}"}, } ], "metadata": {"upload_type": "other"}, } requests_mock.get("https://zenodo.org/api/records/1234", json=mock_response) - requests_mock.get( - "file://{}".format(zen_path), content=open(zen_path, "rb").read() - ) + requests_mock.get(f"file://{zen_path}", content=open(zen_path, "rb").read()) zen = Zenodo() spec = {"host": test_zen.hosts[1], "record": "1234"} @@ -115,7 +113,7 @@ def test_fetch_software_from_github_archive(requests_mock): output.append(l) unpacked_files = set(os.listdir(d)) - expected = set(["some-other-file.txt", "some-file.txt"]) + expected = {"some-other-file.txt", "some-file.txt"} assert expected == unpacked_files @@ -129,15 +127,13 @@ def test_fetch_software(requests_mock): # this is the difference to the GitHub generated one, # the ZIP file isn't in a directory "filename": "afake.zip", - "links": {"download": "file://{}".format(zen_path)}, + "links": {"download": f"file://{zen_path}"}, } ], "metadata": {"upload_type": "software"}, } requests_mock.get("https://zenodo.org/api/records/1234", json=mock_response) - requests_mock.get( - "file://{}".format(zen_path), content=open(zen_path, "rb").read() - ) + requests_mock.get(f"file://{zen_path}", content=open(zen_path, "rb").read()) with TemporaryDirectory() as d: zen = Zenodo() @@ -147,7 +143,7 @@ def test_fetch_software(requests_mock): output.append(l) unpacked_files = set(os.listdir(d)) - expected = set(["some-other-file.txt", "some-file.txt"]) + expected = {"some-other-file.txt", "some-file.txt"} assert expected == unpacked_files @@ -159,21 +155,21 @@ def test_fetch_data(requests_mock): "files": [ { "filename": "afake.zip", - "links": {"download": "file://{}".format(a_zen_path)}, + "links": {"download": f"file://{a_zen_path}"}, }, { "filename": "bfake.zip", - "links": {"download": "file://{}".format(b_zen_path)}, + "links": {"download": f"file://{b_zen_path}"}, }, ], "metadata": {"upload_type": "data"}, } requests_mock.get("https://zenodo.org/api/records/1234", json=mock_response) requests_mock.get( - "file://{}".format(a_zen_path), content=open(a_zen_path, "rb").read() + f"file://{a_zen_path}", content=open(a_zen_path, "rb").read() ) requests_mock.get( - "file://{}".format(b_zen_path), content=open(b_zen_path, "rb").read() + f"file://{b_zen_path}", content=open(b_zen_path, "rb").read() ) with TemporaryDirectory() as d: diff --git a/tests/unit/test_args.py b/tests/unit/test_args.py index e5fd2c1ab..404ee796c 100644 --- a/tests/unit/test_args.py +++ b/tests/unit/test_args.py @@ -13,7 +13,7 @@ def test_version(capsys): """ with pytest.raises(SystemExit): make_r2d(["--version"]) - assert capsys.readouterr().out == "{}\n".format(__version__) + assert capsys.readouterr().out == f"{__version__}\n" def test_simple(): diff --git a/tests/unit/test_connect_url.py b/tests/unit/test_connect_url.py index 681cc6808..3115a8ab3 100644 --- a/tests/unit/test_connect_url.py +++ b/tests/unit/test_connect_url.py @@ -40,8 +40,8 @@ def test_connect_url(tmpdir): app.start() container = app.start_container() - container_url = "http://{}:{}/api".format(app.hostname, app.port) - expected_url = "http://{}:{}".format(app.hostname, app.port) + container_url = f"http://{app.hostname}:{app.port}/api" + expected_url = f"http://{app.hostname}:{app.port}" # wait a bit for the container to be ready # give the container a chance to start diff --git a/tests/unit/test_env.py b/tests/unit/test_env.py index ee01b3615..fde4aed43 100644 --- a/tests/unit/test_env.py +++ b/tests/unit/test_env.py @@ -30,7 +30,7 @@ def test_env(capfd): "repo2docker", # 'key=value' are exported as is in docker "-e", - "FOO={}".format(ts), + f"FOO={ts}", "--env", "BAR=baz", # 'key' is exported with the currently exported value @@ -65,7 +65,7 @@ def test_env(capfd): # stderr should contain lines of output declares = [x for x in captured.err.splitlines() if x.startswith("declare")] - assert 'declare -x FOO="{}"'.format(ts) in declares + assert f'declare -x FOO="{ts}"' in declares assert 'declare -x BAR="baz"' in declares assert 'declare -x SPAM="eggs"' in declares assert "declare -x NO_SPAM" not in declares diff --git a/tests/unit/test_ports.py b/tests/unit/test_ports.py index 09944e873..90148ba41 100644 --- a/tests/unit/test_ports.py +++ b/tests/unit/test_ports.py @@ -82,13 +82,13 @@ def _cleanup(): if all_ports: port = port_mapping["8888/tcp"][0]["HostPort"] - url = "http://{}:{}".format(host, port) + url = f"http://{host}:{port}" for i in range(5): try: r = requests.get(url) r.raise_for_status() except Exception as e: - print("No response from {}: {}".format(url, e)) + print(f"No response from {url}: {e}") container.reload() assert container.status == "running" time.sleep(3) diff --git a/tests/unit/test_r.py b/tests/unit/test_r.py index f13ee7396..3d141cfc7 100644 --- a/tests/unit/test_r.py +++ b/tests/unit/test_r.py @@ -87,6 +87,7 @@ def mock_request_head(url): with patch("requests.head", side_effect=mock_request_head): r = buildpacks.RBuildPack() - assert r.get_mran_snapshot_url( - requested - ) == "https://mran.microsoft.com/snapshot/{}".format(expected.isoformat()) + assert ( + r.get_mran_snapshot_url(requested) + == f"https://mran.microsoft.com/snapshot/{expected.isoformat()}" + ) diff --git a/tests/unit/test_users.py b/tests/unit/test_users.py index 2bceb5ff9..e14eeaf13 100644 --- a/tests/unit/test_users.py +++ b/tests/unit/test_users.py @@ -35,7 +35,7 @@ def test_user(): [ "repo2docker", "-v", - "{}:/home/{}".format(tmpdir, username), + f"{tmpdir}:/home/{username}", "--user-id", userid, "--user-name", @@ -53,7 +53,7 @@ def test_user(): with open(os.path.join(tmpdir, "id")) as f: assert f.read().strip() == userid with open(os.path.join(tmpdir, "pwd")) as f: - assert f.read().strip() == "/home/{}".format(username) + assert f.read().strip() == f"/home/{username}" with open(os.path.join(tmpdir, "name")) as f: assert f.read().strip() == username with open(os.path.join(tmpdir, "name")) as f: diff --git a/tests/unit/test_utils.py b/tests/unit/test_utils.py index ef9a8d38f..28401e33f 100644 --- a/tests/unit/test_utils.py +++ b/tests/unit/test_utils.py @@ -90,7 +90,7 @@ def test_invalid_port_mapping(port_spec): with pytest.raises(ValueError) as e: utils.validate_and_generate_port_mapping([port_spec]) - assert 'Port specification "{}"'.format(port_spec) in str(e.value) + assert f'Port specification "{port_spec}"' in str(e.value) def test_deep_get(): diff --git a/tests/unit/test_volumes.py b/tests/unit/test_volumes.py index db6efba2d..9e108ec82 100644 --- a/tests/unit/test_volumes.py +++ b/tests/unit/test_volumes.py @@ -22,7 +22,7 @@ def test_volume_abspath(): [ "repo2docker", "-v", - "{}:/home/{}".format(tmpdir, username), + f"{tmpdir}:/home/{username}", "--user-id", str(os.geteuid()), "--user-name", @@ -31,7 +31,7 @@ def test_volume_abspath(): "--", "/bin/bash", "-c", - "echo -n {} > ts".format(ts), + f"echo -n {ts} > ts", ] ) @@ -61,7 +61,7 @@ def test_volume_relpath(): "--", "/bin/bash", "-c", - "echo -n {} > ts".format(ts), + f"echo -n {ts} > ts", ] ) diff --git a/versioneer.py b/versioneer.py index 2b5454051..a47088994 100644 --- a/versioneer.py +++ b/versioneer.py @@ -275,7 +275,6 @@ """ -from __future__ import print_function try: import configparser @@ -344,7 +343,7 @@ def get_config_from_root(root): # the top of versioneer.py for instructions on writing your setup.cfg . setup_cfg = os.path.join(root, "setup.cfg") parser = configparser.SafeConfigParser() - with open(setup_cfg, "r") as f: + with open(setup_cfg) as f: parser.readfp(f) VCS = parser.get("versioneer", "VCS") # mandatory @@ -404,7 +403,7 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env= stderr=(subprocess.PIPE if hide_stderr else None), ) break - except EnvironmentError: + except OSError: e = sys.exc_info()[1] if e.errno == errno.ENOENT: continue @@ -414,7 +413,7 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env= return None, None else: if verbose: - print("unable to find command, tried %s" % (commands,)) + print(f"unable to find command, tried {commands}") return None, None stdout = p.communicate()[0].strip() if sys.version_info[0] >= 3: @@ -429,7 +428,7 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env= LONG_VERSION_PY[ "git" -] = ''' +] = r''' # This file helps to compute a version number in source trees obtained from # git-archive tarball (such as those provided by githubs download-from-tag # feature). Distribution tarballs (built by setup.py sdist) and build @@ -961,7 +960,7 @@ def git_get_keywords(versionfile_abs): # _version.py. keywords = {} try: - f = open(versionfile_abs, "r") + f = open(versionfile_abs) for line in f.readlines(): if line.strip().startswith("git_refnames ="): mo = re.search(r'=\s*"(.*)"', line) @@ -976,7 +975,7 @@ def git_get_keywords(versionfile_abs): if mo: keywords["date"] = mo.group(1) f.close() - except EnvironmentError: + except OSError: pass return keywords @@ -1000,11 +999,11 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): if verbose: print("keywords are unexpanded, not using") raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = set([r.strip() for r in refnames.strip("()").split(",")]) + refs = {r.strip() for r in refnames.strip("()").split(",")} # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of # just "foo-1.0". If we see a "tag: " prefix, prefer those. TAG = "tag: " - tags = set([r[len(TAG) :] for r in refs if r.startswith(TAG)]) + tags = {r[len(TAG) :] for r in refs if r.startswith(TAG)} if not tags: # Either we're using git < 1.8.3, or there really are no tags. We use # a heuristic: assume all version tags have a digit. The old git %d @@ -1013,7 +1012,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose): # between branches and tags. By ignoring refnames without digits, we # filter out many common branch names like "release" and # "stabilization", as well as "HEAD" and "master". - tags = set([r for r in refs if re.search(r"\d", r)]) + tags = {r for r in refs if re.search(r"\d", r)} if verbose: print("discarding '%s', no digits" % ",".join(refs - tags)) if verbose: @@ -1116,7 +1115,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): if verbose: fmt = "tag '%s' doesn't start with prefix '%s'" print(fmt % (full_tag, tag_prefix)) - pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % ( + pieces["error"] = "tag '{}' doesn't start with prefix '{}'".format( full_tag, tag_prefix, ) @@ -1166,13 +1165,13 @@ def do_vcs_install(manifest_in, versionfile_source, ipy): files.append(versioneer_file) present = False try: - f = open(".gitattributes", "r") + f = open(".gitattributes") for line in f.readlines(): if line.strip().startswith(versionfile_source): if "export-subst" in line.strip().split()[1:]: present = True f.close() - except EnvironmentError: + except OSError: pass if not present: f = open(".gitattributes", "a+") @@ -1236,7 +1235,7 @@ def versions_from_file(filename): try: with open(filename) as f: contents = f.read() - except EnvironmentError: + except OSError: raise NotThisMethod("unable to read _version.py") mo = re.search( r"version_json = '''\n(.*)''' # END VERSION_JSON", contents, re.M | re.S @@ -1257,7 +1256,7 @@ def write_to_version_file(filename, versions): with open(filename, "w") as f: f.write(SHORT_VERSION_PY % contents) - print("set %s to '%s'" % (filename, versions["version"])) + print("set {} to '{}'".format(filename, versions["version"])) def plus_or_dot(pieces): @@ -1482,7 +1481,7 @@ def get_versions(verbose=False): try: ver = versions_from_file(versionfile_abs) if verbose: - print("got version from file %s %s" % (versionfile_abs, ver)) + print(f"got version from file {versionfile_abs} {ver}") return ver except NotThisMethod: pass @@ -1755,11 +1754,7 @@ def do_setup(): root = get_root() try: cfg = get_config_from_root(root) - except ( - EnvironmentError, - configparser.NoSectionError, - configparser.NoOptionError, - ) as e: + except (OSError, configparser.NoSectionError, configparser.NoOptionError) as e: if isinstance(e, (EnvironmentError, configparser.NoSectionError)): print("Adding sample versioneer config to setup.cfg", file=sys.stderr) with open(os.path.join(root, "setup.cfg"), "a") as f: @@ -1784,9 +1779,9 @@ def do_setup(): ipy = os.path.join(os.path.dirname(cfg.versionfile_source), "__init__.py") if os.path.exists(ipy): try: - with open(ipy, "r") as f: + with open(ipy) as f: old = f.read() - except EnvironmentError: + except OSError: old = "" if INIT_PY_SNIPPET not in old: print(" appending to %s" % ipy) @@ -1805,12 +1800,12 @@ def do_setup(): manifest_in = os.path.join(root, "MANIFEST.in") simple_includes = set() try: - with open(manifest_in, "r") as f: + with open(manifest_in) as f: for line in f: if line.startswith("include "): for include in line.split()[1:]: simple_includes.add(include) - except EnvironmentError: + except OSError: pass # That doesn't cover everything MANIFEST.in can do # (http://docs.python.org/2/distutils/sourcedist.html#commands), so @@ -1844,7 +1839,7 @@ def scan_setup_py(): found = set() setters = False errors = 0 - with open("setup.py", "r") as f: + with open("setup.py") as f: for line in f.readlines(): if "import versioneer" in line: found.add("import") From 15a1fb6e2d22c013523835280e19c186e605b05f Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Sun, 23 Oct 2022 19:18:37 +0200 Subject: [PATCH 035/171] refactor: manually add transitions to f-strings --- docs/source/conf.py | 6 ++-- repo2docker/__main__.py | 4 +-- repo2docker/_version.py | 9 +++--- repo2docker/app.py | 35 +++++++-------------- repo2docker/buildpacks/_r_base.py | 16 +++------- repo2docker/buildpacks/base.py | 7 ++--- repo2docker/buildpacks/conda/__init__.py | 36 +++++++++------------- repo2docker/buildpacks/docker.py | 4 +-- repo2docker/buildpacks/nix/__init__.py | 8 ++--- repo2docker/buildpacks/pipfile/__init__.py | 4 +-- repo2docker/buildpacks/python/__init__.py | 4 +-- repo2docker/buildpacks/r.py | 15 +++------ repo2docker/contentproviders/base.py | 4 +-- repo2docker/contentproviders/dataverse.py | 12 +++----- repo2docker/contentproviders/figshare.py | 6 ++-- repo2docker/contentproviders/git.py | 2 +- repo2docker/contentproviders/hydroshare.py | 6 ++-- repo2docker/contentproviders/mercurial.py | 2 +- repo2docker/contentproviders/zenodo.py | 2 +- repo2docker/utils.py | 18 +++++------ tests/conda/py2/verify | 2 +- tests/conftest.py | 8 ++--- tests/unit/test_connect_url.py | 4 +-- tests/unit/test_subdir.py | 2 +- tests/unit/test_users.py | 13 +++----- tests/venv/usr-bin/verify | 2 +- versioneer.py | 11 +++---- 27 files changed, 90 insertions(+), 152 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 11c156cfe..4e33931a9 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -61,12 +61,10 @@ default_python = CondaBuildPack.major_pythons["3"] -rst_prolog = """ +rst_prolog = f""" .. |default_python| replace:: **Python {default_python}** .. |default_python_version| replace:: {default_python} -""".format( - default_python=default_python -) +""" # -- Options for HTML output ------------------------------------------------- diff --git a/repo2docker/__main__.py b/repo2docker/__main__.py index c3e7ef7e5..2ca17f171 100644 --- a/repo2docker/__main__.py +++ b/repo2docker/__main__.py @@ -304,8 +304,8 @@ def make_r2d(argv=None): r2d.volumes[os.path.abspath(args.repo)] = "." else: r2d.log.error( - 'Cannot mount "{}" in editable mode ' - "as it is not a directory".format(args.repo), + f'Cannot mount "{args.repo}" in editable mode ' + "as it is not a directory", extra=dict(phase=R2dState.FAILED), ) sys.exit(1) diff --git a/repo2docker/_version.py b/repo2docker/_version.py index aca7b127e..017b26612 100644 --- a/repo2docker/_version.py +++ b/repo2docker/_version.py @@ -293,7 +293,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe) if not mo: # unparseable. Maybe git-describe is misbehaving? - pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out + pieces["error"] = f"unable to parse git-describe output: '{describe_out}'" return pieces # tag @@ -302,10 +302,9 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): if verbose: fmt = "tag '%s' doesn't start with prefix '%s'" print(fmt % (full_tag, tag_prefix)) - pieces["error"] = "tag '{}' doesn't start with prefix '{}'".format( - full_tag, - tag_prefix, - ) + pieces[ + "error" + ] = f"tag '{full_tag}' doesn't start with prefix '{tag_prefix}'" return pieces pieces["closest-tag"] = full_tag[len(tag_prefix) :] diff --git a/repo2docker/app.py b/repo2docker/app.py index 718b12b29..5bee81b41 100755 --- a/repo2docker/app.py +++ b/repo2docker/app.py @@ -425,9 +425,7 @@ def get_engine(self): entry = engines[self.engine] except KeyError: raise ContainerEngineException( - "Container engine '{}' not found. Available engines: {}".format( - self.engine, ",".join(engines.keys()) - ) + f"Container engine '{self.engine}' not found. Available engines: {','.join(engines.keys())}" ) engine_class = entry.load() return engine_class(parent=self) @@ -447,16 +445,11 @@ def fetch(self, url, ref, checkout_path): spec = cp.detect(url, ref=ref) if spec is not None: picked_content_provider = cp - self.log.info( - "Picked {cp} content " - "provider.\n".format(cp=cp.__class__.__name__) - ) + self.log.info(f"Picked {cp.__class__.__name__} content provider.\n") break if picked_content_provider is None: - self.log.error( - "No matching content provider found for " "{url}.".format(url=url) - ) + self.log.error(f"No matching content provider found for {url}.") swh_token = self.config.get("swh_token", self.swh_token) if swh_token and isinstance(picked_content_provider, contentproviders.Swhid): @@ -488,8 +481,7 @@ def json_excepthook(self, etype, evalue, traceback): Avoids non-JSON output on errors when using --json-logs """ self.log.error( - "Error during build: %s", - evalue, + f"Error during build: {evalue}", exc_info=(etype, evalue, traceback), extra=dict(phase=R2dState.FAILED), ) @@ -619,11 +611,9 @@ def start_container(self): run_cmd = [ "jupyter", "notebook", - "--ip", - "0.0.0.0", - "--port", - container_port, - f"--NotebookApp.custom_display_url=http://{host_name}:{host_port}" + "--ip=0.0.0.0", + f"--port={container_port}", + f"--NotebookApp.custom_display_url=http://{host_name}:{host_port}", "--NotebookApp.default_url=/lab", ] else: @@ -730,7 +720,7 @@ def build(self): try: docker_client = self.get_engine() except ContainerEngineException as e: - self.log.error("\nContainer engine initialization error: %s\n", e) + self.log.error(f"\nContainer engine initialization error: {e}\n") self.exit(1) # If the source to be executed is a directory, continue using the @@ -751,8 +741,7 @@ def build(self): if self.find_image(): self.log.info( - "Reusing existing image ({}), not " - "building.".format(self.output_image_spec) + f"Reusing existing image ({self.output_image_spec}), not building." ) # no need to build, so skip to the end by `return`ing here # this will still execute the finally clause and let's us @@ -763,8 +752,7 @@ def build(self): checkout_path = os.path.join(checkout_path, self.subdir) if not os.path.isdir(checkout_path): self.log.error( - "Subdirectory %s does not exist", - self.subdir, + f"Subdirectory {self.subdir} does not exist", extra=dict(phase=R2dState.FAILED), ) raise FileNotFoundError(f"Could not find {checkout_path}") @@ -808,8 +796,7 @@ def build(self): ) self.log.info( - "Using %s builder\n", - bp.__class__.__name__, + f"Using {bp.__class__.__name__} builder\n", extra=dict(phase=R2dState.BUILDING), ) diff --git a/repo2docker/buildpacks/_r_base.py b/repo2docker/buildpacks/_r_base.py index c73273793..35a3177b5 100644 --- a/repo2docker/buildpacks/_r_base.py +++ b/repo2docker/buildpacks/_r_base.py @@ -26,7 +26,7 @@ def rstudio_base_scripts(r_version): # we should have --no-install-recommends on all our apt-get install commands, # but here it's important because these recommend r-base, # which will upgrade the installed version of R, undoing our pinned version - r""" + rf""" curl --silent --location --fail {rstudio_url} > /tmp/rstudio.deb && \ curl --silent --location --fail {shiny_server_url} > /tmp/shiny.deb && \ echo '{rstudio_sha256sum} /tmp/rstudio.deb' | sha256sum -c - && \ @@ -37,24 +37,16 @@ def rstudio_base_scripts(r_version): apt-get -qq purge && \ apt-get -qq clean && \ rm -rf /var/lib/apt/lists/* - """.format( - rstudio_url=rstudio_url, - rstudio_sha256sum=rstudio_sha256sum, - shiny_server_url=shiny_server_url, - shiny_sha256sum=shiny_sha256sum, - ), + """, ), ( "${NB_USER}", # Install jupyter-rsession-proxy - r""" + rf""" pip install --no-cache \ jupyter-rsession-proxy=={rsession_proxy_version} \ jupyter-shiny-proxy=={shiny_proxy_version} - """.format( - rsession_proxy_version=rsession_proxy_version, - shiny_proxy_version=shiny_proxy_version, - ), + """, ), ( # Not all of these locations are configurable; so we make sure diff --git a/repo2docker/buildpacks/base.py b/repo2docker/buildpacks/base.py index 16476e9d8..0758afc61 100644 --- a/repo2docker/buildpacks/base.py +++ b/repo2docker/buildpacks/base.py @@ -594,8 +594,8 @@ def _filter_tar(tar): # buildpacks/docker.py where it is duplicated if not isinstance(memory_limit, int): raise ValueError( - "The memory limit has to be specified as an" - "integer but is '{}'".format(type(memory_limit)) + "The memory limit has to be specified as an " + f"integer but is '{type(memory_limit)}'" ) limits = {} if memory_limit: @@ -647,8 +647,7 @@ def get_preassemble_scripts(self): # FIXME: Add support for specifying version numbers if not re.match(r"^[a-z0-9.+-]+", package): raise ValueError( - "Found invalid package name {} in " - "apt.txt".format(package) + f"Found invalid package name {package} in apt.txt" ) extra_apt_packages.append(package) diff --git a/repo2docker/buildpacks/conda/__init__.py b/repo2docker/buildpacks/conda/__init__.py index 662e70bfe..8c4426dc8 100644 --- a/repo2docker/buildpacks/conda/__init__.py +++ b/repo2docker/buildpacks/conda/__init__.py @@ -341,15 +341,13 @@ def get_env_scripts(self): scripts.append( ( "${NB_USER}", - r""" + rf""" TIMEFORMAT='time: %3R' \ - bash -c 'time ${{MAMBA_EXE}} env update -p {0} --file "{1}" && \ + bash -c 'time ${{MAMBA_EXE}} env update -p {env_prefix} --file "{environment_yml}" && \ time ${{MAMBA_EXE}} clean --all -f -y && \ - ${{MAMBA_EXE}} list -p {0} \ + ${{MAMBA_EXE}} list -p {env_prefix} \ ' - """.format( - env_prefix, environment_yml - ), + """, ) ) @@ -361,36 +359,30 @@ def get_env_scripts(self): scripts.append( ( "${NB_USER}", - r""" - ${{MAMBA_EXE}} install -p {0} r-base{1} r-irkernel r-devtools -y && \ + rf""" + ${{MAMBA_EXE}} install -p {env_prefix} r-base{r_pin} r-irkernel r-devtools -y && \ ${{MAMBA_EXE}} clean --all -f -y && \ - ${{MAMBA_EXE}} list -p {0} - """.format( - env_prefix, r_pin - ), + ${{MAMBA_EXE}} list -p {env_prefix} + """, ) ) scripts += rstudio_base_scripts(self.r_version) scripts += [ ( "root", - r""" + rf""" echo auth-none=1 >> /etc/rstudio/rserver.conf && \ echo auth-minimum-user-id=0 >> /etc/rstudio/rserver.conf && \ - echo "rsession-which-r={}/bin/R" >> /etc/rstudio/rserver.conf && \ + echo "rsession-which-r={env_prefix}/bin/R" >> /etc/rstudio/rserver.conf && \ echo www-frame-origin=same >> /etc/rstudio/rserver.conf - """.format( - env_prefix - ), + """, ), ( "${NB_USER}", # Register the jupyter kernel - r""" - R --quiet -e "IRkernel::installspec(prefix='{}')" - """.format( - env_prefix - ), + rf""" + R --quiet -e "IRkernel::installspec(prefix='{env_prefix}')" + """, ), ] return scripts diff --git a/repo2docker/buildpacks/docker.py b/repo2docker/buildpacks/docker.py index e0ccfc95c..6d8bd4698 100644 --- a/repo2docker/buildpacks/docker.py +++ b/repo2docker/buildpacks/docker.py @@ -34,8 +34,8 @@ def build( # buildpacks/base.py where it is duplicated if not isinstance(memory_limit, int): raise ValueError( - "The memory limit has to be specified as an" - "integer but is '{}'".format(type(memory_limit)) + "The memory limit has to be specified as an " + f"integer but is '{type(memory_limit)}'" ) limits = {} if memory_limit: diff --git a/repo2docker/buildpacks/nix/__init__.py b/repo2docker/buildpacks/nix/__init__.py index b7ca105d7..4947b92e5 100644 --- a/repo2docker/buildpacks/nix/__init__.py +++ b/repo2docker/buildpacks/nix/__init__.py @@ -62,13 +62,11 @@ def get_assemble_scripts(self): return super().get_assemble_scripts() + [ ( "${NB_USER}", - """ + f""" nix-channel --add https://nixos.org/channels/nixpkgs-unstable nixpkgs && \ nix-channel --update && \ - nix-shell {} - """.format( - self.binder_path("default.nix") - ), + nix-shell {self.binder_path("default.nix")} + """, ) ] diff --git a/repo2docker/buildpacks/pipfile/__init__.py b/repo2docker/buildpacks/pipfile/__init__.py index e928d01ec..f08a1beba 100644 --- a/repo2docker/buildpacks/pipfile/__init__.py +++ b/repo2docker/buildpacks/pipfile/__init__.py @@ -123,9 +123,7 @@ def get_assemble_scripts(self): assemble_scripts.append( ( "${NB_USER}", - '${{NB_PYTHON_PREFIX}}/bin/pip install --no-cache-dir -r "{}"'.format( - nb_requirements_file - ), + f'${{NB_PYTHON_PREFIX}}/bin/pip install --no-cache-dir -r "{nb_requirements_file}"', ) ) diff --git a/repo2docker/buildpacks/python/__init__.py b/repo2docker/buildpacks/python/__init__.py index 0c12f91b8..bdcaa5209 100644 --- a/repo2docker/buildpacks/python/__init__.py +++ b/repo2docker/buildpacks/python/__init__.py @@ -55,9 +55,7 @@ def _get_pip_scripts(self): "${NB_USER}", # want the $NB_PYHTON_PREFIX environment variable, not for # Python's string formatting to try and replace this - '${{NB_PYTHON_PREFIX}}/bin/pip install --no-cache-dir -r "{}"'.format( - nb_requirements_file - ), + f'${{NB_PYTHON_PREFIX}}/bin/pip install --no-cache-dir -r "{nb_requirements_file}"', ) ) diff --git a/repo2docker/buildpacks/r.py b/repo2docker/buildpacks/r.py index 9009a4d87..3156913f9 100644 --- a/repo2docker/buildpacks/r.py +++ b/repo2docker/buildpacks/r.py @@ -336,12 +336,10 @@ def get_build_scripts(self): ( "${NB_USER}", # Install a pinned version of devtools, IRKernel and shiny - r""" - R --quiet -e "install.packages(c('devtools', 'IRkernel', 'shiny'), repos='{devtools_cran_mirror_url}')" && \ + rf""" + R --quiet -e "install.packages(c('devtools', 'IRkernel', 'shiny'), repos='{self.get_devtools_snapshot_url()}')" && \ R --quiet -e "IRkernel::installspec(prefix='$NB_PYTHON_PREFIX')" - """.format( - devtools_cran_mirror_url=self.get_devtools_snapshot_url() - ), + """, ), ] @@ -374,8 +372,7 @@ def get_preassemble_scripts(self): "${NB_USER}", # Delete /tmp/downloaded_packages only if install.R fails, as the second # invocation of install.R might be able to reuse them - "Rscript %s && touch /tmp/.preassembled || true && rm -rf /tmp/downloaded_packages" - % installR_path, + f"Rscript {installR_path} && touch /tmp/.preassembled || true && rm -rf /tmp/downloaded_packages", ) ] @@ -392,9 +389,7 @@ def get_assemble_scripts(self): "${NB_USER}", # only run install.R if the pre-assembly failed # Delete any downloaded packages in /tmp, as they aren't reused by R - """if [ ! -f /tmp/.preassembled ]; then Rscript {}; rm -rf /tmp/downloaded_packages; fi""".format( - installR_path - ), + f"""if [ ! -f /tmp/.preassembled ]; then Rscript {installR_path}; rm -rf /tmp/downloaded_packages; fi""", ) ] diff --git a/repo2docker/contentproviders/base.py b/repo2docker/contentproviders/base.py index f4f1cbbb0..672c39733 100644 --- a/repo2docker/contentproviders/base.py +++ b/repo2docker/contentproviders/base.py @@ -68,6 +68,6 @@ def detect(self, source, ref=None, extra_args=None): def fetch(self, spec, output_dir, yield_output=False): # nothing to be done if your content is already in the output directory - msg = "Local content provider assumes {} == {}".format(spec["path"], output_dir) + msg = f'Local content provider assumes {spec["path"]} == {output_dir}' assert output_dir == spec["path"], msg - yield "Using local repo {}.\n".format(spec["path"]) + yield f'Using local repo {spec["path"]}.\n' diff --git a/repo2docker/contentproviders/dataverse.py b/repo2docker/contentproviders/dataverse.py index c308c2d09..e6e7da38c 100644 --- a/repo2docker/contentproviders/dataverse.py +++ b/repo2docker/contentproviders/dataverse.py @@ -76,9 +76,7 @@ def detect(self, doi, ref=None, extra_args=None): data = self.urlopen(search_url).json()["data"] if data["count_in_response"] != 1: self.log.debug( - "Dataverse search query failed!\n - doi: {}\n - url: {}\n - resp: {}\n".format( - doi, url, json.dump(data) - ) + f"Dataverse search query failed!\n - doi: {doi}\n - url: {url}\n - resp: {json.dump(data)}\n" ) return @@ -98,16 +96,14 @@ def fetch(self, spec, output_dir, yield_output=False): host = spec["host"] yield f"Fetching Dataverse record {record_id}.\n" - url = "{}/api/datasets/:persistentId?persistentId={}".format( - host["url"], record_id - ) + url = f'{host["url"]}/api/datasets/:persistentId?persistentId={record_id}' resp = self.urlopen(url, headers={"accept": "application/json"}) record = resp.json()["data"] for fobj in deep_get(record, "latestVersion.files"): - file_url = "{}/api/access/datafile/{}".format( - host["url"], deep_get(fobj, "dataFile.id") + file_url = ( + f'{host["url"]}/api/access/datafile/{deep_get(fobj, "dataFile.id")}' ) filename = os.path.join(fobj.get("directoryLabel", ""), fobj["label"]) diff --git a/repo2docker/contentproviders/figshare.py b/repo2docker/contentproviders/figshare.py index 5d27684d1..0735e441c 100644 --- a/repo2docker/contentproviders/figshare.py +++ b/repo2docker/contentproviders/figshare.py @@ -75,11 +75,9 @@ def fetch(self, spec, output_dir, yield_output=False): article_version = spec["version"] host = spec["host"] - yield "Fetching Figshare article {} in version {}.\n".format( - article_id, article_version - ) + yield f"Fetching Figshare article {article_id} in version {article_version}.\n" resp = self.urlopen( - "{}{}/versions/{}".format(host["api"], article_id, article_version), + f'{host["api"]}{article_id}/versions/{article_version}', headers={"accept": "application/json"}, ) diff --git a/repo2docker/contentproviders/git.py b/repo2docker/contentproviders/git.py index 9e5fb48e7..a3d330e6c 100644 --- a/repo2docker/contentproviders/git.py +++ b/repo2docker/contentproviders/git.py @@ -43,7 +43,7 @@ def fetch(self, spec, output_dir, yield_output=False): hash = check_ref(ref, output_dir) if hash is None: self.log.error( - "Failed to check out ref %s", ref, extra=dict(phase=R2dState.FAILED) + f"Failed to check out ref {ref}", extra=dict(phase=R2dState.FAILED) ) if ref == "master": msg = ( diff --git a/repo2docker/contentproviders/hydroshare.py b/repo2docker/contentproviders/hydroshare.py index 3378129ab..886a8f81a 100755 --- a/repo2docker/contentproviders/hydroshare.py +++ b/repo2docker/contentproviders/hydroshare.py @@ -59,7 +59,7 @@ def fetch(self, spec, output_dir, yield_output=False, timeout=120): resource_id = spec["resource"] host = spec["host"] - bag_url = "{}{}".format(host["django_irods"], resource_id) + bag_url = f'{host["django_irods"]}{resource_id}' yield f"Downloading {bag_url}.\n" @@ -76,9 +76,7 @@ def fetch(self, spec, output_dir, yield_output=False, timeout=120): msg = "Bag taking too long to prepare, exiting now, try again later." yield msg raise ContentProviderException(msg) - yield "Bag is being prepared, requesting again in {} seconds.\n".format( - wait_time - ) + yield f"Bag is being prepared, requesting again in {wait_time} seconds.\n" time.sleep(wait_time) conn = self.urlopen(bag_url) if conn.status_code != 200: diff --git a/repo2docker/contentproviders/mercurial.py b/repo2docker/contentproviders/mercurial.py index e29584f29..821f55f37 100644 --- a/repo2docker/contentproviders/mercurial.py +++ b/repo2docker/contentproviders/mercurial.py @@ -60,7 +60,7 @@ def fetch(self, spec, output_dir, yield_output=False): ) except subprocess.CalledProcessError: self.log.error( - "Failed to update to ref %s", ref, extra=dict(phase=R2dState.FAILED) + f"Failed to update to ref {ref}", extra=dict(phase=R2dState.FAILED) ) raise ValueError(f"Failed to update to ref {ref}") diff --git a/repo2docker/contentproviders/zenodo.py b/repo2docker/contentproviders/zenodo.py index a58e295f8..0a8d91084 100644 --- a/repo2docker/contentproviders/zenodo.py +++ b/repo2docker/contentproviders/zenodo.py @@ -68,7 +68,7 @@ def fetch(self, spec, output_dir, yield_output=False): yield f"Fetching Zenodo record {record_id}.\n" resp = self.urlopen( - "{}{}".format(host["api"], record_id), + f'{host["api"]}{record_id}', headers={"accept": "application/json"}, ) diff --git a/repo2docker/utils.py b/repo2docker/utils.py index e8833bd84..852f21e28 100644 --- a/repo2docker/utils.py +++ b/repo2docker/utils.py @@ -136,13 +136,10 @@ def check_port(port): try: p = int(port) except ValueError as e: - raise ValueError( - 'Port specification "{}" has ' "an invalid port.".format(mapping) - ) + raise ValueError(f'Port specification "{mapping}" has an invalid port.') if not 0 < p <= 65535: raise ValueError( - 'Port specification "{}" specifies ' - "a port outside 1-65535.".format(mapping) + f'Port specification "{mapping}" specifies a port outside 1-65535.' ) return port @@ -152,8 +149,7 @@ def check_port_string(p): port, protocol = parts if protocol not in ("tcp", "udp"): raise ValueError( - 'Port specification "{}" has ' - "an invalid protocol.".format(mapping) + f'Port specification "{mapping}" has an invalid protocol.' ) elif len(parts) == 1: port = parts[0] @@ -310,14 +306,14 @@ def validate(self, obj, value): num = float(value[:-1]) except ValueError: raise TraitError( - "{val} is not a valid memory specification. " - "Must be an int or a string with suffix K, M, G, T".format(val=value) + f"{value} is not a valid memory specification. " + "Must be an int or a string with suffix K, M, G, T" ) suffix = value[-1] if suffix not in self.UNIT_SUFFIXES: raise TraitError( - "{val} is not a valid memory specification. " - "Must be an int or a string with suffix K, M, G, T".format(val=value) + f"{value} is not a valid memory specification. " + "Must be an int or a string with suffix K, M, G, T" ) else: return int(float(num) * self.UNIT_SUFFIXES[suffix]) diff --git a/tests/conda/py2/verify b/tests/conda/py2/verify index b251755a6..4a55686cf 100755 --- a/tests/conda/py2/verify +++ b/tests/conda/py2/verify @@ -30,4 +30,4 @@ for pkg in pkgs: assert pkg["version"].startswith("2.7.") break else: - assert False, "python not found in %s" % pkg_names + assert False, f"python not found in {pkg_names}" diff --git a/tests/conftest.py b/tests/conftest.py index eda58223f..e2914801a 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -65,7 +65,7 @@ def build_noop(): container = app.start_container() port = app.port # wait a bit for the container to be ready - container_url = "http://localhost:%s/api" % port + container_url = f"http://localhost:{port}/api" # give the container a chance to start time.sleep(1) try: @@ -77,13 +77,13 @@ def build_noop(): try: info = requests.get(container_url).json() except Exception as e: - print("Error: %s" % e) + print(f"Error: {e}") time.sleep(i * 3) else: print(info) success = True break - assert success, "Notebook never started in %s" % container + assert success, f"Notebook never started in {container}" finally: # stop the container container.stop() @@ -211,7 +211,7 @@ def reportinfo(self): def repr_failure(self, excinfo): err = excinfo.value if isinstance(err, SystemExit): - cmd = "jupyter-repo2docker %s" % " ".join(map(pipes.quote, self.args)) + cmd = f'jupyter-repo2docker {" ".join(map(pipes.quote, self.args))}' return f"{cmd} | exited with status={err.code}" else: return super().repr_failure(excinfo) diff --git a/tests/unit/test_connect_url.py b/tests/unit/test_connect_url.py index 3115a8ab3..7438b8aa3 100644 --- a/tests/unit/test_connect_url.py +++ b/tests/unit/test_connect_url.py @@ -59,13 +59,13 @@ def test_connect_url(tmpdir): try: info = requests.get(container_url).json() except Exception as e: - print("Error: %s" % e) + print(f"Error: {e}") time.sleep(i * 3) else: print(info) success = True break - assert success, "Notebook never started in %s" % container + assert success, f"Notebook never started in {container}" finally: # stop the container container.stop() diff --git a/tests/unit/test_subdir.py b/tests/unit/test_subdir.py index 43d08fce3..4b0cd47ba 100644 --- a/tests/unit/test_subdir.py +++ b/tests/unit/test_subdir.py @@ -21,7 +21,7 @@ def test_subdir(run_repo2docker): run_repo2docker(argv) # check that we restored the current working directory - assert cwd == os.getcwd(), "We should be back in %s" % cwd + assert cwd == os.getcwd(), f"We should be back in {cwd}" def test_subdir_in_image_name(): diff --git a/tests/unit/test_users.py b/tests/unit/test_users.py index e14eeaf13..642e4f3b2 100644 --- a/tests/unit/test_users.py +++ b/tests/unit/test_users.py @@ -34,19 +34,14 @@ def test_user(): subprocess.check_call( [ "repo2docker", - "-v", - f"{tmpdir}:/home/{username}", - "--user-id", - userid, - "--user-name", - username, + f"--volume={tmpdir}:/home/{username}", + f"--user-id={userid}", + f"--user-name={username}", tmpdir, "--", "/bin/bash", "-c", - "id -u > id && pwd > pwd && whoami > name && echo -n $USER > env_user".format( - ts - ), + "id -u > id && pwd > pwd && whoami > name && echo -n $USER > env_user", ] ) diff --git a/tests/venv/usr-bin/verify b/tests/venv/usr-bin/verify index 4370b68ed..c6efe7823 100755 --- a/tests/venv/usr-bin/verify +++ b/tests/venv/usr-bin/verify @@ -4,4 +4,4 @@ import os assert os.path.expanduser("~/.local/bin") in os.getenv("PATH"), os.getenv("PATH") assert os.getcwd() == os.environ["REPO_DIR"] -assert "{}/.local/bin".format(os.environ["REPO_DIR"]) in os.getenv("PATH") +assert f'{os.environ["REPO_DIR"]}/.local/bin' in os.getenv("PATH") diff --git a/versioneer.py b/versioneer.py index a47088994..03a560576 100644 --- a/versioneer.py +++ b/versioneer.py @@ -1106,7 +1106,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe) if not mo: # unparseable. Maybe git-describe is misbehaving? - pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out + pieces["error"] = f"unable to parse git-describe output: '{describe_out}'" return pieces # tag @@ -1115,10 +1115,9 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): if verbose: fmt = "tag '%s' doesn't start with prefix '%s'" print(fmt % (full_tag, tag_prefix)) - pieces["error"] = "tag '{}' doesn't start with prefix '{}'".format( - full_tag, - tag_prefix, - ) + pieces[ + "error" + ] = f"tag '{full_tag}' doesn't start with prefix '{tag_prefix}'" return pieces pieces["closest-tag"] = full_tag[len(tag_prefix) :] @@ -1256,7 +1255,7 @@ def write_to_version_file(filename, versions): with open(filename, "w") as f: f.write(SHORT_VERSION_PY % contents) - print("set {} to '{}'".format(filename, versions["version"])) + print(f"set {filename} to '{versions['version']}'") def plus_or_dot(pieces): From 1926795c8ca3a4be418f45b0b9c2689e2ab3f396 Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Mon, 31 Oct 2022 23:29:57 +0100 Subject: [PATCH 036/171] pre-commit: enable isort --- .pre-commit-config.yaml | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 42d13f19e..8bd52ff20 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -32,14 +32,15 @@ repos: - --target-version=py38 - --target-version=py39 - --target-version=py310 + - --target-version=py311 - # # Autoformat: Python code - # - repo: https://github.com/pycqa/isort - # rev: 5.10.1 - # hooks: - # - id: isort - # args: - # - --profile=black + # Autoformat: Python code + - repo: https://github.com/pycqa/isort + rev: 5.10.1 + hooks: + - id: isort + args: + - --profile=black # # Autoformat: markdown, yaml (but not helm templates) # - repo: https://github.com/pre-commit/mirrors-prettier From 27c2b403dbd3b6bb1b31f687ca4069434301465f Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 31 Oct 2022 22:32:14 +0000 Subject: [PATCH 037/171] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- docs/source/conf.py | 1 - repo2docker/__main__.py | 11 +++++----- repo2docker/app.py | 14 ++++++------- repo2docker/buildpacks/__init__.py | 11 +++++----- repo2docker/buildpacks/base.py | 11 +++++----- repo2docker/buildpacks/conda/__init__.py | 4 ++-- repo2docker/buildpacks/conda/freeze.py | 7 +++---- repo2docker/buildpacks/docker.py | 2 ++ repo2docker/buildpacks/julia/julia_project.py | 2 +- repo2docker/buildpacks/julia/julia_require.py | 2 +- repo2docker/buildpacks/nix/__init__.py | 2 +- repo2docker/buildpacks/python/__init__.py | 2 +- repo2docker/buildpacks/r.py | 8 ++++---- repo2docker/contentproviders/__init__.py | 6 +++--- repo2docker/contentproviders/dataverse.py | 7 +++---- repo2docker/contentproviders/doi.py | 17 +++++++--------- repo2docker/contentproviders/figshare.py | 10 ++++------ repo2docker/contentproviders/git.py | 2 +- repo2docker/contentproviders/hydroshare.py | 9 ++++----- repo2docker/contentproviders/mercurial.py | 2 +- repo2docker/contentproviders/swhid.py | 7 +++---- repo2docker/contentproviders/zenodo.py | 10 ++++------ repo2docker/docker.py | 5 +++-- repo2docker/engine.py | 2 +- repo2docker/utils.py | 11 +++++----- setup.py | 8 +++++--- .../conda/r3.6-target-repo-dir-flag/verify.py | 2 +- tests/conftest.py | 3 +-- tests/memlimit/dockerfile/postBuild | 2 +- tests/memlimit/non-dockerfile/postBuild | 2 +- .../py2-with-server-and-kernel-req/verify | 1 - .../setup-py-explicit-in-binder-dir/setup.py | 2 +- .../setup-py-explicit-in-binder-dir/verify | 2 +- tests/pipfile/setup-py-explicit/setup.py | 2 +- tests/pipfile/setup-py-explicit/verify | 2 +- tests/pipfile/setup-py-implicit/setup.py | 2 +- tests/unit/contentproviders/test_dataverse.py | 7 +++---- tests/unit/contentproviders/test_doi.py | 14 ++++++------- tests/unit/contentproviders/test_figshare.py | 11 +++++----- tests/unit/contentproviders/test_git.py | 4 +++- .../unit/contentproviders/test_hydroshare.py | 9 ++++----- tests/unit/contentproviders/test_local.py | 2 +- tests/unit/contentproviders/test_mercurial.py | 1 - tests/unit/contentproviders/test_swhid.py | 20 +++++++++---------- tests/unit/contentproviders/test_zenodo.py | 8 ++++---- tests/unit/test_app.py | 6 +++--- tests/unit/test_args.py | 4 +++- tests/unit/test_argumentvalidation.py | 1 - tests/unit/test_buildpack.py | 3 ++- tests/unit/test_cache_from.py | 1 - tests/unit/test_clone_depth.py | 2 -- tests/unit/test_connect_url.py | 5 +++-- tests/unit/test_editable.py | 1 - tests/unit/test_env_yml.py | 2 ++ tests/unit/test_external_scripts.py | 1 + tests/unit/test_freeze.py | 3 +-- tests/unit/test_labels.py | 9 +++++---- tests/unit/test_memlimit.py | 5 +---- tests/unit/test_ports.py | 10 +++++----- tests/unit/test_r.py | 2 +- tests/unit/test_semver.py | 1 + tests/unit/test_subdir.py | 2 +- tests/unit/test_utils.py | 8 +++++--- 63 files changed, 162 insertions(+), 173 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index 4e33931a9..ec8294dad 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -4,7 +4,6 @@ # import datetime - # -- Project information ----------------------------------------------------- # ref: https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information # diff --git a/repo2docker/__main__.py b/repo2docker/__main__.py index 2ca17f171..cca1616ce 100644 --- a/repo2docker/__main__.py +++ b/repo2docker/__main__.py @@ -1,14 +1,15 @@ import argparse -import sys -import os import logging +import os +import sys + +from . import __version__ from .app import Repo2Docker from .engine import BuildError, ImageLoadError -from . import __version__ from .utils import ( - validate_and_generate_port_mapping, - is_valid_docker_image_name, R2dState, + is_valid_docker_image_name, + validate_and_generate_port_mapping, ) diff --git a/repo2docker/app.py b/repo2docker/app.py index 5bee81b41..c62a77d63 100755 --- a/repo2docker/app.py +++ b/repo2docker/app.py @@ -7,24 +7,23 @@ python -m repo2docker https://github.com/you/your-repo """ +import getpass import json -import sys import logging import os -import entrypoints -import getpass import shutil +import sys import tempfile import time from urllib.parse import urlparse +import entrypoints import escapism from pythonjsonlogger import jsonlogger - -from traitlets import Any, Dict, Int, List, Unicode, Bool, default +from traitlets import Any, Bool, Dict, Int, List, Unicode, default from traitlets.config import Application -from . import __version__ +from . import __version__, contentproviders from .buildpacks import ( CondaBuildPack, DockerBuildPack, @@ -36,9 +35,8 @@ PythonBuildPack, RBuildPack, ) -from . import contentproviders from .engine import BuildError, ContainerEngineException, ImageLoadError -from .utils import ByteSpecification, chdir, R2dState +from .utils import ByteSpecification, R2dState, chdir class Repo2Docker(Application): diff --git a/repo2docker/buildpacks/__init__.py b/repo2docker/buildpacks/__init__.py index 10fe89a4e..7568000bd 100644 --- a/repo2docker/buildpacks/__init__.py +++ b/repo2docker/buildpacks/__init__.py @@ -1,10 +1,9 @@ -from .base import BuildPack, BaseImage -from .python import PythonBuildPack -from .pipfile import PipfileBuildPack +from .base import BaseImage, BuildPack from .conda import CondaBuildPack -from .julia import JuliaProjectTomlBuildPack -from .julia import JuliaRequireBuildPack from .docker import DockerBuildPack +from .julia import JuliaProjectTomlBuildPack, JuliaRequireBuildPack from .legacy import LegacyBinderDockerBuildPack -from .r import RBuildPack from .nix import NixBuildPack +from .pipfile import PipfileBuildPack +from .python import PythonBuildPack +from .r import RBuildPack diff --git a/repo2docker/buildpacks/base.py b/repo2docker/buildpacks/base.py index 0758afc61..e7c9b537d 100644 --- a/repo2docker/buildpacks/base.py +++ b/repo2docker/buildpacks/base.py @@ -1,14 +1,15 @@ -import textwrap -import jinja2 -import tarfile +import hashlib import io +import logging import os import re -import logging import string import sys -import hashlib +import tarfile +import textwrap + import escapism +import jinja2 # Only use syntax features supported by Docker 17.09 TEMPLATE = r""" diff --git a/repo2docker/buildpacks/conda/__init__.py b/repo2docker/buildpacks/conda/__init__.py index 8c4426dc8..99653177b 100644 --- a/repo2docker/buildpacks/conda/__init__.py +++ b/repo2docker/buildpacks/conda/__init__.py @@ -5,9 +5,9 @@ from ruamel.yaml import YAML -from ..base import BaseImage -from .._r_base import rstudio_base_scripts from ...utils import is_local_pip_requirement +from .._r_base import rstudio_base_scripts +from ..base import BaseImage # pattern for parsing conda dependency line PYTHON_REGEX = re.compile(r"python\s*=+\s*([\d\.]*)") diff --git a/repo2docker/buildpacks/conda/freeze.py b/repo2docker/buildpacks/conda/freeze.py index 84475457f..7bdb444eb 100755 --- a/repo2docker/buildpacks/conda/freeze.py +++ b/repo2docker/buildpacks/conda/freeze.py @@ -9,17 +9,16 @@ python freeze.py [3.8] """ -from argparse import ArgumentParser -from datetime import datetime import os import pathlib import shutil -from subprocess import check_call import sys +from argparse import ArgumentParser +from datetime import datetime +from subprocess import check_call from ruamel.yaml import YAML - HERE = pathlib.Path(os.path.dirname(os.path.abspath(__file__))) ENV_FILE = HERE / "environment.yml" diff --git a/repo2docker/buildpacks/docker.py b/repo2docker/buildpacks/docker.py index 6d8bd4698..6979b8305 100644 --- a/repo2docker/buildpacks/docker.py +++ b/repo2docker/buildpacks/docker.py @@ -1,7 +1,9 @@ """Generates a variety of Dockerfiles based on an input matrix """ import os + import docker + from .base import BuildPack diff --git a/repo2docker/buildpacks/julia/julia_project.py b/repo2docker/buildpacks/julia/julia_project.py index e6e191dc2..d61e65d13 100644 --- a/repo2docker/buildpacks/julia/julia_project.py +++ b/repo2docker/buildpacks/julia/julia_project.py @@ -6,8 +6,8 @@ import semver import toml -from ..python import PythonBuildPack from ...semver import find_semver_match +from ..python import PythonBuildPack class JuliaProjectTomlBuildPack(PythonBuildPack): diff --git a/repo2docker/buildpacks/julia/julia_require.py b/repo2docker/buildpacks/julia/julia_require.py index 075b928e0..b2acbcff6 100644 --- a/repo2docker/buildpacks/julia/julia_require.py +++ b/repo2docker/buildpacks/julia/julia_require.py @@ -2,8 +2,8 @@ import os -from ..python import PythonBuildPack from ...semver import parse_version as V +from ..python import PythonBuildPack class JuliaRequireBuildPack(PythonBuildPack): diff --git a/repo2docker/buildpacks/nix/__init__.py b/repo2docker/buildpacks/nix/__init__.py index 4947b92e5..73dd81af4 100644 --- a/repo2docker/buildpacks/nix/__init__.py +++ b/repo2docker/buildpacks/nix/__init__.py @@ -1,7 +1,7 @@ """BuildPack for nixpkgs environments""" import os -from ..base import BuildPack, BaseImage +from ..base import BaseImage, BuildPack class NixBuildPack(BaseImage): diff --git a/repo2docker/buildpacks/python/__init__.py b/repo2docker/buildpacks/python/__init__.py index bdcaa5209..7aa225642 100644 --- a/repo2docker/buildpacks/python/__init__.py +++ b/repo2docker/buildpacks/python/__init__.py @@ -1,8 +1,8 @@ """Generates Dockerfiles based on an input matrix based on Python.""" import os -from ..conda import CondaBuildPack from ...utils import is_local_pip_requirement, open_guess_encoding +from ..conda import CondaBuildPack class PythonBuildPack(CondaBuildPack): diff --git a/repo2docker/buildpacks/r.py b/repo2docker/buildpacks/r.py index 3156913f9..200f472fd 100644 --- a/repo2docker/buildpacks/r.py +++ b/repo2docker/buildpacks/r.py @@ -1,12 +1,12 @@ -import re -import os import datetime -import requests +import os +import re +import requests from ..semver import parse_version as V -from .python import PythonBuildPack from ._r_base import rstudio_base_scripts +from .python import PythonBuildPack class RBuildPack(PythonBuildPack): diff --git a/repo2docker/contentproviders/__init__.py b/repo2docker/contentproviders/__init__.py index 6398c233e..5c40476df 100755 --- a/repo2docker/contentproviders/__init__.py +++ b/repo2docker/contentproviders/__init__.py @@ -1,8 +1,8 @@ -from .git import Git from .base import Local -from .zenodo import Zenodo -from .figshare import Figshare from .dataverse import Dataverse +from .figshare import Figshare +from .git import Git from .hydroshare import Hydroshare from .mercurial import Mercurial from .swhid import Swhid +from .zenodo import Zenodo diff --git a/repo2docker/contentproviders/dataverse.py b/repo2docker/contentproviders/dataverse.py index e6e7da38c..1998f6bef 100644 --- a/repo2docker/contentproviders/dataverse.py +++ b/repo2docker/contentproviders/dataverse.py @@ -1,11 +1,10 @@ -import os import json +import os import shutil +from urllib.parse import parse_qs, urlparse, urlunparse -from urllib.parse import urlparse, urlunparse, parse_qs - -from .doi import DoiProvider from ..utils import copytree, deep_get +from .doi import DoiProvider class Dataverse(DoiProvider): diff --git a/repo2docker/contentproviders/doi.py b/repo2docker/contentproviders/doi.py index 01d048ec7..03fa0171c 100644 --- a/repo2docker/contentproviders/doi.py +++ b/repo2docker/contentproviders/doi.py @@ -1,18 +1,15 @@ -import os import json -import shutil import logging - -from os import makedirs -from os import path -from requests import Session, HTTPError - +import os +import shutil +from os import makedirs, path from zipfile import ZipFile, is_zipfile -from .base import ContentProvider -from ..utils import copytree, deep_get -from ..utils import normalize_doi, is_doi +from requests import HTTPError, Session + from .. import __version__ +from ..utils import copytree, deep_get, is_doi, normalize_doi +from .base import ContentProvider class DoiProvider(ContentProvider): diff --git a/repo2docker/contentproviders/figshare.py b/repo2docker/contentproviders/figshare.py index 0735e441c..6c7b26c86 100644 --- a/repo2docker/contentproviders/figshare.py +++ b/repo2docker/contentproviders/figshare.py @@ -1,16 +1,14 @@ +import json import os import re -import json import shutil - -from os import makedirs -from os import path -from urllib.request import Request +from os import makedirs, path from urllib.error import HTTPError +from urllib.request import Request from zipfile import is_zipfile -from .doi import DoiProvider from ..utils import copytree, deep_get +from .doi import DoiProvider class Figshare(DoiProvider): diff --git a/repo2docker/contentproviders/git.py b/repo2docker/contentproviders/git.py index a3d330e6c..f35e9a888 100644 --- a/repo2docker/contentproviders/git.py +++ b/repo2docker/contentproviders/git.py @@ -1,7 +1,7 @@ import subprocess +from ..utils import R2dState, check_ref, execute_cmd from .base import ContentProvider, ContentProviderException -from ..utils import execute_cmd, check_ref, R2dState class Git(ContentProvider): diff --git a/repo2docker/contentproviders/hydroshare.py b/repo2docker/contentproviders/hydroshare.py index 886a8f81a..4104d97a6 100755 --- a/repo2docker/contentproviders/hydroshare.py +++ b/repo2docker/contentproviders/hydroshare.py @@ -1,14 +1,13 @@ -import zipfile +import json import os import shutil import time -import json -from datetime import datetime, timezone, timedelta - +import zipfile +from datetime import datetime, timedelta, timezone from urllib.request import urlretrieve -from .doi import DoiProvider from .base import ContentProviderException +from .doi import DoiProvider class Hydroshare(DoiProvider): diff --git a/repo2docker/contentproviders/mercurial.py b/repo2docker/contentproviders/mercurial.py index 821f55f37..e427cc022 100644 --- a/repo2docker/contentproviders/mercurial.py +++ b/repo2docker/contentproviders/mercurial.py @@ -1,7 +1,7 @@ import subprocess +from ..utils import R2dState, execute_cmd from .base import ContentProvider, ContentProviderException -from ..utils import execute_cmd, R2dState args_enabling_topic = ["--config", "extensions.topic="] diff --git a/repo2docker/contentproviders/swhid.py b/repo2docker/contentproviders/swhid.py index 2a964e70f..18dc78a91 100644 --- a/repo2docker/contentproviders/swhid.py +++ b/repo2docker/contentproviders/swhid.py @@ -1,17 +1,16 @@ import io import os +import re import shutil import tarfile import time -import re - from os import path import requests -from .base import ContentProvider -from ..utils import copytree from .. import __version__ +from ..utils import copytree +from .base import ContentProvider def parse_swhid(swhid): diff --git a/repo2docker/contentproviders/zenodo.py b/repo2docker/contentproviders/zenodo.py index 0a8d91084..5d02f723b 100644 --- a/repo2docker/contentproviders/zenodo.py +++ b/repo2docker/contentproviders/zenodo.py @@ -1,14 +1,12 @@ -import os import json +import os import shutil - -from os import makedirs -from os import path -from urllib.request import Request +from os import makedirs, path from urllib.error import HTTPError +from urllib.request import Request -from .doi import DoiProvider from ..utils import copytree, deep_get +from .doi import DoiProvider class Zenodo(DoiProvider): diff --git a/repo2docker/docker.py b/repo2docker/docker.py index 686a70db5..267c16cf6 100644 --- a/repo2docker/docker.py +++ b/repo2docker/docker.py @@ -2,9 +2,10 @@ Docker container engine for repo2docker """ -import docker -from traitlets import Dict from iso8601 import parse_date +from traitlets import Dict + +import docker from .engine import Container, ContainerEngine, ContainerEngineException, Image diff --git a/repo2docker/engine.py b/repo2docker/engine.py index 459b2be83..73276a3a7 100644 --- a/repo2docker/engine.py +++ b/repo2docker/engine.py @@ -3,8 +3,8 @@ """ from abc import ABC, abstractmethod -from traitlets.config import LoggingConfigurable +from traitlets.config import LoggingConfigurable # Based on https://docker-py.readthedocs.io/en/4.2.0/containers.html diff --git a/repo2docker/utils.py b/repo2docker/utils.py index 852f21e28..cd345f4a0 100644 --- a/repo2docker/utils.py +++ b/repo2docker/utils.py @@ -1,13 +1,12 @@ -from contextlib import contextmanager -from enum import Enum -from functools import partial import os import re import subprocess -import chardet - -from shutil import copystat, copy2 +from contextlib import contextmanager +from enum import Enum +from functools import partial +from shutil import copy2, copystat +import chardet from traitlets import Integer, TraitError diff --git a/setup.py b/setup.py index e4eb16a0f..58abff7c0 100644 --- a/setup.py +++ b/setup.py @@ -1,6 +1,8 @@ -from distutils.cmd import Command -from setuptools import setup, find_packages import sys +from distutils.cmd import Command + +from setuptools import find_packages, setup + import versioneer if sys.version_info[0] < 3: @@ -23,8 +25,8 @@ def finalize_options(self): pass def run(self): - from urllib.request import urlopen import json + from urllib.request import urlopen resp = urlopen(self.url, timeout=5) resp_body = resp.read() diff --git a/tests/conda/r3.6-target-repo-dir-flag/verify.py b/tests/conda/r3.6-target-repo-dir-flag/verify.py index d284c28a6..701278364 100755 --- a/tests/conda/r3.6-target-repo-dir-flag/verify.py +++ b/tests/conda/r3.6-target-repo-dir-flag/verify.py @@ -1,6 +1,6 @@ #!/usr/bin/env python -import sys import os +import sys from glob import glob # conda should still be in /srv/conda diff --git a/tests/conftest.py b/tests/conftest.py index e2914801a..13e62b401 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -19,14 +19,13 @@ import os import pipes import shlex -import requests import subprocess import time from tempfile import TemporaryDirectory - import escapism import pytest +import requests import yaml from repo2docker.__main__ import make_r2d diff --git a/tests/memlimit/dockerfile/postBuild b/tests/memlimit/dockerfile/postBuild index 4fe5360f2..1d7819241 100755 --- a/tests/memlimit/dockerfile/postBuild +++ b/tests/memlimit/dockerfile/postBuild @@ -10,8 +10,8 @@ NOTE: This file has to be duplicated & present in all the following locations: - tests/memlimit/dockerfile/postBuild See https://github.com/jupyterhub/repo2docker/issues/160 for reason """ -from ctypes import cdll, c_void_p, memset import os +from ctypes import c_void_p, cdll, memset libc = cdll.LoadLibrary("libc.so.6") libc.malloc.restype = c_void_p diff --git a/tests/memlimit/non-dockerfile/postBuild b/tests/memlimit/non-dockerfile/postBuild index 4fe5360f2..1d7819241 100755 --- a/tests/memlimit/non-dockerfile/postBuild +++ b/tests/memlimit/non-dockerfile/postBuild @@ -10,8 +10,8 @@ NOTE: This file has to be duplicated & present in all the following locations: - tests/memlimit/dockerfile/postBuild See https://github.com/jupyterhub/repo2docker/issues/160 for reason """ -from ctypes import cdll, c_void_p, memset import os +from ctypes import c_void_p, cdll, memset libc = cdll.LoadLibrary("libc.so.6") libc.malloc.restype = c_void_p diff --git a/tests/pipfile/py2-with-server-and-kernel-req/verify b/tests/pipfile/py2-with-server-and-kernel-req/verify index 7246be615..5ff8a889c 100755 --- a/tests/pipfile/py2-with-server-and-kernel-req/verify +++ b/tests/pipfile/py2-with-server-and-kernel-req/verify @@ -2,7 +2,6 @@ import os import sys - # Verify - kernel's Python: use Python 2 print(sys.version_info) assert sys.version_info[:2] == (2, 7) diff --git a/tests/pipfile/setup-py-explicit-in-binder-dir/setup.py b/tests/pipfile/setup-py-explicit-in-binder-dir/setup.py index c67a722a7..ca077f415 100644 --- a/tests/pipfile/setup-py-explicit-in-binder-dir/setup.py +++ b/tests/pipfile/setup-py-explicit-in-binder-dir/setup.py @@ -1,4 +1,4 @@ -from setuptools import setup, find_packages +from setuptools import find_packages, setup setup( name="Dummy", diff --git a/tests/pipfile/setup-py-explicit-in-binder-dir/verify b/tests/pipfile/setup-py-explicit-in-binder-dir/verify index 4c6eaf1e0..80f73003f 100755 --- a/tests/pipfile/setup-py-explicit-in-binder-dir/verify +++ b/tests/pipfile/setup-py-explicit-in-binder-dir/verify @@ -1,6 +1,6 @@ #!/usr/bin/env python -import there import dummy # This package should be available, as it was a dependency for dummy import pypi_pkg_test +import there diff --git a/tests/pipfile/setup-py-explicit/setup.py b/tests/pipfile/setup-py-explicit/setup.py index c67a722a7..ca077f415 100644 --- a/tests/pipfile/setup-py-explicit/setup.py +++ b/tests/pipfile/setup-py-explicit/setup.py @@ -1,4 +1,4 @@ -from setuptools import setup, find_packages +from setuptools import find_packages, setup setup( name="Dummy", diff --git a/tests/pipfile/setup-py-explicit/verify b/tests/pipfile/setup-py-explicit/verify index 4c6eaf1e0..80f73003f 100755 --- a/tests/pipfile/setup-py-explicit/verify +++ b/tests/pipfile/setup-py-explicit/verify @@ -1,6 +1,6 @@ #!/usr/bin/env python -import there import dummy # This package should be available, as it was a dependency for dummy import pypi_pkg_test +import there diff --git a/tests/pipfile/setup-py-implicit/setup.py b/tests/pipfile/setup-py-implicit/setup.py index c67a722a7..ca077f415 100644 --- a/tests/pipfile/setup-py-implicit/setup.py +++ b/tests/pipfile/setup-py-implicit/setup.py @@ -1,4 +1,4 @@ -from setuptools import setup, find_packages +from setuptools import find_packages, setup setup( name="Dummy", diff --git a/tests/unit/contentproviders/test_dataverse.py b/tests/unit/contentproviders/test_dataverse.py index 63a584716..309a22d4a 100644 --- a/tests/unit/contentproviders/test_dataverse.py +++ b/tests/unit/contentproviders/test_dataverse.py @@ -1,15 +1,14 @@ import json import os -import pytest import re - from io import BytesIO from tempfile import TemporaryDirectory from unittest.mock import patch -from urllib.request import urlopen, Request +from urllib.request import Request, urlopen -from repo2docker.contentproviders import Dataverse +import pytest +from repo2docker.contentproviders import Dataverse test_dv = Dataverse() harvard_dv = next(_ for _ in test_dv.hosts if _["name"] == "Harvard Dataverse") diff --git a/tests/unit/contentproviders/test_doi.py b/tests/unit/contentproviders/test_doi.py index ed2dcb736..dab3d7fcd 100644 --- a/tests/unit/contentproviders/test_doi.py +++ b/tests/unit/contentproviders/test_doi.py @@ -1,17 +1,17 @@ import json +import logging import os import re -import urllib -import pytest import tempfile -import logging - -from unittest.mock import patch, MagicMock, mock_open +import urllib +from unittest.mock import MagicMock, mock_open, patch from zipfile import ZipFile -from repo2docker.contentproviders.doi import DoiProvider -from repo2docker.contentproviders.base import ContentProviderException +import pytest + from repo2docker import __version__ +from repo2docker.contentproviders.base import ContentProviderException +from repo2docker.contentproviders.doi import DoiProvider def test_content_id(): diff --git a/tests/unit/contentproviders/test_figshare.py b/tests/unit/contentproviders/test_figshare.py index 3de67e985..b4f42de31 100644 --- a/tests/unit/contentproviders/test_figshare.py +++ b/tests/unit/contentproviders/test_figshare.py @@ -1,18 +1,17 @@ import json import os import re -import pytest - from contextlib import contextmanager from io import BytesIO -from tempfile import TemporaryDirectory, NamedTemporaryFile +from tempfile import NamedTemporaryFile, TemporaryDirectory from unittest.mock import patch -from urllib.request import urlopen, Request +from urllib.request import Request, urlopen from zipfile import ZipFile -from repo2docker.contentproviders import Figshare -from repo2docker.__main__ import make_r2d +import pytest +from repo2docker.__main__ import make_r2d +from repo2docker.contentproviders import Figshare test_content_ids = [ ("https://figshare.com/articles/title/9782777", "9782777.v1"), diff --git a/tests/unit/contentproviders/test_git.py b/tests/unit/contentproviders/test_git.py index 65779bf6d..fd63f9689 100644 --- a/tests/unit/contentproviders/test_git.py +++ b/tests/unit/contentproviders/test_git.py @@ -1,7 +1,9 @@ import os -import pytest import subprocess from tempfile import TemporaryDirectory + +import pytest + from repo2docker.contentproviders import Git diff --git a/tests/unit/contentproviders/test_hydroshare.py b/tests/unit/contentproviders/test_hydroshare.py index b0211c52f..cec541f6f 100755 --- a/tests/unit/contentproviders/test_hydroshare.py +++ b/tests/unit/contentproviders/test_hydroshare.py @@ -1,16 +1,15 @@ import os -import pytest - +import re from contextlib import contextmanager -from tempfile import TemporaryDirectory, NamedTemporaryFile +from tempfile import NamedTemporaryFile, TemporaryDirectory from unittest.mock import patch from zipfile import ZipFile -import re + +import pytest from repo2docker.contentproviders import Hydroshare from repo2docker.contentproviders.base import ContentProviderException - doi_responses = { "https://doi.org/10.4211/hs.b8f6eae9d89241cf8b5904033460af61": ( "https://www.hydroshare.org/resource/b8f6eae9d89241cf8b5904033460af61" diff --git a/tests/unit/contentproviders/test_local.py b/tests/unit/contentproviders/test_local.py index fcb2a6a87..ef288aef7 100644 --- a/tests/unit/contentproviders/test_local.py +++ b/tests/unit/contentproviders/test_local.py @@ -1,5 +1,5 @@ import os -from tempfile import TemporaryDirectory, NamedTemporaryFile +from tempfile import NamedTemporaryFile, TemporaryDirectory from repo2docker.contentproviders import Local diff --git a/tests/unit/contentproviders/test_mercurial.py b/tests/unit/contentproviders/test_mercurial.py index 4619ef862..0acb91d1e 100644 --- a/tests/unit/contentproviders/test_mercurial.py +++ b/tests/unit/contentproviders/test_mercurial.py @@ -8,7 +8,6 @@ from repo2docker.contentproviders import Mercurial from repo2docker.contentproviders.mercurial import args_enabling_topic - SKIP_HG = os.environ.get("REPO2DOCKER_SKIP_HG_TESTS", "").lower() not in { "", "0", diff --git a/tests/unit/contentproviders/test_swhid.py b/tests/unit/contentproviders/test_swhid.py index 48c1fa31e..56fee1dfc 100644 --- a/tests/unit/contentproviders/test_swhid.py +++ b/tests/unit/contentproviders/test_swhid.py @@ -1,22 +1,22 @@ +import io import json +import logging import os -import io -import tarfile -import shutil import re -import urllib -import pytest +import shutil +import tarfile import tempfile -import logging -import requests_mock - +import urllib from os import makedirs from os.path import join -from unittest.mock import patch, MagicMock, mock_open +from unittest.mock import MagicMock, mock_open, patch from zipfile import ZipFile -from repo2docker.contentproviders.swhid import Swhid, parse_swhid +import pytest +import requests_mock + from repo2docker.contentproviders.base import ContentProviderException +from repo2docker.contentproviders.swhid import Swhid, parse_swhid # this is a slightly stripped down copy of swh.model.cli.swhid_of_dir(). diff --git a/tests/unit/contentproviders/test_zenodo.py b/tests/unit/contentproviders/test_zenodo.py index 88e143c60..0755163da 100644 --- a/tests/unit/contentproviders/test_zenodo.py +++ b/tests/unit/contentproviders/test_zenodo.py @@ -1,15 +1,15 @@ import json import os -import pytest import re - from contextlib import contextmanager from io import BytesIO -from tempfile import TemporaryDirectory, NamedTemporaryFile +from tempfile import NamedTemporaryFile, TemporaryDirectory from unittest.mock import patch -from urllib.request import urlopen, Request +from urllib.request import Request, urlopen from zipfile import ZipFile +import pytest + from repo2docker.contentproviders import Zenodo doi_responses = { diff --git a/tests/unit/test_app.py b/tests/unit/test_app.py index 25b39cdb1..d37103e60 100644 --- a/tests/unit/test_app.py +++ b/tests/unit/test_app.py @@ -1,13 +1,13 @@ import errno -import pytest from tempfile import TemporaryDirectory from unittest.mock import patch -import docker import escapism +import pytest -from repo2docker.app import Repo2Docker +import docker from repo2docker.__main__ import make_r2d +from repo2docker.app import Repo2Docker from repo2docker.utils import chdir diff --git a/tests/unit/test_args.py b/tests/unit/test_args.py index 404ee796c..975604ea4 100644 --- a/tests/unit/test_args.py +++ b/tests/unit/test_args.py @@ -2,9 +2,11 @@ Test argument parsing and r2d construction """ import os + import pytest -from repo2docker.__main__ import make_r2d + from repo2docker import __version__ +from repo2docker.__main__ import make_r2d def test_version(capsys): diff --git a/tests/unit/test_argumentvalidation.py b/tests/unit/test_argumentvalidation.py index d2475b89f..33e7d69af 100644 --- a/tests/unit/test_argumentvalidation.py +++ b/tests/unit/test_argumentvalidation.py @@ -7,7 +7,6 @@ import pytest - here = os.path.dirname(os.path.abspath(__file__)) test_dir = os.path.dirname(here) docker_simple = os.path.join(test_dir, "dockerfile", "simple") diff --git a/tests/unit/test_buildpack.py b/tests/unit/test_buildpack.py index eda7bb924..6a8147e30 100644 --- a/tests/unit/test_buildpack.py +++ b/tests/unit/test_buildpack.py @@ -1,7 +1,8 @@ from os.path import join as pjoin +from tempfile import TemporaryDirectory import pytest -from tempfile import TemporaryDirectory + from repo2docker.buildpacks import LegacyBinderDockerBuildPack, PythonBuildPack from repo2docker.utils import chdir diff --git a/tests/unit/test_cache_from.py b/tests/unit/test_cache_from.py index 77797b128..fd186dbc5 100644 --- a/tests/unit/test_cache_from.py +++ b/tests/unit/test_cache_from.py @@ -5,7 +5,6 @@ from unittest.mock import MagicMock import docker - from repo2docker.buildpacks import ( BaseImage, DockerBuildPack, diff --git a/tests/unit/test_clone_depth.py b/tests/unit/test_clone_depth.py index 7989b1175..55102eac1 100644 --- a/tests/unit/test_clone_depth.py +++ b/tests/unit/test_clone_depth.py @@ -8,12 +8,10 @@ """ import os import subprocess - from tempfile import TemporaryDirectory from repo2docker.app import Repo2Docker - URL = "https://github.com/binderhub-ci-repos/repo2docker-ci-clone-depth" diff --git a/tests/unit/test_connect_url.py b/tests/unit/test_connect_url.py index 7438b8aa3..dbc0c2608 100644 --- a/tests/unit/test_connect_url.py +++ b/tests/unit/test_connect_url.py @@ -1,10 +1,11 @@ """ Test if the explict hostname is supplied correctly to the container """ -import requests import time -from repo2docker.app import Repo2Docker +import requests + +from repo2docker.app import Repo2Docker # Minimal Dockerfile to make build as fast as possible DOCKER_FILE = """ diff --git a/tests/unit/test_editable.py b/tests/unit/test_editable.py index 6947b7d21..de4d6261e 100644 --- a/tests/unit/test_editable.py +++ b/tests/unit/test_editable.py @@ -5,7 +5,6 @@ from repo2docker.__main__ import make_r2d - DIR = os.path.join(os.path.dirname(os.path.dirname(__file__)), "dockerfile", "editable") diff --git a/tests/unit/test_env_yml.py b/tests/unit/test_env_yml.py index c744ccf3a..dff142288 100644 --- a/tests/unit/test_env_yml.py +++ b/tests/unit/test_env_yml.py @@ -3,7 +3,9 @@ """ import os import sys + import pytest + from repo2docker import buildpacks diff --git a/tests/unit/test_external_scripts.py b/tests/unit/test_external_scripts.py index d03debe55..278707c87 100644 --- a/tests/unit/test_external_scripts.py +++ b/tests/unit/test_external_scripts.py @@ -1,5 +1,6 @@ """Test if assemble scripts from outside of r2d repo are accepted.""" import time + from repo2docker.app import Repo2Docker from repo2docker.buildpacks import PythonBuildPack diff --git a/tests/unit/test_freeze.py b/tests/unit/test_freeze.py index 66b0c3bbd..ddcd29f3e 100644 --- a/tests/unit/test_freeze.py +++ b/tests/unit/test_freeze.py @@ -2,12 +2,11 @@ from tempfile import TemporaryDirectory from unittest.mock import patch +import pytest from ruamel.yaml import YAML from repo2docker.buildpacks.conda.freeze import set_python -import pytest - V = "3.7" yaml = YAML(typ="rt") diff --git a/tests/unit/test_labels.py b/tests/unit/test_labels.py index c13cff4bf..5520de4d1 100644 --- a/tests/unit/test_labels.py +++ b/tests/unit/test_labels.py @@ -1,12 +1,13 @@ """ Test if labels are supplied correctly to the container """ -from repo2docker.app import Repo2Docker -from repo2docker.buildpacks import BuildPack -from repo2docker import __version__ -import pytest from unittest.mock import Mock +import pytest + +from repo2docker import __version__ +from repo2docker.app import Repo2Docker +from repo2docker.buildpacks import BuildPack URL = "https://github.com/binderhub-ci-repos/repo2docker-ci-clone-depth" diff --git a/tests/unit/test_memlimit.py b/tests/unit/test_memlimit.py index 1e708d4fc..ee2f2b356 100644 --- a/tests/unit/test_memlimit.py +++ b/tests/unit/test_memlimit.py @@ -3,16 +3,13 @@ """ import os - from unittest.mock import MagicMock -import docker - import pytest +import docker from repo2docker.buildpacks import BaseImage, DockerBuildPack - basedir = os.path.dirname(os.path.dirname(os.path.abspath(__file__))) diff --git a/tests/unit/test_ports.py b/tests/unit/test_ports.py index 90148ba41..aaebcdab1 100644 --- a/tests/unit/test_ports.py +++ b/tests/unit/test_ports.py @@ -2,18 +2,18 @@ Test Port mappings work on running non-jupyter workflows """ -import requests -import time import os -import tempfile import random +import tempfile +import time from getpass import getuser -import docker import pytest +import requests -from repo2docker.app import Repo2Docker +import docker from repo2docker.__main__ import make_r2d +from repo2docker.app import Repo2Docker def read_port_mapping_response( diff --git a/tests/unit/test_r.py b/tests/unit/test_r.py index 3d141cfc7..a5d7db7c0 100644 --- a/tests/unit/test_r.py +++ b/tests/unit/test_r.py @@ -1,8 +1,8 @@ from datetime import date +from unittest.mock import patch import pytest from requests.models import Response -from unittest.mock import patch from repo2docker import buildpacks diff --git a/tests/unit/test_semver.py b/tests/unit/test_semver.py index bbbf8ca50..b07272be1 100644 --- a/tests/unit/test_semver.py +++ b/tests/unit/test_semver.py @@ -1,5 +1,6 @@ import pytest from semver import VersionInfo + from repo2docker import semver diff --git a/tests/unit/test_subdir.py b/tests/unit/test_subdir.py index 4b0cd47ba..4e7007311 100644 --- a/tests/unit/test_subdir.py +++ b/tests/unit/test_subdir.py @@ -4,8 +4,8 @@ import os import escapism - import pytest + from repo2docker.app import Repo2Docker TEST_REPO = "https://github.com/binderhub-ci-repos/repo2docker-subdir-support" diff --git a/tests/unit/test_utils.py b/tests/unit/test_utils.py index 28401e33f..cec3dc8cd 100644 --- a/tests/unit/test_utils.py +++ b/tests/unit/test_utils.py @@ -1,13 +1,15 @@ """ Tests for repo2docker/utils.py """ -import traitlets import os -from repo2docker import utils -import pytest import subprocess import tempfile +import pytest +import traitlets + +from repo2docker import utils + def test_capture_cmd_no_capture_success(): # This should succeed From 94bd21e16e32fd868b2d06476b18513a69bcd9e3 Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Mon, 31 Oct 2022 23:40:34 +0100 Subject: [PATCH 038/171] pre-commit: enable prettier for markdown --- .pre-commit-config.yaml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8bd52ff20..842120dae 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -42,8 +42,9 @@ repos: args: - --profile=black - # # Autoformat: markdown, yaml (but not helm templates) - # - repo: https://github.com/pre-commit/mirrors-prettier - # rev: v2.7.1 - # hooks: - # - id: prettier + # Autoformat: markdown + - repo: https://github.com/pre-commit/mirrors-prettier + rev: v2.7.1 + hooks: + - id: prettier + files: ".md" From ae3aeb6dc5dd6deee6d663b7088eb74d225a815f Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 31 Oct 2022 22:40:52 +0000 Subject: [PATCH 039/171] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- .github/ISSUE_TEMPLATE/bug_report.md | 20 ++++--- .github/ISSUE_TEMPLATE/feature_request.md | 18 +++--- .github/ISSUE_TEMPLATE/support-question.md | 7 +-- CONTRIBUTING.md | 23 ++++---- README.md | 7 +-- docs/source/architecture.md | 14 ++--- docs/source/contributing/contributing.md | 66 +++++++++++----------- docs/source/contributing/roadmap.md | 47 ++++++++------- docs/source/contributing/tasks.md | 39 ++++++------- docs/source/design.md | 5 +- tests/conda/README.md | 2 +- 11 files changed, 125 insertions(+), 123 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md index 2171bd672..548df5785 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.md +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -1,23 +1,27 @@ --- name: Bug report about: Create a report to help us repair something that is currently broken -title: '' -labels: '' -assignees: '' - +title: "" +labels: "" +assignees: "" --- + ### Bug description + #### Expected behaviour + #### Actual behaviour + ### How to reproduce + 1. Go to '...' @@ -26,9 +30,9 @@ assignees: '' 4. See error ### Your personal set up - - - OS: [e.g. linux, OSX] - - Docker version: `docker version` - - repo2docker version `repo2docker --version` + +- OS: [e.g. linux, OSX] +- Docker version: `docker version` +- repo2docker version `repo2docker --version` diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md index 833ba6e5f..a0bcd5a2f 100644 --- a/.github/ISSUE_TEMPLATE/feature_request.md +++ b/.github/ISSUE_TEMPLATE/feature_request.md @@ -1,29 +1,29 @@ --- name: Feature request about: Suggest a new feature or a big change to repo2docker -title: '' -labels: 'needs: discussion' -assignees: '' - +title: "" +labels: "needs: discussion" +assignees: "" --- + ### Proposed change - + ### Alternative options - + ### Who would use this feature? - + ### How much effort will adding it take? - + ### Who can do this work? - + diff --git a/.github/ISSUE_TEMPLATE/support-question.md b/.github/ISSUE_TEMPLATE/support-question.md index bf10a69a4..e7b543e50 100644 --- a/.github/ISSUE_TEMPLATE/support-question.md +++ b/.github/ISSUE_TEMPLATE/support-question.md @@ -1,10 +1,9 @@ --- name: Support question about: Ask a question about using repo2docker -title: '' -labels: '' -assignees: '' - +title: "" +labels: "" +assignees: "" --- 🚨 Please do **not** open an issue for support questions. Instead please search for similar issues or post on http://discourse.jupyter.org/c/questions. 🚨 diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index f1a583d59..1dfc19576 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -8,19 +8,20 @@ The repo2docker developer documentation is all rendered on our documentation web If you're here, you're probably looking for the [Contributing to repo2docker development](https://repo2docker.readthedocs.io/en/latest/contributing/contributing.html) page. Please make sure you've read the following sections before opening an issue/pull request: -* [Process for making a contribution](https://repo2docker.readthedocs.io/en/latest/contributing/contributing.html#process-for-making-a-contribution). - * These steps talk you through choosing the right issue template (bug report or feature request) and making a change. -* [Guidelines to getting a Pull Request merged](https://repo2docker.readthedocs.io/en/latest/contributing/contributing.html#guidelines-to-getting-a-pull-request-merged). - * These are tips and tricks to help make your contribution as smooth as possible for you and for the repo2docker maintenance team. + +- [Process for making a contribution](https://repo2docker.readthedocs.io/en/latest/contributing/contributing.html#process-for-making-a-contribution). + - These steps talk you through choosing the right issue template (bug report or feature request) and making a change. +- [Guidelines to getting a Pull Request merged](https://repo2docker.readthedocs.io/en/latest/contributing/contributing.html#guidelines-to-getting-a-pull-request-merged). + - These are tips and tricks to help make your contribution as smooth as possible for you and for the repo2docker maintenance team. There are a few other pages to highlight: -* [Our roadmap](https://repo2docker.readthedocs.io/en/latest/contributing/roadmap.html) - * We use the roadmap to develop a shared understanding of the project's vision and direction amongst the community of users, contributors, and maintainers. +- [Our roadmap](https://repo2docker.readthedocs.io/en/latest/contributing/roadmap.html) + - We use the roadmap to develop a shared understanding of the project's vision and direction amongst the community of users, contributors, and maintainers. This is a great place to get a feel for what the maintainers are thinking about for the short, medium, and long term future of the project. -* [Design of repo2docker](https://repo2docker.readthedocs.io/en/latest/design.html) - * This page explains some of the design principles behind repo2docker. +- [Design of repo2docker](https://repo2docker.readthedocs.io/en/latest/design.html) + - This page explains some of the design principles behind repo2docker. Its a good place to understand _why_ the team have made the decisions that they have along the way! - * We absolutely encourage discussion around refactoring, updating or extending repo2docker, but please make sure that you've understood this page before opening an issue to discuss the change you'd like to propose. -* [Common developer tasks and how-tos](https://repo2docker.readthedocs.io/en/latest/contributing/tasks.html) - * Some notes on running tests, buildpack dependencies, creating a release, and keeping the pip files up to date. + - We absolutely encourage discussion around refactoring, updating or extending repo2docker, but please make sure that you've understood this page before opening an issue to discuss the change you'd like to propose. +- [Common developer tasks and how-tos](https://repo2docker.readthedocs.io/en/latest/contributing/tasks.html) + - Some notes on running tests, buildpack dependencies, creating a release, and keeping the pip files up to date. diff --git a/README.md b/README.md index 84949e84f..01d60eebc 100644 --- a/README.md +++ b/README.md @@ -31,6 +31,7 @@ For more information, please visit --- ## Using repo2docker + ### Prerequisites 1. Docker to build & run the repositories. The [community edition](https://store.docker.com/search?type=edition&offering=community) @@ -83,21 +84,19 @@ something like: If you copy paste that URL into your browser you will see a Jupyter Notebook with the contents of the repository you had just built! -For more information on how to use ``repo2docker``, see the +For more information on how to use `repo2docker`, see the [usage guide](http://repo2docker.readthedocs.io/en/latest/usage.html). - ## Repository specifications Repo2Docker looks for configuration files in the source repository to determine how the Docker image should be built. For a list of the configuration -files that ``repo2docker`` can use, see the +files that `repo2docker` can use, see the [complete list of configuration files](https://repo2docker.readthedocs.io/en/latest/config_files.html). The philosophy of repo2docker is inspired by [Heroku Build Packs](https://devcenter.heroku.com/articles/buildpacks). - ## Docker Image Repo2Docker can be run inside a Docker container if access to the Docker Daemon is provided, for example see [BinderHub](https://github.com/jupyterhub/binderhub). Docker images are [published to quay.io](https://quay.io/repository/jupyterhub/repo2docker?tab=tags). The old [Docker Hub image](https://hub.docker.com/r/jupyter/repo2docker) is no longer supported. diff --git a/docs/source/architecture.md b/docs/source/architecture.md index 153855188..0153c8ae4 100644 --- a/docs/source/architecture.md +++ b/docs/source/architecture.md @@ -4,6 +4,7 @@ This is a living document talking about the architecture of repo2docker from various perspectives. (buildpacks)= + ## Buildpacks The **buildpack** concept comes from [Heroku](https://devcenter.heroku.com/articles/buildpacks) @@ -57,7 +58,7 @@ and basic notebook packages (from `repo2docker/buildpacks/conda/environment.yml` to be the same for most repositories built with `CondaBuildPack`, so we want to use [docker layer caching](https://thenewstack.io/understanding-the-docker-cache-for-faster-builds/) as much as possible for performance reasons. Next time a repository is built with `CondaBuildPack`, -we can skip straight to the **copy** step (since the base environment docker image *layers* have +we can skip straight to the **copy** step (since the base environment docker image _layers_ have already been built and cached). The `get_build_scripts` and `get_build_script_files` methods are primarily used for this. @@ -65,11 +66,11 @@ The `get_build_scripts` and `get_build_script_files` methods are primarily used and `get_build_script_files` is used to copy specific scripts (such as a conda installer) into the image to be run as pat of `get_build_scripts`. Code in either has following constraints: -1. You can *not* use the contents of repository in them, since this happens before the repository +1. You can _not_ use the contents of repository in them, since this happens before the repository is copied into the image. For example, `pip install -r requirements.txt` will not work, since there's no `requirements.txt` inside the image at this point. This is an explicit design decision, to enable better layer caching. -2. You *may*, however, read the contents of the repository and modify the scripts emitted based +2. You _may_, however, read the contents of the repository and modify the scripts emitted based on that! For example, in `CondaBuildPack`, if there's Python 2 specified in `environment.yml`, a different kind of environment is set up. The reading of the `environment.yml` is performed in the BuildPack itself, and not in the scripts returned by `get_build_scripts`. This is fine. @@ -118,7 +119,7 @@ a path to a repository. This might be a local path or a URL. Upon being called, `repo2docker` will loop through all ContentProviders and perform the following commands: -* Run the `detect()` method on the repository path given to `repo2docker`. This +- Run the `detect()` method on the repository path given to `repo2docker`. This should return any value other than `None` if the path matches what the ContentProvider is looking for. @@ -126,12 +127,11 @@ commands: > checks whether the argument is a valid local path. If so, then `detect(` > returns a dictionary: `{'path': source}` which defines the path to the repository. > This path is used by `fetch()` to check that it matches the output directory. -* If `detect()` returns something other than `None`, run `fetch()` with the + +- If `detect()` returns something other than `None`, run `fetch()` with the returned value as its argument. This should result in the contents of the repository being placed locally to a folder. For more information on ContentProviders, take a look at [the ContentProvider base class](https://github.com/jupyterhub/repo2docker/blob/80b979f8580ddef184d2ba7d354e7a833cfa38a4/repo2docker/contentproviders/base.py#L16-L60) which has more explanation. - - diff --git a/docs/source/contributing/contributing.md b/docs/source/contributing/contributing.md index 7d101dfe6..8e26bcda2 100644 --- a/docs/source/contributing/contributing.md +++ b/docs/source/contributing/contributing.md @@ -2,33 +2,33 @@ Thank you for thinking about contributing to repo2docker! This is an open source project that is developed and maintained entirely by volunteers. -*Your contribution* is integral to the future of the project. +_Your contribution_ is integral to the future of the project. THANK YOU! ## Types of contribution There are many ways to contribute to repo2docker: -* **Update the documentation.** +- **Update the documentation.** If you're reading a page or docstring and it doesn't make sense (or doesn't exist!), please let us know by opening a bug report. It's even more amazing if you can give us a suggested change. -* **Fix bugs or add requested features.** +- **Fix bugs or add requested features.** Have a look through the [issue tracker](https://github.com/jupyterhub/repo2docker/issues) and see if there are any tagged as ["help wanted"](https://github.com/jupyterhub/repo2docker/issues?q=is%3Aissue+is%3Aopen+label%3A%22help+wanted%22). As the label suggests, we'd love your help! -* **Report a bug.** +- **Report a bug.** If repo2docker isn't doing what you thought it would do then open a [bug report](https://github.com/jupyterhub/repo2docker/issues/new?template=bug_report.md). That issue template will ask you a few questions described in more detail below. -* **Suggest a new feature.** +- **Suggest a new feature.** We know that there are lots of ways to extend repo2docker! If you're interested in adding a feature then please open a [feature request](https://github.com/jupyterhub/repo2docker/issues/new?template=feature_request.md). That issue template will ask you a few questions described in detail below. -* **Review someone's Pull Request.** +- **Review someone's Pull Request.** Whenever somebody proposes changes to the repo2docker codebase, the community reviews the changes, and provides feedback, edits, and suggestions. Check out the [open pull requests](https://github.com/jupyterhub/repo2docker/pulls?q=is%3Apr+is%3Aopen+sort%3Aupdated-desc) and provide feedback that helps improve the PR and get it merged. Please keep your feedback positive and constructive! -* **Tell people about repo2docker.** +- **Tell people about repo2docker.** As we said above, repo2docker is built by and for its community. If you know anyone who would like to use repo2docker, please tell them about the project! You could give a talk about it, or run a demonstration. @@ -42,31 +42,31 @@ This outlines the process for getting changes to the repo2docker project merged. 1. Identify the correct issue template: [bug report](https://github.com/jupyterhub/repo2docker/issues/new?template=bug_report.md) or [feature request](https://github.com/jupyterhub/repo2docker/issues/new?template=feature_request.md). - **Bug reports** ([examples](https://github.com/jupyterhub/repo2docker/issues?q=is%3Aissue+is%3Aopen+label%3Abug), [new issue](https://github.com/jupyterhub/repo2docker/issues/new?template=bug_report.md)) will ask you for a description of the problem, the expected behaviour, the actual behaviour, how to reproduce the problem, and your personal set up. - Bugs can include problems with the documentation, or code not running as expected. + **Bug reports** ([examples](https://github.com/jupyterhub/repo2docker/issues?q=is%3Aissue+is%3Aopen+label%3Abug), [new issue](https://github.com/jupyterhub/repo2docker/issues/new?template=bug_report.md)) will ask you for a description of the problem, the expected behaviour, the actual behaviour, how to reproduce the problem, and your personal set up. + Bugs can include problems with the documentation, or code not running as expected. - It is really important that you make it easy for the maintainers to reproduce the problem you're having. - This guide on creating a [minimal, complete and verifiable example](https://stackoverflow.com/help/mcve) is a great place to start. + It is really important that you make it easy for the maintainers to reproduce the problem you're having. + This guide on creating a [minimal, complete and verifiable example](https://stackoverflow.com/help/mcve) is a great place to start. - **Feature requests** ([examples](https://github.com/jupyterhub/repo2docker/labels/needs%3A%20discussion), [new issue](https://github.com/jupyterhub/repo2docker/issues/new?template=feature_request.md)) will ask you for the proposed change, any alternatives that you have considered, a description of who would use this feature, and a best-guess of how much work it will take and what skills are required to accomplish. + **Feature requests** ([examples](https://github.com/jupyterhub/repo2docker/labels/needs%3A%20discussion), [new issue](https://github.com/jupyterhub/repo2docker/issues/new?template=feature_request.md)) will ask you for the proposed change, any alternatives that you have considered, a description of who would use this feature, and a best-guess of how much work it will take and what skills are required to accomplish. - Very easy feature requests might be updates to the documentation to clarify steps for new users. - Harder feature requests may be to add new functionality to the project and will need more in depth discussion about who can complete and maintain the work. + Very easy feature requests might be updates to the documentation to clarify steps for new users. + Harder feature requests may be to add new functionality to the project and will need more in depth discussion about who can complete and maintain the work. - Feature requests are a great opportunity for you to advocate for the use case you're suggesting. - They help others understand how much effort it would be to integrate the work,and - if you're successful at convincing them that this effort is worth it - make it more likely that they to choose to work on it with you. + Feature requests are a great opportunity for you to advocate for the use case you're suggesting. + They help others understand how much effort it would be to integrate the work,and - if you're successful at convincing them that this effort is worth it - make it more likely that they to choose to work on it with you. 2. Open an issue. - Getting consensus with the community is a great way to save time later. + Getting consensus with the community is a great way to save time later. 3. Make edits in [your fork](https://help.github.com/en/articles/fork-a-repo) of the [repo2docker repository](https://github.com/jupyterhub/repo2docker). 4. Make a [pull request](https://help.github.com/en/articles/about-pull-requests). -Read the [next section](guidelines-to-getting-a-pull-request-merged) for guidelines for both reviewers and contributors on merging a PR. -6. Wait for a community member to merge your changes. - Remember that **someone else must merge your pull request**. - That goes for new contributors and long term maintainers alike. - Because `main` is continuously deployed to mybinder.org it is essential - that `main` is always in a deployable state. -7. (optional) Deploy a new version of repo2docker to mybinder.org by [following these steps](http://mybinder-sre.readthedocs.io/en/latest/deployment/how.html) + Read the [next section](guidelines-to-getting-a-pull-request-merged) for guidelines for both reviewers and contributors on merging a PR. +5. Wait for a community member to merge your changes. + Remember that **someone else must merge your pull request**. + That goes for new contributors and long term maintainers alike. + Because `main` is continuously deployed to mybinder.org it is essential + that `main` is always in a deployable state. +6. (optional) Deploy a new version of repo2docker to mybinder.org by [following these steps](http://mybinder-sre.readthedocs.io/en/latest/deployment/how.html) (guidelines-to-getting-a-pull-request-merged)= @@ -74,26 +74,27 @@ Read the [next section](guidelines-to-getting-a-pull-request-merged) for guideli These are not hard rules to be enforced by 🚓 but they are suggestions written by the repo2docker maintainers to help complete your contribution as smoothly as possible for both you and for them. -* **Create a PR as early as possible**, marking it with `[WIP]` while you work on it. +- **Create a PR as early as possible**, marking it with `[WIP]` while you work on it. This avoids duplicated work, lets you get high level feedback on functionality or API changes, and/or helps find collaborators to work with you. -* **Keep your PR focused.** +- **Keep your PR focused.** The best PRs solve one problem. If you end up changing multiple things, please open separate PRs for the different conceptual changes. -* **Add tests to your code.** +- **Add tests to your code.** PRs will not be merged if Travis is failing. -* **Apply [PEP8](https://www.python.org/dev/peps/pep-0008/)** as much as possible, but not too much. +- **Apply [PEP8](https://www.python.org/dev/peps/pep-0008/)** as much as possible, but not too much. If in doubt, ask. -* **Use merge commits** instead of merge-by-squashing/-rebasing. +- **Use merge commits** instead of merge-by-squashing/-rebasing. This makes it easier to find all changes since the last deployment `git log --merges --pretty=format:"%h %<(10,trunc)%an %<(15)%ar %s" ..` and your PR easier to review. -* **Make it clear when your PR is ready for review.** +- **Make it clear when your PR is ready for review.** Prefix the title of your pull request (PR) with `[MRG]` if the contribution is complete and should be subjected to a detailed review. -* **Use commit messages to describe _why_ you are proposing the changes you are proposing.** -* **Try to not rush changes** (the definition of rush depends on how big your changes are). +- **Use commit messages to describe _why_ you are proposing the changes you are proposing.** +- **Try to not rush changes** (the definition of rush depends on how big your changes are). Remember that everyone in the repo2docker team is a volunteer and we can not (nor would we want to) control their time or interests. Wait patiently for a reviewer to merge the PR. (Remember that **someone else** must merge your PR, even if you have the admin rights to do so.) (contributing:local-dev)= + ## Setting up for Local Development To develop & test repo2docker locally, you need: @@ -149,7 +150,6 @@ according to black's style guide. You can activate it with `pre-commit install`. As part of our continuous integration tests we will check that code is formatted properly and the tests will fail if this is not the case. - ### Verify that docker is installed and running If you do not already have [Docker](https://www.docker.com/), you should be able diff --git a/docs/source/contributing/roadmap.md b/docs/source/contributing/roadmap.md index 0a620cadc..4148a7a79 100644 --- a/docs/source/contributing/roadmap.md +++ b/docs/source/contributing/roadmap.md @@ -7,6 +7,7 @@ The goal is to communicate priorities and upcoming release plans. It is not a aimed at limiting contributions to what is listed here. ## Using the roadmap + ### Sharing Feedback on the Roadmap All of the community is encouraged to provide feedback as well as share new @@ -16,24 +17,22 @@ After submitting the issue, others from the community will probably respond with questions or comments they have to clarify the issue. The maintainers will help identify what a good next step is for the issue. - ### What do we mean by "next step"? When submitting an issue, think about what "next step" category best describes your issue: -* **now**, concrete/actionable step that is ready for someone to start work on. -These might be items that have a link to an issue or more abstract like -"decrease typos and dead links in the documentation" -* **soon**, less concrete/actionable step that is going to happen soon, -discussions around the topic are coming close to an end at which point it can -move into the "now" category -* **later**, abstract ideas or tasks, need a lot of discussion or -experimentation to shape the idea so that it can be executed. Can also -contain concrete/actionable steps that have been postponed on purpose -(these are steps that could be in "now" but the decision was taken to work on -them later) - +- **now**, concrete/actionable step that is ready for someone to start work on. + These might be items that have a link to an issue or more abstract like + "decrease typos and dead links in the documentation" +- **soon**, less concrete/actionable step that is going to happen soon, + discussions around the topic are coming close to an end at which point it can + move into the "now" category +- **later**, abstract ideas or tasks, need a lot of discussion or + experimentation to shape the idea so that it can be executed. Can also + contain concrete/actionable steps that have been postponed on purpose + (these are steps that could be in "now" but the decision was taken to work on + them later) ### Reviewing and Updating the Roadmap @@ -48,22 +47,21 @@ For those please create a The roadmap should give the reader an idea of what is happening next, what needs input and discussion before it can happen and what has been postponed. - ## The roadmap proper + ### Project vision Repo2docker is a dependable tool used by humans that reduces the complexity of creating the environment in which a piece of software can be executed. - ### Now The "Now" items are being actively worked on by the project: -* reduce documentation typos and syntax errors -* increase test coverage to 80% (see https://codecov.io/gh/jupyterhub/repo2docker/tree/main/repo2docker for low coverage files) -* mounting repository contents in locations that is not `/home/jovyan` -* investigate options for pinning repo2docker versions ([#490](https://github.com/jupyterhub/repo2docker/issues/490)) +- reduce documentation typos and syntax errors +- increase test coverage to 80% (see https://codecov.io/gh/jupyterhub/repo2docker/tree/main/repo2docker for low coverage files) +- mounting repository contents in locations that is not `/home/jovyan` +- investigate options for pinning repo2docker versions ([#490](https://github.com/jupyterhub/repo2docker/issues/490)) ### Soon @@ -71,15 +69,16 @@ The "Soon" items are being discussed/a plan of action is being made. Once an item reaches the point of an actionable plan and person who wants to work on it, the item will be moved to the "Now" section. Typically, these will be moved at a future review of the roadmap. -* create the contributor highway, define the route from newcomer to project lead -* add Julia Manifest support (https://docs.julialang.org/en/v1/stdlib/Pkg/index.html, [#486](https://github.com/jupyterhub/repo2docker/issues/486)) -* support different base images/build pack stacks ([#487](https://github.com/jupyterhub/repo2docker/issues/487)) +- create the contributor highway, define the route from newcomer to project lead +- add Julia Manifest support (https://docs.julialang.org/en/v1/stdlib/Pkg/index.html, [#486](https://github.com/jupyterhub/repo2docker/issues/486)) +- support different base images/build pack stacks ([#487](https://github.com/jupyterhub/repo2docker/issues/487)) ### Later The "Later" items are things that are at the back of the project's mind. At this time there is no active plan for an item. The project would like to find the resources and time to discuss and then execute these ideas. -* support execution on a remote host (with more resources than available locally) via the command-line -* add support for using ZIP files as the repo (`repo2docker https://example.com/an-archive.zip`) + +- support execution on a remote host (with more resources than available locally) via the command-line +- add support for using ZIP files as the repo (`repo2docker https://example.com/an-archive.zip`) diff --git a/docs/source/contributing/tasks.md b/docs/source/contributing/tasks.md index 3fe47585c..6deae1c0f 100644 --- a/docs/source/contributing/tasks.md +++ b/docs/source/contributing/tasks.md @@ -32,17 +32,18 @@ py.test -s tests/ To skip the tests related to Mercurial repositories (to avoid to install Mercurial and hg-evolve), one can use the environment variable -``REPO2DOCKER_SKIP_HG_TESTS``. +`REPO2DOCKER_SKIP_HG_TESTS`. ### Troubleshooting Tests Some of the tests have non-python requirements for your development machine. They are: - `git-lfs` must be installed ([instructions](https://github.com/git-lfs/git-lfs)). It need not be activated -- there is no need to run the `git lfs install` command. It just needs to be available to the test suite. - - If your test failure messages include "`git-lfs filter-process: git-lfs: command not found`", this step should address the problem. + + - If your test failure messages include "`git-lfs filter-process: git-lfs: command not found`", this step should address the problem. - Minimum Docker Image size of 128GB is required. If you are not running docker on a linux OS, you may need to expand the runtime image size for your installation. See Docker's instructions for [macOS](https://docs.docker.com/docker-for-mac/space/) or [Windows 10](https://docs.docker.com/docker-for-windows/#resources) for more information. - - If your test failure messages include "`No space left on device: '/home/...`", this step should address the problem. + - If your test failure messages include "`No space left on device: '/home/...`", this step should address the problem. ## Update and Freeze BuildPack Dependencies @@ -51,35 +52,36 @@ dependencies that are installed by default for several buildpacks. For both the `conda` and `virtualenv` (`pip`) base environments in the **Conda BuildPack** and **Python BuildPack**, we install specific pinned versions of all dependencies. We explicitly list the dependencies -we want, then *freeze* them at commit time to explicitly list all the +we want, then _freeze_ them at commit time to explicitly list all the transitive dependencies at current versions. This way, we know that all dependencies will have the exact same version installed at all times. To update one of the dependencies shared across all `repo2docker` builds, you must follow these steps (with more detailed information in the sections below): -1. Bump the version numbers of the dependencies you want to update in the `conda` environment ([link](tasks:conda-dependencies)) +1. Bump the version numbers of the dependencies you want to update in the `conda` environment ([link](tasks:conda-dependencies)) 2. Make a pull request with your changes ([link](https://github.com/jupyterhub/repo2docker/blob/HEAD/CONTRIBUTING.md#make-a-pull-request)) See the subsections below for more detailed instructions. (tasks:conda-dependencies)= + ### Conda dependencies 1. There are two files related to conda dependencies. Edit as needed. - - `repo2docker/buildpacks/conda/environment.yml` + - `repo2docker/buildpacks/conda/environment.yml` - Contains list of packages to install in Python3 conda environments, - which are the default. **This is where all Notebook versions & - notebook extensions (such as JupyterLab / nteract) go**. + Contains list of packages to install in Python3 conda environments, + which are the default. **This is where all Notebook versions & + notebook extensions (such as JupyterLab / nteract) go**. - - `repo2docker/buildpacks/conda/environment.py-2.7.yml` + - `repo2docker/buildpacks/conda/environment.py-2.7.yml` - Contains list of packages to install in Python2 conda environments, which - can be specifically requested by users. **This only needs `IPyKernel` - and kernel related libraries**. Notebook / Notebook Extension need - not be installed here. + Contains list of packages to install in Python2 conda environments, which + can be specifically requested by users. **This only needs `IPyKernel` + and kernel related libraries**. Notebook / Notebook Extension need + not be installed here. 2. Once you edit either of these files to add a new package / bump version on an existing package, you should then run: @@ -147,14 +149,13 @@ Once this has completed, make sure that the new version has been updated. Once the new release has been pushed to PyPI, we need to create a new release on the [GitHub repository releases page](https://github.com/jupyterhub/repo2docker/releases). Once on that page, follow these steps: -* Click "Draft a new release" -* Choose a tag version using the same tag you just created above -* The release name is simply the tag version -* Finally, click "Publish release" +- Click "Draft a new release" +- Choose a tag version using the same tag you just created above +- The release name is simply the tag version +- Finally, click "Publish release" That's it! - # Uncommon tasks ## Compare generated Dockerfiles between repo2docker versions diff --git a/docs/source/design.md b/docs/source/design.md index e70835637..7f6536941 100644 --- a/docs/source/design.md +++ b/docs/source/design.md @@ -7,8 +7,7 @@ The philosophy for the repo2docker buildpacks includes: - using common configuration files for familiar installation and packaging tools - allowing configuration files to be combined to compose more complex setups - specifying default locations for configuration files -(in the repository's root, `binder` or `.binder` directory) - + (in the repository's root, `binder` or `.binder` directory) When designing `repo2docker` and adding to it in the future, the developers are influenced by two primary use cases. @@ -79,7 +78,7 @@ is a highly recommended quick read. Although other projects, like [s2i](https://github.com/openshift/source-to-image), exist to convert source to Docker images, `repo2docker` provides the additional functionality to support -*composable* environments. We want to easily have an image with +_composable_ environments. We want to easily have an image with Python3+Julia+R-3.2 environments, rather than just one single language environment. While generally one language environment per container works well, in many scientific / datascience computing environments you need multiple diff --git a/tests/conda/README.md b/tests/conda/README.md index 156976194..6f137f615 100644 --- a/tests/conda/README.md +++ b/tests/conda/README.md @@ -57,7 +57,7 @@ `--target-repo-dir` is meant to support custom paths where repositories can be copied to besides `${HOME}`. - + This test makes use of the `test-extra-args.yaml` file to influence additional arguments passed to `repo2docker` during the test. In this test, specify `--target-repo-dir=/srv/repo`. From ff586d0e10b989c466d226f2bfed0ae414a180ac Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Wed, 2 Nov 2022 16:42:29 +0100 Subject: [PATCH 040/171] docker image: update alpine to 3.16 --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index e60edab3f..0f7d08ed5 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,5 +1,5 @@ # syntax = docker/dockerfile:1.3 -ARG ALPINE_VERSION=3.15.0 +ARG ALPINE_VERSION=3.16 FROM alpine:${ALPINE_VERSION} AS builder RUN apk add --no-cache git python3 python3-dev py-pip build-base From 3e5a64f82f515f38ae887000baf4903737282a02 Mon Sep 17 00:00:00 2001 From: Sylvain Corlay Date: Thu, 3 Nov 2022 00:50:34 +0100 Subject: [PATCH 041/171] Upgrade to mamba 1.0 --- repo2docker/buildpacks/conda/install-base-env.bash | 2 +- tests/conda/py35-binder-dir/verify | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/repo2docker/buildpacks/conda/install-base-env.bash b/repo2docker/buildpacks/conda/install-base-env.bash index 33b917735..10b196979 100755 --- a/repo2docker/buildpacks/conda/install-base-env.bash +++ b/repo2docker/buildpacks/conda/install-base-env.bash @@ -5,7 +5,7 @@ set -ex cd $(dirname $0) -export MAMBA_VERSION=0.25.0 +export MAMBA_VERSION=1.0.0 export CONDA_VERSION=4.13.0 URL="https://anaconda.org/conda-forge/micromamba/${MAMBA_VERSION}/download/linux-64/micromamba-${MAMBA_VERSION}-0.tar.bz2" diff --git a/tests/conda/py35-binder-dir/verify b/tests/conda/py35-binder-dir/verify index c43376a87..32e73c428 100755 --- a/tests/conda/py35-binder-dir/verify +++ b/tests/conda/py35-binder-dir/verify @@ -5,12 +5,12 @@ from subprocess import check_output assert sys.version_info[:2] == (3, 5), sys.version out = check_output(["micromamba", "--version"]).decode("utf8").strip() -assert out == "0.25.0", out +assert out == "1.0.0", out out = check_output(["mamba", "--version"]).decode("utf8").strip() assert ( out - == """mamba 0.25.0 + == """mamba 1.0.0 conda 4.13.0""" ), out From 61b76f622d0300eb4730ee36e03d848e8c0b827d Mon Sep 17 00:00:00 2001 From: Frankie Robertson Date: Tue, 8 Nov 2022 14:48:47 +0200 Subject: [PATCH 042/171] Create Julia projects based on binder/Project.toml when found --- repo2docker/buildpacks/julia/julia_project.py | 23 ++++++++++++++----- 1 file changed, 17 insertions(+), 6 deletions(-) diff --git a/repo2docker/buildpacks/julia/julia_project.py b/repo2docker/buildpacks/julia/julia_project.py index d61e65d13..70853b26a 100644 --- a/repo2docker/buildpacks/julia/julia_project.py +++ b/repo2docker/buildpacks/julia/julia_project.py @@ -93,8 +93,15 @@ def get_build_env(self): ("JUPYTER_DATA_DIR", "${NB_PYTHON_PREFIX}/share/jupyter"), ] + @property + def project_dir(self): + if self.binder_dir: + return "${REPO_DIR}/" + self.binder_dir + else: + return "${REPO_DIR}" + def get_env(self): - return super().get_env() + [("JULIA_PROJECT", "${REPO_DIR}")] + return super().get_env() + [("JULIA_PROJECT", self.project_dir)] def get_path(self): """Adds path to Julia binaries to user's PATH. @@ -148,15 +155,19 @@ def get_assemble_scripts(self): The parent, CondaBuildPack, will add the build steps for any needed Python packages found in environment.yml. """ - return super().get_assemble_scripts() + [ + scripts = super().get_assemble_scripts() + scripts.append( ( "${NB_USER}", r""" - JULIA_PROJECT="" julia -e "using Pkg; Pkg.add(\"IJulia\"); using IJulia; installkernel(\"Julia\", \"--project=${REPO_DIR}\");" && \ - julia --project=${REPO_DIR} -e 'using Pkg; Pkg.instantiate(); Pkg.resolve(); pkg"precompile"' - """, + JULIA_PROJECT="" julia -e "using Pkg; Pkg.add(\"IJulia\"); using IJulia; installkernel(\"Julia\", \"--project={project}\");" && \ + julia --project={project} -e 'using Pkg; Pkg.instantiate(); Pkg.resolve(); pkg"precompile"' + """.format( + project=self.project_dir + ), ) - ] + ) + return scripts def detect(self): """ From e99a1061719cec892ffab2c11350df8c2220a32f Mon Sep 17 00:00:00 2001 From: Frankie Robertson Date: Tue, 8 Nov 2022 14:50:07 +0200 Subject: [PATCH 043/171] Add test for Julia project.toml in binder subdirectory --- tests/julia/project-binder-dir/Manifest.toml | 10 ++++++ tests/julia/project-binder-dir/Project.toml | 2 ++ .../project-binder-dir/binder/Manifest.toml | 36 +++++++++++++++++++ .../project-binder-dir/binder/Project.toml | 2 ++ tests/julia/project-binder-dir/verify | 27 ++++++++++++++ 5 files changed, 77 insertions(+) create mode 100644 tests/julia/project-binder-dir/Manifest.toml create mode 100644 tests/julia/project-binder-dir/Project.toml create mode 100644 tests/julia/project-binder-dir/binder/Manifest.toml create mode 100644 tests/julia/project-binder-dir/binder/Project.toml create mode 100755 tests/julia/project-binder-dir/verify diff --git a/tests/julia/project-binder-dir/Manifest.toml b/tests/julia/project-binder-dir/Manifest.toml new file mode 100644 index 000000000..1b72c7cd7 --- /dev/null +++ b/tests/julia/project-binder-dir/Manifest.toml @@ -0,0 +1,10 @@ +# This file is machine-generated - editing it directly is not advised + +julia_version = "1.8.2" +manifest_format = "2.0" +project_hash = "8a6b9faef104dfa92a55997106baee3560dc25bc" + +[[deps.IteratorInterfaceExtensions]] +git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" +uuid = "82899510-4779-5014-852e-03e436cf321d" +version = "1.0.0" diff --git a/tests/julia/project-binder-dir/Project.toml b/tests/julia/project-binder-dir/Project.toml new file mode 100644 index 000000000..ee7dad5c3 --- /dev/null +++ b/tests/julia/project-binder-dir/Project.toml @@ -0,0 +1,2 @@ +[deps] +IteratorInterfaceExtensions = "82899510-4779-5014-852e-03e436cf321d" diff --git a/tests/julia/project-binder-dir/binder/Manifest.toml b/tests/julia/project-binder-dir/binder/Manifest.toml new file mode 100644 index 000000000..7e4afe015 --- /dev/null +++ b/tests/julia/project-binder-dir/binder/Manifest.toml @@ -0,0 +1,36 @@ +# This file is machine-generated - editing it directly is not advised + +julia_version = "1.8.2" +manifest_format = "2.0" +project_hash = "663bcf2fe6af67425c484706d7562ccb3a370117" + +[[deps.Adapt]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "195c5505521008abea5aee4f96930717958eac6f" +uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" +version = "3.4.0" + +[[deps.Artifacts]] +uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" + +[[deps.CompilerSupportLibraries_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" +version = "0.5.2+0" + +[[deps.Libdl]] +uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" + +[[deps.LinearAlgebra]] +deps = ["Libdl", "libblastrampoline_jll"] +uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" + +[[deps.OpenBLAS_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] +uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" +version = "0.3.20+0" + +[[deps.libblastrampoline_jll]] +deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] +uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" +version = "5.1.1+0" diff --git a/tests/julia/project-binder-dir/binder/Project.toml b/tests/julia/project-binder-dir/binder/Project.toml new file mode 100644 index 000000000..b14e0e605 --- /dev/null +++ b/tests/julia/project-binder-dir/binder/Project.toml @@ -0,0 +1,2 @@ +[deps] +Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" diff --git a/tests/julia/project-binder-dir/verify b/tests/julia/project-binder-dir/verify new file mode 100755 index 000000000..32ce2c44b --- /dev/null +++ b/tests/julia/project-binder-dir/verify @@ -0,0 +1,27 @@ +#!/usr/bin/env julia + +if VERSION != v"1.8.2" + println("Julia version should be 1.8.2") + exit(1) +end + +# Verify that the environment variables are set correctly for julia 1.0+ +@assert "julia" ∈ readdir(Sys.BINDIR) + +try + # Test that the package was installed. + using Adapt +catch + println("Should be able to load Adapt") + exit(1) +end + +try + using IteratorInterfaceExtensions + # Test that the package was not installed. + println("Should not be able to load IteratorInterfaceExtensions") + exit(1) +catch +end + +exit(0) From b841dea4ac6cd65f0db30b369174489b5b909783 Mon Sep 17 00:00:00 2001 From: Min RK Date: Wed, 2 Nov 2022 14:51:58 +0100 Subject: [PATCH 044/171] reconcile CLI/config priority - avoid CLI defaults clobbering values from config. Mostly by using `default=None`, and adding `if args.name is not None` checks before assigning attributes --- repo2docker/__main__.py | 54 ++++++++++++++++++++++++++--------------- repo2docker/app.py | 2 +- 2 files changed, 35 insertions(+), 21 deletions(-) diff --git a/repo2docker/__main__.py b/repo2docker/__main__.py index cca1616ce..41bc5c38e 100644 --- a/repo2docker/__main__.py +++ b/repo2docker/__main__.py @@ -93,7 +93,7 @@ def get_argparser(): argparser.add_argument( "--json-logs", - default=False, + default=None, action="store_true", help="Emit JSON logs instead of human readable logs", ) @@ -108,7 +108,7 @@ def get_argparser(): argparser.add_argument( "--image-name", - help=("Name of image to be built. If unspecified will be " "autogenerated"), + help="Name of image to be built. If unspecified will be autogenerated", type=validate_image_name, ) @@ -126,9 +126,7 @@ def get_argparser(): "--no-build", dest="build", action="store_false", - help=( - "Do not actually build the image. Useful in conjunction " "with --debug." - ), + help="Do not actually build the image. Useful in conjunction with --debug.", ) argparser.add_argument( @@ -164,6 +162,7 @@ def get_argparser(): "--publish-all", "-P", dest="all_ports", + default=None, action="store_true", help="Publish all exposed ports to random host ports.", ) @@ -171,6 +170,7 @@ def get_argparser(): argparser.add_argument( "--no-clean", dest="clean", + default=None, action="store_false", help="Don't clean up remote checkouts after we are done", ) @@ -250,6 +250,7 @@ def get_argparser(): return argparser +# Note: only used by sphinx-autoprogram argparser = get_argparser() @@ -274,12 +275,18 @@ def make_r2d(argv=None): args, traitlet_args = argparser.parse_known_args(argv) r2d = Repo2Docker() - r2d.parse_command_line(traitlet_args) if args.debug: r2d.log_level = logging.DEBUG + # load CLI after config file, for correct priority r2d.load_config_file(args.config) + r2d.parse_command_line(traitlet_args) + + if args.debug: + # re-apply debug in case log_level was also set via config + r2d.log_level = logging.DEBUG + if args.appendix: r2d.appendix = args.appendix @@ -317,7 +324,8 @@ def make_r2d(argv=None): # we will pick a name after fetching the repository r2d.output_image_spec = "" - r2d.json_logs = args.json_logs + if args.json_logs is not None: + r2d.json_logs = args.json_logs r2d.dry_run = not args.build @@ -341,29 +349,33 @@ def make_r2d(argv=None): src, dest = v.split(":") r2d.volumes[src] = dest - r2d.run_cmd = args.cmd + if args.cmd: + r2d.run_cmd = args.cmd if args.all_ports and not r2d.run: - print( - "To publish user defined port mappings, the container must " "also be run" - ) + print("To publish user-defined port mappings, the container must also be run") sys.exit(1) if args.ports and not r2d.run: - print( - "To publish user defined port mappings, the container must " "also be run" - ) + print("To publish user-defined port mappings, the container must also be run") sys.exit(1) if args.ports and len(args.ports) > 1 and not r2d.run_cmd: print( - "To publish user defined port mapping, user must specify " - "the command to run in the container" + "To publish user-defined port mapping, " + "you must specify the command to run in the container" ) sys.exit(1) - r2d.ports = validate_and_generate_port_mapping(args.ports) - r2d.all_ports = args.all_ports + if args.ports: + # override or update, if also defined in config file? + if r2d.ports: + r2d.log.warning( + f"Ignoring port configuration from config (ports={r2d.ports}), overridden by CLI" + ) + r2d.ports = validate_and_generate_port_mapping(args.ports) + if args.all_ports is not None: + r2d.all_ports = args.all_ports if args.user_id: r2d.user_id = args.user_id @@ -401,13 +413,15 @@ def make_r2d(argv=None): if args.engine: r2d.engine = args.engine - r2d.environment = args.environment + if args.environment: + # extend any environment config from a config file + r2d.environment.extend(args.environment) # if the source exists locally we don't want to delete it at the end # FIXME: Find a better way to figure out if repo is 'local'. Push this into ContentProvider? if os.path.exists(args.repo): r2d.cleanup_checkout = False - else: + elif args.clean is not None: r2d.cleanup_checkout = args.clean if args.target_repo_dir: diff --git a/repo2docker/app.py b/repo2docker/app.py index c62a77d63..e3e2ebc51 100755 --- a/repo2docker/app.py +++ b/repo2docker/app.py @@ -332,7 +332,7 @@ def _user_name_default(self): ) run = Bool( - False, + True, help=""" Run docker image after building """, From 98724fb2556203fa8d3ff1940c19e02e1f861c68 Mon Sep 17 00:00:00 2001 From: Min RK Date: Tue, 8 Nov 2022 15:40:23 +0100 Subject: [PATCH 045/171] handle more options from config - warn if repo is specified in config, because it doesn't make sense and will be ignored - only override config for ref/image/run/build if specified on the cli requires both-directions config for run and build, to handle the default being inverted in a config file --- repo2docker/__main__.py | 44 ++++++++++++++++++++++++++++++++++------- 1 file changed, 37 insertions(+), 7 deletions(-) diff --git a/repo2docker/__main__.py b/repo2docker/__main__.py index 41bc5c38e..56a78c225 100644 --- a/repo2docker/__main__.py +++ b/repo2docker/__main__.py @@ -114,6 +114,7 @@ def get_argparser(): argparser.add_argument( "--ref", + default=None, help=( "Reference to build instead of default reference. For example" " branch name or commit for a Git repository." @@ -129,6 +130,14 @@ def get_argparser(): help="Do not actually build the image. Useful in conjunction with --debug.", ) + argparser.add_argument( + "--build", + dest="build", + action="store_true", + help="Build the image (default)", + ) + argparser.set_defaults(build=None) + argparser.add_argument( "--build-memory-limit", help="Total Memory that can be used by the docker build process", @@ -147,6 +156,14 @@ def get_argparser(): help="Do not run container after it has been built", ) + argparser.add_argument( + "--run", + dest="run", + action="store_true", + help="Run container after it has been built (default).", + ) + argparser.set_defaults(run=None) + argparser.add_argument( "--publish", "-p", @@ -181,6 +198,13 @@ def get_argparser(): action="store_true", help="Push docker image to repository", ) + argparser.add_argument( + "--no-push", + dest="push", + action="store_false", + help="Don't push docker image to repository (default).", + ) + argparser.set_defaults(push=None) argparser.add_argument( "--volume", @@ -298,8 +322,14 @@ def make_r2d(argv=None): key, _, val = a.partition("=") r2d.extra_build_args[key] = val + # repo is a required arg, and should never come from config: + if "repo" in r2d.config.Repo2Docker: + r2d.log.warning( + f"Ignoring Repo2Docker.repo={r2d.repo!r} configuration, using {args.repo!r} from CLI." + ) r2d.repo = args.repo - r2d.ref = args.ref + if args.ref is not None: + r2d.ref = args.ref # user wants to mount a local directory into the container for # editing @@ -320,22 +350,22 @@ def make_r2d(argv=None): if args.image_name: r2d.output_image_spec = args.image_name - else: - # we will pick a name after fetching the repository - r2d.output_image_spec = "" if args.json_logs is not None: r2d.json_logs = args.json_logs - r2d.dry_run = not args.build + if args.build is not None: + r2d.dry_run = not args.build if r2d.dry_run: # Can't push nor run if we aren't building args.run = False args.push = False - r2d.run = args.run - r2d.push = args.push + if args.run is not None: + r2d.run = args.run + if args.push is not None: + r2d.push = args.push # check against r2d.run and not args.run as r2d.run is false on # --no-build. Also r2d.volumes and not args.volumes since --editable From 2a9dab13f863e552f8402b6cbfb74584d109a090 Mon Sep 17 00:00:00 2001 From: Min RK Date: Tue, 8 Nov 2022 16:01:31 +0100 Subject: [PATCH 046/171] test some cli > config > defaults priority not full coverage, but covers some important cases --- tests/unit/test_args.py | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/tests/unit/test_args.py b/tests/unit/test_args.py index 975604ea4..53913d944 100644 --- a/tests/unit/test_args.py +++ b/tests/unit/test_args.py @@ -95,3 +95,36 @@ def test_invalid_image_name(): """ with pytest.raises(SystemExit): make_r2d(["--image-name", "_invalid", "."]) + + +def test_build_config_priority(tmp_path): + config_file = str(tmp_path.joinpath("repo2docker_config.py")) + with open(config_file, "w") as f: + f.write("c.Repo2Docker.dry_run = True") + r2d = make_r2d(["--config", config_file, "."]) + assert r2d.dry_run + r2d = make_r2d(["--config", config_file, "--build", "."]) + assert not r2d.dry_run + with open(config_file, "w") as f: + f.write("c.Repo2Docker.dry_run = False") + r2d = make_r2d(["--config", config_file, "--no-build", "."]) + assert r2d.dry_run + + +@pytest.mark.parametrize( + "trait, arg, default", + [ + ("output_image_spec", "--image-name", ""), + ("ref", "--ref", None), + ], +) +def test_config_priority(tmp_path, trait, arg, default): + config_file = str(tmp_path.joinpath("repo2docker_config.py")) + r2d = make_r2d(["."]) + assert getattr(r2d, trait) == default + with open(config_file, "w") as f: + f.write(f"c.Repo2Docker.{trait} = 'config'") + r2d = make_r2d(["--config", config_file, "."]) + assert getattr(r2d, trait) == "config" + r2d = make_r2d(["--config", config_file, arg, "cli", "."]) + assert getattr(r2d, trait) == "cli" From d5f291bec1898207146c7d99344a45bdb009f391 Mon Sep 17 00:00:00 2001 From: Min RK Date: Tue, 8 Nov 2022 16:27:45 +0100 Subject: [PATCH 047/171] move cleanup_checkout / local repo, dry_run/push/run relationships to app so app behaves more consistently when run without cli --- repo2docker/__main__.py | 4 ---- repo2docker/app.py | 19 +++++++++++++++++-- 2 files changed, 17 insertions(+), 6 deletions(-) diff --git a/repo2docker/__main__.py b/repo2docker/__main__.py index 56a78c225..085d2e9ee 100644 --- a/repo2docker/__main__.py +++ b/repo2docker/__main__.py @@ -447,10 +447,6 @@ def make_r2d(argv=None): # extend any environment config from a config file r2d.environment.extend(args.environment) - # if the source exists locally we don't want to delete it at the end - # FIXME: Find a better way to figure out if repo is 'local'. Push this into ContentProvider? - if os.path.exists(args.repo): - r2d.cleanup_checkout = False elif args.clean is not None: r2d.cleanup_checkout = args.clean diff --git a/repo2docker/app.py b/repo2docker/app.py index e3e2ebc51..94384984e 100755 --- a/repo2docker/app.py +++ b/repo2docker/app.py @@ -20,7 +20,7 @@ import entrypoints import escapism from pythonjsonlogger import jsonlogger -from traitlets import Any, Bool, Dict, Int, List, Unicode, default +from traitlets import Any, Bool, Dict, Int, List, Unicode, default, observe from traitlets.config import Application from . import __version__, contentproviders @@ -304,7 +304,7 @@ def _user_name_default(self): ) cleanup_checkout = Bool( - False, + True, help=""" Delete source repository after building is done. @@ -313,6 +313,12 @@ def _user_name_default(self): config=True, ) + @default("cleanup_checkout") + def _defaut_cleanup_checkout(self): + # if the source exists locally we don't want to delete it at the end + # FIXME: Find a better way to figure out if repo is 'local'. Push this into ContentProvider? + return not os.path.exists(self.repo) + output_image_spec = Unicode( "", help=""" @@ -349,6 +355,12 @@ def _user_name_default(self): config=True, ) + @observe("dry_run") + def _dry_run_changed(self, change): + if change.new: + # dry_run forces run and push to be False + self.push = self.run = False + # FIXME: Refactor classes to separate build & run steps run_cmd = List( [], @@ -727,6 +739,8 @@ def build(self): # making a copy of it as it might contain large files that would be # expensive to copy. if os.path.isdir(self.repo): + # never cleanup when we are working in a local repo + self.cleanup_checkout = False checkout_path = self.repo else: if self.git_workdir is None: @@ -828,6 +842,7 @@ def build(self): finally: # Cleanup checkout if necessary + # never cleanup when checking out a local repo if self.cleanup_checkout: shutil.rmtree(checkout_path, ignore_errors=True) From 8802ca2a30248447eaf47cbcdd8ca3daa0e4457b Mon Sep 17 00:00:00 2001 From: Min RK Date: Tue, 8 Nov 2022 16:28:01 +0100 Subject: [PATCH 048/171] update test expectations of log messages --- tests/unit/test_argumentvalidation.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/unit/test_argumentvalidation.py b/tests/unit/test_argumentvalidation.py index 33e7d69af..78b964649 100644 --- a/tests/unit/test_argumentvalidation.py +++ b/tests/unit/test_argumentvalidation.py @@ -162,7 +162,7 @@ def test_port_mapping_no_run_fail(temp_cwd): assert not validate_arguments( builddir, args_list, - "To publish user defined port mappings, the container must also be run", + "To publish user-defined port mappings, the container must also be run", ) @@ -175,7 +175,7 @@ def test_all_ports_mapping_no_run_fail(temp_cwd): assert not validate_arguments( builddir, args_list, - "To publish user defined port mappings, the container must also be run", + "To publish user-defined port mappings, the container must also be run", ) From 31e9722c82951aa7370ce5ce7795270a2a8c32e9 Mon Sep 17 00:00:00 2001 From: Min RK Date: Wed, 9 Nov 2022 16:31:20 +0100 Subject: [PATCH 049/171] add --clean for consistency with other both-ways boolean flags --- repo2docker/__main__.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/repo2docker/__main__.py b/repo2docker/__main__.py index 085d2e9ee..70cc8da14 100644 --- a/repo2docker/__main__.py +++ b/repo2docker/__main__.py @@ -187,10 +187,16 @@ def get_argparser(): argparser.add_argument( "--no-clean", dest="clean", - default=None, action="store_false", help="Don't clean up remote checkouts after we are done", ) + argparser.add_argument( + "--clean", + dest="clean", + action="store_true", + help="Clean up remote checkouts after we are done (default).", + ) + argparser.set_defaults(clean=None) argparser.add_argument( "--push", From 430565faf7d18bf7282e56be351b01855b9bae47 Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Wed, 9 Nov 2022 17:13:12 +0100 Subject: [PATCH 050/171] ci: coalesce tests to avoid increasing test durations --- tests/julia/README.md | 4 ++- .../.binder}/Project.toml | 0 .../project-1.0.2-binder-dir/Project.toml | 8 +++++ .../verify | 0 tests/julia/project-binder-dir/Manifest.toml | 10 ------ tests/julia/project-binder-dir/Project.toml | 2 -- .../project-binder-dir/binder/Manifest.toml | 36 ------------------- .../project-binder-dir/binder/Project.toml | 2 -- tests/julia/project-binder-dir/verify | 27 -------------- 9 files changed, 11 insertions(+), 78 deletions(-) rename tests/julia/{project-1.0.2 => project-1.0.2-binder-dir/.binder}/Project.toml (100%) create mode 100644 tests/julia/project-1.0.2-binder-dir/Project.toml rename tests/julia/{project-1.0.2 => project-1.0.2-binder-dir}/verify (100%) delete mode 100644 tests/julia/project-binder-dir/Manifest.toml delete mode 100644 tests/julia/project-binder-dir/Project.toml delete mode 100644 tests/julia/project-binder-dir/binder/Manifest.toml delete mode 100644 tests/julia/project-binder-dir/binder/Project.toml delete mode 100755 tests/julia/project-binder-dir/verify diff --git a/tests/julia/README.md b/tests/julia/README.md index f6d2996f9..be3277c33 100644 --- a/tests/julia/README.md +++ b/tests/julia/README.md @@ -13,11 +13,13 @@ - Tests use of a `Project.toml` file for Julia, using the repo2docker default version of Julia as specified in `julia_project.py`. -### project-1.0.2 +### project-1.0.2-binder-dir - Tests use of a `Project.toml` file for Julia, using a version of Julia specified via `julia = "=1.0.2"` in `Project.toml`'s `[compat]` section. +- Test use of a `.binder` directory. + ### require - Tests use of a `REQUIRE` file for Julia, using the repo2docker default version diff --git a/tests/julia/project-1.0.2/Project.toml b/tests/julia/project-1.0.2-binder-dir/.binder/Project.toml similarity index 100% rename from tests/julia/project-1.0.2/Project.toml rename to tests/julia/project-1.0.2-binder-dir/.binder/Project.toml diff --git a/tests/julia/project-1.0.2-binder-dir/Project.toml b/tests/julia/project-1.0.2-binder-dir/Project.toml new file mode 100644 index 000000000..6fdcca7fa --- /dev/null +++ b/tests/julia/project-1.0.2-binder-dir/Project.toml @@ -0,0 +1,8 @@ +# A broken Project.toml, but the idea is that the test should ignore this file +# anyhow as there is a .binder folder. +# +[deps] +IteratorInterfaceExtensions = "invalid" + +[compat] +julia = "=1.0.invalid" diff --git a/tests/julia/project-1.0.2/verify b/tests/julia/project-1.0.2-binder-dir/verify similarity index 100% rename from tests/julia/project-1.0.2/verify rename to tests/julia/project-1.0.2-binder-dir/verify diff --git a/tests/julia/project-binder-dir/Manifest.toml b/tests/julia/project-binder-dir/Manifest.toml deleted file mode 100644 index 1b72c7cd7..000000000 --- a/tests/julia/project-binder-dir/Manifest.toml +++ /dev/null @@ -1,10 +0,0 @@ -# This file is machine-generated - editing it directly is not advised - -julia_version = "1.8.2" -manifest_format = "2.0" -project_hash = "8a6b9faef104dfa92a55997106baee3560dc25bc" - -[[deps.IteratorInterfaceExtensions]] -git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" -uuid = "82899510-4779-5014-852e-03e436cf321d" -version = "1.0.0" diff --git a/tests/julia/project-binder-dir/Project.toml b/tests/julia/project-binder-dir/Project.toml deleted file mode 100644 index ee7dad5c3..000000000 --- a/tests/julia/project-binder-dir/Project.toml +++ /dev/null @@ -1,2 +0,0 @@ -[deps] -IteratorInterfaceExtensions = "82899510-4779-5014-852e-03e436cf321d" diff --git a/tests/julia/project-binder-dir/binder/Manifest.toml b/tests/julia/project-binder-dir/binder/Manifest.toml deleted file mode 100644 index 7e4afe015..000000000 --- a/tests/julia/project-binder-dir/binder/Manifest.toml +++ /dev/null @@ -1,36 +0,0 @@ -# This file is machine-generated - editing it directly is not advised - -julia_version = "1.8.2" -manifest_format = "2.0" -project_hash = "663bcf2fe6af67425c484706d7562ccb3a370117" - -[[deps.Adapt]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "195c5505521008abea5aee4f96930717958eac6f" -uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.4.0" - -[[deps.Artifacts]] -uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" - -[[deps.CompilerSupportLibraries_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -version = "0.5.2+0" - -[[deps.Libdl]] -uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" - -[[deps.LinearAlgebra]] -deps = ["Libdl", "libblastrampoline_jll"] -uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" - -[[deps.OpenBLAS_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] -uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" -version = "0.3.20+0" - -[[deps.libblastrampoline_jll]] -deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] -uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.1.1+0" diff --git a/tests/julia/project-binder-dir/binder/Project.toml b/tests/julia/project-binder-dir/binder/Project.toml deleted file mode 100644 index b14e0e605..000000000 --- a/tests/julia/project-binder-dir/binder/Project.toml +++ /dev/null @@ -1,2 +0,0 @@ -[deps] -Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" diff --git a/tests/julia/project-binder-dir/verify b/tests/julia/project-binder-dir/verify deleted file mode 100755 index 32ce2c44b..000000000 --- a/tests/julia/project-binder-dir/verify +++ /dev/null @@ -1,27 +0,0 @@ -#!/usr/bin/env julia - -if VERSION != v"1.8.2" - println("Julia version should be 1.8.2") - exit(1) -end - -# Verify that the environment variables are set correctly for julia 1.0+ -@assert "julia" ∈ readdir(Sys.BINDIR) - -try - # Test that the package was installed. - using Adapt -catch - println("Should be able to load Adapt") - exit(1) -end - -try - using IteratorInterfaceExtensions - # Test that the package was not installed. - println("Should not be able to load IteratorInterfaceExtensions") - exit(1) -catch -end - -exit(0) From e6a66316ab107abf5e67b1ff1c55988666af7db6 Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Fri, 11 Nov 2022 07:55:12 +0100 Subject: [PATCH 051/171] ci: update outdated comment in node test --- tests/base/node/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/base/node/README.md b/tests/base/node/README.md index 9b21a5000..09007cc86 100644 --- a/tests/base/node/README.md +++ b/tests/base/node/README.md @@ -1 +1 @@ -Test that node 12 and npm 6 are installed and runnable. +Test that node 16 and npm 8 are installed and runnable. From 98aceac76d93277ed3bcc3a7bb25681050bd93d1 Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Fri, 11 Nov 2022 07:55:42 +0100 Subject: [PATCH 052/171] tests: cleanup legacy logic These files are no longer used as of repo2docker PR 912 --- tests/memlimit/.gitignore | 1 - tests/memlimit/dockerfile/Dockerfile | 6 ------ tests/memlimit/dockerfile/postBuild | 27 ------------------------- tests/memlimit/non-dockerfile/postBuild | 27 ------------------------- tests/unit/test_memlimit.py | 19 ----------------- 5 files changed, 80 deletions(-) delete mode 100644 tests/memlimit/.gitignore delete mode 100644 tests/memlimit/dockerfile/Dockerfile delete mode 100755 tests/memlimit/dockerfile/postBuild delete mode 100755 tests/memlimit/non-dockerfile/postBuild diff --git a/tests/memlimit/.gitignore b/tests/memlimit/.gitignore deleted file mode 100644 index 1320de820..000000000 --- a/tests/memlimit/.gitignore +++ /dev/null @@ -1 +0,0 @@ -cachebust diff --git a/tests/memlimit/dockerfile/Dockerfile b/tests/memlimit/dockerfile/Dockerfile deleted file mode 100644 index 9513e5e44..000000000 --- a/tests/memlimit/dockerfile/Dockerfile +++ /dev/null @@ -1,6 +0,0 @@ -FROM ubuntu:bionic - -RUN apt-get update && apt-get install --yes python3 - -COPY . . -RUN ./postBuild diff --git a/tests/memlimit/dockerfile/postBuild b/tests/memlimit/dockerfile/postBuild deleted file mode 100755 index 1d7819241..000000000 --- a/tests/memlimit/dockerfile/postBuild +++ /dev/null @@ -1,27 +0,0 @@ -#!/usr/bin/env python3 -""" -Simplest program that tries to allocate a large amount of RAM. - -malloc lies on Linux by default, so we use memset to force the -kernel to actually give us real memory. - -NOTE: This file has to be duplicated & present in all the following locations: - - tests/memlimit/dockerfile/postBuild - - tests/memlimit/dockerfile/postBuild -See https://github.com/jupyterhub/repo2docker/issues/160 for reason -""" -import os -from ctypes import c_void_p, cdll, memset - -libc = cdll.LoadLibrary("libc.so.6") -libc.malloc.restype = c_void_p - -with open("mem_allocate_mb") as f: - mem_allocate_mb = int(f.read().strip()) - -size = 1024 * 1024 * mem_allocate_mb -print(f"trying to allocate {mem_allocate_mb}MB") - -ret = libc.malloc(size) - -memset(ret, 0, size) diff --git a/tests/memlimit/non-dockerfile/postBuild b/tests/memlimit/non-dockerfile/postBuild deleted file mode 100755 index 1d7819241..000000000 --- a/tests/memlimit/non-dockerfile/postBuild +++ /dev/null @@ -1,27 +0,0 @@ -#!/usr/bin/env python3 -""" -Simplest program that tries to allocate a large amount of RAM. - -malloc lies on Linux by default, so we use memset to force the -kernel to actually give us real memory. - -NOTE: This file has to be duplicated & present in all the following locations: - - tests/memlimit/dockerfile/postBuild - - tests/memlimit/dockerfile/postBuild -See https://github.com/jupyterhub/repo2docker/issues/160 for reason -""" -import os -from ctypes import c_void_p, cdll, memset - -libc = cdll.LoadLibrary("libc.so.6") -libc.malloc.restype = c_void_p - -with open("mem_allocate_mb") as f: - mem_allocate_mb = int(f.read().strip()) - -size = 1024 * 1024 * mem_allocate_mb -print(f"trying to allocate {mem_allocate_mb}MB") - -ret = libc.malloc(size) - -memset(ret, 0, size) diff --git a/tests/unit/test_memlimit.py b/tests/unit/test_memlimit.py index ee2f2b356..7fcb541fc 100644 --- a/tests/unit/test_memlimit.py +++ b/tests/unit/test_memlimit.py @@ -47,25 +47,6 @@ def test_memory_limit_enforced(tmpdir): } -def test_memlimit_same_postbuild(): - """ - Validate that the postBuild files for the dockerfile and non-dockerfile - tests are the same - - Until https://github.com/jupyterhub/repo2docker/issues/160 gets fixed. - """ - filepaths = [ - os.path.join(basedir, "memlimit", t, "postBuild") - for t in ("dockerfile", "non-dockerfile") - ] - file_contents = [] - for fp in filepaths: - with open(fp) as f: - file_contents.append(f.read()) - # Make sure they're all the same - assert len(set(file_contents)) == 1 - - @pytest.mark.parametrize("BuildPack", [BaseImage, DockerBuildPack]) def test_memlimit_argument_type(BuildPack): # check that an exception is raised when the memory limit isn't an int From 485a8ad097e0bfeda06777110702e79ca9c01a0c Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 15 Nov 2022 00:13:39 +0000 Subject: [PATCH 053/171] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/asottile/pyupgrade: v3.2.0 → v3.2.2](https://github.com/asottile/pyupgrade/compare/v3.2.0...v3.2.2) - [github.com/pre-commit/mirrors-prettier: v2.7.1 → v3.0.0-alpha.4](https://github.com/pre-commit/mirrors-prettier/compare/v2.7.1...v3.0.0-alpha.4) --- .pre-commit-config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 842120dae..89c4d33d1 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -11,7 +11,7 @@ repos: # Autoformat: Python code, syntax patterns are modernized - repo: https://github.com/asottile/pyupgrade - rev: v3.2.0 + rev: v3.2.2 hooks: - id: pyupgrade args: @@ -44,7 +44,7 @@ repos: # Autoformat: markdown - repo: https://github.com/pre-commit/mirrors-prettier - rev: v2.7.1 + rev: v3.0.0-alpha.4 hooks: - id: prettier files: ".md" From ad5ecaa8656df92f8d8959f19e4631801e659d2e Mon Sep 17 00:00:00 2001 From: YuviPanda Date: Fri, 18 Nov 2022 14:36:05 -0800 Subject: [PATCH 054/171] Switch default python to 3.10 3.7 is *quite* old, and folks get caught up in it because it also sometimes forces much older versions of packages - and it can be quite confusing to debug (see https://github.com/2i2c-org/infrastructure/issues/1934) for example. --- repo2docker/buildpacks/conda/environment.lock | 145 +++++++++--------- .../buildpacks/conda/environment.py-3.10.lock | 133 ++++++++-------- .../buildpacks/conda/environment.py-3.10.yml | 2 +- .../buildpacks/conda/environment.py-3.7.lock | 100 ++++++------ .../buildpacks/conda/environment.py-3.7.yml | 2 +- .../buildpacks/conda/environment.py-3.8.lock | 133 ++++++++-------- .../buildpacks/conda/environment.py-3.8.yml | 2 +- .../buildpacks/conda/environment.py-3.9.lock | 135 ++++++++-------- .../buildpacks/conda/environment.py-3.9.yml | 2 +- repo2docker/buildpacks/conda/freeze.py | 2 +- 10 files changed, 333 insertions(+), 323 deletions(-) diff --git a/repo2docker/buildpacks/conda/environment.lock b/repo2docker/buildpacks/conda/environment.lock index a1fe2ebbb..e8acce8a9 100644 --- a/repo2docker/buildpacks/conda/environment.lock +++ b/repo2docker/buildpacks/conda/environment.lock @@ -1,17 +1,18 @@ -# AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY -# Frozen on 2022-10-13 14:39:03 UTC +# AUTO GENERATED FROM environment.py-3.10.yml, DO NOT MANUALLY MODIFY +# Frozen on 2022-11-18 22:33:53 UTC # Generated by conda-lock. # platform: linux-64 -# input_hash: f39cf3a86cdaeb58bee45974ccbdaf3fb51ad41f0bb6f3caf9340c5aad0dfa3b +# input_hash: 64c9dcb0ab6e1e70f0b3695ec95ddb9d269f1442f5172e7995f643aee3e9226b @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.9.24-ha878542_0.tar.bz2#41e4e87062433e283696cf384f952ef6 -https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.36.1-hea4e1c9_2.tar.bz2#bd4f2e711b39af170e7ff15163fe87ee -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-12.1.0-ha89aaad_16.tar.bz2#6f5ba041a41eb102a1027d9e68731be7 -https://conda.anaconda.org/conda-forge/linux-64/pandoc-2.19.2-ha770c72_0.tar.bz2#f17322ae18898607521b3fa90df84235 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-12.1.0-h8d9b700_16.tar.bz2#f013cf7749536ce43d82afbffdf499ab +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.39-hc81fddc_0.tar.bz2#c2719e2faa7bd7076d3a4b52271e5622 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-12.2.0-h46fd767_19.tar.bz2#1030b1f38c129f2634eae026f704fe60 +https://conda.anaconda.org/conda-forge/noarch/tzdata-2022f-h191b570_0.tar.bz2#e366350e2343a798e29833286abe2560 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-12.2.0-h65d4601_19.tar.bz2#cedcee7c064c01c403f962c9e8d3c373 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-12.1.0-h8d9b700_16.tar.bz2#4f05bc9844f7c101e6e147dab3c88d5c +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-12.2.0-h65d4601_19.tar.bz2#e4c94f80aef025c17ab0828cd85ef535 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2#a1fd65c7ccbf10880423d82bca54eb54 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a/repo2docker/buildpacks/conda/environment.py-3.8.yml b/repo2docker/buildpacks/conda/environment.py-3.8.yml index 5a4e68c18..4c89d9743 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.8.yml +++ b/repo2docker/buildpacks/conda/environment.py-3.8.yml @@ -1,5 +1,5 @@ # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY -# Generated on 2022-10-13 14:39:03 UTC +# Generated on 2022-11-18 22:33:01 UTC channels: - conda-forge dependencies: diff --git a/repo2docker/buildpacks/conda/environment.py-3.9.lock b/repo2docker/buildpacks/conda/environment.py-3.9.lock index 263d528f8..d0df1cbfc 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.9.lock +++ b/repo2docker/buildpacks/conda/environment.py-3.9.lock @@ -1,18 +1,17 @@ # AUTO GENERATED FROM environment.py-3.9.yml, DO NOT MANUALLY MODIFY -# Frozen on 2022-10-13 14:39:39 UTC +# Frozen on 2022-11-18 22:33:38 UTC # Generated by conda-lock. # platform: linux-64 # input_hash: 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+https://conda.anaconda.org/conda-forge/noarch/jupyterlab_server-2.16.3-pyhd8ed1ab_0.tar.bz2#7141271af36d1e0a1c6d5a955528bc1e +https://conda.anaconda.org/conda-forge/noarch/nbconvert-7.2.5-pyhd8ed1ab_0.tar.bz2#14cfcab1c236866c4590970ee25d618c +https://conda.anaconda.org/conda-forge/noarch/notebook-shim-0.2.2-pyhd8ed1ab_0.tar.bz2#40be846cd4e78672a40e43db9dae753c +https://conda.anaconda.org/conda-forge/noarch/nbclassic-0.4.8-pyhd8ed1ab_0.tar.bz2#f4f150f83ed90a1b833e6081bbf38257 https://conda.anaconda.org/conda-forge/noarch/notebook-6.4.12-pyha770c72_0.tar.bz2#77fc67c5bbea44fd41e8bbe2ac82d1ad https://conda.anaconda.org/conda-forge/noarch/jupyter-offlinenotebook-0.2.2-pyh1d7be83_0.tar.bz2#fe55056ce4bc4bd4953ba440270735fb https://conda.anaconda.org/conda-forge/linux-64/jupyterhub-singleuser-1.5.0-py39hf3d152e_1.tar.bz2#31dba5dc15564c19d36836786fafe297 diff --git a/repo2docker/buildpacks/conda/environment.py-3.9.yml b/repo2docker/buildpacks/conda/environment.py-3.9.yml index a854684eb..1050e2ddb 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.9.yml +++ b/repo2docker/buildpacks/conda/environment.py-3.9.yml @@ -1,5 +1,5 @@ # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY -# Generated on 2022-10-13 14:39:21 UTC +# Generated on 2022-11-18 22:33:18 UTC channels: - conda-forge dependencies: diff --git a/repo2docker/buildpacks/conda/freeze.py b/repo2docker/buildpacks/conda/freeze.py index 7bdb444eb..be294ab8d 100755 --- a/repo2docker/buildpacks/conda/freeze.py +++ b/repo2docker/buildpacks/conda/freeze.py @@ -120,7 +120,7 @@ def set_python(py_env_file, py): default=("3.7", "3.8", "3.9", "3.10"), ) args = parser.parse_args() - default_py = "3.7" + default_py = "3.10" for py in args.py: env_file = pathlib.Path(str(ENV_FILE_T).format(py=py)) set_python(env_file, py) From 5058eca99fb4a9c3d195ad77340c9ceefc2b80c3 Mon Sep 17 00:00:00 2001 From: YuviPanda Date: Fri, 18 Nov 2022 15:07:57 -0800 Subject: [PATCH 055/171] Fix a couple of failing tests --- tests/conda/py-r-postbuild-file/verify.py | 4 ++-- tests/conda/py2/verify | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/conda/py-r-postbuild-file/verify.py b/tests/conda/py-r-postbuild-file/verify.py index 549a05a13..46ca44f25 100755 --- a/tests/conda/py-r-postbuild-file/verify.py +++ b/tests/conda/py-r-postbuild-file/verify.py @@ -4,8 +4,8 @@ def test_sys_version(): - """The default python version should be 3.7""" - assert sys.version_info[:2] == (3, 7) + """The default python version should be 3.10""" + assert sys.version_info[:2] == (3, 10) def test_there(): diff --git a/tests/conda/py2/verify b/tests/conda/py2/verify index 4a55686cf..da667ec25 100755 --- a/tests/conda/py2/verify +++ b/tests/conda/py2/verify @@ -1,7 +1,7 @@ #!/usr/bin/env python import sys -assert sys.version_info[:2] == (3, 7), sys.version +assert sys.version_info[:2] == (3, 10), sys.version # verify that we have Python 2 and Python 3 kernelspecs from jupyter_client.kernelspec import KernelSpecManager From 592ccb75966ef450fbec07f4203918c4bf7ebac8 Mon Sep 17 00:00:00 2001 From: YuviPanda Date: Tue, 9 Jun 2020 11:23:50 +0530 Subject: [PATCH 056/171] Set ubuntu 20.04 as new base image We would at some point need to set this as the default. To prepare for that, I think we should make this an option that is available, and run our tests on this too. The R stack seems possibly currently unavailable for 20.04 (see https://community.rstudio.com/t/rstudio-server-ubuntu-20-04/64188) but I'll try it out --- repo2docker/buildpacks/base.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/repo2docker/buildpacks/base.py b/repo2docker/buildpacks/base.py index e7c9b537d..570cb81a0 100644 --- a/repo2docker/buildpacks/base.py +++ b/repo2docker/buildpacks/base.py @@ -13,7 +13,7 @@ # Only use syntax features supported by Docker 17.09 TEMPLATE = r""" -FROM buildpack-deps:bionic +FROM buildpack-deps:focal # Avoid prompts from apt ENV DEBIAN_FRONTEND=noninteractive From b724c02c6a6aac48248594d2b2fa9d55c0f16a08 Mon Sep 17 00:00:00 2001 From: YuviPanda Date: Sat, 4 Jun 2022 01:31:00 +0530 Subject: [PATCH 057/171] Switch RSPM to use focal, not bionic --- repo2docker/buildpacks/r.py | 4 ++-- tests/unit/test_r.py | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/repo2docker/buildpacks/r.py b/repo2docker/buildpacks/r.py index 200f472fd..ca0929463 100644 --- a/repo2docker/buildpacks/r.py +++ b/repo2docker/buildpacks/r.py @@ -210,7 +210,7 @@ def get_rspm_snapshot_url(self, snapshot_date, max_days_prior=7): # Construct a snapshot URL that will give us binary packages for Ubuntu Bionic (18.04) if "upsi" in snapshots: return ( - "https://packagemanager.rstudio.com/all/__linux__/bionic/" + "https://packagemanager.rstudio.com/all/__linux__/focal/" + snapshots["upsi"] ) raise ValueError( @@ -253,7 +253,7 @@ def get_devtools_snapshot_url(self): # Hardcoded rather than dynamically determined from a date to avoid extra API calls # Plus, we can always use packagemanager.rstudio.com here as we always install the # necessary apt packages. - return "https://packagemanager.rstudio.com/all/__linux__/bionic/2022-01-04+Y3JhbiwyOjQ1MjYyMTU7NzlBRkJEMzg" + return "https://packagemanager.rstudio.com/all/__linux__/focal/2022-06-03+Y3JhbiwyOjQ1MjYyMTU7RkM5ODcwN0M" def get_build_scripts(self): """ diff --git a/tests/unit/test_r.py b/tests/unit/test_r.py index a5d7db7c0..a03d631ee 100644 --- a/tests/unit/test_r.py +++ b/tests/unit/test_r.py @@ -65,7 +65,7 @@ def test_snapshot_rspm_date(): for requested, expected in test_dates.items(): snapshot_url = r.get_rspm_snapshot_url(requested) assert snapshot_url.startswith( - "https://packagemanager.rstudio.com/all/__linux__/bionic/" + "https://packagemanager.rstudio.com/all/__linux__/focal/" + expected.strftime("%Y-%m-%d") ) From 808693744577641071127f6e7741f0e15179177c Mon Sep 17 00:00:00 2001 From: YuviPanda Date: Wed, 22 Jun 2022 15:38:20 -0700 Subject: [PATCH 058/171] Don't hardcode ubuntu codename when getting r packages --- repo2docker/buildpacks/base.py | 2 ++ repo2docker/buildpacks/r.py | 20 ++++++++++++++------ 2 files changed, 16 insertions(+), 6 deletions(-) diff --git a/repo2docker/buildpacks/base.py b/repo2docker/buildpacks/base.py index 570cb81a0..4eace92f6 100644 --- a/repo2docker/buildpacks/base.py +++ b/repo2docker/buildpacks/base.py @@ -253,6 +253,8 @@ def get_base_packages(self): # Utils! "less", "unzip", + # Gives us envsubst + "gettext-base", } def get_build_env(self): diff --git a/repo2docker/buildpacks/r.py b/repo2docker/buildpacks/r.py index ca0929463..0dc533572 100644 --- a/repo2docker/buildpacks/r.py +++ b/repo2docker/buildpacks/r.py @@ -210,7 +210,10 @@ def get_rspm_snapshot_url(self, snapshot_date, max_days_prior=7): # Construct a snapshot URL that will give us binary packages for Ubuntu Bionic (18.04) if "upsi" in snapshots: return ( - "https://packagemanager.rstudio.com/all/__linux__/focal/" + # Env variables here are expanded by envsubst in the Dockerfile, after sourcing + # /etc/os-release. This allows us to use distro specific variables here to get + # appropriate binary packages without having to hard code version names here. + "https://packagemanager.rstudio.com/all/__linux__/${VERSION_CODENAME}/" + snapshots["upsi"] ) raise ValueError( @@ -253,7 +256,10 @@ def get_devtools_snapshot_url(self): # Hardcoded rather than dynamically determined from a date to avoid extra API calls # Plus, we can always use packagemanager.rstudio.com here as we always install the # necessary apt packages. - return "https://packagemanager.rstudio.com/all/__linux__/focal/2022-06-03+Y3JhbiwyOjQ1MjYyMTU7RkM5ODcwN0M" + # Env variables here are expanded by envsubst in the Dockerfile, after sourcing + # /etc/os-release. This allows us to use distro specific variables here to get + # appropriate binary packages without having to hard code version names here. + return "https://packagemanager.rstudio.com/all/__linux__/${VERSION_CODENAME}/2022-06-03+Y3JhbiwyOjQ1MjYyMTU7RkM5ODcwN0M" def get_build_scripts(self): """ @@ -329,15 +335,17 @@ def get_build_scripts(self): rf""" R RHOME && \ mkdir -p /etc/rstudio && \ - echo 'options(repos = c(CRAN = "{cran_mirror_url}"))' > /opt/R/{self.r_version}/lib/R/etc/Rprofile.site && \ - echo 'r-cran-repos={cran_mirror_url}' > /etc/rstudio/rsession.conf + EXPANDED_CRAN_MIRROR_URL="$(. /etc/os-release && echo {cran_mirror_url} | envsubst)" && \ + echo "options(repos = c(CRAN = \"${{EXPANDED_CRAN_MIRROR_URL}}\"))" > /opt/R/{self.r_version}/lib/R/etc/Rprofile.site && \ + echo "r-cran-repos=${{EXPANDED_CRAN_MIRROR_URL}}" > /etc/rstudio/rsession.conf """, ), ( "${NB_USER}", # Install a pinned version of devtools, IRKernel and shiny - rf""" - R --quiet -e "install.packages(c('devtools', 'IRkernel', 'shiny'), repos='{self.get_devtools_snapshot_url()}')" && \ + r""" + EXPANDED_CRAN_MIRROR_URL="$(. /etc/os-release && echo {self.devtools_cran_mirror_url()} | envsubst)" && \ + R --quiet -e "install.packages(c('devtools', 'IRkernel', 'shiny'), repos='${{EXPANDED_CRAN_MIRROR_URL}}')" && \ R --quiet -e "IRkernel::installspec(prefix='$NB_PYTHON_PREFIX')" """, ), From 20b081525785fdc6ac524e06150028796b8787ec Mon Sep 17 00:00:00 2001 From: YuviPanda Date: Fri, 24 Jun 2022 18:13:53 -0700 Subject: [PATCH 059/171] Make base_image configurable Fixes https://github.com/jupyterhub/repo2docker/issues/487 --- repo2docker/app.py | 12 +++++++++++- repo2docker/buildpacks/base.py | 10 +++++++--- repo2docker/buildpacks/legacy/__init__.py | 3 +++ 3 files changed, 21 insertions(+), 4 deletions(-) diff --git a/repo2docker/app.py b/repo2docker/app.py index 94384984e..96e2e1d30 100755 --- a/repo2docker/app.py +++ b/repo2docker/app.py @@ -425,6 +425,16 @@ def _dry_run_changed(self, change): """, ) + base_image = Unicode( + "buildpack-deps:bionic", + config=True, + help=""" + Base image to use when building docker images. + + Should be an ubuntu derivative, minimum 18.04. + """, + ) + def get_engine(self): """Return an instance of the container engine. @@ -771,7 +781,7 @@ def build(self): with chdir(checkout_path): for BP in self.buildpacks: - bp = BP() + bp = BP(base_image=self.base_image) if bp.detect(): picked_buildpack = bp break diff --git a/repo2docker/buildpacks/base.py b/repo2docker/buildpacks/base.py index 4eace92f6..41355445c 100644 --- a/repo2docker/buildpacks/base.py +++ b/repo2docker/buildpacks/base.py @@ -13,7 +13,7 @@ # Only use syntax features supported by Docker 17.09 TEMPLATE = r""" -FROM buildpack-deps:focal +FROM {{base_image}} # Avoid prompts from apt ENV DEBIAN_FRONTEND=noninteractive @@ -210,7 +210,6 @@ class BuildPack: Specifically used for creating Dockerfiles for use with repo2docker only. Things that are kept constant: - - base image - some environment variables (such as locale) - user creation & ownership of home directory - working directory @@ -220,9 +219,13 @@ class BuildPack: """ - def __init__(self): + def __init__(self, base_image): + """ + base_image specifies the base image to use when building docker images + """ self.log = logging.getLogger("repo2docker") self.appendix = "" + self.base_image = base_image self.labels = {} if sys.platform.startswith("win"): self.log.warning( @@ -522,6 +525,7 @@ def render(self, build_args=None): appendix=self.appendix, # For docker 17.09 `COPY --chown`, 19.03 would allow using $NBUSER user=build_args.get("NB_UID", DEFAULT_NB_UID), + base_image=self.base_image, ) @staticmethod diff --git a/repo2docker/buildpacks/legacy/__init__.py b/repo2docker/buildpacks/legacy/__init__.py index a1b91e026..31980f9f7 100644 --- a/repo2docker/buildpacks/legacy/__init__.py +++ b/repo2docker/buildpacks/legacy/__init__.py @@ -16,6 +16,9 @@ class LegacyBinderDockerBuildPack: This buildpack has been deprecated. """ + def __init__(self, *args, **kwargs): + pass + def detect(self): """Check if current repo should be built with the Legacy BuildPack.""" log = logging.getLogger("repo2docker") From f35a948e75551d3df11d811a38998ba93943ca45 Mon Sep 17 00:00:00 2001 From: YuviPanda Date: Sat, 23 Jul 2022 08:48:56 -0700 Subject: [PATCH 060/171] Set base image for default buildpack too --- repo2docker/app.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/repo2docker/app.py b/repo2docker/app.py index 96e2e1d30..5ac6b953d 100755 --- a/repo2docker/app.py +++ b/repo2docker/app.py @@ -786,7 +786,9 @@ def build(self): picked_buildpack = bp break else: - picked_buildpack = self.default_buildpack() + picked_buildpack = self.default_buildpack( + base_image=self.base_image + ) picked_buildpack.appendix = self.appendix # Add metadata labels From 446e67820e1c73091743ca31177071baa7aa26f1 Mon Sep 17 00:00:00 2001 From: YuviPanda Date: Sat, 23 Jul 2022 09:17:30 -0700 Subject: [PATCH 061/171] Add test fixture for setting base image --- tests/conftest.py | 8 ++++++++ tests/unit/test_binder_dir.py | 8 ++++---- tests/unit/test_buildpack.py | 13 +++++++------ tests/unit/test_cache_from.py | 4 ++-- tests/unit/test_env_yml.py | 8 ++++---- tests/unit/test_labels.py | 4 ++-- tests/unit/test_memlimit.py | 6 ++++-- tests/unit/test_preassemble.py | 4 ++-- tests/unit/test_r.py | 20 ++++++++++---------- 9 files changed, 43 insertions(+), 32 deletions(-) diff --git a/tests/conftest.py b/tests/conftest.py index 13e62b401..a09ef0420 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -100,6 +100,14 @@ def run_test(args): return run_test +@pytest.fixture() +def base_image(): + """ + Base ubuntu image to use when testing specific BuildPacks + """ + return "buildpack-deps:bionic" + + def _add_content_to_git(repo_dir): """Add content to file 'test' in git repository and commit.""" # use append mode so this can be called multiple times diff --git a/tests/unit/test_binder_dir.py b/tests/unit/test_binder_dir.py index 9e777b0ab..3d7f6eb23 100644 --- a/tests/unit/test_binder_dir.py +++ b/tests/unit/test_binder_dir.py @@ -6,21 +6,21 @@ @pytest.mark.parametrize("binder_dir", ["binder", ".binder", ""]) -def test_binder_dir(tmpdir, binder_dir): +def test_binder_dir(tmpdir, binder_dir, base_image): tmpdir.chdir() if binder_dir: os.mkdir(binder_dir) - bp = buildpacks.BuildPack() + bp = buildpacks.BuildPack(base_image) assert binder_dir == bp.binder_dir assert bp.binder_path("foo.yaml") == os.path.join(binder_dir, "foo.yaml") -def test_exclusive_binder_dir(tmpdir): +def test_exclusive_binder_dir(tmpdir, base_image): tmpdir.chdir() os.mkdir("./binder") os.mkdir("./.binder") - bp = buildpacks.BuildPack() + bp = buildpacks.BuildPack(base_image) with pytest.raises(RuntimeError): _ = bp.binder_dir diff --git a/tests/unit/test_buildpack.py b/tests/unit/test_buildpack.py index 6a8147e30..46d9cb786 100644 --- a/tests/unit/test_buildpack.py +++ b/tests/unit/test_buildpack.py @@ -5,36 +5,37 @@ from repo2docker.buildpacks import LegacyBinderDockerBuildPack, PythonBuildPack from repo2docker.utils import chdir +from tests.conftest import base_image -def test_legacy_raises(): +def test_legacy_raises(base_image): # check legacy buildpack raises on a repo that triggers it with TemporaryDirectory() as repodir: with open(pjoin(repodir, "Dockerfile"), "w") as d: d.write("FROM andrewosh/binder-base") with chdir(repodir): - bp = LegacyBinderDockerBuildPack() + bp = LegacyBinderDockerBuildPack(base_image) with pytest.raises(RuntimeError): bp.detect() -def test_legacy_doesnt_detect(): +def test_legacy_doesnt_detect(base_image): # check legacy buildpack doesn't trigger with TemporaryDirectory() as repodir: with open(pjoin(repodir, "Dockerfile"), "w") as d: d.write("FROM andrewosh/some-image") with chdir(repodir): - bp = LegacyBinderDockerBuildPack() + bp = LegacyBinderDockerBuildPack(base_image) assert not bp.detect() -def test_legacy_on_repo_without_dockerfile(): +def test_legacy_on_repo_without_dockerfile(base_image): # check legacy buildpack doesn't trigger on a repo w/o Dockerfile with TemporaryDirectory() as repodir: with chdir(repodir): - bp = LegacyBinderDockerBuildPack() + bp = LegacyBinderDockerBuildPack(base_image) assert not bp.detect() diff --git a/tests/unit/test_cache_from.py b/tests/unit/test_cache_from.py index fd186dbc5..f5752b181 100644 --- a/tests/unit/test_cache_from.py +++ b/tests/unit/test_cache_from.py @@ -30,7 +30,7 @@ def test_cache_from_base(tmpdir): assert called_kwargs["cache_from"] == cache_from -def test_cache_from_docker(tmpdir): +def test_cache_from_docker(tmpdir, base_image): cache_from = ["image-1:latest"] fake_log_value = {"stream": "fake"} fake_client = MagicMock(spec=docker.APIClient) @@ -42,7 +42,7 @@ def test_cache_from_docker(tmpdir): with tmpdir.join("Dockerfile").open("w") as f: f.write("FROM scratch\n") - for line in DockerBuildPack().build( + for line in DockerBuildPack(base_image).build( fake_client, "image-2", 100, {}, cache_from, extra_build_kwargs ): assert line == fake_log_value diff --git a/tests/unit/test_env_yml.py b/tests/unit/test_env_yml.py index dff142288..fa45417dc 100644 --- a/tests/unit/test_env_yml.py +++ b/tests/unit/test_env_yml.py @@ -9,20 +9,20 @@ from repo2docker import buildpacks -def test_empty_env_yml(tmpdir): +def test_empty_env_yml(tmpdir, base_image): tmpdir.chdir() p = tmpdir.join("environment.yml") p.write("") - bp = buildpacks.CondaBuildPack() + bp = buildpacks.CondaBuildPack(base_image) py_ver = bp.python_version # If the environment.yml is empty python_version will get an empty string assert py_ver == "" -def test_no_dict_env_yml(tmpdir): +def test_no_dict_env_yml(tmpdir, base_image): tmpdir.chdir() q = tmpdir.join("environment.yml") q.write("numpy\n " "matplotlib\n") - bq = buildpacks.CondaBuildPack() + bq = buildpacks.CondaBuildPack(base_image) with pytest.raises(TypeError): py_ver = bq.python_version diff --git a/tests/unit/test_labels.py b/tests/unit/test_labels.py index 5520de4d1..e6e1f2e9e 100644 --- a/tests/unit/test_labels.py +++ b/tests/unit/test_labels.py @@ -12,8 +12,8 @@ URL = "https://github.com/binderhub-ci-repos/repo2docker-ci-clone-depth" -def test_buildpack_labels_rendered(): - bp = BuildPack() +def test_buildpack_labels_rendered(base_image): + bp = BuildPack(base_image) assert "LABEL" not in bp.render() bp.labels["first_label"] = "firstlabel" assert 'LABEL first_label="firstlabel"\n' in bp.render() diff --git a/tests/unit/test_memlimit.py b/tests/unit/test_memlimit.py index 7fcb541fc..7846bdab6 100644 --- a/tests/unit/test_memlimit.py +++ b/tests/unit/test_memlimit.py @@ -48,14 +48,16 @@ def test_memory_limit_enforced(tmpdir): @pytest.mark.parametrize("BuildPack", [BaseImage, DockerBuildPack]) -def test_memlimit_argument_type(BuildPack): +def test_memlimit_argument_type(BuildPack, base_image): # check that an exception is raised when the memory limit isn't an int fake_log_value = {"stream": "fake"} fake_client = MagicMock(spec=docker.APIClient) fake_client.build.return_value = iter([fake_log_value]) with pytest.raises(ValueError) as exc_info: - for line in BuildPack().build(fake_client, "image-2", "10Gi", {}, [], {}): + for line in BuildPack(base_image).build( + fake_client, "image-2", "10Gi", {}, [], {} + ): pass assert "The memory limit has to be specified as an" in str(exc_info.value) diff --git a/tests/unit/test_preassemble.py b/tests/unit/test_preassemble.py index d3a08f773..70dad5337 100644 --- a/tests/unit/test_preassemble.py +++ b/tests/unit/test_preassemble.py @@ -6,7 +6,7 @@ @pytest.mark.parametrize("binder_dir", ["", ".binder", "binder"]) -def test_combine_preassemble_steps(tmpdir, binder_dir): +def test_combine_preassemble_steps(tmpdir, binder_dir, base_image): tmpdir.chdir() if binder_dir: os.mkdir(binder_dir) @@ -19,7 +19,7 @@ def test_combine_preassemble_steps(tmpdir, binder_dir): with open(os.path.join(binder_dir, "runtime.txt"), "w") as f: f.write("r-2019-01-30") - bp = buildpacks.RBuildPack() + bp = buildpacks.RBuildPack(base_image) files = bp.get_preassemble_script_files() assert len(files) == 2 diff --git a/tests/unit/test_r.py b/tests/unit/test_r.py index a03d631ee..31f483c60 100644 --- a/tests/unit/test_r.py +++ b/tests/unit/test_r.py @@ -10,7 +10,7 @@ @pytest.mark.parametrize( "runtime_version, expected", [("", "4.2"), ("3.6", "3.6"), ("3.5.1", "3.5")] ) -def test_version_specification(tmpdir, runtime_version, expected): +def test_version_specification(tmpdir, runtime_version, expected, base_image): tmpdir.chdir() with open("runtime.txt", "w") as f: @@ -18,17 +18,17 @@ def test_version_specification(tmpdir, runtime_version, expected): runtime_version += "-" f.write(f"r-{runtime_version}2019-01-01") - r = buildpacks.RBuildPack() + r = buildpacks.RBuildPack(base_image) assert r.r_version.startswith(expected) -def test_version_completion(tmpdir): +def test_version_completion(tmpdir, base_image): tmpdir.chdir() with open("runtime.txt", "w") as f: f.write(f"r-3.6-2019-01-01") - r = buildpacks.RBuildPack() + r = buildpacks.RBuildPack(base_image) assert r.r_version == "3.6.3" @@ -40,17 +40,17 @@ def test_version_completion(tmpdir): ("r-3.5-2019-01-01", (2019, 1, 1)), ], ) -def test_mran_date(tmpdir, runtime, expected): +def test_mran_date(tmpdir, runtime, expected, base_image): tmpdir.chdir() with open("runtime.txt", "w") as f: f.write(runtime) - r = buildpacks.RBuildPack() + r = buildpacks.RBuildPack(base_image) assert r.checkpoint_date == date(*expected) -def test_snapshot_rspm_date(): +def test_snapshot_rspm_date(base_image): test_dates = { # Even though there is no snapshot specified in the interface at https://packagemanager.rstudio.com/client/#/repos/1/overview # For 2021 Oct 22, the API still returns a valid URL that one can install @@ -61,7 +61,7 @@ def test_snapshot_rspm_date(): date(2022, 1, 1): date(2022, 1, 1), } - r = buildpacks.RBuildPack() + r = buildpacks.RBuildPack(base_image) for requested, expected in test_dates.items(): snapshot_url = r.get_rspm_snapshot_url(requested) assert snapshot_url.startswith( @@ -75,7 +75,7 @@ def test_snapshot_rspm_date(): @pytest.mark.parametrize("expected", [date(2019, 12, 29), date(2019, 12, 26)]) @pytest.mark.parametrize("requested", [date(2019, 12, 31)]) -def test_snapshot_mran_date(requested, expected): +def test_snapshot_mran_date(requested, expected, base_image): def mock_request_head(url): r = Response() if url == "https://mran.microsoft.com/snapshot/" + expected.isoformat(): @@ -86,7 +86,7 @@ def mock_request_head(url): return r with patch("requests.head", side_effect=mock_request_head): - r = buildpacks.RBuildPack() + r = buildpacks.RBuildPack(base_image) assert ( r.get_mran_snapshot_url(requested) == f"https://mran.microsoft.com/snapshot/{expected.isoformat()}" From 9ff14c1907aee5febdfeb595afd4ce6753fa48f1 Mon Sep 17 00:00:00 2001 From: YuviPanda Date: Sun, 24 Jul 2022 11:58:48 -0700 Subject: [PATCH 062/171] Remove accidental import vscode inserted --- tests/unit/test_buildpack.py | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/unit/test_buildpack.py b/tests/unit/test_buildpack.py index 46d9cb786..bf8163c5b 100644 --- a/tests/unit/test_buildpack.py +++ b/tests/unit/test_buildpack.py @@ -5,7 +5,6 @@ from repo2docker.buildpacks import LegacyBinderDockerBuildPack, PythonBuildPack from repo2docker.utils import chdir -from tests.conftest import base_image def test_legacy_raises(base_image): From b58fd1508d373551114cb162519c482ad1be6cd5 Mon Sep 17 00:00:00 2001 From: YuviPanda Date: Mon, 25 Jul 2022 11:38:40 -0700 Subject: [PATCH 063/171] Fix rspm test for VERSION_CODENAME --- tests/unit/test_r.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/tests/unit/test_r.py b/tests/unit/test_r.py index 31f483c60..364945d71 100644 --- a/tests/unit/test_r.py +++ b/tests/unit/test_r.py @@ -65,7 +65,8 @@ def test_snapshot_rspm_date(base_image): for requested, expected in test_dates.items(): snapshot_url = r.get_rspm_snapshot_url(requested) assert snapshot_url.startswith( - "https://packagemanager.rstudio.com/all/__linux__/focal/" + # VERSION_CODENAME is handled at runtime during the build + "https://packagemanager.rstudio.com/all/__linux__/${VERSION_CODENAME}/" + expected.strftime("%Y-%m-%d") ) From 7eb143eab01b8059e1edbebd8ca39c6290ab840f Mon Sep 17 00:00:00 2001 From: YuviPanda Date: Mon, 25 Jul 2022 11:39:43 -0700 Subject: [PATCH 064/171] Set base_image in a few more places --- tests/unit/test_cache_from.py | 4 ++-- tests/unit/test_memlimit.py | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/unit/test_cache_from.py b/tests/unit/test_cache_from.py index f5752b181..a7697a246 100644 --- a/tests/unit/test_cache_from.py +++ b/tests/unit/test_cache_from.py @@ -12,7 +12,7 @@ ) -def test_cache_from_base(tmpdir): +def test_cache_from_base(tmpdir, base_image): cache_from = ["image-1:latest"] fake_log_value = {"stream": "fake"} fake_client = MagicMock(spec=docker.APIClient) @@ -21,7 +21,7 @@ def test_cache_from_base(tmpdir): # Test base image build pack tmpdir.chdir() - for line in BaseImage().build( + for line in BaseImage(base_image).build( fake_client, "image-2", 100, {}, cache_from, extra_build_kwargs ): assert line == fake_log_value diff --git a/tests/unit/test_memlimit.py b/tests/unit/test_memlimit.py index 7846bdab6..c1896c9c7 100644 --- a/tests/unit/test_memlimit.py +++ b/tests/unit/test_memlimit.py @@ -13,7 +13,7 @@ basedir = os.path.dirname(os.path.dirname(os.path.abspath(__file__))) -def test_memory_limit_enforced(tmpdir): +def test_memory_limit_enforced(tmpdir, base_image): fake_cache_from = ["image-1:latest"] fake_log_value = {"stream": "fake"} fake_client = MagicMock(spec=docker.APIClient) @@ -27,7 +27,7 @@ def test_memory_limit_enforced(tmpdir): # Test that the buildpack passes the right arguments to the docker # client in order to enforce the memory limit tmpdir.chdir() - for line in BaseImage().build( + for line in BaseImage(base_image).build( fake_client, "image-2", memory_limit, From c21374d305178798887c8e102185e83c64ce42e4 Mon Sep 17 00:00:00 2001 From: Yuvi Panda Date: Tue, 26 Jul 2022 11:51:15 -0700 Subject: [PATCH 065/171] Fix typo Co-authored-by: Simon Li --- repo2docker/app.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/repo2docker/app.py b/repo2docker/app.py index 5ac6b953d..f809480e4 100755 --- a/repo2docker/app.py +++ b/repo2docker/app.py @@ -431,7 +431,7 @@ def _dry_run_changed(self, change): help=""" Base image to use when building docker images. - Should be an ubuntu derivative, minimum 18.04. + Should be an Ubuntu derivative, minimum 18.04. """, ) From f776d8efcb967e89f0ec0f0ca7a2cf89cb9cd4b8 Mon Sep 17 00:00:00 2001 From: Yuvi Panda Date: Tue, 26 Jul 2022 11:51:42 -0700 Subject: [PATCH 066/171] Use full image tag Fixes #1146 Co-authored-by: Simon Li --- repo2docker/app.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/repo2docker/app.py b/repo2docker/app.py index f809480e4..bf642870f 100755 --- a/repo2docker/app.py +++ b/repo2docker/app.py @@ -426,7 +426,7 @@ def _dry_run_changed(self, change): ) base_image = Unicode( - "buildpack-deps:bionic", + "docker.io/library/buildpack-deps:bionic", config=True, help=""" Base image to use when building docker images. From 4d83abc2df1f8e9bda7719ca764a5dd0ee09f686 Mon Sep 17 00:00:00 2001 From: YuviPanda Date: Tue, 26 Jul 2022 11:53:33 -0700 Subject: [PATCH 067/171] Add note about what base images are supported --- repo2docker/app.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/repo2docker/app.py b/repo2docker/app.py index bf642870f..8719656e2 100755 --- a/repo2docker/app.py +++ b/repo2docker/app.py @@ -431,7 +431,12 @@ def _dry_run_changed(self, change): help=""" Base image to use when building docker images. - Should be an Ubuntu derivative, minimum 18.04. + Only images that match the following criteria are supported: + - Ubuntu based distributions, minimum 18.04 + - Contains set of base packages installed with the buildpack-deps + image family: https://hub.docker.com/_/buildpack-deps + + Other images *may* work, but are not officially supported. """, ) From 389334a4a3f4d777f241e8f21f9419bc03a3fd36 Mon Sep 17 00:00:00 2001 From: Bartosz Kardas Date: Sat, 10 Dec 2022 21:37:42 +0100 Subject: [PATCH 068/171] Added missing base_image argument --- tests/unit/test_buildpack.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/unit/test_buildpack.py b/tests/unit/test_buildpack.py index bf8163c5b..38fc5c237 100644 --- a/tests/unit/test_buildpack.py +++ b/tests/unit/test_buildpack.py @@ -39,9 +39,9 @@ def test_legacy_on_repo_without_dockerfile(base_image): @pytest.mark.parametrize("python_version", ["2.6", "3.0", "4.10", "3.99"]) -def test_unsupported_python(tmpdir, python_version): +def test_unsupported_python(tmpdir, python_version, base_image): tmpdir.chdir() - bp = PythonBuildPack() + bp = PythonBuildPack(base_image) bp._python_version = python_version assert bp.python_version == python_version with pytest.raises(ValueError): From 90c375c5f75398038521430ec839da331aad802b Mon Sep 17 00:00:00 2001 From: YuviPanda Date: Sat, 10 Dec 2022 13:24:09 -0800 Subject: [PATCH 069/171] Add setuptools to built image hg-evolve seems to need it, as otherwise it is failing with: 16 4.520 Downloading hg-evolve-10.5.3.tar.gz (847 kB) --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 0f7d08ed5..68a7f20fe 100644 --- a/Dockerfile +++ b/Dockerfile @@ -21,7 +21,7 @@ RUN --mount=type=cache,target=${PIP_CACHE_DIR} \ FROM alpine:${ALPINE_VERSION} # install python, git, bash, mercurial -RUN apk add --no-cache git git-lfs python3 py-pip bash docker mercurial +RUN apk add --no-cache git git-lfs python3 py-pip py3-setuptools bash docker mercurial # repeat ARG from above ARG PIP_CACHE_DIR=/tmp/pip-cache From aae6a71621eff9879014ad17b71df50710c1e938 Mon Sep 17 00:00:00 2001 From: YuviPanda Date: Sat, 10 Dec 2022 13:29:44 -0800 Subject: [PATCH 070/171] Try using py3-pip when installing in Alpine Seems to be perhaps different than py-pip --- Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 68a7f20fe..e09e62e07 100644 --- a/Dockerfile +++ b/Dockerfile @@ -2,7 +2,7 @@ ARG ALPINE_VERSION=3.16 FROM alpine:${ALPINE_VERSION} AS builder -RUN apk add --no-cache git python3 python3-dev py-pip build-base +RUN apk add --no-cache git python3 python3-dev py3-pip build-base # set pip's cache directory using this environment variable, and use # ARG instead of ENV to ensure its only set when the image is built @@ -21,7 +21,7 @@ RUN --mount=type=cache,target=${PIP_CACHE_DIR} \ FROM alpine:${ALPINE_VERSION} # install python, git, bash, mercurial -RUN apk add --no-cache git git-lfs python3 py-pip py3-setuptools bash docker mercurial +RUN apk add --no-cache git git-lfs python3 py3-pip bash docker mercurial # repeat ARG from above ARG PIP_CACHE_DIR=/tmp/pip-cache From 8a359f9c0048b08c855f35263d889186f754650a Mon Sep 17 00:00:00 2001 From: Bartosz Kardas Date: Sun, 11 Dec 2022 01:11:21 +0100 Subject: [PATCH 071/171] Readded setuptools --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index e09e62e07..7166cb198 100644 --- a/Dockerfile +++ b/Dockerfile @@ -21,7 +21,7 @@ RUN --mount=type=cache,target=${PIP_CACHE_DIR} \ FROM alpine:${ALPINE_VERSION} # install python, git, bash, mercurial -RUN apk add --no-cache git git-lfs python3 py3-pip bash docker mercurial +RUN apk add --no-cache git git-lfs python3 py3-pip py3-setuptools bash docker mercurial # repeat ARG from above ARG PIP_CACHE_DIR=/tmp/pip-cache From c3d257519bdc51cafb26af1a0e5f25aa6b7f5b03 Mon Sep 17 00:00:00 2001 From: Bartosz Kardas Date: Sun, 11 Dec 2022 22:00:41 +0100 Subject: [PATCH 072/171] Fixd shell command for buildpacks/r --- repo2docker/buildpacks/r.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/repo2docker/buildpacks/r.py b/repo2docker/buildpacks/r.py index 0dc533572..217ac0e7f 100644 --- a/repo2docker/buildpacks/r.py +++ b/repo2docker/buildpacks/r.py @@ -343,8 +343,8 @@ def get_build_scripts(self): ( "${NB_USER}", # Install a pinned version of devtools, IRKernel and shiny - r""" - EXPANDED_CRAN_MIRROR_URL="$(. /etc/os-release && echo {self.devtools_cran_mirror_url()} | envsubst)" && \ + rf""" + EXPANDED_CRAN_MIRROR_URL="$(. /etc/os-release && echo {cran_mirror_url} | envsubst)" && \ R --quiet -e "install.packages(c('devtools', 'IRkernel', 'shiny'), repos='${{EXPANDED_CRAN_MIRROR_URL}}')" && \ R --quiet -e "IRkernel::installspec(prefix='$NB_PYTHON_PREFIX')" """, From 76731c885b5ad99087060e2a03527897b1a6c581 Mon Sep 17 00:00:00 2001 From: Bartosz Kardas Date: Sun, 11 Dec 2022 22:08:18 +0100 Subject: [PATCH 073/171] Added setuptools --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 7166cb198..6a1605af2 100644 --- a/Dockerfile +++ b/Dockerfile @@ -2,7 +2,7 @@ ARG ALPINE_VERSION=3.16 FROM alpine:${ALPINE_VERSION} AS builder -RUN apk add --no-cache git python3 python3-dev py3-pip build-base +RUN apk add --no-cache git python3 python3-dev py3-pip py3-setuptools build-base # set pip's cache directory using this environment variable, and use # ARG instead of ENV to ensure its only set when the image is built From 21ad4cac543a456d65ba964939b5737064abbc70 Mon Sep 17 00:00:00 2001 From: Bartosz Kardas Date: Sun, 11 Dec 2022 23:04:03 +0100 Subject: [PATCH 074/171] Bump linux alpine to 3.17 due to setuptools bug --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 6a1605af2..dd4d85877 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,5 +1,5 @@ # syntax = docker/dockerfile:1.3 -ARG ALPINE_VERSION=3.16 +ARG ALPINE_VERSION=3.17 FROM alpine:${ALPINE_VERSION} AS builder RUN apk add --no-cache git python3 python3-dev py3-pip py3-setuptools build-base From 52e80769b0cfb7887613c7248dc729e4515a78d8 Mon Sep 17 00:00:00 2001 From: Bartosz Kardas Date: Sun, 11 Dec 2022 23:26:24 +0100 Subject: [PATCH 075/171] Renamed branch to main --- repo2docker/contentproviders/git.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/repo2docker/contentproviders/git.py b/repo2docker/contentproviders/git.py index f35e9a888..1427bd09f 100644 --- a/repo2docker/contentproviders/git.py +++ b/repo2docker/contentproviders/git.py @@ -45,10 +45,10 @@ def fetch(self, spec, output_dir, yield_output=False): self.log.error( f"Failed to check out ref {ref}", extra=dict(phase=R2dState.FAILED) ) - if ref == "master": + if ref == "main": msg = ( - "Failed to check out the 'master' branch. " - "Maybe the default branch is not named 'master' " + "Failed to check out the 'main' branch. " + "Maybe the default branch is not named 'main' " "for this repository.\n\nTry not explicitly " "specifying `--ref`." ) From b85df8f9933b5b3294c8a4ce8fecce797d0a4602 Mon Sep 17 00:00:00 2001 From: Bartosz Kardas Date: Sun, 11 Dec 2022 23:38:27 +0100 Subject: [PATCH 076/171] Refactored R command --- repo2docker/buildpacks/r.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/repo2docker/buildpacks/r.py b/repo2docker/buildpacks/r.py index 217ac0e7f..9cb59f3fb 100644 --- a/repo2docker/buildpacks/r.py +++ b/repo2docker/buildpacks/r.py @@ -344,9 +344,9 @@ def get_build_scripts(self): "${NB_USER}", # Install a pinned version of devtools, IRKernel and shiny rf""" - EXPANDED_CRAN_MIRROR_URL="$(. /etc/os-release && echo {cran_mirror_url} | envsubst)" && \ - R --quiet -e "install.packages(c('devtools', 'IRkernel', 'shiny'), repos='${{EXPANDED_CRAN_MIRROR_URL}}')" && \ - R --quiet -e "IRkernel::installspec(prefix='$NB_PYTHON_PREFIX')" + export EXPANDED_CRAN_MIRROR_URL="$(. /etc/os-release && echo {cran_mirror_url} | envsubst)" && \ + R --quiet -e "install.packages(c('devtools', 'IRkernel', 'shiny'), repos=Sys.getenv(\"EXPANDED_CRAN_MIRROR_URL\"))" && \ + R --quiet -e "IRkernel::installspec(prefix=Sys.getenv(\"NB_PYTHON_PREFIX\"))" """, ), ] From 0b9154ae2b3e213627e0971ae0b141f0406513de Mon Sep 17 00:00:00 2001 From: Bartosz Kardas Date: Mon, 12 Dec 2022 00:04:09 +0100 Subject: [PATCH 077/171] Updated master/main branches error info --- repo2docker/contentproviders/git.py | 6 +++--- tests/external/reproductions.repos.yaml | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/repo2docker/contentproviders/git.py b/repo2docker/contentproviders/git.py index 1427bd09f..905fa4eee 100644 --- a/repo2docker/contentproviders/git.py +++ b/repo2docker/contentproviders/git.py @@ -45,10 +45,10 @@ def fetch(self, spec, output_dir, yield_output=False): self.log.error( f"Failed to check out ref {ref}", extra=dict(phase=R2dState.FAILED) ) - if ref == "main": + if ref == "master" or ref == "main": msg = ( - "Failed to check out the 'main' branch. " - "Maybe the default branch is not named 'main' " + f"Failed to check out the '{ref}' branch. " + f"Maybe the default branch is not named '{ref}' " "for this repository.\n\nTry not explicitly " "specifying `--ref`." ) diff --git a/tests/external/reproductions.repos.yaml b/tests/external/reproductions.repos.yaml index d019bc10e..74f1085c4 100644 --- a/tests/external/reproductions.repos.yaml +++ b/tests/external/reproductions.repos.yaml @@ -12,12 +12,12 @@ # Test that a full remote/ref works - name: Binder Examples - Requirements url: https://github.com/binder-examples/requirements - ref: origin/master + ref: origin/main verify: python -c 'import matplotlib' # Test that ref is added to branch if not present - name: Binder Examples - Requirements url: https://github.com/binder-examples/requirements - ref: master + ref: main verify: python -c 'import matplotlib' # Test that tags work + ref is added to tag if not present - name: Binder Examples - Requirements From dc337e9e36341f3b487beb1cb2934557a5f81334 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 12 Dec 2022 05:10:38 +0000 Subject: [PATCH 078/171] build(deps): bump pypa/gh-action-pypi-publish from 1.5.1 to 1.6.4 Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.5.1 to 1.6.4. - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.5.1...v1.6.4) --- updated-dependencies: - dependency-name: pypa/gh-action-pypi-publish dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- .github/workflows/release.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 6f1b274ef..37ca8be28 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -55,7 +55,7 @@ jobs: # all previous steps always run in order to exercise them - name: Publish distribution to PyPI if: startsWith(github.ref, 'refs/tags') - uses: pypa/gh-action-pypi-publish@v1.5.1 + uses: pypa/gh-action-pypi-publish@v1.6.4 with: password: ${{ secrets.PYPI_PASSWORD }} From 5e75258f2fdfc2813179966165467263e3b22d39 Mon Sep 17 00:00:00 2001 From: Chris Holdgraf Date: Tue, 13 Dec 2022 10:50:03 +0100 Subject: [PATCH 079/171] Document base image --- docs/source/howto/base_image.md | 21 +++++++++++++++++++++ docs/source/howto/index.rst | 1 + 2 files changed, 22 insertions(+) create mode 100644 docs/source/howto/base_image.md diff --git a/docs/source/howto/base_image.md b/docs/source/howto/base_image.md new file mode 100644 index 000000000..4ce12f745 --- /dev/null +++ b/docs/source/howto/base_image.md @@ -0,0 +1,21 @@ +# Change the base image used by Docker + +You may change the base image used in the `Dockerfile` that creates images by repo2docker. +This is equivalent to changing the `FROM ` in the Dockerfile. + +To do so, use the `base_image` traitlet when invoking `repo2docker`. +Note that this is not configurable by individual repositories, it is configured when you invoke the `repo2docker` command. + +```{note} +By default repo2docker builds on top of the `buildpack-deps:bionic` base image, an Ubuntu-based image. +``` + +## Requirements for your base image + +`repo2docker` will only work if a specific set of packages exists in the base image. +Only images that match the following criteria are supported: + +- Ubuntu based distributions (minimum `18.04`) +- Contains a set of base packages installed with [the `buildpack-deps` image family](https://hub.docker.com/_/buildpack-deps). + +Other images *may* work, but are not officially supported. diff --git a/docs/source/howto/index.rst b/docs/source/howto/index.rst index c7ee34a3c..426837edd 100644 --- a/docs/source/howto/index.rst +++ b/docs/source/howto/index.rst @@ -15,3 +15,4 @@ Select from the pages listed below to get started. lab_workspaces jupyterhub_images deploy + base_image From 4eaf096bf90053ee9054f54a5e03bf30f6967d3e Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 13 Dec 2022 09:50:16 +0000 Subject: [PATCH 080/171] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- docs/source/howto/base_image.md | 42 ++++++++++++++++----------------- 1 file changed, 21 insertions(+), 21 deletions(-) diff --git a/docs/source/howto/base_image.md b/docs/source/howto/base_image.md index 4ce12f745..b662042bc 100644 --- a/docs/source/howto/base_image.md +++ b/docs/source/howto/base_image.md @@ -1,21 +1,21 @@ -# Change the base image used by Docker - -You may change the base image used in the `Dockerfile` that creates images by repo2docker. -This is equivalent to changing the `FROM ` in the Dockerfile. - -To do so, use the `base_image` traitlet when invoking `repo2docker`. -Note that this is not configurable by individual repositories, it is configured when you invoke the `repo2docker` command. - -```{note} -By default repo2docker builds on top of the `buildpack-deps:bionic` base image, an Ubuntu-based image. -``` - -## Requirements for your base image - -`repo2docker` will only work if a specific set of packages exists in the base image. -Only images that match the following criteria are supported: - -- Ubuntu based distributions (minimum `18.04`) -- Contains a set of base packages installed with [the `buildpack-deps` image family](https://hub.docker.com/_/buildpack-deps). - -Other images *may* work, but are not officially supported. +# Change the base image used by Docker + +You may change the base image used in the `Dockerfile` that creates images by repo2docker. +This is equivalent to changing the `FROM ` in the Dockerfile. + +To do so, use the `base_image` traitlet when invoking `repo2docker`. +Note that this is not configurable by individual repositories, it is configured when you invoke the `repo2docker` command. + +```{note} +By default repo2docker builds on top of the `buildpack-deps:bionic` base image, an Ubuntu-based image. +``` + +## Requirements for your base image + +`repo2docker` will only work if a specific set of packages exists in the base image. +Only images that match the following criteria are supported: + +- Ubuntu based distributions (minimum `18.04`) +- Contains a set of base packages installed with [the `buildpack-deps` image family](https://hub.docker.com/_/buildpack-deps). + +Other images _may_ work, but are not officially supported. From 4a5ff3c37e0081a2882a3411e5ba6d0370e077bb Mon Sep 17 00:00:00 2001 From: Chris Holdgraf Date: Tue, 13 Dec 2022 11:32:00 +0100 Subject: [PATCH 081/171] Add note on reproducibility --- docs/source/howto/base_image.md | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/docs/source/howto/base_image.md b/docs/source/howto/base_image.md index b662042bc..9a77a8122 100644 --- a/docs/source/howto/base_image.md +++ b/docs/source/howto/base_image.md @@ -19,3 +19,15 @@ Only images that match the following criteria are supported: - Contains a set of base packages installed with [the `buildpack-deps` image family](https://hub.docker.com/_/buildpack-deps). Other images _may_ work, but are not officially supported. + +## This will affect reproducibility 🚨 + +Changing the base image may have an impact on the reproducibility of repositories that are built. +There are **no guarantees that repositories will behave the same way as other repo2docker builds if you change the base image**. +For example these are two scenarios that would make your repositories non-reproducible: + +- **Your base image is different from `Ubuntu:bionic`.** + If you change the base image in a way that is different from repo2docker's default (the Ubuntu `bionic` image), then repositories that **you** build with repo2docker may be significantly different from those that **other** instances of repo2docker build (e.g., those from [`mybinder.org`](https://mybinder.org)). +- **Your base image changes over time.** + If you choose a base image that changes its composition over time (e.g., an image provided by some other community), then it may cause repositories build with your base image to change in unpredictable ways. + We recommend choosing a base image that you know to be stable and trustworthy. \ No newline at end of file From e956501d67ee86257fd907f1a807bf25fb9bf674 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 13 Dec 2022 10:32:43 +0000 Subject: [PATCH 082/171] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- docs/source/howto/base_image.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/howto/base_image.md b/docs/source/howto/base_image.md index 9a77a8122..6fa8f5173 100644 --- a/docs/source/howto/base_image.md +++ b/docs/source/howto/base_image.md @@ -30,4 +30,4 @@ For example these are two scenarios that would make your repositories non-reprod If you change the base image in a way that is different from repo2docker's default (the Ubuntu `bionic` image), then repositories that **you** build with repo2docker may be significantly different from those that **other** instances of repo2docker build (e.g., those from [`mybinder.org`](https://mybinder.org)). - **Your base image changes over time.** If you choose a base image that changes its composition over time (e.g., an image provided by some other community), then it may cause repositories build with your base image to change in unpredictable ways. - We recommend choosing a base image that you know to be stable and trustworthy. \ No newline at end of file + We recommend choosing a base image that you know to be stable and trustworthy. From b72fde073268b63f16ec20e92b8f5c0a4700b705 Mon Sep 17 00:00:00 2001 From: Florian Kohrt Date: Thu, 15 Dec 2022 18:34:06 +0100 Subject: [PATCH 083/171] Fix typo --- docs/source/howto/user_interface.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/howto/user_interface.rst b/docs/source/howto/user_interface.rst index efee01dc6..92a9bc01b 100644 --- a/docs/source/howto/user_interface.rst +++ b/docs/source/howto/user_interface.rst @@ -97,7 +97,7 @@ http://mybinder.org/v2/gh/binder-examples/r/HEAD?urlpath=rstudio Shiny ===== -`Shiny lets you create interactive visualizaions with R `_. +`Shiny lets you create interactive visualizations with R `_. Shiny is automatically enabled if a configuration file for R is detected (i.e. an R version specified in ``runtime.txt``). If this is detected, Shiny will be accessible by appending From aa07af045c1762fde5c55ab183a522e0679309a1 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 20 Dec 2022 01:20:51 +0000 Subject: [PATCH 084/171] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/asottile/pyupgrade: v3.2.2 → v3.3.1](https://github.com/asottile/pyupgrade/compare/v3.2.2...v3.3.1) - [github.com/psf/black: 22.10.0 → 22.12.0](https://github.com/psf/black/compare/22.10.0...22.12.0) - [github.com/pycqa/isort: 5.10.1 → v5.11.3](https://github.com/pycqa/isort/compare/5.10.1...v5.11.3) --- .pre-commit-config.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 89c4d33d1..6fb4a0f24 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -11,7 +11,7 @@ repos: # Autoformat: Python code, syntax patterns are modernized - repo: https://github.com/asottile/pyupgrade - rev: v3.2.2 + rev: v3.3.1 hooks: - id: pyupgrade args: @@ -23,7 +23,7 @@ repos: # Autoformat: Python code - repo: https://github.com/psf/black - rev: 22.10.0 + rev: 22.12.0 hooks: - id: black args: @@ -36,7 +36,7 @@ repos: # Autoformat: Python code - repo: https://github.com/pycqa/isort - rev: 5.10.1 + rev: v5.11.3 hooks: - id: isort args: From ec6f28408b82d8c3e7a0aba01a3c98ff97b8a5ad Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Tue, 20 Dec 2022 10:17:04 +0100 Subject: [PATCH 085/171] pre-commit.ci: update monthly --- .pre-commit-config.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 6fb4a0f24..58d567767 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -48,3 +48,7 @@ repos: hooks: - id: prettier files: ".md" + +# pre-commit.ci config reference: https://pre-commit.ci/#configuration +ci: + autoupdate_schedule: monthly From 0fffbf8873ae372de6ba7a5ba600cc089431f360 Mon Sep 17 00:00:00 2001 From: Simon Li Date: Sun, 1 Jan 2023 00:00:29 +0000 Subject: [PATCH 086/171] Revert "mount wheels from build stage instead of copying them" This reverts commit ed82b83ebad77d7c5893e23a73777de4812545dd. --- Dockerfile | 24 +++++++----------------- 1 file changed, 7 insertions(+), 17 deletions(-) diff --git a/Dockerfile b/Dockerfile index 0f7d08ed5..9c28f765d 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,21 +1,16 @@ # syntax = docker/dockerfile:1.3 ARG ALPINE_VERSION=3.16 -FROM alpine:${ALPINE_VERSION} AS builder +FROM alpine:${ALPINE_VERSION} RUN apk add --no-cache git python3 python3-dev py-pip build-base -# set pip's cache directory using this environment variable, and use -# ARG instead of ENV to ensure its only set when the image is built -ARG PIP_CACHE_DIR=/tmp/pip-cache - # build wheels in first image ADD . /tmp/src RUN cd /tmp/src && git clean -xfd && git status -RUN --mount=type=cache,target=${PIP_CACHE_DIR} \ - mkdir /tmp/wheelhouse \ +RUN mkdir /tmp/wheelhouse \ && cd /tmp/wheelhouse \ && pip3 install wheel \ - && pip3 wheel /tmp/src \ + && pip3 wheel --no-cache-dir /tmp/src \ && ls -l /tmp/wheelhouse FROM alpine:${ALPINE_VERSION} @@ -23,17 +18,12 @@ FROM alpine:${ALPINE_VERSION} # install python, git, bash, mercurial RUN apk add --no-cache git git-lfs python3 py-pip bash docker mercurial -# repeat ARG from above -ARG PIP_CACHE_DIR=/tmp/pip-cache +# install hg-evolve (Mercurial extensions) +RUN pip3 install hg-evolve --user --no-cache-dir # install repo2docker -# and hg-evolve (Mercurial extensions) -# mount /tmp/wheelhouse from build stage -# avoids extra layer when using COPY --from -RUN --mount=type=cache,target=${PIP_CACHE_DIR} \ - --mount=type=cache,from=builder,source=/tmp/wheelhouse,target=/tmp/wheelhouse \ - pip3 install --ignore-installed --no-deps /tmp/wheelhouse/*.whl \ - && pip3 install hg-evolve \ +COPY --from=0 /tmp/wheelhouse /tmp/wheelhouse +RUN pip3 install --no-cache-dir --ignore-installed --no-deps /tmp/wheelhouse/*.whl \ && pip3 list # add git-credential helper From e498f1df47c3903922cba46ea12890fc8bf947c5 Mon Sep 17 00:00:00 2001 From: Simon Li Date: Sun, 1 Jan 2023 00:08:46 +0000 Subject: [PATCH 087/171] Update tests/external/reproductions.repos.yaml --- tests/external/reproductions.repos.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/external/reproductions.repos.yaml b/tests/external/reproductions.repos.yaml index d019bc10e..74f1085c4 100644 --- a/tests/external/reproductions.repos.yaml +++ b/tests/external/reproductions.repos.yaml @@ -12,12 +12,12 @@ # Test that a full remote/ref works - name: Binder Examples - Requirements url: https://github.com/binder-examples/requirements - ref: origin/master + ref: origin/main verify: python -c 'import matplotlib' # Test that ref is added to branch if not present - name: Binder Examples - Requirements url: https://github.com/binder-examples/requirements - ref: master + ref: main verify: python -c 'import matplotlib' # Test that tags work + ref is added to tag if not present - name: Binder Examples - Requirements From 268e86b0f7ce57a0d3f0be6080b9ccdb54e116b7 Mon Sep 17 00:00:00 2001 From: Simon Li Date: Sun, 1 Jan 2023 00:10:37 +0000 Subject: [PATCH 088/171] Docker release: add `linux/arm64` --- .github/workflows/release.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 37ca8be28..d711d75ff 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -125,6 +125,6 @@ jobs: uses: docker/build-push-action@v3 with: context: . - platforms: linux/amd64 + platforms: linux/amd64,linux/arm64 push: true tags: ${{ env.TAGS }} From d0d55c07baa9f055e9f9ac404e07aae61028e394 Mon Sep 17 00:00:00 2001 From: Simon Li Date: Sat, 31 Dec 2022 14:41:42 +0000 Subject: [PATCH 089/171] =?UTF-8?q?Rename=20`environment*.lock`=20?= =?UTF-8?q?=E2=9E=A1=EF=B8=8F=20=20`environment*-linux-64.lock`?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../conda/{environment.lock => environment-linux-64.lock} | 0 .../{environment.py-2.7.lock => environment.py-2.7-linux-64.lock} | 0 ...environment.py-3.10.lock => environment.py-3.10-linux-64.lock} | 0 .../{environment.py-3.5.lock => environment.py-3.5-linux-64.lock} | 0 .../{environment.py-3.6.lock => environment.py-3.6-linux-64.lock} | 0 .../{environment.py-3.7.lock => environment.py-3.7-linux-64.lock} | 0 .../{environment.py-3.8.lock => environment.py-3.8-linux-64.lock} | 0 .../{environment.py-3.9.lock => environment.py-3.9-linux-64.lock} | 0 8 files changed, 0 insertions(+), 0 deletions(-) rename repo2docker/buildpacks/conda/{environment.lock => environment-linux-64.lock} (100%) rename repo2docker/buildpacks/conda/{environment.py-2.7.lock => environment.py-2.7-linux-64.lock} (100%) rename repo2docker/buildpacks/conda/{environment.py-3.10.lock => environment.py-3.10-linux-64.lock} (100%) rename repo2docker/buildpacks/conda/{environment.py-3.5.lock => environment.py-3.5-linux-64.lock} (100%) rename repo2docker/buildpacks/conda/{environment.py-3.6.lock => environment.py-3.6-linux-64.lock} (100%) rename repo2docker/buildpacks/conda/{environment.py-3.7.lock => environment.py-3.7-linux-64.lock} (100%) rename repo2docker/buildpacks/conda/{environment.py-3.8.lock => environment.py-3.8-linux-64.lock} (100%) rename repo2docker/buildpacks/conda/{environment.py-3.9.lock => environment.py-3.9-linux-64.lock} (100%) diff --git a/repo2docker/buildpacks/conda/environment.lock b/repo2docker/buildpacks/conda/environment-linux-64.lock similarity index 100% rename from repo2docker/buildpacks/conda/environment.lock rename to repo2docker/buildpacks/conda/environment-linux-64.lock diff --git a/repo2docker/buildpacks/conda/environment.py-2.7.lock b/repo2docker/buildpacks/conda/environment.py-2.7-linux-64.lock similarity index 100% rename from repo2docker/buildpacks/conda/environment.py-2.7.lock rename to repo2docker/buildpacks/conda/environment.py-2.7-linux-64.lock diff --git a/repo2docker/buildpacks/conda/environment.py-3.10.lock b/repo2docker/buildpacks/conda/environment.py-3.10-linux-64.lock similarity index 100% rename from repo2docker/buildpacks/conda/environment.py-3.10.lock rename to repo2docker/buildpacks/conda/environment.py-3.10-linux-64.lock diff --git a/repo2docker/buildpacks/conda/environment.py-3.5.lock b/repo2docker/buildpacks/conda/environment.py-3.5-linux-64.lock similarity index 100% rename from repo2docker/buildpacks/conda/environment.py-3.5.lock rename to repo2docker/buildpacks/conda/environment.py-3.5-linux-64.lock diff --git a/repo2docker/buildpacks/conda/environment.py-3.6.lock b/repo2docker/buildpacks/conda/environment.py-3.6-linux-64.lock similarity index 100% rename from repo2docker/buildpacks/conda/environment.py-3.6.lock rename to repo2docker/buildpacks/conda/environment.py-3.6-linux-64.lock diff --git a/repo2docker/buildpacks/conda/environment.py-3.7.lock b/repo2docker/buildpacks/conda/environment.py-3.7-linux-64.lock similarity index 100% rename from repo2docker/buildpacks/conda/environment.py-3.7.lock rename to repo2docker/buildpacks/conda/environment.py-3.7-linux-64.lock diff --git a/repo2docker/buildpacks/conda/environment.py-3.8.lock b/repo2docker/buildpacks/conda/environment.py-3.8-linux-64.lock similarity index 100% rename from repo2docker/buildpacks/conda/environment.py-3.8.lock rename to repo2docker/buildpacks/conda/environment.py-3.8-linux-64.lock diff --git a/repo2docker/buildpacks/conda/environment.py-3.9.lock b/repo2docker/buildpacks/conda/environment.py-3.9-linux-64.lock similarity index 100% rename from repo2docker/buildpacks/conda/environment.py-3.9.lock rename to repo2docker/buildpacks/conda/environment.py-3.9-linux-64.lock From e774709744d00309243b3186bd3c1eef2359a57e Mon Sep 17 00:00:00 2001 From: Simon Li Date: Sun, 1 Jan 2023 11:35:45 +0000 Subject: [PATCH 090/171] Update freeze.py to handle linux-aarch64 --- repo2docker/buildpacks/conda/freeze.py | 21 ++++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/repo2docker/buildpacks/conda/freeze.py b/repo2docker/buildpacks/conda/freeze.py index 7bdb444eb..670b863cb 100755 --- a/repo2docker/buildpacks/conda/freeze.py +++ b/repo2docker/buildpacks/conda/freeze.py @@ -22,7 +22,7 @@ HERE = pathlib.Path(os.path.dirname(os.path.abspath(__file__))) ENV_FILE = HERE / "environment.yml" -FROZEN_FILE = os.path.splitext(ENV_FILE)[0] + ".lock" +FROZEN_FILE_T = os.path.splitext(ENV_FILE)[0] + "-{platform}.lock" ENV_FILE_T = HERE / "environment.py-{py}.yml" @@ -119,12 +119,19 @@ def set_python(py_env_file, py): help="Python version(s) to update and freeze", default=("3.7", "3.8", "3.9", "3.10"), ) + parser.add_argument( + "platform", + nargs="*", + help="Platform(s) to update and freeze", + default=("linux-64", "linux-aarch64"), + ) args = parser.parse_args() default_py = "3.7" for py in args.py: - env_file = pathlib.Path(str(ENV_FILE_T).format(py=py)) - set_python(env_file, py) - frozen_file = pathlib.Path(os.path.splitext(env_file)[0] + ".lock") - freeze(env_file, frozen_file) - if py == default_py: - shutil.copy(frozen_file, FROZEN_FILE) + for platform in args.platform: + env_file = pathlib.Path(str(ENV_FILE_T).format(py=py)) + set_python(env_file, py) + frozen_file = pathlib.Path(os.path.splitext(env_file)[0] + f"-{platform}.lock") + freeze(env_file, frozen_file, platform) + if py == default_py: + shutil.copy(frozen_file, FROZEN_FILE_T.format(platform=platform)) From 33eee4a4407c4e8fca55ece887303d99abd4209d Mon Sep 17 00:00:00 2001 From: Simon Li Date: Sun, 1 Jan 2023 11:36:09 +0000 Subject: [PATCH 091/171] refreeze --- .../conda/environment-linux-64.lock | 151 ++++++++------- .../conda/environment-linux-aarch64.lock | 148 +++++++++++++++ .../conda/environment.py-3.10-linux-64.lock | 171 ++++++++--------- .../environment.py-3.10-linux-aarch64.lock | 158 ++++++++++++++++ .../buildpacks/conda/environment.py-3.10.yml | 2 +- .../conda/environment.py-3.7-linux-64.lock | 151 ++++++++------- .../environment.py-3.7-linux-aarch64.lock | 148 +++++++++++++++ .../buildpacks/conda/environment.py-3.7.yml | 2 +- .../conda/environment.py-3.8-linux-64.lock | 170 ++++++++--------- .../environment.py-3.8-linux-aarch64.lock | 157 ++++++++++++++++ .../buildpacks/conda/environment.py-3.8.yml | 2 +- .../conda/environment.py-3.9-linux-64.lock | 172 +++++++++--------- .../environment.py-3.9-linux-aarch64.lock | 158 ++++++++++++++++ .../buildpacks/conda/environment.py-3.9.yml | 2 +- 14 files changed, 1183 insertions(+), 409 deletions(-) create mode 100644 repo2docker/buildpacks/conda/environment-linux-aarch64.lock create mode 100644 repo2docker/buildpacks/conda/environment.py-3.10-linux-aarch64.lock create mode 100644 repo2docker/buildpacks/conda/environment.py-3.7-linux-aarch64.lock create mode 100644 repo2docker/buildpacks/conda/environment.py-3.8-linux-aarch64.lock create mode 100644 repo2docker/buildpacks/conda/environment.py-3.9-linux-aarch64.lock diff --git a/repo2docker/buildpacks/conda/environment-linux-64.lock b/repo2docker/buildpacks/conda/environment-linux-64.lock index a1fe2ebbb..541c2d19f 100644 --- a/repo2docker/buildpacks/conda/environment-linux-64.lock +++ b/repo2docker/buildpacks/conda/environment-linux-64.lock @@ -1,17 +1,17 @@ # AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY -# Frozen on 2022-10-13 14:39:03 UTC +# Frozen on 2023-01-01 11:29:43 UTC # Generated by conda-lock. # platform: linux-64 # input_hash: f39cf3a86cdaeb58bee45974ccbdaf3fb51ad41f0bb6f3caf9340c5aad0dfa3b @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.9.24-ha878542_0.tar.bz2#41e4e87062433e283696cf384f952ef6 -https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.36.1-hea4e1c9_2.tar.bz2#bd4f2e711b39af170e7ff15163fe87ee -https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-12.1.0-ha89aaad_16.tar.bz2#6f5ba041a41eb102a1027d9e68731be7 -https://conda.anaconda.org/conda-forge/linux-64/pandoc-2.19.2-ha770c72_0.tar.bz2#f17322ae18898607521b3fa90df84235 -https://conda.anaconda.org/conda-forge/linux-64/libgomp-12.1.0-h8d9b700_16.tar.bz2#f013cf7749536ce43d82afbffdf499ab +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.12.7-ha878542_0.conda#ff9f73d45c4a07d6f424495288a26080 +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.39-hcc3a1bd_1.conda#737be0d34c22d24432049ab7a3214de4 +https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-12.2.0-h46fd767_19.tar.bz2#1030b1f38c129f2634eae026f704fe60 +https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.7-3_cp37m.conda#46277e9cf1ecd46926a31cea47079009 +https://conda.anaconda.org/conda-forge/linux-64/libgomp-12.2.0-h65d4601_19.tar.bz2#cedcee7c064c01c403f962c9e8d3c373 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d -https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-12.1.0-h8d9b700_16.tar.bz2#4f05bc9844f7c101e6e147dab3c88d5c +https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-12.2.0-h65d4601_19.tar.bz2#e4c94f80aef025c17ab0828cd85ef535 https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.18.1-h7f98852_0.tar.bz2#f26ef8098fab1f719c91eb760d63381a https://conda.anaconda.org/conda-forge/linux-64/icu-70.1-h27087fc_0.tar.bz2#87473a15119779e021c314249d4b4aed https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3 @@ -20,129 +20,128 @@ 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https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1 -https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.47.0-hdcd2b5c_1.tar.bz2#6fe9e31c2b8d0b022626ccac13e6ca3c -https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.39.4-h753d276_0.tar.bz2#978924c298fc2215f129e8171bbea688 -https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.10.0-haa6b8db_3.tar.bz2#89acee135f0809a18a1f4537390aa2dd +https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.47.0-hff17c54_1.tar.bz2#2b7dbfa6988a41f9d23ba6d4f0e1d74e +https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.40.0-h753d276_0.tar.bz2#2e5f9a37d487e1019fd4d8113adb2f9f +https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.10.0-hf14f497_3.tar.bz2#d85acad4b47dff4e3def14a769a97906 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+https://conda.anaconda.org/conda-forge/noarch/argon2-cffi-21.3.0-pyhd8ed1ab_0.tar.bz2#a0b402db58f73aaab8ee0ca1025a362e +https://conda.anaconda.org/conda-forge/linux-aarch64/jupyter_core-5.1.1-py39h4420490_0.conda#000c9bd1bde07a73caf4e2b333faeb43 +https://conda.anaconda.org/conda-forge/noarch/jupyter_telemetry-0.1.0-pyhd8ed1ab_1.tar.bz2#bb9ebdb6d5aa2622484aff1faceee181 +https://conda.anaconda.org/conda-forge/noarch/oauthlib-3.2.2-pyhd8ed1ab_0.tar.bz2#8f882b197fd9c4941a787926baea4868 +https://conda.anaconda.org/conda-forge/noarch/prompt-toolkit-3.0.36-pyha770c72_0.conda#4d79ec192e0bfd530a254006d123b9a6 +https://conda.anaconda.org/conda-forge/noarch/pyopenssl-22.1.0-pyhd8ed1ab_0.tar.bz2#fbfa0a180d48c800f922a10a114a8632 +https://conda.anaconda.org/conda-forge/noarch/certipy-0.1.3-py_0.tar.bz2#23486713ef5712923e7c57cae609b22e +https://conda.anaconda.org/conda-forge/noarch/ipython-8.7.0-pyh41d4057_0.conda#adc2f96edf35423c091dba93b642573a +https://conda.anaconda.org/conda-forge/noarch/jupyter_client-7.4.8-pyhd8ed1ab_0.conda#bd4951aa5fbf3336a249e25c90f50333 +https://conda.anaconda.org/conda-forge/noarch/nbformat-5.7.1-pyhd8ed1ab_0.conda#facb42913140f1a399a5ebb65b30915e +https://conda.anaconda.org/conda-forge/noarch/urllib3-1.26.13-pyhd8ed1ab_0.conda#3078ef2359efd6ecadbc7e085c5e0592 +https://conda.anaconda.org/conda-forge/noarch/ipykernel-6.19.4-pyh210e3f2_0.conda#65372b6dd819e2c36345cf91eeb4ff06 +https://conda.anaconda.org/conda-forge/noarch/nbclient-0.7.2-pyhd8ed1ab_0.conda#6c7b0d75b66a220274bb5a28c23197f2 +https://conda.anaconda.org/conda-forge/noarch/requests-2.28.1-pyhd8ed1ab_1.tar.bz2#089382ee0e2dc2eae33a04cc3c2bddb0 +https://conda.anaconda.org/conda-forge/noarch/ipywidgets-8.0.2-pyhd8ed1ab_1.tar.bz2#81b7f46918555bf911ad2ba2f3259094 +https://conda.anaconda.org/conda-forge/linux-aarch64/jupyterhub-base-1.5.0-py39ha65689a_1.tar.bz2#4a9725abb86dbd756dc201db57022055 +https://conda.anaconda.org/conda-forge/noarch/nbconvert-core-7.2.7-pyhd8ed1ab_0.conda#dce063b1f5d6193646fc2ac43f88b77f +https://conda.anaconda.org/conda-forge/noarch/jupyter_server-1.23.4-pyhd8ed1ab_0.conda#35b7e9267926e864cc70ce137e6588ca +https://conda.anaconda.org/conda-forge/noarch/nbconvert-pandoc-7.2.7-pyhd8ed1ab_0.conda#7d48776bb3fdfa6447267c413a480ccd +https://conda.anaconda.org/conda-forge/noarch/jupyter-resource-usage-0.6.3-pyhd8ed1ab_0.tar.bz2#9d26ebd67e0e22aba13ac8a490d88d9e +https://conda.anaconda.org/conda-forge/noarch/jupyterlab_server-2.17.0-pyhd8ed1ab_0.conda#68364b266a989bb9829943bfd33187d8 +https://conda.anaconda.org/conda-forge/noarch/nbconvert-7.2.7-pyhd8ed1ab_0.conda#b019fe41e6f6b88e0557532514f39cff +https://conda.anaconda.org/conda-forge/noarch/notebook-shim-0.2.2-pyhd8ed1ab_0.tar.bz2#40be846cd4e78672a40e43db9dae753c +https://conda.anaconda.org/conda-forge/noarch/nbclassic-0.4.8-pyhd8ed1ab_0.tar.bz2#f4f150f83ed90a1b833e6081bbf38257 +https://conda.anaconda.org/conda-forge/noarch/notebook-6.4.12-pyha770c72_0.tar.bz2#77fc67c5bbea44fd41e8bbe2ac82d1ad +https://conda.anaconda.org/conda-forge/noarch/jupyter-offlinenotebook-0.2.2-pyh1d7be83_0.tar.bz2#fe55056ce4bc4bd4953ba440270735fb +https://conda.anaconda.org/conda-forge/linux-aarch64/jupyterhub-singleuser-1.5.0-py39ha65689a_1.tar.bz2#428f24f44794a428a875ee08be6eee31 +https://conda.anaconda.org/conda-forge/noarch/jupyterlab-3.4.8-pyhd8ed1ab_0.tar.bz2#6fbf13b0e8a6fa24bbae91205e8ce467 +https://conda.anaconda.org/conda-forge/noarch/nteract_on_jupyter-2.1.3-py_0.tar.bz2#1430ccd983ae6b161e2fbf4377965f7a diff --git a/repo2docker/buildpacks/conda/environment.py-3.9.yml b/repo2docker/buildpacks/conda/environment.py-3.9.yml index a854684eb..a08e59022 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.9.yml +++ b/repo2docker/buildpacks/conda/environment.py-3.9.yml @@ -1,5 +1,5 @@ # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY -# Generated on 2022-10-13 14:39:21 UTC +# Generated on 2023-01-01 11:30:44 UTC channels: - conda-forge dependencies: From 064d91ae22480ae4afe3b39321813bff86501ab1 Mon Sep 17 00:00:00 2001 From: Simon Li Date: Sun, 1 Jan 2023 15:52:19 +0000 Subject: [PATCH 092/171] BuildPacks: support arm64 where possible (i.e. not R) --- repo2docker/buildpacks/_r_base.py | 4 ++++ repo2docker/buildpacks/base.py | 3 +++ repo2docker/buildpacks/conda/__init__.py | 11 +++++++---- repo2docker/buildpacks/conda/freeze.py | 4 +++- .../buildpacks/conda/install-base-env.bash | 2 +- repo2docker/buildpacks/julia/julia_project.py | 11 ++++++++++- repo2docker/buildpacks/julia/julia_require.py | 11 ++++++++++- repo2docker/buildpacks/nix/__init__.py | 11 ++++++++--- repo2docker/buildpacks/nix/install-nix.bash | 16 ++++++++++------ repo2docker/buildpacks/r.py | 3 +++ repo2docker/docker.py | 9 ++++++++- repo2docker/utils.py | 17 +++++++++++++++++ 12 files changed, 84 insertions(+), 18 deletions(-) diff --git a/repo2docker/buildpacks/_r_base.py b/repo2docker/buildpacks/_r_base.py index 35a3177b5..27e11eba4 100644 --- a/repo2docker/buildpacks/_r_base.py +++ b/repo2docker/buildpacks/_r_base.py @@ -4,11 +4,15 @@ Keeping this in r.py would lead to cyclic imports. """ from ..semver import parse_version as V +from ..utils import get_platform def rstudio_base_scripts(r_version): """Base steps to install RStudio and shiny-server.""" + if get_platform() != "linux-64": + raise RuntimeError("RStudio is only available for linux-64") + # Shiny server (not the package!) seems to be the same version for all R versions shiny_server_url = "https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.17.973-amd64.deb" shiny_proxy_version = "1.1" diff --git a/repo2docker/buildpacks/base.py b/repo2docker/buildpacks/base.py index e7c9b537d..51677ee3a 100644 --- a/repo2docker/buildpacks/base.py +++ b/repo2docker/buildpacks/base.py @@ -11,6 +11,8 @@ import escapism import jinja2 +from ..utils import get_platform + # Only use syntax features supported by Docker 17.09 TEMPLATE = r""" FROM buildpack-deps:bionic @@ -229,6 +231,7 @@ def __init__(self): "Windows environment detected. Note that Windows " "support is experimental in repo2docker." ) + self.platform = get_platform() def get_packages(self): """ diff --git a/repo2docker/buildpacks/conda/__init__.py b/repo2docker/buildpacks/conda/__init__.py index 99653177b..5bf403fe6 100644 --- a/repo2docker/buildpacks/conda/__init__.py +++ b/repo2docker/buildpacks/conda/__init__.py @@ -59,6 +59,7 @@ def get_build_env(self): # this exe should be used for installs after bootstrap with micromamba # switch this to /usr/local/bin/micromamba to use it for all installs ("MAMBA_EXE", "${CONDA_DIR}/bin/mamba"), + ("CONDA_PLATFORM", self.platform), ] if self._nb_requirements_file: env.append(("NB_REQUIREMENTS_FILE", self._nb_requirements_file)) @@ -160,13 +161,13 @@ def get_build_script_files(self): # major Python versions during upgrade. # If no version is specified or no matching X.Y version is found, # the default base environment is used. - frozen_name = "environment.lock" + frozen_name = f"environment-{self.platform}.lock" pip_frozen_name = "requirements.txt" if py_version: if self.python_version == "2.7": # python 2 goes in a different env files[ - "conda/environment.py-2.7.lock" + "conda/environment.py-2.7-linux-64.lock" ] = self._kernel_environment_file = "/tmp/env/kernel-environment.lock" # additional pip requirements for kernel env if os.path.exists(os.path.join(HERE, "requirements.py-2.7.txt")): @@ -176,12 +177,14 @@ def get_build_script_files(self): self._kernel_requirements_file ) = "/tmp/env/kernel-requirements.txt" else: - py_frozen_name = f"environment.py-{py_version}.lock" + py_frozen_name = f"environment.py-{py_version}-{self.platform}.lock" if os.path.exists(os.path.join(HERE, py_frozen_name)): frozen_name = py_frozen_name pip_frozen_name = f"requirements.py-{py_version}.pip" else: - raise ValueError(f"Python version {py_version} is not supported!") + raise ValueError( + f"Python version {py_version} {self.platform} is not supported!" + ) files[ "conda/" + frozen_name ] = self._nb_environment_file = "/tmp/env/environment.lock" diff --git a/repo2docker/buildpacks/conda/freeze.py b/repo2docker/buildpacks/conda/freeze.py index 670b863cb..e800b714e 100755 --- a/repo2docker/buildpacks/conda/freeze.py +++ b/repo2docker/buildpacks/conda/freeze.py @@ -131,7 +131,9 @@ def set_python(py_env_file, py): for platform in args.platform: env_file = pathlib.Path(str(ENV_FILE_T).format(py=py)) set_python(env_file, py) - frozen_file = pathlib.Path(os.path.splitext(env_file)[0] + f"-{platform}.lock") + frozen_file = pathlib.Path( + os.path.splitext(env_file)[0] + f"-{platform}.lock" + ) freeze(env_file, frozen_file, platform) if py == default_py: shutil.copy(frozen_file, FROZEN_FILE_T.format(platform=platform)) diff --git a/repo2docker/buildpacks/conda/install-base-env.bash b/repo2docker/buildpacks/conda/install-base-env.bash index 10b196979..875fe3b16 100755 --- a/repo2docker/buildpacks/conda/install-base-env.bash +++ b/repo2docker/buildpacks/conda/install-base-env.bash @@ -8,7 +8,7 @@ cd $(dirname $0) export MAMBA_VERSION=1.0.0 export CONDA_VERSION=4.13.0 -URL="https://anaconda.org/conda-forge/micromamba/${MAMBA_VERSION}/download/linux-64/micromamba-${MAMBA_VERSION}-0.tar.bz2" +URL="https://anaconda.org/conda-forge/micromamba/${MAMBA_VERSION}/download/${CONDA_PLATFORM}/micromamba-${MAMBA_VERSION}-0.tar.bz2" # make sure we don't do anything funky with user's $HOME # since this is run as root diff --git a/repo2docker/buildpacks/julia/julia_project.py b/repo2docker/buildpacks/julia/julia_project.py index 70853b26a..d77415520 100644 --- a/repo2docker/buildpacks/julia/julia_project.py +++ b/repo2docker/buildpacks/julia/julia_project.py @@ -79,16 +79,25 @@ def get_build_env(self): will be installed - `JULIA_DEPOT_PATH`: path where Julia libraries are installed. - `JULIA_VERSION`: default version of julia to be installed + - `JULIA_ARCH`: machine architecture used in Julia download URLs + - `JULIA_ARCH_SHORT`: machine architecture used in Julia download URLs - `JUPYTER`: environment variable required by IJulia to point to the `jupyter` executable For example, a tuple may be `('JULIA_VERSION', '0.6.0')`. """ + if self.platform == "linux-aarch64": + julia_arch = julia_arch_short = "aarch64" + else: + julia_arch = "x86_64" + julia_arch_short = "x64" return super().get_build_env() + [ ("JULIA_PATH", "${APP_BASE}/julia"), ("JULIA_DEPOT_PATH", "${JULIA_PATH}/pkg"), ("JULIA_VERSION", self.julia_version), + ("JULIA_ARCH", julia_arch), + ("JULIA_ARCH_SHORT", julia_arch_short), ("JUPYTER", "${NB_PYTHON_PREFIX}/bin/jupyter"), ("JUPYTER_DATA_DIR", "${NB_PYTHON_PREFIX}/share/jupyter"), ] @@ -129,7 +138,7 @@ def get_build_scripts(self): "root", r""" mkdir -p ${JULIA_PATH} && \ - curl -sSL "https://julialang-s3.julialang.org/bin/linux/x64/${JULIA_VERSION%[.-]*}/julia-${JULIA_VERSION}-linux-x86_64.tar.gz" | tar -xz -C ${JULIA_PATH} --strip-components 1 + curl -sSL "https://julialang-s3.julialang.org/bin/linux/${JULIA_ARCH_SHORT}/${JULIA_VERSION%[.-]*}/julia-${JULIA_VERSION}-linux-${JULIA_ARCH}.tar.gz" | tar -xz -C ${JULIA_PATH} --strip-components 1 """, ), ( diff --git a/repo2docker/buildpacks/julia/julia_require.py b/repo2docker/buildpacks/julia/julia_require.py index b2acbcff6..aef1f1bab 100644 --- a/repo2docker/buildpacks/julia/julia_require.py +++ b/repo2docker/buildpacks/julia/julia_require.py @@ -69,12 +69,19 @@ def get_build_env(self): - `JULIA_DEPOT_PATH`: path where Julia libraries are installed. Similar to JULIA_PKGDIR, used in 1.x. - `JULIA_VERSION`: default version of julia to be installed + - `JULIA_ARCH`: machine architecture used in Julia download URLs + - `JULIA_ARCH_SHORT`: machine architecture used in Julia download URLs - `JUPYTER`: environment variable required by IJulia to point to the `jupyter` executable For example, a tuple may be `('JULIA_VERSION', '0.6.0')`. """ + if self.platform == "linux-aarch64": + julia_arch = julia_arch_short = "aarch64" + else: + julia_arch = "x86_64" + julia_arch_short = "x64" return super().get_build_env() + [ ("JULIA_PATH", "${APP_BASE}/julia"), ("JULIA_HOME", "${JULIA_PATH}/bin"), # julia <= 0.6 @@ -82,6 +89,8 @@ def get_build_env(self): ("JULIA_PKGDIR", "${JULIA_PATH}/pkg"), ("JULIA_DEPOT_PATH", "${JULIA_PKGDIR}"), # julia >= 0.7 ("JULIA_VERSION", self.julia_version), + ("JULIA_ARCH", julia_arch), + ("JULIA_ARCH_SHORT", julia_arch_short), ("JUPYTER", "${NB_PYTHON_PREFIX}/bin/jupyter"), ] @@ -111,7 +120,7 @@ def get_build_scripts(self): "root", r""" mkdir -p ${JULIA_PATH} && \ - curl -sSL "https://julialang-s3.julialang.org/bin/linux/x64/${JULIA_VERSION%[.-]*}/julia-${JULIA_VERSION}-linux-x86_64.tar.gz" | tar -xz -C ${JULIA_PATH} --strip-components 1 + curl -sSL "https://julialang-s3.julialang.org/bin/linux/${JULIA_ARCH_SHORT}/${JULIA_VERSION%[.-]*}/julia-${JULIA_VERSION}-linux-${JULIA_ARCH}.tar.gz" | tar -xz -C ${JULIA_PATH} --strip-components 1 """, ), ( diff --git a/repo2docker/buildpacks/nix/__init__.py b/repo2docker/buildpacks/nix/__init__.py index 73dd81af4..cd121997a 100644 --- a/repo2docker/buildpacks/nix/__init__.py +++ b/repo2docker/buildpacks/nix/__init__.py @@ -13,6 +13,7 @@ def get_path(self): def get_env(self): """Ordered list of environment variables to be set for this image""" + return super().get_env() + [ ("NIX_PATH", "nixpkgs=/home/${NB_USER}/.nix-defexpr/channels/nixpkgs"), ("NIX_SSL_CERT_FILE", "/etc/ssl/certs/ca-certificates.crt"), @@ -30,6 +31,10 @@ def get_build_scripts(self): - install nix package manager for user """ + if self.platform == "linux-aarch64": + nix_arch = "aarch64" + else: + nix_arch = "x86_64" return super().get_build_scripts() + [ ( "root", @@ -43,9 +48,9 @@ def get_build_scripts(self): ), ( "${NB_USER}", - """ - bash /home/${NB_USER}/.local/bin/install-nix.bash && \ - rm /home/${NB_USER}/.local/bin/install-nix.bash + f""" + NIX_ARCH={nix_arch} bash /home/${{NB_USER}}/.local/bin/install-nix.bash && \ + rm /home/${{NB_USER}}/.local/bin/install-nix.bash """, ), ] diff --git a/repo2docker/buildpacks/nix/install-nix.bash b/repo2docker/buildpacks/nix/install-nix.bash index 1eb657966..be0cb1a5d 100644 --- a/repo2docker/buildpacks/nix/install-nix.bash +++ b/repo2docker/buildpacks/nix/install-nix.bash @@ -3,12 +3,16 @@ set -ex NIX_VERSION="2.3.9" -NIX_SHA256="49763fd7fa06bcb712ced2f3f11afd275e3a4d7bc5ff0d6fd1d50a4c3ce7bbf4" +if [ "$NIX_ARCH" = "aarch64" ]; then + NIX_SHA256="733a26911193fdd44d5d68342075af5924d8c0701aae877e51a38d74ee9f4ff8" +else + NIX_SHA256="49763fd7fa06bcb712ced2f3f11afd275e3a4d7bc5ff0d6fd1d50a4c3ce7bbf4" +fi # Do all our operations in /tmp, since we can't rely on current directory being writeable yet. cd /tmp -wget --quiet https://nixos.org/releases/nix/nix-$NIX_VERSION/nix-$NIX_VERSION-x86_64-linux.tar.xz -echo "$NIX_SHA256 nix-$NIX_VERSION-x86_64-linux.tar.xz" | sha256sum -c -tar xJf nix-*-x86_64-linux.tar.xz -sh nix-*-x86_64-linux/install -rm -r nix-*-x86_64-linux* +wget --quiet https://nixos.org/releases/nix/nix-$NIX_VERSION/nix-$NIX_VERSION-$NIX_ARCH-linux.tar.xz +echo "$NIX_SHA256 nix-$NIX_VERSION-$NIX_ARCH-linux.tar.xz" | sha256sum -c +tar xJf nix-*-$NIX_ARCH-linux.tar.xz +sh nix-*-$NIX_ARCH-linux/install +rm -r nix-*-$NIX_ARCH-linux* diff --git a/repo2docker/buildpacks/r.py b/repo2docker/buildpacks/r.py index 200f472fd..2d5ed26e3 100644 --- a/repo2docker/buildpacks/r.py +++ b/repo2docker/buildpacks/r.py @@ -5,6 +5,7 @@ import requests from ..semver import parse_version as V +from ..utils import get_platform from ._r_base import rstudio_base_scripts from .python import PythonBuildPack @@ -277,6 +278,8 @@ def get_build_scripts(self): cran_mirror_url = self.get_cran_mirror_url(self.checkpoint_date) + if get_platform() != "linux-64": + raise RuntimeError("RStudio is only available for linux-64") scripts = [ ( "root", diff --git a/repo2docker/docker.py b/repo2docker/docker.py index 267c16cf6..d52709f6b 100644 --- a/repo2docker/docker.py +++ b/repo2docker/docker.py @@ -8,6 +8,7 @@ import docker from .engine import Container, ContainerEngine, ContainerEngineException, Image +from .utils import get_platform class DockerContainer(Container): @@ -93,6 +94,12 @@ def build( labels=None, **kwargs, ): + platform = get_platform() + if platform == "linux-aarch64": + docker_platform = "linux/arm64" + else: + docker_platform = "linux/amd64" + return self._apiclient.build( buildargs=buildargs, cache_from=cache_from, @@ -106,7 +113,7 @@ def build( fileobj=fileobj, path=path, labels=labels, - platform="linux/amd64", + platform=docker_platform, **kwargs, ) diff --git a/repo2docker/utils.py b/repo2docker/utils.py index cd345f4a0..6aaa8f2c6 100644 --- a/repo2docker/utils.py +++ b/repo2docker/utils.py @@ -1,6 +1,8 @@ import os +import platform import re import subprocess +import warnings from contextlib import contextmanager from enum import Enum from functools import partial @@ -524,3 +526,18 @@ def is_local_pip_requirement(line): return True return False + + +def get_platform(): + """Return the platform of the image + + Returns either `linux-64` or `linux-aarch64` + """ + m = platform.machine() + if m == "x86_64": + return "linux-64" + elif m == "aarch64": + return "linux-aarch64" + else: + warnings.warn(f"Unexpected platform '{m}', defaulting to linux-64") + return "linux-64" From 8f3f57ada73861cc8be43dabcaecf0c919199733 Mon Sep 17 00:00:00 2001 From: Simon Li Date: Mon, 2 Jan 2023 12:11:34 +0000 Subject: [PATCH 093/171] Make platform configurable instead of only auto-detecting --- repo2docker/app.py | 26 ++++++++++++++++++- repo2docker/buildpacks/_r_base.py | 4 --- repo2docker/buildpacks/base.py | 6 ++--- repo2docker/buildpacks/conda/__init__.py | 22 +++++++++++++--- repo2docker/buildpacks/docker.py | 2 ++ repo2docker/buildpacks/julia/julia_project.py | 2 +- repo2docker/buildpacks/julia/julia_require.py | 2 +- repo2docker/buildpacks/nix/__init__.py | 2 +- repo2docker/buildpacks/r.py | 7 ++--- repo2docker/docker.py | 10 ++----- repo2docker/engine.py | 3 +++ repo2docker/utils.py | 12 ++++----- tests/unit/test_utils.py | 14 ++++++++++ 13 files changed, 80 insertions(+), 32 deletions(-) diff --git a/repo2docker/app.py b/repo2docker/app.py index 94384984e..18ce5f974 100755 --- a/repo2docker/app.py +++ b/repo2docker/app.py @@ -15,6 +15,7 @@ import sys import tempfile import time +import warnings from urllib.parse import urlparse import entrypoints @@ -36,7 +37,7 @@ RBuildPack, ) from .engine import BuildError, ContainerEngineException, ImageLoadError -from .utils import ByteSpecification, R2dState, chdir +from .utils import ByteSpecification, R2dState, chdir, get_platform class Repo2Docker(Application): @@ -250,6 +251,27 @@ def _user_name_default(self): config=True, ) + platform = Unicode( + config=True, + help=""" + Platform to build for, linux/amd64 (recommended) or linux/arm64 (experimental). + """, + ) + + @default("platform") + def _platform_default(self): + """ + Default platform + """ + p = get_platform() + if p == "linux/arm64": + warnings.warn( + "Building for linux/arm64 is experimental. " + "To use the recommended platform set --Repo2Docker.platform=linux/amd64. " + "To silence this warning set --Repo2Docker.platform=linux/arm64." + ) + return p + extra_build_args = Dict( {}, help=""" @@ -778,6 +800,7 @@ def build(self): else: picked_buildpack = self.default_buildpack() + picked_buildpack.platform = self.platform picked_buildpack.appendix = self.appendix # Add metadata labels picked_buildpack.labels["repo2docker.version"] = self.version @@ -819,6 +842,7 @@ def build(self): build_args, self.cache_from, self.extra_build_kwargs, + platform=self.platform, ): if docker_client.string_output: self.log.info(l, extra=dict(phase=R2dState.BUILDING)) diff --git a/repo2docker/buildpacks/_r_base.py b/repo2docker/buildpacks/_r_base.py index 27e11eba4..35a3177b5 100644 --- a/repo2docker/buildpacks/_r_base.py +++ b/repo2docker/buildpacks/_r_base.py @@ -4,15 +4,11 @@ Keeping this in r.py would lead to cyclic imports. """ from ..semver import parse_version as V -from ..utils import get_platform def rstudio_base_scripts(r_version): """Base steps to install RStudio and shiny-server.""" - if get_platform() != "linux-64": - raise RuntimeError("RStudio is only available for linux-64") - # Shiny server (not the package!) seems to be the same version for all R versions shiny_server_url = "https://download3.rstudio.org/ubuntu-14.04/x86_64/shiny-server-1.5.17.973-amd64.deb" shiny_proxy_version = "1.1" diff --git a/repo2docker/buildpacks/base.py b/repo2docker/buildpacks/base.py index 51677ee3a..ceed91ce4 100644 --- a/repo2docker/buildpacks/base.py +++ b/repo2docker/buildpacks/base.py @@ -11,8 +11,6 @@ import escapism import jinja2 -from ..utils import get_platform - # Only use syntax features supported by Docker 17.09 TEMPLATE = r""" FROM buildpack-deps:bionic @@ -231,7 +229,7 @@ def __init__(self): "Windows environment detected. Note that Windows " "support is experimental in repo2docker." ) - self.platform = get_platform() + self.platform = "" def get_packages(self): """ @@ -562,6 +560,7 @@ def build( build_args, cache_from, extra_build_kwargs, + platform=None, ): tarf = io.BytesIO() tar = tarfile.open(fileobj=tarf, mode="w") @@ -616,6 +615,7 @@ def _filter_tar(tar): buildargs=build_args, container_limits=limits, cache_from=cache_from, + platform=platform, ) build_kwargs.update(extra_build_kwargs) diff --git a/repo2docker/buildpacks/conda/__init__.py b/repo2docker/buildpacks/conda/__init__.py index 5bf403fe6..b538aafb1 100644 --- a/repo2docker/buildpacks/conda/__init__.py +++ b/repo2docker/buildpacks/conda/__init__.py @@ -35,6 +35,14 @@ class CondaBuildPack(BaseImage): # extra pip requirements.txt for the notebook env _nb_requirements_file = "" + def _conda_platform(self): + """Return the conda platform name for the current platform""" + if self.platform == "linux/amd64": + return "linux-64" + if self.platform == "linux/arm64": + return "linux-aarch64" + raise ValueError(f"Unknown platform {self.platform}") + def get_build_env(self): """Return environment variables to be set. @@ -59,7 +67,7 @@ def get_build_env(self): # this exe should be used for installs after bootstrap with micromamba # switch this to /usr/local/bin/micromamba to use it for all installs ("MAMBA_EXE", "${CONDA_DIR}/bin/mamba"), - ("CONDA_PLATFORM", self.platform), + ("CONDA_PLATFORM", self._conda_platform()), ] if self._nb_requirements_file: env.append(("NB_REQUIREMENTS_FILE", self._nb_requirements_file)) @@ -161,7 +169,7 @@ def get_build_script_files(self): # major Python versions during upgrade. # If no version is specified or no matching X.Y version is found, # the default base environment is used. - frozen_name = f"environment-{self.platform}.lock" + frozen_name = f"environment-{self._conda_platform()}.lock" pip_frozen_name = "requirements.txt" if py_version: if self.python_version == "2.7": @@ -177,13 +185,15 @@ def get_build_script_files(self): self._kernel_requirements_file ) = "/tmp/env/kernel-requirements.txt" else: - py_frozen_name = f"environment.py-{py_version}-{self.platform}.lock" + py_frozen_name = ( + f"environment.py-{py_version}-{self._conda_platform()}.lock" + ) if os.path.exists(os.path.join(HERE, py_frozen_name)): frozen_name = py_frozen_name pip_frozen_name = f"requirements.py-{py_version}.pip" else: raise ValueError( - f"Python version {py_version} {self.platform} is not supported!" + f"Python version {py_version} {self._conda_platform()} is not supported!" ) files[ "conda/" + frozen_name @@ -369,6 +379,10 @@ def get_env_scripts(self): """, ) ) + if self.platform != "linux/amd64": + raise RuntimeError( + f"RStudio is only available for linux/amd64 ({self.platform})" + ) scripts += rstudio_base_scripts(self.r_version) scripts += [ ( diff --git a/repo2docker/buildpacks/docker.py b/repo2docker/buildpacks/docker.py index 6979b8305..d1dfe4926 100644 --- a/repo2docker/buildpacks/docker.py +++ b/repo2docker/buildpacks/docker.py @@ -30,6 +30,7 @@ def build( build_args, cache_from, extra_build_kwargs, + platform=None, ): """Build a Docker image based on the Dockerfile in the source repo.""" # If you work on this bit of code check the corresponding code in @@ -55,6 +56,7 @@ def build( container_limits=limits, cache_from=cache_from, labels=self.get_labels(), + platform=platform, ) build_kwargs.update(extra_build_kwargs) diff --git a/repo2docker/buildpacks/julia/julia_project.py b/repo2docker/buildpacks/julia/julia_project.py index d77415520..b7eab5c3f 100644 --- a/repo2docker/buildpacks/julia/julia_project.py +++ b/repo2docker/buildpacks/julia/julia_project.py @@ -87,7 +87,7 @@ def get_build_env(self): For example, a tuple may be `('JULIA_VERSION', '0.6.0')`. """ - if self.platform == "linux-aarch64": + if self.platform == "linux/arm64": julia_arch = julia_arch_short = "aarch64" else: julia_arch = "x86_64" diff --git a/repo2docker/buildpacks/julia/julia_require.py b/repo2docker/buildpacks/julia/julia_require.py index aef1f1bab..b3b8cecf2 100644 --- a/repo2docker/buildpacks/julia/julia_require.py +++ b/repo2docker/buildpacks/julia/julia_require.py @@ -77,7 +77,7 @@ def get_build_env(self): For example, a tuple may be `('JULIA_VERSION', '0.6.0')`. """ - if self.platform == "linux-aarch64": + if self.platform == "linux/arm64": julia_arch = julia_arch_short = "aarch64" else: julia_arch = "x86_64" diff --git a/repo2docker/buildpacks/nix/__init__.py b/repo2docker/buildpacks/nix/__init__.py index cd121997a..9dbb412ab 100644 --- a/repo2docker/buildpacks/nix/__init__.py +++ b/repo2docker/buildpacks/nix/__init__.py @@ -31,7 +31,7 @@ def get_build_scripts(self): - install nix package manager for user """ - if self.platform == "linux-aarch64": + if self.platform == "linux/arm64": nix_arch = "aarch64" else: nix_arch = "x86_64" diff --git a/repo2docker/buildpacks/r.py b/repo2docker/buildpacks/r.py index 2d5ed26e3..8d8ae6b1b 100644 --- a/repo2docker/buildpacks/r.py +++ b/repo2docker/buildpacks/r.py @@ -5,7 +5,6 @@ import requests from ..semver import parse_version as V -from ..utils import get_platform from ._r_base import rstudio_base_scripts from .python import PythonBuildPack @@ -278,8 +277,10 @@ def get_build_scripts(self): cran_mirror_url = self.get_cran_mirror_url(self.checkpoint_date) - if get_platform() != "linux-64": - raise RuntimeError("RStudio is only available for linux-64") + if self.platform != "linux/amd64": + raise RuntimeError( + f"RStudio is only available for linux/amd64 ({self.platform})" + ) scripts = [ ( "root", diff --git a/repo2docker/docker.py b/repo2docker/docker.py index d52709f6b..39d9e0441 100644 --- a/repo2docker/docker.py +++ b/repo2docker/docker.py @@ -8,7 +8,6 @@ import docker from .engine import Container, ContainerEngine, ContainerEngineException, Image -from .utils import get_platform class DockerContainer(Container): @@ -92,14 +91,9 @@ def build( fileobj=None, path="", labels=None, + platform=None, **kwargs, ): - platform = get_platform() - if platform == "linux-aarch64": - docker_platform = "linux/arm64" - else: - docker_platform = "linux/amd64" - return self._apiclient.build( buildargs=buildargs, cache_from=cache_from, @@ -113,7 +107,7 @@ def build( fileobj=fileobj, path=path, labels=labels, - platform=docker_platform, + platform=platform, **kwargs, ) diff --git a/repo2docker/engine.py b/repo2docker/engine.py index 73276a3a7..f3febccc0 100644 --- a/repo2docker/engine.py +++ b/repo2docker/engine.py @@ -177,6 +177,7 @@ def build( fileobj=None, path="", labels=None, + platform=None, **kwargs, ): """ @@ -207,6 +208,8 @@ def build( path to the Dockerfile labels : dict Dictionary of labels to set on the image + platform: str + Platform to build for Returns ------- diff --git a/repo2docker/utils.py b/repo2docker/utils.py index 6aaa8f2c6..e3590274f 100644 --- a/repo2docker/utils.py +++ b/repo2docker/utils.py @@ -529,15 +529,15 @@ def is_local_pip_requirement(line): def get_platform(): - """Return the platform of the image + """Return the target platform of the container image - Returns either `linux-64` or `linux-aarch64` + Returns either `linux/amd64` or `linux/arm64` """ m = platform.machine() if m == "x86_64": - return "linux-64" + return "linux/amd64" elif m == "aarch64": - return "linux-aarch64" + return "linux/arm64" else: - warnings.warn(f"Unexpected platform '{m}', defaulting to linux-64") - return "linux-64" + warnings.warn(f"Unexpected platform '{m}', defaulting to linux/amd64") + return "linux/amd64" diff --git a/tests/unit/test_utils.py b/tests/unit/test_utils.py index cec3dc8cd..39a4ffc4d 100644 --- a/tests/unit/test_utils.py +++ b/tests/unit/test_utils.py @@ -2,6 +2,7 @@ Tests for repo2docker/utils.py """ import os +import platform import subprocess import tempfile @@ -160,3 +161,16 @@ def test_open_guess_encoding(): ) def test_local_pip_requirement(req, is_local): assert utils.is_local_pip_requirement(req) == is_local + + +@pytest.mark.parametrize( + "machine_name,expected", + [ + ("x86_64", "linux/amd64"), + ("aarch64", "linux/arm64"), + ("other", "linux/amd64"), + ], +) +def test_get_platform(monkeypatch, machine_name, expected): + monkeypatch.setattr(platform, "machine", lambda: machine_name) + assert utils.get_platform() == expected From 2308cfe2324bfe7f83ce26d9dda624e8582cfbca Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 3 Jan 2023 01:51:52 +0000 Subject: [PATCH 094/171] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/pycqa/isort: v5.11.3 → 5.11.4](https://github.com/pycqa/isort/compare/v5.11.3...5.11.4) --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 58d567767..c9518890c 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -36,7 +36,7 @@ repos: # Autoformat: Python code - repo: https://github.com/pycqa/isort - rev: v5.11.3 + rev: 5.11.4 hooks: - id: isort args: From cdd0d5634255279b0bffe1fd991fecdb6099e0d4 Mon Sep 17 00:00:00 2001 From: Simon Li Date: Wed, 4 Jan 2023 15:04:49 +0000 Subject: [PATCH 095/171] OSX reports arm64 (Linux reports aarch64) --- repo2docker/utils.py | 4 ++++ tests/unit/test_utils.py | 1 + 2 files changed, 5 insertions(+) diff --git a/repo2docker/utils.py b/repo2docker/utils.py index e3590274f..9c2769e1d 100644 --- a/repo2docker/utils.py +++ b/repo2docker/utils.py @@ -537,6 +537,10 @@ def get_platform(): if m == "x86_64": return "linux/amd64" elif m == "aarch64": + # Linux reports aarch64 + return "linux/arm64" + elif m == "arm64": + # OSX reports arm64 return "linux/arm64" else: warnings.warn(f"Unexpected platform '{m}', defaulting to linux/amd64") diff --git a/tests/unit/test_utils.py b/tests/unit/test_utils.py index 39a4ffc4d..c518bbd23 100644 --- a/tests/unit/test_utils.py +++ b/tests/unit/test_utils.py @@ -168,6 +168,7 @@ def test_local_pip_requirement(req, is_local): [ ("x86_64", "linux/amd64"), ("aarch64", "linux/arm64"), + ("arm64", "linux/arm64"), ("other", "linux/amd64"), ], ) From 8f818645f9490866714b5826b390906af3dc272c Mon Sep 17 00:00:00 2001 From: Simon Li Date: Wed, 4 Jan 2023 15:08:26 +0000 Subject: [PATCH 096/171] Raise error if Python 2.7 is used on arm64 --- repo2docker/buildpacks/conda/__init__.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/repo2docker/buildpacks/conda/__init__.py b/repo2docker/buildpacks/conda/__init__.py index b538aafb1..66aff037a 100644 --- a/repo2docker/buildpacks/conda/__init__.py +++ b/repo2docker/buildpacks/conda/__init__.py @@ -173,6 +173,11 @@ def get_build_script_files(self): pip_frozen_name = "requirements.txt" if py_version: if self.python_version == "2.7": + if "linux-64" != self._conda_platform(): + raise ValueError( + f"Python version 2.7 {self._conda_platform()} is not supported!" + ) + # python 2 goes in a different env files[ "conda/environment.py-2.7-linux-64.lock" From 0a3846f5d9c66645b302eb8c8e0139dabccb8036 Mon Sep 17 00:00:00 2001 From: YuviPanda Date: Sat, 7 Jan 2023 01:12:15 -0800 Subject: [PATCH 097/171] Support installing RStudio on distros without openssl1.1 --- repo2docker/buildpacks/_r_base.py | 28 +++++++++++++++++++++------- 1 file changed, 21 insertions(+), 7 deletions(-) diff --git a/repo2docker/buildpacks/_r_base.py b/repo2docker/buildpacks/_r_base.py index 35a3177b5..d833c1d51 100644 --- a/repo2docker/buildpacks/_r_base.py +++ b/repo2docker/buildpacks/_r_base.py @@ -14,10 +14,17 @@ def rstudio_base_scripts(r_version): shiny_proxy_version = "1.1" shiny_sha256sum = "80f1e48f6c824be7ef9c843bb7911d4981ac7e8a963e0eff823936a8b28476ee" - rstudio_url = "https://download2.rstudio.org/server/bionic/amd64/rstudio-server-2022.02.1-461-amd64.deb" - rstudio_sha256sum = ( - "239e8d93e103872e7c6d827113d88871965f82ffb0397f5638025100520d8a54" - ) + + # RStudio server has different builds based on wether OpenSSL 3 or 1.1 is available in the base + # image. 3 is present Jammy+, 1.1 until then. Instead of hardcoding URLs based on distro, we actually + # check for the dependency itself directly in the code below. You can find these URLs in + # https://posit.co/download/rstudio-server/, toggling between Ubuntu 22 (for openssl3) vs earlier versions (openssl 1.1) + # you may forget about openssl, but openssl never forgets you. + rstudio_openssl3_url = 'https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2022.12.0-353-amd64.deb' + rstudio_openssl3_sha256sum = 'a5aa2202786f9017a6de368a410488ea2e4fc6c739f78998977af214df0d6288' + + rstudio_openssl1_url = 'https://download2.rstudio.org/server/bionic/amd64/rstudio-server-2022.12.0-353-amd64.deb' + rstudio_openssl1_sha256sum = 'bb88e37328c304881e60d6205d7dac145525a5c2aaaf9da26f1cb625b7d47e6e' rsession_proxy_version = "2.0.1" return [ @@ -27,11 +34,18 @@ def rstudio_base_scripts(r_version): # but here it's important because these recommend r-base, # which will upgrade the installed version of R, undoing our pinned version rf""" - curl --silent --location --fail {rstudio_url} > /tmp/rstudio.deb && \ + apt-get update > /dev/null && \ + if apt-cache search libssl3 > /dev/null; then \ + RSTUDIO_URL="{rstudio_openssl3_url}" ;\ + RSTUDIO_HASH="{rstudio_openssl3_sha256sum}" ;\ + else \ + RSTUDIO_URL="{rstudio_openssl1_url}" ;\ + RSTUDIO_HASH="{rstudio_openssl1_sha256sum}" ;\ + fi && \ + curl --silent --location --fail ${{RSTUDIO_URL}} > /tmp/rstudio.deb && \ curl --silent --location --fail {shiny_server_url} > /tmp/shiny.deb && \ - echo '{rstudio_sha256sum} /tmp/rstudio.deb' | sha256sum -c - && \ + echo "${{RSTUDIO_HASH}} /tmp/rstudio.deb' | sha256sum -c - && \ echo '{shiny_sha256sum} /tmp/shiny.deb' | sha256sum -c - && \ - apt-get update > /dev/null && \ apt install -y --no-install-recommends /tmp/rstudio.deb /tmp/shiny.deb && \ rm /tmp/*.deb && \ apt-get -qq purge && \ From 01c142b8c2e5410fce14b969c8828aa69aa113e7 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Sat, 7 Jan 2023 09:12:38 +0000 Subject: [PATCH 098/171] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- repo2docker/buildpacks/_r_base.py | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/repo2docker/buildpacks/_r_base.py b/repo2docker/buildpacks/_r_base.py index d833c1d51..8bd7a9419 100644 --- a/repo2docker/buildpacks/_r_base.py +++ b/repo2docker/buildpacks/_r_base.py @@ -14,17 +14,20 @@ def rstudio_base_scripts(r_version): shiny_proxy_version = "1.1" shiny_sha256sum = "80f1e48f6c824be7ef9c843bb7911d4981ac7e8a963e0eff823936a8b28476ee" - # RStudio server has different builds based on wether OpenSSL 3 or 1.1 is available in the base # image. 3 is present Jammy+, 1.1 until then. Instead of hardcoding URLs based on distro, we actually # check for the dependency itself directly in the code below. You can find these URLs in # https://posit.co/download/rstudio-server/, toggling between Ubuntu 22 (for openssl3) vs earlier versions (openssl 1.1) # you may forget about openssl, but openssl never forgets you. - rstudio_openssl3_url = 'https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2022.12.0-353-amd64.deb' - rstudio_openssl3_sha256sum = 'a5aa2202786f9017a6de368a410488ea2e4fc6c739f78998977af214df0d6288' + rstudio_openssl3_url = "https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2022.12.0-353-amd64.deb" + rstudio_openssl3_sha256sum = ( + "a5aa2202786f9017a6de368a410488ea2e4fc6c739f78998977af214df0d6288" + ) - rstudio_openssl1_url = 'https://download2.rstudio.org/server/bionic/amd64/rstudio-server-2022.12.0-353-amd64.deb' - rstudio_openssl1_sha256sum = 'bb88e37328c304881e60d6205d7dac145525a5c2aaaf9da26f1cb625b7d47e6e' + rstudio_openssl1_url = "https://download2.rstudio.org/server/bionic/amd64/rstudio-server-2022.12.0-353-amd64.deb" + rstudio_openssl1_sha256sum = ( + "bb88e37328c304881e60d6205d7dac145525a5c2aaaf9da26f1cb625b7d47e6e" + ) rsession_proxy_version = "2.0.1" return [ From a6ccf815cc82fd3c371791373540aa0a0cf2b4de Mon Sep 17 00:00:00 2001 From: YuviPanda Date: Sat, 7 Jan 2023 01:55:06 -0800 Subject: [PATCH 099/171] Fix mismatched quotes --- repo2docker/buildpacks/_r_base.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/repo2docker/buildpacks/_r_base.py b/repo2docker/buildpacks/_r_base.py index 8bd7a9419..772b2d80c 100644 --- a/repo2docker/buildpacks/_r_base.py +++ b/repo2docker/buildpacks/_r_base.py @@ -47,7 +47,7 @@ def rstudio_base_scripts(r_version): fi && \ curl --silent --location --fail ${{RSTUDIO_URL}} > /tmp/rstudio.deb && \ curl --silent --location --fail {shiny_server_url} > /tmp/shiny.deb && \ - echo "${{RSTUDIO_HASH}} /tmp/rstudio.deb' | sha256sum -c - && \ + echo "${{RSTUDIO_HASH}} /tmp/rstudio.deb" | sha256sum -c - && \ echo '{shiny_sha256sum} /tmp/shiny.deb' | sha256sum -c - && \ apt install -y --no-install-recommends /tmp/rstudio.deb /tmp/shiny.deb && \ rm /tmp/*.deb && \ From 75a8bd74b21a7c4ffbced395bc2ff801e840a972 Mon Sep 17 00:00:00 2001 From: Sylvain Corlay Date: Wed, 11 Jan 2023 07:49:42 +0100 Subject: [PATCH 100/171] Upgrade to mamba 1.1 and enable rich SAT error messages --- repo2docker/buildpacks/conda/install-base-env.bash | 3 ++- tests/conda/py35-binder-dir/verify | 4 ++-- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/repo2docker/buildpacks/conda/install-base-env.bash b/repo2docker/buildpacks/conda/install-base-env.bash index 875fe3b16..e8b3bb3ed 100755 --- a/repo2docker/buildpacks/conda/install-base-env.bash +++ b/repo2docker/buildpacks/conda/install-base-env.bash @@ -5,7 +5,7 @@ set -ex cd $(dirname $0) -export MAMBA_VERSION=1.0.0 +export MAMBA_VERSION=1.1.0 export CONDA_VERSION=4.13.0 URL="https://anaconda.org/conda-forge/micromamba/${MAMBA_VERSION}/download/${CONDA_PLATFORM}/micromamba-${MAMBA_VERSION}-0.tar.bz2" @@ -34,6 +34,7 @@ channels: auto_update_conda: false show_channel_urls: true update_dependencies: false +experimental_sat_error_message: true # channel_priority: flexible EOT diff --git a/tests/conda/py35-binder-dir/verify b/tests/conda/py35-binder-dir/verify index 32e73c428..8bad344de 100755 --- a/tests/conda/py35-binder-dir/verify +++ b/tests/conda/py35-binder-dir/verify @@ -5,12 +5,12 @@ from subprocess import check_output assert sys.version_info[:2] == (3, 5), sys.version out = check_output(["micromamba", "--version"]).decode("utf8").strip() -assert out == "1.0.0", out +assert out == "1.1.0", out out = check_output(["mamba", "--version"]).decode("utf8").strip() assert ( out - == """mamba 1.0.0 + == """mamba 1.1.0 conda 4.13.0""" ), out From 348efa2efe0f5950df5965a612fa8ac25985ba0f Mon Sep 17 00:00:00 2001 From: Tim <37033036+TimStewartJ@users.noreply.github.com> Date: Sun, 15 Jan 2023 15:29:03 -0800 Subject: [PATCH 101/171] add conda env lib path to r config --- repo2docker/buildpacks/conda/__init__.py | 1 + 1 file changed, 1 insertion(+) diff --git a/repo2docker/buildpacks/conda/__init__.py b/repo2docker/buildpacks/conda/__init__.py index 66aff037a..f56a84ce9 100644 --- a/repo2docker/buildpacks/conda/__init__.py +++ b/repo2docker/buildpacks/conda/__init__.py @@ -396,6 +396,7 @@ def get_env_scripts(self): echo auth-none=1 >> /etc/rstudio/rserver.conf && \ echo auth-minimum-user-id=0 >> /etc/rstudio/rserver.conf && \ echo "rsession-which-r={env_prefix}/bin/R" >> /etc/rstudio/rserver.conf && \ + echo "rsession-ld-library-path={env_prefix}/lib" >> /etc/rstudio/rserver.conf && \ echo www-frame-origin=same >> /etc/rstudio/rserver.conf """, ), From 6e508d2b2369b67a16902cc3852daf11c4076e5a Mon Sep 17 00:00:00 2001 From: Jeremy Tuloup Date: Fri, 20 Jan 2023 16:37:44 +0100 Subject: [PATCH 102/171] Also install dev requirements on Gitpod --- .gitpod.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.gitpod.yml b/.gitpod.yml index 717449570..69e7aa86d 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -1,10 +1,12 @@ tasks: - init: | pip3 install sphinx-autobuild + pip3 install -r dev-requirements.txt pip3 install -r docs/requirements.txt pip3 install -e . command: | sphinx-autobuild docs/source/ docs/_build/html/ name: Sphinx preview + ports: - port: 8000 From 498cb68210260a8d563738d886b0d6f95923f9b6 Mon Sep 17 00:00:00 2001 From: Jeremy Tuloup Date: Fri, 20 Jan 2023 15:52:19 +0000 Subject: [PATCH 103/171] Update to `jupyter-resource-usage==0.7.0` --- .../conda/environment-linux-64.lock | 40 ++++++------ .../conda/environment-linux-aarch64.lock | 40 ++++++------ .../conda/environment.py-3.10-linux-64.lock | 63 +++++++++---------- .../environment.py-3.10-linux-aarch64.lock | 63 +++++++++---------- .../buildpacks/conda/environment.py-3.10.yml | 4 +- .../conda/environment.py-3.7-linux-64.lock | 40 ++++++------ .../environment.py-3.7-linux-aarch64.lock | 40 ++++++------ .../buildpacks/conda/environment.py-3.7.yml | 4 +- .../conda/environment.py-3.8-linux-64.lock | 63 +++++++++---------- .../environment.py-3.8-linux-aarch64.lock | 63 +++++++++---------- .../buildpacks/conda/environment.py-3.8.yml | 4 +- .../conda/environment.py-3.9-linux-64.lock | 63 +++++++++---------- .../environment.py-3.9-linux-aarch64.lock | 63 +++++++++---------- .../buildpacks/conda/environment.py-3.9.yml | 4 +- repo2docker/buildpacks/conda/environment.yml | 2 +- 15 files changed, 275 insertions(+), 281 deletions(-) diff --git a/repo2docker/buildpacks/conda/environment-linux-64.lock b/repo2docker/buildpacks/conda/environment-linux-64.lock index 541c2d19f..8a2809ea1 100644 --- a/repo2docker/buildpacks/conda/environment-linux-64.lock +++ b/repo2docker/buildpacks/conda/environment-linux-64.lock @@ -1,8 +1,8 @@ # AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY -# Frozen on 2023-01-01 11:29:43 UTC +# Frozen on 2023-01-20 15:37:02 UTC # Generated by conda-lock. # platform: linux-64 -# input_hash: f39cf3a86cdaeb58bee45974ccbdaf3fb51ad41f0bb6f3caf9340c5aad0dfa3b +# input_hash: cee196dc9fb70d2989f32b1256c94555f5d711492cbd4ce63c1a49ef58f5180f @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.12.7-ha878542_0.conda#ff9f73d45c4a07d6f424495288a26080 @@ -25,7 +25,7 @@ https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.3-h27087fc_1.tar.bz2#4 https://conda.anaconda.org/conda-forge/linux-64/openssl-3.0.7-h0b41bf4_1.conda#7adaac6ff98219bcb99b45e408b80f4e https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1 -https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.47.0-hff17c54_1.tar.bz2#2b7dbfa6988a41f9d23ba6d4f0e1d74e +https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.51.0-hff17c54_0.conda#dd682f0b6d65e75b2bc868fc8e93d87e https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.40.0-h753d276_0.tar.bz2#2e5f9a37d487e1019fd4d8113adb2f9f https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.10.0-hf14f497_3.tar.bz2#d85acad4b47dff4e3def14a769a97906 https://conda.anaconda.org/conda-forge/linux-64/pandoc-2.19.2-h32600fe_1.tar.bz2#35a82883468c85ac8bf41f083c1933cf @@ -58,7 +58,7 @@ https://conda.anaconda.org/conda-forge/noarch/jupyterlab_widgets-3.0.5-pyhd8ed1a https://conda.anaconda.org/conda-forge/linux-64/markupsafe-2.1.1-py37h540881e_1.tar.bz2#a9123517674ab0589d955a5adbf58573 https://conda.anaconda.org/conda-forge/noarch/mistune-2.0.4-pyhd8ed1ab_0.tar.bz2#78e0a90393b79b378b8ff6d32893d58a https://conda.anaconda.org/conda-forge/noarch/nest-asyncio-1.5.6-pyhd8ed1ab_0.tar.bz2#7b868f21adde0d9b8b38f9c16836589b -https://conda.anaconda.org/conda-forge/noarch/packaging-22.0-pyhd8ed1ab_0.conda#0e8e1bd93998978fc3125522266d12db +https://conda.anaconda.org/conda-forge/noarch/packaging-23.0-pyhd8ed1ab_0.conda#1ff2e3ca41f0ce16afec7190db28288b https://conda.anaconda.org/conda-forge/noarch/pamela-1.0.0-py_0.tar.bz2#36f6f18d2f3ae0c93d77a9dbedad08c3 https://conda.anaconda.org/conda-forge/noarch/pandocfilters-1.5.0-pyhd8ed1ab_0.tar.bz2#457c2c8c08e54905d6954e79cb5b5db9 https://conda.anaconda.org/conda-forge/noarch/parso-0.8.3-pyhd8ed1ab_0.tar.bz2#17a565a0c3899244e938cdf417e7b094 @@ -74,17 +74,17 @@ https://conda.anaconda.org/conda-forge/linux-64/pyrsistent-0.18.1-py37h540881e_1 https://conda.anaconda.org/conda-forge/linux-64/pysocks-1.7.1-py37h89c1867_5.tar.bz2#8c4b0563f96363ee99f1ab864616ac63 https://conda.anaconda.org/conda-forge/noarch/python-fastjsonschema-2.16.2-pyhd8ed1ab_0.tar.bz2#5fe4b6002f505336734ce92961b3e6a0 https://conda.anaconda.org/conda-forge/noarch/python-json-logger-2.0.4-pyhd8ed1ab_0.conda#6d1f4215f123c18aed06fb4104bcb11a -https://conda.anaconda.org/conda-forge/noarch/pytz-2022.7-pyhd8ed1ab_0.conda#c8d7e34ca76d6ecc03b84bedfd99d689 +https://conda.anaconda.org/conda-forge/noarch/pytz-2022.7.1-pyhd8ed1ab_0.conda#f59d49a7b464901cf714b9e7984d01a2 https://conda.anaconda.org/conda-forge/linux-64/pyzmq-24.0.1-py37h0c0c2a8_0.tar.bz2#732c98a38c84984262940c868793ebb4 https://conda.anaconda.org/conda-forge/linux-64/ruamel.yaml.clib-0.2.6-py37h540881e_1.tar.bz2#f3c703ac09e7810d6c9baec89e901fb5 https://conda.anaconda.org/conda-forge/noarch/send2trash-1.8.0-pyhd8ed1ab_0.tar.bz2#edab14119efe85c3bf131ad747e9005c -https://conda.anaconda.org/conda-forge/noarch/setuptools-65.6.3-pyhd8ed1ab_0.conda#9600fc9524d3f821e6a6d58c52f5bf5a +https://conda.anaconda.org/conda-forge/noarch/setuptools-66.0.0-pyhd8ed1ab_0.conda#88ec352fde1a5561ce5f93a302539f7f https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2#e5f25f8dbc060e9a8d912e432202afc2 https://conda.anaconda.org/conda-forge/noarch/sniffio-1.3.0-pyhd8ed1ab_0.tar.bz2#dd6cbc539e74cb1f430efbd4575b9303 https://conda.anaconda.org/conda-forge/noarch/soupsieve-2.3.2.post1-pyhd8ed1ab_0.tar.bz2#146f4541d643d48fc8a75cacf69f03ae https://conda.anaconda.org/conda-forge/noarch/tomli-2.0.1-pyhd8ed1ab_0.tar.bz2#5844808ffab9ebdb694585b50ba02a96 https://conda.anaconda.org/conda-forge/linux-64/tornado-6.2-py37h540881e_0.tar.bz2#2f0863ba6b29d1d2872b064dd697a492 -https://conda.anaconda.org/conda-forge/noarch/traitlets-5.8.0-pyhd8ed1ab_0.conda#75fa7ac3992a41e6a06102594bbf67d0 +https://conda.anaconda.org/conda-forge/noarch/traitlets-5.8.1-pyhd8ed1ab_0.conda#ef5179bcc6a9acc23b12ac92936e05ab https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.4.0-pyha770c72_0.tar.bz2#2d93b130d148d7fc77e583677792fc6a https://conda.anaconda.org/conda-forge/noarch/webencodings-0.5.1-py_1.tar.bz2#3563be4c5611a44210d9ba0c16113136 https://conda.anaconda.org/conda-forge/noarch/websocket-client-1.4.2-pyhd8ed1ab_0.tar.bz2#5309fca1777cfdd2d7ab582edb8cc41a @@ -98,14 +98,14 @@ https://conda.anaconda.org/conda-forge/noarch/beautifulsoup4-4.11.1-pyha770c72_0 https://conda.anaconda.org/conda-forge/noarch/bleach-5.0.1-pyhd8ed1ab_0.tar.bz2#1f5151d37e4a2b1137f81c89a3a769f2 https://conda.anaconda.org/conda-forge/linux-64/cffi-1.15.1-py37h43b0acd_1.tar.bz2#5111b64bdfdd72d85086ec49c952fe0d https://conda.anaconda.org/conda-forge/linux-64/importlib-metadata-4.11.4-py37h89c1867_0.tar.bz2#71107630527e4bd82932952351231efe -https://conda.anaconda.org/conda-forge/noarch/importlib_resources-5.10.1-pyhd8ed1ab_1.conda#5b48ca365913b08b819884bc21d4fb56 +https://conda.anaconda.org/conda-forge/noarch/importlib_resources-5.10.2-pyhd8ed1ab_0.conda#de76905f801c22fc43e624058574eab3 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e0b85a766..2c5fdb8b0 100644 --- a/repo2docker/buildpacks/conda/environment-linux-aarch64.lock +++ b/repo2docker/buildpacks/conda/environment-linux-aarch64.lock @@ -1,8 +1,8 @@ # AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY -# Frozen on 2023-01-01 11:29:53 UTC +# Frozen on 2023-01-20 15:38:19 UTC # Generated by conda-lock. # platform: linux-aarch64 -# input_hash: a623ebdc4f4a6b9c05e667ad83a83f99bc96451d4d23e680cd12966e0398a255 +# input_hash: cadb4a6d02f2ff0c65698515aa840b348774bdef253c8b11b4a1a1283bcf9d5e @EXPLICIT https://conda.anaconda.org/conda-forge/linux-aarch64/ca-certificates-2022.12.7-h4fd8a4c_0.conda#2450fbcaf65634e0d071e47e2b8487b4 https://conda.anaconda.org/conda-forge/linux-aarch64/ld_impl_linux-aarch64-2.39-h16cd69b_1.conda#9daf385ebefaea92087d3a315e398964 @@ -25,7 +25,7 @@ https://conda.anaconda.org/conda-forge/linux-aarch64/ncurses-6.3-headf329_1.tar. 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https://conda.anaconda.org/conda-forge/noarch/nbclassic-0.4.8-pyhd8ed1ab_0.tar.bz2#f4f150f83ed90a1b833e6081bbf38257 https://conda.anaconda.org/conda-forge/noarch/notebook-6.4.12-pyha770c72_0.tar.bz2#77fc67c5bbea44fd41e8bbe2ac82d1ad diff --git a/repo2docker/buildpacks/conda/environment.py-3.10.yml b/repo2docker/buildpacks/conda/environment.py-3.10.yml index c3207ec34..d379bdea9 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.10.yml +++ b/repo2docker/buildpacks/conda/environment.py-3.10.yml @@ -1,5 +1,5 @@ # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY -# Generated on 2023-01-01 11:31:15 UTC +# Generated on 2023-01-20 15:47:50 UTC channels: - conda-forge dependencies: @@ -8,7 +8,7 @@ dependencies: - pip - ipywidgets==8.0.2 - jupyter-offlinenotebook==0.2.2 -- jupyter-resource-usage==0.6.3 +- jupyter-resource-usage==0.7.0 - jupyterlab==3.4.8 - jupyterhub-singleuser==1.5.0 - notebook==6.4.12 diff --git a/repo2docker/buildpacks/conda/environment.py-3.7-linux-64.lock b/repo2docker/buildpacks/conda/environment.py-3.7-linux-64.lock index 541c2d19f..8a2809ea1 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.7-linux-64.lock +++ b/repo2docker/buildpacks/conda/environment.py-3.7-linux-64.lock @@ -1,8 +1,8 @@ # AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY -# Frozen on 2023-01-01 11:29:43 UTC +# Frozen on 2023-01-20 15:37:02 UTC # Generated by conda-lock. # platform: linux-64 -# input_hash: f39cf3a86cdaeb58bee45974ccbdaf3fb51ad41f0bb6f3caf9340c5aad0dfa3b +# input_hash: cee196dc9fb70d2989f32b1256c94555f5d711492cbd4ce63c1a49ef58f5180f @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.12.7-ha878542_0.conda#ff9f73d45c4a07d6f424495288a26080 @@ -25,7 +25,7 @@ https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.3-h27087fc_1.tar.bz2#4 https://conda.anaconda.org/conda-forge/linux-64/openssl-3.0.7-h0b41bf4_1.conda#7adaac6ff98219bcb99b45e408b80f4e https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0 https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1 -https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.47.0-hff17c54_1.tar.bz2#2b7dbfa6988a41f9d23ba6d4f0e1d74e +https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.51.0-hff17c54_0.conda#dd682f0b6d65e75b2bc868fc8e93d87e https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.40.0-h753d276_0.tar.bz2#2e5f9a37d487e1019fd4d8113adb2f9f https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.10.0-hf14f497_3.tar.bz2#d85acad4b47dff4e3def14a769a97906 https://conda.anaconda.org/conda-forge/linux-64/pandoc-2.19.2-h32600fe_1.tar.bz2#35a82883468c85ac8bf41f083c1933cf @@ -58,7 +58,7 @@ 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@@ -74,17 +74,17 @@ https://conda.anaconda.org/conda-forge/linux-64/pyrsistent-0.18.1-py37h540881e_1 https://conda.anaconda.org/conda-forge/linux-64/pysocks-1.7.1-py37h89c1867_5.tar.bz2#8c4b0563f96363ee99f1ab864616ac63 https://conda.anaconda.org/conda-forge/noarch/python-fastjsonschema-2.16.2-pyhd8ed1ab_0.tar.bz2#5fe4b6002f505336734ce92961b3e6a0 https://conda.anaconda.org/conda-forge/noarch/python-json-logger-2.0.4-pyhd8ed1ab_0.conda#6d1f4215f123c18aed06fb4104bcb11a -https://conda.anaconda.org/conda-forge/noarch/pytz-2022.7-pyhd8ed1ab_0.conda#c8d7e34ca76d6ecc03b84bedfd99d689 +https://conda.anaconda.org/conda-forge/noarch/pytz-2022.7.1-pyhd8ed1ab_0.conda#f59d49a7b464901cf714b9e7984d01a2 https://conda.anaconda.org/conda-forge/linux-64/pyzmq-24.0.1-py37h0c0c2a8_0.tar.bz2#732c98a38c84984262940c868793ebb4 https://conda.anaconda.org/conda-forge/linux-64/ruamel.yaml.clib-0.2.6-py37h540881e_1.tar.bz2#f3c703ac09e7810d6c9baec89e901fb5 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-https://conda.anaconda.org/conda-forge/noarch/traitlets-5.8.0-pyhd8ed1ab_0.conda#75fa7ac3992a41e6a06102594bbf67d0 +https://conda.anaconda.org/conda-forge/noarch/traitlets-5.8.1-pyhd8ed1ab_0.conda#ef5179bcc6a9acc23b12ac92936e05ab https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.4.0-pyha770c72_0.tar.bz2#2d93b130d148d7fc77e583677792fc6a https://conda.anaconda.org/conda-forge/noarch/webencodings-0.5.1-py_1.tar.bz2#3563be4c5611a44210d9ba0c16113136 https://conda.anaconda.org/conda-forge/noarch/websocket-client-1.4.2-pyhd8ed1ab_0.tar.bz2#5309fca1777cfdd2d7ab582edb8cc41a @@ -98,14 +98,14 @@ https://conda.anaconda.org/conda-forge/noarch/beautifulsoup4-4.11.1-pyha770c72_0 https://conda.anaconda.org/conda-forge/noarch/bleach-5.0.1-pyhd8ed1ab_0.tar.bz2#1f5151d37e4a2b1137f81c89a3a769f2 https://conda.anaconda.org/conda-forge/linux-64/cffi-1.15.1-py37h43b0acd_1.tar.bz2#5111b64bdfdd72d85086ec49c952fe0d 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@@ # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY -# Generated on 2023-01-01 11:29:43 UTC +# Generated on 2023-01-20 15:37:02 UTC channels: - conda-forge dependencies: @@ -8,7 +8,7 @@ dependencies: - pip - ipywidgets==8.0.2 - jupyter-offlinenotebook==0.2.2 -- jupyter-resource-usage==0.6.3 +- jupyter-resource-usage==0.7.0 - jupyterlab==3.4.8 - jupyterhub-singleuser==1.5.0 - notebook==6.4.12 diff --git a/repo2docker/buildpacks/conda/environment.py-3.8-linux-64.lock b/repo2docker/buildpacks/conda/environment.py-3.8-linux-64.lock index fd8b8c9b9..c5974bdf7 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.8-linux-64.lock +++ b/repo2docker/buildpacks/conda/environment.py-3.8-linux-64.lock @@ -1,8 +1,8 @@ # AUTO GENERATED FROM environment.py-3.8.yml, DO NOT MANUALLY MODIFY -# Frozen on 2023-01-01 11:30:13 UTC +# Frozen on 2023-01-20 15:40:41 UTC # Generated by conda-lock. # platform: linux-64 -# input_hash: 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https://conda.anaconda.org/conda-forge/noarch/notebook-shim-0.2.2-pyhd8ed1ab_0.tar.bz2#40be846cd4e78672a40e43db9dae753c https://conda.anaconda.org/conda-forge/noarch/nbclassic-0.4.8-pyhd8ed1ab_0.tar.bz2#f4f150f83ed90a1b833e6081bbf38257 https://conda.anaconda.org/conda-forge/noarch/notebook-6.4.12-pyha770c72_0.tar.bz2#77fc67c5bbea44fd41e8bbe2ac82d1ad diff --git a/repo2docker/buildpacks/conda/environment.py-3.8.yml b/repo2docker/buildpacks/conda/environment.py-3.8.yml index d7bd45da0..788294273 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.8.yml +++ b/repo2docker/buildpacks/conda/environment.py-3.8.yml @@ -1,5 +1,5 @@ # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY -# Generated on 2023-01-01 11:30:13 UTC +# Generated on 2023-01-20 15:40:41 UTC channels: - conda-forge dependencies: @@ -8,7 +8,7 @@ dependencies: - pip - ipywidgets==8.0.2 - jupyter-offlinenotebook==0.2.2 -- jupyter-resource-usage==0.6.3 +- jupyter-resource-usage==0.7.0 - jupyterlab==3.4.8 - jupyterhub-singleuser==1.5.0 - notebook==6.4.12 diff --git a/repo2docker/buildpacks/conda/environment.py-3.9-linux-64.lock b/repo2docker/buildpacks/conda/environment.py-3.9-linux-64.lock index 0138b6aff..e6909e694 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.9-linux-64.lock +++ b/repo2docker/buildpacks/conda/environment.py-3.9-linux-64.lock @@ -1,8 +1,8 @@ # AUTO GENERATED FROM environment.py-3.9.yml, DO NOT MANUALLY MODIFY -# Frozen on 2023-01-01 11:30:44 UTC +# Frozen on 2023-01-20 15:44:21 UTC # Generated by conda-lock. # platform: linux-64 -# input_hash: f0b7020f912d4c25c1482bcd0774212f9f4f041ec6eaea0b34676693729dcaf0 +# input_hash: cf2fc57d67e2975358e9bb39eb35d65c5a98a54b911f2aca3030cdb63900ce7e @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.12.7-ha878542_0.conda#ff9f73d45c4a07d6f424495288a26080 @@ -28,7 +28,7 @@ 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a/repo2docker/buildpacks/conda/environment.py-3.9.yml b/repo2docker/buildpacks/conda/environment.py-3.9.yml index a08e59022..9f986dfab 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.9.yml +++ b/repo2docker/buildpacks/conda/environment.py-3.9.yml @@ -1,5 +1,5 @@ # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY -# Generated on 2023-01-01 11:30:44 UTC +# Generated on 2023-01-20 15:44:21 UTC channels: - conda-forge dependencies: @@ -8,7 +8,7 @@ dependencies: - pip - ipywidgets==8.0.2 - jupyter-offlinenotebook==0.2.2 -- jupyter-resource-usage==0.6.3 +- jupyter-resource-usage==0.7.0 - jupyterlab==3.4.8 - jupyterhub-singleuser==1.5.0 - notebook==6.4.12 diff --git a/repo2docker/buildpacks/conda/environment.yml b/repo2docker/buildpacks/conda/environment.yml index fc3f00da1..68cc1b1e8 100644 --- a/repo2docker/buildpacks/conda/environment.yml +++ b/repo2docker/buildpacks/conda/environment.yml @@ -6,7 +6,7 @@ dependencies: - pip - ipywidgets==8.0.2 - jupyter-offlinenotebook==0.2.2 - - jupyter-resource-usage==0.6.3 + - jupyter-resource-usage==0.7.0 - jupyterlab==3.4.8 - jupyterhub-singleuser==1.5.0 - notebook==6.4.12 From 971caee73f8a22178b17cb086123c97b70c954ea Mon Sep 17 00:00:00 2001 From: Jeremy Tuloup Date: Wed, 18 Jan 2023 13:12:06 +0000 Subject: [PATCH 104/171] Bump to Node 18 --- repo2docker/buildpacks/conda/environment-linux-64.lock | 2 +- repo2docker/buildpacks/conda/environment-linux-aarch64.lock | 2 +- repo2docker/buildpacks/conda/environment.py-3.10-linux-64.lock | 2 +- .../buildpacks/conda/environment.py-3.10-linux-aarch64.lock | 2 +- repo2docker/buildpacks/conda/environment.py-3.10.yml | 2 +- repo2docker/buildpacks/conda/environment.py-3.7-linux-64.lock | 2 +- .../buildpacks/conda/environment.py-3.7-linux-aarch64.lock | 2 +- repo2docker/buildpacks/conda/environment.py-3.7.yml | 2 +- repo2docker/buildpacks/conda/environment.py-3.8-linux-64.lock | 2 +- .../buildpacks/conda/environment.py-3.8-linux-aarch64.lock | 2 +- repo2docker/buildpacks/conda/environment.py-3.8.yml | 2 +- repo2docker/buildpacks/conda/environment.py-3.9-linux-64.lock | 2 +- .../buildpacks/conda/environment.py-3.9-linux-aarch64.lock | 2 +- repo2docker/buildpacks/conda/environment.py-3.9.yml | 2 +- repo2docker/buildpacks/conda/environment.yml | 2 +- tests/base/node/verify | 2 +- 16 files changed, 16 insertions(+), 16 deletions(-) diff --git a/repo2docker/buildpacks/conda/environment-linux-64.lock b/repo2docker/buildpacks/conda/environment-linux-64.lock index 8a2809ea1..c8d7acb5b 100644 --- a/repo2docker/buildpacks/conda/environment-linux-64.lock +++ b/repo2docker/buildpacks/conda/environment-linux-64.lock @@ -34,7 +34,7 @@ https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.12-h27826a3_0.tar.bz2#5b8 https://conda.anaconda.org/conda-forge/linux-64/zeromq-4.3.4-h9c3ff4c_1.tar.bz2#21743a8d2ea0c8cfbbf8fe489b0347df https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-h166bdaf_4.tar.bz2#4b11e365c0275b808be78b30f904e295 https://conda.anaconda.org/conda-forge/linux-64/krb5-1.20.1-h81ceb04_0.conda#89a41adce7106749573d883b2f657d78 -https://conda.anaconda.org/conda-forge/linux-64/nodejs-16.17.1-h8839609_0.tar.bz2#1a19c5a76422549640a6824d6db189cf +https://conda.anaconda.org/conda-forge/linux-64/nodejs-18.12.1-h8839609_0.tar.bz2#305f25b78340b0f7b391a6919d1246f2 https://conda.anaconda.org/conda-forge/linux-64/sqlite-3.40.0-h4ff8645_0.tar.bz2#bb11803129cbbb53ed56f9506ff74145 https://conda.anaconda.org/conda-forge/linux-64/libcurl-7.87.0-hdc1c0ab_0.conda#bc302fa1cf8eda15c60f669b7524a320 https://conda.anaconda.org/conda-forge/linux-64/python-3.7.12-hf930737_100_cpython.tar.bz2#416558a6f46b7a1fa8db7d0e98aff56a diff --git a/repo2docker/buildpacks/conda/environment-linux-aarch64.lock b/repo2docker/buildpacks/conda/environment-linux-aarch64.lock index 2c5fdb8b0..c1028cea7 100644 --- a/repo2docker/buildpacks/conda/environment-linux-aarch64.lock +++ b/repo2docker/buildpacks/conda/environment-linux-aarch64.lock @@ -33,7 +33,7 @@ https://conda.anaconda.org/conda-forge/linux-aarch64/tk-8.6.12-hd8af866_0.tar.bz https://conda.anaconda.org/conda-forge/linux-aarch64/zeromq-4.3.4-h01db608_1.tar.bz2#dd56c9ce3f1f689a5e71941830349279 https://conda.anaconda.org/conda-forge/linux-aarch64/zlib-1.2.13-h4e544f5_4.tar.bz2#dc8395f4a79bb0b13ca7d855c72482d4 https://conda.anaconda.org/conda-forge/linux-aarch64/krb5-1.20.1-h113d92e_0.conda#c0ac34c76019d6ebfef2d47a5687459c -https://conda.anaconda.org/conda-forge/linux-aarch64/nodejs-16.17.1-h928fb59_0.tar.bz2#53413e70d6594c79b6b70d2038a62f1c +https://conda.anaconda.org/conda-forge/linux-aarch64/nodejs-18.12.1-h928fb59_0.tar.bz2#b0ff8fc996c6e50ac2b3e1a5dcc14d34 https://conda.anaconda.org/conda-forge/linux-aarch64/sqlite-3.40.0-h69ca7e5_0.tar.bz2#ef70a4737971a336d0dbb8913280e5ce https://conda.anaconda.org/conda-forge/linux-aarch64/libcurl-7.87.0-h6ad7c7a_0.conda#6e8310f3e0b523e64faa9012d4151ff0 https://conda.anaconda.org/conda-forge/linux-aarch64/python-3.7.12-h47f6e27_100_cpython.tar.bz2#d7b2c7500aa702c992c285854bef95a7 diff --git a/repo2docker/buildpacks/conda/environment.py-3.10-linux-64.lock b/repo2docker/buildpacks/conda/environment.py-3.10-linux-64.lock index 56d48649b..cd4585988 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.10-linux-64.lock +++ b/repo2docker/buildpacks/conda/environment.py-3.10-linux-64.lock @@ -37,7 +37,7 @@ https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.12-h27826a3_0.tar.bz2#5b8 https://conda.anaconda.org/conda-forge/linux-64/zeromq-4.3.4-h9c3ff4c_1.tar.bz2#21743a8d2ea0c8cfbbf8fe489b0347df https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-h166bdaf_4.tar.bz2#4b11e365c0275b808be78b30f904e295 https://conda.anaconda.org/conda-forge/linux-64/krb5-1.20.1-h81ceb04_0.conda#89a41adce7106749573d883b2f657d78 -https://conda.anaconda.org/conda-forge/linux-64/nodejs-16.17.1-h8839609_0.tar.bz2#1a19c5a76422549640a6824d6db189cf +https://conda.anaconda.org/conda-forge/linux-64/nodejs-18.12.1-h8839609_0.tar.bz2#305f25b78340b0f7b391a6919d1246f2 https://conda.anaconda.org/conda-forge/linux-64/python-3.10.8-h4a9ceb5_0_cpython.conda#be2a6d78752c2ab85f360ce37d2c64e2 https://conda.anaconda.org/conda-forge/noarch/async_generator-1.10-py_0.tar.bz2#d56c596e61b1c4952acf0a9920856c12 https://conda.anaconda.org/conda-forge/noarch/attrs-22.2.0-pyh71513ae_0.conda#8b76db7818a4e401ed4486c4c1635cd9 diff --git a/repo2docker/buildpacks/conda/environment.py-3.10-linux-aarch64.lock b/repo2docker/buildpacks/conda/environment.py-3.10-linux-aarch64.lock index 93c5b1ebe..f12710988 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.10-linux-aarch64.lock +++ b/repo2docker/buildpacks/conda/environment.py-3.10-linux-aarch64.lock @@ -36,7 +36,7 @@ https://conda.anaconda.org/conda-forge/linux-aarch64/tk-8.6.12-hd8af866_0.tar.bz https://conda.anaconda.org/conda-forge/linux-aarch64/zeromq-4.3.4-h01db608_1.tar.bz2#dd56c9ce3f1f689a5e71941830349279 https://conda.anaconda.org/conda-forge/linux-aarch64/zlib-1.2.13-h4e544f5_4.tar.bz2#dc8395f4a79bb0b13ca7d855c72482d4 https://conda.anaconda.org/conda-forge/linux-aarch64/krb5-1.20.1-h113d92e_0.conda#c0ac34c76019d6ebfef2d47a5687459c -https://conda.anaconda.org/conda-forge/linux-aarch64/nodejs-16.17.1-h928fb59_0.tar.bz2#53413e70d6594c79b6b70d2038a62f1c +https://conda.anaconda.org/conda-forge/linux-aarch64/nodejs-18.12.1-h928fb59_0.tar.bz2#b0ff8fc996c6e50ac2b3e1a5dcc14d34 https://conda.anaconda.org/conda-forge/linux-aarch64/python-3.10.8-hac3cb69_0_cpython.conda#2d1529dcafcc4ae83a6d2d020b1c604e https://conda.anaconda.org/conda-forge/noarch/async_generator-1.10-py_0.tar.bz2#d56c596e61b1c4952acf0a9920856c12 https://conda.anaconda.org/conda-forge/noarch/attrs-22.2.0-pyh71513ae_0.conda#8b76db7818a4e401ed4486c4c1635cd9 diff --git a/repo2docker/buildpacks/conda/environment.py-3.10.yml b/repo2docker/buildpacks/conda/environment.py-3.10.yml index d379bdea9..b1888ca7a 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.10.yml +++ b/repo2docker/buildpacks/conda/environment.py-3.10.yml @@ -4,7 +4,7 @@ channels: - conda-forge dependencies: - python=3.10.* -- nodejs=16 +- nodejs=18 - pip - ipywidgets==8.0.2 - jupyter-offlinenotebook==0.2.2 diff --git a/repo2docker/buildpacks/conda/environment.py-3.7-linux-64.lock b/repo2docker/buildpacks/conda/environment.py-3.7-linux-64.lock index 8a2809ea1..c8d7acb5b 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.7-linux-64.lock +++ b/repo2docker/buildpacks/conda/environment.py-3.7-linux-64.lock @@ -34,7 +34,7 @@ https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.12-h27826a3_0.tar.bz2#5b8 https://conda.anaconda.org/conda-forge/linux-64/zeromq-4.3.4-h9c3ff4c_1.tar.bz2#21743a8d2ea0c8cfbbf8fe489b0347df https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-h166bdaf_4.tar.bz2#4b11e365c0275b808be78b30f904e295 https://conda.anaconda.org/conda-forge/linux-64/krb5-1.20.1-h81ceb04_0.conda#89a41adce7106749573d883b2f657d78 -https://conda.anaconda.org/conda-forge/linux-64/nodejs-16.17.1-h8839609_0.tar.bz2#1a19c5a76422549640a6824d6db189cf +https://conda.anaconda.org/conda-forge/linux-64/nodejs-18.12.1-h8839609_0.tar.bz2#305f25b78340b0f7b391a6919d1246f2 https://conda.anaconda.org/conda-forge/linux-64/sqlite-3.40.0-h4ff8645_0.tar.bz2#bb11803129cbbb53ed56f9506ff74145 https://conda.anaconda.org/conda-forge/linux-64/libcurl-7.87.0-hdc1c0ab_0.conda#bc302fa1cf8eda15c60f669b7524a320 https://conda.anaconda.org/conda-forge/linux-64/python-3.7.12-hf930737_100_cpython.tar.bz2#416558a6f46b7a1fa8db7d0e98aff56a diff --git a/repo2docker/buildpacks/conda/environment.py-3.7-linux-aarch64.lock b/repo2docker/buildpacks/conda/environment.py-3.7-linux-aarch64.lock index 2c5fdb8b0..c1028cea7 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.7-linux-aarch64.lock +++ b/repo2docker/buildpacks/conda/environment.py-3.7-linux-aarch64.lock @@ -33,7 +33,7 @@ https://conda.anaconda.org/conda-forge/linux-aarch64/tk-8.6.12-hd8af866_0.tar.bz https://conda.anaconda.org/conda-forge/linux-aarch64/zeromq-4.3.4-h01db608_1.tar.bz2#dd56c9ce3f1f689a5e71941830349279 https://conda.anaconda.org/conda-forge/linux-aarch64/zlib-1.2.13-h4e544f5_4.tar.bz2#dc8395f4a79bb0b13ca7d855c72482d4 https://conda.anaconda.org/conda-forge/linux-aarch64/krb5-1.20.1-h113d92e_0.conda#c0ac34c76019d6ebfef2d47a5687459c -https://conda.anaconda.org/conda-forge/linux-aarch64/nodejs-16.17.1-h928fb59_0.tar.bz2#53413e70d6594c79b6b70d2038a62f1c +https://conda.anaconda.org/conda-forge/linux-aarch64/nodejs-18.12.1-h928fb59_0.tar.bz2#b0ff8fc996c6e50ac2b3e1a5dcc14d34 https://conda.anaconda.org/conda-forge/linux-aarch64/sqlite-3.40.0-h69ca7e5_0.tar.bz2#ef70a4737971a336d0dbb8913280e5ce https://conda.anaconda.org/conda-forge/linux-aarch64/libcurl-7.87.0-h6ad7c7a_0.conda#6e8310f3e0b523e64faa9012d4151ff0 https://conda.anaconda.org/conda-forge/linux-aarch64/python-3.7.12-h47f6e27_100_cpython.tar.bz2#d7b2c7500aa702c992c285854bef95a7 diff --git a/repo2docker/buildpacks/conda/environment.py-3.7.yml b/repo2docker/buildpacks/conda/environment.py-3.7.yml index 1cd52b808..da41a56d3 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.7.yml +++ b/repo2docker/buildpacks/conda/environment.py-3.7.yml @@ -4,7 +4,7 @@ channels: - conda-forge dependencies: - python=3.7.* -- nodejs=16 +- nodejs=18 - pip - ipywidgets==8.0.2 - jupyter-offlinenotebook==0.2.2 diff --git a/repo2docker/buildpacks/conda/environment.py-3.8-linux-64.lock b/repo2docker/buildpacks/conda/environment.py-3.8-linux-64.lock index c5974bdf7..7bde3a9bc 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.8-linux-64.lock +++ b/repo2docker/buildpacks/conda/environment.py-3.8-linux-64.lock @@ -36,7 +36,7 @@ https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.12-h27826a3_0.tar.bz2#5b8 https://conda.anaconda.org/conda-forge/linux-64/zeromq-4.3.4-h9c3ff4c_1.tar.bz2#21743a8d2ea0c8cfbbf8fe489b0347df https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-h166bdaf_4.tar.bz2#4b11e365c0275b808be78b30f904e295 https://conda.anaconda.org/conda-forge/linux-64/krb5-1.20.1-h81ceb04_0.conda#89a41adce7106749573d883b2f657d78 -https://conda.anaconda.org/conda-forge/linux-64/nodejs-16.17.1-h8839609_0.tar.bz2#1a19c5a76422549640a6824d6db189cf +https://conda.anaconda.org/conda-forge/linux-64/nodejs-18.12.1-h8839609_0.tar.bz2#305f25b78340b0f7b391a6919d1246f2 https://conda.anaconda.org/conda-forge/linux-64/python-3.8.15-h4a9ceb5_0_cpython.conda#dc29a8a79d0f2c80004cc06d3190104f https://conda.anaconda.org/conda-forge/noarch/async_generator-1.10-py_0.tar.bz2#d56c596e61b1c4952acf0a9920856c12 https://conda.anaconda.org/conda-forge/noarch/attrs-22.2.0-pyh71513ae_0.conda#8b76db7818a4e401ed4486c4c1635cd9 diff --git a/repo2docker/buildpacks/conda/environment.py-3.8-linux-aarch64.lock b/repo2docker/buildpacks/conda/environment.py-3.8-linux-aarch64.lock index c96550748..6f1e124ef 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.8-linux-aarch64.lock +++ b/repo2docker/buildpacks/conda/environment.py-3.8-linux-aarch64.lock @@ -35,7 +35,7 @@ https://conda.anaconda.org/conda-forge/linux-aarch64/tk-8.6.12-hd8af866_0.tar.bz https://conda.anaconda.org/conda-forge/linux-aarch64/zeromq-4.3.4-h01db608_1.tar.bz2#dd56c9ce3f1f689a5e71941830349279 https://conda.anaconda.org/conda-forge/linux-aarch64/zlib-1.2.13-h4e544f5_4.tar.bz2#dc8395f4a79bb0b13ca7d855c72482d4 https://conda.anaconda.org/conda-forge/linux-aarch64/krb5-1.20.1-h113d92e_0.conda#c0ac34c76019d6ebfef2d47a5687459c -https://conda.anaconda.org/conda-forge/linux-aarch64/nodejs-16.17.1-h928fb59_0.tar.bz2#53413e70d6594c79b6b70d2038a62f1c +https://conda.anaconda.org/conda-forge/linux-aarch64/nodejs-18.12.1-h928fb59_0.tar.bz2#b0ff8fc996c6e50ac2b3e1a5dcc14d34 https://conda.anaconda.org/conda-forge/linux-aarch64/python-3.8.15-hac3cb69_0_cpython.conda#0b32f8b75efd53332d5a29b7afe3715c https://conda.anaconda.org/conda-forge/noarch/async_generator-1.10-py_0.tar.bz2#d56c596e61b1c4952acf0a9920856c12 https://conda.anaconda.org/conda-forge/noarch/attrs-22.2.0-pyh71513ae_0.conda#8b76db7818a4e401ed4486c4c1635cd9 diff --git a/repo2docker/buildpacks/conda/environment.py-3.8.yml b/repo2docker/buildpacks/conda/environment.py-3.8.yml index 788294273..b122a9550 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.8.yml +++ b/repo2docker/buildpacks/conda/environment.py-3.8.yml @@ -4,7 +4,7 @@ channels: - conda-forge dependencies: - python=3.8.* -- nodejs=16 +- nodejs=18 - pip - ipywidgets==8.0.2 - jupyter-offlinenotebook==0.2.2 diff --git a/repo2docker/buildpacks/conda/environment.py-3.9-linux-64.lock b/repo2docker/buildpacks/conda/environment.py-3.9-linux-64.lock index e6909e694..b577d7606 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.9-linux-64.lock +++ b/repo2docker/buildpacks/conda/environment.py-3.9-linux-64.lock @@ -37,7 +37,7 @@ https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.12-h27826a3_0.tar.bz2#5b8 https://conda.anaconda.org/conda-forge/linux-64/zeromq-4.3.4-h9c3ff4c_1.tar.bz2#21743a8d2ea0c8cfbbf8fe489b0347df https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-h166bdaf_4.tar.bz2#4b11e365c0275b808be78b30f904e295 https://conda.anaconda.org/conda-forge/linux-64/krb5-1.20.1-h81ceb04_0.conda#89a41adce7106749573d883b2f657d78 -https://conda.anaconda.org/conda-forge/linux-64/nodejs-16.17.1-h8839609_0.tar.bz2#1a19c5a76422549640a6824d6db189cf +https://conda.anaconda.org/conda-forge/linux-64/nodejs-18.12.1-h8839609_0.tar.bz2#305f25b78340b0f7b391a6919d1246f2 https://conda.anaconda.org/conda-forge/linux-64/python-3.9.15-hba424b6_0_cpython.conda#7b9485fce17fac2dd4aca6117a9936c2 https://conda.anaconda.org/conda-forge/noarch/async_generator-1.10-py_0.tar.bz2#d56c596e61b1c4952acf0a9920856c12 https://conda.anaconda.org/conda-forge/noarch/attrs-22.2.0-pyh71513ae_0.conda#8b76db7818a4e401ed4486c4c1635cd9 diff --git a/repo2docker/buildpacks/conda/environment.py-3.9-linux-aarch64.lock b/repo2docker/buildpacks/conda/environment.py-3.9-linux-aarch64.lock index dadce2151..8d5e8f66d 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.9-linux-aarch64.lock +++ b/repo2docker/buildpacks/conda/environment.py-3.9-linux-aarch64.lock @@ -36,7 +36,7 @@ https://conda.anaconda.org/conda-forge/linux-aarch64/tk-8.6.12-hd8af866_0.tar.bz https://conda.anaconda.org/conda-forge/linux-aarch64/zeromq-4.3.4-h01db608_1.tar.bz2#dd56c9ce3f1f689a5e71941830349279 https://conda.anaconda.org/conda-forge/linux-aarch64/zlib-1.2.13-h4e544f5_4.tar.bz2#dc8395f4a79bb0b13ca7d855c72482d4 https://conda.anaconda.org/conda-forge/linux-aarch64/krb5-1.20.1-h113d92e_0.conda#c0ac34c76019d6ebfef2d47a5687459c -https://conda.anaconda.org/conda-forge/linux-aarch64/nodejs-16.17.1-h928fb59_0.tar.bz2#53413e70d6594c79b6b70d2038a62f1c +https://conda.anaconda.org/conda-forge/linux-aarch64/nodejs-18.12.1-h928fb59_0.tar.bz2#b0ff8fc996c6e50ac2b3e1a5dcc14d34 https://conda.anaconda.org/conda-forge/linux-aarch64/python-3.9.15-hcd6f746_0_cpython.conda#4f20c6aad727bf0e2c9bb13a82f9a5fd https://conda.anaconda.org/conda-forge/noarch/async_generator-1.10-py_0.tar.bz2#d56c596e61b1c4952acf0a9920856c12 https://conda.anaconda.org/conda-forge/noarch/attrs-22.2.0-pyh71513ae_0.conda#8b76db7818a4e401ed4486c4c1635cd9 diff --git a/repo2docker/buildpacks/conda/environment.py-3.9.yml b/repo2docker/buildpacks/conda/environment.py-3.9.yml index 9f986dfab..e2857b69e 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.9.yml +++ b/repo2docker/buildpacks/conda/environment.py-3.9.yml @@ -4,7 +4,7 @@ channels: - conda-forge dependencies: - python=3.9.* -- nodejs=16 +- nodejs=18 - pip - ipywidgets==8.0.2 - jupyter-offlinenotebook==0.2.2 diff --git a/repo2docker/buildpacks/conda/environment.yml b/repo2docker/buildpacks/conda/environment.yml index 68cc1b1e8..3245f58c0 100644 --- a/repo2docker/buildpacks/conda/environment.yml +++ b/repo2docker/buildpacks/conda/environment.yml @@ -2,7 +2,7 @@ channels: - conda-forge dependencies: - python=3.7 - - nodejs=16 + - nodejs=18 - pip - ipywidgets==8.0.2 - jupyter-offlinenotebook==0.2.2 diff --git a/tests/base/node/verify b/tests/base/node/verify index 7a4ba351a..555426126 100755 --- a/tests/base/node/verify +++ b/tests/base/node/verify @@ -5,7 +5,7 @@ set -ex # check node system package and its version which node node --version -node --version | grep v16 +node --version | grep v18 which npm npm --version From 32fada9b0e216adf43fa167b8ba17f499f519eb8 Mon Sep 17 00:00:00 2001 From: Jeremy Tuloup Date: Mon, 23 Jan 2023 12:13:34 +0000 Subject: [PATCH 105/171] Refreeze --- repo2docker/buildpacks/conda/environment-linux-64.lock | 6 +++--- repo2docker/buildpacks/conda/environment-linux-aarch64.lock | 6 +++--- .../buildpacks/conda/environment.py-3.10-linux-64.lock | 6 +++--- .../buildpacks/conda/environment.py-3.10-linux-aarch64.lock | 6 +++--- repo2docker/buildpacks/conda/environment.py-3.10.yml | 2 +- .../buildpacks/conda/environment.py-3.7-linux-64.lock | 6 +++--- .../buildpacks/conda/environment.py-3.7-linux-aarch64.lock | 6 +++--- repo2docker/buildpacks/conda/environment.py-3.7.yml | 2 +- .../buildpacks/conda/environment.py-3.8-linux-64.lock | 6 +++--- .../buildpacks/conda/environment.py-3.8-linux-aarch64.lock | 6 +++--- repo2docker/buildpacks/conda/environment.py-3.8.yml | 2 +- .../buildpacks/conda/environment.py-3.9-linux-64.lock | 6 +++--- .../buildpacks/conda/environment.py-3.9-linux-aarch64.lock | 6 +++--- repo2docker/buildpacks/conda/environment.py-3.9.yml | 2 +- 14 files changed, 34 insertions(+), 34 deletions(-) diff --git a/repo2docker/buildpacks/conda/environment-linux-64.lock b/repo2docker/buildpacks/conda/environment-linux-64.lock index c8d7acb5b..84f3a5bc9 100644 --- a/repo2docker/buildpacks/conda/environment-linux-64.lock +++ b/repo2docker/buildpacks/conda/environment-linux-64.lock @@ -1,8 +1,8 @@ # AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY -# Frozen on 2023-01-20 15:37:02 UTC +# Frozen on 2023-01-23 11:59:03 UTC # Generated by conda-lock. # platform: linux-64 -# input_hash: cee196dc9fb70d2989f32b1256c94555f5d711492cbd4ce63c1a49ef58f5180f +# input_hash: 3b780a798011d21422fbbea52f1c94325fc806c944f506d41d0bdf397b93c604 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.12.7-ha878542_0.conda#ff9f73d45c4a07d6f424495288a26080 @@ -78,7 +78,7 @@ https://conda.anaconda.org/conda-forge/noarch/pytz-2022.7.1-pyhd8ed1ab_0.conda#f https://conda.anaconda.org/conda-forge/linux-64/pyzmq-24.0.1-py37h0c0c2a8_0.tar.bz2#732c98a38c84984262940c868793ebb4 https://conda.anaconda.org/conda-forge/linux-64/ruamel.yaml.clib-0.2.6-py37h540881e_1.tar.bz2#f3c703ac09e7810d6c9baec89e901fb5 https://conda.anaconda.org/conda-forge/noarch/send2trash-1.8.0-pyhd8ed1ab_0.tar.bz2#edab14119efe85c3bf131ad747e9005c -https://conda.anaconda.org/conda-forge/noarch/setuptools-66.0.0-pyhd8ed1ab_0.conda#88ec352fde1a5561ce5f93a302539f7f +https://conda.anaconda.org/conda-forge/noarch/setuptools-66.1.1-pyhd8ed1ab_0.conda#9467d520d1457018e055bbbfdf9b7567 https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2#e5f25f8dbc060e9a8d912e432202afc2 https://conda.anaconda.org/conda-forge/noarch/sniffio-1.3.0-pyhd8ed1ab_0.tar.bz2#dd6cbc539e74cb1f430efbd4575b9303 https://conda.anaconda.org/conda-forge/noarch/soupsieve-2.3.2.post1-pyhd8ed1ab_0.tar.bz2#146f4541d643d48fc8a75cacf69f03ae diff --git a/repo2docker/buildpacks/conda/environment-linux-aarch64.lock b/repo2docker/buildpacks/conda/environment-linux-aarch64.lock index c1028cea7..ed64b223c 100644 --- a/repo2docker/buildpacks/conda/environment-linux-aarch64.lock +++ b/repo2docker/buildpacks/conda/environment-linux-aarch64.lock @@ -1,8 +1,8 @@ # AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY -# Frozen on 2023-01-20 15:38:19 UTC +# Frozen on 2023-01-23 12:00:09 UTC # Generated by conda-lock. # platform: linux-aarch64 -# input_hash: cadb4a6d02f2ff0c65698515aa840b348774bdef253c8b11b4a1a1283bcf9d5e +# input_hash: 0a4a7f1713025e05325e2cb2a1336c042deaeb35413c3a951b07a3c8e06390a6 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-aarch64/ca-certificates-2022.12.7-h4fd8a4c_0.conda#2450fbcaf65634e0d071e47e2b8487b4 https://conda.anaconda.org/conda-forge/linux-aarch64/ld_impl_linux-aarch64-2.39-h16cd69b_1.conda#9daf385ebefaea92087d3a315e398964 @@ -77,7 +77,7 @@ https://conda.anaconda.org/conda-forge/noarch/pytz-2022.7.1-pyhd8ed1ab_0.conda#f https://conda.anaconda.org/conda-forge/linux-aarch64/pyzmq-24.0.1-py37h7cb28e0_0.tar.bz2#97e6c8c18201d08a2eb5f87ce28cb55e https://conda.anaconda.org/conda-forge/linux-aarch64/ruamel.yaml.clib-0.2.6-py37h795501a_1.tar.bz2#65038418d32470b70045205dd1bd7579 https://conda.anaconda.org/conda-forge/noarch/send2trash-1.8.0-pyhd8ed1ab_0.tar.bz2#edab14119efe85c3bf131ad747e9005c -https://conda.anaconda.org/conda-forge/noarch/setuptools-66.0.0-pyhd8ed1ab_0.conda#88ec352fde1a5561ce5f93a302539f7f +https://conda.anaconda.org/conda-forge/noarch/setuptools-66.1.1-pyhd8ed1ab_0.conda#9467d520d1457018e055bbbfdf9b7567 https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2#e5f25f8dbc060e9a8d912e432202afc2 https://conda.anaconda.org/conda-forge/noarch/sniffio-1.3.0-pyhd8ed1ab_0.tar.bz2#dd6cbc539e74cb1f430efbd4575b9303 https://conda.anaconda.org/conda-forge/noarch/soupsieve-2.3.2.post1-pyhd8ed1ab_0.tar.bz2#146f4541d643d48fc8a75cacf69f03ae diff --git a/repo2docker/buildpacks/conda/environment.py-3.10-linux-64.lock b/repo2docker/buildpacks/conda/environment.py-3.10-linux-64.lock index cd4585988..7e92bdc0d 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.10-linux-64.lock +++ b/repo2docker/buildpacks/conda/environment.py-3.10-linux-64.lock @@ -1,8 +1,8 @@ # AUTO GENERATED FROM environment.py-3.10.yml, DO NOT MANUALLY MODIFY -# Frozen on 2023-01-20 15:47:50 UTC +# Frozen on 2023-01-23 12:08:19 UTC # Generated by conda-lock. # platform: linux-64 -# input_hash: ad5bb61470d67b72818e63bd0fc00bccaa4e95fe982c2e73381eaeacbc00a613 +# input_hash: a3c35e1cf5cf3f900f8a304aa0b72221317c0c98cea5f5f807e9f50a631a6799 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.12.7-ha878542_0.conda#ff9f73d45c4a07d6f424495288a26080 @@ -81,7 +81,7 @@ https://conda.anaconda.org/conda-forge/noarch/pytz-2022.7.1-pyhd8ed1ab_0.conda#f https://conda.anaconda.org/conda-forge/linux-64/pyzmq-25.0.0-py310h059b190_0.conda#125d2a047e37a0ff0676912c91a622ae https://conda.anaconda.org/conda-forge/linux-64/ruamel.yaml.clib-0.2.7-py310h1fa729e_1.conda#2f9b517412af46255cef5e53a22c264e https://conda.anaconda.org/conda-forge/noarch/send2trash-1.8.0-pyhd8ed1ab_0.tar.bz2#edab14119efe85c3bf131ad747e9005c -https://conda.anaconda.org/conda-forge/noarch/setuptools-66.0.0-pyhd8ed1ab_0.conda#88ec352fde1a5561ce5f93a302539f7f +https://conda.anaconda.org/conda-forge/noarch/setuptools-66.1.1-pyhd8ed1ab_0.conda#9467d520d1457018e055bbbfdf9b7567 https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2#e5f25f8dbc060e9a8d912e432202afc2 https://conda.anaconda.org/conda-forge/noarch/sniffio-1.3.0-pyhd8ed1ab_0.tar.bz2#dd6cbc539e74cb1f430efbd4575b9303 https://conda.anaconda.org/conda-forge/noarch/soupsieve-2.3.2.post1-pyhd8ed1ab_0.tar.bz2#146f4541d643d48fc8a75cacf69f03ae diff --git a/repo2docker/buildpacks/conda/environment.py-3.10-linux-aarch64.lock b/repo2docker/buildpacks/conda/environment.py-3.10-linux-aarch64.lock index f12710988..a9c2ef413 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.10-linux-aarch64.lock +++ b/repo2docker/buildpacks/conda/environment.py-3.10-linux-aarch64.lock @@ -1,8 +1,8 @@ # AUTO GENERATED FROM environment.py-3.10.yml, DO NOT MANUALLY MODIFY -# Frozen on 2023-01-20 15:49:08 UTC +# Frozen on 2023-01-23 12:09:22 UTC # Generated by conda-lock. # platform: linux-aarch64 -# input_hash: d4619e9db1f41ca736489466f5413db9e20bfa062d7773fd079e30720fc2fb5b +# input_hash: 1d93d4ce5d477d06c8dfeffbc518efe25e14cb1cdb318f4a421b8392b591d068 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-aarch64/ca-certificates-2022.12.7-h4fd8a4c_0.conda#2450fbcaf65634e0d071e47e2b8487b4 https://conda.anaconda.org/conda-forge/linux-aarch64/ld_impl_linux-aarch64-2.39-h16cd69b_1.conda#9daf385ebefaea92087d3a315e398964 @@ -80,7 +80,7 @@ https://conda.anaconda.org/conda-forge/noarch/pytz-2022.7.1-pyhd8ed1ab_0.conda#f https://conda.anaconda.org/conda-forge/linux-aarch64/pyzmq-25.0.0-py310h1438264_0.conda#c1fc6b100d824f9431564e5c26943ee9 https://conda.anaconda.org/conda-forge/linux-aarch64/ruamel.yaml.clib-0.2.7-py310hb89b984_1.conda#89972c78c36ed3261c22bde7c012be03 https://conda.anaconda.org/conda-forge/noarch/send2trash-1.8.0-pyhd8ed1ab_0.tar.bz2#edab14119efe85c3bf131ad747e9005c -https://conda.anaconda.org/conda-forge/noarch/setuptools-66.0.0-pyhd8ed1ab_0.conda#88ec352fde1a5561ce5f93a302539f7f +https://conda.anaconda.org/conda-forge/noarch/setuptools-66.1.1-pyhd8ed1ab_0.conda#9467d520d1457018e055bbbfdf9b7567 https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2#e5f25f8dbc060e9a8d912e432202afc2 https://conda.anaconda.org/conda-forge/noarch/sniffio-1.3.0-pyhd8ed1ab_0.tar.bz2#dd6cbc539e74cb1f430efbd4575b9303 https://conda.anaconda.org/conda-forge/noarch/soupsieve-2.3.2.post1-pyhd8ed1ab_0.tar.bz2#146f4541d643d48fc8a75cacf69f03ae diff --git a/repo2docker/buildpacks/conda/environment.py-3.10.yml b/repo2docker/buildpacks/conda/environment.py-3.10.yml index b1888ca7a..c6500cee7 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.10.yml +++ b/repo2docker/buildpacks/conda/environment.py-3.10.yml @@ -1,5 +1,5 @@ # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY -# Generated on 2023-01-20 15:47:50 UTC +# Generated on 2023-01-23 12:08:19 UTC channels: - conda-forge dependencies: diff --git a/repo2docker/buildpacks/conda/environment.py-3.7-linux-64.lock b/repo2docker/buildpacks/conda/environment.py-3.7-linux-64.lock index c8d7acb5b..84f3a5bc9 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.7-linux-64.lock +++ b/repo2docker/buildpacks/conda/environment.py-3.7-linux-64.lock @@ -1,8 +1,8 @@ # AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY -# Frozen on 2023-01-20 15:37:02 UTC +# Frozen on 2023-01-23 11:59:03 UTC # Generated by conda-lock. # platform: linux-64 -# input_hash: cee196dc9fb70d2989f32b1256c94555f5d711492cbd4ce63c1a49ef58f5180f +# input_hash: 3b780a798011d21422fbbea52f1c94325fc806c944f506d41d0bdf397b93c604 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.12.7-ha878542_0.conda#ff9f73d45c4a07d6f424495288a26080 @@ -78,7 +78,7 @@ https://conda.anaconda.org/conda-forge/noarch/pytz-2022.7.1-pyhd8ed1ab_0.conda#f https://conda.anaconda.org/conda-forge/linux-64/pyzmq-24.0.1-py37h0c0c2a8_0.tar.bz2#732c98a38c84984262940c868793ebb4 https://conda.anaconda.org/conda-forge/linux-64/ruamel.yaml.clib-0.2.6-py37h540881e_1.tar.bz2#f3c703ac09e7810d6c9baec89e901fb5 https://conda.anaconda.org/conda-forge/noarch/send2trash-1.8.0-pyhd8ed1ab_0.tar.bz2#edab14119efe85c3bf131ad747e9005c -https://conda.anaconda.org/conda-forge/noarch/setuptools-66.0.0-pyhd8ed1ab_0.conda#88ec352fde1a5561ce5f93a302539f7f +https://conda.anaconda.org/conda-forge/noarch/setuptools-66.1.1-pyhd8ed1ab_0.conda#9467d520d1457018e055bbbfdf9b7567 https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2#e5f25f8dbc060e9a8d912e432202afc2 https://conda.anaconda.org/conda-forge/noarch/sniffio-1.3.0-pyhd8ed1ab_0.tar.bz2#dd6cbc539e74cb1f430efbd4575b9303 https://conda.anaconda.org/conda-forge/noarch/soupsieve-2.3.2.post1-pyhd8ed1ab_0.tar.bz2#146f4541d643d48fc8a75cacf69f03ae diff --git a/repo2docker/buildpacks/conda/environment.py-3.7-linux-aarch64.lock b/repo2docker/buildpacks/conda/environment.py-3.7-linux-aarch64.lock index c1028cea7..ed64b223c 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.7-linux-aarch64.lock +++ b/repo2docker/buildpacks/conda/environment.py-3.7-linux-aarch64.lock @@ -1,8 +1,8 @@ # AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY -# Frozen on 2023-01-20 15:38:19 UTC +# Frozen on 2023-01-23 12:00:09 UTC # Generated by conda-lock. # platform: linux-aarch64 -# input_hash: cadb4a6d02f2ff0c65698515aa840b348774bdef253c8b11b4a1a1283bcf9d5e +# input_hash: 0a4a7f1713025e05325e2cb2a1336c042deaeb35413c3a951b07a3c8e06390a6 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-aarch64/ca-certificates-2022.12.7-h4fd8a4c_0.conda#2450fbcaf65634e0d071e47e2b8487b4 https://conda.anaconda.org/conda-forge/linux-aarch64/ld_impl_linux-aarch64-2.39-h16cd69b_1.conda#9daf385ebefaea92087d3a315e398964 @@ -77,7 +77,7 @@ https://conda.anaconda.org/conda-forge/noarch/pytz-2022.7.1-pyhd8ed1ab_0.conda#f https://conda.anaconda.org/conda-forge/linux-aarch64/pyzmq-24.0.1-py37h7cb28e0_0.tar.bz2#97e6c8c18201d08a2eb5f87ce28cb55e https://conda.anaconda.org/conda-forge/linux-aarch64/ruamel.yaml.clib-0.2.6-py37h795501a_1.tar.bz2#65038418d32470b70045205dd1bd7579 https://conda.anaconda.org/conda-forge/noarch/send2trash-1.8.0-pyhd8ed1ab_0.tar.bz2#edab14119efe85c3bf131ad747e9005c -https://conda.anaconda.org/conda-forge/noarch/setuptools-66.0.0-pyhd8ed1ab_0.conda#88ec352fde1a5561ce5f93a302539f7f +https://conda.anaconda.org/conda-forge/noarch/setuptools-66.1.1-pyhd8ed1ab_0.conda#9467d520d1457018e055bbbfdf9b7567 https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2#e5f25f8dbc060e9a8d912e432202afc2 https://conda.anaconda.org/conda-forge/noarch/sniffio-1.3.0-pyhd8ed1ab_0.tar.bz2#dd6cbc539e74cb1f430efbd4575b9303 https://conda.anaconda.org/conda-forge/noarch/soupsieve-2.3.2.post1-pyhd8ed1ab_0.tar.bz2#146f4541d643d48fc8a75cacf69f03ae diff --git a/repo2docker/buildpacks/conda/environment.py-3.7.yml b/repo2docker/buildpacks/conda/environment.py-3.7.yml index da41a56d3..a0afd3d70 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.7.yml +++ b/repo2docker/buildpacks/conda/environment.py-3.7.yml @@ -1,5 +1,5 @@ # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY -# Generated on 2023-01-20 15:37:02 UTC +# Generated on 2023-01-23 11:59:03 UTC channels: - conda-forge dependencies: diff --git a/repo2docker/buildpacks/conda/environment.py-3.8-linux-64.lock b/repo2docker/buildpacks/conda/environment.py-3.8-linux-64.lock index 7bde3a9bc..72bc5afb5 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.8-linux-64.lock +++ b/repo2docker/buildpacks/conda/environment.py-3.8-linux-64.lock @@ -1,8 +1,8 @@ # AUTO GENERATED FROM environment.py-3.8.yml, DO NOT MANUALLY MODIFY -# Frozen on 2023-01-20 15:40:41 UTC +# Frozen on 2023-01-23 12:02:13 UTC # Generated by conda-lock. # platform: linux-64 -# input_hash: c24af796da7ce1b38126170a1e3e6a9c2d5cd8b38bb891e12ea6edb3d9c870cc +# input_hash: 3ee9f169b42eac9c4b87b9717811f649e435daf083090ac5504090183c941cce @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.12.7-ha878542_0.conda#ff9f73d45c4a07d6f424495288a26080 @@ -80,7 +80,7 @@ https://conda.anaconda.org/conda-forge/noarch/pytz-2022.7.1-pyhd8ed1ab_0.conda#f https://conda.anaconda.org/conda-forge/linux-64/pyzmq-25.0.0-py38he24dcef_0.conda#b7527850daeb11074c2d316fdb9e573e https://conda.anaconda.org/conda-forge/linux-64/ruamel.yaml.clib-0.2.7-py38h1de0b5d_1.conda#9afa2fc3c51cc4e7d1589c38e4e00d5c https://conda.anaconda.org/conda-forge/noarch/send2trash-1.8.0-pyhd8ed1ab_0.tar.bz2#edab14119efe85c3bf131ad747e9005c -https://conda.anaconda.org/conda-forge/noarch/setuptools-66.0.0-pyhd8ed1ab_0.conda#88ec352fde1a5561ce5f93a302539f7f +https://conda.anaconda.org/conda-forge/noarch/setuptools-66.1.1-pyhd8ed1ab_0.conda#9467d520d1457018e055bbbfdf9b7567 https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2#e5f25f8dbc060e9a8d912e432202afc2 https://conda.anaconda.org/conda-forge/noarch/sniffio-1.3.0-pyhd8ed1ab_0.tar.bz2#dd6cbc539e74cb1f430efbd4575b9303 https://conda.anaconda.org/conda-forge/noarch/soupsieve-2.3.2.post1-pyhd8ed1ab_0.tar.bz2#146f4541d643d48fc8a75cacf69f03ae diff --git a/repo2docker/buildpacks/conda/environment.py-3.8-linux-aarch64.lock b/repo2docker/buildpacks/conda/environment.py-3.8-linux-aarch64.lock index 6f1e124ef..cbaa1dc10 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.8-linux-aarch64.lock +++ b/repo2docker/buildpacks/conda/environment.py-3.8-linux-aarch64.lock @@ -1,8 +1,8 @@ # AUTO GENERATED FROM environment.py-3.8.yml, DO NOT MANUALLY MODIFY -# Frozen on 2023-01-20 15:41:58 UTC +# Frozen on 2023-01-23 12:03:18 UTC # Generated by conda-lock. # platform: linux-aarch64 -# input_hash: 9c56eb9ac9b1988fc6a0486df3913ae538e55d61b4d902864ed52d30173b6816 +# input_hash: ee16c54e01819e63190fba74576e2d110a2657abfb395e71346210349b48c082 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-aarch64/ca-certificates-2022.12.7-h4fd8a4c_0.conda#2450fbcaf65634e0d071e47e2b8487b4 https://conda.anaconda.org/conda-forge/linux-aarch64/ld_impl_linux-aarch64-2.39-h16cd69b_1.conda#9daf385ebefaea92087d3a315e398964 @@ -79,7 +79,7 @@ https://conda.anaconda.org/conda-forge/noarch/pytz-2022.7.1-pyhd8ed1ab_0.conda#f https://conda.anaconda.org/conda-forge/linux-aarch64/pyzmq-25.0.0-py38ha599cda_0.conda#625205531c7d9a8a167d48f71010b9ae https://conda.anaconda.org/conda-forge/linux-aarch64/ruamel.yaml.clib-0.2.7-py38hda48048_1.conda#0c48b738ee78083aab440dc39c967828 https://conda.anaconda.org/conda-forge/noarch/send2trash-1.8.0-pyhd8ed1ab_0.tar.bz2#edab14119efe85c3bf131ad747e9005c -https://conda.anaconda.org/conda-forge/noarch/setuptools-66.0.0-pyhd8ed1ab_0.conda#88ec352fde1a5561ce5f93a302539f7f +https://conda.anaconda.org/conda-forge/noarch/setuptools-66.1.1-pyhd8ed1ab_0.conda#9467d520d1457018e055bbbfdf9b7567 https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2#e5f25f8dbc060e9a8d912e432202afc2 https://conda.anaconda.org/conda-forge/noarch/sniffio-1.3.0-pyhd8ed1ab_0.tar.bz2#dd6cbc539e74cb1f430efbd4575b9303 https://conda.anaconda.org/conda-forge/noarch/soupsieve-2.3.2.post1-pyhd8ed1ab_0.tar.bz2#146f4541d643d48fc8a75cacf69f03ae diff --git a/repo2docker/buildpacks/conda/environment.py-3.8.yml b/repo2docker/buildpacks/conda/environment.py-3.8.yml index b122a9550..eaf5fc906 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.8.yml +++ b/repo2docker/buildpacks/conda/environment.py-3.8.yml @@ -1,5 +1,5 @@ # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY -# Generated on 2023-01-20 15:40:41 UTC +# Generated on 2023-01-23 12:02:13 UTC channels: - conda-forge dependencies: diff --git a/repo2docker/buildpacks/conda/environment.py-3.9-linux-64.lock b/repo2docker/buildpacks/conda/environment.py-3.9-linux-64.lock index b577d7606..6fc15bb25 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.9-linux-64.lock +++ b/repo2docker/buildpacks/conda/environment.py-3.9-linux-64.lock @@ -1,8 +1,8 @@ # AUTO GENERATED FROM environment.py-3.9.yml, DO NOT MANUALLY MODIFY -# Frozen on 2023-01-20 15:44:21 UTC +# Frozen on 2023-01-23 12:05:17 UTC # Generated by conda-lock. # platform: linux-64 -# input_hash: cf2fc57d67e2975358e9bb39eb35d65c5a98a54b911f2aca3030cdb63900ce7e +# input_hash: 3e8d6c21102d42dc26862fa21fbba8f868f97a08b274d8fb41d88a36b73e8c77 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.12.7-ha878542_0.conda#ff9f73d45c4a07d6f424495288a26080 @@ -81,7 +81,7 @@ https://conda.anaconda.org/conda-forge/noarch/pytz-2022.7.1-pyhd8ed1ab_0.conda#f https://conda.anaconda.org/conda-forge/linux-64/pyzmq-25.0.0-py39h0be026e_0.conda#7ed232c22ecbe2cabdebafa7d422f51d https://conda.anaconda.org/conda-forge/linux-64/ruamel.yaml.clib-0.2.7-py39h72bdee0_1.conda#d9da3b1d13895666f4cc2559d37b8de4 https://conda.anaconda.org/conda-forge/noarch/send2trash-1.8.0-pyhd8ed1ab_0.tar.bz2#edab14119efe85c3bf131ad747e9005c -https://conda.anaconda.org/conda-forge/noarch/setuptools-66.0.0-pyhd8ed1ab_0.conda#88ec352fde1a5561ce5f93a302539f7f +https://conda.anaconda.org/conda-forge/noarch/setuptools-66.1.1-pyhd8ed1ab_0.conda#9467d520d1457018e055bbbfdf9b7567 https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2#e5f25f8dbc060e9a8d912e432202afc2 https://conda.anaconda.org/conda-forge/noarch/sniffio-1.3.0-pyhd8ed1ab_0.tar.bz2#dd6cbc539e74cb1f430efbd4575b9303 https://conda.anaconda.org/conda-forge/noarch/soupsieve-2.3.2.post1-pyhd8ed1ab_0.tar.bz2#146f4541d643d48fc8a75cacf69f03ae diff --git a/repo2docker/buildpacks/conda/environment.py-3.9-linux-aarch64.lock b/repo2docker/buildpacks/conda/environment.py-3.9-linux-aarch64.lock index 8d5e8f66d..e85cb05bd 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.9-linux-aarch64.lock +++ b/repo2docker/buildpacks/conda/environment.py-3.9-linux-aarch64.lock @@ -1,8 +1,8 @@ # AUTO GENERATED FROM environment.py-3.9.yml, DO NOT MANUALLY MODIFY -# Frozen on 2023-01-20 15:45:33 UTC +# Frozen on 2023-01-23 12:06:23 UTC # Generated by conda-lock. # platform: linux-aarch64 -# input_hash: f9cecfedb6d82690580c12b5fc3a67f089f5ed66cf2d534f94a5b9ec21e50662 +# input_hash: e0f0a4acb21d21a7d3572227f14d5f4dde74c1ef1084ed2b597ab60e25bdbdbb @EXPLICIT https://conda.anaconda.org/conda-forge/linux-aarch64/ca-certificates-2022.12.7-h4fd8a4c_0.conda#2450fbcaf65634e0d071e47e2b8487b4 https://conda.anaconda.org/conda-forge/linux-aarch64/ld_impl_linux-aarch64-2.39-h16cd69b_1.conda#9daf385ebefaea92087d3a315e398964 @@ -80,7 +80,7 @@ https://conda.anaconda.org/conda-forge/noarch/pytz-2022.7.1-pyhd8ed1ab_0.conda#f https://conda.anaconda.org/conda-forge/linux-aarch64/pyzmq-25.0.0-py39h693dd76_0.conda#fee60123ee6a34dac6efdf37d3963cd1 https://conda.anaconda.org/conda-forge/linux-aarch64/ruamel.yaml.clib-0.2.7-py39h24fc6b6_1.conda#ad937086fe2828084067e5967a4000a4 https://conda.anaconda.org/conda-forge/noarch/send2trash-1.8.0-pyhd8ed1ab_0.tar.bz2#edab14119efe85c3bf131ad747e9005c -https://conda.anaconda.org/conda-forge/noarch/setuptools-66.0.0-pyhd8ed1ab_0.conda#88ec352fde1a5561ce5f93a302539f7f +https://conda.anaconda.org/conda-forge/noarch/setuptools-66.1.1-pyhd8ed1ab_0.conda#9467d520d1457018e055bbbfdf9b7567 https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2#e5f25f8dbc060e9a8d912e432202afc2 https://conda.anaconda.org/conda-forge/noarch/sniffio-1.3.0-pyhd8ed1ab_0.tar.bz2#dd6cbc539e74cb1f430efbd4575b9303 https://conda.anaconda.org/conda-forge/noarch/soupsieve-2.3.2.post1-pyhd8ed1ab_0.tar.bz2#146f4541d643d48fc8a75cacf69f03ae diff --git a/repo2docker/buildpacks/conda/environment.py-3.9.yml b/repo2docker/buildpacks/conda/environment.py-3.9.yml index e2857b69e..14f7f0cb4 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.9.yml +++ b/repo2docker/buildpacks/conda/environment.py-3.9.yml @@ -1,5 +1,5 @@ # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY -# Generated on 2023-01-20 15:44:21 UTC +# Generated on 2023-01-23 12:05:17 UTC channels: - conda-forge dependencies: From fc2ce1f3aae4f326fb3ffb9142b0a6156b422eef Mon Sep 17 00:00:00 2001 From: Min RK Date: Fri, 3 Feb 2023 15:19:33 +0100 Subject: [PATCH 106/171] pre-commit update fixes isort crash --- .pre-commit-config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index c9518890c..75f0ab42a 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,7 +23,7 @@ repos: # Autoformat: Python code - repo: https://github.com/psf/black - rev: 22.12.0 + rev: 23.1.0 hooks: - id: black args: @@ -36,7 +36,7 @@ repos: # Autoformat: Python code - repo: https://github.com/pycqa/isort - rev: 5.11.4 + rev: 5.12.0 hooks: - id: isort args: From 4bffe3df6a30262db618baf6d051183481e7c102 Mon Sep 17 00:00:00 2001 From: Min RK Date: Fri, 3 Feb 2023 15:21:07 +0100 Subject: [PATCH 107/171] ignore pre-commit changes in github workflows --- .github/workflows/docker.yml | 2 ++ .github/workflows/release.yml | 2 ++ .github/workflows/test.yml | 2 ++ 3 files changed, 6 insertions(+) diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml index 33b744735..283de494f 100644 --- a/.github/workflows/docker.yml +++ b/.github/workflows/docker.yml @@ -11,6 +11,7 @@ on: - "**.rst" - ".github/workflows/*" - "!.github/workflows/docker.yml" + - ".pre-commit-config.yaml" push: paths-ignore: - "docs/**" @@ -18,6 +19,7 @@ on: - "**.rst" - ".github/workflows/*" - "!.github/workflows/docker.yml" + - ".pre-commit-config.yaml" branches-ignore: - "dependabot/**" - "pre-commit-ci-update-config" diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index d711d75ff..16ebfff71 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -11,6 +11,7 @@ on: - "**.rst" - ".github/workflows/*" - "!.github/workflows/release.yml" + - ".pre-commit-config.yaml" push: paths-ignore: - "docs/**" @@ -18,6 +19,7 @@ on: - "**.rst" - ".github/workflows/*" - "!.github/workflows/release.yml" + - ".pre-commit-config.yaml" branches-ignore: - "dependabot/**" - "pre-commit-ci-update-config" diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 4995d238c..798f07723 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -11,6 +11,7 @@ on: - "**.rst" - ".github/workflows/*" - "!.github/workflows/test.yml" + - ".pre-commit-config.yaml" push: paths-ignore: - "docs/**" @@ -18,6 +19,7 @@ on: - "**.rst" - ".github/workflows/*" - "!.github/workflows/test.yml" + - ".pre-commit-config.yaml" branches-ignore: - "dependabot/**" - "pre-commit-ci-update-config" From 3e6951c02ea38867f4c9a05683553712b092b703 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Fri, 3 Feb 2023 14:22:05 +0000 Subject: [PATCH 108/171] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- tests/unit/contentproviders/test_dataverse.py | 1 - tests/unit/contentproviders/test_hydroshare.py | 1 - 2 files changed, 2 deletions(-) diff --git a/tests/unit/contentproviders/test_dataverse.py b/tests/unit/contentproviders/test_dataverse.py index 309a22d4a..1603b9cdd 100644 --- a/tests/unit/contentproviders/test_dataverse.py +++ b/tests/unit/contentproviders/test_dataverse.py @@ -95,7 +95,6 @@ def doi_resolver(req, context): @pytest.fixture def dv_files(tmpdir): - f1 = tmpdir.join("some-file.txt") f1.write("some content") diff --git a/tests/unit/contentproviders/test_hydroshare.py b/tests/unit/contentproviders/test_hydroshare.py index cec541f6f..0c8acfd14 100755 --- a/tests/unit/contentproviders/test_hydroshare.py +++ b/tests/unit/contentproviders/test_hydroshare.py @@ -35,7 +35,6 @@ def doi_resolver(req, context): def test_content_id(requests_mock): - requests_mock.get(re.compile("https://"), json=hydroshare_data) requests_mock.get(re.compile("https://doi.org"), json=doi_resolver) From ca51f8fc004171ca3cde97fbfc114ae5f3211705 Mon Sep 17 00:00:00 2001 From: Min RK Date: Fri, 3 Feb 2023 13:49:09 +0100 Subject: [PATCH 109/171] add Python 3.11, jupyterhub 3.1.1 --- .../conda/environment-linux-64.lock | 45 +++--- .../conda/environment-linux-aarch64.lock | 45 +++--- .../conda/environment.py-3.10-linux-64.lock | 62 ++++---- .../environment.py-3.10-linux-aarch64.lock | 62 ++++---- .../buildpacks/conda/environment.py-3.10.yml | 4 +- .../conda/environment.py-3.11-linux-64.lock | 150 ++++++++++++++++++ .../environment.py-3.11-linux-aarch64.lock | 149 +++++++++++++++++ .../buildpacks/conda/environment.py-3.11.lock | 150 ++++++++++++++++++ .../buildpacks/conda/environment.py-3.11.yml | 15 ++ .../conda/environment.py-3.7-linux-64.lock | 45 +++--- .../environment.py-3.7-linux-aarch64.lock | 45 +++--- .../buildpacks/conda/environment.py-3.7.yml | 4 +- .../conda/environment.py-3.8-linux-64.lock | 62 ++++---- .../environment.py-3.8-linux-aarch64.lock | 62 ++++---- .../buildpacks/conda/environment.py-3.8.yml | 4 +- .../conda/environment.py-3.9-linux-64.lock | 62 ++++---- .../environment.py-3.9-linux-aarch64.lock | 62 ++++---- .../buildpacks/conda/environment.py-3.9.yml | 4 +- repo2docker/buildpacks/conda/environment.yml | 2 +- repo2docker/buildpacks/conda/freeze.py | 2 +- 20 files changed, 708 insertions(+), 328 deletions(-) create mode 100644 repo2docker/buildpacks/conda/environment.py-3.11-linux-64.lock create mode 100644 repo2docker/buildpacks/conda/environment.py-3.11-linux-aarch64.lock create mode 100644 repo2docker/buildpacks/conda/environment.py-3.11.lock create mode 100644 repo2docker/buildpacks/conda/environment.py-3.11.yml diff --git a/repo2docker/buildpacks/conda/environment-linux-64.lock b/repo2docker/buildpacks/conda/environment-linux-64.lock index 84f3a5bc9..c185ab8bb 100644 --- a/repo2docker/buildpacks/conda/environment-linux-64.lock +++ b/repo2docker/buildpacks/conda/environment-linux-64.lock @@ -1,42 +1,34 @@ # AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY -# Frozen on 2023-01-23 11:59:03 UTC +# Frozen on 2023-02-03 12:33:27 UTC # Generated by conda-lock. # platform: linux-64 -# input_hash: 3b780a798011d21422fbbea52f1c94325fc806c944f506d41d0bdf397b93c604 +# input_hash: 56d66ed1f6b5535bd09b3fb8546cc5bdb3cea65aa2ed89ffaf52424a63c739aa @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.12.7-ha878542_0.conda#ff9f73d45c4a07d6f424495288a26080 -https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.39-hcc3a1bd_1.conda#737be0d34c22d24432049ab7a3214de4 +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3 https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-12.2.0-h46fd767_19.tar.bz2#1030b1f38c129f2634eae026f704fe60 https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.7-3_cp37m.conda#46277e9cf1ecd46926a31cea47079009 https://conda.anaconda.org/conda-forge/linux-64/libgomp-12.2.0-h65d4601_19.tar.bz2#cedcee7c064c01c403f962c9e8d3c373 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-12.2.0-h65d4601_19.tar.bz2#e4c94f80aef025c17ab0828cd85ef535 -https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.18.1-h7f98852_0.tar.bz2#f26ef8098fab1f719c91eb760d63381a https://conda.anaconda.org/conda-forge/linux-64/icu-70.1-h27087fc_0.tar.bz2#87473a15119779e021c314249d4b4aed -https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3 -https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-h516909a_1.tar.bz2#6f8720dff19e17ce5d48cfe7f3d2f0a3 https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.0-h7f98852_0.tar.bz2#39b1328babf85c7c3a61636d9cd50206 https://conda.anaconda.org/conda-forge/linux-64/libsodium-1.0.18-h36c2ea0_1.tar.bz2#c3788462a6fbddafdb413a9f9053e58d https://conda.anaconda.org/conda-forge/linux-64/libuv-1.44.2-h166bdaf_0.tar.bz2#e5cb4fe581a18ca2185a016eb848fc00 https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-h166bdaf_4.tar.bz2#f3f9de449d32ca9b9c66a22863c96f41 https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.3-h27087fc_1.tar.bz2#4acfc691e64342b9dae57cf2adc63238 -https://conda.anaconda.org/conda-forge/linux-64/openssl-3.0.7-h0b41bf4_1.conda#7adaac6ff98219bcb99b45e408b80f4e +https://conda.anaconda.org/conda-forge/linux-64/openssl-3.0.7-h0b41bf4_2.conda#45758f4ece9c8b7b5f99328bd5caae51 https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0 -https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1 -https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.51.0-hff17c54_0.conda#dd682f0b6d65e75b2bc868fc8e93d87e https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.40.0-h753d276_0.tar.bz2#2e5f9a37d487e1019fd4d8113adb2f9f -https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.10.0-hf14f497_3.tar.bz2#d85acad4b47dff4e3def14a769a97906 https://conda.anaconda.org/conda-forge/linux-64/pandoc-2.19.2-h32600fe_1.tar.bz2#35a82883468c85ac8bf41f083c1933cf https://conda.anaconda.org/conda-forge/linux-64/readline-8.1.2-h0f457ee_0.tar.bz2#db2ebbe2943aae81ed051a6a9af8e0fa https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.12-h27826a3_0.tar.bz2#5b8c42eb62e9fc961af70bdd6a26e168 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mode 100644 index 000000000..7c49ec704 --- /dev/null +++ b/repo2docker/buildpacks/conda/environment.py-3.11.yml @@ -0,0 +1,15 @@ +# AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY +# Generated on 2023-02-03 12:31:38 UTC +channels: +- conda-forge +dependencies: +- python=3.11.* +- nodejs=18 +- pip +- ipywidgets==8.0.2 +- jupyter-offlinenotebook==0.2.2 +- jupyter-resource-usage==0.7.0 +- jupyterlab==3.4.8 +- jupyterhub-singleuser==3.1.1 +- notebook==6.4.12 +- nteract_on_jupyter==2.1.3 diff --git a/repo2docker/buildpacks/conda/environment.py-3.7-linux-64.lock b/repo2docker/buildpacks/conda/environment.py-3.7-linux-64.lock index 84f3a5bc9..c185ab8bb 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.7-linux-64.lock +++ b/repo2docker/buildpacks/conda/environment.py-3.7-linux-64.lock @@ -1,42 +1,34 @@ # AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY -# Frozen on 2023-01-23 11:59:03 UTC +# Frozen on 2023-02-03 12:33:27 UTC # Generated by conda-lock. # 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https://conda.anaconda.org/conda-forge/noarch/jupyter_server-1.23.5-pyhd8ed1ab_0.conda#e3ae1d46749f48a1875b560fca41cb0c -https://conda.anaconda.org/conda-forge/noarch/nbconvert-pandoc-7.2.8-pyhd8ed1ab_0.conda#701b0db88fe192e1685de29b8ca0840e +https://conda.anaconda.org/conda-forge/noarch/nbconvert-pandoc-7.2.9-pyhd8ed1ab_0.conda#4a8dc94c7c2f3736dc4b91ec345d5b4b https://conda.anaconda.org/conda-forge/noarch/jupyter-resource-usage-0.7.0-pyhd8ed1ab_0.conda#c57567d49d926826b1f852712ac8acfa https://conda.anaconda.org/conda-forge/noarch/jupyterlab_server-2.19.0-pyhd8ed1ab_0.conda#9dc0706ec2f8e13b7a0db9d6a19051ff -https://conda.anaconda.org/conda-forge/noarch/nbconvert-7.2.8-pyhd8ed1ab_0.conda#8b5cb7073f66beef0d7161406fdb6e8b +https://conda.anaconda.org/conda-forge/noarch/nbconvert-7.2.9-pyhd8ed1ab_0.conda#523aaa3affb003ab0e68dbc24c9027f4 https://conda.anaconda.org/conda-forge/noarch/notebook-shim-0.2.2-pyhd8ed1ab_0.tar.bz2#40be846cd4e78672a40e43db9dae753c -https://conda.anaconda.org/conda-forge/noarch/nbclassic-0.4.8-pyhd8ed1ab_0.tar.bz2#f4f150f83ed90a1b833e6081bbf38257 +https://conda.anaconda.org/conda-forge/noarch/nbclassic-0.5.1-pyhd8ed1ab_0.conda#cf832e3d48ef22528c676ed6e4b4085a https://conda.anaconda.org/conda-forge/noarch/notebook-6.4.12-pyha770c72_0.tar.bz2#77fc67c5bbea44fd41e8bbe2ac82d1ad https://conda.anaconda.org/conda-forge/noarch/jupyter-offlinenotebook-0.2.2-pyh1d7be83_0.tar.bz2#fe55056ce4bc4bd4953ba440270735fb -https://conda.anaconda.org/conda-forge/linux-aarch64/jupyterhub-singleuser-1.5.0-py39ha65689a_1.tar.bz2#428f24f44794a428a875ee08be6eee31 https://conda.anaconda.org/conda-forge/noarch/jupyterlab-3.4.8-pyhd8ed1ab_0.tar.bz2#6fbf13b0e8a6fa24bbae91205e8ce467 https://conda.anaconda.org/conda-forge/noarch/nteract_on_jupyter-2.1.3-py_0.tar.bz2#1430ccd983ae6b161e2fbf4377965f7a +https://conda.anaconda.org/conda-forge/noarch/jupyterhub-singleuser-3.1.1-pyh2a2186d_0.conda#6d0a3394efe9ff7c0ad1ed03a6ca3720 diff --git a/repo2docker/buildpacks/conda/environment.py-3.9.yml b/repo2docker/buildpacks/conda/environment.py-3.9.yml index 14f7f0cb4..852d7eba5 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.9.yml +++ b/repo2docker/buildpacks/conda/environment.py-3.9.yml @@ -1,5 +1,5 @@ # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY -# Generated on 2023-01-23 12:05:17 UTC +# Generated on 2023-02-03 12:34:00 UTC channels: - conda-forge dependencies: @@ -10,6 +10,6 @@ dependencies: - jupyter-offlinenotebook==0.2.2 - jupyter-resource-usage==0.7.0 - jupyterlab==3.4.8 -- jupyterhub-singleuser==1.5.0 +- jupyterhub-singleuser==3.1.1 - notebook==6.4.12 - nteract_on_jupyter==2.1.3 diff --git a/repo2docker/buildpacks/conda/environment.yml b/repo2docker/buildpacks/conda/environment.yml index 3245f58c0..c34a43d83 100644 --- a/repo2docker/buildpacks/conda/environment.yml +++ b/repo2docker/buildpacks/conda/environment.yml @@ -8,6 +8,6 @@ dependencies: - jupyter-offlinenotebook==0.2.2 - jupyter-resource-usage==0.7.0 - jupyterlab==3.4.8 - - jupyterhub-singleuser==1.5.0 + - jupyterhub-singleuser==3.1.1 - notebook==6.4.12 - nteract_on_jupyter==2.1.3 diff --git a/repo2docker/buildpacks/conda/freeze.py b/repo2docker/buildpacks/conda/freeze.py index e800b714e..b464fcc21 100755 --- a/repo2docker/buildpacks/conda/freeze.py +++ b/repo2docker/buildpacks/conda/freeze.py @@ -117,7 +117,7 @@ def set_python(py_env_file, py): "py", nargs="*", help="Python version(s) to update and freeze", - default=("3.7", "3.8", "3.9", "3.10"), + default=("3.7", "3.8", "3.9", "3.10", "3.11"), ) parser.add_argument( "platform", From b8c76448a35b66a27ae52ced3cb4db089fc0f6e2 Mon Sep 17 00:00:00 2001 From: Min RK Date: Fri, 3 Feb 2023 15:27:07 +0100 Subject: [PATCH 110/171] generalize separate kernel environment from server for old Python replaces `.py2` special-case with a general `separate_kernel_env` flag, currently triggered by requesting Python < 3.7. Python 3.6 and 3.5 are now treated as Python 2.7 --- repo2docker/buildpacks/conda/__init__.py | 50 +++++++++++++++++----- repo2docker/buildpacks/pipfile/__init__.py | 4 +- repo2docker/buildpacks/python/__init__.py | 4 +- 3 files changed, 43 insertions(+), 15 deletions(-) diff --git a/repo2docker/buildpacks/conda/__init__.py b/repo2docker/buildpacks/conda/__init__.py index 66aff037a..9a3c97be2 100644 --- a/repo2docker/buildpacks/conda/__init__.py +++ b/repo2docker/buildpacks/conda/__init__.py @@ -1,10 +1,12 @@ """BuildPack for conda environments""" import os import re +import warnings from collections.abc import Mapping from ruamel.yaml import YAML +from ...semver import parse_version as V from ...utils import is_local_pip_requirement from .._r_base import rstudio_base_scripts from ..base import BaseImage @@ -98,7 +100,7 @@ def get_path(self): """ path = super().get_path() path.insert(0, "${CONDA_DIR}/bin") - if self.py2: + if self.separate_kernel_env: path.insert(0, "${KERNEL_PYTHON_PREFIX}/bin") path.insert(0, "${NB_PYTHON_PREFIX}/bin") # This is at the end of $PATH, for backwards compat reasons @@ -172,20 +174,24 @@ def get_build_script_files(self): frozen_name = f"environment-{self._conda_platform()}.lock" pip_frozen_name = "requirements.txt" if py_version: - if self.python_version == "2.7": - if "linux-64" != self._conda_platform(): + conda_platform = self._conda_platform() + if self.separate_kernel_env: + self.log.warning( + f"User-requested packages for legacy Python version {py_version} will be installed in a separate kernel environment.\n" + ) + lockfile_name = f"environment.py-{py_version}-{conda_platform}.lock" + if not os.path.exists(os.path.join(HERE, lockfile_name)): raise ValueError( - f"Python version 2.7 {self._conda_platform()} is not supported!" + f"Python version {py_version} on {conda_platform} is not supported!" ) - - # python 2 goes in a different env files[ - "conda/environment.py-2.7-linux-64.lock" + f"conda/{lockfile_name}" ] = self._kernel_environment_file = "/tmp/env/kernel-environment.lock" - # additional pip requirements for kernel env - if os.path.exists(os.path.join(HERE, "requirements.py-2.7.txt")): + + requirements_file_name = f"requirements.py-{py_version}.pip" + if os.path.exists(os.path.join(HERE, requirements_file_name)): files[ - "conda/requirements.py-2.7.txt" + f"conda/{requirements_file_name}" ] = ( self._kernel_requirements_file ) = "/tmp/env/kernel-requirements.txt" @@ -333,8 +339,26 @@ def uses_r(self): @property def py2(self): """Am I building a Python 2 kernel environment?""" + warnings.warn( + "CondaBuildPack.py2 is deprecated in 2023.2. Use CondaBuildPack.separate_kernel_env.", + DeprecationWarning, + stacklevel=2, + ) return self.python_version and self.python_version.split(".")[0] == "2" + # Python versions _older_ than this get a separate kernel env + kernel_env_cutoff_version = "3.7" + + @property + def separate_kernel_env(self): + """Whether the kernel should be installed into a separate env from the server + + Applies to older versions of Python that aren't kept up-to-date + """ + return self.python_version and V(self.python_version) < V( + self.kernel_env_cutoff_version + ) + def get_preassemble_script_files(self): """preassembly only requires environment.yml @@ -352,7 +376,11 @@ def get_env_scripts(self): """Return series of build-steps specific to this source repository.""" scripts = [] environment_yml = self.binder_path("environment.yml") - env_prefix = "${KERNEL_PYTHON_PREFIX}" if self.py2 else "${NB_PYTHON_PREFIX}" + env_prefix = ( + "${KERNEL_PYTHON_PREFIX}" + if self.separate_kernel_env + else "${NB_PYTHON_PREFIX}" + ) if os.path.exists(environment_yml): # TODO: when using micromamba, we call $MAMBA_EXE install -p ... # whereas mamba/conda need `env update -p ...` when it's an env.yaml file diff --git a/repo2docker/buildpacks/pipfile/__init__.py b/repo2docker/buildpacks/pipfile/__init__.py index f08a1beba..7f8ec53b6 100644 --- a/repo2docker/buildpacks/pipfile/__init__.py +++ b/repo2docker/buildpacks/pipfile/__init__.py @@ -113,8 +113,8 @@ def get_assemble_scripts(self): # environment. assemble_scripts = super().get_assemble_scripts() - if self.py2: - # using Python 2 as a kernel, but Python 3 for the notebook server + if self.separate_kernel_env: + # using legacy Python (e.g. 2.7) as a kernel # requirements3.txt allows for packages to be installed to the # notebook servers Python environment diff --git a/repo2docker/buildpacks/python/__init__.py b/repo2docker/buildpacks/python/__init__.py index 7aa225642..a96a6cabf 100644 --- a/repo2docker/buildpacks/python/__init__.py +++ b/repo2docker/buildpacks/python/__init__.py @@ -45,8 +45,8 @@ def _get_pip_scripts(self): # whether it's distinct from the notebook or the same. pip = "${KERNEL_PYTHON_PREFIX}/bin/pip" scripts = [] - if self.py2: - # using python 2 kernel, + if self.separate_kernel_env: + # using legacy Python kernel # requirements3.txt allows installation in the notebook server env nb_requirements_file = self.binder_path("requirements3.txt") if os.path.exists(nb_requirements_file): From a9d77e21f10f781662dfb36b04b932f03da33ca3 Mon Sep 17 00:00:00 2001 From: Min RK Date: Fri, 3 Feb 2023 15:27:32 +0100 Subject: [PATCH 111/171] No longer install notebook/jupyterhub packages on Python 3.5 now that it's a kernel-only environment --- .../buildpacks/conda/requirements.py-3.5.pip | 17 ----------------- 1 file changed, 17 deletions(-) delete mode 100644 repo2docker/buildpacks/conda/requirements.py-3.5.pip diff --git a/repo2docker/buildpacks/conda/requirements.py-3.5.pip b/repo2docker/buildpacks/conda/requirements.py-3.5.pip deleted file mode 100644 index 416274ad2..000000000 --- a/repo2docker/buildpacks/conda/requirements.py-3.5.pip +++ /dev/null @@ -1,17 +0,0 @@ -# pip-installed packages for Python 3.5 -# these should only be packages -# whose versions are too new to have builds available for Python 3.5 -alembic==1.0.3 -async-generator==1.10 -chardet==3.0.4 -idna==2.7 -jupyterhub==0.9.4 -mako==1.0.7 -notebook==5.7.8 -nteract-on-jupyter==1.9.6 -pamela==0.3.0 -python-editor==1.0.3 -python-oauth2==1.1.0 -requests==2.20.1 -sqlalchemy==1.2.14 -urllib3==1.24.1 From 18cbf55b90c27a977ca299a82048310e9c7816ee Mon Sep 17 00:00:00 2001 From: Min RK Date: Fri, 3 Feb 2023 15:28:37 +0100 Subject: [PATCH 112/171] test postBuild behavior with legacy Python 3.6 --- tests/conda/py36-postBuild/environment.yml | 3 + tests/conda/py36-postBuild/postBuild | 9 +++ tests/conda/py36-postBuild/verify | 3 + tests/conda/py36-postBuild/verify.py | 85 ++++++++++++++++++++++ 4 files changed, 100 insertions(+) create mode 100644 tests/conda/py36-postBuild/environment.yml create mode 100755 tests/conda/py36-postBuild/postBuild create mode 100755 tests/conda/py36-postBuild/verify create mode 100644 tests/conda/py36-postBuild/verify.py diff --git a/tests/conda/py36-postBuild/environment.yml b/tests/conda/py36-postBuild/environment.yml new file mode 100644 index 000000000..c6ce14436 --- /dev/null +++ b/tests/conda/py36-postBuild/environment.yml @@ -0,0 +1,3 @@ +dependencies: + - python=3.6 + - numpy diff --git a/tests/conda/py36-postBuild/postBuild b/tests/conda/py36-postBuild/postBuild new file mode 100755 index 000000000..cf0db0125 --- /dev/null +++ b/tests/conda/py36-postBuild/postBuild @@ -0,0 +1,9 @@ +#!/bin/bash +set -ex + +# mamba/conda installs in kernel env +mamba install -y make + +# note `pip` on path is _not_ the kernel env! +# is this what we (or users) want? +pip install pytest diff --git a/tests/conda/py36-postBuild/verify b/tests/conda/py36-postBuild/verify new file mode 100755 index 000000000..e576d7ab5 --- /dev/null +++ b/tests/conda/py36-postBuild/verify @@ -0,0 +1,3 @@ +#!/bin/bash +set -ex +pytest -vs ./verify.py diff --git a/tests/conda/py36-postBuild/verify.py b/tests/conda/py36-postBuild/verify.py new file mode 100644 index 000000000..806a5c9a5 --- /dev/null +++ b/tests/conda/py36-postBuild/verify.py @@ -0,0 +1,85 @@ +""" +tests to be run with pytest inside the container + +can't be called test_whatever.py because then _host_ pytest will try to run it! +""" + +import json +import os +import shutil +from subprocess import check_output + +from pytest import fixture + +kernel_prefix = os.environ.get("KERNEL_PYTHON_PREFIX") +server_prefix = os.environ.get("NB_PYTHON_PREFIX") + + +def json_cmd(cmd): + """Run a command and decode its JSON output""" + out = check_output(cmd) + return json.loads(out.decode("utf8", "replace")) + + +def conda_pkgs(prefix): + """Conda package list as a dict""" + conda_json = json_cmd(["conda", "list", "--json", "-p", prefix]) + return {pkg["name"]: pkg for pkg in conda_json} + + +def pip_pkgs(prefix): + """Pip package list as a dict""" + pip_json = json_cmd([f"{prefix}/bin/pip", "list", "--format=json"]) + return {pkg["name"]: pkg for pkg in pip_json} + + +@fixture(scope="session") +def kernel_conda(): + return conda_pkgs(kernel_prefix) + + +@fixture(scope="session") +def server_conda(): + return conda_pkgs(server_prefix) + + +@fixture(scope="session") +def kernel_pip(): + return pip_pkgs(kernel_prefix) + + +@fixture(scope="session") +def server_pip(): + return pip_pkgs(server_prefix) + + +def test_which_python(): + # server python comes first. Is this expected? + assert shutil.which("python3") == f"{server_prefix}/bin/python3" + + +def test_kernel_env(kernel_conda): + assert kernel_prefix != server_prefix + kernel_python = kernel_conda["python"]["version"] + assert kernel_python[:3] == "3.6" + # test environment.yml packages + assert "numpy" in kernel_conda + + +def test_server_env(server_conda): + # this should be the default version + # it will need updating when the default changes + assert server_conda["python"]["version"][:3] == "3.7" + + +def test_conda_install(kernel_conda, server_conda): + # test that postBuild conda install went in the kernel env + assert "make" in kernel_conda + assert "make" not in server_conda + + +def test_pip_install(kernel_pip, server_pip): + # server env comes first for pip + # is this expected? + assert "pytest" not in kernel_pip + assert "pytest" in server_pip From 738a56dcd5b5169b14ed5b535514cf4cf3fb8e63 Mon Sep 17 00:00:00 2001 From: Min RK Date: Fri, 3 Feb 2023 16:08:40 +0100 Subject: [PATCH 113/171] refreeze after merge --- .../conda/environment-linux-64.lock | 136 ++++++++--------- .../conda/environment-linux-aarch64.lock | 104 +++++++------ .../conda/environment.py-3.10-linux-64.lock | 137 +++++++++--------- .../environment.py-3.10-linux-aarch64.lock | 49 ++++--- .../buildpacks/conda/environment.py-3.10.yml | 2 +- .../conda/environment.py-3.7-linux-64.lock | 106 +++++++------- .../environment.py-3.7-linux-aarch64.lock | 32 ++-- .../buildpacks/conda/environment.py-3.7.yml | 2 +- .../conda/environment.py-3.8-linux-64.lock | 132 ++++++++--------- .../environment.py-3.8-linux-aarch64.lock | 49 ++++--- .../buildpacks/conda/environment.py-3.8.yml | 2 +- .../conda/environment.py-3.9-linux-64.lock | 134 +++++++++-------- .../environment.py-3.9-linux-aarch64.lock | 49 ++++--- .../buildpacks/conda/environment.py-3.9.yml | 2 +- repo2docker/buildpacks/conda/environment.yml | 2 +- 15 files changed, 469 insertions(+), 469 deletions(-) diff --git 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a/repo2docker/buildpacks/conda/environment.py-3.10.yml b/repo2docker/buildpacks/conda/environment.py-3.10.yml index 91a56e331..97e5361e7 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.10.yml +++ b/repo2docker/buildpacks/conda/environment.py-3.10.yml @@ -1,5 +1,5 @@ # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY -# Generated on 2022-11-18 22:33:38 UTC +# Generated on 2023-02-03 15:07:27 UTC channels: - conda-forge dependencies: diff --git a/repo2docker/buildpacks/conda/environment.py-3.7-linux-64.lock b/repo2docker/buildpacks/conda/environment.py-3.7-linux-64.lock index 1dda0b4cd..483141faf 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.7-linux-64.lock +++ b/repo2docker/buildpacks/conda/environment.py-3.7-linux-64.lock @@ -1,13 +1,14 @@ # AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY -# Frozen on 2022-11-18 22:33:01 UTC +# Frozen on 2023-02-03 15:06:11 UTC # Generated by conda-lock. # platform: linux-64 -# input_hash: 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UTC +# Generated on 2023-02-03 15:06:35 UTC channels: - conda-forge dependencies: diff --git a/repo2docker/buildpacks/conda/environment.py-3.9-linux-64.lock b/repo2docker/buildpacks/conda/environment.py-3.9-linux-64.lock index 09a2d3c0c..dd761e3dd 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.9-linux-64.lock +++ b/repo2docker/buildpacks/conda/environment.py-3.9-linux-64.lock @@ -1,14 +1,15 @@ # AUTO GENERATED FROM environment.py-3.9.yml, DO NOT MANUALLY MODIFY -# Frozen on 2022-11-18 22:33:38 UTC +# Frozen on 2023-02-03 15:07:03 UTC # Generated by conda-lock. # platform: linux-64 -# input_hash: 3e8d6c21102d42dc26862fa21fbba8f868f97a08b274d8fb41d88a36b73e8c77 +# input_hash: 7f7fc460068d618879d5a59d02e2ed8cdeda20ec3692dc18b5ded1cb5a4fd1eb @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 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-https://conda.anaconda.org/conda-forge/noarch/nbclassic-0.4.8-pyhd8ed1ab_0.tar.bz2#f4f150f83ed90a1b833e6081bbf38257 +https://conda.anaconda.org/conda-forge/noarch/nbclassic-0.5.1-pyhd8ed1ab_0.conda#cf832e3d48ef22528c676ed6e4b4085a https://conda.anaconda.org/conda-forge/noarch/notebook-6.4.12-pyha770c72_0.tar.bz2#77fc67c5bbea44fd41e8bbe2ac82d1ad https://conda.anaconda.org/conda-forge/noarch/jupyter-offlinenotebook-0.2.2-pyh1d7be83_0.tar.bz2#fe55056ce4bc4bd4953ba440270735fb https://conda.anaconda.org/conda-forge/linux-aarch64/jupyterhub-singleuser-1.5.0-py39ha65689a_1.tar.bz2#428f24f44794a428a875ee08be6eee31 diff --git a/repo2docker/buildpacks/conda/environment.py-3.9.yml b/repo2docker/buildpacks/conda/environment.py-3.9.yml index 8a9a89784..c1a7f162e 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.9.yml +++ b/repo2docker/buildpacks/conda/environment.py-3.9.yml @@ -1,5 +1,5 @@ # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY -# Generated on 2022-11-18 22:33:18 UTC +# Generated on 2023-02-03 15:07:03 UTC channels: - conda-forge dependencies: diff --git a/repo2docker/buildpacks/conda/environment.yml b/repo2docker/buildpacks/conda/environment.yml index 3245f58c0..f08f7dd4d 100644 --- a/repo2docker/buildpacks/conda/environment.yml +++ b/repo2docker/buildpacks/conda/environment.yml @@ -1,7 +1,7 @@ channels: - conda-forge dependencies: - - python=3.7 + - python=3.10 - nodejs=18 - pip - ipywidgets==8.0.2 From 6e92cdd05bf7f866d2bad15c15b2c3fbf686d5a9 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 6 Feb 2023 05:10:11 +0000 Subject: [PATCH 114/171] build(deps): bump docker/build-push-action from 3 to 4 Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 3 to 4. - [Release notes](https://github.com/docker/build-push-action/releases) - [Commits](https://github.com/docker/build-push-action/compare/v3...v4) --- updated-dependencies: - dependency-name: docker/build-push-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- .github/workflows/docker.yml | 2 +- .github/workflows/release.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml index 283de494f..c9d588590 100644 --- a/.github/workflows/docker.yml +++ b/.github/workflows/docker.yml @@ -38,7 +38,7 @@ jobs: # https://github.com/docker/build-push-action - name: Build Docker image - uses: docker/build-push-action@v3 + uses: docker/build-push-action@v4 with: context: . tags: jupyter/repo2docker:pr diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 16ebfff71..e9c5d89a6 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -124,7 +124,7 @@ jobs: echo "TAGS=$TAGS" >> $GITHUB_ENV - name: Build and push repo2docker - uses: docker/build-push-action@v3 + uses: docker/build-push-action@v4 with: context: . platforms: linux/amd64,linux/arm64 From fbab2cd3307e900a0854b0da51a3e34333f6d1ef Mon Sep 17 00:00:00 2001 From: Min RK Date: Wed, 8 Feb 2023 12:52:59 +0100 Subject: [PATCH 115/171] actually change the default Python version to 3.10 this default lives too many places! --- repo2docker/buildpacks/conda/__init__.py | 2 +- tests/venv/default/verify | 2 +- tests/venv/numpy/verify | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/repo2docker/buildpacks/conda/__init__.py b/repo2docker/buildpacks/conda/__init__.py index 66aff037a..781d5d3d1 100644 --- a/repo2docker/buildpacks/conda/__init__.py +++ b/repo2docker/buildpacks/conda/__init__.py @@ -141,7 +141,7 @@ def get_build_scripts(self): ), ] - major_pythons = {"2": "2.7", "3": "3.7"} + major_pythons = {"2": "2.7", "3": "3.10"} def get_build_script_files(self): """ diff --git a/tests/venv/default/verify b/tests/venv/default/verify index 559670863..b5b2b9920 100755 --- a/tests/venv/default/verify +++ b/tests/venv/default/verify @@ -2,7 +2,7 @@ # Verify that the default just provides a py3 environment with jupyter import sys -assert sys.version_info[:2] == (3, 7), sys.version +assert sys.version_info[:2] == (3, 10), sys.version import jupyter with open("/tmp/appendix") as f: diff --git a/tests/venv/numpy/verify b/tests/venv/numpy/verify index 34769ecb1..ef098d21a 100755 --- a/tests/venv/numpy/verify +++ b/tests/venv/numpy/verify @@ -1,6 +1,6 @@ #!/usr/bin/env python import sys -assert sys.version_info[:2] == (3, 7) +assert sys.version_info[:2] == (3, 10) import numpy From abe2cc859841712378bd0d9f5a0253afaf600e84 Mon Sep 17 00:00:00 2001 From: Min RK Date: Wed, 8 Feb 2023 13:51:04 +0100 Subject: [PATCH 116/171] import downgrade test rather than building old xeus-cling, which requires a downgrade of Python from 3.10 to 3.9, which is _not_ supported, run the build with a 3.9 pin. This still results in patch-level downgrade of Python, major downgrade of openssl, etc. --- tests/conda/downgrade/environment.yml | 11 +++++++++ tests/conda/downgrade/verify | 30 +++++++++++++++++++++++++ tests/external/reproductions.repos.yaml | 6 ----- 3 files changed, 41 insertions(+), 6 deletions(-) create mode 100644 tests/conda/downgrade/environment.yml create mode 100755 tests/conda/downgrade/verify diff --git a/tests/conda/downgrade/environment.yml b/tests/conda/downgrade/environment.yml new file mode 100644 index 000000000..319f8d5dd --- /dev/null +++ b/tests/conda/downgrade/environment.yml @@ -0,0 +1,11 @@ +# originally xeus-cling@0.6.0 +# added python=3.9 pin because implicit downgrade of Python from 3.10 to 3.9 isn't allowed +name: xeus-cling +channels: + - conda-forge +dependencies: + - python=3.9 + - xeus-cling=0.6.0 + - xtensor=0.20.8 + - xtensor-blas=0.16.1 + - notebook diff --git a/tests/conda/downgrade/verify b/tests/conda/downgrade/verify new file mode 100755 index 000000000..07b409408 --- /dev/null +++ b/tests/conda/downgrade/verify @@ -0,0 +1,30 @@ +#!/usr/bin/env python3 +import json +import pprint +from subprocess import check_output + + +def json_sh(cmd): + """Run a command that produces JSON on stdout and return the parsed result""" + buf = check_output(cmd) + return json.loads(buf.decode("utf8", "replace")) + + +conda_pkg_list = json_sh(["conda", "list", "--json"]) +pprint.pprint(conda_pkg_list) +# make it a dict +pkgs = {pkg["name"]: pkg for pkg in conda_pkg_list} + +# base env resolved +assert pkgs["python"]["version"].startswith("3.9"), pkgs["python"] +assert "xeus-cling" in pkgs +assert pkgs["xeus-cling"]["version"] == "0.6.0" + +# verify downgrade +# this may be brittle, but it's unlikely any of these old versions +# of packages will be rebuilt +# xeus-cling 0.6.0 pins xeus 0.20, which pins openssl 1.1.1, +# which in turn downgrades Python from >=3.9.16 to 3.9.6 + +assert pkgs["openssl"]["version"].startswith("1.1.1"), pkgs["openssl"]["version"] +assert pkgs["python"]["version"] == "3.9.6", pkgs["python"]["version"] diff --git a/tests/external/reproductions.repos.yaml b/tests/external/reproductions.repos.yaml index 74f1085c4..55509a019 100644 --- a/tests/external/reproductions.repos.yaml +++ b/tests/external/reproductions.repos.yaml @@ -24,12 +24,6 @@ url: https://github.com/binder-examples/requirements ref: python-3.7 verify: python -c 'import matplotlib' -# Test that custom channels and downgrades don't -# get blocked by pinning -- name: Xeus-Cling - url: https://github.com/QuantStack/xeus-cling - ref: 0.6.0 - verify: jupyter kernelspec list # Zenodo record of https://github.com/binder-examples/requirements - name: 10.5281/zenodo.3242074 url: 10.5281/zenodo.3242074 From 62f5dbfe4e7ab0d89b75e98ed03d86ee3b3753cb Mon Sep 17 00:00:00 2001 From: Min RK Date: Wed, 8 Feb 2023 14:26:12 +0100 Subject: [PATCH 117/171] update binder-examples/requirements tag test to one with specified Python version --- tests/external/reproductions.repos.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/tests/external/reproductions.repos.yaml b/tests/external/reproductions.repos.yaml index 55509a019..060c33313 100644 --- a/tests/external/reproductions.repos.yaml +++ b/tests/external/reproductions.repos.yaml @@ -10,19 +10,19 @@ ref: b8259dac9eb verify: python -c 'import matplotlib' # Test that a full remote/ref works -- name: Binder Examples - Requirements +- name: Binder Examples - Requirements - origin/main url: https://github.com/binder-examples/requirements ref: origin/main verify: python -c 'import matplotlib' # Test that ref is added to branch if not present -- name: Binder Examples - Requirements +- name: Binder Examples - Requirements - main url: https://github.com/binder-examples/requirements ref: main verify: python -c 'import matplotlib' # Test that tags work + ref is added to tag if not present -- name: Binder Examples - Requirements +- name: Binder Examples - Requirements - tag url: https://github.com/binder-examples/requirements - ref: python-3.7 + ref: python-3.8 verify: python -c 'import matplotlib' # Zenodo record of https://github.com/binder-examples/requirements - name: 10.5281/zenodo.3242074 From b84abf3b775a035b039a0b7dcb14b45a39a19490 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Roberto=20Di=20Remigio=20Eik=C3=A5s?= Date: Sat, 11 Feb 2023 11:34:32 +0100 Subject: [PATCH 118/171] Update install-nix.bash --- repo2docker/buildpacks/nix/install-nix.bash | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/repo2docker/buildpacks/nix/install-nix.bash b/repo2docker/buildpacks/nix/install-nix.bash index be0cb1a5d..f3524e627 100644 --- a/repo2docker/buildpacks/nix/install-nix.bash +++ b/repo2docker/buildpacks/nix/install-nix.bash @@ -2,11 +2,11 @@ # This downloads and installs a pinned version of nix set -ex -NIX_VERSION="2.3.9" +NIX_VERSION="2.13.2" if [ "$NIX_ARCH" = "aarch64" ]; then - NIX_SHA256="733a26911193fdd44d5d68342075af5924d8c0701aae877e51a38d74ee9f4ff8" + NIX_SHA256="4ae275a46a2441d3459ae389a90ce6e8f7eff12c2a084b2d003ba6f8d0899603" else - NIX_SHA256="49763fd7fa06bcb712ced2f3f11afd275e3a4d7bc5ff0d6fd1d50a4c3ce7bbf4" + NIX_SHA256="beaec0f28899c22f33adbe30e4ecfceef87b797278c5210ee693e22e9719dfb4" fi # Do all our operations in /tmp, since we can't rely on current directory being writeable yet. From 5e8ee1ca7ddfba1af89be6147fbfca1fa7b75f07 Mon Sep 17 00:00:00 2001 From: Simon Li Date: Sun, 12 Feb 2023 00:16:14 +0000 Subject: [PATCH 119/171] Add registry optional credentials to push() --- repo2docker/docker.py | 2 ++ repo2docker/engine.py | 37 +++++++++++++++++++++++++++++++++ tests/unit/test_docker.py | 43 +++++++++++++++++++++++++++++++++++++++ 3 files changed, 82 insertions(+) diff --git a/repo2docker/docker.py b/repo2docker/docker.py index 39d9e0441..170eea3fb 100644 --- a/repo2docker/docker.py +++ b/repo2docker/docker.py @@ -120,6 +120,8 @@ def inspect_image(self, image): return Image(tags=image["RepoTags"], config=image["ContainerConfig"]) def push(self, image_spec): + if self.registry_credentials: + self._apiclient.login(**self.registry_credentials) return self._apiclient.push(image_spec, stream=True) def run( diff --git a/repo2docker/engine.py b/repo2docker/engine.py index f3febccc0..a8897a64e 100644 --- a/repo2docker/engine.py +++ b/repo2docker/engine.py @@ -2,8 +2,11 @@ Interface for a repo2docker container engine """ +import json +import os from abc import ABC, abstractmethod +from traitlets import Dict, default from traitlets.config import LoggingConfigurable # Based on https://docker-py.readthedocs.io/en/4.2.0/containers.html @@ -142,6 +145,37 @@ class ContainerEngine(LoggingConfigurable): Initialised with a reference to the parent so can also be configured using traitlets. """ + registry_credentials = Dict( + help=""" + Credentials dictionary, if set will be used to authenticate with + the registry. Typically this will include the keys: + + - `username`: The registry username + - `password`: The registry password or token + - `registry`: The registry URL + + This can also be set by passing a JSON object in the + CONTAINER_ENGINE_REGISTRY_CREDENTIALS environment variable. + """, + config=True, + ) + + @default("registry_credentials") + def _registry_credentials_default(self): + """ + Set the registry credentials from CONTAINER_ENGINE_REGISTRY_CREDENTIALS + """ + obj = os.getenv("CONTAINER_ENGINE_REGISTRY_CREDENTIALS") + if obj: + try: + return json.loads(obj) + except json.JSONDecodeError: + self.log.error( + "CONTAINER_ENGINE_REGISTRY_CREDENTIALS is not valid JSON" + ) + raise + return {} + string_output = True """ Whether progress events should be strings or an object. @@ -251,6 +285,9 @@ def push(self, image_spec): """ Push image to a registry + If the registry_credentials traitlets is set it should be used to + authenticate with the registry before pushing. + Parameters ---------- image_spec : str diff --git a/tests/unit/test_docker.py b/tests/unit/test_docker.py index 2fe0b6f5e..c47aa4fa0 100644 --- a/tests/unit/test_docker.py +++ b/tests/unit/test_docker.py @@ -2,6 +2,9 @@ import os from subprocess import check_output +from unittest.mock import Mock, patch + +from repo2docker.docker import DockerEngine repo_root = os.path.abspath( os.path.join(os.path.dirname(__file__), os.pardir, os.pardir) @@ -19,3 +22,43 @@ def test_git_credential_env(): .strip() ) assert out == credential_env + + +class MockDockerEngine(DockerEngine): + def __init__(self, *args, **kwargs): + self._apiclient = Mock() + + +def test_docker_push_no_credentials(): + engine = MockDockerEngine() + + engine.push("image") + + assert len(engine._apiclient.method_calls) == 1 + engine._apiclient.push.assert_called_once_with("image", stream=True) + + +def test_docker_push_dict_credentials(): + engine = MockDockerEngine() + engine.registry_credentials = {"username": "abc", "password": "def"} + + engine.push("image") + + assert len(engine._apiclient.method_calls) == 2 + engine._apiclient.login.assert_called_once_with(username="abc", password="def") + engine._apiclient.push.assert_called_once_with("image", stream=True) + + +def test_docker_push_env_credentials(): + engine = MockDockerEngine() + with patch.dict( + "os.environ", + { + "CONTAINER_ENGINE_REGISTRY_CREDENTIALS": '{"username": "abc", "password": "def"}' + }, + ): + engine.push("image") + + assert len(engine._apiclient.method_calls) == 2 + engine._apiclient.login.assert_called_once_with(username="abc", password="def") + engine._apiclient.push.assert_called_once_with("image", stream=True) From 0f328e67e774b4fe864b998d713cf641b1255b02 Mon Sep 17 00:00:00 2001 From: Min RK Date: Wed, 15 Feb 2023 14:10:59 +0100 Subject: [PATCH 120/171] Julia 0.6 needs Jupyter from py35 environment --- repo2docker/buildpacks/julia/julia_require.py | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/repo2docker/buildpacks/julia/julia_require.py b/repo2docker/buildpacks/julia/julia_require.py index b3b8cecf2..ad3f5448d 100644 --- a/repo2docker/buildpacks/julia/julia_require.py +++ b/repo2docker/buildpacks/julia/julia_require.py @@ -82,6 +82,14 @@ def get_build_env(self): else: julia_arch = "x86_64" julia_arch_short = "x64" + + if V(self.julia_version) < V("0.7"): + # IJulia with Julia 0.6 isn't compatible with more recent jupyter-core + # point it to the one in the kernel env + # I _think_ this is only relevant during installation + jupyter = "${KERNEL_PYTHON_PREFIX}/bin/jupyter" + else: + jupyter = "${NB_PYTHON_PREFIX}/bin/jupyter" return super().get_build_env() + [ ("JULIA_PATH", "${APP_BASE}/julia"), ("JULIA_HOME", "${JULIA_PATH}/bin"), # julia <= 0.6 @@ -91,7 +99,7 @@ def get_build_env(self): ("JULIA_VERSION", self.julia_version), ("JULIA_ARCH", julia_arch), ("JULIA_ARCH_SHORT", julia_arch_short), - ("JUPYTER", "${NB_PYTHON_PREFIX}/bin/jupyter"), + ("JUPYTER", jupyter), ] def get_path(self): From 5f6d76764b8f650fb27fbda462b537e8b16e4ec0 Mon Sep 17 00:00:00 2001 From: Min RK Date: Wed, 15 Feb 2023 12:53:08 +0100 Subject: [PATCH 121/171] update test expectations in py35/py36 tests `/usr/bin/env python` is no longer the kernel python --- tests/conda/py35-binder-dir/verify | 21 ++++++++++++++++----- tests/external/reproductions.repos.yaml | 2 +- tests/pipfile/py36/verify | 8 ++++---- tests/venv/py35/verify | 2 +- 4 files changed, 22 insertions(+), 11 deletions(-) diff --git a/tests/conda/py35-binder-dir/verify b/tests/conda/py35-binder-dir/verify index 8bad344de..dc2d9a60d 100755 --- a/tests/conda/py35-binder-dir/verify +++ b/tests/conda/py35-binder-dir/verify @@ -1,17 +1,28 @@ #!/usr/bin/env python +import os import sys -from subprocess import check_output +from subprocess import STDOUT, check_output -assert sys.version_info[:2] == (3, 5), sys.version +assert sys.version_info[:2] == (3, 7), sys.version -out = check_output(["micromamba", "--version"]).decode("utf8").strip() + +def sh(cmd, **kwargs): + return check_output(cmd, **kwargs).decode("utf8").strip() + + +kernel_python = os.path.join(os.environ["KERNEL_PYTHON_PREFIX"], "bin", "python") +out = sh([kernel_python, "--version"], stderr=STDOUT) +v = out.split()[1] +assert v[:3] == "3.5", out + +out = sh(["micromamba", "--version"]) assert out == "1.1.0", out -out = check_output(["mamba", "--version"]).decode("utf8").strip() +out = sh(["mamba", "--version"]) assert ( out == """mamba 1.1.0 conda 4.13.0""" ), out -import numpy +sh([kernel_python, "-c", "import numpy"]) diff --git a/tests/external/reproductions.repos.yaml b/tests/external/reproductions.repos.yaml index 74f1085c4..6f9c3459f 100644 --- a/tests/external/reproductions.repos.yaml +++ b/tests/external/reproductions.repos.yaml @@ -33,7 +33,7 @@ # Zenodo record of https://github.com/binder-examples/requirements - name: 10.5281/zenodo.3242074 url: 10.5281/zenodo.3242074 - verify: python -c 'import matplotlib' + verify: /srv/conda/envs/kernel/bin/python -c 'import matplotlib' # Test that files in git-lfs are properly cloned - name: LFS url: https://github.com/binderhub-ci-repos/lfs diff --git a/tests/pipfile/py36/verify b/tests/pipfile/py36/verify index f71a6daa8..f54d226ad 100755 --- a/tests/pipfile/py36/verify +++ b/tests/pipfile/py36/verify @@ -1,8 +1,8 @@ -#!/usr/bin/env python +#!/srv/conda/envs/kernel/bin/python import sys -import pypi_pkg_test -import there - print(sys.version_info) assert sys.version_info[:2] == (3, 6) + +import pypi_pkg_test # noqa +import there # noqa diff --git a/tests/venv/py35/verify b/tests/venv/py35/verify index 4abec3090..6475d4f3c 100755 --- a/tests/venv/py35/verify +++ b/tests/venv/py35/verify @@ -1,4 +1,4 @@ -#!/usr/bin/env python3 +#!/srv/conda/envs/kernel/bin/python import sys print(sys.version_info) From 1a2438d34ec82774eca5ba92f604fa388702fc51 Mon Sep 17 00:00:00 2001 From: Min RK Date: Thu, 16 Feb 2023 12:44:18 +0100 Subject: [PATCH 122/171] default env is 3.10 --- .../conda/environment-linux-64.lock | 27 ++++++++++--------- .../conda/environment-linux-aarch64.lock | 27 ++++++++++--------- 2 files changed, 28 insertions(+), 26 deletions(-) diff --git a/repo2docker/buildpacks/conda/environment-linux-64.lock b/repo2docker/buildpacks/conda/environment-linux-64.lock index 34daf8aa2..a934da5e8 100644 --- a/repo2docker/buildpacks/conda/environment-linux-64.lock +++ b/repo2docker/buildpacks/conda/environment-linux-64.lock @@ -1,8 +1,8 @@ -# AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY -# Frozen on 2023-02-03 12:33:27 UTC +# AUTO GENERATED FROM environment.py-3.10.yml, DO NOT MANUALLY MODIFY +# Frozen on 2023-02-03 12:34:24 UTC # Generated by conda-lock. # platform: linux-64 -# input_hash: 56d66ed1f6b5535bd09b3fb8546cc5bdb3cea65aa2ed89ffaf52424a63c739aa +# input_hash: 9fd16b0f6d64e86a62e326694b74a429aef5dd7b227a96b4f0e2425851e4e016 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.12.7-ha878542_0.conda#ff9f73d45c4a07d6f424495288a26080 @@ -13,6 +13,7 @@ https://conda.anaconda.org/conda-forge/noarch/tzdata-2022g-h191b570_0.conda#51fc https://conda.anaconda.org/conda-forge/linux-64/libgomp-12.2.0-h65d4601_19.tar.bz2#cedcee7c064c01c403f962c9e8d3c373 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-12.2.0-h65d4601_19.tar.bz2#e4c94f80aef025c17ab0828cd85ef535 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h7f98852_4.tar.bz2#a1fd65c7ccbf10880423d82bca54eb54 https://conda.anaconda.org/conda-forge/linux-64/icu-70.1-h27087fc_0.tar.bz2#87473a15119779e021c314249d4b4aed https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.0-h7f98852_0.tar.bz2#39b1328babf85c7c3a61636d9cd50206 @@ -30,8 +31,7 @@ https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.12-h27826a3_0.tar.bz2#5b8 https://conda.anaconda.org/conda-forge/linux-64/zeromq-4.3.4-h9c3ff4c_1.tar.bz2#21743a8d2ea0c8cfbbf8fe489b0347df https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-h166bdaf_4.tar.bz2#4b11e365c0275b808be78b30f904e295 https://conda.anaconda.org/conda-forge/linux-64/nodejs-18.12.1-h8839609_0.tar.bz2#305f25b78340b0f7b391a6919d1246f2 -https://conda.anaconda.org/conda-forge/linux-64/sqlite-3.40.0-h4ff8645_0.tar.bz2#bb11803129cbbb53ed56f9506ff74145 -https://conda.anaconda.org/conda-forge/linux-64/python-3.7.12-hf930737_100_cpython.tar.bz2#416558a6f46b7a1fa8db7d0e98aff56a +https://conda.anaconda.org/conda-forge/linux-64/python-3.10.9-he550d4f_0_cpython.conda#3cb3e91b3fe66baa68a12c85f39b9b40 https://conda.anaconda.org/conda-forge/noarch/async_generator-1.10-py_0.tar.bz2#d56c596e61b1c4952acf0a9920856c12 https://conda.anaconda.org/conda-forge/noarch/attrs-22.2.0-pyh71513ae_0.conda#8b76db7818a4e401ed4486c4c1635cd9 https://conda.anaconda.org/conda-forge/noarch/backcall-0.2.0-pyh9f0ad1d_0.tar.bz2#6006a6d08a3fa99268a2681c7fb55213 @@ -50,7 +50,6 @@ https://conda.anaconda.org/conda-forge/noarch/idna-3.4-pyhd8ed1ab_0.tar.bz2#3427 https://conda.anaconda.org/conda-forge/noarch/ipython_genutils-0.2.0-py_1.tar.bz2#5071c982548b3a20caf70462f04f5287 https://conda.anaconda.org/conda-forge/noarch/json5-0.9.5-pyh9f0ad1d_0.tar.bz2#10759827a94e6b14996e81fb002c0bda https://conda.anaconda.org/conda-forge/noarch/jupyterlab_widgets-3.0.5-pyhd8ed1ab_0.conda#953a312b272f37d39fe9d09f46734622 -https://conda.anaconda.org/conda-forge/linux-64/libcurl-7.87.0-hdc1c0ab_0.conda#bc302fa1cf8eda15c60f669b7524a320 https://conda.anaconda.org/conda-forge/linux-64/markupsafe-2.1.2-py310h1fa729e_0.conda#a1f0db6709778b77b5903541eeac4032 https://conda.anaconda.org/conda-forge/noarch/mistune-2.0.4-pyhd8ed1ab_0.tar.bz2#78e0a90393b79b378b8ff6d32893d58a https://conda.anaconda.org/conda-forge/noarch/nest-asyncio-1.5.6-pyhd8ed1ab_0.tar.bz2#7b868f21adde0d9b8b38f9c16836589b @@ -61,7 +60,7 @@ https://conda.anaconda.org/conda-forge/noarch/parso-0.8.3-pyhd8ed1ab_0.tar.bz2#1 https://conda.anaconda.org/conda-forge/noarch/pickleshare-0.7.5-py_1003.tar.bz2#415f0ebb6198cc2801c73438a9fb5761 https://conda.anaconda.org/conda-forge/noarch/pkgutil-resolve-name-1.3.10-pyhd8ed1ab_0.tar.bz2#89e3c7cdde7d3aaa2aee933b604dd07f https://conda.anaconda.org/conda-forge/noarch/prometheus_client-0.16.0-pyhd8ed1ab_0.conda#8efaddc1c8b8ce262c4d1a7c6571c799 -https://conda.anaconda.org/conda-forge/linux-64/psutil-5.9.3-py37h540881e_0.tar.bz2#0c813ad118e926df328bf74899a48047 +https://conda.anaconda.org/conda-forge/linux-64/psutil-5.9.4-py310h5764c6d_0.tar.bz2#c3c55664e9becc48e6a652e2b641961f https://conda.anaconda.org/conda-forge/noarch/ptyprocess-0.7.0-pyhd3deb0d_0.tar.bz2#359eeb6536da0e687af562ed265ec263 https://conda.anaconda.org/conda-forge/noarch/pure_eval-0.2.2-pyhd8ed1ab_0.tar.bz2#6784285c7e55cb7212efabc79e4c2883 https://conda.anaconda.org/conda-forge/noarch/pycparser-2.21-pyhd8ed1ab_0.tar.bz2#076becd9e05608f8dc72757d5f3a91ff @@ -79,7 +78,7 @@ https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2#e5 https://conda.anaconda.org/conda-forge/noarch/sniffio-1.3.0-pyhd8ed1ab_0.tar.bz2#dd6cbc539e74cb1f430efbd4575b9303 https://conda.anaconda.org/conda-forge/noarch/soupsieve-2.3.2.post1-pyhd8ed1ab_0.tar.bz2#146f4541d643d48fc8a75cacf69f03ae https://conda.anaconda.org/conda-forge/noarch/tomli-2.0.1-pyhd8ed1ab_0.tar.bz2#5844808ffab9ebdb694585b50ba02a96 -https://conda.anaconda.org/conda-forge/linux-64/tornado-6.2-py37h540881e_0.tar.bz2#2f0863ba6b29d1d2872b064dd697a492 +https://conda.anaconda.org/conda-forge/linux-64/tornado-6.2-py310h5764c6d_1.tar.bz2#be4a201ac582c11d89ed7d15b3157cc3 https://conda.anaconda.org/conda-forge/noarch/traitlets-5.9.0-pyhd8ed1ab_0.conda#d0b4f5c87cd35ac3fb3d47b223263a64 https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.4.0-pyha770c72_0.tar.bz2#2d93b130d148d7fc77e583677792fc6a https://conda.anaconda.org/conda-forge/noarch/webencodings-0.5.1-py_1.tar.bz2#3563be4c5611a44210d9ba0c16113136 @@ -93,8 +92,9 @@ https://conda.anaconda.org/conda-forge/noarch/babel-2.11.0-pyhd8ed1ab_0.tar.bz2# https://conda.anaconda.org/conda-forge/noarch/backports.functools_lru_cache-1.6.4-pyhd8ed1ab_0.tar.bz2#c5b3edc62d6309088f4970b3eaaa65a6 https://conda.anaconda.org/conda-forge/noarch/beautifulsoup4-4.11.2-pyha770c72_0.conda#88b59f6989f0ed5ab3433af0b82555e1 https://conda.anaconda.org/conda-forge/noarch/bleach-6.0.0-pyhd8ed1ab_0.conda#d48b143d01385872a88ef8417e96c30e -https://conda.anaconda.org/conda-forge/linux-64/cffi-1.15.1-py37h43b0acd_1.tar.bz2#5111b64bdfdd72d85086ec49c952fe0d -https://conda.anaconda.org/conda-forge/linux-64/importlib-metadata-4.11.4-py37h89c1867_0.tar.bz2#71107630527e4bd82932952351231efe +https://conda.anaconda.org/conda-forge/linux-64/cffi-1.15.1-py310h255011f_3.conda#800596144bb613cd7ac58b80900ce835 +https://conda.anaconda.org/conda-forge/noarch/comm-0.1.2-pyhd8ed1ab_0.conda#3c78af4752bb1600ebe5e83ef4588eaa +https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-6.0.0-pyha770c72_0.conda#691644becbcdca9f73243450b1c63e62 https://conda.anaconda.org/conda-forge/noarch/importlib_resources-5.10.2-pyhd8ed1ab_0.conda#de76905f801c22fc43e624058574eab3 https://conda.anaconda.org/conda-forge/noarch/jedi-0.18.2-pyhd8ed1ab_0.conda#b5e695ef9c3f0d27d6cd96bf5adc9e07 https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.2-pyhd8ed1ab_1.tar.bz2#c8490ed5c70966d232fdd389d0dbed37 @@ -130,12 +130,13 @@ https://conda.anaconda.org/conda-forge/noarch/ipython-8.9.0-pyh41d4057_0.conda#3 https://conda.anaconda.org/conda-forge/noarch/jupyter_client-8.0.2-pyhd8ed1ab_0.conda#cbb8d182b6053ce14b5fe60ef1e36fbb https://conda.anaconda.org/conda-forge/noarch/nbformat-5.7.3-pyhd8ed1ab_0.conda#9714111cb6c7dbbc9a9f34de205c2f29 https://conda.anaconda.org/conda-forge/noarch/urllib3-1.26.14-pyhd8ed1ab_0.conda#01f33ad2e0aaf6b5ba4add50dad5ad29 -https://conda.anaconda.org/conda-forge/noarch/ipykernel-6.16.2-pyh210e3f2_0.tar.bz2#6b0f40821b784cac8a33d0c5eb7602c0 -https://conda.anaconda.org/conda-forge/noarch/nbconvert-core-7.2.9-pyhd8ed1ab_0.conda#a9e1826152e79416db71c51b0d3af28c +https://conda.anaconda.org/conda-forge/noarch/ipykernel-6.21.1-pyh210e3f2_0.conda#225e7869419b8bcae5d3165eba50204d +https://conda.anaconda.org/conda-forge/noarch/nbclient-0.7.2-pyhd8ed1ab_0.conda#6c7b0d75b66a220274bb5a28c23197f2 https://conda.anaconda.org/conda-forge/noarch/requests-2.28.2-pyhd8ed1ab_0.conda#11d178fc55199482ee48d6812ea83983 https://conda.anaconda.org/conda-forge/noarch/ipywidgets-8.0.2-pyhd8ed1ab_1.tar.bz2#81b7f46918555bf911ad2ba2f3259094 -https://conda.anaconda.org/conda-forge/noarch/jupyter_server-1.23.4-pyhd8ed1ab_0.conda#35b7e9267926e864cc70ce137e6588ca https://conda.anaconda.org/conda-forge/noarch/jupyterhub-base-3.1.1-pyh2a2186d_0.conda#78fc5dfd4577a7ba172fa65eb64b6afb +https://conda.anaconda.org/conda-forge/noarch/nbconvert-core-7.2.9-pyhd8ed1ab_0.conda#a9e1826152e79416db71c51b0d3af28c +https://conda.anaconda.org/conda-forge/noarch/jupyter_server-1.23.5-pyhd8ed1ab_0.conda#e3ae1d46749f48a1875b560fca41cb0c https://conda.anaconda.org/conda-forge/noarch/nbconvert-pandoc-7.2.9-pyhd8ed1ab_0.conda#4a8dc94c7c2f3736dc4b91ec345d5b4b https://conda.anaconda.org/conda-forge/noarch/jupyter-resource-usage-0.7.0-pyhd8ed1ab_0.conda#c57567d49d926826b1f852712ac8acfa https://conda.anaconda.org/conda-forge/noarch/jupyterlab_server-2.19.0-pyhd8ed1ab_0.conda#9dc0706ec2f8e13b7a0db9d6a19051ff diff --git a/repo2docker/buildpacks/conda/environment-linux-aarch64.lock b/repo2docker/buildpacks/conda/environment-linux-aarch64.lock index b15d9dffb..3bc2523a4 100644 --- a/repo2docker/buildpacks/conda/environment-linux-aarch64.lock +++ b/repo2docker/buildpacks/conda/environment-linux-aarch64.lock @@ -1,8 +1,8 @@ -# AUTO GENERATED FROM environment.py-3.7.yml, DO NOT MANUALLY MODIFY -# Frozen on 2023-02-03 12:33:35 UTC +# AUTO GENERATED FROM environment.py-3.10.yml, DO NOT MANUALLY MODIFY +# Frozen on 2023-02-03 12:34:31 UTC # Generated by conda-lock. # platform: linux-aarch64 -# input_hash: 5d827030b8550a7c54b1799a2f8975f8c422c8cd7f555193fcd4912380c6d3cb +# input_hash: c039d9a57d204f210d3832a8744df6e5ed536030655439a29ff883148f704b60 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-aarch64/ca-certificates-2022.12.7-h4fd8a4c_0.conda#2450fbcaf65634e0d071e47e2b8487b4 https://conda.anaconda.org/conda-forge/linux-aarch64/ld_impl_linux-aarch64-2.40-h2d8c526_0.conda#16246d69e945d0b1969a6099e7c5d457 @@ -13,6 +13,7 @@ https://conda.anaconda.org/conda-forge/linux-aarch64/python_abi-3.10-3_cp310.con https://conda.anaconda.org/conda-forge/noarch/tzdata-2022g-h191b570_0.conda#51fc4fcfb19f5d95ffc8c339db5068e8 https://conda.anaconda.org/conda-forge/linux-aarch64/_openmp_mutex-4.5-2_gnu.tar.bz2#6168d71addc746e8f2b8d57dfd2edcea https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-ng-12.2.0-h607ecd0_19.tar.bz2#8456a29b6d9fc3123ccb9a966b6b2c49 +https://conda.anaconda.org/conda-forge/linux-aarch64/bzip2-1.0.8-hf897c2e_4.tar.bz2#2d787570a729e273a4e75775ddf3348a 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-https://conda.anaconda.org/conda-forge/linux-aarch64/python-3.7.12-h47f6e27_100_cpython.tar.bz2#d7b2c7500aa702c992c285854bef95a7 +https://conda.anaconda.org/conda-forge/linux-aarch64/python-3.10.9-ha43d526_0_cpython.conda#24478dd738f2d557efe2a4fc6a248eb3 https://conda.anaconda.org/conda-forge/noarch/async_generator-1.10-py_0.tar.bz2#d56c596e61b1c4952acf0a9920856c12 https://conda.anaconda.org/conda-forge/noarch/attrs-22.2.0-pyh71513ae_0.conda#8b76db7818a4e401ed4486c4c1635cd9 https://conda.anaconda.org/conda-forge/noarch/backcall-0.2.0-pyh9f0ad1d_0.tar.bz2#6006a6d08a3fa99268a2681c7fb55213 @@ -49,7 +49,6 @@ https://conda.anaconda.org/conda-forge/noarch/idna-3.4-pyhd8ed1ab_0.tar.bz2#3427 https://conda.anaconda.org/conda-forge/noarch/ipython_genutils-0.2.0-py_1.tar.bz2#5071c982548b3a20caf70462f04f5287 https://conda.anaconda.org/conda-forge/noarch/json5-0.9.5-pyh9f0ad1d_0.tar.bz2#10759827a94e6b14996e81fb002c0bda https://conda.anaconda.org/conda-forge/noarch/jupyterlab_widgets-3.0.5-pyhd8ed1ab_0.conda#953a312b272f37d39fe9d09f46734622 -https://conda.anaconda.org/conda-forge/linux-aarch64/libcurl-7.87.0-h6ad7c7a_0.conda#6e8310f3e0b523e64faa9012d4151ff0 https://conda.anaconda.org/conda-forge/linux-aarch64/markupsafe-2.1.2-py310h734f5e8_0.conda#e511c7fb8abad744ecbf1dee01603cde https://conda.anaconda.org/conda-forge/noarch/mistune-2.0.4-pyhd8ed1ab_0.tar.bz2#78e0a90393b79b378b8ff6d32893d58a https://conda.anaconda.org/conda-forge/noarch/nest-asyncio-1.5.6-pyhd8ed1ab_0.tar.bz2#7b868f21adde0d9b8b38f9c16836589b @@ -60,7 +59,7 @@ https://conda.anaconda.org/conda-forge/noarch/parso-0.8.3-pyhd8ed1ab_0.tar.bz2#1 https://conda.anaconda.org/conda-forge/noarch/pickleshare-0.7.5-py_1003.tar.bz2#415f0ebb6198cc2801c73438a9fb5761 https://conda.anaconda.org/conda-forge/noarch/pkgutil-resolve-name-1.3.10-pyhd8ed1ab_0.tar.bz2#89e3c7cdde7d3aaa2aee933b604dd07f https://conda.anaconda.org/conda-forge/noarch/prometheus_client-0.16.0-pyhd8ed1ab_0.conda#8efaddc1c8b8ce262c4d1a7c6571c799 -https://conda.anaconda.org/conda-forge/linux-aarch64/psutil-5.9.3-py37h795501a_0.tar.bz2#4fd90f8ee043a535f1effd3b2260d46c +https://conda.anaconda.org/conda-forge/linux-aarch64/psutil-5.9.4-py310h761cc84_0.tar.bz2#50a75748a7239960359f38a13db42c4c https://conda.anaconda.org/conda-forge/noarch/ptyprocess-0.7.0-pyhd3deb0d_0.tar.bz2#359eeb6536da0e687af562ed265ec263 https://conda.anaconda.org/conda-forge/noarch/pure_eval-0.2.2-pyhd8ed1ab_0.tar.bz2#6784285c7e55cb7212efabc79e4c2883 https://conda.anaconda.org/conda-forge/noarch/pycparser-2.21-pyhd8ed1ab_0.tar.bz2#076becd9e05608f8dc72757d5f3a91ff @@ -78,7 +77,7 @@ https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2#e5 https://conda.anaconda.org/conda-forge/noarch/sniffio-1.3.0-pyhd8ed1ab_0.tar.bz2#dd6cbc539e74cb1f430efbd4575b9303 https://conda.anaconda.org/conda-forge/noarch/soupsieve-2.3.2.post1-pyhd8ed1ab_0.tar.bz2#146f4541d643d48fc8a75cacf69f03ae https://conda.anaconda.org/conda-forge/noarch/tomli-2.0.1-pyhd8ed1ab_0.tar.bz2#5844808ffab9ebdb694585b50ba02a96 -https://conda.anaconda.org/conda-forge/linux-aarch64/tornado-6.2-py37heeccf27_0.tar.bz2#e87e4ac6adb1b6564b5910ddb967401b +https://conda.anaconda.org/conda-forge/linux-aarch64/tornado-6.2-py310hdc54845_1.tar.bz2#343c5468b69f14f4009cfcf8ae286f98 https://conda.anaconda.org/conda-forge/noarch/traitlets-5.9.0-pyhd8ed1ab_0.conda#d0b4f5c87cd35ac3fb3d47b223263a64 https://conda.anaconda.org/conda-forge/noarch/typing_extensions-4.4.0-pyha770c72_0.tar.bz2#2d93b130d148d7fc77e583677792fc6a https://conda.anaconda.org/conda-forge/noarch/webencodings-0.5.1-py_1.tar.bz2#3563be4c5611a44210d9ba0c16113136 @@ -92,8 +91,9 @@ https://conda.anaconda.org/conda-forge/noarch/babel-2.11.0-pyhd8ed1ab_0.tar.bz2# https://conda.anaconda.org/conda-forge/noarch/backports.functools_lru_cache-1.6.4-pyhd8ed1ab_0.tar.bz2#c5b3edc62d6309088f4970b3eaaa65a6 https://conda.anaconda.org/conda-forge/noarch/beautifulsoup4-4.11.2-pyha770c72_0.conda#88b59f6989f0ed5ab3433af0b82555e1 https://conda.anaconda.org/conda-forge/noarch/bleach-6.0.0-pyhd8ed1ab_0.conda#d48b143d01385872a88ef8417e96c30e -https://conda.anaconda.org/conda-forge/linux-aarch64/cffi-1.15.1-py37h828e148_1.tar.bz2#50a7437124b0618862af25f390dc259f -https://conda.anaconda.org/conda-forge/linux-aarch64/importlib-metadata-4.11.4-py37hd9ded2f_0.tar.bz2#0f8204faf4756a6f66a609a51992dec0 +https://conda.anaconda.org/conda-forge/linux-aarch64/cffi-1.15.1-py310hf0c4615_3.conda#a2bedcb1d205485ea32fe5d2bd6fd970 +https://conda.anaconda.org/conda-forge/noarch/comm-0.1.2-pyhd8ed1ab_0.conda#3c78af4752bb1600ebe5e83ef4588eaa +https://conda.anaconda.org/conda-forge/noarch/importlib-metadata-6.0.0-pyha770c72_0.conda#691644becbcdca9f73243450b1c63e62 https://conda.anaconda.org/conda-forge/noarch/importlib_resources-5.10.2-pyhd8ed1ab_0.conda#de76905f801c22fc43e624058574eab3 https://conda.anaconda.org/conda-forge/noarch/jedi-0.18.2-pyhd8ed1ab_0.conda#b5e695ef9c3f0d27d6cd96bf5adc9e07 https://conda.anaconda.org/conda-forge/noarch/jinja2-3.1.2-pyhd8ed1ab_1.tar.bz2#c8490ed5c70966d232fdd389d0dbed37 @@ -129,12 +129,13 @@ https://conda.anaconda.org/conda-forge/noarch/ipython-8.9.0-pyh41d4057_0.conda#3 https://conda.anaconda.org/conda-forge/noarch/jupyter_client-8.0.2-pyhd8ed1ab_0.conda#cbb8d182b6053ce14b5fe60ef1e36fbb https://conda.anaconda.org/conda-forge/noarch/nbformat-5.7.3-pyhd8ed1ab_0.conda#9714111cb6c7dbbc9a9f34de205c2f29 https://conda.anaconda.org/conda-forge/noarch/urllib3-1.26.14-pyhd8ed1ab_0.conda#01f33ad2e0aaf6b5ba4add50dad5ad29 -https://conda.anaconda.org/conda-forge/noarch/ipykernel-6.16.2-pyh210e3f2_0.tar.bz2#6b0f40821b784cac8a33d0c5eb7602c0 -https://conda.anaconda.org/conda-forge/noarch/nbconvert-core-7.2.9-pyhd8ed1ab_0.conda#a9e1826152e79416db71c51b0d3af28c +https://conda.anaconda.org/conda-forge/noarch/ipykernel-6.21.1-pyh210e3f2_0.conda#225e7869419b8bcae5d3165eba50204d +https://conda.anaconda.org/conda-forge/noarch/nbclient-0.7.2-pyhd8ed1ab_0.conda#6c7b0d75b66a220274bb5a28c23197f2 https://conda.anaconda.org/conda-forge/noarch/requests-2.28.2-pyhd8ed1ab_0.conda#11d178fc55199482ee48d6812ea83983 https://conda.anaconda.org/conda-forge/noarch/ipywidgets-8.0.2-pyhd8ed1ab_1.tar.bz2#81b7f46918555bf911ad2ba2f3259094 -https://conda.anaconda.org/conda-forge/noarch/jupyter_server-1.23.4-pyhd8ed1ab_0.conda#35b7e9267926e864cc70ce137e6588ca https://conda.anaconda.org/conda-forge/noarch/jupyterhub-base-3.1.1-pyh2a2186d_0.conda#78fc5dfd4577a7ba172fa65eb64b6afb +https://conda.anaconda.org/conda-forge/noarch/nbconvert-core-7.2.9-pyhd8ed1ab_0.conda#a9e1826152e79416db71c51b0d3af28c +https://conda.anaconda.org/conda-forge/noarch/jupyter_server-1.23.5-pyhd8ed1ab_0.conda#e3ae1d46749f48a1875b560fca41cb0c https://conda.anaconda.org/conda-forge/noarch/nbconvert-pandoc-7.2.9-pyhd8ed1ab_0.conda#4a8dc94c7c2f3736dc4b91ec345d5b4b https://conda.anaconda.org/conda-forge/noarch/jupyter-resource-usage-0.7.0-pyhd8ed1ab_0.conda#c57567d49d926826b1f852712ac8acfa https://conda.anaconda.org/conda-forge/noarch/jupyterlab_server-2.19.0-pyhd8ed1ab_0.conda#9dc0706ec2f8e13b7a0db9d6a19051ff From 52be2d3d64cb2be3f876d00c8d575b15924ff215 Mon Sep 17 00:00:00 2001 From: Min RK Date: Thu, 16 Feb 2023 13:13:09 +0100 Subject: [PATCH 123/171] memoize getters ensures `get_` functions are called only once, avoiding duplicate log statements --- repo2docker/buildpacks/base.py | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/repo2docker/buildpacks/base.py b/repo2docker/buildpacks/base.py index ceed91ce4..60f33edd9 100644 --- a/repo2docker/buildpacks/base.py +++ b/repo2docker/buildpacks/base.py @@ -7,6 +7,7 @@ import sys import tarfile import textwrap +from functools import lru_cache import escapism import jinja2 @@ -230,6 +231,18 @@ def __init__(self): "support is experimental in repo2docker." ) self.platform = "" + self._memoize() + + def _memoize(self): + """Memoize `get_foo` methods with lru_cache() + + Avoids duplicate log statements when calling what should be idempotent methods more than once + """ + for method_name in dir(self): + if method_name.startswith("get_"): + method = getattr(self, method_name) + if callable(method): + setattr(self, method_name, lru_cache()(method)) def get_packages(self): """ From 847fdffe017aa9e7980849ca8e130e1d5a1f3eb5 Mon Sep 17 00:00:00 2001 From: Min RK Date: Thu, 16 Feb 2023 13:25:01 +0100 Subject: [PATCH 124/171] update default env expectations in seperate kernel envs --- tests/conda/py35-binder-dir/verify | 2 +- tests/conda/py36-postBuild/verify.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/conda/py35-binder-dir/verify b/tests/conda/py35-binder-dir/verify index dc2d9a60d..67ea6827b 100755 --- a/tests/conda/py35-binder-dir/verify +++ b/tests/conda/py35-binder-dir/verify @@ -3,7 +3,7 @@ import os import sys from subprocess import STDOUT, check_output -assert sys.version_info[:2] == (3, 7), sys.version +assert sys.version_info[:2] == (3, 10), sys.version def sh(cmd, **kwargs): diff --git a/tests/conda/py36-postBuild/verify.py b/tests/conda/py36-postBuild/verify.py index 806a5c9a5..78c47c3e9 100644 --- a/tests/conda/py36-postBuild/verify.py +++ b/tests/conda/py36-postBuild/verify.py @@ -69,7 +69,7 @@ def test_kernel_env(kernel_conda): def test_server_env(server_conda): # this should be the default version # it will need updating when the default changes - assert server_conda["python"]["version"][:3] == "3.7" + assert server_conda["python"]["version"].split(".")[:2] == ["3", "10"] def test_conda_install(kernel_conda, server_conda): From c1d12ad06d5bad14ce4d50f05c46bc60f3c1f519 Mon Sep 17 00:00:00 2001 From: Min RK Date: Fri, 17 Feb 2023 10:09:21 +0100 Subject: [PATCH 125/171] update docs for default and supported Python versions --- docs/source/config_files.rst | 4 ++-- docs/source/faq.rst | 19 ++++++++++++++++--- 2 files changed, 18 insertions(+), 5 deletions(-) diff --git a/docs/source/config_files.rst b/docs/source/config_files.rst index fe7470970..8d14f7a49 100644 --- a/docs/source/config_files.rst +++ b/docs/source/config_files.rst @@ -43,8 +43,8 @@ specified in your ``environment.yml``. You can also specify which Python version to install in your built environment with ``environment.yml``. By default, ``repo2docker`` installs |default_python| with your ``environment.yml`` unless you include the version of -Python in this file. ``conda`` supports all versions of Python, -though ``repo2docker`` support is best with Python 3.7, 3.6, 3.5 and 2.7. +Python in this file. ``conda`` Should support all versions of Python, +though ``repo2docker`` support is best with Python 3.7-3.11. .. warning:: If you include a Python version in a ``runtime.txt`` file in addition to your diff --git a/docs/source/faq.rst b/docs/source/faq.rst index 50e35276a..ce442d04e 100644 --- a/docs/source/faq.rst +++ b/docs/source/faq.rst @@ -22,6 +22,10 @@ Repo2docker officially supports the following versions of Python (specified in your :ref:`environment.yml ` or :ref:`runtime.txt ` file): +- 3.11 (added in 2023) +- 3.10 (added in 2022, default in 2023) +- 3.9 (added in 2021) +- 3.8 (added in 0.11) - 3.7 (added in 0.7, default in 0.8) - 3.6 (default in 0.7 and earlier) - 3.5 @@ -35,9 +39,18 @@ in the base environment is not packaged for your Python, either because the version of the package is too new and your chosen Python is too old, or vice versa. -I Python 2.7 is specified, a separate environment for the kernel will be -installed with Python 2. The notebook server will run in the default Python 3.7 -environment. +If an old version of Python is specified (3.6 or earlier in 2023), a separate environment for the kernel will be installed with your requested Python version. +The notebook server will run in the default |default_python| environment. +That is, your _notebooks_ will run with Python 3.6, while your notebook _server_ will run with |default_python|. + +These two environments can be distinguished with ``$NB_PYTHON_PREFIX/bin/python`` for the server and ``$KERNEL_PYTHON_PREFIX/bin/python`` for the kernel. +Both of these environment variables area always defined, even when they are the same. + +Starting in 2023, the default version of Python used when Python version is unspecified will be updated more often. +Python itself releases a new version every year now, and repo2docker will follow, with the default Python version generally trailing the latest stable version of Python itself by 1-2 versions. + +If you choose not to specify a Python version, your repository is _guaranteed_ to stop working, eventually. +We **strongly** recommend specifying a Python version (in environment.yml, runtime.txt, Pipfile, etc.) Julia ~~~~~ From 66b8765c6993ddfb2ed61d6154862246045880d9 Mon Sep 17 00:00:00 2001 From: Min RK Date: Wed, 15 Feb 2023 14:38:05 +0100 Subject: [PATCH 126/171] Remove unspecified Python version case - removes lockfile copies without version - enforces that `buildpack.python_version` is always specified (major_pythons['3'] in cases where it could have been falsy before) - warns when Python version is unspecified, which ensures future reproducibility failures --- repo2docker/buildpacks/conda/__init__.py | 94 ++++++----- .../conda/environment-linux-64.lock | 150 ------------------ .../conda/environment-linux-aarch64.lock | 149 ----------------- repo2docker/buildpacks/conda/freeze.py | 7 - repo2docker/buildpacks/pipfile/__init__.py | 10 +- repo2docker/buildpacks/python/__init__.py | 3 + tests/unit/test_env_yml.py | 6 +- 7 files changed, 64 insertions(+), 355 deletions(-) delete mode 100644 repo2docker/buildpacks/conda/environment-linux-64.lock delete mode 100644 repo2docker/buildpacks/conda/environment-linux-aarch64.lock diff --git a/repo2docker/buildpacks/conda/__init__.py b/repo2docker/buildpacks/conda/__init__.py index 688ef04e6..802dfb292 100644 --- a/repo2docker/buildpacks/conda/__init__.py +++ b/repo2docker/buildpacks/conda/__init__.py @@ -165,49 +165,54 @@ def get_build_script_files(self): "conda/activate-conda.sh": "/etc/profile.d/activate-conda.sh", } py_version = self.python_version + if not py_version or len(py_version.split(".")) != 2: + raise ValueError( + f"{self.__class__.__name__}.python_version must always be specified as 'x.y', e.g. '3.10', got {py_version}." + ) self.log.info(f"Building conda environment for python={py_version}\n") # Select the frozen base environment based on Python version. # avoids expensive and possibly conflicting upgrades when changing # major Python versions during upgrade. - # If no version is specified or no matching X.Y version is found, - # the default base environment is used. - frozen_name = f"environment-{self._conda_platform()}.lock" - pip_frozen_name = "requirements.txt" - if py_version: - conda_platform = self._conda_platform() - if self.separate_kernel_env: - self.log.warning( - f"User-requested packages for legacy Python version {py_version} will be installed in a separate kernel environment.\n" + conda_platform = self._conda_platform() + + if self.separate_kernel_env: + # setup kernel environment (separate from server) + # server runs with default env + server_py_version = self.major_pythons["3"] + self.log.warning( + f"User-requested packages for legacy Python version {py_version} will be installed in a separate kernel environment in $KERNEL_PYTHON_PREFIX.\n" + f"Jupyter Server will run with {server_py_version} in $NB_PYTHON_PREFIX.\n" + ) + lockfile_name = f"environment.py-{py_version}-{conda_platform}.lock" + if not os.path.exists(os.path.join(HERE, lockfile_name)): + raise ValueError( + f"Python version {py_version} on {conda_platform} is not supported!" ) - lockfile_name = f"environment.py-{py_version}-{conda_platform}.lock" - if not os.path.exists(os.path.join(HERE, lockfile_name)): - raise ValueError( - f"Python version {py_version} on {conda_platform} is not supported!" - ) + files[ + f"conda/{lockfile_name}" + ] = self._kernel_environment_file = "/tmp/env/kernel-environment.lock" + + requirements_file_name = f"requirements.py-{py_version}.pip" + if os.path.exists(os.path.join(HERE, requirements_file_name)): files[ - f"conda/{lockfile_name}" - ] = self._kernel_environment_file = "/tmp/env/kernel-environment.lock" - - requirements_file_name = f"requirements.py-{py_version}.pip" - if os.path.exists(os.path.join(HERE, requirements_file_name)): - files[ - f"conda/{requirements_file_name}" - ] = ( - self._kernel_requirements_file - ) = "/tmp/env/kernel-requirements.txt" - else: - py_frozen_name = ( - f"environment.py-{py_version}-{self._conda_platform()}.lock" - ) - if os.path.exists(os.path.join(HERE, py_frozen_name)): - frozen_name = py_frozen_name - pip_frozen_name = f"requirements.py-{py_version}.pip" - else: - raise ValueError( - f"Python version {py_version} {self._conda_platform()} is not supported!" - ) + f"conda/{requirements_file_name}" + ] = self._kernel_requirements_file = "/tmp/env/kernel-requirements.txt" + else: + # server and kernel are the same + server_py_version = py_version + + # setup the server Python environment + conda_frozen_name = f"environment.py-{server_py_version}-{conda_platform}.lock" + pip_frozen_name = f"requirements.py-{server_py_version}.pip" + + if not os.path.exists(os.path.join(HERE, conda_frozen_name)): + # no env, not supported + raise ValueError( + f"Python version {server_py_version} on {conda_platform} is not supported!" + ) + files[ - "conda/" + frozen_name + "conda/" + conda_frozen_name ] = self._nb_environment_file = "/tmp/env/environment.lock" # add requirements.txt, if present @@ -267,8 +272,9 @@ def _should_preassemble_env(self): def python_version(self): """Detect the Python version for a given `environment.yml` - Will return 'x.y' if version is found (e.g '3.6'), - or a Falsy empty string '' if not found. + Will always return an `x.y` version. + If no version is found, the default Python version is used, + via self.major_pythons['3']. Version information below the minor level is dropped. """ @@ -286,13 +292,17 @@ def python_version(self): # extract major.minor if py_version: - if len(py_version) == 1: - self._python_version = self.major_pythons.get(py_version[0]) + py_version_info = py_version.split(".") + if len(py_version_info) == 1: + self._python_version = self.major_pythons[py_version_info[0]] else: # return major.minor - self._python_version = ".".join(py_version.split(".")[:2]) + self._python_version = ".".join(py_version_info[:2]) else: - self._python_version = "" + self._python_version = self.major_pythons["3"] + self.log.warning( + f"Python version unspecified, using current default Python version {self._python_version}. This will change in the future." + ) return self._python_version diff --git a/repo2docker/buildpacks/conda/environment-linux-64.lock b/repo2docker/buildpacks/conda/environment-linux-64.lock deleted file mode 100644 index a934da5e8..000000000 --- a/repo2docker/buildpacks/conda/environment-linux-64.lock +++ /dev/null @@ -1,150 +0,0 @@ -# AUTO GENERATED FROM environment.py-3.10.yml, DO NOT MANUALLY MODIFY -# Frozen on 2023-02-03 12:34:24 UTC -# Generated by conda-lock. -# platform: linux-64 -# input_hash: 9fd16b0f6d64e86a62e326694b74a429aef5dd7b227a96b4f0e2425851e4e016 -@EXPLICIT -https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.12.7-ha878542_0.conda#ff9f73d45c4a07d6f424495288a26080 -https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3 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-https://conda.anaconda.org/conda-forge/noarch/nbclient-0.7.2-pyhd8ed1ab_0.conda#6c7b0d75b66a220274bb5a28c23197f2 -https://conda.anaconda.org/conda-forge/noarch/requests-2.28.2-pyhd8ed1ab_0.conda#11d178fc55199482ee48d6812ea83983 -https://conda.anaconda.org/conda-forge/noarch/ipywidgets-8.0.2-pyhd8ed1ab_1.tar.bz2#81b7f46918555bf911ad2ba2f3259094 -https://conda.anaconda.org/conda-forge/noarch/jupyterhub-base-3.1.1-pyh2a2186d_0.conda#78fc5dfd4577a7ba172fa65eb64b6afb -https://conda.anaconda.org/conda-forge/noarch/nbconvert-core-7.2.9-pyhd8ed1ab_0.conda#a9e1826152e79416db71c51b0d3af28c -https://conda.anaconda.org/conda-forge/noarch/jupyter_server-1.23.5-pyhd8ed1ab_0.conda#e3ae1d46749f48a1875b560fca41cb0c -https://conda.anaconda.org/conda-forge/noarch/nbconvert-pandoc-7.2.9-pyhd8ed1ab_0.conda#4a8dc94c7c2f3736dc4b91ec345d5b4b -https://conda.anaconda.org/conda-forge/noarch/jupyter-resource-usage-0.7.0-pyhd8ed1ab_0.conda#c57567d49d926826b1f852712ac8acfa -https://conda.anaconda.org/conda-forge/noarch/jupyterlab_server-2.19.0-pyhd8ed1ab_0.conda#9dc0706ec2f8e13b7a0db9d6a19051ff -https://conda.anaconda.org/conda-forge/noarch/nbconvert-7.2.9-pyhd8ed1ab_0.conda#523aaa3affb003ab0e68dbc24c9027f4 -https://conda.anaconda.org/conda-forge/noarch/notebook-shim-0.2.2-pyhd8ed1ab_0.tar.bz2#40be846cd4e78672a40e43db9dae753c -https://conda.anaconda.org/conda-forge/noarch/nbclassic-0.5.1-pyhd8ed1ab_0.conda#cf832e3d48ef22528c676ed6e4b4085a -https://conda.anaconda.org/conda-forge/noarch/notebook-6.4.12-pyha770c72_0.tar.bz2#77fc67c5bbea44fd41e8bbe2ac82d1ad -https://conda.anaconda.org/conda-forge/noarch/jupyter-offlinenotebook-0.2.2-pyh1d7be83_0.tar.bz2#fe55056ce4bc4bd4953ba440270735fb -https://conda.anaconda.org/conda-forge/noarch/jupyterlab-3.4.8-pyhd8ed1ab_0.tar.bz2#6fbf13b0e8a6fa24bbae91205e8ce467 -https://conda.anaconda.org/conda-forge/noarch/nteract_on_jupyter-2.1.3-py_0.tar.bz2#1430ccd983ae6b161e2fbf4377965f7a -https://conda.anaconda.org/conda-forge/noarch/jupyterhub-singleuser-3.1.1-pyh2a2186d_0.conda#6d0a3394efe9ff7c0ad1ed03a6ca3720 diff --git a/repo2docker/buildpacks/conda/freeze.py b/repo2docker/buildpacks/conda/freeze.py index 2bcf06b9e..a3a18b2b0 100755 --- a/repo2docker/buildpacks/conda/freeze.py +++ b/repo2docker/buildpacks/conda/freeze.py @@ -11,8 +11,6 @@ import os import pathlib -import shutil -import sys from argparse import ArgumentParser from datetime import datetime from subprocess import check_call @@ -22,8 +20,6 @@ HERE = pathlib.Path(os.path.dirname(os.path.abspath(__file__))) ENV_FILE = HERE / "environment.yml" -FROZEN_FILE_T = os.path.splitext(ENV_FILE)[0] + "-{platform}.lock" - ENV_FILE_T = HERE / "environment.py-{py}.yml" yaml = YAML(typ="rt") @@ -126,7 +122,6 @@ def set_python(py_env_file, py): default=("linux-64", "linux-aarch64"), ) args = parser.parse_args() - default_py = "3.10" for py in args.py: for platform in args.platform: env_file = pathlib.Path(str(ENV_FILE_T).format(py=py)) @@ -135,5 +130,3 @@ def set_python(py_env_file, py): os.path.splitext(env_file)[0] + f"-{platform}.lock" ) freeze(env_file, frozen_file, platform) - if py == default_py: - shutil.copy(frozen_file, FROZEN_FILE_T.format(platform=platform)) diff --git a/repo2docker/buildpacks/pipfile/__init__.py b/repo2docker/buildpacks/pipfile/__init__.py index 7f8ec53b6..fa14d83b9 100644 --- a/repo2docker/buildpacks/pipfile/__init__.py +++ b/repo2docker/buildpacks/pipfile/__init__.py @@ -64,15 +64,19 @@ def python_version(self): # extract major.minor if py_version: - if len(py_version.split(".")) == 1: - self._python_version = self.major_pythons.get(py_version[0]) + py_version_info = py_version.split(".") + if len(py_version_info) == 1: + self._python_version = self.major_pythons[py_version_info[0]] else: # return major.minor - self._python_version = ".".join(py_version.split(".")[:2]) + self._python_version = ".".join(py_version_info[:2]) return self._python_version else: # use the default Python self._python_version = self.major_pythons["3"] + self.log.warning( + f"Python version unspecified, using current default Python version {self._python_version}. This will change in the future." + ) return self._python_version def get_preassemble_script_files(self): diff --git a/repo2docker/buildpacks/python/__init__.py b/repo2docker/buildpacks/python/__init__.py index a96a6cabf..17975da3a 100644 --- a/repo2docker/buildpacks/python/__init__.py +++ b/repo2docker/buildpacks/python/__init__.py @@ -23,6 +23,9 @@ def python_version(self): # not a Python runtime (e.g. R, which subclasses this) # use the default Python self._python_version = self.major_pythons["3"] + self.log.warning( + f"Python version unspecified, using current default Python version {self._python_version}. This will change in the future." + ) return self._python_version py_version_info = runtime.split("-", 1)[1].split(".") diff --git a/tests/unit/test_env_yml.py b/tests/unit/test_env_yml.py index dff142288..671de12f9 100644 --- a/tests/unit/test_env_yml.py +++ b/tests/unit/test_env_yml.py @@ -1,8 +1,6 @@ """ Test if the environment.yml is empty or it constains other data structure than a dictionary """ -import os -import sys import pytest @@ -15,8 +13,8 @@ def test_empty_env_yml(tmpdir): p.write("") bp = buildpacks.CondaBuildPack() py_ver = bp.python_version - # If the environment.yml is empty python_version will get an empty string - assert py_ver == "" + # If the environment.yml is empty, python_version will get the default Python version + assert py_ver == bp.major_pythons["3"] def test_no_dict_env_yml(tmpdir): From 1faf4b88fce4b4e1f131dc4d1f6ff0c8a7317f8d Mon Sep 17 00:00:00 2001 From: Min RK Date: Tue, 21 Feb 2023 09:32:02 +0100 Subject: [PATCH 127/171] disable codecov status it's unreliable, and we don't want to waste time with incorrect failed status checks the links in the checks are the main value, not the pass/fail --- .codecov.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.codecov.yml b/.codecov.yml index 8836913fb..72e51fd76 100644 --- a/.codecov.yml +++ b/.codecov.yml @@ -6,7 +6,7 @@ coverage: status: project: default: - target: auto + target: "0%" patch: default: - target: 20% + target: "0%" From 39b563c47d7984d6e57b44939a4309828e63b894 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 7 Mar 2023 03:45:48 +0000 Subject: [PATCH 128/171] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/pre-commit/mirrors-prettier: v3.0.0-alpha.4 → v3.0.0-alpha.6](https://github.com/pre-commit/mirrors-prettier/compare/v3.0.0-alpha.4...v3.0.0-alpha.6) --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 75f0ab42a..bc9dad7bf 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -44,7 +44,7 @@ repos: # Autoformat: markdown - repo: https://github.com/pre-commit/mirrors-prettier - rev: v3.0.0-alpha.4 + rev: v3.0.0-alpha.6 hooks: - id: prettier files: ".md" From 938d91c9ca5b044368afd237a1adf0e1666f44b6 Mon Sep 17 00:00:00 2001 From: Philip Durbin Date: Fri, 10 Mar 2023 16:46:05 -0500 Subject: [PATCH 129/171] download original file formats from Dataverse #1242 Dataverse creates plain-text, preservation-friendly copies of certain file formats (some of which are proprietary, such as Stata or SPSS) and this .tab (tab-separated) file is downloaded unless you supply `format=original`, which is what this pull request does. The original filename (e.g. foo.dta, a Stata file) comes from `originalFileName`, which is only populated when the preservation copy (e.g. foo.tab) has been successfully created. Additional variables were created to distinguish between `filename`, `original_filename`, and `filename_with_path`. If `original_filename` is available, it's the right one to use. To allow the tests to continue passing, the query parameters are now removed so just the file id can be cast as an int. --- repo2docker/contentproviders/dataverse.py | 13 ++++++++++--- tests/unit/contentproviders/test_dataverse.py | 4 +++- 2 files changed, 13 insertions(+), 4 deletions(-) diff --git a/repo2docker/contentproviders/dataverse.py b/repo2docker/contentproviders/dataverse.py index 1998f6bef..9054f53ce 100644 --- a/repo2docker/contentproviders/dataverse.py +++ b/repo2docker/contentproviders/dataverse.py @@ -102,11 +102,18 @@ def fetch(self, spec, output_dir, yield_output=False): for fobj in deep_get(record, "latestVersion.files"): file_url = ( - f'{host["url"]}/api/access/datafile/{deep_get(fobj, "dataFile.id")}' + # without format=original you get the preservation format (plain text, tab separated) + f'{host["url"]}/api/access/datafile/{deep_get(fobj, "dataFile.id")}?format=original' ) - filename = os.path.join(fobj.get("directoryLabel", ""), fobj["label"]) + filename = fobj["label"] + original_filename = fobj["dataFile"].get("originalFileName", None) + if original_filename: + # replace preservation format filename (foo.tab) with original filename (foo.dta) + filename = original_filename - file_ref = {"download": file_url, "filename": filename} + filename_with_path = os.path.join(fobj.get("directoryLabel", ""), filename) + + file_ref = {"download": file_url, "filename": filename_with_path} fetch_map = {key: key for key in file_ref.keys()} yield from self.fetch_file(file_ref, fetch_map, output_dir) diff --git a/tests/unit/contentproviders/test_dataverse.py b/tests/unit/contentproviders/test_dataverse.py index 1603b9cdd..c5c0d1cb6 100644 --- a/tests/unit/contentproviders/test_dataverse.py +++ b/tests/unit/contentproviders/test_dataverse.py @@ -5,6 +5,7 @@ from tempfile import TemporaryDirectory from unittest.mock import patch from urllib.request import Request, urlopen +from urllib.parse import urlsplit import pytest @@ -131,7 +132,8 @@ def test_dataverse_fetch(dv_files, requests_mock): spec = {"host": harvard_dv, "record": "doi:10.7910/DVN/6ZXAGT"} def mock_filecontent(req, context): - file_no = int(req.url.split("/")[-1]) - 1 + parts = urlsplit(req.url) + file_no = int(parts.path.split("/")[-1]) - 1 return open(dv_files[file_no], "rb").read() requests_mock.get( From f848c81073a4d5f15d922de90cae1f65775301d6 Mon Sep 17 00:00:00 2001 From: YuviPanda Date: Thu, 23 Mar 2023 20:02:49 +0530 Subject: [PATCH 130/171] Install libssl-dev unconditionally for R --- repo2docker/buildpacks/r.py | 1 + 1 file changed, 1 insertion(+) diff --git a/repo2docker/buildpacks/r.py b/repo2docker/buildpacks/r.py index 5c147bd94..e2a92a07c 100644 --- a/repo2docker/buildpacks/r.py +++ b/repo2docker/buildpacks/r.py @@ -191,6 +191,7 @@ def get_packages(self): "libapparmor1", "sudo", "lsb-release", + "libssl-dev", ] return super().get_packages().union(packages) From 1e1d6ac20fb192962011fcab04741b16353fcd8d Mon Sep 17 00:00:00 2001 From: Min RK Date: Thu, 23 Mar 2023 15:58:27 +0100 Subject: [PATCH 131/171] memoize all getters explicitly rather than automatically --- repo2docker/buildpacks/base.py | 31 ++++++++++++------- repo2docker/buildpacks/conda/__init__.py | 10 ++++++ repo2docker/buildpacks/julia/julia_project.py | 8 ++++- repo2docker/buildpacks/julia/julia_require.py | 6 ++++ repo2docker/buildpacks/nix/__init__.py | 9 +++++- repo2docker/buildpacks/pipfile/__init__.py | 4 +++ repo2docker/buildpacks/python/__init__.py | 4 +++ repo2docker/buildpacks/r.py | 13 ++++++++ 8 files changed, 71 insertions(+), 14 deletions(-) diff --git a/repo2docker/buildpacks/base.py b/repo2docker/buildpacks/base.py index 60f33edd9..9afabf7ec 100644 --- a/repo2docker/buildpacks/base.py +++ b/repo2docker/buildpacks/base.py @@ -231,19 +231,8 @@ def __init__(self): "support is experimental in repo2docker." ) self.platform = "" - self._memoize() - - def _memoize(self): - """Memoize `get_foo` methods with lru_cache() - - Avoids duplicate log statements when calling what should be idempotent methods more than once - """ - for method_name in dir(self): - if method_name.startswith("get_"): - method = getattr(self, method_name) - if callable(method): - setattr(self, method_name, lru_cache()(method)) + @lru_cache def get_packages(self): """ List of packages that are installed in this BuildPack. @@ -253,6 +242,7 @@ def get_packages(self): """ return set() + @lru_cache def get_base_packages(self): """ Base set of apt packages that are installed for all images. @@ -269,6 +259,7 @@ def get_base_packages(self): "unzip", } + @lru_cache def get_build_env(self): """ Ordered list of environment variables to be set for this image. @@ -284,6 +275,7 @@ def get_build_env(self): """ return [] + @lru_cache def get_env(self): """ Ordered list of environment variables to be set for this image. @@ -298,6 +290,7 @@ def get_env(self): """ return [] + @lru_cache def get_path(self): """ Ordered list of file system paths to look for executables in. @@ -307,12 +300,14 @@ def get_path(self): """ return [] + @lru_cache def get_labels(self): """ Docker labels to set on the built image. """ return self.labels + @lru_cache def get_build_script_files(self): """ Dict of files to be copied to the container image for use in building. @@ -337,6 +332,7 @@ def _check_stencila(self): f"Found a stencila manifest.xml at {root}. Stencila is no longer supported." ) + @lru_cache def get_build_scripts(self): """ Ordered list of shell script snippets to build the base image. @@ -358,6 +354,7 @@ def get_build_scripts(self): return [] + @lru_cache def get_preassemble_script_files(self): """ Dict of files to be copied to the container image for use in preassembly. @@ -371,6 +368,7 @@ def get_preassemble_script_files(self): """ return {} + @lru_cache def get_preassemble_scripts(self): """ Ordered list of shell snippets to build an image for this repository. @@ -387,6 +385,7 @@ def get_preassemble_scripts(self): """ return [] + @lru_cache def get_assemble_scripts(self): """ Ordered list of shell script snippets to build the repo into the image. @@ -413,6 +412,7 @@ def get_assemble_scripts(self): """ return [] + @lru_cache def get_post_build_scripts(self): """ An ordered list of executable scripts to execute after build. @@ -425,6 +425,7 @@ def get_post_build_scripts(self): """ return [] + @lru_cache def get_start_script(self): """ The path to a script to be executed at container start up. @@ -637,12 +638,14 @@ def _filter_tar(tar): class BaseImage(BuildPack): + @lru_cache def get_build_env(self): """Return env directives required for build""" return [ ("APP_BASE", "/srv"), ] + @lru_cache def get_env(self): """Return env directives to be set after build""" return [] @@ -650,6 +653,7 @@ def get_env(self): def detect(self): return True + @lru_cache def get_preassemble_scripts(self): scripts = [] try: @@ -689,16 +693,19 @@ def get_preassemble_scripts(self): return scripts + @lru_cache def get_assemble_scripts(self): """Return directives to run after the entire repository has been added to the image""" return [] + @lru_cache def get_post_build_scripts(self): post_build = self.binder_path("postBuild") if os.path.exists(post_build): return [post_build] return [] + @lru_cache def get_start_script(self): start = self.binder_path("start") if os.path.exists(start): diff --git a/repo2docker/buildpacks/conda/__init__.py b/repo2docker/buildpacks/conda/__init__.py index 29682c7e2..7dc24481d 100644 --- a/repo2docker/buildpacks/conda/__init__.py +++ b/repo2docker/buildpacks/conda/__init__.py @@ -3,6 +3,7 @@ import re import warnings from collections.abc import Mapping +from functools import lru_cache from ruamel.yaml import YAML @@ -45,6 +46,7 @@ def _conda_platform(self): return "linux-aarch64" raise ValueError(f"Unknown platform {self.platform}") + @lru_cache def get_build_env(self): """Return environment variables to be set. @@ -88,11 +90,13 @@ def get_build_env(self): env.append(("KERNEL_PYTHON_PREFIX", "${NB_PYTHON_PREFIX}")) return env + @lru_cache def get_env(self): """Make kernel env the default for `conda install`""" env = super().get_env() + [("CONDA_DEFAULT_ENV", "${KERNEL_PYTHON_PREFIX}")] return env + @lru_cache def get_path(self): """Return paths (including conda environment path) to be added to the PATH environment variable. @@ -107,6 +111,7 @@ def get_path(self): path.append("${NPM_DIR}/bin") return path + @lru_cache def get_build_scripts(self): """ Return series of build-steps common to all Python 3 repositories. @@ -145,6 +150,7 @@ def get_build_scripts(self): major_pythons = {"2": "2.7", "3": "3.7"} + @lru_cache def get_build_script_files(self): """ Dict of files to be copied to the container image for use in building. @@ -359,6 +365,7 @@ def separate_kernel_env(self): self.kernel_env_cutoff_version ) + @lru_cache def get_preassemble_script_files(self): """preassembly only requires environment.yml @@ -372,6 +379,7 @@ def get_preassemble_script_files(self): assemble_files[environment_yml] = environment_yml return assemble_files + @lru_cache def get_env_scripts(self): """Return series of build-steps specific to this source repository.""" scripts = [] @@ -438,12 +446,14 @@ def get_env_scripts(self): ] return scripts + @lru_cache def get_preassemble_scripts(self): scripts = super().get_preassemble_scripts() if self._should_preassemble_env: scripts.extend(self.get_env_scripts()) return scripts + @lru_cache def get_assemble_scripts(self): scripts = super().get_assemble_scripts() if not self._should_preassemble_env: diff --git a/repo2docker/buildpacks/julia/julia_project.py b/repo2docker/buildpacks/julia/julia_project.py index b7eab5c3f..c9f72a1e1 100644 --- a/repo2docker/buildpacks/julia/julia_project.py +++ b/repo2docker/buildpacks/julia/julia_project.py @@ -1,6 +1,7 @@ """Generates a Dockerfile based on an input matrix for Julia""" import functools import os +from functools import lru_cache import requests import semver @@ -19,7 +20,7 @@ class JuliaProjectTomlBuildPack(PythonBuildPack): # Note that these must remain ordered, in order for the find_semver_match() # function to behave correctly. @property - @functools.lru_cache(maxsize=1) + @lru_cache(maxsize=1) def all_julias(self): try: json = requests.get( @@ -67,6 +68,7 @@ def julia_version(self): raise RuntimeError("Failed to find a matching Julia version: {compat}") return match + @lru_cache def get_build_env(self): """Get additional environment settings for Julia and Jupyter @@ -109,9 +111,11 @@ def project_dir(self): else: return "${REPO_DIR}" + @lru_cache def get_env(self): return super().get_env() + [("JULIA_PROJECT", self.project_dir)] + @lru_cache def get_path(self): """Adds path to Julia binaries to user's PATH. @@ -122,6 +126,7 @@ def get_path(self): """ return super().get_path() + ["${JULIA_PATH}/bin"] + @lru_cache def get_build_scripts(self): """ Return series of build-steps common to "ALL" Julia repositories @@ -150,6 +155,7 @@ def get_build_scripts(self): ), ] + @lru_cache def get_assemble_scripts(self): """ Return series of build-steps specific to "this" Julia repository diff --git a/repo2docker/buildpacks/julia/julia_require.py b/repo2docker/buildpacks/julia/julia_require.py index ad3f5448d..10046800c 100644 --- a/repo2docker/buildpacks/julia/julia_require.py +++ b/repo2docker/buildpacks/julia/julia_require.py @@ -1,6 +1,7 @@ """Generates a Dockerfile based on an input matrix with REQUIRE for legacy Julia""" import os +from functools import lru_cache from ...semver import parse_version as V from ..python import PythonBuildPack @@ -54,6 +55,7 @@ def julia_version(self): self._julia_version = julia_version return self._julia_version + @lru_cache def get_build_env(self): """Get additional environment settings for Julia and Jupyter @@ -102,6 +104,7 @@ def get_build_env(self): ("JUPYTER", jupyter), ] + @lru_cache def get_path(self): """Adds path to Julia binaries to user's PATH. @@ -112,6 +115,7 @@ def get_path(self): """ return super().get_path() + ["${JULIA_HOME}"] + @lru_cache def get_build_scripts(self): """ Return series of build-steps common to "ALL" Julia repositories @@ -149,6 +153,7 @@ def get_build_scripts(self): ), ] + @lru_cache def get_assemble_scripts(self): """ Return series of build-steps specific to "this" Julia repository @@ -176,6 +181,7 @@ def get_assemble_scripts(self): ) ] + @lru_cache def get_build_script_files(self): files = { "julia/install-repo-dependencies.jl": "/tmp/install-repo-dependencies.jl" diff --git a/repo2docker/buildpacks/nix/__init__.py b/repo2docker/buildpacks/nix/__init__.py index 9dbb412ab..93b6c6fc9 100644 --- a/repo2docker/buildpacks/nix/__init__.py +++ b/repo2docker/buildpacks/nix/__init__.py @@ -1,16 +1,19 @@ """BuildPack for nixpkgs environments""" import os +from functools import lru_cache -from ..base import BaseImage, BuildPack +from ..base import BaseImage class NixBuildPack(BaseImage): """A nix Package Manager BuildPack""" + @lru_cache def get_path(self): """Return paths to be added to PATH environemnt variable""" return super().get_path() + ["/home/${NB_USER}/.nix-profile/bin"] + @lru_cache def get_env(self): """Ordered list of environment variables to be set for this image""" @@ -20,6 +23,7 @@ def get_env(self): ("GIT_SSL_CAINFO", "/etc/ssl/certs/ca-certificates.crt"), ] + @lru_cache def get_build_scripts(self): """ Return series of build-steps common to all nix repositories. @@ -55,6 +59,7 @@ def get_build_scripts(self): ), ] + @lru_cache def get_build_script_files(self): """Dict of files to be copied to the container image for use in building""" return { @@ -62,6 +67,7 @@ def get_build_script_files(self): "nix/nix-shell-wrapper": "/usr/local/bin/nix-shell-wrapper", } + @lru_cache def get_assemble_scripts(self): """Return series of build-steps specific to this source repository.""" return super().get_assemble_scripts() + [ @@ -75,6 +81,7 @@ def get_assemble_scripts(self): ) ] + @lru_cache def get_start_script(self): """The path to a script to be executed as ENTRYPOINT""" # the shell wrapper script duplicates the behaviour of other buildpacks diff --git a/repo2docker/buildpacks/pipfile/__init__.py b/repo2docker/buildpacks/pipfile/__init__.py index 7f8ec53b6..29ba6ef33 100644 --- a/repo2docker/buildpacks/pipfile/__init__.py +++ b/repo2docker/buildpacks/pipfile/__init__.py @@ -8,6 +8,7 @@ import json import os import re +from functools import lru_cache import toml @@ -75,6 +76,7 @@ def python_version(self): self._python_version = self.major_pythons["3"] return self._python_version + @lru_cache def get_preassemble_script_files(self): """Return files needed for preassembly""" files = super().get_preassemble_script_files() @@ -84,6 +86,7 @@ def get_preassemble_script_files(self): files[path] = path return files + @lru_cache def get_preassemble_scripts(self): """scripts to run prior to staging the repo contents""" scripts = super().get_preassemble_scripts() @@ -101,6 +104,7 @@ def get_preassemble_scripts(self): ) return scripts + @lru_cache def get_assemble_scripts(self): """Return series of build-steps specific to this repository.""" # If we have either Pipfile.lock, Pipfile, or runtime.txt declare the diff --git a/repo2docker/buildpacks/python/__init__.py b/repo2docker/buildpacks/python/__init__.py index a96a6cabf..89a783756 100644 --- a/repo2docker/buildpacks/python/__init__.py +++ b/repo2docker/buildpacks/python/__init__.py @@ -1,5 +1,6 @@ """Generates Dockerfiles based on an input matrix based on Python.""" import os +from functools import lru_cache from ...utils import is_local_pip_requirement, open_guess_encoding from ..conda import CondaBuildPack @@ -93,6 +94,7 @@ def _should_preassemble_pip(self): # allow assembly from subset return True + @lru_cache def get_preassemble_script_files(self): assemble_files = super().get_preassemble_script_files() for name in ("requirements.txt", "requirements3.txt"): @@ -101,6 +103,7 @@ def get_preassemble_script_files(self): assemble_files[requirements_txt] = requirements_txt return assemble_files + @lru_cache def get_preassemble_scripts(self): """Return scripts to run before adding the full repository""" scripts = super().get_preassemble_scripts() @@ -108,6 +111,7 @@ def get_preassemble_scripts(self): scripts.extend(self._get_pip_scripts()) return scripts + @lru_cache def get_assemble_scripts(self): """Return series of build steps that require the full repository""" # If we have a runtime.txt & that's set to python-2.7, diff --git a/repo2docker/buildpacks/r.py b/repo2docker/buildpacks/r.py index 8d8ae6b1b..a3c8badef 100644 --- a/repo2docker/buildpacks/r.py +++ b/repo2docker/buildpacks/r.py @@ -1,6 +1,7 @@ import datetime import os import re +from functools import lru_cache import requests @@ -142,6 +143,7 @@ def detect(self): self._runtime = f"r-{str(self._checkpoint_date)}" return True + @lru_cache def get_env(self): """ Set custom env vars needed for RStudio to load @@ -156,6 +158,7 @@ def get_env(self): ("LD_LIBRARY_PATH", "${R_HOME}/lib:${LD_LIBRARY_PATH}"), ] + @lru_cache def get_path(self): """ Return paths to be added to the PATH environment variable. @@ -165,6 +168,7 @@ def get_path(self): """ return super().get_path() + ["/usr/lib/rstudio-server/bin/"] + @lru_cache def get_build_env(self): """ Return environment variables to be set. @@ -178,6 +182,7 @@ def get_build_env(self): ("R_LIBS_USER", "${APP_BASE}/rlibs") ] + @lru_cache def get_packages(self): """ Return list of packages to be installed. @@ -195,6 +200,7 @@ def get_packages(self): return super().get_packages().union(packages) + @lru_cache def get_rspm_snapshot_url(self, snapshot_date, max_days_prior=7): for i in range(max_days_prior): snapshots = requests.post( @@ -219,6 +225,7 @@ def get_rspm_snapshot_url(self, snapshot_date, max_days_prior=7): ) ) + @lru_cache def get_mran_snapshot_url(self, snapshot_date, max_days_prior=7): for i in range(max_days_prior): try_date = snapshot_date - datetime.timedelta(days=i) @@ -233,6 +240,7 @@ def get_mran_snapshot_url(self, snapshot_date, max_days_prior=7): ) ) + @lru_cache def get_cran_mirror_url(self, snapshot_date): # Date after which we will use rspm + binary packages instead of MRAN + source packages rspm_cutoff_date = datetime.date(2022, 1, 1) @@ -242,6 +250,7 @@ def get_cran_mirror_url(self, snapshot_date): else: return self.get_mran_snapshot_url(snapshot_date) + @lru_cache def get_devtools_snapshot_url(self): """ Return url of snapshot to use for getting devtools install @@ -255,6 +264,7 @@ def get_devtools_snapshot_url(self): # necessary apt packages. return "https://packagemanager.rstudio.com/all/__linux__/bionic/2022-01-04+Y3JhbiwyOjQ1MjYyMTU7NzlBRkJEMzg" + @lru_cache def get_build_scripts(self): """ Return series of build-steps common to all R repositories @@ -349,6 +359,7 @@ def get_build_scripts(self): return super().get_build_scripts() + scripts + @lru_cache def get_preassemble_script_files(self): files = super().get_preassemble_script_files() installR_path = self.binder_path("install.R") @@ -357,6 +368,7 @@ def get_preassemble_script_files(self): return files + @lru_cache def get_preassemble_scripts(self): """Install contents of install.R @@ -382,6 +394,7 @@ def get_preassemble_scripts(self): return super().get_preassemble_scripts() + scripts + @lru_cache def get_assemble_scripts(self): """Install the dependencies of or the repository itself""" assemble_scripts = super().get_assemble_scripts() From 70a2de4e1234372f81b343bd57092d511fff04f1 Mon Sep 17 00:00:00 2001 From: Min RK Date: Thu, 23 Mar 2023 16:00:23 +0100 Subject: [PATCH 132/171] @lru_cache requires Python 3.8, use older @lru_cache() --- repo2docker/buildpacks/base.py | 38 +++++++++---------- repo2docker/buildpacks/conda/__init__.py | 18 ++++----- repo2docker/buildpacks/julia/julia_project.py | 10 ++--- repo2docker/buildpacks/julia/julia_require.py | 10 ++--- repo2docker/buildpacks/nix/__init__.py | 12 +++--- repo2docker/buildpacks/pipfile/__init__.py | 6 +-- repo2docker/buildpacks/python/__init__.py | 6 +-- repo2docker/buildpacks/r.py | 24 ++++++------ 8 files changed, 62 insertions(+), 62 deletions(-) diff --git a/repo2docker/buildpacks/base.py b/repo2docker/buildpacks/base.py index 9afabf7ec..62f94e87a 100644 --- a/repo2docker/buildpacks/base.py +++ b/repo2docker/buildpacks/base.py @@ -232,7 +232,7 @@ def __init__(self): ) self.platform = "" - @lru_cache + @lru_cache() def get_packages(self): """ List of packages that are installed in this BuildPack. @@ -242,7 +242,7 @@ def get_packages(self): """ return set() - @lru_cache + @lru_cache() def get_base_packages(self): """ Base set of apt packages that are installed for all images. @@ -259,7 +259,7 @@ def get_base_packages(self): "unzip", } - @lru_cache + @lru_cache() def get_build_env(self): """ Ordered list of environment variables to be set for this image. @@ -275,7 +275,7 @@ def get_build_env(self): """ return [] - @lru_cache + @lru_cache() def get_env(self): """ Ordered list of environment variables to be set for this image. @@ -290,7 +290,7 @@ def get_env(self): """ return [] - @lru_cache + @lru_cache() def get_path(self): """ Ordered list of file system paths to look for executables in. @@ -300,14 +300,14 @@ def get_path(self): """ return [] - @lru_cache + @lru_cache() def get_labels(self): """ Docker labels to set on the built image. """ return self.labels - @lru_cache + @lru_cache() def get_build_script_files(self): """ Dict of files to be copied to the container image for use in building. @@ -332,7 +332,7 @@ def _check_stencila(self): f"Found a stencila manifest.xml at {root}. Stencila is no longer supported." ) - @lru_cache + @lru_cache() def get_build_scripts(self): """ Ordered list of shell script snippets to build the base image. @@ -354,7 +354,7 @@ def get_build_scripts(self): return [] - @lru_cache + @lru_cache() def get_preassemble_script_files(self): """ Dict of files to be copied to the container image for use in preassembly. @@ -368,7 +368,7 @@ def get_preassemble_script_files(self): """ return {} - @lru_cache + @lru_cache() def get_preassemble_scripts(self): """ Ordered list of shell snippets to build an image for this repository. @@ -385,7 +385,7 @@ def get_preassemble_scripts(self): """ return [] - @lru_cache + @lru_cache() def get_assemble_scripts(self): """ Ordered list of shell script snippets to build the repo into the image. @@ -412,7 +412,7 @@ def get_assemble_scripts(self): """ return [] - @lru_cache + @lru_cache() def get_post_build_scripts(self): """ An ordered list of executable scripts to execute after build. @@ -425,7 +425,7 @@ def get_post_build_scripts(self): """ return [] - @lru_cache + @lru_cache() def get_start_script(self): """ The path to a script to be executed at container start up. @@ -638,14 +638,14 @@ def _filter_tar(tar): class BaseImage(BuildPack): - @lru_cache + @lru_cache() def get_build_env(self): """Return env directives required for build""" return [ ("APP_BASE", "/srv"), ] - @lru_cache + @lru_cache() def get_env(self): """Return env directives to be set after build""" return [] @@ -653,7 +653,7 @@ def get_env(self): def detect(self): return True - @lru_cache + @lru_cache() def get_preassemble_scripts(self): scripts = [] try: @@ -693,19 +693,19 @@ def get_preassemble_scripts(self): return scripts - @lru_cache + @lru_cache() def get_assemble_scripts(self): """Return directives to run after the entire repository has been added to the image""" return [] - @lru_cache + @lru_cache() def get_post_build_scripts(self): post_build = self.binder_path("postBuild") if os.path.exists(post_build): return [post_build] return [] - @lru_cache + @lru_cache() def get_start_script(self): start = self.binder_path("start") if os.path.exists(start): diff --git a/repo2docker/buildpacks/conda/__init__.py b/repo2docker/buildpacks/conda/__init__.py index 7dc24481d..f4791f127 100644 --- a/repo2docker/buildpacks/conda/__init__.py +++ b/repo2docker/buildpacks/conda/__init__.py @@ -46,7 +46,7 @@ def _conda_platform(self): return "linux-aarch64" raise ValueError(f"Unknown platform {self.platform}") - @lru_cache + @lru_cache() def get_build_env(self): """Return environment variables to be set. @@ -90,13 +90,13 @@ def get_build_env(self): env.append(("KERNEL_PYTHON_PREFIX", "${NB_PYTHON_PREFIX}")) return env - @lru_cache + @lru_cache() def get_env(self): """Make kernel env the default for `conda install`""" env = super().get_env() + [("CONDA_DEFAULT_ENV", "${KERNEL_PYTHON_PREFIX}")] return env - @lru_cache + @lru_cache() def get_path(self): """Return paths (including conda environment path) to be added to the PATH environment variable. @@ -111,7 +111,7 @@ def get_path(self): path.append("${NPM_DIR}/bin") return path - @lru_cache + @lru_cache() def get_build_scripts(self): """ Return series of build-steps common to all Python 3 repositories. @@ -150,7 +150,7 @@ def get_build_scripts(self): major_pythons = {"2": "2.7", "3": "3.7"} - @lru_cache + @lru_cache() def get_build_script_files(self): """ Dict of files to be copied to the container image for use in building. @@ -365,7 +365,7 @@ def separate_kernel_env(self): self.kernel_env_cutoff_version ) - @lru_cache + @lru_cache() def get_preassemble_script_files(self): """preassembly only requires environment.yml @@ -379,7 +379,7 @@ def get_preassemble_script_files(self): assemble_files[environment_yml] = environment_yml return assemble_files - @lru_cache + @lru_cache() def get_env_scripts(self): """Return series of build-steps specific to this source repository.""" scripts = [] @@ -446,14 +446,14 @@ def get_env_scripts(self): ] return scripts - @lru_cache + @lru_cache() def get_preassemble_scripts(self): scripts = super().get_preassemble_scripts() if self._should_preassemble_env: scripts.extend(self.get_env_scripts()) return scripts - @lru_cache + @lru_cache() def get_assemble_scripts(self): scripts = super().get_assemble_scripts() if not self._should_preassemble_env: diff --git a/repo2docker/buildpacks/julia/julia_project.py b/repo2docker/buildpacks/julia/julia_project.py index c9f72a1e1..cce56abf7 100644 --- a/repo2docker/buildpacks/julia/julia_project.py +++ b/repo2docker/buildpacks/julia/julia_project.py @@ -68,7 +68,7 @@ def julia_version(self): raise RuntimeError("Failed to find a matching Julia version: {compat}") return match - @lru_cache + @lru_cache() def get_build_env(self): """Get additional environment settings for Julia and Jupyter @@ -111,11 +111,11 @@ def project_dir(self): else: return "${REPO_DIR}" - @lru_cache + @lru_cache() def get_env(self): return super().get_env() + [("JULIA_PROJECT", self.project_dir)] - @lru_cache + @lru_cache() def get_path(self): """Adds path to Julia binaries to user's PATH. @@ -126,7 +126,7 @@ def get_path(self): """ return super().get_path() + ["${JULIA_PATH}/bin"] - @lru_cache + @lru_cache() def get_build_scripts(self): """ Return series of build-steps common to "ALL" Julia repositories @@ -155,7 +155,7 @@ def get_build_scripts(self): ), ] - @lru_cache + @lru_cache() def get_assemble_scripts(self): """ Return series of build-steps specific to "this" Julia repository diff --git a/repo2docker/buildpacks/julia/julia_require.py b/repo2docker/buildpacks/julia/julia_require.py index 10046800c..ab41ffc26 100644 --- a/repo2docker/buildpacks/julia/julia_require.py +++ b/repo2docker/buildpacks/julia/julia_require.py @@ -55,7 +55,7 @@ def julia_version(self): self._julia_version = julia_version return self._julia_version - @lru_cache + @lru_cache() def get_build_env(self): """Get additional environment settings for Julia and Jupyter @@ -104,7 +104,7 @@ def get_build_env(self): ("JUPYTER", jupyter), ] - @lru_cache + @lru_cache() def get_path(self): """Adds path to Julia binaries to user's PATH. @@ -115,7 +115,7 @@ def get_path(self): """ return super().get_path() + ["${JULIA_HOME}"] - @lru_cache + @lru_cache() def get_build_scripts(self): """ Return series of build-steps common to "ALL" Julia repositories @@ -153,7 +153,7 @@ def get_build_scripts(self): ), ] - @lru_cache + @lru_cache() def get_assemble_scripts(self): """ Return series of build-steps specific to "this" Julia repository @@ -181,7 +181,7 @@ def get_assemble_scripts(self): ) ] - @lru_cache + @lru_cache() def get_build_script_files(self): files = { "julia/install-repo-dependencies.jl": "/tmp/install-repo-dependencies.jl" diff --git a/repo2docker/buildpacks/nix/__init__.py b/repo2docker/buildpacks/nix/__init__.py index 93b6c6fc9..94fd7b7c5 100644 --- a/repo2docker/buildpacks/nix/__init__.py +++ b/repo2docker/buildpacks/nix/__init__.py @@ -8,12 +8,12 @@ class NixBuildPack(BaseImage): """A nix Package Manager BuildPack""" - @lru_cache + @lru_cache() def get_path(self): """Return paths to be added to PATH environemnt variable""" return super().get_path() + ["/home/${NB_USER}/.nix-profile/bin"] - @lru_cache + @lru_cache() def get_env(self): """Ordered list of environment variables to be set for this image""" @@ -23,7 +23,7 @@ def get_env(self): ("GIT_SSL_CAINFO", "/etc/ssl/certs/ca-certificates.crt"), ] - @lru_cache + @lru_cache() def get_build_scripts(self): """ Return series of build-steps common to all nix repositories. @@ -59,7 +59,7 @@ def get_build_scripts(self): ), ] - @lru_cache + @lru_cache() def get_build_script_files(self): """Dict of files to be copied to the container image for use in building""" return { @@ -67,7 +67,7 @@ def get_build_script_files(self): "nix/nix-shell-wrapper": "/usr/local/bin/nix-shell-wrapper", } - @lru_cache + @lru_cache() def get_assemble_scripts(self): """Return series of build-steps specific to this source repository.""" return super().get_assemble_scripts() + [ @@ -81,7 +81,7 @@ def get_assemble_scripts(self): ) ] - @lru_cache + @lru_cache() def get_start_script(self): """The path to a script to be executed as ENTRYPOINT""" # the shell wrapper script duplicates the behaviour of other buildpacks diff --git a/repo2docker/buildpacks/pipfile/__init__.py b/repo2docker/buildpacks/pipfile/__init__.py index 29ba6ef33..5a99f49d0 100644 --- a/repo2docker/buildpacks/pipfile/__init__.py +++ b/repo2docker/buildpacks/pipfile/__init__.py @@ -76,7 +76,7 @@ def python_version(self): self._python_version = self.major_pythons["3"] return self._python_version - @lru_cache + @lru_cache() def get_preassemble_script_files(self): """Return files needed for preassembly""" files = super().get_preassemble_script_files() @@ -86,7 +86,7 @@ def get_preassemble_script_files(self): files[path] = path return files - @lru_cache + @lru_cache() def get_preassemble_scripts(self): """scripts to run prior to staging the repo contents""" scripts = super().get_preassemble_scripts() @@ -104,7 +104,7 @@ def get_preassemble_scripts(self): ) return scripts - @lru_cache + @lru_cache() def get_assemble_scripts(self): """Return series of build-steps specific to this repository.""" # If we have either Pipfile.lock, Pipfile, or runtime.txt declare the diff --git a/repo2docker/buildpacks/python/__init__.py b/repo2docker/buildpacks/python/__init__.py index 89a783756..32986cff5 100644 --- a/repo2docker/buildpacks/python/__init__.py +++ b/repo2docker/buildpacks/python/__init__.py @@ -94,7 +94,7 @@ def _should_preassemble_pip(self): # allow assembly from subset return True - @lru_cache + @lru_cache() def get_preassemble_script_files(self): assemble_files = super().get_preassemble_script_files() for name in ("requirements.txt", "requirements3.txt"): @@ -103,7 +103,7 @@ def get_preassemble_script_files(self): assemble_files[requirements_txt] = requirements_txt return assemble_files - @lru_cache + @lru_cache() def get_preassemble_scripts(self): """Return scripts to run before adding the full repository""" scripts = super().get_preassemble_scripts() @@ -111,7 +111,7 @@ def get_preassemble_scripts(self): scripts.extend(self._get_pip_scripts()) return scripts - @lru_cache + @lru_cache() def get_assemble_scripts(self): """Return series of build steps that require the full repository""" # If we have a runtime.txt & that's set to python-2.7, diff --git a/repo2docker/buildpacks/r.py b/repo2docker/buildpacks/r.py index a3c8badef..03aa4ae61 100644 --- a/repo2docker/buildpacks/r.py +++ b/repo2docker/buildpacks/r.py @@ -143,7 +143,7 @@ def detect(self): self._runtime = f"r-{str(self._checkpoint_date)}" return True - @lru_cache + @lru_cache() def get_env(self): """ Set custom env vars needed for RStudio to load @@ -158,7 +158,7 @@ def get_env(self): ("LD_LIBRARY_PATH", "${R_HOME}/lib:${LD_LIBRARY_PATH}"), ] - @lru_cache + @lru_cache() def get_path(self): """ Return paths to be added to the PATH environment variable. @@ -168,7 +168,7 @@ def get_path(self): """ return super().get_path() + ["/usr/lib/rstudio-server/bin/"] - @lru_cache + @lru_cache() def get_build_env(self): """ Return environment variables to be set. @@ -182,7 +182,7 @@ def get_build_env(self): ("R_LIBS_USER", "${APP_BASE}/rlibs") ] - @lru_cache + @lru_cache() def get_packages(self): """ Return list of packages to be installed. @@ -200,7 +200,7 @@ def get_packages(self): return super().get_packages().union(packages) - @lru_cache + @lru_cache() def get_rspm_snapshot_url(self, snapshot_date, max_days_prior=7): for i in range(max_days_prior): snapshots = requests.post( @@ -225,7 +225,7 @@ def get_rspm_snapshot_url(self, snapshot_date, max_days_prior=7): ) ) - @lru_cache + @lru_cache() def get_mran_snapshot_url(self, snapshot_date, max_days_prior=7): for i in range(max_days_prior): try_date = snapshot_date - datetime.timedelta(days=i) @@ -240,7 +240,7 @@ def get_mran_snapshot_url(self, snapshot_date, max_days_prior=7): ) ) - @lru_cache + @lru_cache() def get_cran_mirror_url(self, snapshot_date): # Date after which we will use rspm + binary packages instead of MRAN + source packages rspm_cutoff_date = datetime.date(2022, 1, 1) @@ -250,7 +250,7 @@ def get_cran_mirror_url(self, snapshot_date): else: return self.get_mran_snapshot_url(snapshot_date) - @lru_cache + @lru_cache() def get_devtools_snapshot_url(self): """ Return url of snapshot to use for getting devtools install @@ -264,7 +264,7 @@ def get_devtools_snapshot_url(self): # necessary apt packages. return "https://packagemanager.rstudio.com/all/__linux__/bionic/2022-01-04+Y3JhbiwyOjQ1MjYyMTU7NzlBRkJEMzg" - @lru_cache + @lru_cache() def get_build_scripts(self): """ Return series of build-steps common to all R repositories @@ -359,7 +359,7 @@ def get_build_scripts(self): return super().get_build_scripts() + scripts - @lru_cache + @lru_cache() def get_preassemble_script_files(self): files = super().get_preassemble_script_files() installR_path = self.binder_path("install.R") @@ -368,7 +368,7 @@ def get_preassemble_script_files(self): return files - @lru_cache + @lru_cache() def get_preassemble_scripts(self): """Install contents of install.R @@ -394,7 +394,7 @@ def get_preassemble_scripts(self): return super().get_preassemble_scripts() + scripts - @lru_cache + @lru_cache() def get_assemble_scripts(self): """Install the dependencies of or the repository itself""" assemble_scripts = super().get_assemble_scripts() From de908c92131f4147812bc43bd02d69e5610862a2 Mon Sep 17 00:00:00 2001 From: Sylvain Corlay Date: Thu, 23 Mar 2023 16:45:57 +0100 Subject: [PATCH 133/171] Update to mamba 1.4.0 and conda 23.1.0 --- repo2docker/buildpacks/conda/install-base-env.bash | 5 ++--- tests/conda/py35-binder-dir/verify | 6 +++--- 2 files changed, 5 insertions(+), 6 deletions(-) diff --git a/repo2docker/buildpacks/conda/install-base-env.bash b/repo2docker/buildpacks/conda/install-base-env.bash index e8b3bb3ed..ebaf7fbbc 100755 --- a/repo2docker/buildpacks/conda/install-base-env.bash +++ b/repo2docker/buildpacks/conda/install-base-env.bash @@ -5,8 +5,8 @@ set -ex cd $(dirname $0) -export MAMBA_VERSION=1.1.0 -export CONDA_VERSION=4.13.0 +export MAMBA_VERSION=1.4.0 +export CONDA_VERSION=23.1.0 URL="https://anaconda.org/conda-forge/micromamba/${MAMBA_VERSION}/download/${CONDA_PLATFORM}/micromamba-${MAMBA_VERSION}-0.tar.bz2" @@ -34,7 +34,6 @@ channels: auto_update_conda: false show_channel_urls: true update_dependencies: false -experimental_sat_error_message: true # channel_priority: flexible EOT diff --git a/tests/conda/py35-binder-dir/verify b/tests/conda/py35-binder-dir/verify index 67ea6827b..8cd1f0a9b 100755 --- a/tests/conda/py35-binder-dir/verify +++ b/tests/conda/py35-binder-dir/verify @@ -16,13 +16,13 @@ v = out.split()[1] assert v[:3] == "3.5", out out = sh(["micromamba", "--version"]) -assert out == "1.1.0", out +assert out == "1.4.0", out out = sh(["mamba", "--version"]) assert ( out - == """mamba 1.1.0 -conda 4.13.0""" + == """mamba 1.4.0 +conda 23.1.0""" ), out sh([kernel_python, "-c", "import numpy"]) From 6b68e5aaf936c7926fa1d68548eab6adadf2b5b6 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 27 Mar 2023 06:05:59 +0000 Subject: [PATCH 134/171] build(deps): bump pypa/gh-action-pypi-publish from 1.6.4 to 1.8.3 Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.6.4 to 1.8.3. - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.6.4...v1.8.3) --- updated-dependencies: - dependency-name: pypa/gh-action-pypi-publish dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- .github/workflows/release.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 16ebfff71..d881a14b3 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -57,7 +57,7 @@ jobs: # all previous steps always run in order to exercise them - name: Publish distribution to PyPI if: startsWith(github.ref, 'refs/tags') - uses: pypa/gh-action-pypi-publish@v1.6.4 + uses: pypa/gh-action-pypi-publish@v1.8.3 with: password: ${{ secrets.PYPI_PASSWORD }} From 48f4cc630eac137dd9c1394dab886cb07c93563c Mon Sep 17 00:00:00 2001 From: Philip Durbin Date: Wed, 29 Mar 2023 05:35:08 -0400 Subject: [PATCH 135/171] make isort happy with pre-commit run --all-files #1242 --- tests/unit/contentproviders/test_dataverse.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/unit/contentproviders/test_dataverse.py b/tests/unit/contentproviders/test_dataverse.py index c5c0d1cb6..abdfe456d 100644 --- a/tests/unit/contentproviders/test_dataverse.py +++ b/tests/unit/contentproviders/test_dataverse.py @@ -4,8 +4,8 @@ from io import BytesIO from tempfile import TemporaryDirectory from unittest.mock import patch -from urllib.request import Request, urlopen from urllib.parse import urlsplit +from urllib.request import Request, urlopen import pytest From b4b8629a456785798ad2332cce971eff3e1d66c5 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 3 Apr 2023 06:00:35 +0000 Subject: [PATCH 136/171] build(deps): bump pypa/gh-action-pypi-publish from 1.8.3 to 1.8.4 Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.3 to 1.8.4. - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.3...v1.8.4) --- updated-dependencies: - dependency-name: pypa/gh-action-pypi-publish dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- .github/workflows/release.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index bbfcec1af..dc769fd36 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -57,7 +57,7 @@ jobs: # all previous steps always run in order to exercise them - name: Publish distribution to PyPI if: startsWith(github.ref, 'refs/tags') - uses: pypa/gh-action-pypi-publish@v1.8.3 + uses: pypa/gh-action-pypi-publish@v1.8.4 with: password: ${{ secrets.PYPI_PASSWORD }} From 438e696c808778e53fd11f564c258706819a783f Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 4 Apr 2023 06:23:02 +0000 Subject: [PATCH 137/171] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/psf/black: 23.1.0 → 23.3.0](https://github.com/psf/black/compare/23.1.0...23.3.0) --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index bc9dad7bf..d7eb34473 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,7 +23,7 @@ repos: # Autoformat: Python code - repo: https://github.com/psf/black - rev: 23.1.0 + rev: 23.3.0 hooks: - id: black args: From 7e1c89fde7ac24ef5b4a56d0d5ca5ab99af84cb2 Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Tue, 4 Apr 2023 22:57:33 +0200 Subject: [PATCH 138/171] dependabot: monthly updates of github actions --- .github/dependabot.yml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/.github/dependabot.yml b/.github/dependabot.yml index ac88b7c69..9787ecdda 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -9,8 +9,9 @@ version: 2 updates: # Maintain dependencies in our GitHub Workflows - package-ecosystem: github-actions - directory: "/" # This should be / rather than .github/workflows + directory: / + labels: [ci] schedule: - interval: weekly + interval: monthly time: "05:00" - timezone: "Etc/UTC" + timezone: Etc/UTC From 1e7cd82722d0c683054f3564b690727d62e7c25c Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Wed, 5 Apr 2023 10:16:47 +0200 Subject: [PATCH 139/171] dependabot: rename to .yaml --- .github/{dependabot.yml => dependabot.yaml} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename .github/{dependabot.yml => dependabot.yaml} (72%) diff --git a/.github/dependabot.yml b/.github/dependabot.yaml similarity index 72% rename from .github/dependabot.yml rename to .github/dependabot.yaml index 9787ecdda..ec797f62c 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yaml @@ -1,4 +1,4 @@ -# dependabot.yml reference: https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file +# dependabot.yaml reference: https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file # # Notes: # - Status and logs from dependabot are provided at From 30f3cb368d46077056fe30da7325bea8c2206cf1 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 7 Apr 2023 13:58:14 +0000 Subject: [PATCH 140/171] build(deps): bump pypa/gh-action-pypi-publish from 1.8.4 to 1.8.5 Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.4 to 1.8.5. - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.4...v1.8.5) --- updated-dependencies: - dependency-name: pypa/gh-action-pypi-publish dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- .github/workflows/release.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index dc769fd36..be33ebfda 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -57,7 +57,7 @@ jobs: # all previous steps always run in order to exercise them - name: Publish distribution to PyPI if: startsWith(github.ref, 'refs/tags') - uses: pypa/gh-action-pypi-publish@v1.8.4 + uses: pypa/gh-action-pypi-publish@v1.8.5 with: password: ${{ secrets.PYPI_PASSWORD }} From 5f383fd8cdebe03c3b1489657a71e4c407cf28fc Mon Sep 17 00:00:00 2001 From: YuviPanda Date: Mon, 27 Mar 2023 17:07:41 +0530 Subject: [PATCH 141/171] Remove deprecated nteract_on_jupyter Last release was in 2019, and it has been explicilty deprecated for a while https://github.com/nteract/nteract/issues/5554#issuecomment-852434391 TLJH plans to remove it in https://github.com/jupyterhub/the-littlest-jupyterhub/pull/869 --- docs/source/contributing/tasks.md | 2 +- docs/source/howto/user_interface.rst | 31 -------------------- repo2docker/buildpacks/conda/__init__.py | 1 - repo2docker/buildpacks/conda/environment.yml | 1 - 4 files changed, 1 insertion(+), 34 deletions(-) diff --git a/docs/source/contributing/tasks.md b/docs/source/contributing/tasks.md index 6deae1c0f..30be8c662 100644 --- a/docs/source/contributing/tasks.md +++ b/docs/source/contributing/tasks.md @@ -74,7 +74,7 @@ See the subsections below for more detailed instructions. Contains list of packages to install in Python3 conda environments, which are the default. **This is where all Notebook versions & - notebook extensions (such as JupyterLab / nteract) go**. + notebook extensions (such as JupyterLab) go**. - `repo2docker/buildpacks/conda/environment.py-2.7.yml` diff --git a/docs/source/howto/user_interface.rst b/docs/source/howto/user_interface.rst index 92a9bc01b..588c270c4 100644 --- a/docs/source/howto/user_interface.rst +++ b/docs/source/howto/user_interface.rst @@ -46,37 +46,6 @@ And you can switch back to JupyterLab by replacing ``/tree/`` with ``/lab/``: http(s):///lab/ - -nteract -======= - -`nteract is a notebook interface `_ built with React. -It is similar to a more feature-filled version of the traditional -Jupyter Notebook interface. - -nteract comes pre-installed in any session that has been built from -a Python repository. - -You can launch nteract from within a user -session by replacing ``/tree`` with ``/nteract`` at the end of a notebook -server's URL like so: - -.. code-block:: none - - http(s):///nteract - -For example, the following Binder URL will open the -`pyTudes repository `_ -and begin an nteract session in the ``ipynb`` folder: - -https://mybinder.org/v2/gh/norvig/pytudes/HEAD?urlpath=nteract/tree/ipynb - -The ``/tree/ipynb`` above is how nteract directs you to a specific file -or folder. - -To learn more about nteract, visit `the nteract website `_. - - RStudio ======= diff --git a/repo2docker/buildpacks/conda/__init__.py b/repo2docker/buildpacks/conda/__init__.py index 508d5cd1e..aed5de6f6 100644 --- a/repo2docker/buildpacks/conda/__init__.py +++ b/repo2docker/buildpacks/conda/__init__.py @@ -127,7 +127,6 @@ def get_build_scripts(self): - a frozen base set of requirements, including: - support for Jupyter widgets - support for JupyterLab - - support for nteract """ return super().get_build_scripts() + [ diff --git a/repo2docker/buildpacks/conda/environment.yml b/repo2docker/buildpacks/conda/environment.yml index 258062bdb..538bdbbf5 100644 --- a/repo2docker/buildpacks/conda/environment.yml +++ b/repo2docker/buildpacks/conda/environment.yml @@ -10,4 +10,3 @@ dependencies: - jupyterlab==3.4.8 - jupyterhub-singleuser==3.1.1 - notebook==6.4.12 - - nteract_on_jupyter==2.1.3 From f87c86c625e7149934b2e4399d59b959d5834eae Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Sun, 9 Apr 2023 17:25:53 +0200 Subject: [PATCH 142/171] conda buildpack: refreeze environments --- .../conda/environment.py-3.10-linux-64.lock | 110 ++++++++--------- .../environment.py-3.10-linux-aarch64.lock | 110 ++++++++--------- .../buildpacks/conda/environment.py-3.10.yml | 3 +- .../conda/environment.py-3.11-linux-64.lock | 111 +++++++++--------- .../environment.py-3.11-linux-aarch64.lock | 111 +++++++++--------- .../buildpacks/conda/environment.py-3.11.yml | 3 +- .../conda/environment.py-3.7-linux-64.lock | 70 +++++------ .../environment.py-3.7-linux-aarch64.lock | 70 +++++------ .../buildpacks/conda/environment.py-3.7.yml | 3 +- .../conda/environment.py-3.8-linux-64.lock | 106 ++++++++--------- .../environment.py-3.8-linux-aarch64.lock | 106 ++++++++--------- .../buildpacks/conda/environment.py-3.8.yml | 3 +- .../conda/environment.py-3.9-linux-64.lock | 108 ++++++++--------- .../environment.py-3.9-linux-aarch64.lock | 108 ++++++++--------- .../buildpacks/conda/environment.py-3.9.yml | 3 +- 15 files changed, 511 insertions(+), 514 deletions(-) diff --git a/repo2docker/buildpacks/conda/environment.py-3.10-linux-64.lock b/repo2docker/buildpacks/conda/environment.py-3.10-linux-64.lock index a934da5e8..ecdeefec9 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.10-linux-64.lock +++ b/repo2docker/buildpacks/conda/environment.py-3.10-linux-64.lock @@ -1,15 +1,15 @@ # AUTO GENERATED FROM environment.py-3.10.yml, DO NOT MANUALLY MODIFY -# Frozen on 2023-02-03 12:34:24 UTC +# Frozen on 2023-04-09 15:23:40 UTC # Generated by conda-lock. # platform: linux-64 -# input_hash: 9fd16b0f6d64e86a62e326694b74a429aef5dd7b227a96b4f0e2425851e4e016 +# input_hash: 999dec5129d8880d536f4005b8c79138df000d64e6626932b69eee478a0c6c4e @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.12.7-ha878542_0.conda#ff9f73d45c4a07d6f424495288a26080 https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h41732ed_0.conda#7aca3059a1729aa76c597603f10b0dd3 https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-12.2.0-h46fd767_19.tar.bz2#1030b1f38c129f2634eae026f704fe60 https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.10-3_cp310.conda#4eb33d14d794b0f4be116443ffed3853 -https://conda.anaconda.org/conda-forge/noarch/tzdata-2022g-h191b570_0.conda#51fc4fcfb19f5d95ffc8c339db5068e8 +https://conda.anaconda.org/conda-forge/noarch/tzdata-2023c-h71feb2d_0.conda#939e3e74d8be4dac89ce83b20de2492a https://conda.anaconda.org/conda-forge/linux-64/libgomp-12.2.0-h65d4601_19.tar.bz2#cedcee7c064c01c403f962c9e8d3c373 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-12.2.0-h65d4601_19.tar.bz2#e4c94f80aef025c17ab0828cd85ef535 @@ -18,28 +18,27 @@ https://conda.anaconda.org/conda-forge/linux-64/icu-70.1-h27087fc_0.tar.bz2#8747 https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.0-h7f98852_0.tar.bz2#39b1328babf85c7c3a61636d9cd50206 https://conda.anaconda.org/conda-forge/linux-64/libsodium-1.0.18-h36c2ea0_1.tar.bz2#c3788462a6fbddafdb413a9f9053e58d -https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.32.1-h7f98852_1000.tar.bz2#772d69f030955d9646d3d0eaf21d859d 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a/repo2docker/buildpacks/conda/environment.py-3.7.yml b/repo2docker/buildpacks/conda/environment.py-3.7.yml index d20195340..e4038edf9 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.7.yml +++ b/repo2docker/buildpacks/conda/environment.py-3.7.yml @@ -1,5 +1,5 @@ # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY -# Generated on 2023-02-03 12:33:27 UTC +# Generated on 2023-04-09 15:22:03 UTC channels: - conda-forge dependencies: @@ -12,4 +12,3 @@ dependencies: - jupyterlab==3.4.8 - jupyterhub-singleuser==3.1.1 - notebook==6.4.12 -- nteract_on_jupyter==2.1.3 diff --git a/repo2docker/buildpacks/conda/environment.py-3.8-linux-64.lock b/repo2docker/buildpacks/conda/environment.py-3.8-linux-64.lock index c1c0ff49f..7b2d061d3 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.8-linux-64.lock +++ b/repo2docker/buildpacks/conda/environment.py-3.8-linux-64.lock @@ -1,8 +1,8 @@ # AUTO GENERATED FROM environment.py-3.8.yml, DO NOT MANUALLY MODIFY -# Frozen on 2023-02-03 12:32:57 UTC +# Frozen on 2023-04-09 15:22:34 UTC # Generated by conda-lock. # platform: linux-64 -# input_hash: 2fe7881a5392503fd6a9f83c6e0faba6d5cc08834c94af8545dde81cf2a35991 +# input_hash: 996b633ac0ff8e2641d62cbcef669cba45c12aebd71fd687d4fa93caa00f2078 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.12.7-ha878542_0.conda#ff9f73d45c4a07d6f424495288a26080 @@ -17,28 +17,27 @@ https://conda.anaconda.org/conda-forge/linux-64/icu-70.1-h27087fc_0.tar.bz2#8747 https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3 https://conda.anaconda.org/conda-forge/linux-64/libnsl-2.0.0-h7f98852_0.tar.bz2#39b1328babf85c7c3a61636d9cd50206 https://conda.anaconda.org/conda-forge/linux-64/libsodium-1.0.18-h36c2ea0_1.tar.bz2#c3788462a6fbddafdb413a9f9053e58d 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a/repo2docker/buildpacks/conda/environment.py-3.8.yml +++ b/repo2docker/buildpacks/conda/environment.py-3.8.yml @@ -1,5 +1,5 @@ # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY -# Generated on 2023-02-03 12:32:57 UTC +# Generated on 2023-04-09 15:22:34 UTC channels: - conda-forge dependencies: @@ -12,4 +12,3 @@ dependencies: - jupyterlab==3.4.8 - jupyterhub-singleuser==3.1.1 - notebook==6.4.12 -- nteract_on_jupyter==2.1.3 diff --git a/repo2docker/buildpacks/conda/environment.py-3.9-linux-64.lock b/repo2docker/buildpacks/conda/environment.py-3.9-linux-64.lock index 5d7d29c63..27fc7fb7c 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.9-linux-64.lock +++ b/repo2docker/buildpacks/conda/environment.py-3.9-linux-64.lock @@ -1,15 +1,15 @@ # AUTO GENERATED FROM environment.py-3.9.yml, DO NOT MANUALLY MODIFY -# Frozen on 2023-02-03 12:34:00 UTC +# Frozen on 2023-04-09 15:23:05 UTC # Generated by conda-lock. # platform: linux-64 -# input_hash: 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+https://conda.anaconda.org/conda-forge/noarch/nbconvert-core-7.3.0-pyhd8ed1ab_2.conda#ed94c1fe002035e89035733f7b81c698 +https://conda.anaconda.org/conda-forge/noarch/ipywidgets-8.0.2-pyhd8ed1ab_1.tar.bz2#81b7f46918555bf911ad2ba2f3259094 +https://conda.anaconda.org/conda-forge/noarch/jupyter_server-1.23.6-pyhd8ed1ab_0.conda#5016f7c6845a6efd270fcee63af9a2a0 +https://conda.anaconda.org/conda-forge/noarch/nbconvert-pandoc-7.3.0-pyhd8ed1ab_2.conda#e8970dddb374e0df96830efa6adc6257 https://conda.anaconda.org/conda-forge/noarch/jupyter-resource-usage-0.7.0-pyhd8ed1ab_0.conda#c57567d49d926826b1f852712ac8acfa -https://conda.anaconda.org/conda-forge/noarch/jupyterlab_server-2.19.0-pyhd8ed1ab_0.conda#9dc0706ec2f8e13b7a0db9d6a19051ff -https://conda.anaconda.org/conda-forge/noarch/nbconvert-7.2.9-pyhd8ed1ab_0.conda#523aaa3affb003ab0e68dbc24c9027f4 +https://conda.anaconda.org/conda-forge/noarch/jupyterlab_server-2.22.0-pyhd8ed1ab_0.conda#9e2780151926e61ed169a2e87140f2c6 +https://conda.anaconda.org/conda-forge/noarch/nbconvert-7.3.0-pyhd8ed1ab_2.conda#6e1101bee7a04177535ee6c1a5306bf6 https://conda.anaconda.org/conda-forge/noarch/notebook-shim-0.2.2-pyhd8ed1ab_0.tar.bz2#40be846cd4e78672a40e43db9dae753c -https://conda.anaconda.org/conda-forge/noarch/nbclassic-0.5.1-pyhd8ed1ab_0.conda#cf832e3d48ef22528c676ed6e4b4085a +https://conda.anaconda.org/conda-forge/noarch/nbclassic-0.5.5-pyhb4ecaf3_1.conda#a29d9080cb29c25b6a36c1d2f3da3ece https://conda.anaconda.org/conda-forge/noarch/notebook-6.4.12-pyha770c72_0.tar.bz2#77fc67c5bbea44fd41e8bbe2ac82d1ad https://conda.anaconda.org/conda-forge/noarch/jupyter-offlinenotebook-0.2.2-pyh1d7be83_0.tar.bz2#fe55056ce4bc4bd4953ba440270735fb https://conda.anaconda.org/conda-forge/noarch/jupyterlab-3.4.8-pyhd8ed1ab_0.tar.bz2#6fbf13b0e8a6fa24bbae91205e8ce467 -https://conda.anaconda.org/conda-forge/noarch/nteract_on_jupyter-2.1.3-py_0.tar.bz2#1430ccd983ae6b161e2fbf4377965f7a https://conda.anaconda.org/conda-forge/noarch/jupyterhub-singleuser-3.1.1-pyh2a2186d_0.conda#6d0a3394efe9ff7c0ad1ed03a6ca3720 diff --git a/repo2docker/buildpacks/conda/environment.py-3.9.yml b/repo2docker/buildpacks/conda/environment.py-3.9.yml index 852d7eba5..81763a4bd 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.9.yml +++ b/repo2docker/buildpacks/conda/environment.py-3.9.yml @@ -1,5 +1,5 @@ # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY -# Generated on 2023-02-03 12:34:00 UTC +# Generated on 2023-04-09 15:23:05 UTC channels: - conda-forge dependencies: @@ -12,4 +12,3 @@ dependencies: - jupyterlab==3.4.8 - jupyterhub-singleuser==3.1.1 - notebook==6.4.12 -- nteract_on_jupyter==2.1.3 From 3068954c4d81cca0f0454d1b26c9b9b98608856d Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Sun, 9 Apr 2023 17:40:36 +0200 Subject: [PATCH 143/171] conda buildpack: accept that refreeze brought in npm 9 --- tests/base/node/verify | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/tests/base/node/verify b/tests/base/node/verify index 555426126..8f662b65f 100755 --- a/tests/base/node/verify +++ b/tests/base/node/verify @@ -7,6 +7,12 @@ which node node --version node --version | grep v18 +# npm comes with the nodejs conda-forge package that we have pinned, but we +# don't have npm pinned. For example nodejs 18.13.0 brought npm 8.19.3, but +# nodejs 18.14.0 brought npm 9.3.1. +# +# Since we have no npm version pinning, we just test that some version is +# installed. +# which npm npm --version -npm --version | grep 8. From 39d203cc80a020e8d4bd6d88cd5025c058c3a012 Mon Sep 17 00:00:00 2001 From: Min RK Date: Tue, 11 Apr 2023 12:01:43 +0200 Subject: [PATCH 144/171] missing `f` in julia fetch error f-string --- repo2docker/buildpacks/julia/julia_project.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/repo2docker/buildpacks/julia/julia_project.py b/repo2docker/buildpacks/julia/julia_project.py index cce56abf7..7b6771c28 100644 --- a/repo2docker/buildpacks/julia/julia_project.py +++ b/repo2docker/buildpacks/julia/julia_project.py @@ -27,7 +27,7 @@ def all_julias(self): "https://julialang-s3.julialang.org/bin/versions.json" ).json() except Exception as e: - raise RuntimeError("Failed to fetch available Julia versions: {e}") + raise RuntimeError(f"Failed to fetch available Julia versions: {e}") vers = [semver.VersionInfo.parse(v) for v in json.keys()] # filter out pre-release versions not supported by find_semver_match() filtered_vers = [v for v in vers if v.prerelease is None] From 7bf02d8101175c3acc2de1d953a6b27695677ace Mon Sep 17 00:00:00 2001 From: "Kacper Kowalik (Xarthisius)" Date: Mon, 22 May 2023 12:55:50 -0500 Subject: [PATCH 145/171] Update the location of R packagemanager Fixes #1272 --- docs/source/howto/languages.rst | 4 ++-- repo2docker/buildpacks/r.py | 18 +++++++++--------- tests/r/r4.0-rspm/verify | 4 ++-- tests/unit/test_r.py | 6 +++--- 4 files changed, 16 insertions(+), 16 deletions(-) diff --git a/docs/source/howto/languages.rst b/docs/source/howto/languages.rst index abf76e0a1..75ea7e537 100644 --- a/docs/source/howto/languages.rst +++ b/docs/source/howto/languages.rst @@ -66,11 +66,11 @@ by adding a :ref:`install.R` file to your repo. RStudio and IRKernel installed by default for all R versions. If you request R 4.1 or later, or specify a snapshot date newer than -``2022-01-01``, `packagemanager.rstudio.com `_ +``2022-01-01``, `packagemanager.posit.co `_ will be used to provide much faster installations via `binary packages `_. For *some* packages, this might require you install underlying system libraries using :ref:`apt.txt` - look at the page for the CRAN package you are interested in at -`packagemanager.rstudio.com `_ to find +`packagemanager.posit.co `_ to find a list. For older R versions with an older snapshot date, `MRAN `_ diff --git a/repo2docker/buildpacks/r.py b/repo2docker/buildpacks/r.py index 03aa4ae61..26190c742 100644 --- a/repo2docker/buildpacks/r.py +++ b/repo2docker/buildpacks/r.py @@ -22,8 +22,8 @@ class RBuildPack(PythonBuildPack): Where 'year', 'month' and 'date' refer to a specific date whose CRAN snapshot we will use to fetch packages. - Uses https://packagemanager.rstudio.com, or MRAN if no snapshot - is found on packagemanager.rstudio.com + Uses https://packagemanager.posit.co, or MRAN if no snapshot + is found on packagemanager.posit.co 2. A `DESCRIPTION` file signaling an R package @@ -204,7 +204,7 @@ def get_packages(self): def get_rspm_snapshot_url(self, snapshot_date, max_days_prior=7): for i in range(max_days_prior): snapshots = requests.post( - "https://packagemanager.rstudio.com/__api__/url", + "https://packagemanager.posit.co/__api__/url", # Ask for midnight UTC snapshot json={ "repo": "all", @@ -216,11 +216,11 @@ def get_rspm_snapshot_url(self, snapshot_date, max_days_prior=7): # Construct a snapshot URL that will give us binary packages for Ubuntu Bionic (18.04) if "upsi" in snapshots: return ( - "https://packagemanager.rstudio.com/all/__linux__/bionic/" + "https://packagemanager.posit.co/all/__linux__/bionic/" + snapshots["upsi"] ) raise ValueError( - "No snapshot found for {} or {} days prior in packagemanager.rstudio.com".format( + "No snapshot found for {} or {} days prior in packagemanager.posit.co".format( snapshot_date.strftime("%Y-%m-%d"), max_days_prior ) ) @@ -229,7 +229,7 @@ def get_rspm_snapshot_url(self, snapshot_date, max_days_prior=7): def get_mran_snapshot_url(self, snapshot_date, max_days_prior=7): for i in range(max_days_prior): try_date = snapshot_date - datetime.timedelta(days=i) - # Fall back to MRAN if packagemanager.rstudio.com doesn't have it + # Fall back to MRAN if packagemanager.posit.co doesn't have it url = f"https://mran.microsoft.com/snapshot/{try_date.isoformat()}" r = requests.head(url) if r.ok: @@ -258,11 +258,11 @@ def get_devtools_snapshot_url(self): devtools is part of our 'core' base install, so we should have some control over what version we install here. """ - # Picked from https://packagemanager.rstudio.com/client/#/repos/1/overview + # Picked from https://packagemanager.posit.co/client/#/repos/1/overview # Hardcoded rather than dynamically determined from a date to avoid extra API calls - # Plus, we can always use packagemanager.rstudio.com here as we always install the + # Plus, we can always use packagemanager.posit.co here as we always install the # necessary apt packages. - return "https://packagemanager.rstudio.com/all/__linux__/bionic/2022-01-04+Y3JhbiwyOjQ1MjYyMTU7NzlBRkJEMzg" + return "https://packagemanager.posit.co/all/__linux__/bionic/2022-01-04+Y3JhbiwyOjQ1MjYyMTU7NzlBRkJEMzg" @lru_cache() def get_build_scripts(self): diff --git a/tests/r/r4.0-rspm/verify b/tests/r/r4.0-rspm/verify index 21bac29d8..835f141c0 100755 --- a/tests/r/r4.0-rspm/verify +++ b/tests/r/r4.0-rspm/verify @@ -8,6 +8,6 @@ if (!(version$major == "4" && as.double(version$minor) >= 0 && as.double(version } # The date we have chosen should give us an rspm mirror -if (!(startsWith(options()$repos["CRAN"], "https://packagemanager.rstudio.com"))) { +if (!(startsWith(options()$repos["CRAN"], "https://packagemanager.posit.co"))) { quit("yes", 1) -} \ No newline at end of file +} diff --git a/tests/unit/test_r.py b/tests/unit/test_r.py index a5d7db7c0..7f7e5a0e1 100644 --- a/tests/unit/test_r.py +++ b/tests/unit/test_r.py @@ -26,7 +26,7 @@ def test_version_completion(tmpdir): tmpdir.chdir() with open("runtime.txt", "w") as f: - f.write(f"r-3.6-2019-01-01") + f.write("r-3.6-2019-01-01") r = buildpacks.RBuildPack() assert r.r_version == "3.6.3" @@ -52,7 +52,7 @@ def test_mran_date(tmpdir, runtime, expected): def test_snapshot_rspm_date(): test_dates = { - # Even though there is no snapshot specified in the interface at https://packagemanager.rstudio.com/client/#/repos/1/overview + # Even though there is no snapshot specified in the interface at https://packagemanager.posit.co/client/#/repos/1/overview # For 2021 Oct 22, the API still returns a valid URL that one can install # packages from - probably some server side magic that repeats our client side logic. # No snapshot for this date from @@ -65,7 +65,7 @@ def test_snapshot_rspm_date(): for requested, expected in test_dates.items(): snapshot_url = r.get_rspm_snapshot_url(requested) assert snapshot_url.startswith( - "https://packagemanager.rstudio.com/all/__linux__/bionic/" + "https://packagemanager.posit.co/all/__linux__/bionic/" + expected.strftime("%Y-%m-%d") ) From 2f46bccb7b66ab4d0fc83c9dd62e9461eb346ec3 Mon Sep 17 00:00:00 2001 From: Min RK Date: Wed, 24 May 2023 13:06:00 +0200 Subject: [PATCH 146/171] fix github link templates missing `%s` raises error on sphinx 6 --- docs/source/conf.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index ec8294dad..2dcb08615 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -29,9 +29,9 @@ exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] templates_path = ["_templates"] extlinks = { - "issue": ("https://github.com/jupyterhub/repo2docker/issues/%s", "Issue #"), - "pr": ("https://github.com/jupyterhub/repo2docker/pull/%s", "PR #"), - "user": ("https://github.com/%s", "@"), + "issue": ("https://github.com/jupyterhub/repo2docker/issues/%s", "Issue #%s"), + "pr": ("https://github.com/jupyterhub/repo2docker/pull/%s", "PR #%s"), + "user": ("https://github.com/%s", "@%s"), } From 44e4697cafbd2f6651b1def3aebe91b17ffc3649 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 1 Jun 2023 05:57:45 +0000 Subject: [PATCH 147/171] build(deps): bump pypa/gh-action-pypi-publish from 1.8.5 to 1.8.6 Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.5 to 1.8.6. - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](https://github.com/pypa/gh-action-pypi-publish/compare/v1.8.5...v1.8.6) --- updated-dependencies: - dependency-name: pypa/gh-action-pypi-publish dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- .github/workflows/release.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index be33ebfda..74c429441 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -57,7 +57,7 @@ jobs: # all previous steps always run in order to exercise them - name: Publish distribution to PyPI if: startsWith(github.ref, 'refs/tags') - uses: pypa/gh-action-pypi-publish@v1.8.5 + uses: pypa/gh-action-pypi-publish@v1.8.6 with: password: ${{ secrets.PYPI_PASSWORD }} From f13d80e51d7add8f90f5b3e500ef3f6f96c43712 Mon Sep 17 00:00:00 2001 From: YuviPanda Date: Tue, 6 Jun 2023 01:21:40 +0530 Subject: [PATCH 148/171] Recreate changelog as markdown github-activity, used for other JupyterHub release processes, now outputs markdown. This PR moves the existing changelog to use markdown, and provides a more complete list of changes too. Ref https://github.com/jupyterhub/repo2docker/issues/1280 --- CHANGES.rst | 2 +- docs/source/changelog.md | 726 ++++++++++++++++++++++++++++++++++++++ docs/source/changelog.rst | 523 --------------------------- 3 files changed, 727 insertions(+), 524 deletions(-) create mode 100644 docs/source/changelog.md delete mode 100644 docs/source/changelog.rst diff --git a/CHANGES.rst b/CHANGES.rst index 8441ef9f4..5beccbf12 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -1 +1 @@ -The ``repo2docker`` changelog has been moved. It can be viewed online at https://repo2docker.readthedocs.io/en/latest/changelog.html. In the ``repo2docker`` repository, the changelog is located at ``docs/source/changelog.rst``. +The ``repo2docker`` changelog has been moved. It can be viewed online at https://repo2docker.readthedocs.io/en/latest/changelog.html. In the ``repo2docker`` repository, the changelog is located at ``docs/source/changelog.md``. diff --git a/docs/source/changelog.md b/docs/source/changelog.md new file mode 100644 index 000000000..62b49ffc4 --- /dev/null +++ b/docs/source/changelog.md @@ -0,0 +1,726 @@ +# Changelog + +## 2022.10.0 + +([full changelog](https://github.com/jupyterhub/repo2docker/compare/e40242c...e0d5b9b)) + +### Maintenance and upkeep improvements + +- Use enum to standardise `phase` [#1185](https://github.com/jupyterhub/repo2docker/pull/1185) ([@manics](https://github.com/manics)) +- get CI working again [#1178](https://github.com/jupyterhub/repo2docker/pull/1178) ([@minrk](https://github.com/minrk)) +- Freeze.py update [#1173](https://github.com/jupyterhub/repo2docker/pull/1173) ([@manics](https://github.com/manics)) +- Bump default R version to 4.2 from 4.1, and let R 3.4 go from 3.4.0 to 3.4.4 [#1165](https://github.com/jupyterhub/repo2docker/pull/1165) ([@yuvipanda](https://github.com/yuvipanda)) + +### Documentation improvements + +- Post release fixes [#1133](https://github.com/jupyterhub/repo2docker/pull/1133) ([@manics](https://github.com/manics)) + +### Other merged PRs + +- Initial changelog for 2022.10.0 [#1194](https://github.com/jupyterhub/repo2docker/pull/1194) ([@manics](https://github.com/manics)) +- [MRG] Update Jupyter dependencies [#1193](https://github.com/jupyterhub/repo2docker/pull/1193) ([@jtpio](https://github.com/jtpio)) +- Remove conda buildpacks pin of r-irkernel to 1.2 [#1191](https://github.com/jupyterhub/repo2docker/pull/1191) ([@consideRatio](https://github.com/consideRatio)) +- ci: refactor julia/r/conda tests - now ~25 min instead of ~50 min [#1188](https://github.com/jupyterhub/repo2docker/pull/1188) ([@consideRatio](https://github.com/consideRatio)) +- ci: general refresh of github workflows, update gha versions and let dependabot do it, etc. [#1186](https://github.com/jupyterhub/repo2docker/pull/1186) ([@consideRatio](https://github.com/consideRatio)) +- fail on unsupported Python [#1184](https://github.com/jupyterhub/repo2docker/pull/1184) ([@minrk](https://github.com/minrk)) +- mount wheels from build stage instead of copying them [#1182](https://github.com/jupyterhub/repo2docker/pull/1182) ([@minrk](https://github.com/minrk)) +- consistent log handling when not using JSON loggers [#1177](https://github.com/jupyterhub/repo2docker/pull/1177) ([@minrk](https://github.com/minrk)) +- explicitly build linux/amd64 images [#1176](https://github.com/jupyterhub/repo2docker/pull/1176) ([@minrk](https://github.com/minrk)) +- add Python 3.10 base environment [#1175](https://github.com/jupyterhub/repo2docker/pull/1175) ([@minrk](https://github.com/minrk)) +- Bump version of nodejs [#1172](https://github.com/jupyterhub/repo2docker/pull/1172) ([@yuvipanda](https://github.com/yuvipanda)) +- Update mamba [#1171](https://github.com/jupyterhub/repo2docker/pull/1171) ([@SylvainCorlay](https://github.com/SylvainCorlay)) +- Support pulling from zenodo sandbox too [#1169](https://github.com/jupyterhub/repo2docker/pull/1169) ([@yuvipanda](https://github.com/yuvipanda)) +- Add MPDL Dataverse [#1167](https://github.com/jupyterhub/repo2docker/pull/1167) ([@wilhelmfrank](https://github.com/wilhelmfrank)) +- ci: switch to using a 2fa enabled accounts pypi api-token [#1166](https://github.com/jupyterhub/repo2docker/pull/1166) ([@consideRatio](https://github.com/consideRatio)) +- Add JPL Dataverse [#1163](https://github.com/jupyterhub/repo2docker/pull/1163) ([@foobarbecue](https://github.com/foobarbecue)) +- Get R from RStudio provided apt packages (.deb files) [#1161](https://github.com/jupyterhub/repo2docker/pull/1161) ([@yuvipanda](https://github.com/yuvipanda)) +- [MRG] Shallow clone HEAD [#1160](https://github.com/jupyterhub/repo2docker/pull/1160) ([@daradib](https://github.com/daradib)) +- Fix Read-Only filesystem permission issue for log file [#1156](https://github.com/jupyterhub/repo2docker/pull/1156) ([@timeu](https://github.com/timeu)) +- handle permission issue writing .jupyter-server-log.txt in REPO_DIR [#1151](https://github.com/jupyterhub/repo2docker/pull/1151) ([@pymonger](https://github.com/pymonger)) +- Update black version [#1150](https://github.com/jupyterhub/repo2docker/pull/1150) ([@yuvipanda](https://github.com/yuvipanda)) +- Update base notebook packages [#1149](https://github.com/jupyterhub/repo2docker/pull/1149) ([@yuvipanda](https://github.com/yuvipanda)) +- [MRG] upgrade RStudio Server to v2022.02.1 [#1148](https://github.com/jupyterhub/repo2docker/pull/1148) ([@aplamada](https://github.com/aplamada)) +- Update 'how to get R' section [#1147](https://github.com/jupyterhub/repo2docker/pull/1147) ([@yuvipanda](https://github.com/yuvipanda)) +- handle r version being unspecified in environment.yml [#1141](https://github.com/jupyterhub/repo2docker/pull/1141) ([@minrk](https://github.com/minrk)) +- [MRG] Update Dockerfile to current Alpine (ALPINE_VERSION=3.15.0) [#1136](https://github.com/jupyterhub/repo2docker/pull/1136) ([@holzman](https://github.com/holzman)) +- [MRG] Pass build_args to `render()` during `--no-build` for consistency with regular builds [#1135](https://github.com/jupyterhub/repo2docker/pull/1135) ([@yoogottamk](https://github.com/yoogottamk)) +- Update Changelog for release 2022.02.0 [#1113](https://github.com/jupyterhub/repo2docker/pull/1113) ([@manics](https://github.com/manics)) + +### Contributors to this release + +([GitHub contributors page for this release](https://github.com/jupyterhub/repo2docker/graphs/contributors?from=2022-02-06&to=2022-10-18&type=c)) + +[@aplamada](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aaplamada+updated%3A2022-02-06..2022-10-18&type=Issues) | [@betatim](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abetatim+updated%3A2022-02-06..2022-10-18&type=Issues) | [@consideRatio](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AconsideRatio+updated%3A2022-02-06..2022-10-18&type=Issues) | [@daradib](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Adaradib+updated%3A2022-02-06..2022-10-18&type=Issues) | [@foobarbecue](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Afoobarbecue+updated%3A2022-02-06..2022-10-18&type=Issues) | [@holzman](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aholzman+updated%3A2022-02-06..2022-10-18&type=Issues) | [@jameshowison](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajameshowison+updated%3A2022-02-06..2022-10-18&type=Issues) | [@jtpio](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajtpio+updated%3A2022-02-06..2022-10-18&type=Issues) | [@manics](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Amanics+updated%3A2022-02-06..2022-10-18&type=Issues) | [@minrk](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aminrk+updated%3A2022-02-06..2022-10-18&type=Issues) | [@pymonger](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Apymonger+updated%3A2022-02-06..2022-10-18&type=Issues) | [@SylvainCorlay](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3ASylvainCorlay+updated%3A2022-02-06..2022-10-18&type=Issues) | [@timeu](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Atimeu+updated%3A2022-02-06..2022-10-18&type=Issues) | [@welcome](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awelcome+updated%3A2022-02-06..2022-10-18&type=Issues) | [@wilhelmfrank](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awilhelmfrank+updated%3A2022-02-06..2022-10-18&type=Issues) | [@yoogottamk](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayoogottamk+updated%3A2022-02-06..2022-10-18&type=Issues) | [@yuvipanda](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayuvipanda+updated%3A2022-02-06..2022-10-18&type=Issues) + +## 2022.02.0 + +([full changelog](https://github.com/jupyterhub/repo2docker/compare/c73321c...e40242c)) + +### Enhancements made + +- Update jupyterlab 3.2.5 jupyter-resource-usage 0.6.1 [#1105](https://github.com/jupyterhub/repo2docker/pull/1105) ([@manics](https://github.com/manics)) + +### Maintenance and upkeep improvements + +- Add help message to freeze.py [#1106](https://github.com/jupyterhub/repo2docker/pull/1106) ([@manics](https://github.com/manics)) + +### Documentation improvements + +- [MRG] Release 2021.08.0 [#1067](https://github.com/jupyterhub/repo2docker/pull/1067) ([@manics](https://github.com/manics)) + +### Other merged PRs + +- put micromamba in /usr/local/bin and use mamba for installs [#1128](https://github.com/jupyterhub/repo2docker/pull/1128) ([@minrk](https://github.com/minrk)) +- Update ipywidgets jupyter-offlinenotebook jupyterlab [#1127](https://github.com/jupyterhub/repo2docker/pull/1127) ([@manics](https://github.com/manics)) +- Allow passing in extra args to Docker initialization [#1124](https://github.com/jupyterhub/repo2docker/pull/1124) ([@yuvipanda](https://github.com/yuvipanda)) +- Allow passing in traitlets via commandline [#1123](https://github.com/jupyterhub/repo2docker/pull/1123) ([@yuvipanda](https://github.com/yuvipanda)) +- Delete /tmp/downloaded_packages after running install.R [#1119](https://github.com/jupyterhub/repo2docker/pull/1119) ([@yuvipanda](https://github.com/yuvipanda)) +- Use a smaller R library in our tests [#1118](https://github.com/jupyterhub/repo2docker/pull/1118) ([@yuvipanda](https://github.com/yuvipanda)) +- Only get R itself (r-base-core) from apt, not CRAN packages [#1117](https://github.com/jupyterhub/repo2docker/pull/1117) ([@minrk](https://github.com/minrk)) +- set USER root after each directive block [#1115](https://github.com/jupyterhub/repo2docker/pull/1115) ([@minrk](https://github.com/minrk)) +- Update Changelog for release 2022.02.0 [#1113](https://github.com/jupyterhub/repo2docker/pull/1113) ([@manics](https://github.com/manics)) +- Say 'apt repository' rather than PPA [#1111](https://github.com/jupyterhub/repo2docker/pull/1111) ([@yuvipanda](https://github.com/yuvipanda)) +- Bump default R version to 4.1 [#1107](https://github.com/jupyterhub/repo2docker/pull/1107) ([@yuvipanda](https://github.com/yuvipanda)) +- Get binary R packages from packagemanager.rstudio.com [#1104](https://github.com/jupyterhub/repo2docker/pull/1104) ([@yuvipanda](https://github.com/yuvipanda)) +- Quieter R builds [#1103](https://github.com/jupyterhub/repo2docker/pull/1103) ([@yuvipanda](https://github.com/yuvipanda)) +- Support R 4.1 [#1102](https://github.com/jupyterhub/repo2docker/pull/1102) ([@yuvipanda](https://github.com/yuvipanda)) +- Add command line option to pass extra build args [#1100](https://github.com/jupyterhub/repo2docker/pull/1100) ([@TimoRoth](https://github.com/TimoRoth)) +- Set labels when building image from Dockerfile [#1097](https://github.com/jupyterhub/repo2docker/pull/1097) ([@TimoRoth](https://github.com/TimoRoth)) +- jupyterlab 3.1.17 [#1092](https://github.com/jupyterhub/repo2docker/pull/1092) ([@minrk](https://github.com/minrk)) +- update user_interface doc to reflect that lab is default [#1085](https://github.com/jupyterhub/repo2docker/pull/1085) ([@minrk](https://github.com/minrk)) +- Updates to dev docs + Recommonmark -> MyST Parser [#1082](https://github.com/jupyterhub/repo2docker/pull/1082) ([@choldgraf](https://github.com/choldgraf)) +- Bump JupyterLab to 3.1.11 [#1081](https://github.com/jupyterhub/repo2docker/pull/1081) ([@choldgraf](https://github.com/choldgraf)) +- Fix Docker build (again) [#1078](https://github.com/jupyterhub/repo2docker/pull/1078) ([@manics](https://github.com/manics)) +- Typo fix in utils docstring [#1072](https://github.com/jupyterhub/repo2docker/pull/1072) ([@jgarte](https://github.com/jgarte)) +- Rename requirements.py-3.5.txt to requirements.py-3.5.pip [#1061](https://github.com/jupyterhub/repo2docker/pull/1061) ([@manics](https://github.com/manics)) +- Default UI to JupyterLab [#1035](https://github.com/jupyterhub/repo2docker/pull/1035) ([@SylvainCorlay](https://github.com/SylvainCorlay)) + +### Contributors to this release + +([GitHub contributors page for this release](https://github.com/jupyterhub/repo2docker/graphs/contributors?from=2021-08-24&to=2022-02-06&type=c)) + +[@andrewjohnlowe](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aandrewjohnlowe+updated%3A2021-08-24..2022-02-06&type=Issues) | [@aplamada](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aaplamada+updated%3A2021-08-24..2022-02-06&type=Issues) | 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[@daroczig](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Adaroczig+updated%3A2021-08-24..2022-02-06&type=Issues) | [@exaexa](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aexaexa+updated%3A2021-08-24..2022-02-06&type=Issues) | [@jgarte](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajgarte+updated%3A2021-08-24..2022-02-06&type=Issues) | [@jtpio](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajtpio+updated%3A2021-08-24..2022-02-06&type=Issues) | [@kkmann](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Akkmann+updated%3A2021-08-24..2022-02-06&type=Issues) | [@mael-le-gal](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Amael-le-gal+updated%3A2021-08-24..2022-02-06&type=Issues) | [@manics](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Amanics+updated%3A2021-08-24..2022-02-06&type=Issues) | [@mattwigway](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Amattwigway+updated%3A2021-08-24..2022-02-06&type=Issues) | [@meeseeksmachine](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ameeseeksmachine+updated%3A2021-08-24..2022-02-06&type=Issues) | [@minrk](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aminrk+updated%3A2021-08-24..2022-02-06&type=Issues) | [@petersudmant](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Apetersudmant+updated%3A2021-08-24..2022-02-06&type=Issues) | [@RaoOfPhysics](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3ARaoOfPhysics+updated%3A2021-08-24..2022-02-06&type=Issues) | [@sje30](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Asje30+updated%3A2021-08-24..2022-02-06&type=Issues) | [@SylvainCorlay](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3ASylvainCorlay+updated%3A2021-08-24..2022-02-06&type=Issues) | [@TimoRoth](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3ATimoRoth+updated%3A2021-08-24..2022-02-06&type=Issues) | [@welcome](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awelcome+updated%3A2021-08-24..2022-02-06&type=Issues) | [@yuvipanda](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayuvipanda+updated%3A2021-08-24..2022-02-06&type=Issues) + +## 2021.08.0 + +([full changelog](https://github.com/jupyterhub/repo2docker/compare/71eb805...c73321c)) + +### Bugs fixed + +- fix: add chardet, a not explicitly declared dependency [#1064](https://github.com/jupyterhub/repo2docker/pull/1064) ([@johnhoman](https://github.com/johnhoman)) + +### Documentation improvements + +- [MRG] Release 2021.08.0 [#1067](https://github.com/jupyterhub/repo2docker/pull/1067) ([@manics](https://github.com/manics)) + +### Other merged PRs + +- Update README quay.io URL, Add docker latest tag [#1075](https://github.com/jupyterhub/repo2docker/pull/1075) ([@manics](https://github.com/manics)) +- GitHub workflow build and push to Docker hub [#1071](https://github.com/jupyterhub/repo2docker/pull/1071) ([@manics](https://github.com/manics)) +- Bump environment [#1069](https://github.com/jupyterhub/repo2docker/pull/1069) ([@manics](https://github.com/manics)) +- Rename master branch to main [#1068](https://github.com/jupyterhub/repo2docker/pull/1068) ([@manics](https://github.com/manics)) +- Workaround docker-py dependency's failure to import six [#1066](https://github.com/jupyterhub/repo2docker/pull/1066) ([@consideRatio](https://github.com/consideRatio)) +- Remove Pipfile & Pipfile.lock [#1054](https://github.com/jupyterhub/repo2docker/pull/1054) ([@yuvipanda](https://github.com/yuvipanda)) +- Remove CircleCI docs build [#1053](https://github.com/jupyterhub/repo2docker/pull/1053) ([@yuvipanda](https://github.com/yuvipanda)) +- Pin doc requirements to avoid CI breakages [#1052](https://github.com/jupyterhub/repo2docker/pull/1052) ([@manics](https://github.com/manics)) +- Stop using deprecated add_stylesheet in sphinx [#1050](https://github.com/jupyterhub/repo2docker/pull/1050) ([@yuvipanda](https://github.com/yuvipanda)) +- Add study participation notice to readme [#1046](https://github.com/jupyterhub/repo2docker/pull/1046) ([@sgibson91](https://github.com/sgibson91)) +- Bump urllib3 from 1.26.4 to 1.26.5 [#1045](https://github.com/jupyterhub/repo2docker/pull/1045) ([@dependabot](https://github.com/dependabot)) +- always unpack a single zenodo zip [#1043](https://github.com/jupyterhub/repo2docker/pull/1043) ([@akhmerov](https://github.com/akhmerov)) +- State newly used installation command [#1040](https://github.com/jupyterhub/repo2docker/pull/1040) ([@fkohrt](https://github.com/fkohrt)) +- Fix regression in hydroshare introduced after moving to requests [#1034](https://github.com/jupyterhub/repo2docker/pull/1034) ([@MridulS](https://github.com/MridulS)) +- Bump pyyaml from 5.1.1 to 5.4 [#1029](https://github.com/jupyterhub/repo2docker/pull/1029) ([@dependabot](https://github.com/dependabot)) +- Set default Julia version to 1.6 [#1028](https://github.com/jupyterhub/repo2docker/pull/1028) ([@tomyun](https://github.com/tomyun)) +- Fix logo URL in README [#1027](https://github.com/jupyterhub/repo2docker/pull/1027) ([@betatim](https://github.com/betatim)) +- Refine buffered output debugging [#1016](https://github.com/jupyterhub/repo2docker/pull/1016) ([@minrk](https://github.com/minrk)) +- reimplement entrypoint in Python [#1014](https://github.com/jupyterhub/repo2docker/pull/1014) ([@minrk](https://github.com/minrk)) +- [MRG] Define an interface for Container engines [#848](https://github.com/jupyterhub/repo2docker/pull/848) ([@manics](https://github.com/manics)) + +### Contributors to this release + +([GitHub contributors page for this release](https://github.com/jupyterhub/repo2docker/graphs/contributors?from=2021-03-12&to=2021-08-24&type=c)) + +[@akhmerov](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aakhmerov+updated%3A2021-03-12..2021-08-24&type=Issues) | [@aplamada](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aaplamada+updated%3A2021-03-12..2021-08-24&type=Issues) | [@betatim](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abetatim+updated%3A2021-03-12..2021-08-24&type=Issues) | [@choldgraf](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acholdgraf+updated%3A2021-03-12..2021-08-24&type=Issues) | [@civodul](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acivodul+updated%3A2021-03-12..2021-08-24&type=Issues) | [@consideRatio](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AconsideRatio+updated%3A2021-03-12..2021-08-24&type=Issues) | [@dependabot](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Adependabot+updated%3A2021-03-12..2021-08-24&type=Issues) | [@dkleissa](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Adkleissa+updated%3A2021-03-12..2021-08-24&type=Issues) | [@fkohrt](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Afkohrt+updated%3A2021-03-12..2021-08-24&type=Issues) | [@johnhoman](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajohnhoman+updated%3A2021-03-12..2021-08-24&type=Issues) | [@jzf2101](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajzf2101+updated%3A2021-03-12..2021-08-24&type=Issues) | [@ltetrel](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Altetrel+updated%3A2021-03-12..2021-08-24&type=Issues) | [@manics](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Amanics+updated%3A2021-03-12..2021-08-24&type=Issues) | [@meeseeksmachine](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ameeseeksmachine+updated%3A2021-03-12..2021-08-24&type=Issues) | [@minrk](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aminrk+updated%3A2021-03-12..2021-08-24&type=Issues) | [@MridulS](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AMridulS+updated%3A2021-03-12..2021-08-24&type=Issues) | [@ocefpaf](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aocefpaf+updated%3A2021-03-12..2021-08-24&type=Issues) | [@paugier](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Apaugier+updated%3A2021-03-12..2021-08-24&type=Issues) | [@rnestler](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Arnestler+updated%3A2021-03-12..2021-08-24&type=Issues) | [@sgibson91](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Asgibson91+updated%3A2021-03-12..2021-08-24&type=Issues) | [@SylvainCorlay](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3ASylvainCorlay+updated%3A2021-03-12..2021-08-24&type=Issues) | [@tomyun](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Atomyun+updated%3A2021-03-12..2021-08-24&type=Issues) | [@welcome](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awelcome+updated%3A2021-03-12..2021-08-24&type=Issues) | [@willingc](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awillingc+updated%3A2021-03-12..2021-08-24&type=Issues) | [@xhochy](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Axhochy+updated%3A2021-03-12..2021-08-24&type=Issues) | [@yuvipanda](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayuvipanda+updated%3A2021-03-12..2021-08-24&type=Issues) + +## 2021.03.0 + +([full changelog](https://github.com/jupyterhub/repo2docker/compare/40f475f...71eb805)) + +### Merged PRs + +- [MRG] Cleanup install_requires including duplicates [#1020](https://github.com/jupyterhub/repo2docker/pull/1020) ([@manics](https://github.com/manics)) +- buildpacks.r: dont use apt-key directly to respect *_proxy env vars [#1019](https://github.com/jupyterhub/repo2docker/pull/1019) ([@g-braeunlich](https://github.com/g-braeunlich)) +- freeze with mamba, add 3.9 [#1017](https://github.com/jupyterhub/repo2docker/pull/1017) ([@minrk](https://github.com/minrk)) +- bump python in circleci test [#1013](https://github.com/jupyterhub/repo2docker/pull/1013) ([@minrk](https://github.com/minrk)) +- fix dataverse regression introduced in last release [#1011](https://github.com/jupyterhub/repo2docker/pull/1011) ([@MridulS](https://github.com/MridulS)) +- Add GH workflow to push releases to PYPi and introduce CalVer [#1004](https://github.com/jupyterhub/repo2docker/pull/1004) ([@betatim](https://github.com/betatim)) +- Add entrypoint script which automatically propagates *_PROXY env vars… [#1003](https://github.com/jupyterhub/repo2docker/pull/1003) ([@g-braeunlich](https://github.com/g-braeunlich)) +- Update to JupyterLab 3.0 [#996](https://github.com/jupyterhub/repo2docker/pull/996) ([@jtpio](https://github.com/jtpio)) +- Add a contentprovider for Software Heritage persistent ID (SWHID) [#988](https://github.com/jupyterhub/repo2docker/pull/988) ([@douardda](https://github.com/douardda)) +- [MRG] Stream jupyter server logs to a file [#987](https://github.com/jupyterhub/repo2docker/pull/987) ([@betatim](https://github.com/betatim)) +- [MRG] Experiment with different install mechanism to get code coverage stats again [#982](https://github.com/jupyterhub/repo2docker/pull/982) ([@betatim](https://github.com/betatim)) +- add 4.0, 4.0.2 to list of supported R versions [#960](https://github.com/jupyterhub/repo2docker/pull/960) ([@minrk](https://github.com/minrk)) + +### Contributors to this release + +([GitHub contributors page for this release](https://github.com/jupyterhub/repo2docker/graphs/contributors?from=2021-01-23&to=2021-03-12&type=c)) + +[@betatim](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abetatim+updated%3A2021-01-23..2021-03-12&type=Issues) | [@choldgraf](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acholdgraf+updated%3A2021-01-23..2021-03-12&type=Issues) | [@ctr26](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Actr26+updated%3A2021-01-23..2021-03-12&type=Issues) | [@douardda](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Adouardda+updated%3A2021-01-23..2021-03-12&type=Issues) | [@g-braeunlich](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ag-braeunlich+updated%3A2021-01-23..2021-03-12&type=Issues) | [@jabbera](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajabbera+updated%3A2021-01-23..2021-03-12&type=Issues) | [@jtpio](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajtpio+updated%3A2021-01-23..2021-03-12&type=Issues) | [@manics](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Amanics+updated%3A2021-01-23..2021-03-12&type=Issues) | [@minrk](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aminrk+updated%3A2021-01-23..2021-03-12&type=Issues) | [@MridulS](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AMridulS+updated%3A2021-01-23..2021-03-12&type=Issues) | [@scottyhq](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ascottyhq+updated%3A2021-01-23..2021-03-12&type=Issues) | [@SylvainCorlay](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3ASylvainCorlay+updated%3A2021-01-23..2021-03-12&type=Issues) | [@trybik](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Atrybik+updated%3A2021-01-23..2021-03-12&type=Issues) | [@welcome](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awelcome+updated%3A2021-01-23..2021-03-12&type=Issues) | [@yuvipanda](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayuvipanda+updated%3A2021-01-23..2021-03-12&type=Issues) + +## 2021.01.0 + +([full changelog](https://github.com/jupyterhub/repo2docker/compare/2e477dd...40f475f)) + +### Merged PRs + +- MRG: Fix figshare test [#1001](https://github.com/jupyterhub/repo2docker/pull/1001) ([@manics](https://github.com/manics)) +- [MRG] Weekly test of master to check for external failures [#998](https://github.com/jupyterhub/repo2docker/pull/998) ([@manics](https://github.com/manics)) +- Replace urllib by requests in contentproviders [#993](https://github.com/jupyterhub/repo2docker/pull/993) ([@douardda](https://github.com/douardda)) +- Use mambaforge instead of miniforge [#992](https://github.com/jupyterhub/repo2docker/pull/992) ([@SylvainCorlay](https://github.com/SylvainCorlay)) +- buildpacks/nix: 2.3 -> 2.3.9 [#991](https://github.com/jupyterhub/repo2docker/pull/991) ([@FRidh](https://github.com/FRidh)) +- buildpacks/nix: disable sandboxing (bugfix) [#990](https://github.com/jupyterhub/repo2docker/pull/990) ([@FRidh](https://github.com/FRidh)) +- Add Julia 1.5.3 support [#984](https://github.com/jupyterhub/repo2docker/pull/984) ([@tomyun](https://github.com/tomyun)) +- [MRG] Update to node 14 [#983](https://github.com/jupyterhub/repo2docker/pull/983) ([@jtpio](https://github.com/jtpio)) +- Mamba 0.6.1 [#979](https://github.com/jupyterhub/repo2docker/pull/979) ([@minrk](https://github.com/minrk)) +- [MRG] Remove reference to `master` branch from CLI doc [#977](https://github.com/jupyterhub/repo2docker/pull/977) ([@betatim](https://github.com/betatim)) +- [MRG] Ensure REPO_DIR owned by NB_USER [#975](https://github.com/jupyterhub/repo2docker/pull/975) ([@tomyun](https://github.com/tomyun)) +- add chown to COPY commands to reduce layer count [#969](https://github.com/jupyterhub/repo2docker/pull/969) ([@bollwyvl](https://github.com/bollwyvl)) +- MRG: set TIMEFORMAT for timed bash conda commands [#966](https://github.com/jupyterhub/repo2docker/pull/966) ([@manics](https://github.com/manics)) +- MRG: Disable jupyterlab extension build minimize [#963](https://github.com/jupyterhub/repo2docker/pull/963) ([@manics](https://github.com/manics)) +- Bump Black version to 20.8b1 and use --target-version=py36 [#955](https://github.com/jupyterhub/repo2docker/pull/955) ([@paugier](https://github.com/paugier)) +- MRG: Add workflow to build Docker image [#954](https://github.com/jupyterhub/repo2docker/pull/954) ([@manics](https://github.com/manics)) +- [MRG] Crosslink 'Configuring your repository' with usage [#952](https://github.com/jupyterhub/repo2docker/pull/952) ([@manics](https://github.com/manics)) +- [MRG] Bump Python requirement to 3.6 from 3.5 [#951](https://github.com/jupyterhub/repo2docker/pull/951) ([@betatim](https://github.com/betatim)) +- [MRG] Add a Mercurial contentprovider [#950](https://github.com/jupyterhub/repo2docker/pull/950) ([@paugier](https://github.com/paugier)) +- [MRG] Handle requirements.txt with `--pre` lines [#943](https://github.com/jupyterhub/repo2docker/pull/943) ([@betatim](https://github.com/betatim)) +- GitHub Actions [#942](https://github.com/jupyterhub/repo2docker/pull/942) ([@minrk](https://github.com/minrk)) +- stop running tests on travis [#940](https://github.com/jupyterhub/repo2docker/pull/940) ([@minrk](https://github.com/minrk)) +- update repo URLs for jupyterhub/repo2docker [#939](https://github.com/jupyterhub/repo2docker/pull/939) ([@minrk](https://github.com/minrk)) +- Add Julia 1.5.0 support [#938](https://github.com/jupyterhub/repo2docker/pull/938) ([@tomyun](https://github.com/tomyun)) +- Upgrade custom test infrastructure for pytest 6.0.0 [#936](https://github.com/jupyterhub/repo2docker/pull/936) ([@betatim](https://github.com/betatim)) +- validate_image_name: mention lowercase, fix formatting [#934](https://github.com/jupyterhub/repo2docker/pull/934) ([@manics](https://github.com/manics)) +- Update JupyterLab to 2.2.0 [#933](https://github.com/jupyterhub/repo2docker/pull/933) ([@manics](https://github.com/manics)) +- [MRG] Update snapshot date for simple R test [#930](https://github.com/jupyterhub/repo2docker/pull/930) ([@betatim](https://github.com/betatim)) +- little improvement for testing binder_dir [#928](https://github.com/jupyterhub/repo2docker/pull/928) ([@bitnik](https://github.com/bitnik)) +- update docs for config dirs [#927](https://github.com/jupyterhub/repo2docker/pull/927) ([@bitnik](https://github.com/bitnik)) +- avoid deprecated import of collections.abc [#924](https://github.com/jupyterhub/repo2docker/pull/924) ([@minrk](https://github.com/minrk)) +- Bump nix version to 2.3 [#915](https://github.com/jupyterhub/repo2docker/pull/915) ([@jboynyc](https://github.com/jboynyc)) +- doc: runtime.txt installs python x.y (& concise rewording) [#914](https://github.com/jupyterhub/repo2docker/pull/914) ([@mdeff](https://github.com/mdeff)) +- doc: environment.yml installs a conda env, not only python [#913](https://github.com/jupyterhub/repo2docker/pull/913) ([@mdeff](https://github.com/mdeff)) +- [MRG] Add gitpod.io config for docs [#908](https://github.com/jupyterhub/repo2docker/pull/908) ([@betatim](https://github.com/betatim)) +- [MRG] - fix repo2docker logo in Sphinx docs [#906](https://github.com/jupyterhub/repo2docker/pull/906) ([@trallard](https://github.com/trallard)) +- [MRG] Add nbresuse==0.3.3 (full freeze.py) [#904](https://github.com/jupyterhub/repo2docker/pull/904) ([@manics](https://github.com/manics)) +- Add missing “:” for R code [#900](https://github.com/jupyterhub/repo2docker/pull/900) ([@adamhsparks](https://github.com/adamhsparks)) +- Add Julia 1.4.2 support [#899](https://github.com/jupyterhub/repo2docker/pull/899) ([@davidanthoff](https://github.com/davidanthoff)) +- Update Dockerfile to add Docker [#896](https://github.com/jupyterhub/repo2docker/pull/896) ([@hamelsmu](https://github.com/hamelsmu)) +- [MRG] Fix RShiny proxy [#893](https://github.com/jupyterhub/repo2docker/pull/893) ([@betatim](https://github.com/betatim)) +- [MRG] Bump version of irkernel for R 4.0 [#892](https://github.com/jupyterhub/repo2docker/pull/892) ([@betatim](https://github.com/betatim)) +- [MRG] chmod start script from repo2docker-entrypoint [#886](https://github.com/jupyterhub/repo2docker/pull/886) ([@danlester](https://github.com/danlester)) +- [MRG] Workaround Docker issue impacting some tests on macOS [#882](https://github.com/jupyterhub/repo2docker/pull/882) ([@hwine](https://github.com/hwine)) +- [MRG] pypi jupyter-offlinenotebook==0.1.0 [#880](https://github.com/jupyterhub/repo2docker/pull/880) ([@manics](https://github.com/manics)) +- Work around a Julia bug [#879](https://github.com/jupyterhub/repo2docker/pull/879) ([@davidanthoff](https://github.com/davidanthoff)) +- [MRG] Change --env option to work like docker's [#874](https://github.com/jupyterhub/repo2docker/pull/874) ([@hwine](https://github.com/hwine)) +- [docs] fix grammatical error in section title [#872](https://github.com/jupyterhub/repo2docker/pull/872) ([@jameslamb](https://github.com/jameslamb)) +- Add support for Julia 1.4.0 [#870](https://github.com/jupyterhub/repo2docker/pull/870) ([@davidanthoff](https://github.com/davidanthoff)) +- [MRG] Update server proxy and rsession proxy [#869](https://github.com/jupyterhub/repo2docker/pull/869) ([@betatim](https://github.com/betatim)) +- Adopt new Sphinx theme name [#864](https://github.com/jupyterhub/repo2docker/pull/864) ([@xhochy](https://github.com/xhochy)) +- Document loose conda export with --from-history [#863](https://github.com/jupyterhub/repo2docker/pull/863) ([@xhochy](https://github.com/xhochy)) +- Fix typo [#862](https://github.com/jupyterhub/repo2docker/pull/862) ([@jtpio](https://github.com/jtpio)) +- Use miniforge instead of miniconda to get conda [#859](https://github.com/jupyterhub/repo2docker/pull/859) ([@yuvipanda](https://github.com/yuvipanda)) +- [MRG] If looking for latest MRAN URL try earlier snapshots too [#851](https://github.com/jupyterhub/repo2docker/pull/851) ([@manics](https://github.com/manics)) +- [MRG] Update black 19.10b0, target Python 3.5 [#849](https://github.com/jupyterhub/repo2docker/pull/849) ([@manics](https://github.com/manics)) +- [MRG] Add jupyter-offlinenotebook extension [#845](https://github.com/jupyterhub/repo2docker/pull/845) ([@betatim](https://github.com/betatim)) +- docs: postBuild warn about shell script errors being ignored [#844](https://github.com/jupyterhub/repo2docker/pull/844) ([@manics](https://github.com/manics)) +- [MRG] Update changelog for 0.11.0 [#842](https://github.com/jupyterhub/repo2docker/pull/842) ([@betatim](https://github.com/betatim)) + +### Contributors to this release + +([GitHub contributors page for this release](https://github.com/jupyterhub/repo2docker/graphs/contributors?from=2020-02-05&to=2021-01-23&type=c)) + +[@adamhsparks](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aadamhsparks+updated%3A2020-02-05..2021-01-23&type=Issues) | [@AliMirlou](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AAliMirlou+updated%3A2020-02-05..2021-01-23&type=Issues) | [@betatim](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abetatim+updated%3A2020-02-05..2021-01-23&type=Issues) | [@bitnik](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abitnik+updated%3A2020-02-05..2021-01-23&type=Issues) | [@blink1073](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ablink1073+updated%3A2020-02-05..2021-01-23&type=Issues) | [@bollwyvl](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abollwyvl+updated%3A2020-02-05..2021-01-23&type=Issues) | [@cboettig](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acboettig+updated%3A2020-02-05..2021-01-23&type=Issues) | [@ccordoba12](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Accordoba12+updated%3A2020-02-05..2021-01-23&type=Issues) | [@choldgraf](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acholdgraf+updated%3A2020-02-05..2021-01-23&type=Issues) | [@consideRatio](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AconsideRatio+updated%3A2020-02-05..2021-01-23&type=Issues) | [@danlester](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Adanlester+updated%3A2020-02-05..2021-01-23&type=Issues) | [@davidanthoff](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Adavidanthoff+updated%3A2020-02-05..2021-01-23&type=Issues) | [@dolfinus](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Adolfinus+updated%3A2020-02-05..2021-01-23&type=Issues) | [@douardda](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Adouardda+updated%3A2020-02-05..2021-01-23&type=Issues) | [@FRidh](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AFRidh+updated%3A2020-02-05..2021-01-23&type=Issues) | [@gracinet](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Agracinet+updated%3A2020-02-05..2021-01-23&type=Issues) | [@hamelsmu](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ahamelsmu+updated%3A2020-02-05..2021-01-23&type=Issues) | [@hwine](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ahwine+updated%3A2020-02-05..2021-01-23&type=Issues) | [@ivergara](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aivergara+updated%3A2020-02-05..2021-01-23&type=Issues) | [@jameslamb](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajameslamb+updated%3A2020-02-05..2021-01-23&type=Issues) | [@jasongrout](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajasongrout+updated%3A2020-02-05..2021-01-23&type=Issues) | [@jboynyc](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajboynyc+updated%3A2020-02-05..2021-01-23&type=Issues) | [@jtpio](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajtpio+updated%3A2020-02-05..2021-01-23&type=Issues) | [@jzf2101](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajzf2101+updated%3A2020-02-05..2021-01-23&type=Issues) | [@kkmann](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Akkmann+updated%3A2020-02-05..2021-01-23&type=Issues) | [@manics](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Amanics+updated%3A2020-02-05..2021-01-23&type=Issues) | [@mdeff](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Amdeff+updated%3A2020-02-05..2021-01-23&type=Issues) | [@meeseeksmachine](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ameeseeksmachine+updated%3A2020-02-05..2021-01-23&type=Issues) | [@minrk](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aminrk+updated%3A2020-02-05..2021-01-23&type=Issues) | [@nokome](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Anokome+updated%3A2020-02-05..2021-01-23&type=Issues) | [@nuest](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Anuest+updated%3A2020-02-05..2021-01-23&type=Issues) | [@ocefpaf](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aocefpaf+updated%3A2020-02-05..2021-01-23&type=Issues) | [@paugier](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Apaugier+updated%3A2020-02-05..2021-01-23&type=Issues) | [@scottyhq](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ascottyhq+updated%3A2020-02-05..2021-01-23&type=Issues) | [@sgibson91](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Asgibson91+updated%3A2020-02-05..2021-01-23&type=Issues) | [@support](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Asupport+updated%3A2020-02-05..2021-01-23&type=Issues) | [@SylvainCorlay](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3ASylvainCorlay+updated%3A2020-02-05..2021-01-23&type=Issues) | [@tomyun](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Atomyun+updated%3A2020-02-05..2021-01-23&type=Issues) | [@trallard](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Atrallard+updated%3A2020-02-05..2021-01-23&type=Issues) | [@welcome](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awelcome+updated%3A2020-02-05..2021-01-23&type=Issues) | [@westurner](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awesturner+updated%3A2020-02-05..2021-01-23&type=Issues) | [@willingc](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awillingc+updated%3A2020-02-05..2021-01-23&type=Issues) | [@xhochy](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Axhochy+updated%3A2020-02-05..2021-01-23&type=Issues) | [@yuvipanda](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayuvipanda+updated%3A2020-02-05..2021-01-23&type=Issues) + +## 0.11.0 + +([full changelog](https://github.com/jupyterhub/repo2docker/compare/69c09ae...2e477dd)) + +### Enhancements made + +- [MRG] Allow absolute paths in build_script_files [#681](https://github.com/jupyterhub/repo2docker/pull/681) ([@Xarthisius](https://github.com/Xarthisius)) + +### Maintenance and upkeep improvements + +- adduser: useradd --no-log-init to reduce lastlog size [#804](https://github.com/jupyterhub/repo2docker/pull/804) ([@manics](https://github.com/manics)) +- [MRG] Bumped conda version to 4.7.12 [#802](https://github.com/jupyterhub/repo2docker/pull/802) ([@davidrpugh](https://github.com/davidrpugh)) +- Use port 80 to download GPG keys to avoid firewall problems [#797](https://github.com/jupyterhub/repo2docker/pull/797) ([@betatim](https://github.com/betatim)) +- [MRG] Update nteract-on-jupyter to 2.1.3 [#794](https://github.com/jupyterhub/repo2docker/pull/794) ([@betatim](https://github.com/betatim)) +- use getpass.getuser instead of os.getlogin [#789](https://github.com/jupyterhub/repo2docker/pull/789) ([@minrk](https://github.com/minrk)) +- Add baseline infra for Azure Pipelines [#787](https://github.com/jupyterhub/repo2docker/pull/787) ([@willingc](https://github.com/willingc)) +- [MRG] Restore the hooks directory when building the docker image [#786](https://github.com/jupyterhub/repo2docker/pull/786) ([@betatim](https://github.com/betatim)) +- Add script to compare Dockerfiles generated by current and older… [#785](https://github.com/jupyterhub/repo2docker/pull/785) ([@nuest](https://github.com/nuest)) +- Print Dockerfile to stdout when --no-build [#784](https://github.com/jupyterhub/repo2docker/pull/784) ([@minrk](https://github.com/minrk)) +- add hooks to dockerignore [#782](https://github.com/jupyterhub/repo2docker/pull/782) ([@minrk](https://github.com/minrk)) +- add explicit log message on failing Docker connection [#779](https://github.com/jupyterhub/repo2docker/pull/779) ([@nuest](https://github.com/nuest)) +- [WIP] Upgrade IRKernel version to 1.0.2 [#770](https://github.com/jupyterhub/repo2docker/pull/770) ([@GeorgianaElena](https://github.com/GeorgianaElena)) +- Bump Miniconda from 4.6.14 to 4.7.10 [#769](https://github.com/jupyterhub/repo2docker/pull/769) ([@davidrpugh](https://github.com/davidrpugh)) +- Add support for Julia 1.2.0 [#768](https://github.com/jupyterhub/repo2docker/pull/768) ([@davidanthoff](https://github.com/davidanthoff)) +- include full docker progress events in push progress events [#727](https://github.com/jupyterhub/repo2docker/pull/727) ([@minrk](https://github.com/minrk)) + +### Documentation improvements + +- [MRG] Add docs for Figshare and Dataverse; update Dataverse installations file formatting [#796](https://github.com/jupyterhub/repo2docker/pull/796) ([@nuest](https://github.com/nuest)) +- Provide help text for commandline arguments [#517](https://github.com/jupyterhub/repo2docker/pull/517) ([@yuvipanda](https://github.com/yuvipanda)) + +### Other merged PRs + +- [MRG] Update changelog for 0.11.0 [#842](https://github.com/jupyterhub/repo2docker/pull/842) ([@betatim](https://github.com/betatim)) +- Merge pull request #840 from minrk/py38 [#840](https://github.com/jupyterhub/repo2docker/pull/840) ([@minrk](https://github.com/minrk)) +- [MRG] update base environment [#839](https://github.com/jupyterhub/repo2docker/pull/839) ([@minrk](https://github.com/minrk)) +- Start RStudio if R is installed via conda [#838](https://github.com/jupyterhub/repo2docker/pull/838) ([@xhochy](https://github.com/xhochy)) +- Merge pull request #834 from GeorgianaElena/new_badge [#834](https://github.com/jupyterhub/repo2docker/pull/834) ([@GeorgianaElena](https://github.com/GeorgianaElena)) +- Add support for Julia 1.3.1 [#831](https://github.com/jupyterhub/repo2docker/pull/831) ([@davidanthoff](https://github.com/davidanthoff)) +- [WIP] r build-pack: when using ppa install r-recommended [#830](https://github.com/jupyterhub/repo2docker/pull/830) ([@manics](https://github.com/manics)) +- [MRG] Deprecate legacy buildpack [#829](https://github.com/jupyterhub/repo2docker/pull/829) ([@betatim](https://github.com/betatim)) +- [MRG] Fix a broken link, update favicon [#826](https://github.com/jupyterhub/repo2docker/pull/826) ([@betatim](https://github.com/betatim)) +- adding instructions for contentprovider extension [#824](https://github.com/jupyterhub/repo2docker/pull/824) ([@choldgraf](https://github.com/choldgraf)) +- Add support for Julia 1.0.5 and 1.3.0 [#822](https://github.com/jupyterhub/repo2docker/pull/822) ([@davidanthoff](https://github.com/davidanthoff)) +- updating theme to pandas sphinx [#816](https://github.com/jupyterhub/repo2docker/pull/816) ([@choldgraf](https://github.com/choldgraf)) +- [MRG] Fixes link rendering [#811](https://github.com/jupyterhub/repo2docker/pull/811) ([@arokem](https://github.com/arokem)) +- [MRG] Remove explicit checkout when ref given [#810](https://github.com/jupyterhub/repo2docker/pull/810) ([@betatim](https://github.com/betatim)) +- [MRG] Fix submodule check out [#809](https://github.com/jupyterhub/repo2docker/pull/809) ([@davidbrochart](https://github.com/davidbrochart)) +- [MRG] add Hydroshare as a content provider [#800](https://github.com/jupyterhub/repo2docker/pull/800) ([@sblack-usu](https://github.com/sblack-usu)) +- [MRG] Add support for installing different versions of R [#772](https://github.com/jupyterhub/repo2docker/pull/772) ([@betatim](https://github.com/betatim)) +- Handle different file encodings [#771](https://github.com/jupyterhub/repo2docker/pull/771) ([@GeorgianaElena](https://github.com/GeorgianaElena)) +- Tiny typo in docs/source/index.rst [#760](https://github.com/jupyterhub/repo2docker/pull/760) ([@AartGoossens](https://github.com/AartGoossens)) +- [MRG] Dataverse content provider [#739](https://github.com/jupyterhub/repo2docker/pull/739) ([@Xarthisius](https://github.com/Xarthisius)) + +### Contributors to this release + +([GitHub contributors page for this release](https://github.com/jupyterhub/repo2docker/graphs/contributors?from=2019-08-07&to=2020-02-05&type=c)) + +[@AartGoossens](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AAartGoossens+updated%3A2019-08-07..2020-02-05&type=Issues) | [@andrewjohnlowe](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aandrewjohnlowe+updated%3A2019-08-07..2020-02-05&type=Issues) | [@arokem](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aarokem+updated%3A2019-08-07..2020-02-05&type=Issues) | [@betatim](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abetatim+updated%3A2019-08-07..2020-02-05&type=Issues) | [@cboettig](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acboettig+updated%3A2019-08-07..2020-02-05&type=Issues) | [@choldgraf](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acholdgraf+updated%3A2019-08-07..2020-02-05&type=Issues) | [@consideRatio](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AconsideRatio+updated%3A2019-08-07..2020-02-05&type=Issues) | [@daroczig](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Adaroczig+updated%3A2019-08-07..2020-02-05&type=Issues) | [@davidanthoff](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Adavidanthoff+updated%3A2019-08-07..2020-02-05&type=Issues) | [@davidbrochart](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Adavidbrochart+updated%3A2019-08-07..2020-02-05&type=Issues) | [@davidrpugh](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Adavidrpugh+updated%3A2019-08-07..2020-02-05&type=Issues) | [@dlowenberg](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Adlowenberg+updated%3A2019-08-07..2020-02-05&type=Issues) | [@DominikGlodzik](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3ADominikGlodzik+updated%3A2019-08-07..2020-02-05&type=Issues) | [@GeorgianaElena](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AGeorgianaElena+updated%3A2019-08-07..2020-02-05&type=Issues) | 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[@psychemedia](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Apsychemedia+updated%3A2019-08-07..2020-02-05&type=Issues) | [@rdbisme](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ardbisme+updated%3A2019-08-07..2020-02-05&type=Issues) | [@ryanlovett](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aryanlovett+updated%3A2019-08-07..2020-02-05&type=Issues) | [@saulshanabrook](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Asaulshanabrook+updated%3A2019-08-07..2020-02-05&type=Issues) | [@sblack-usu](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Asblack-usu+updated%3A2019-08-07..2020-02-05&type=Issues) | [@scottyhq](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ascottyhq+updated%3A2019-08-07..2020-02-05&type=Issues) | [@trallard](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Atrallard+updated%3A2019-08-07..2020-02-05&type=Issues) | [@travigd](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Atravigd+updated%3A2019-08-07..2020-02-05&type=Issues) | [@willingc](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awillingc+updated%3A2019-08-07..2020-02-05&type=Issues) | [@Xarthisius](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AXarthisius+updated%3A2019-08-07..2020-02-05&type=Issues) | [@xhochy](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Axhochy+updated%3A2019-08-07..2020-02-05&type=Issues) | [@yuvipanda](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayuvipanda+updated%3A2019-08-07..2020-02-05&type=Issues) + +## 0.10.0 + +([full changelog](https://github.com/jupyterhub/repo2docker/compare/734664a...69c09ae)) + +### Enhancements made + +- [MRG/REVIEW] Support Pipfile / Pipfile.lock with pipenv [#649](https://github.com/jupyterhub/repo2docker/pull/649) ([@consideRatio](https://github.com/consideRatio)) + +### Maintenance and upkeep improvements + +- [MRG] Rewrite tests in test_semver.py #615 [#757](https://github.com/jupyterhub/repo2docker/pull/757) ([@Geektrovert](https://github.com/Geektrovert)) +- [MRG] switch pip packages to conda-forge in conda buildpack [#728](https://github.com/jupyterhub/repo2docker/pull/728) ([@scottyhq](https://github.com/scottyhq)) + +### Other merged PRs + +- [MRG] Call parent preassemble scripts methods [#752](https://github.com/jupyterhub/repo2docker/pull/752) ([@betatim](https://github.com/betatim)) +- parse pipfiles to determine Python version [#748](https://github.com/jupyterhub/repo2docker/pull/748) ([@minrk](https://github.com/minrk)) +- typo in doi regexp [#746](https://github.com/jupyterhub/repo2docker/pull/746) ([@minrk](https://github.com/minrk)) +- refreeze 2019-07-16 [#745](https://github.com/jupyterhub/repo2docker/pull/745) ([@minrk](https://github.com/minrk)) +- [MRG] preassembly for conda/python [#743](https://github.com/jupyterhub/repo2docker/pull/743) ([@minrk](https://github.com/minrk)) +- [MRG] Adding bash to Dockerfile to fix git-credential-env [#738](https://github.com/jupyterhub/repo2docker/pull/738) ([@eexwhyzee](https://github.com/eexwhyzee)) +- bump xeus-cling in tests [#735](https://github.com/jupyterhub/repo2docker/pull/735) ([@minrk](https://github.com/minrk)) +- [MRG] Switch to binder-examples/requirements for our tests [#732](https://github.com/jupyterhub/repo2docker/pull/732) ([@betatim](https://github.com/betatim)) +- [MRG] Remove print statement and unused import [#730](https://github.com/jupyterhub/repo2docker/pull/730) ([@betatim](https://github.com/betatim)) +- [MRG] Handle root user case more gracefully. Fixes #696 [#723](https://github.com/jupyterhub/repo2docker/pull/723) ([@Xarthisius](https://github.com/Xarthisius)) +- Update target_repo_dir docstring [#721](https://github.com/jupyterhub/repo2docker/pull/721) ([@fmaussion](https://github.com/fmaussion)) +- [WIP] Version bump Conda from 4.6.14 to 4.7.5 [#719](https://github.com/jupyterhub/repo2docker/pull/719) ([@davidrpugh](https://github.com/davidrpugh)) +- [MRG] Install APT packages before copying the repo contents [#716](https://github.com/jupyterhub/repo2docker/pull/716) ([@betatim](https://github.com/betatim)) +- updated link for the community edition of docker [#715](https://github.com/jupyterhub/repo2docker/pull/715) ([@johnjarmitage](https://github.com/johnjarmitage)) +- Revert "[MRG] Remove more files during the image build to slimdown the image" [#712](https://github.com/jupyterhub/repo2docker/pull/712) ([@betatim](https://github.com/betatim)) +- Add support for julia 1.0.4 and 1.1.1 [#710](https://github.com/jupyterhub/repo2docker/pull/710) ([@davidanthoff](https://github.com/davidanthoff)) +- [MRG] Remove more files during the image build to slimdown the image [#709](https://github.com/jupyterhub/repo2docker/pull/709) ([@betatim](https://github.com/betatim)) +- base docker image on alpine [#705](https://github.com/jupyterhub/repo2docker/pull/705) ([@minrk](https://github.com/minrk)) +- [MRG] Generalize Zenodo content provider to support other Invenio repositories [#704](https://github.com/jupyterhub/repo2docker/pull/704) ([@tmorrell](https://github.com/tmorrell)) +- add `git-lfs` to dockerfile used for the repo2docker image [#703](https://github.com/jupyterhub/repo2docker/pull/703) ([@minrk](https://github.com/minrk)) +- [MRG] Add auto-formatting setup [#699](https://github.com/jupyterhub/repo2docker/pull/699) ([@betatim](https://github.com/betatim)) +- [MRG] Update verification of Node install [#695](https://github.com/jupyterhub/repo2docker/pull/695) ([@betatim](https://github.com/betatim)) +- [MRG] Zenodo content provider [#693](https://github.com/jupyterhub/repo2docker/pull/693) ([@betatim](https://github.com/betatim)) +- Adding contentprovider documentation [#692](https://github.com/jupyterhub/repo2docker/pull/692) ([@choldgraf](https://github.com/choldgraf)) +- set CONDA_DEFAULT_ENV [#690](https://github.com/jupyterhub/repo2docker/pull/690) ([@minrk](https://github.com/minrk)) +- Switch Travis CI to Ubuntu Xenial 16.04 [#689](https://github.com/jupyterhub/repo2docker/pull/689) ([@jrbourbeau](https://github.com/jrbourbeau)) +- [MRG] Drop support for Python 3.4 [#684](https://github.com/jupyterhub/repo2docker/pull/684) ([@betatim](https://github.com/betatim)) +- [MRG] Use getpass instead of pwd to fetch username [#683](https://github.com/jupyterhub/repo2docker/pull/683) ([@betatim](https://github.com/betatim)) +- Do not try to build the image with root as the primary user [#679](https://github.com/jupyterhub/repo2docker/pull/679) ([@Xarthisius](https://github.com/Xarthisius)) +- Revert "[MRG] Do not try to build the image with root as the primary user." [#678](https://github.com/jupyterhub/repo2docker/pull/678) ([@betatim](https://github.com/betatim)) +- [MRG] Update base image used for memory limit checks [#677](https://github.com/jupyterhub/repo2docker/pull/677) ([@betatim](https://github.com/betatim)) +- [MRG] Do not try to build the image with root as the primary user. [#676](https://github.com/jupyterhub/repo2docker/pull/676) ([@Xarthisius](https://github.com/Xarthisius)) +- bumping release date [#669](https://github.com/jupyterhub/repo2docker/pull/669) ([@choldgraf](https://github.com/choldgraf)) +- [MRG] release info updates [#668](https://github.com/jupyterhub/repo2docker/pull/668) ([@choldgraf](https://github.com/choldgraf)) +- [MRG] Remove the conda package cache as we can't hardlink to it [#666](https://github.com/jupyterhub/repo2docker/pull/666) ([@betatim](https://github.com/betatim)) + +### Contributors to this release + +([GitHub contributors page for this release](https://github.com/jupyterhub/repo2docker/graphs/contributors?from=2019-05-05&to=2019-08-07&type=c)) + +[@AliMirlou](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AAliMirlou+updated%3A2019-05-05..2019-08-07&type=Issues) | [@arnavs](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aarnavs+updated%3A2019-05-05..2019-08-07&type=Issues) | [@arokem](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aarokem+updated%3A2019-05-05..2019-08-07&type=Issues) | [@betatim](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abetatim+updated%3A2019-05-05..2019-08-07&type=Issues) | [@cboettig](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acboettig+updated%3A2019-05-05..2019-08-07&type=Issues) | [@choldgraf](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acholdgraf+updated%3A2019-05-05..2019-08-07&type=Issues) | [@consideRatio](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AconsideRatio+updated%3A2019-05-05..2019-08-07&type=Issues) | [@davidanthoff](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Adavidanthoff+updated%3A2019-05-05..2019-08-07&type=Issues) | [@davidrpugh](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Adavidrpugh+updated%3A2019-05-05..2019-08-07&type=Issues) | [@eexwhyzee](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aeexwhyzee+updated%3A2019-05-05..2019-08-07&type=Issues) | [@fmaussion](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Afmaussion+updated%3A2019-05-05..2019-08-07&type=Issues) | [@Geektrovert](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AGeektrovert+updated%3A2019-05-05..2019-08-07&type=Issues) | [@henchc](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ahenchc+updated%3A2019-05-05..2019-08-07&type=Issues) | [@jchesterpivotal](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajchesterpivotal+updated%3A2019-05-05..2019-08-07&type=Issues) | [@jlperla](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajlperla+updated%3A2019-05-05..2019-08-07&type=Issues) | [@johnjarmitage](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajohnjarmitage+updated%3A2019-05-05..2019-08-07&type=Issues) | [@jrbourbeau](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajrbourbeau+updated%3A2019-05-05..2019-08-07&type=Issues) | [@jzf2101](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajzf2101+updated%3A2019-05-05..2019-08-07&type=Issues) | [@mael-le-gal](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Amael-le-gal+updated%3A2019-05-05..2019-08-07&type=Issues) | [@manics](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Amanics+updated%3A2019-05-05..2019-08-07&type=Issues) | [@MattF-NSIDC](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AMattF-NSIDC+updated%3A2019-05-05..2019-08-07&type=Issues) | [@meeseeksmachine](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ameeseeksmachine+updated%3A2019-05-05..2019-08-07&type=Issues) | [@minrk](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aminrk+updated%3A2019-05-05..2019-08-07&type=Issues) | [@nuest](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Anuest+updated%3A2019-05-05..2019-08-07&type=Issues) | [@pdurbin](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Apdurbin+updated%3A2019-05-05..2019-08-07&type=Issues) | [@psychemedia](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Apsychemedia+updated%3A2019-05-05..2019-08-07&type=Issues) | [@saulshanabrook](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Asaulshanabrook+updated%3A2019-05-05..2019-08-07&type=Issues) | [@scopatz](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ascopatz+updated%3A2019-05-05..2019-08-07&type=Issues) | [@scottyhq](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ascottyhq+updated%3A2019-05-05..2019-08-07&type=Issues) | [@sgibson91](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Asgibson91+updated%3A2019-05-05..2019-08-07&type=Issues) | [@SylvainCorlay](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3ASylvainCorlay+updated%3A2019-05-05..2019-08-07&type=Issues) | [@tmorrell](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Atmorrell+updated%3A2019-05-05..2019-08-07&type=Issues) | [@trallard](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Atrallard+updated%3A2019-05-05..2019-08-07&type=Issues) | [@willingc](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awillingc+updated%3A2019-05-05..2019-08-07&type=Issues) | [@Xarthisius](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AXarthisius+updated%3A2019-05-05..2019-08-07&type=Issues) | [@yuvipanda](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayuvipanda+updated%3A2019-05-05..2019-08-07&type=Issues) | [@zmackie](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Azmackie+updated%3A2019-05-05..2019-08-07&type=Issues) + +## 0.9.0 + +([full changelog](https://github.com/jupyterhub/repo2docker/compare/b6c4e7e...734664a)) + +### Merged PRs + +- [MRG] Update change log in preparation for releasing v0.9.0 [#664](https://github.com/jupyterhub/repo2docker/pull/664) ([@betatim](https://github.com/betatim)) +- tweak language to make clear `exec "$@"` works [#663](https://github.com/jupyterhub/repo2docker/pull/663) ([@fomightez](https://github.com/fomightez)) +- specification info page [#662](https://github.com/jupyterhub/repo2docker/pull/662) ([@choldgraf](https://github.com/choldgraf)) +- add note to changelog [#659](https://github.com/jupyterhub/repo2docker/pull/659) ([@jhamman](https://github.com/jhamman)) +- Make sure ENTRYPOINT is an absolute path [#657](https://github.com/jupyterhub/repo2docker/pull/657) ([@yuvipanda](https://github.com/yuvipanda)) +- [MRG] Update contributing guidelines and issue templates [#655](https://github.com/jupyterhub/repo2docker/pull/655) ([@KirstieJane](https://github.com/KirstieJane)) +- [MRG] Update issue templates [#654](https://github.com/jupyterhub/repo2docker/pull/654) ([@betatim](https://github.com/betatim)) +- Support .binder directory [#653](https://github.com/jupyterhub/repo2docker/pull/653) ([@jhamman](https://github.com/jhamman)) +- [MRG] Fix handling of memory limit command line argument [#652](https://github.com/jupyterhub/repo2docker/pull/652) ([@betatim](https://github.com/betatim)) +- [MRG] install notebook in its own env [#651](https://github.com/jupyterhub/repo2docker/pull/651) ([@minrk](https://github.com/minrk)) +- [MRG] Bump nteract-on-jupyter to 2.0.12 and notebook to 5.7.8 [#650](https://github.com/jupyterhub/repo2docker/pull/650) ([@betatim](https://github.com/betatim)) +- [MRG] Unpin pip again [#647](https://github.com/jupyterhub/repo2docker/pull/647) ([@betatim](https://github.com/betatim)) +- [MRG] Fix up the server proxy package to get websockets back [#646](https://github.com/jupyterhub/repo2docker/pull/646) ([@betatim](https://github.com/betatim)) +- mentioning s2i in faq [#642](https://github.com/jupyterhub/repo2docker/pull/642) ([@choldgraf](https://github.com/choldgraf)) +- [MRG] Update change log [#641](https://github.com/jupyterhub/repo2docker/pull/641) ([@betatim](https://github.com/betatim)) +- [MRG] Fix sphinx deprecation for recommonmark [#640](https://github.com/jupyterhub/repo2docker/pull/640) ([@betatim](https://github.com/betatim)) +- [MRG] Ensure git submodules are updated and initialized [#639](https://github.com/jupyterhub/repo2docker/pull/639) ([@djhoese](https://github.com/djhoese)) +- [MRG] Remove conda package directory [#638](https://github.com/jupyterhub/repo2docker/pull/638) ([@betatim](https://github.com/betatim)) +- [MRG] Update the source links used by the legacy buildpack [#633](https://github.com/jupyterhub/repo2docker/pull/633) ([@betatim](https://github.com/betatim)) +- [MRG] Python 3.7 as the default in the docs [#631](https://github.com/jupyterhub/repo2docker/pull/631) ([@jtpio](https://github.com/jtpio)) +- [MRG] Bump notebook package version [#628](https://github.com/jupyterhub/repo2docker/pull/628) ([@betatim](https://github.com/betatim)) +- [MRG] Add issue template [#624](https://github.com/jupyterhub/repo2docker/pull/624) ([@betatim](https://github.com/betatim)) +- [MRG] Julia: Two small doc updates [#623](https://github.com/jupyterhub/repo2docker/pull/623) ([@fredrikekre](https://github.com/fredrikekre)) +- Install IJulia kernel into proper directory [#622](https://github.com/jupyterhub/repo2docker/pull/622) ([@davidanthoff](https://github.com/davidanthoff)) +- added some debug for R shiny [#614](https://github.com/jupyterhub/repo2docker/pull/614) ([@drmowinckels](https://github.com/drmowinckels)) +- [MRG] Add tests for Julia semver matching [#613](https://github.com/jupyterhub/repo2docker/pull/613) ([@betatim](https://github.com/betatim)) +- Use JULIA_PROJECT env variable to activate julia env [#612](https://github.com/jupyterhub/repo2docker/pull/612) ([@davidanthoff](https://github.com/davidanthoff)) +- [MRG] Add PR template with links to contrib docs and less focus on code contributions [#607](https://github.com/jupyterhub/repo2docker/pull/607) ([@betatim](https://github.com/betatim)) +- [MRG] Reopen change log [#606](https://github.com/jupyterhub/repo2docker/pull/606) ([@betatim](https://github.com/betatim)) +- [MRG] Add FAQ entry and Howto on exporting conda environments [#598](https://github.com/jupyterhub/repo2docker/pull/598) ([@betatim](https://github.com/betatim)) +- [MRG] Add tests for setting Python version during freeze [#592](https://github.com/jupyterhub/repo2docker/pull/592) ([@betatim](https://github.com/betatim)) +- Fix release date of 0.8.0 [#590](https://github.com/jupyterhub/repo2docker/pull/590) ([@betatim](https://github.com/betatim)) + +### Contributors to this release + +([GitHub contributors page for this release](https://github.com/jupyterhub/repo2docker/graphs/contributors?from=2019-02-21&to=2019-05-05&type=c)) + +[@alimanfoo](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aalimanfoo+updated%3A2019-02-21..2019-05-05&type=Issues) | [@betatim](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abetatim+updated%3A2019-02-21..2019-05-05&type=Issues) | [@captainsafia](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acaptainsafia+updated%3A2019-02-21..2019-05-05&type=Issues) | [@cboettig](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acboettig+updated%3A2019-02-21..2019-05-05&type=Issues) | [@choldgraf](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acholdgraf+updated%3A2019-02-21..2019-05-05&type=Issues) | [@consideRatio](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AconsideRatio+updated%3A2019-02-21..2019-05-05&type=Issues) | [@davidanthoff](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Adavidanthoff+updated%3A2019-02-21..2019-05-05&type=Issues) | [@djhoese](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Adjhoese+updated%3A2019-02-21..2019-05-05&type=Issues) | [@drmowinckels](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Adrmowinckels+updated%3A2019-02-21..2019-05-05&type=Issues) | [@fomightez](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Afomightez+updated%3A2019-02-21..2019-05-05&type=Issues) | [@fredrikekre](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Afredrikekre+updated%3A2019-02-21..2019-05-05&type=Issues) | [@Geektrovert](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AGeektrovert+updated%3A2019-02-21..2019-05-05&type=Issues) | [@jdblischak](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajdblischak+updated%3A2019-02-21..2019-05-05&type=Issues) | [@jhamman](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajhamman+updated%3A2019-02-21..2019-05-05&type=Issues) | [@jtpio](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajtpio+updated%3A2019-02-21..2019-05-05&type=Issues) | [@karthik](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Akarthik+updated%3A2019-02-21..2019-05-05&type=Issues) | [@KirstieJane](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AKirstieJane+updated%3A2019-02-21..2019-05-05&type=Issues) | [@LucianaMarques](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3ALucianaMarques+updated%3A2019-02-21..2019-05-05&type=Issues) | [@manics](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Amanics+updated%3A2019-02-21..2019-05-05&type=Issues) | [@meeseeksmachine](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ameeseeksmachine+updated%3A2019-02-21..2019-05-05&type=Issues) | [@minrk](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aminrk+updated%3A2019-02-21..2019-05-05&type=Issues) | [@NHDaly](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3ANHDaly+updated%3A2019-02-21..2019-05-05&type=Issues) | [@nuest](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Anuest+updated%3A2019-02-21..2019-05-05&type=Issues) | [@pat-s](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Apat-s+updated%3A2019-02-21..2019-05-05&type=Issues) | [@rabernat](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Arabernat+updated%3A2019-02-21..2019-05-05&type=Issues) | [@rgbkrk](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Argbkrk+updated%3A2019-02-21..2019-05-05&type=Issues) | [@trallard](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Atrallard+updated%3A2019-02-21..2019-05-05&type=Issues) | [@willingc](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awillingc+updated%3A2019-02-21..2019-05-05&type=Issues) | [@yuvipanda](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayuvipanda+updated%3A2019-02-21..2019-05-05&type=Issues) + +## 0.8.0 + +([full changelog](https://github.com/jupyterhub/repo2docker/compare/72d7634...b6c4e7e)) + +### Merged PRs + +- Fix release date of 0.8.0 [#590](https://github.com/jupyterhub/repo2docker/pull/590) ([@betatim](https://github.com/betatim)) +- Fix up double label trouble in the config file docs [#588](https://github.com/jupyterhub/repo2docker/pull/588) ([@betatim](https://github.com/betatim)) +- fix "Possible nested set" warning [#587](https://github.com/jupyterhub/repo2docker/pull/587) ([@minrk](https://github.com/minrk)) +- regen Pipfile.lock [#586](https://github.com/jupyterhub/repo2docker/pull/586) ([@minrk](https://github.com/minrk)) +- [MRG] Update documentation with more cross references [#585](https://github.com/jupyterhub/repo2docker/pull/585) ([@betatim](https://github.com/betatim)) +- install: one-liner to install most recent upstream code [#583](https://github.com/jupyterhub/repo2docker/pull/583) ([@haraldschilly](https://github.com/haraldschilly)) +- pin conda during Python-switch step [#576](https://github.com/jupyterhub/repo2docker/pull/576) ([@minrk](https://github.com/minrk)) +- Check if '--debug' is set properly [#575](https://github.com/jupyterhub/repo2docker/pull/575) ([@yuvipanda](https://github.com/yuvipanda)) +- npm installation [#573](https://github.com/jupyterhub/repo2docker/pull/573) ([@GladysNalvarte](https://github.com/GladysNalvarte)) +- missing quotes in GIT_CREDENTIAL_ENV [#572](https://github.com/jupyterhub/repo2docker/pull/572) ([@minrk](https://github.com/minrk)) +- Update conf.py [#569](https://github.com/jupyterhub/repo2docker/pull/569) ([@lheagy](https://github.com/lheagy)) +- updating interfaces page and adding jupyterlab workspaces page [#568](https://github.com/jupyterhub/repo2docker/pull/568) ([@choldgraf](https://github.com/choldgraf)) +- fix docker commit tag [#562](https://github.com/jupyterhub/repo2docker/pull/562) ([@minrk](https://github.com/minrk)) +- Set JULIA_DEPOT_PATH [#555](https://github.com/jupyterhub/repo2docker/pull/555) ([@yuvipanda](https://github.com/yuvipanda)) +- Updated log info for local content provider [#551](https://github.com/jupyterhub/repo2docker/pull/551) ([@GladysNalvarte](https://github.com/GladysNalvarte)) +- Fixes Travis build errors related to pytest and Sphinx [#547](https://github.com/jupyterhub/repo2docker/pull/547) ([@craig-willis](https://github.com/craig-willis)) +- Spurious comment in `Dockerfile` #543 [#544](https://github.com/jupyterhub/repo2docker/pull/544) ([@benjaminr](https://github.com/benjaminr)) +- Bump default python version to 3.7 [#539](https://github.com/jupyterhub/repo2docker/pull/539) ([@yuvipanda](https://github.com/yuvipanda)) +- Use a minimal hand-crafted Dockerfile for speed [#536](https://github.com/jupyterhub/repo2docker/pull/536) ([@betatim](https://github.com/betatim)) +- [MRG] Add tests for port mapping conversion [#534](https://github.com/jupyterhub/repo2docker/pull/534) ([@betatim](https://github.com/betatim)) +- adding a roadmap link to the root [#532](https://github.com/jupyterhub/repo2docker/pull/532) ([@choldgraf](https://github.com/choldgraf)) +- Minor howto doc fixes [#531](https://github.com/jupyterhub/repo2docker/pull/531) ([@jrbourbeau](https://github.com/jrbourbeau)) +- fix commit hash truncation on docker images [#530](https://github.com/jupyterhub/repo2docker/pull/530) ([@minrk](https://github.com/minrk)) +- Run docker builds on docker hub [#527](https://github.com/jupyterhub/repo2docker/pull/527) ([@minrk](https://github.com/minrk)) +- Add tag command snippet [#526](https://github.com/jupyterhub/repo2docker/pull/526) ([@minrk](https://github.com/minrk)) +- Remove f-strings [#520](https://github.com/jupyterhub/repo2docker/pull/520) ([@jrbourbeau](https://github.com/jrbourbeau)) +- refreeze with notebook 5.7.4 [#519](https://github.com/jupyterhub/repo2docker/pull/519) ([@minrk](https://github.com/minrk)) +- Update RTD to install repo2docker [#518](https://github.com/jupyterhub/repo2docker/pull/518) ([@jrbourbeau](https://github.com/jrbourbeau)) +- Fix cache-busting when running tests locally [#509](https://github.com/jupyterhub/repo2docker/pull/509) ([@yuvipanda](https://github.com/yuvipanda)) +- Copy repo to ${REPO_DIR} rather than ${HOME} [#507](https://github.com/jupyterhub/repo2docker/pull/507) ([@yuvipanda](https://github.com/yuvipanda)) +- Fix typos and syntax errors in the documentation [#505](https://github.com/jupyterhub/repo2docker/pull/505) ([@betatim](https://github.com/betatim)) +- fix push-tags condition [#501](https://github.com/jupyterhub/repo2docker/pull/501) ([@minrk](https://github.com/minrk)) +- Add repo2docker Dockerfile labels [#500](https://github.com/jupyterhub/repo2docker/pull/500) ([@jrbourbeau](https://github.com/jrbourbeau)) +- push tagged images on travis [#499](https://github.com/jupyterhub/repo2docker/pull/499) ([@minrk](https://github.com/minrk)) +- Update changelog in preparation for releasing v0.7.0 [#498](https://github.com/jupyterhub/repo2docker/pull/498) ([@betatim](https://github.com/betatim)) +- Make repo2docker easier to use as a library - Part 1 [#496](https://github.com/jupyterhub/repo2docker/pull/496) ([@yuvipanda](https://github.com/yuvipanda)) +- Make apt-get install be quiet [#483](https://github.com/jupyterhub/repo2docker/pull/483) ([@yuvipanda](https://github.com/yuvipanda)) + +### Contributors to this release + +([GitHub contributors page for this release](https://github.com/jupyterhub/repo2docker/graphs/contributors?from=2018-12-12&to=2019-02-21&type=c)) + +[@alimanfoo](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aalimanfoo+updated%3A2018-12-12..2019-02-21&type=Issues) | [@annakrystalli](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aannakrystalli+updated%3A2018-12-12..2019-02-21&type=Issues) | [@benjaminr](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abenjaminr+updated%3A2018-12-12..2019-02-21&type=Issues) | [@betatim](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abetatim+updated%3A2018-12-12..2019-02-21&type=Issues) | [@captainsafia](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acaptainsafia+updated%3A2018-12-12..2019-02-21&type=Issues) | [@choldgraf](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acholdgraf+updated%3A2018-12-12..2019-02-21&type=Issues) | [@craig-willis](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acraig-willis+updated%3A2018-12-12..2019-02-21&type=Issues) | [@GladysNalvarte](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AGladysNalvarte+updated%3A2018-12-12..2019-02-21&type=Issues) | [@haraldschilly](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aharaldschilly+updated%3A2018-12-12..2019-02-21&type=Issues) | [@jrbourbeau](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajrbourbeau+updated%3A2018-12-12..2019-02-21&type=Issues) | [@lheagy](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Alheagy+updated%3A2018-12-12..2019-02-21&type=Issues) | [@LucianaMarques](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3ALucianaMarques+updated%3A2018-12-12..2019-02-21&type=Issues) | [@manics](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Amanics+updated%3A2018-12-12..2019-02-21&type=Issues) | [@MatthewBM](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AMatthewBM+updated%3A2018-12-12..2019-02-21&type=Issues) | [@minrk](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aminrk+updated%3A2018-12-12..2019-02-21&type=Issues) | [@psychemedia](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Apsychemedia+updated%3A2018-12-12..2019-02-21&type=Issues) | [@rgbkrk](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Argbkrk+updated%3A2018-12-12..2019-02-21&type=Issues) | [@VladimirVisnovsky](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AVladimirVisnovsky+updated%3A2018-12-12..2019-02-21&type=Issues) | [@WillKoehrsen](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AWillKoehrsen+updated%3A2018-12-12..2019-02-21&type=Issues) | [@yuvipanda](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayuvipanda+updated%3A2018-12-12..2019-02-21&type=Issues) + +## 0.7.0 + +([full changelog](https://github.com/jupyterhub/repo2docker/compare/1b8e16a...72d7634)) + +### Merged PRs + +- Update changelog in preparation for releasing v0.7.0 [#498](https://github.com/jupyterhub/repo2docker/pull/498) ([@betatim](https://github.com/betatim)) +- Remove duplicate codecov config [#495](https://github.com/jupyterhub/repo2docker/pull/495) ([@betatim](https://github.com/betatim)) +- Bump nbrsessionproxy version [#493](https://github.com/jupyterhub/repo2docker/pull/493) ([@yuvipanda](https://github.com/yuvipanda)) +- Add codecov configuration [#492](https://github.com/jupyterhub/repo2docker/pull/492) ([@betatim](https://github.com/betatim)) +- Update the roadmap [#491](https://github.com/jupyterhub/repo2docker/pull/491) ([@betatim](https://github.com/betatim)) +- Log a 'success' message when push is complete [#482](https://github.com/jupyterhub/repo2docker/pull/482) ([@yuvipanda](https://github.com/yuvipanda)) +- Revert "[MRG] Start reusing existing docker images if content hasn't changed" [#481](https://github.com/jupyterhub/repo2docker/pull/481) ([@yuvipanda](https://github.com/yuvipanda)) +- Make apt be quieter [#479](https://github.com/jupyterhub/repo2docker/pull/479) ([@yuvipanda](https://github.com/yuvipanda)) +- Allow specifying images to reuse cache from [#478](https://github.com/jupyterhub/repo2docker/pull/478) ([@yuvipanda](https://github.com/yuvipanda)) +- removing note that env.yml is needed for julia [#477](https://github.com/jupyterhub/repo2docker/pull/477) ([@choldgraf](https://github.com/choldgraf)) +- [MRG] Tweak docstring to make it more understandable [#474](https://github.com/jupyterhub/repo2docker/pull/474) ([@betatim](https://github.com/betatim)) +- Ensure Python3 before reading README with encoding arg [#472](https://github.com/jupyterhub/repo2docker/pull/472) ([@nokome](https://github.com/nokome)) +- Add space between logo and title in README [#468](https://github.com/jupyterhub/repo2docker/pull/468) ([@willingc](https://github.com/willingc)) +- Add jupyterhub to base environment [#467](https://github.com/jupyterhub/repo2docker/pull/467) ([@yuvipanda](https://github.com/yuvipanda)) +- [MRG] Add a first roadmap [#465](https://github.com/jupyterhub/repo2docker/pull/465) ([@betatim](https://github.com/betatim)) +- Update CHANGES.rst [#464](https://github.com/jupyterhub/repo2docker/pull/464) ([@betatim](https://github.com/betatim)) +- [MRG] Add and use new logo [#463](https://github.com/jupyterhub/repo2docker/pull/463) ([@betatim](https://github.com/betatim)) +- [MRG] Start reusing existing docker images if content hasn't changed [#461](https://github.com/jupyterhub/repo2docker/pull/461) ([@betatim](https://github.com/betatim)) +- Updates for Stencila [#457](https://github.com/jupyterhub/repo2docker/pull/457) ([@nuest](https://github.com/nuest)) +- Update changelog [#454](https://github.com/jupyterhub/repo2docker/pull/454) ([@betatim](https://github.com/betatim)) +- adding back sidebars [#451](https://github.com/jupyterhub/repo2docker/pull/451) ([@choldgraf](https://github.com/choldgraf)) +- [MRG] Switch to BaseImage for nix build pack [#448](https://github.com/jupyterhub/repo2docker/pull/448) ([@betatim](https://github.com/betatim)) +- [MRG] Pipfile for repo2Docker [#447](https://github.com/jupyterhub/repo2docker/pull/447) ([@trallard](https://github.com/trallard)) +- adding circleci preview and jupyterhub docs theme [#446](https://github.com/jupyterhub/repo2docker/pull/446) ([@choldgraf](https://github.com/choldgraf)) +- [MRG] Change back into main repository directory [#436](https://github.com/jupyterhub/repo2docker/pull/436) ([@betatim](https://github.com/betatim)) +- PEP8 styling [#435](https://github.com/jupyterhub/repo2docker/pull/435) ([@betatim](https://github.com/betatim)) +- [MRG] Switch to right sub-directory for coverage reports [#432](https://github.com/jupyterhub/repo2docker/pull/432) ([@betatim](https://github.com/betatim)) +- Add pip install doc-requirements.txt to setup of virtual environment instructions [#431](https://github.com/jupyterhub/repo2docker/pull/431) ([@matthewfeickert](https://github.com/matthewfeickert)) +- [MRG] Only check beginning of name of Python shared library [#429](https://github.com/jupyterhub/repo2docker/pull/429) ([@betatim](https://github.com/betatim)) +- Adjust css for header links [#428](https://github.com/jupyterhub/repo2docker/pull/428) ([@evertrol](https://github.com/evertrol)) +- [MRG] Update the contributing docs [#427](https://github.com/jupyterhub/repo2docker/pull/427) ([@betatim](https://github.com/betatim)) +- Add a change log [#426](https://github.com/jupyterhub/repo2docker/pull/426) ([@evertrol](https://github.com/evertrol)) +- Change faq to rst [#425](https://github.com/jupyterhub/repo2docker/pull/425) ([@evertrol](https://github.com/evertrol)) +- Fix documentation: avoid clashing markup [#422](https://github.com/jupyterhub/repo2docker/pull/422) ([@evertrol](https://github.com/evertrol)) +- Add an edit-mode option [#421](https://github.com/jupyterhub/repo2docker/pull/421) ([@evertrol](https://github.com/evertrol)) +- Speed up cloning by using a depth of 1 if there is no refspec [#420](https://github.com/jupyterhub/repo2docker/pull/420) ([@evertrol](https://github.com/evertrol)) +- fix my heading mistake in the docs for DESCRIPTION files [#418](https://github.com/jupyterhub/repo2docker/pull/418) ([@gedankenstuecke](https://github.com/gedankenstuecke)) +- Subdirectory support [#413](https://github.com/jupyterhub/repo2docker/pull/413) ([@dsludwig](https://github.com/dsludwig)) +- updating index, usage, and install docs [#409](https://github.com/jupyterhub/repo2docker/pull/409) ([@choldgraf](https://github.com/choldgraf)) +- Adding support for nix buildpack in repo2docker [#407](https://github.com/jupyterhub/repo2docker/pull/407) ([@costrouc](https://github.com/costrouc)) +- add R DESCRIPTION support [#406](https://github.com/jupyterhub/repo2docker/pull/406) ([@gedankenstuecke](https://github.com/gedankenstuecke)) +- Support python 3.7 [#405](https://github.com/jupyterhub/repo2docker/pull/405) ([@minrk](https://github.com/minrk)) +- [MRG] Make travis fail when pytest fails [#401](https://github.com/jupyterhub/repo2docker/pull/401) ([@betatim](https://github.com/betatim)) +- Fix relative location of the start script [#400](https://github.com/jupyterhub/repo2docker/pull/400) ([@giovannipizzi](https://github.com/giovannipizzi)) +- Add more details to our setup() command [#394](https://github.com/jupyterhub/repo2docker/pull/394) ([@betatim](https://github.com/betatim)) +- Julia v1.0 support: Add option to specify julia version in REQUIRE [#393](https://github.com/jupyterhub/repo2docker/pull/393) ([@NHDaly](https://github.com/NHDaly)) +- Bump nteract-on-jupyter version [#390](https://github.com/jupyterhub/repo2docker/pull/390) ([@yuvipanda](https://github.com/yuvipanda)) + +### Contributors to this release + +([GitHub contributors page for this release](https://github.com/jupyterhub/repo2docker/graphs/contributors?from=2018-09-09&to=2018-12-12&type=c)) + +[@agahkarakuzu](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aagahkarakuzu+updated%3A2018-09-09..2018-12-12&type=Issues) | [@betatim](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abetatim+updated%3A2018-09-09..2018-12-12&type=Issues) | [@blairhudson](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ablairhudson+updated%3A2018-09-09..2018-12-12&type=Issues) | [@cboettig](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acboettig+updated%3A2018-09-09..2018-12-12&type=Issues) | [@choldgraf](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acholdgraf+updated%3A2018-09-09..2018-12-12&type=Issues) | [@consideRatio](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AconsideRatio+updated%3A2018-09-09..2018-12-12&type=Issues) | [@costrouc](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acostrouc+updated%3A2018-09-09..2018-12-12&type=Issues) | [@craig-willis](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acraig-willis+updated%3A2018-09-09..2018-12-12&type=Issues) | [@ctr26](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Actr26+updated%3A2018-09-09..2018-12-12&type=Issues) | [@davidanthoff](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Adavidanthoff+updated%3A2018-09-09..2018-12-12&type=Issues) | [@dsludwig](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Adsludwig+updated%3A2018-09-09..2018-12-12&type=Issues) | [@evertrol](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aevertrol+updated%3A2018-09-09..2018-12-12&type=Issues) | [@gedankenstuecke](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Agedankenstuecke+updated%3A2018-09-09..2018-12-12&type=Issues) | [@giovannipizzi](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Agiovannipizzi+updated%3A2018-09-09..2018-12-12&type=Issues) | [@jhamman](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajhamman+updated%3A2018-09-09..2018-12-12&type=Issues) | [@jzf2101](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajzf2101+updated%3A2018-09-09..2018-12-12&type=Issues) | [@karthik](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Akarthik+updated%3A2018-09-09..2018-12-12&type=Issues) | [@KristofferC](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AKristofferC+updated%3A2018-09-09..2018-12-12&type=Issues) | [@ltalirz](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Altalirz+updated%3A2018-09-09..2018-12-12&type=Issues) | [@ltetrel](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Altetrel+updated%3A2018-09-09..2018-12-12&type=Issues) | [@manics](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Amanics+updated%3A2018-09-09..2018-12-12&type=Issues) | [@matthewfeickert](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Amatthewfeickert+updated%3A2018-09-09..2018-12-12&type=Issues) | [@minrk](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aminrk+updated%3A2018-09-09..2018-12-12&type=Issues) | [@NHDaly](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3ANHDaly+updated%3A2018-09-09..2018-12-12&type=Issues) | [@nokome](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Anokome+updated%3A2018-09-09..2018-12-12&type=Issues) | [@nuest](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Anuest+updated%3A2018-09-09..2018-12-12&type=Issues) | [@pdurbin](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Apdurbin+updated%3A2018-09-09..2018-12-12&type=Issues) | [@psychemedia](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Apsychemedia+updated%3A2018-09-09..2018-12-12&type=Issues) | [@rbavery](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Arbavery+updated%3A2018-09-09..2018-12-12&type=Issues) | [@rgbkrk](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Argbkrk+updated%3A2018-09-09..2018-12-12&type=Issues) | [@ryanlovett](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aryanlovett+updated%3A2018-09-09..2018-12-12&type=Issues) | [@spMohanty](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AspMohanty+updated%3A2018-09-09..2018-12-12&type=Issues) | [@tgeorgeux](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Atgeorgeux+updated%3A2018-09-09..2018-12-12&type=Issues) | [@trallard](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Atrallard+updated%3A2018-09-09..2018-12-12&type=Issues) | [@trybik](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Atrybik+updated%3A2018-09-09..2018-12-12&type=Issues) | [@willingc](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awillingc+updated%3A2018-09-09..2018-12-12&type=Issues) | [@WillKoehrsen](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AWillKoehrsen+updated%3A2018-09-09..2018-12-12&type=Issues) | [@yuvipanda](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayuvipanda+updated%3A2018-09-09..2018-12-12&type=Issues) + +## 0.6.0 + +([full changelog](https://github.com/jupyterhub/repo2docker/compare/d97eee9...1b8e16a)) + +### Documentation improvements + +- Add architecture document [#235](https://github.com/jupyterhub/repo2docker/pull/235) ([@yuvipanda](https://github.com/yuvipanda)) + +### Other merged PRs + +- Add more details to our setup() command [#394](https://github.com/jupyterhub/repo2docker/pull/394) ([@betatim](https://github.com/betatim)) +- Bump conda version to 4.5.11 [#391](https://github.com/jupyterhub/repo2docker/pull/391) ([@yuvipanda](https://github.com/yuvipanda)) +- Issue #388 - Use bash echo for git-credential-env [#389](https://github.com/jupyterhub/repo2docker/pull/389) ([@zymergen-luke](https://github.com/zymergen-luke)) +- Change PyPI deploy account to mybinderteam [#385](https://github.com/jupyterhub/repo2docker/pull/385) ([@betatim](https://github.com/betatim)) +- [MRG] Update contributing documentation [#384](https://github.com/jupyterhub/repo2docker/pull/384) ([@betatim](https://github.com/betatim)) +- Update to JupyterLab 0.34 [#378](https://github.com/jupyterhub/repo2docker/pull/378) ([@blink1073](https://github.com/blink1073)) +- [MRG] Escape environment variable when using Python string formatting [#377](https://github.com/jupyterhub/repo2docker/pull/377) ([@betatim](https://github.com/betatim)) +- Split out tests, tweak docs, and a style change [#375](https://github.com/jupyterhub/repo2docker/pull/375) ([@betatim](https://github.com/betatim)) +- remove conda-meta/history [#373](https://github.com/jupyterhub/repo2docker/pull/373) ([@minrk](https://github.com/minrk)) +- Fix warnings in the documentation build and add to CI [#372](https://github.com/jupyterhub/repo2docker/pull/372) ([@betatim](https://github.com/betatim)) +- adding message and changing header characters for config files [#370](https://github.com/jupyterhub/repo2docker/pull/370) ([@choldgraf](https://github.com/choldgraf)) +- Install nodejs/npm from nodesource [#364](https://github.com/jupyterhub/repo2docker/pull/364) ([@GladysNalvarte](https://github.com/GladysNalvarte)) +- Add launch script [#363](https://github.com/jupyterhub/repo2docker/pull/363) ([@jhamman](https://github.com/jhamman)) +- Specify custom_display_url argument [#358](https://github.com/jupyterhub/repo2docker/pull/358) ([@GladysNalvarte](https://github.com/GladysNalvarte)) +- Switch from PyDataScienceHandbook to Pytudes [#355](https://github.com/jupyterhub/repo2docker/pull/355) ([@betatim](https://github.com/betatim)) +- bump versions and refreeze [#354](https://github.com/jupyterhub/repo2docker/pull/354) ([@minrk](https://github.com/minrk)) +- [MRG] Add version argument [#352](https://github.com/jupyterhub/repo2docker/pull/352) ([@vsoch](https://github.com/vsoch)) +- Add CircleCI Deploy Option [#351](https://github.com/jupyterhub/repo2docker/pull/351) ([@vsoch](https://github.com/vsoch)) +- from traitlets import TraitError in utils.py [#348](https://github.com/jupyterhub/repo2docker/pull/348) ([@cclauss](https://github.com/cclauss)) +- scinece -> science [#347](https://github.com/jupyterhub/repo2docker/pull/347) ([@danielleberre](https://github.com/danielleberre)) +- Fix some rst weirdness in the uage docs [#346](https://github.com/jupyterhub/repo2docker/pull/346) ([@betatim](https://github.com/betatim)) +- Add DockerSpawner command in JupyterHub config [#344](https://github.com/jupyterhub/repo2docker/pull/344) ([@rprimet](https://github.com/rprimet)) +- Test that images can start notebook servers in all the builders [#343](https://github.com/jupyterhub/repo2docker/pull/343) ([@GladysNalvarte](https://github.com/GladysNalvarte)) +- Setup auto releasing on GitHub tagging [#342](https://github.com/jupyterhub/repo2docker/pull/342) ([@betatim](https://github.com/betatim)) +- documentation improvements based on reviews for walkthrough and configuration details [#338](https://github.com/jupyterhub/repo2docker/pull/338) ([@jzf2101](https://github.com/jzf2101)) +- Tweaking Docs for Readability [#335](https://github.com/jupyterhub/repo2docker/pull/335) ([@jzf2101](https://github.com/jzf2101)) +- Include LICENSE file in wheels [#327](https://github.com/jupyterhub/repo2docker/pull/327) ([@toddrme2178](https://github.com/toddrme2178)) +- Switch to miniconda v4.5.1 [#324](https://github.com/jupyterhub/repo2docker/pull/324) ([@betatim](https://github.com/betatim)) +- Support shiny apps [#320](https://github.com/jupyterhub/repo2docker/pull/320) ([@ryanlovett](https://github.com/ryanlovett)) +- prefer R to conda in buildpack order [#317](https://github.com/jupyterhub/repo2docker/pull/317) ([@minrk](https://github.com/minrk)) +- Use XDG standard ~/.local for user software installs [#313](https://github.com/jupyterhub/repo2docker/pull/313) ([@yuvipanda](https://github.com/yuvipanda)) +- To add the user bin folder to the path [#311](https://github.com/jupyterhub/repo2docker/pull/311) ([@aborruso](https://github.com/aborruso)) +- stencila support [#309](https://github.com/jupyterhub/repo2docker/pull/309) ([@minrk](https://github.com/minrk)) +- Add links to the front page and modify travis [#308](https://github.com/jupyterhub/repo2docker/pull/308) ([@betatim](https://github.com/betatim)) +- Bump nteract jupyter extension [#306](https://github.com/jupyterhub/repo2docker/pull/306) ([@yuvipanda](https://github.com/yuvipanda)) +- remove _nb_ext_conf from legacy env [#303](https://github.com/jupyterhub/repo2docker/pull/303) ([@minrk](https://github.com/minrk)) +- bump base image to ubuntu 18.04 [#302](https://github.com/jupyterhub/repo2docker/pull/302) ([@minrk](https://github.com/minrk)) +- Documentation and warning improvements [#300](https://github.com/jupyterhub/repo2docker/pull/300) ([@choldgraf](https://github.com/choldgraf)) +- Fix two typos [#299](https://github.com/jupyterhub/repo2docker/pull/299) ([@darabos](https://github.com/darabos)) +- Always install Python with conda [#298](https://github.com/jupyterhub/repo2docker/pull/298) ([@minrk](https://github.com/minrk)) +- split post build script command in Docker file [#294](https://github.com/jupyterhub/repo2docker/pull/294) ([@bitnik](https://github.com/bitnik)) +- Add guidelines on merging work [#292](https://github.com/jupyterhub/repo2docker/pull/292) ([@betatim](https://github.com/betatim)) +- Support setup.py in Python buildpacks [#289](https://github.com/jupyterhub/repo2docker/pull/289) ([@GladysNalvarte](https://github.com/GladysNalvarte)) +- Use travis_retry to run tests [#288](https://github.com/jupyterhub/repo2docker/pull/288) ([@betatim](https://github.com/betatim)) +- Add a test to select Python 3 via runtime.txt [#287](https://github.com/jupyterhub/repo2docker/pull/287) ([@betatim](https://github.com/betatim)) +- Enables Python2 just with runtime.txt file [#284](https://github.com/jupyterhub/repo2docker/pull/284) ([@GladysNalvarte](https://github.com/GladysNalvarte)) +- Add note about os support and update example repo [#283](https://github.com/jupyterhub/repo2docker/pull/283) ([@willingc](https://github.com/willingc)) +- Add codecov configuration to enable PR comments [#279](https://github.com/jupyterhub/repo2docker/pull/279) ([@betatim](https://github.com/betatim)) +- fixing python2 search [#277](https://github.com/jupyterhub/repo2docker/pull/277) ([@choldgraf](https://github.com/choldgraf)) +- Freeze legacy environment [#276](https://github.com/jupyterhub/repo2docker/pull/276) ([@GladysNalvarte](https://github.com/GladysNalvarte)) +- Refreeze environments [#274](https://github.com/jupyterhub/repo2docker/pull/274) ([@willingc](https://github.com/willingc)) +- add docstrings to docker buildpack [#272](https://github.com/jupyterhub/repo2docker/pull/272) ([@willingc](https://github.com/willingc)) +- add docstrings for conda buildpack [#271](https://github.com/jupyterhub/repo2docker/pull/271) ([@willingc](https://github.com/willingc)) +- add docstrings for legacy buildpack [#270](https://github.com/jupyterhub/repo2docker/pull/270) ([@willingc](https://github.com/willingc)) +- Add docstrings to python3 and python2 buildpacks [#265](https://github.com/jupyterhub/repo2docker/pull/265) ([@willingc](https://github.com/willingc)) +- Add doc for new buildpacks [#264](https://github.com/jupyterhub/repo2docker/pull/264) ([@willingc](https://github.com/willingc)) +- Fix detecting dependency files in binder/ subidr [#261](https://github.com/jupyterhub/repo2docker/pull/261) ([@betatim](https://github.com/betatim)) +- refreeze environments [#260](https://github.com/jupyterhub/repo2docker/pull/260) ([@minrk](https://github.com/minrk)) +- Adding unzip to base packages [#259](https://github.com/jupyterhub/repo2docker/pull/259) ([@kmader](https://github.com/kmader)) +- Revert "Add shiny-server." [#258](https://github.com/jupyterhub/repo2docker/pull/258) ([@yuvipanda](https://github.com/yuvipanda)) +- make sure there's a newline before each 'File: ' heading [#255](https://github.com/jupyterhub/repo2docker/pull/255) ([@ctb](https://github.com/ctb)) +- [MRG] Setup R libraries path for RStudio [#254](https://github.com/jupyterhub/repo2docker/pull/254) ([@betatim](https://github.com/betatim)) +- upgrade nteract_on_jupyter to 1.5.0 [#252](https://github.com/jupyterhub/repo2docker/pull/252) ([@rgbkrk](https://github.com/rgbkrk)) +- remove -v from conda env update [#248](https://github.com/jupyterhub/repo2docker/pull/248) ([@minrk](https://github.com/minrk)) +- [WIP] Specify plans for stability in repo2docker dependency [#244](https://github.com/jupyterhub/repo2docker/pull/244) ([@betatim](https://github.com/betatim)) +- Do not require postBuild to be executable [#241](https://github.com/jupyterhub/repo2docker/pull/241) ([@yuvipanda](https://github.com/yuvipanda)) +- Add shiny-server. [#239](https://github.com/jupyterhub/repo2docker/pull/239) ([@ryanlovett](https://github.com/ryanlovett)) +- clone recursively [#233](https://github.com/jupyterhub/repo2docker/pull/233) ([@minrk](https://github.com/minrk)) +- instantiate Repo2Docker to run tests [#229](https://github.com/jupyterhub/repo2docker/pull/229) ([@minrk](https://github.com/minrk)) +- do not reuse BuildPack instances [#228](https://github.com/jupyterhub/repo2docker/pull/228) ([@minrk](https://github.com/minrk)) +- Bump jupyterlab and jupyter notebook to latest versions [#225](https://github.com/jupyterhub/repo2docker/pull/225) ([@betatim](https://github.com/betatim)) +- Add a CONTRIBUTING.md [#224](https://github.com/jupyterhub/repo2docker/pull/224) ([@yuvipanda](https://github.com/yuvipanda)) +- Install from wheel when testing in travis [#222](https://github.com/jupyterhub/repo2docker/pull/222) ([@yuvipanda](https://github.com/yuvipanda)) +- Bump version to v0.5 [#221](https://github.com/jupyterhub/repo2docker/pull/221) ([@yuvipanda](https://github.com/yuvipanda)) +- Switch freeze guidance to not be a directive [#220](https://github.com/jupyterhub/repo2docker/pull/220) ([@rgbkrk](https://github.com/rgbkrk)) +- pin nteract_on_jupyter to 1.4.0 [#219](https://github.com/jupyterhub/repo2docker/pull/219) ([@rgbkrk](https://github.com/rgbkrk)) +- Add docstrings and minor style fixes for application files and JuliaBuildPack [#213](https://github.com/jupyterhub/repo2docker/pull/213) ([@willingc](https://github.com/willingc)) +- Add native R + IRKernel + RStudio support [#210](https://github.com/jupyterhub/repo2docker/pull/210) ([@yuvipanda](https://github.com/yuvipanda)) +- Fix Python version detection for conda [#209](https://github.com/jupyterhub/repo2docker/pull/209) ([@minrk](https://github.com/minrk)) +- Clarify that --debug and --no-build are for debugging only [#205](https://github.com/jupyterhub/repo2docker/pull/205) ([@yuvipanda](https://github.com/yuvipanda)) +- Remove outdated builder info from docs [#204](https://github.com/jupyterhub/repo2docker/pull/204) ([@yuvipanda](https://github.com/yuvipanda)) +- Add nteract jupyter extension to requirements.txt based setups [#200](https://github.com/jupyterhub/repo2docker/pull/200) ([@yuvipanda](https://github.com/yuvipanda)) +- Emergency Bump to artful [#197](https://github.com/jupyterhub/repo2docker/pull/197) ([@yuvipanda](https://github.com/yuvipanda)) +- Refreeze conda environment [#193](https://github.com/jupyterhub/repo2docker/pull/193) ([@yuvipanda](https://github.com/yuvipanda)) +- refreeze conda environments [#187](https://github.com/jupyterhub/repo2docker/pull/187) ([@minrk](https://github.com/minrk)) +- Provide a flag to pass environment variables at runtime [#186](https://github.com/jupyterhub/repo2docker/pull/186) ([@rprimet](https://github.com/rprimet)) +- Stop using alpine base images [#183](https://github.com/jupyterhub/repo2docker/pull/183) ([@yuvipanda](https://github.com/yuvipanda)) +- Fix indentation causing only last line of apt.txt to be parsed [#181](https://github.com/jupyterhub/repo2docker/pull/181) ([@nmih](https://github.com/nmih)) +- Fixed run argument check for mounting volumes. [#179](https://github.com/jupyterhub/repo2docker/pull/179) ([@mukundans91](https://github.com/mukundans91)) +- Add default command to base Dockerfile template [#176](https://github.com/jupyterhub/repo2docker/pull/176) ([@AaronWatters](https://github.com/AaronWatters)) +- Added regex pattern based validation for image name argument [#175](https://github.com/jupyterhub/repo2docker/pull/175) ([@mukundans91](https://github.com/mukundans91)) +- Allow mounting arbitrary volumes into the repo2docker container [#172](https://github.com/jupyterhub/repo2docker/pull/172) ([@yuvipanda](https://github.com/yuvipanda)) +- adding runtime to preparing + improving config section [#168](https://github.com/jupyterhub/repo2docker/pull/168) ([@choldgraf](https://github.com/choldgraf)) +- improving docs [#165](https://github.com/jupyterhub/repo2docker/pull/165) ([@choldgraf](https://github.com/choldgraf)) +- Remove symlink & just copy postBuild file instead [#161](https://github.com/jupyterhub/repo2docker/pull/161) ([@yuvipanda](https://github.com/yuvipanda)) +- Set limits for how much memory docker build can use [#159](https://github.com/jupyterhub/repo2docker/pull/159) ([@yuvipanda](https://github.com/yuvipanda)) +- update venv freeze and conda versions [#158](https://github.com/jupyterhub/repo2docker/pull/158) ([@minrk](https://github.com/minrk)) +- don't run tests in parallel on travis [#157](https://github.com/jupyterhub/repo2docker/pull/157) ([@minrk](https://github.com/minrk)) +- Use a frozen requirements.txt for base install in venv buildpacks [#156](https://github.com/jupyterhub/repo2docker/pull/156) ([@yuvipanda](https://github.com/yuvipanda)) +- Split detector.py into multiple files [#155](https://github.com/jupyterhub/repo2docker/pull/155) ([@yuvipanda](https://github.com/yuvipanda)) +- Make conda env update be verbose [#153](https://github.com/jupyterhub/repo2docker/pull/153) ([@choldgraf](https://github.com/choldgraf)) +- Suggest editable install when installed from source [#152](https://github.com/jupyterhub/repo2docker/pull/152) ([@GladysNalvarte](https://github.com/GladysNalvarte)) +- fixing empty lines and comments in apt.txt [#151](https://github.com/jupyterhub/repo2docker/pull/151) ([@GladysNalvarte](https://github.com/GladysNalvarte)) +- Bump notebook version to 5.2.2 [#150](https://github.com/jupyterhub/repo2docker/pull/150) ([@yuvipanda](https://github.com/yuvipanda)) +- Make all bash verify scripts fail on error [#147](https://github.com/jupyterhub/repo2docker/pull/147) ([@yuvipanda](https://github.com/yuvipanda)) +- Add tests for binder/apt.txt and binder/postBuild [#145](https://github.com/jupyterhub/repo2docker/pull/145) ([@oschuett](https://github.com/oschuett)) +- Fix binder/apt.txt detection [#140](https://github.com/jupyterhub/repo2docker/pull/140) ([@oschuett](https://github.com/oschuett)) +- RFC: Ignore "julia" in REQUIRE file when precompiling [#137](https://github.com/jupyterhub/repo2docker/pull/137) ([@darwindarak](https://github.com/darwindarak)) +- Fully remove jupyterhub references [#132](https://github.com/jupyterhub/repo2docker/pull/132) ([@yuvipanda](https://github.com/yuvipanda)) +- Revert "[MRG] Add limit on git clone depth" [#131](https://github.com/jupyterhub/repo2docker/pull/131) ([@yuvipanda](https://github.com/yuvipanda)) +- Revert "Add handling for no ref being provided" [#130](https://github.com/jupyterhub/repo2docker/pull/130) ([@yuvipanda](https://github.com/yuvipanda)) +- Add handling for no ref being provided [#128](https://github.com/jupyterhub/repo2docker/pull/128) ([@betatim](https://github.com/betatim)) +- Add 'repo2docker' as a script alias [#121](https://github.com/jupyterhub/repo2docker/pull/121) ([@yuvipanda](https://github.com/yuvipanda)) +- [MRG] Use stdlib tempfile module [#118](https://github.com/jupyterhub/repo2docker/pull/118) ([@betatim](https://github.com/betatim)) +- Add a basic FAQ doc + 1 entry [#117](https://github.com/jupyterhub/repo2docker/pull/117) ([@yuvipanda](https://github.com/yuvipanda)) +- adding jupyter logos [#112](https://github.com/jupyterhub/repo2docker/pull/112) ([@choldgraf](https://github.com/choldgraf)) +- Remove jupyterhub from default installs [#111](https://github.com/jupyterhub/repo2docker/pull/111) ([@willingc](https://github.com/willingc)) +- Add doc badge [#108](https://github.com/jupyterhub/repo2docker/pull/108) ([@willingc](https://github.com/willingc)) +- reorganizing arguments [#107](https://github.com/jupyterhub/repo2docker/pull/107) ([@choldgraf](https://github.com/choldgraf)) +- Replace theme with alabaster [#106](https://github.com/jupyterhub/repo2docker/pull/106) ([@willingc](https://github.com/willingc)) +- Attempt to add some info about design principles [#105](https://github.com/jupyterhub/repo2docker/pull/105) ([@yuvipanda](https://github.com/yuvipanda)) +- Only parse `REQUIRE` file in `binder` (if exists) [#104](https://github.com/jupyterhub/repo2docker/pull/104) ([@darwindarak](https://github.com/darwindarak)) +- Remove intermediate containers in failed builds [#101](https://github.com/jupyterhub/repo2docker/pull/101) ([@yuvipanda](https://github.com/yuvipanda)) +- Upgrade to jupyterlab 0.28.0 [#99](https://github.com/jupyterhub/repo2docker/pull/99) ([@gnestor](https://github.com/gnestor)) +- avoid producing non-JSON output on errors [#97](https://github.com/jupyterhub/repo2docker/pull/97) ([@minrk](https://github.com/minrk)) +- docs type-o [#95](https://github.com/jupyterhub/repo2docker/pull/95) ([@choldgraf](https://github.com/choldgraf)) +- Updating postBuild docs + doc build script [#90](https://github.com/jupyterhub/repo2docker/pull/90) ([@choldgraf](https://github.com/choldgraf)) +- Add git to the repo2docker docker image [#89](https://github.com/jupyterhub/repo2docker/pull/89) ([@yuvipanda](https://github.com/yuvipanda)) +- Explicitly echo what image is built in travis [#88](https://github.com/jupyterhub/repo2docker/pull/88) ([@yuvipanda](https://github.com/yuvipanda)) +- Switch base image to alpine + fix typo causing CI to fail [#87](https://github.com/jupyterhub/repo2docker/pull/87) ([@yuvipanda](https://github.com/yuvipanda)) +- make binder directory visible [#86](https://github.com/jupyterhub/repo2docker/pull/86) ([@minrk](https://github.com/minrk)) +- Look in .binder directory for files [#83](https://github.com/jupyterhub/repo2docker/pull/83) ([@minrk](https://github.com/minrk)) +- Update virtualenv base to use jupyterlab 0.27 [#81](https://github.com/jupyterhub/repo2docker/pull/81) ([@ellisonbg](https://github.com/ellisonbg)) +- Update JupyterLab to 0.27 [#80](https://github.com/jupyterhub/repo2docker/pull/80) ([@ellisonbg](https://github.com/ellisonbg)) +- document `--debug` [#79](https://github.com/jupyterhub/repo2docker/pull/79) ([@choldgraf](https://github.com/choldgraf)) +- make JUPYTERHUB_VERSION a build arg [#76](https://github.com/jupyterhub/repo2docker/pull/76) ([@minrk](https://github.com/minrk)) +- typo: --print-dockerfile ended up falling under --debug [#75](https://github.com/jupyterhub/repo2docker/pull/75) ([@minrk](https://github.com/minrk)) +- don't install requirements.txt if environment.yml is present [#74](https://github.com/jupyterhub/repo2docker/pull/74) ([@minrk](https://github.com/minrk)) + +### Contributors to this release + +([GitHub contributors page for this release](https://github.com/jupyterhub/repo2docker/graphs/contributors?from=2017-09-06&to=2018-09-09&type=c)) + +[@AaronWatters](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AAaronWatters+updated%3A2017-09-06..2018-09-09&type=Issues) | [@aborruso](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aaborruso+updated%3A2017-09-06..2018-09-09&type=Issues) | 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[@GladysNalvarte](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AGladysNalvarte+updated%3A2017-09-06..2018-09-09&type=Issues) | [@gnestor](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Agnestor+updated%3A2017-09-06..2018-09-09&type=Issues) | [@hydrosquall](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ahydrosquall+updated%3A2017-09-06..2018-09-09&type=Issues) | [@jasongrout](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajasongrout+updated%3A2017-09-06..2018-09-09&type=Issues) | [@jhamman](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajhamman+updated%3A2017-09-06..2018-09-09&type=Issues) | [@juanesarango](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajuanesarango+updated%3A2017-09-06..2018-09-09&type=Issues) | [@jzf2101](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajzf2101+updated%3A2017-09-06..2018-09-09&type=Issues) | [@kmader](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Akmader+updated%3A2017-09-06..2018-09-09&type=Issues) | [@KristofferC](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AKristofferC+updated%3A2017-09-06..2018-09-09&type=Issues) | [@Madhu94](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AMadhu94+updated%3A2017-09-06..2018-09-09&type=Issues) | [@manics](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Amanics+updated%3A2017-09-06..2018-09-09&type=Issues) | [@minrk](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aminrk+updated%3A2017-09-06..2018-09-09&type=Issues) | [@mpacer](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ampacer+updated%3A2017-09-06..2018-09-09&type=Issues) | 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[@slayoo](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aslayoo+updated%3A2017-09-06..2018-09-09&type=Issues) | [@spendyala](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aspendyala+updated%3A2017-09-06..2018-09-09&type=Issues) | [@SylvainCorlay](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3ASylvainCorlay+updated%3A2017-09-06..2018-09-09&type=Issues) | [@taylorreiter](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ataylorreiter+updated%3A2017-09-06..2018-09-09&type=Issues) | [@toddrme2178](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Atoddrme2178+updated%3A2017-09-06..2018-09-09&type=Issues) | [@trallard](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Atrallard+updated%3A2017-09-06..2018-09-09&type=Issues) | [@vsoch](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Avsoch+updated%3A2017-09-06..2018-09-09&type=Issues) | [@willingc](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awillingc+updated%3A2017-09-06..2018-09-09&type=Issues) | [@yuvipanda](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayuvipanda+updated%3A2017-09-06..2018-09-09&type=Issues) | [@zymergen-luke](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Azymergen-luke+updated%3A2017-09-06..2018-09-09&type=Issues) + +## v0.4.1 + +([full changelog](https://github.com/jupyterhub/repo2docker/compare/e7674ce...d97eee9)) + +### Merged PRs + +- Add --debug & --no-build options [#68](https://github.com/jupyterhub/repo2docker/pull/68) ([@yuvipanda](https://github.com/yuvipanda)) +- Moved old COPYING.md to LICENSE, and updated with current language. [#67](https://github.com/jupyterhub/repo2docker/pull/67) ([@tdalseide](https://github.com/tdalseide)) +- Add license - Issue #64 [#65](https://github.com/jupyterhub/repo2docker/pull/65) ([@sumalaika](https://github.com/sumalaika)) +- Include package_data in setup.py [#59](https://github.com/jupyterhub/repo2docker/pull/59) ([@yuvipanda](https://github.com/yuvipanda)) +- Include package_data in setup.py [#58](https://github.com/jupyterhub/repo2docker/pull/58) ([@yuvipanda](https://github.com/yuvipanda)) +- Add npm to base image [#57](https://github.com/jupyterhub/repo2docker/pull/57) ([@yuvipanda](https://github.com/yuvipanda)) +- config file for RTD [#56](https://github.com/jupyterhub/repo2docker/pull/56) ([@choldgraf](https://github.com/choldgraf)) +- fixing RTD build [#54](https://github.com/jupyterhub/repo2docker/pull/54) ([@choldgraf](https://github.com/choldgraf)) +- updating autogen examples [#53](https://github.com/jupyterhub/repo2docker/pull/53) ([@choldgraf](https://github.com/choldgraf)) +- adding doc generation from the tests [#51](https://github.com/jupyterhub/repo2docker/pull/51) ([@choldgraf](https://github.com/choldgraf)) +- Validate that Julia is using our pre-installed conda [#50](https://github.com/jupyterhub/repo2docker/pull/50) ([@yuvipanda](https://github.com/yuvipanda)) +- Cleanup conda [#49](https://github.com/jupyterhub/repo2docker/pull/49) ([@yuvipanda](https://github.com/yuvipanda)) +- Add back --no-clean support [#48](https://github.com/jupyterhub/repo2docker/pull/48) ([@yuvipanda](https://github.com/yuvipanda)) +- Add a little more info to README [#47](https://github.com/jupyterhub/repo2docker/pull/47) ([@yuvipanda](https://github.com/yuvipanda)) +- Print stdout for all the tests! [#46](https://github.com/jupyterhub/repo2docker/pull/46) ([@yuvipanda](https://github.com/yuvipanda)) +- Fix legacy dockerfile support and add tests [#43](https://github.com/jupyterhub/repo2docker/pull/43) ([@yuvipanda](https://github.com/yuvipanda)) +- Fix dockerfile builds and add tests for them [#42](https://github.com/jupyterhub/repo2docker/pull/42) ([@yuvipanda](https://github.com/yuvipanda)) +- fix the python2 kernelspec [#35](https://github.com/jupyterhub/repo2docker/pull/35) ([@minrk](https://github.com/minrk)) +- julia version bump [#30](https://github.com/jupyterhub/repo2docker/pull/30) ([@choldgraf](https://github.com/choldgraf)) +- Add support for Julia buildpack [#29](https://github.com/jupyterhub/repo2docker/pull/29) ([@yuvipanda](https://github.com/yuvipanda)) +- Add initial sphinx docs [#26](https://github.com/jupyterhub/repo2docker/pull/26) ([@willingc](https://github.com/willingc)) +- Add JupyterLab to the default environment for venv + conda builders [#22](https://github.com/jupyterhub/repo2docker/pull/22) ([@yuvipanda](https://github.com/yuvipanda)) +- Cleanup docker pull hack [#21](https://github.com/jupyterhub/repo2docker/pull/21) ([@yuvipanda](https://github.com/yuvipanda)) +- Add a default build pack [#20](https://github.com/jupyterhub/repo2docker/pull/20) ([@yuvipanda](https://github.com/yuvipanda)) +- add LegacyBinderDockerfile buildpack [#16](https://github.com/jupyterhub/repo2docker/pull/16) ([@minrk](https://github.com/minrk)) + +### Contributors to this release + +([GitHub contributors page for this release](https://github.com/jupyterhub/repo2docker/graphs/contributors?from=2017-05-25&to=2017-09-06&type=c)) + +[@arokem](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aarokem+updated%3A2017-05-25..2017-09-06&type=Issues) | [@betatim](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abetatim+updated%3A2017-05-25..2017-09-06&type=Issues) | [@cboettig](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acboettig+updated%3A2017-05-25..2017-09-06&type=Issues) | [@choldgraf](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acholdgraf+updated%3A2017-05-25..2017-09-06&type=Issues) | [@consideRatio](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AconsideRatio+updated%3A2017-05-25..2017-09-06&type=Issues) | [@dpsanders](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Adpsanders+updated%3A2017-05-25..2017-09-06&type=Issues) | [@jzf2101](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajzf2101+updated%3A2017-05-25..2017-09-06&type=Issues) | [@minrk](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aminrk+updated%3A2017-05-25..2017-09-06&type=Issues) | [@rprimet](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Arprimet+updated%3A2017-05-25..2017-09-06&type=Issues) | [@sje30](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Asje30+updated%3A2017-05-25..2017-09-06&type=Issues) | [@sumalaika](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Asumalaika+updated%3A2017-05-25..2017-09-06&type=Issues) | [@taylorreiter](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ataylorreiter+updated%3A2017-05-25..2017-09-06&type=Issues) | [@tdalseide](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Atdalseide+updated%3A2017-05-25..2017-09-06&type=Issues) | [@tkelman](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Atkelman+updated%3A2017-05-25..2017-09-06&type=Issues) | [@willingc](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awillingc+updated%3A2017-05-25..2017-09-06&type=Issues) | [@yuvipanda](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayuvipanda+updated%3A2017-05-25..2017-09-06&type=Issues) + +## 0.2.0 + +([full changelog](https://github.com/jupyterhub/repo2docker/compare/efd55a9...e7674ce)) + +### Merged PRs + +- line endings! [#14](https://github.com/jupyterhub/repo2docker/pull/14) ([@minrk](https://github.com/minrk)) +- bundle s2i in wheels [#12](https://github.com/jupyterhub/repo2docker/pull/12) ([@minrk](https://github.com/minrk)) +- Add builder creation doc [#11](https://github.com/jupyterhub/repo2docker/pull/11) ([@willingc](https://github.com/willingc)) +- Use same port in host and docker container [#10](https://github.com/jupyterhub/repo2docker/pull/10) ([@yuvipanda](https://github.com/yuvipanda)) +- support repo as positional arg [#8](https://github.com/jupyterhub/repo2docker/pull/8) ([@minrk](https://github.com/minrk)) +- further simplify s2i buildpacks [#7](https://github.com/jupyterhub/repo2docker/pull/7) ([@minrk](https://github.com/minrk)) +- add conda detector [#2](https://github.com/jupyterhub/repo2docker/pull/2) ([@minrk](https://github.com/minrk)) + +### Contributors to this release + +([GitHub contributors page for this release](https://github.com/jupyterhub/repo2docker/graphs/contributors?from=2017-04-19&to=2017-05-25&type=c)) + +[@choldgraf](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acholdgraf+updated%3A2017-04-19..2017-05-25&type=Issues) | [@minrk](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aminrk+updated%3A2017-04-19..2017-05-25&type=Issues) | [@willingc](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awillingc+updated%3A2017-04-19..2017-05-25&type=Issues) | [@yuvipanda](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayuvipanda+updated%3A2017-04-19..2017-05-25&type=Issues) + diff --git a/docs/source/changelog.rst b/docs/source/changelog.rst deleted file mode 100644 index 23a4ed9d6..000000000 --- a/docs/source/changelog.rst +++ /dev/null @@ -1,523 +0,0 @@ -========= -Changelog -========= - -Version 2022.10.0 -================= - -`Full changelog `__ - -New features ------------- - -- Update Jupyter dependencies :pr:`1193` by :user:`jtpio` -- add Python 3.10 base environment :pr:`1175` by :user:`minrk` -- Bump default R version to 4.2 from 4.1, and let R 3.4 go from 3.4.0 to 3.4.4 :pr:`1165` by :user:`yuvipanda` -- Support pulling from zenodo sandbox too :pr:`1169` by :user:`yuvipanda` -- Add MPDL Dataverse :pr:`1167` by :user:`wilhelmfrank` -- Add JPL Dataverse :pr:`1163` by :user:`foobarbecue` -- upgrade RStudio Server to v2022.02.1 :pr:`1148` by :user:`aplamada` -- Pass build_args to `render()` during `--no-build` for consistency with regular builds :pr:`1135` by :user:`yoogottamk` - -Documentation improvements --------------------------- - -- Update 'how to get R' section :pr:`1147` by :user:`yuvipanda` -- Post release fixes :pr:`1133` by :user:`manics` - -API changes ------------ - -Bug fixes ---------- -- consistent log handling when not using JSON loggers :pr:`1177` by :user:`minrk` -- Fix Read-Only filesystem permission issue for log file :pr:`1156` by :user:`timeu` -- handle permission issue writing .jupyter-server-log.txt in REPO_DIR :pr:`1151` by :user:`pymonger` -- handle r version being unspecified in environment.yml :pr:`1141` by :user:`minrk` - -Other merged PRs ----------------- - -- Remove conda buildpacks pin of r-irkernel to 1.2 :pr:`1191` by :user:`consideRatio` -- ci: refactor julia/r/conda tests - now ~25 min instead of ~50 min :pr:`1188` by :user:`consideRatio` -- ci: general refresh of github workflows, update gha versions and let dependabot do it, etc. :pr:`1186` by :user:`consideRatio` -- Use enum to standardise `phase` :pr:`1185` by :user:`manics` -- fail on unsupported Python :pr:`1184` by :user:`minrk` -- mount wheels from build stage instead of copying them :pr:`1182` by :user:`minrk` -- get CI working again :pr:`1178` by :user:`minrk` -- explicitly build linux/amd64 images :pr:`1176` by :user:`minrk` -- Freeze.py update :pr:`1173` by :user:`manics` -- Bump version of nodejs :pr:`1172` by :user:`yuvipanda` -- Update mamba :pr:`1171` by :user:`SylvainCorlay` -- ci: switch to using a 2fa enabled accounts pypi api-token :pr:`1166` by :user:`consideRatio` -- Get R from RStudio provided apt packages (.deb files) :pr:`1161` by :user:`yuvipanda` -- Shallow clone HEAD :pr:`1160` by :user:`daradib` -- Update black version :pr:`1150` by :user:`yuvipanda` -- Update base notebook packages :pr:`1149` by :user:`yuvipanda` -- Update Dockerfile to current Alpine (ALPINE_VERSION=3.15.0) :pr:`1136` by :user:`holzman` -- update Python in some dockerfile tests :pr:`1130` by :user:`minrk` - - -Version 2022.02.0 -================= - -`Full changelog `__ - -New features ------------- - -- Update ipywidgets jupyter-offlinenotebook jupyterlab :pr:`1127` by :user:`manics` -- Allow passing in extra args to Docker initialization :pr:`1124` by :user:`yuvipanda` -- Allow passing in traitlets via commandline :pr:`1123` by :user:`yuvipanda` -- Bump default R version to 4.1 :pr:`1107` by :user:`yuvipanda` -- Update jupyterlab 3.2.5 jupyter-resource-usage 0.6.1 :pr:`1105` by :user:`manics` -- Get binary R packages from packagemanager.rstudio.com :pr:`1104` by :user:`yuvipanda` -- Support R 4.1 :pr:`1102` by :user:`yuvipanda` -- Add command line option to pass extra build args :pr:`1100` by :user:`TimoRoth` -- Set labels when building image from Dockerfile :pr:`1097` by :user:`TimoRoth` -- jupyterlab 3.1.17 :pr:`1092` by :user:`minrk` -- Bump JupyterLab to 3.1.11 :pr:`1081` by :user:`choldgraf` -- Bootstrap base env with micromamba :pr:`1062` by :user:`wolfv` -- Default UI to JupyterLab :pr:`1035` by :user:`SylvainCorlay` - -API changes ------------ - -Bug fixes ---------- - -Other merged PRs ----------------- - -- Put micromamba in /usr/local/bin and use mamba for installs :pr:`1128` by :user:`minrk` -- Remove deprecated calls to distutils :pr:`1122` by :user:`minrk` -- Delete /tmp/downloaded_packages after running install.R :pr:`1119` by :user:`yuvipanda` -- Use a smaller R library in our tests :pr:`1118` by :user:`yuvipanda` -- Only get R itself (r-base-core) from apt, not CRAN packages :pr:`1117` by :user:`minrk` -- set USER root after each directive block :pr:`1115` by :user:`minrk` -- Say 'apt repository' rather than PPA :pr:`1111` by :user:`yuvipanda` -- add tests for R conda :pr:`1108` by :user:`aplamada` -- Add help message to freeze.py :pr:`1106` by :user:`manics` -- Quieter R builds :pr:`1103` by :user:`yuvipanda` -- update user_interface doc to reflect that lab is default :pr:`1085` by :user:`minrk` -- Updates to dev docs + Recommonmark -> MyST Parser :pr:`1082` by :user:`choldgraf` -- Fix Docker build (again) :pr:`1078` by :user:`manics` -- [mrg] __init__.py: r_version: fixed description :pr:`1074` by :user:`magnush0lm` -- Typo fix in utils docstring :pr:`1072` by :user:`jgarte` -- Rename requirements.py-3.5.txt to requirements.py-3.5.pip :pr:`1061` by :user:`manics` -- Remove nodesource' nodejs :pr:`847` by :user:`yuvipanda` - - -Version 2021.08.0 -================= - -`Full changelog `__ - -The repo2docker container image has moved to `quay.io/jupyterhub/repo2docker `_ - -New features ------------- - -- always unpack a single zenodo zip :pr:`1043` by :user:`akhmerov` -- Refreeze with conda-lock :pr:`1024` by :user:`minrk` -- Refine buffered output debugging :pr:`1016` by :user:`minrk` -- reimplement entrypoint in Python :pr:`1014` by :user:`minrk` -- Fetch available Julia versions from hosted json :pr:`994` by :user:`tomyun` -- Define an interface for Container engines :pr:`848` by :user:`manics` - -API changes ------------ - -Bug fixes ---------- - -- Workaround docker-py dependency's failure to import six :pr:`1066:` by :user:`consideratio` -- fix: add chardet, a not explicitly declared dependency :pr:`1064` by :user:`johnhoman` -- Add build-base to build stage of docker image :pr:`1051` by :user:`yuvipanda` -- Fix regression in hydroshare introduced after moving to requests :pr:`1034` by :user:`MridulS` - -Other merged PRs ----------------- - -- Update README quay.io URL, Add docker latest tag :pr:`1075` by :user:`manics` -- GitHub workflow build and push to Docker hub :pr:`1071` by :user:`manics` -- Rename master branch to main :pr:`1068` by :user:`manics` -- Remove Pipfile & Pipfile.lock :pr:`1054` by :user:`yuvipanda` -- Remove CircleCI docs build :pr:`1053` by :user:`yuvipanda` -- Pin doc requirements to avoid CI breakages :pr:`1052` by :user:`manics` -- Stop using deprecated add_stylesheet in sphinx :pr:`1050` by :user:`yuvipanda` -- Add study participation notice to readme :pr:`1046` by :user:`sgibson91` -- Bump urllib3 from 1.26.4 to 1.26.5 :pr:`1045` by :user:`dependabot` -- State newly used installation command :pr:`1040` by :user:`fkohrt` -- Bump pyyaml from 5.1.1 to 5.4 :pr:`1029` by :user:`dependabot` -- Set default Julia version to 1.6 :pr:`1028` by :user:`tomyun` -- Fix logo URL in README :pr:`1027` by :user:`betatim` - - -Version 2021.03.0 -================= - -`Full changelog `__ - -New features ------------- - -- freeze with mamba, add 3.9 :pr:`1017` by :user:`minrk` -- Add GH workflow to push releases to PYPi and introduce CalVer :pr:`1004` by :user:`betatim` -- Add entrypoint script which automatically propagates \*_PROXY env vars… :pr:`1003` ([@g-braeunlich](https://github.com/g-braeunlich)) -- Update to JupyterLab 3.0 :pr:`996` by :user:`jtpio` -- Fetch available Julia versions from hosted json :pr:`994` by :user:`tomyun` -- Add a contentprovider for Software Heritage persistent ID (SWHID) :pr:`988` by :user:`douardda` -- Stream jupyter server logs to a file :pr:`987` by :user:`betatim` -- add 4.0, 4.0.2 to list of supported R versions :pr:`960` by :user:`minrk` - -API changes ------------ - -Bug fixes ---------- - -- fix dataverse regression introduced in last release :pr:`1011` by :user:`MridulS` -- buildpacks.r: dont use apt-key directly to respect \*_proxy env vars :pr:`1019` ([@g-braeunlich](https://github.com/g-braeunlich)) - -Other merged PRs ----------------- - -- Cleanup install_requires including duplicates :pr:`1020` by :user:`manics` -- bump docker action version :pr:`1018` by :user:`minrk` -- bump python in circleci test :pr:`1013` by :user:`minrk` -- Investigating the missing logs :pr:`1008` by :user:`betatim` -- Experiment with different install mechanism to get code coverage stats again :pr:`982` by :user:`betatim` - - -Version 2021.01.0 -================= - -`Full changelog `__ - -New features ------------- - -- Replace urllib by requests in contentproviders :pr:`993` by :user:`douardda` -- Use mambaforge instead of miniforge :pr:`992` by :user:`SylvainCorlay` -- buildpacks/nix: 2.3 -> 2.3.9 :pr:`991` by :user:`FRidh` -- Drop support for stencila :pr:`985` by :user:`minrk` -- Add Julia 1.5.3 support :pr:`984` by :user:`tomyun` -- Update to node 14 :pr:`983` by :user:`jtpio` -- Mamba 0.6.1 :pr:`979` by :user:`minrk` -- Ensure REPO_DIR owned by NB_USER :pr:`975` by :user:`tomyun` -- Add Julia 1.5.2 support :pr:`965` by :user:`tomyun` -- Mamba number three :pr:`962` by :user:`SylvainCorlay` -- Add a Mercurial contentprovider :pr:`950` by :user:`paugier` -- Add Julia 1.5.1 support :pr:`949` by :user:`tomyun` -- Handle requirements.txt with `--pre` lines :pr:`943` by :user:`betatim` -- Add Julia 1.5.0 support :pr:`938` by :user:`tomyun` -- Update JupyterLab to 2.2.0 :pr:`933` by :user:`manics` -- Bump nix version to 2.3 :pr:`915` by :user:`jboynyc` -- Add nbresuse==0.3.3 (full freeze.py) :pr:`904` by :user:`manics` -- Add Julia 1.4.2 support :pr:`899` by :user:`davidanthoff` -- Bump version of irkernel for R 4.0 :pr:`892` by :user:`betatim` -- chmod start script from repo2docker-entrypoint :pr:`886` by :user:`danlester` -- pypi jupyter-offlinenotebook==0.1.0 :pr:`880` by :user:`manics` -- Add support for Julia 1.4.1 :pr:`878` by :user:`davidanthoff` -- Change --env option to work like docker's :pr:`874` by :user:`hwine` -- Add support for Julia 1.4.0 :pr:`870` by :user:`davidanthoff` -- Update server proxy and rsession proxy :pr:`869` by :user:`betatim` -- Use miniforge instead of miniconda to get conda :pr:`859` by :user:`yuvipanda` -- If looking for latest MRAN URL try earlier snapshots too :pr:`851` by :user:`manics` -- Add jupyter-offlinenotebook extension :pr:`845` by :user:`betatim` - -API changes ------------ - -- Bump Python requirement to 3.6 from 3.5 :pr:`951` by :user:`betatim` - -Bug fixes ---------- - -- buildpacks/nix: disable sandboxing (bugfix) :pr:`990` by :user:`FRidh` -- avoid deprecated import of collections.abc :pr:`924` by :user:`minrk` -- Add missing “:” for R code :pr:`900` by :user:`adamhsparks` -- Fix RShiny proxy :pr:`893` by :user:`betatim` -- Work around a Julia bug :pr:`879` by :user:`davidanthoff` -- Fix typo :pr:`862` by :user:`jtpio` - -Other merged PRs ----------------- - -- Fix figshare test :pr:`1001` by :user:`manics` -- Weekly test of master to check for external failures :pr:`998` by :user:`manics` -- Remove reference to `master` branch from CLI doc :pr:`977` by :user:`betatim` -- add chown to COPY commands to reduce layer count :pr:`969` by :user:`bollwyvl` -- set TIMEFORMAT for timed bash conda commands :pr:`966` by :user:`manics` -- Disable jupyterlab extension build minimize :pr:`963` by :user:`manics` -- Bump Black version to 20.8b1 and use --target-version=py36 :pr:`955` by :user:`paugier` -- Add workflow to build Docker image :pr:`954` by :user:`manics` -- Crosslink 'Configuring your repository' with usage :pr:`952` by :user:`manics` -- Add `www-frame-origin=same` to /etc/rstudio/rserver.conf :pr:`944` ([@rkevin-arch](https://github.com/rkevin-arch)) -- GitHub Actions :pr:`942` by :user:`minrk` -- stop running tests on travis :pr:`940` by :user:`minrk` -- update repo URLs for jupyterhub/repo2docker :pr:`939` by :user:`minrk` -- Upgrade custom test infrastructure for pytest 6.0.0 :pr:`936` by :user:`betatim` -- validate_image_name: mention lowercase, fix formatting :pr:`934` by :user:`manics` -- Update snapshot date for simple R test :pr:`930` by :user:`betatim` -- little improvement for testing binder_dir :pr:`928` by :user:`bitnik` -- update docs for config dirs :pr:`927` by :user:`bitnik` -- doc: runtime.txt installs python x.y (& concise rewording) :pr:`914` by :user:`mdeff` -- doc: environment.yml installs a conda env, not only python :pr:`913` by :user:`mdeff` -- Make the memory limit test simpler :pr:`912` by :user:`betatim` -- Add gitpod.io config for docs :pr:`908` by :user:`betatim` -- fix repo2docker logo in Sphinx docs :pr:`906` by :user:`trallard` -- Update Dockerfile to add Docker :pr:`896` by :user:`hamelsmu` -- Document test failure workarounds :pr:`890` by :user:`hwine` -- Workaround Docker issue impacting some tests on macOS :pr:`882` by :user:`hwine` -- [docs] fix grammatical error in section title :pr:`872` by :user:`jameslamb` -- Fix long form args requirements :pr:`866` by :user:`betatim` -- Adopt new Sphinx theme name :pr:`864` by :user:`xhochy` -- Document loose conda export with --from-history :pr:`863` by :user:`xhochy` -- utils.execute_cmd flush buffer if no EOL :pr:`850` by :user:`manics` -- Update black 19.10b0, target Python 3.5 :pr:`849` by :user:`manics` -- docs: postBuild warn about shell script errors being ignored :pr:`844` by :user:`manics` -- Update changelog for 0.11.0 :pr:`842` by :user:`betatim` - - -Version 0.11.0 -============== - -Release date: 2020-02-05 - -New features ------------- -- Add support for Figshare in :pr:`788` by :user:`nuest`. -- Add support for Dataverse in :pr:`739` by :user:`Xarthisius`. -- Add support for configuring the version of R installed in :pr:`772` by - :user:`betatim`. -- Add support for Julia 1.2.0 in :pr:`768` by :user:`davidanthoff`. -- Add support for Julia 1.3.0 and 1.0.5 in :pr:`822` by :user:`davidanthoff`. -- Add support for Julia 1.3.1 in :pr:`831` by :user:`davidanthoff`. -- Update Miniconda to 4.7.10 in :pr:`769` by :user:`davidrpugh`. -- Update IRKernel to 1.0.2 in :pr:`770` by :user:`GeorgianaElena`. -- Update RStudio to 1.2 in :pr:`803` by :user:`pablobernabeu`. -- Switch to "pandas" sphinx theme for documentation in :pr:`816` by :user:`choldgraf`. -- Add content provider documentation in :pr:`824` by :user:`choldgraf`. -- Remove legacy buildpack in :pr:`829` by :user:`betatim`. -- Add support for automatic RStudio install when using R packages via conda - in :pr:`838` by :user:`xhochy`. -- Add support for Python 3.8 in :pr:`840` by :user:`minrk`. -- Add Hydroshare as content provider in :pr:`800` by :user:`sblack-usu`. -- Update to Jupyter Notebook 6 and Lab 1.2 in :pr:`839` by :user:`minrk`. - - -Bug fixes ---------- -- Fix for submodule check out in :pr:`809` by :user:`davidbrochart`. -- Handle `requirements.txt` files with different encodings in :pr:`771` - by :user:`GeorgianaElena`. -- Update to nteract-on-jupyter 2.1.3 in :pr:`2.1.3 by :user:`betatim`. -- Use `useradd --no-log-init` to fix exhausting disk space in :pr:`804` by - :user:`manics.` -- Add help text for commandline arguments in :pr:`517` by :user:`yuvipanda`. -- Fix submodule checkout in :pr:`809` by :user:`davidbrochart`. - - -Version 0.10.0 -============== - -Release date: 2019-08-07 - -New features ------------- -- Increased minimum Python version supported for running `repo2docker` itself - to Python 3.5 in :pr:`684` by :user:`betatim`. -- Support for `Pipfile` and `Pipfile.lock` implemented in :pr:`649` by - :user:`consideratio`. -- Use only conda packages for our base environments in :pr:`728` by - :user:`scottyhq`. -- Fast rebuilds when repo dependencies haven't changed by :user:`minrk` and - :user:`betatim` in :pr:`743`, :pr:`752`, :pr:`718` and :pr:`716`. -- Add support for Zenodo in :pr:`693` by :user:`betatim`. -- Add support for general Invenio repositories in :pr:`704` by :user:`tmorrell`. -- Add support for julia 1.0.4 and 1.1.1 in :pr:`710` by :user:`davidanthoff`. -- Bump Conda from 4.6.14 to 4.7.5 in :pr:`719` by :user:`davidrpugh`. - - -API changes ------------ - -Bug fixes ---------- -- Prevent building the image as root if --user-id and --user-name are not specified - in :pr:`676` by :user:`Xarthisius`. -- Add bash to Dockerfile to fix usage of private repos with git-crendential-env in - :pr:`738` by :user:`eexwhyzee`. -- Fix memory limit enforcement in :pr:`677` by :user:`betatim`. - - -Version 0.9.0 -============= - -Release date: 2019-05-05 - -New features ------------- -- Support for julia `Project.toml`, `JuliaProject.toml` and `Manifest.toml` files in :pr:`595` by - :user:`davidanthoff` -- Set JULIA_PROJECT globally, so that every julia instance starts with the - julia environment activated in :pr:`612` by :user:`davidanthoff`. -- Update Miniconda version to 4.6.14 and Conda version to 4.6.14 in :pr:`637` by - :user:`jhamman` -- Install notebook into `notebook` env instead of `root`. - Activate conda environments and shell integration via ENTRYPOINT - in :pr:`651` by :user:`minrk` -- Support for `.binder` directory in addition to `binder` directory for location of - configuration files, in :pr:`653` by :user:`jhamman`. -- Updated contributor guide and issue templates for bugs, feature requests, - and support questions in :pr:`654` and :pr:`655` by :user:`KirstieJane` and - :user:`betatim`. -- Create a page naming and describing the "Reproducible Execution - Environment Specification" (the specification used by repo2docker) - in :pr:`662` by :user:`choldgraf`. - -API changes ------------ - -Bug fixes ---------- -- Install IJulia kernel into ${NB_PYTHON_PREFIX}/share/jupyter in :pr:`622` by - :user:`davidanthoff`. -- Ensure git submodules are updated and initilized correctly in :pr:`639` by - :user:`djhoese`. -- Use archive.debian.org as source for the debian jessie based legacy - buildpack in :pr:`633` by :user:`betatim`. -- Update to version 5.7.6 of the `notebook` package used in all environments - in :pr:`628` by :user:`betatim`. -- Update to version 5.7.8 of the `notebook` package and version 2.0.12 of - `nteract-on-jupyter` in :pr:`650` by :user:`betatim`. -- Switch to newer version of jupyter-server-proxy to fix websocket handling - in :pr:`646` by :user:`betatim`. -- Update to pip version 19.0.3 in :pr:`647` by :user:`betatim`. -- Ensure ENTRYPOINT is an absolute path in :pr:`657` by :user:`yuvipanda`. -- Fix handling of `--build-memory-limit` values without a postfix in :pr:`652` - by :user:`betatim`. - - -Version 0.8.0 -============= - -Release date: 2019-02-21 - -New features ------------- -- Add additional metadata to docker images about how they were built :pr:`500` by - :user:`jrbourbeau`. -- Allow users to install global NPM packages: :pr:`573` by :user:`GladysNalvarte`. -- Add documentation on switching the user interface presented by a - container. :pr:`568` by user:`choldgraf`. -- Increased test coverage to ~87% by :user:`betatim` and :user:`yuvipanda`. -- Documentation improvements and additions by :user:`lheagy`, :user:`choldgraf`. -- Remove f-strings from code base, repo2docker is compatible with Python 3.4+ - again by :user:`jrbourbeau` in :pr:`520`. -- Local caching of previously built repostories to speed up launch times - by :user:`betatim` in :pr:`511`. -- Make destination of repository content in the container image configurable - on the CLI via ``--target-repo-dir``. By :user:`yuvipanda` in :pr:`507`. -- Expose CPU limit settings for building and running containers. By - :user:`GladysNalvarte` in :pr:`579`. -- Make Python 3.7 the default version. By :user:`yuvipanda` and :user:`minrk` in - :pr:`539`. - -API changes ------------ - -Bug fixes ---------- -- In some cases the version of conda installed in images was not pinned and got - upgraded by user actions. Fixed in :pr:`576` by :user:`minrk`. -- Fix an error related to checking if debug output was enabled or not: - :pr:`575` by :user:`yuvipanda`. -- Update nteract frontend to version 2.0.0 by :user:`yuvipanda` in :pr:`571`. -- Fix quoting issue in ``GIT_CREDENTIAL_ENV`` environment variable by - :user:`minrk` in :pr:`572`. -- Change to using the first 8 characters of each Git commit, not the last 8, - to tag each built docker image of repo2docker itself. :user:`minrk` in :pr:`562`. -- Allow users to select the Julia when using a ``requirements.txt`` by - :user:`yuvipanda` in :pr:`557`. -- Set ``JULIA_DEPOT_PATH`` to install packages outside the home directory by - :user:`yuvipanda` in :pr:`555`. -- Update to Jupyter notebook 5.7.4 :pr:`519` by :user:`minrk`. - - -Version 0.7.0 -============= - -Release date: 2018-12-12 - -New features ------------- - -- Build from sub-directory: build the image based on a sub-directory of a - repository :pr:`413` by :user:`dsludwig`. -- Editable mode: allows editing a local repository from a live container - :pr:`421` by :user:`evertrol`. -- Change log added :pr:`426` by :user:`evertrol`. -- Documentation: improved the documentation for contributors :pr:`453` by - :user:`choldgraf`. -- Buildpack: added support for the nix package manager :pr:`407` by - :user:`costrouc`. -- Log a 'success' message when push is complete :pr:`482` by - :user:`yuvipanda`. -- Allow specifying images to reuse cache from :pr:`478` by - :user:`yuvipanda`. -- Add JupyterHub back to base environment :pr:`476` by :user:`yuvipanda`. -- Repo2docker has a logo! by :user:`agahkarakuzu` and :user:`blairhudson`. -- Improve support for Stencila, including identifying stencila runtime from - document context :pr:`457` by :user:`nuest`. - - -API changes ------------ - -- Add content provider abstraction :pr:`421` by :user:`betatim`. - - -Bug fixes ---------- - -- Update to Jupyter notebook 5.7 :pr:`475` by :user:`betatim` and :user:`minrk`. - - - -Version 0.6 -=========== - -Released 2018-09-09 - - -Version 0.5 -=========== - -Released 2018-02-07 - - -Version 0.4.1 -============= - -Released 2018-09-06 - - -Version 0.2 -=========== - -Released 2018-05-25 - - -Version 0.1.1 -============= - -Released 2017-04-19 - - -Version 0.1 -=========== - -Released 2017-04-14 From ad028f665fb2a414b9f7f75f5bc943276d37f1c9 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 5 Jun 2023 19:52:45 +0000 Subject: [PATCH 149/171] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- docs/source/changelog.md | 21 ++++++++++----------- 1 file changed, 10 insertions(+), 11 deletions(-) diff --git a/docs/source/changelog.md b/docs/source/changelog.md index 62b49ffc4..4f4e7ea3b 100644 --- a/docs/source/changelog.md +++ b/docs/source/changelog.md @@ -149,12 +149,12 @@ ### Merged PRs - [MRG] Cleanup install_requires including duplicates [#1020](https://github.com/jupyterhub/repo2docker/pull/1020) ([@manics](https://github.com/manics)) -- buildpacks.r: dont use apt-key directly to respect *_proxy env vars [#1019](https://github.com/jupyterhub/repo2docker/pull/1019) ([@g-braeunlich](https://github.com/g-braeunlich)) +- buildpacks.r: dont use apt-key directly to respect \*\_proxy env vars [#1019](https://github.com/jupyterhub/repo2docker/pull/1019) ([@g-braeunlich](https://github.com/g-braeunlich)) - freeze with mamba, add 3.9 [#1017](https://github.com/jupyterhub/repo2docker/pull/1017) ([@minrk](https://github.com/minrk)) -- bump python in circleci test [#1013](https://github.com/jupyterhub/repo2docker/pull/1013) ([@minrk](https://github.com/minrk)) +- bump python in circleci test [#1013](https://github.com/jupyterhub/repo2docker/pull/1013) ([@minrk](https://github.com/minrk)) - fix dataverse regression introduced in last release [#1011](https://github.com/jupyterhub/repo2docker/pull/1011) ([@MridulS](https://github.com/MridulS)) - Add GH workflow to push releases to PYPi and introduce CalVer [#1004](https://github.com/jupyterhub/repo2docker/pull/1004) ([@betatim](https://github.com/betatim)) -- Add entrypoint script which automatically propagates *_PROXY env vars… [#1003](https://github.com/jupyterhub/repo2docker/pull/1003) ([@g-braeunlich](https://github.com/g-braeunlich)) +- Add entrypoint script which automatically propagates \*\_PROXY env vars… [#1003](https://github.com/jupyterhub/repo2docker/pull/1003) ([@g-braeunlich](https://github.com/g-braeunlich)) - Update to JupyterLab 3.0 [#996](https://github.com/jupyterhub/repo2docker/pull/996) ([@jtpio](https://github.com/jtpio)) - Add a contentprovider for Software Heritage persistent ID (SWHID) [#988](https://github.com/jupyterhub/repo2docker/pull/988) ([@douardda](https://github.com/douardda)) - [MRG] Stream jupyter server logs to a file [#987](https://github.com/jupyterhub/repo2docker/pull/987) ([@betatim](https://github.com/betatim)) @@ -422,7 +422,7 @@ - fix docker commit tag [#562](https://github.com/jupyterhub/repo2docker/pull/562) ([@minrk](https://github.com/minrk)) - Set JULIA_DEPOT_PATH [#555](https://github.com/jupyterhub/repo2docker/pull/555) ([@yuvipanda](https://github.com/yuvipanda)) - Updated log info for local content provider [#551](https://github.com/jupyterhub/repo2docker/pull/551) ([@GladysNalvarte](https://github.com/GladysNalvarte)) -- Fixes Travis build errors related to pytest and Sphinx [#547](https://github.com/jupyterhub/repo2docker/pull/547) ([@craig-willis](https://github.com/craig-willis)) +- Fixes Travis build errors related to pytest and Sphinx [#547](https://github.com/jupyterhub/repo2docker/pull/547) ([@craig-willis](https://github.com/craig-willis)) - Spurious comment in `Dockerfile` #543 [#544](https://github.com/jupyterhub/repo2docker/pull/544) ([@benjaminr](https://github.com/benjaminr)) - Bump default python version to 3.7 [#539](https://github.com/jupyterhub/repo2docker/pull/539) ([@yuvipanda](https://github.com/yuvipanda)) - Use a minimal hand-crafted Dockerfile for speed [#536](https://github.com/jupyterhub/repo2docker/pull/536) ([@betatim](https://github.com/betatim)) @@ -543,10 +543,10 @@ - scinece -> science [#347](https://github.com/jupyterhub/repo2docker/pull/347) ([@danielleberre](https://github.com/danielleberre)) - Fix some rst weirdness in the uage docs [#346](https://github.com/jupyterhub/repo2docker/pull/346) ([@betatim](https://github.com/betatim)) - Add DockerSpawner command in JupyterHub config [#344](https://github.com/jupyterhub/repo2docker/pull/344) ([@rprimet](https://github.com/rprimet)) -- Test that images can start notebook servers in all the builders [#343](https://github.com/jupyterhub/repo2docker/pull/343) ([@GladysNalvarte](https://github.com/GladysNalvarte)) +- Test that images can start notebook servers in all the builders [#343](https://github.com/jupyterhub/repo2docker/pull/343) ([@GladysNalvarte](https://github.com/GladysNalvarte)) - Setup auto releasing on GitHub tagging [#342](https://github.com/jupyterhub/repo2docker/pull/342) ([@betatim](https://github.com/betatim)) - documentation improvements based on reviews for walkthrough and configuration details [#338](https://github.com/jupyterhub/repo2docker/pull/338) ([@jzf2101](https://github.com/jzf2101)) -- Tweaking Docs for Readability [#335](https://github.com/jupyterhub/repo2docker/pull/335) ([@jzf2101](https://github.com/jzf2101)) +- Tweaking Docs for Readability [#335](https://github.com/jupyterhub/repo2docker/pull/335) ([@jzf2101](https://github.com/jzf2101)) - Include LICENSE file in wheels [#327](https://github.com/jupyterhub/repo2docker/pull/327) ([@toddrme2178](https://github.com/toddrme2178)) - Switch to miniconda v4.5.1 [#324](https://github.com/jupyterhub/repo2docker/pull/324) ([@betatim](https://github.com/betatim)) - Support shiny apps [#320](https://github.com/jupyterhub/repo2docker/pull/320) ([@ryanlovett](https://github.com/ryanlovett)) @@ -556,12 +556,12 @@ - stencila support [#309](https://github.com/jupyterhub/repo2docker/pull/309) ([@minrk](https://github.com/minrk)) - Add links to the front page and modify travis [#308](https://github.com/jupyterhub/repo2docker/pull/308) ([@betatim](https://github.com/betatim)) - Bump nteract jupyter extension [#306](https://github.com/jupyterhub/repo2docker/pull/306) ([@yuvipanda](https://github.com/yuvipanda)) -- remove _nb_ext_conf from legacy env [#303](https://github.com/jupyterhub/repo2docker/pull/303) ([@minrk](https://github.com/minrk)) +- remove \_nb_ext_conf from legacy env [#303](https://github.com/jupyterhub/repo2docker/pull/303) ([@minrk](https://github.com/minrk)) - bump base image to ubuntu 18.04 [#302](https://github.com/jupyterhub/repo2docker/pull/302) ([@minrk](https://github.com/minrk)) - Documentation and warning improvements [#300](https://github.com/jupyterhub/repo2docker/pull/300) ([@choldgraf](https://github.com/choldgraf)) - Fix two typos [#299](https://github.com/jupyterhub/repo2docker/pull/299) ([@darabos](https://github.com/darabos)) - Always install Python with conda [#298](https://github.com/jupyterhub/repo2docker/pull/298) ([@minrk](https://github.com/minrk)) -- split post build script command in Docker file [#294](https://github.com/jupyterhub/repo2docker/pull/294) ([@bitnik](https://github.com/bitnik)) +- split post build script command in Docker file [#294](https://github.com/jupyterhub/repo2docker/pull/294) ([@bitnik](https://github.com/bitnik)) - Add guidelines on merging work [#292](https://github.com/jupyterhub/repo2docker/pull/292) ([@betatim](https://github.com/betatim)) - Support setup.py in Python buildpacks [#289](https://github.com/jupyterhub/repo2docker/pull/289) ([@GladysNalvarte](https://github.com/GladysNalvarte)) - Use travis_retry to run tests [#288](https://github.com/jupyterhub/repo2docker/pull/288) ([@betatim](https://github.com/betatim)) @@ -570,7 +570,7 @@ - Add note about os support and update example repo [#283](https://github.com/jupyterhub/repo2docker/pull/283) ([@willingc](https://github.com/willingc)) - Add codecov configuration to enable PR comments [#279](https://github.com/jupyterhub/repo2docker/pull/279) ([@betatim](https://github.com/betatim)) - fixing python2 search [#277](https://github.com/jupyterhub/repo2docker/pull/277) ([@choldgraf](https://github.com/choldgraf)) -- Freeze legacy environment [#276](https://github.com/jupyterhub/repo2docker/pull/276) ([@GladysNalvarte](https://github.com/GladysNalvarte)) +- Freeze legacy environment [#276](https://github.com/jupyterhub/repo2docker/pull/276) ([@GladysNalvarte](https://github.com/GladysNalvarte)) - Refreeze environments [#274](https://github.com/jupyterhub/repo2docker/pull/274) ([@willingc](https://github.com/willingc)) - add docstrings to docker buildpack [#272](https://github.com/jupyterhub/repo2docker/pull/272) ([@willingc](https://github.com/willingc)) - add docstrings for conda buildpack [#271](https://github.com/jupyterhub/repo2docker/pull/271) ([@willingc](https://github.com/willingc)) @@ -609,7 +609,7 @@ - Provide a flag to pass environment variables at runtime [#186](https://github.com/jupyterhub/repo2docker/pull/186) ([@rprimet](https://github.com/rprimet)) - Stop using alpine base images [#183](https://github.com/jupyterhub/repo2docker/pull/183) ([@yuvipanda](https://github.com/yuvipanda)) - Fix indentation causing only last line of apt.txt to be parsed [#181](https://github.com/jupyterhub/repo2docker/pull/181) ([@nmih](https://github.com/nmih)) -- Fixed run argument check for mounting volumes. [#179](https://github.com/jupyterhub/repo2docker/pull/179) ([@mukundans91](https://github.com/mukundans91)) +- Fixed run argument check for mounting volumes. [#179](https://github.com/jupyterhub/repo2docker/pull/179) ([@mukundans91](https://github.com/mukundans91)) - Add default command to base Dockerfile template [#176](https://github.com/jupyterhub/repo2docker/pull/176) ([@AaronWatters](https://github.com/AaronWatters)) - Added regex pattern based validation for image name argument [#175](https://github.com/jupyterhub/repo2docker/pull/175) ([@mukundans91](https://github.com/mukundans91)) - Allow mounting arbitrary volumes into the repo2docker container [#172](https://github.com/jupyterhub/repo2docker/pull/172) ([@yuvipanda](https://github.com/yuvipanda)) @@ -723,4 +723,3 @@ ([GitHub contributors page for this release](https://github.com/jupyterhub/repo2docker/graphs/contributors?from=2017-04-19&to=2017-05-25&type=c)) [@choldgraf](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acholdgraf+updated%3A2017-04-19..2017-05-25&type=Issues) | [@minrk](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aminrk+updated%3A2017-04-19..2017-05-25&type=Issues) | [@willingc](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awillingc+updated%3A2017-04-19..2017-05-25&type=Issues) | [@yuvipanda](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayuvipanda+updated%3A2017-04-19..2017-05-25&type=Issues) - From 8efd8c5b2628b2f8a0f9edf9afa77744f183ecae Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 6 Jun 2023 04:13:40 +0000 Subject: [PATCH 150/171] [pre-commit.ci] pre-commit autoupdate MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit updates: - [github.com/asottile/pyupgrade: v3.3.1 → v3.4.0](https://github.com/asottile/pyupgrade/compare/v3.3.1...v3.4.0) - [github.com/pre-commit/mirrors-prettier: v3.0.0-alpha.6 → v3.0.0-alpha.9-for-vscode](https://github.com/pre-commit/mirrors-prettier/compare/v3.0.0-alpha.6...v3.0.0-alpha.9-for-vscode) --- .pre-commit-config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index d7eb34473..3040ce88e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -11,7 +11,7 @@ repos: # Autoformat: Python code, syntax patterns are modernized - repo: https://github.com/asottile/pyupgrade - rev: v3.3.1 + rev: v3.4.0 hooks: - id: pyupgrade args: @@ -44,7 +44,7 @@ repos: # Autoformat: markdown - repo: https://github.com/pre-commit/mirrors-prettier - rev: v3.0.0-alpha.6 + rev: v3.0.0-alpha.9-for-vscode hooks: - id: prettier files: ".md" From be74e4ae42890c15dc50a842fb9de12089dbdac7 Mon Sep 17 00:00:00 2001 From: Min RK Date: Tue, 6 Jun 2023 13:26:54 +0200 Subject: [PATCH 151/171] use rst2myst to migrate changelog to .md no content change, only syntax --- docs/source/changelog.md | 1104 +++++++++++++++----------------------- 1 file changed, 419 insertions(+), 685 deletions(-) diff --git a/docs/source/changelog.md b/docs/source/changelog.md index 4f4e7ea3b..6bd03fd64 100644 --- a/docs/source/changelog.md +++ b/docs/source/changelog.md @@ -1,725 +1,459 @@ # Changelog -## 2022.10.0 +## Version 2022.10.0 -([full changelog](https://github.com/jupyterhub/repo2docker/compare/e40242c...e0d5b9b)) +[Full changelog](https://github.com/jupyterhub/repo2docker/compare/2022.02.0...2022.10.0) -### Maintenance and upkeep improvements +### New features -- Use enum to standardise `phase` [#1185](https://github.com/jupyterhub/repo2docker/pull/1185) ([@manics](https://github.com/manics)) -- get CI working again [#1178](https://github.com/jupyterhub/repo2docker/pull/1178) ([@minrk](https://github.com/minrk)) -- Freeze.py update [#1173](https://github.com/jupyterhub/repo2docker/pull/1173) ([@manics](https://github.com/manics)) -- Bump default R version to 4.2 from 4.1, and let R 3.4 go from 3.4.0 to 3.4.4 [#1165](https://github.com/jupyterhub/repo2docker/pull/1165) ([@yuvipanda](https://github.com/yuvipanda)) +- Update Jupyter dependencies {pr}`1193` by {user}`jtpio` +- add Python 3.10 base environment {pr}`1175` by {user}`minrk` +- Bump default R version to 4.2 from 4.1, and let R 3.4 go from 3.4.0 to 3.4.4 {pr}`1165` by {user}`yuvipanda` +- Support pulling from zenodo sandbox too {pr}`1169` by {user}`yuvipanda` +- Add MPDL Dataverse {pr}`1167` by {user}`wilhelmfrank` +- Add JPL Dataverse {pr}`1163` by {user}`foobarbecue` +- upgrade RStudio Server to v2022.02.1 {pr}`1148` by {user}`aplamada` +- Pass build_args to `render()` during `--no-build` for consistency with regular builds {pr}`1135` by {user}`yoogottamk` ### Documentation improvements -- Post release fixes [#1133](https://github.com/jupyterhub/repo2docker/pull/1133) ([@manics](https://github.com/manics)) +- Update 'how to get R' section {pr}`1147` by {user}`yuvipanda` +- Post release fixes {pr}`1133` by {user}`manics` -### Other merged PRs +### API changes -- Initial changelog for 2022.10.0 [#1194](https://github.com/jupyterhub/repo2docker/pull/1194) ([@manics](https://github.com/manics)) -- [MRG] Update Jupyter dependencies [#1193](https://github.com/jupyterhub/repo2docker/pull/1193) ([@jtpio](https://github.com/jtpio)) -- Remove conda buildpacks pin of r-irkernel to 1.2 [#1191](https://github.com/jupyterhub/repo2docker/pull/1191) ([@consideRatio](https://github.com/consideRatio)) -- ci: refactor julia/r/conda tests - now ~25 min instead of ~50 min [#1188](https://github.com/jupyterhub/repo2docker/pull/1188) ([@consideRatio](https://github.com/consideRatio)) -- ci: general refresh of github workflows, update gha versions and let dependabot do it, etc. [#1186](https://github.com/jupyterhub/repo2docker/pull/1186) ([@consideRatio](https://github.com/consideRatio)) -- fail on unsupported Python [#1184](https://github.com/jupyterhub/repo2docker/pull/1184) ([@minrk](https://github.com/minrk)) -- mount wheels from build stage instead of copying them [#1182](https://github.com/jupyterhub/repo2docker/pull/1182) ([@minrk](https://github.com/minrk)) -- consistent log handling when not using JSON loggers [#1177](https://github.com/jupyterhub/repo2docker/pull/1177) ([@minrk](https://github.com/minrk)) -- explicitly build linux/amd64 images [#1176](https://github.com/jupyterhub/repo2docker/pull/1176) ([@minrk](https://github.com/minrk)) -- add Python 3.10 base environment [#1175](https://github.com/jupyterhub/repo2docker/pull/1175) ([@minrk](https://github.com/minrk)) -- Bump version of nodejs [#1172](https://github.com/jupyterhub/repo2docker/pull/1172) ([@yuvipanda](https://github.com/yuvipanda)) -- Update mamba [#1171](https://github.com/jupyterhub/repo2docker/pull/1171) ([@SylvainCorlay](https://github.com/SylvainCorlay)) -- Support pulling from zenodo sandbox too [#1169](https://github.com/jupyterhub/repo2docker/pull/1169) ([@yuvipanda](https://github.com/yuvipanda)) -- Add MPDL Dataverse [#1167](https://github.com/jupyterhub/repo2docker/pull/1167) ([@wilhelmfrank](https://github.com/wilhelmfrank)) -- ci: switch to using a 2fa enabled accounts pypi api-token [#1166](https://github.com/jupyterhub/repo2docker/pull/1166) ([@consideRatio](https://github.com/consideRatio)) -- Add JPL Dataverse [#1163](https://github.com/jupyterhub/repo2docker/pull/1163) ([@foobarbecue](https://github.com/foobarbecue)) -- Get R from RStudio provided apt packages (.deb files) [#1161](https://github.com/jupyterhub/repo2docker/pull/1161) ([@yuvipanda](https://github.com/yuvipanda)) -- [MRG] Shallow clone HEAD [#1160](https://github.com/jupyterhub/repo2docker/pull/1160) ([@daradib](https://github.com/daradib)) -- Fix Read-Only filesystem permission issue for log file [#1156](https://github.com/jupyterhub/repo2docker/pull/1156) ([@timeu](https://github.com/timeu)) -- handle permission issue writing .jupyter-server-log.txt in REPO_DIR [#1151](https://github.com/jupyterhub/repo2docker/pull/1151) ([@pymonger](https://github.com/pymonger)) -- Update black version [#1150](https://github.com/jupyterhub/repo2docker/pull/1150) ([@yuvipanda](https://github.com/yuvipanda)) -- Update base notebook packages [#1149](https://github.com/jupyterhub/repo2docker/pull/1149) ([@yuvipanda](https://github.com/yuvipanda)) -- [MRG] upgrade RStudio Server to v2022.02.1 [#1148](https://github.com/jupyterhub/repo2docker/pull/1148) ([@aplamada](https://github.com/aplamada)) -- Update 'how to get R' section [#1147](https://github.com/jupyterhub/repo2docker/pull/1147) ([@yuvipanda](https://github.com/yuvipanda)) -- handle r version being unspecified in environment.yml [#1141](https://github.com/jupyterhub/repo2docker/pull/1141) ([@minrk](https://github.com/minrk)) -- [MRG] Update Dockerfile to current Alpine (ALPINE_VERSION=3.15.0) [#1136](https://github.com/jupyterhub/repo2docker/pull/1136) ([@holzman](https://github.com/holzman)) -- [MRG] Pass build_args to `render()` during `--no-build` for consistency with regular builds [#1135](https://github.com/jupyterhub/repo2docker/pull/1135) ([@yoogottamk](https://github.com/yoogottamk)) -- Update Changelog for release 2022.02.0 [#1113](https://github.com/jupyterhub/repo2docker/pull/1113) ([@manics](https://github.com/manics)) - -### Contributors to this release - -([GitHub contributors page for this release](https://github.com/jupyterhub/repo2docker/graphs/contributors?from=2022-02-06&to=2022-10-18&type=c)) - -[@aplamada](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aaplamada+updated%3A2022-02-06..2022-10-18&type=Issues) | [@betatim](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abetatim+updated%3A2022-02-06..2022-10-18&type=Issues) | [@consideRatio](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AconsideRatio+updated%3A2022-02-06..2022-10-18&type=Issues) | 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[@pymonger](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Apymonger+updated%3A2022-02-06..2022-10-18&type=Issues) | [@SylvainCorlay](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3ASylvainCorlay+updated%3A2022-02-06..2022-10-18&type=Issues) | [@timeu](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Atimeu+updated%3A2022-02-06..2022-10-18&type=Issues) | [@welcome](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awelcome+updated%3A2022-02-06..2022-10-18&type=Issues) | [@wilhelmfrank](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awilhelmfrank+updated%3A2022-02-06..2022-10-18&type=Issues) | [@yoogottamk](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayoogottamk+updated%3A2022-02-06..2022-10-18&type=Issues) | [@yuvipanda](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayuvipanda+updated%3A2022-02-06..2022-10-18&type=Issues) - -## 2022.02.0 - -([full changelog](https://github.com/jupyterhub/repo2docker/compare/c73321c...e40242c)) - -### Enhancements made - -- Update jupyterlab 3.2.5 jupyter-resource-usage 0.6.1 [#1105](https://github.com/jupyterhub/repo2docker/pull/1105) ([@manics](https://github.com/manics)) - -### Maintenance and upkeep improvements - -- Add help message to freeze.py [#1106](https://github.com/jupyterhub/repo2docker/pull/1106) ([@manics](https://github.com/manics)) +### Bug fixes -### Documentation improvements +- consistent log handling when not using JSON loggers {pr}`1177` by {user}`minrk` +- Fix Read-Only filesystem permission issue for log file {pr}`1156` by {user}`timeu` +- handle permission issue writing .jupyter-server-log.txt in REPO_DIR {pr}`1151` by {user}`pymonger` +- handle r version being unspecified in environment.yml {pr}`1141` by {user}`minrk` + +### Other merged PRs -- [MRG] Release 2021.08.0 [#1067](https://github.com/jupyterhub/repo2docker/pull/1067) ([@manics](https://github.com/manics)) +- Remove conda buildpacks pin of r-irkernel to 1.2 {pr}`1191` by {user}`consideRatio` +- ci: refactor julia/r/conda tests - now ~25 min instead of ~50 min {pr}`1188` by {user}`consideRatio` +- ci: general refresh of github workflows, update gha versions and let dependabot do it, etc. {pr}`1186` by {user}`consideRatio` +- Use enum to standardise `phase` {pr}`1185` by {user}`manics` +- fail on unsupported Python {pr}`1184` by {user}`minrk` +- mount wheels from build stage instead of copying them {pr}`1182` by {user}`minrk` +- get CI working again {pr}`1178` by {user}`minrk` +- explicitly build linux/amd64 images {pr}`1176` by {user}`minrk` +- Freeze.py update {pr}`1173` by {user}`manics` +- Bump version of nodejs {pr}`1172` by {user}`yuvipanda` +- Update mamba {pr}`1171` by {user}`SylvainCorlay` +- ci: switch to using a 2fa enabled accounts pypi api-token {pr}`1166` by {user}`consideRatio` +- Get R from RStudio provided apt packages (.deb files) {pr}`1161` by {user}`yuvipanda` +- Shallow clone HEAD {pr}`1160` by {user}`daradib` +- Update black version {pr}`1150` by {user}`yuvipanda` +- Update base notebook packages {pr}`1149` by {user}`yuvipanda` +- Update Dockerfile to current Alpine (ALPINE_VERSION=3.15.0) {pr}`1136` by {user}`holzman` +- update Python in some dockerfile tests {pr}`1130` by {user}`minrk` + +## Version 2022.02.0 + +[Full changelog](https://github.com/jupyterhub/repo2docker/compare/2021.08.0...2022.02.0) + +### New features + +- Update ipywidgets jupyter-offlinenotebook jupyterlab {pr}`1127` by {user}`manics` +- Allow passing in extra args to Docker initialization {pr}`1124` by {user}`yuvipanda` +- Allow passing in traitlets via commandline {pr}`1123` by {user}`yuvipanda` +- Bump default R version to 4.1 {pr}`1107` by {user}`yuvipanda` +- Update jupyterlab 3.2.5 jupyter-resource-usage 0.6.1 {pr}`1105` by {user}`manics` +- Get binary R packages from packagemanager.rstudio.com {pr}`1104` by {user}`yuvipanda` +- Support R 4.1 {pr}`1102` by {user}`yuvipanda` +- Add command line option to pass extra build args {pr}`1100` by {user}`TimoRoth` +- Set labels when building image from Dockerfile {pr}`1097` by {user}`TimoRoth` +- jupyterlab 3.1.17 {pr}`1092` by {user}`minrk` +- Bump JupyterLab to 3.1.11 {pr}`1081` by {user}`choldgraf` +- Bootstrap base env with micromamba {pr}`1062` by {user}`wolfv` +- Default UI to JupyterLab {pr}`1035` by {user}`SylvainCorlay` + +### API changes + +### Bug fixes ### Other merged PRs -- put micromamba in /usr/local/bin and use mamba for installs [#1128](https://github.com/jupyterhub/repo2docker/pull/1128) ([@minrk](https://github.com/minrk)) -- Update ipywidgets jupyter-offlinenotebook jupyterlab [#1127](https://github.com/jupyterhub/repo2docker/pull/1127) ([@manics](https://github.com/manics)) -- Allow passing in extra args to Docker initialization [#1124](https://github.com/jupyterhub/repo2docker/pull/1124) ([@yuvipanda](https://github.com/yuvipanda)) -- Allow passing in traitlets via commandline [#1123](https://github.com/jupyterhub/repo2docker/pull/1123) ([@yuvipanda](https://github.com/yuvipanda)) -- Delete /tmp/downloaded_packages after running install.R [#1119](https://github.com/jupyterhub/repo2docker/pull/1119) ([@yuvipanda](https://github.com/yuvipanda)) -- Use a smaller R library in our tests [#1118](https://github.com/jupyterhub/repo2docker/pull/1118) ([@yuvipanda](https://github.com/yuvipanda)) -- Only get R itself (r-base-core) from apt, not CRAN packages [#1117](https://github.com/jupyterhub/repo2docker/pull/1117) ([@minrk](https://github.com/minrk)) -- set USER root after each directive block [#1115](https://github.com/jupyterhub/repo2docker/pull/1115) ([@minrk](https://github.com/minrk)) -- Update Changelog for release 2022.02.0 [#1113](https://github.com/jupyterhub/repo2docker/pull/1113) ([@manics](https://github.com/manics)) -- Say 'apt repository' rather than PPA [#1111](https://github.com/jupyterhub/repo2docker/pull/1111) ([@yuvipanda](https://github.com/yuvipanda)) -- Bump default R version to 4.1 [#1107](https://github.com/jupyterhub/repo2docker/pull/1107) ([@yuvipanda](https://github.com/yuvipanda)) -- Get binary R packages from packagemanager.rstudio.com [#1104](https://github.com/jupyterhub/repo2docker/pull/1104) ([@yuvipanda](https://github.com/yuvipanda)) -- Quieter R builds [#1103](https://github.com/jupyterhub/repo2docker/pull/1103) ([@yuvipanda](https://github.com/yuvipanda)) -- Support R 4.1 [#1102](https://github.com/jupyterhub/repo2docker/pull/1102) ([@yuvipanda](https://github.com/yuvipanda)) -- Add command line option to pass extra build args [#1100](https://github.com/jupyterhub/repo2docker/pull/1100) ([@TimoRoth](https://github.com/TimoRoth)) -- Set labels when building image from Dockerfile [#1097](https://github.com/jupyterhub/repo2docker/pull/1097) ([@TimoRoth](https://github.com/TimoRoth)) -- jupyterlab 3.1.17 [#1092](https://github.com/jupyterhub/repo2docker/pull/1092) ([@minrk](https://github.com/minrk)) -- update user_interface doc to reflect that lab is default [#1085](https://github.com/jupyterhub/repo2docker/pull/1085) ([@minrk](https://github.com/minrk)) -- Updates to dev docs + Recommonmark -> MyST Parser [#1082](https://github.com/jupyterhub/repo2docker/pull/1082) ([@choldgraf](https://github.com/choldgraf)) -- Bump JupyterLab to 3.1.11 [#1081](https://github.com/jupyterhub/repo2docker/pull/1081) ([@choldgraf](https://github.com/choldgraf)) -- Fix Docker build (again) [#1078](https://github.com/jupyterhub/repo2docker/pull/1078) ([@manics](https://github.com/manics)) -- Typo fix in utils docstring [#1072](https://github.com/jupyterhub/repo2docker/pull/1072) ([@jgarte](https://github.com/jgarte)) -- Rename requirements.py-3.5.txt to requirements.py-3.5.pip [#1061](https://github.com/jupyterhub/repo2docker/pull/1061) ([@manics](https://github.com/manics)) -- Default UI to JupyterLab [#1035](https://github.com/jupyterhub/repo2docker/pull/1035) ([@SylvainCorlay](https://github.com/SylvainCorlay)) - -### Contributors to this release - -([GitHub contributors page for this release](https://github.com/jupyterhub/repo2docker/graphs/contributors?from=2021-08-24&to=2022-02-06&type=c)) - -[@andrewjohnlowe](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aandrewjohnlowe+updated%3A2021-08-24..2022-02-06&type=Issues) | [@aplamada](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aaplamada+updated%3A2021-08-24..2022-02-06&type=Issues) | [@betatim](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abetatim+updated%3A2021-08-24..2022-02-06&type=Issues) | [@bollwyvl](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abollwyvl+updated%3A2021-08-24..2022-02-06&type=Issues) | [@cboettig](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acboettig+updated%3A2021-08-24..2022-02-06&type=Issues) | 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[@jtpio](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajtpio+updated%3A2021-08-24..2022-02-06&type=Issues) | [@kkmann](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Akkmann+updated%3A2021-08-24..2022-02-06&type=Issues) | [@mael-le-gal](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Amael-le-gal+updated%3A2021-08-24..2022-02-06&type=Issues) | [@manics](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Amanics+updated%3A2021-08-24..2022-02-06&type=Issues) | [@mattwigway](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Amattwigway+updated%3A2021-08-24..2022-02-06&type=Issues) | [@meeseeksmachine](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ameeseeksmachine+updated%3A2021-08-24..2022-02-06&type=Issues) | [@minrk](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aminrk+updated%3A2021-08-24..2022-02-06&type=Issues) | 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-## 2021.08.0 - -([full changelog](https://github.com/jupyterhub/repo2docker/compare/71eb805...c73321c)) - -### Bugs fixed - -- fix: add chardet, a not explicitly declared dependency [#1064](https://github.com/jupyterhub/repo2docker/pull/1064) ([@johnhoman](https://github.com/johnhoman)) +- Put micromamba in /usr/local/bin and use mamba for installs {pr}`1128` by {user}`minrk` +- Remove deprecated calls to distutils {pr}`1122` by {user}`minrk` +- Delete /tmp/downloaded_packages after running install.R {pr}`1119` by {user}`yuvipanda` +- Use a smaller R library in our tests {pr}`1118` by {user}`yuvipanda` +- Only get R itself (r-base-core) from apt, not CRAN packages {pr}`1117` by {user}`minrk` +- set USER root after each directive block {pr}`1115` by {user}`minrk` +- Say 'apt repository' rather than PPA {pr}`1111` by {user}`yuvipanda` +- add tests for R conda {pr}`1108` by {user}`aplamada` +- Add help message to freeze.py {pr}`1106` by {user}`manics` +- Quieter R builds {pr}`1103` by {user}`yuvipanda` +- update user_interface doc to reflect that lab is default {pr}`1085` by {user}`minrk` +- Updates to dev docs + Recommonmark -> MyST Parser {pr}`1082` by {user}`choldgraf` +- Fix Docker build (again) {pr}`1078` by {user}`manics` +- \[mrg\] \_\_init\_\_.py: r_version: fixed description {pr}`1074` by {user}`magnush0lm` +- Typo fix in utils docstring {pr}`1072` by {user}`jgarte` +- Rename requirements.py-3.5.txt to requirements.py-3.5.pip {pr}`1061` by {user}`manics` +- Remove nodesource' nodejs {pr}`847` by {user}`yuvipanda` -### Documentation improvements +## Version 2021.08.0 -- [MRG] Release 2021.08.0 [#1067](https://github.com/jupyterhub/repo2docker/pull/1067) ([@manics](https://github.com/manics)) +[Full changelog](https://github.com/jupyterhub/repo2docker/compare/2021.03.0...2021.08.0) -### Other merged PRs +The repo2docker container image has moved to [quay.io/jupyterhub/repo2docker](https://quay.io/repository/jupyterhub/repo2docker?tab=tags) -- Update README quay.io URL, Add docker latest tag [#1075](https://github.com/jupyterhub/repo2docker/pull/1075) ([@manics](https://github.com/manics)) -- GitHub workflow build and push to Docker hub [#1071](https://github.com/jupyterhub/repo2docker/pull/1071) ([@manics](https://github.com/manics)) -- Bump environment [#1069](https://github.com/jupyterhub/repo2docker/pull/1069) ([@manics](https://github.com/manics)) -- Rename master branch to main [#1068](https://github.com/jupyterhub/repo2docker/pull/1068) ([@manics](https://github.com/manics)) -- Workaround docker-py dependency's failure to import six [#1066](https://github.com/jupyterhub/repo2docker/pull/1066) ([@consideRatio](https://github.com/consideRatio)) -- Remove Pipfile & Pipfile.lock [#1054](https://github.com/jupyterhub/repo2docker/pull/1054) ([@yuvipanda](https://github.com/yuvipanda)) -- Remove CircleCI docs build [#1053](https://github.com/jupyterhub/repo2docker/pull/1053) ([@yuvipanda](https://github.com/yuvipanda)) -- Pin doc requirements to avoid CI breakages [#1052](https://github.com/jupyterhub/repo2docker/pull/1052) ([@manics](https://github.com/manics)) -- Stop using deprecated add_stylesheet in sphinx [#1050](https://github.com/jupyterhub/repo2docker/pull/1050) ([@yuvipanda](https://github.com/yuvipanda)) -- Add study participation notice to readme [#1046](https://github.com/jupyterhub/repo2docker/pull/1046) ([@sgibson91](https://github.com/sgibson91)) -- Bump urllib3 from 1.26.4 to 1.26.5 [#1045](https://github.com/jupyterhub/repo2docker/pull/1045) ([@dependabot](https://github.com/dependabot)) -- always unpack a single zenodo zip [#1043](https://github.com/jupyterhub/repo2docker/pull/1043) ([@akhmerov](https://github.com/akhmerov)) -- State newly used installation command [#1040](https://github.com/jupyterhub/repo2docker/pull/1040) ([@fkohrt](https://github.com/fkohrt)) -- Fix regression in hydroshare introduced after moving to requests [#1034](https://github.com/jupyterhub/repo2docker/pull/1034) ([@MridulS](https://github.com/MridulS)) -- Bump pyyaml from 5.1.1 to 5.4 [#1029](https://github.com/jupyterhub/repo2docker/pull/1029) ([@dependabot](https://github.com/dependabot)) -- Set default Julia version to 1.6 [#1028](https://github.com/jupyterhub/repo2docker/pull/1028) ([@tomyun](https://github.com/tomyun)) -- Fix logo URL in README [#1027](https://github.com/jupyterhub/repo2docker/pull/1027) ([@betatim](https://github.com/betatim)) -- Refine buffered output debugging [#1016](https://github.com/jupyterhub/repo2docker/pull/1016) ([@minrk](https://github.com/minrk)) -- reimplement entrypoint in Python [#1014](https://github.com/jupyterhub/repo2docker/pull/1014) ([@minrk](https://github.com/minrk)) -- [MRG] Define an interface for Container engines [#848](https://github.com/jupyterhub/repo2docker/pull/848) ([@manics](https://github.com/manics)) - -### Contributors to this release - -([GitHub contributors page for this release](https://github.com/jupyterhub/repo2docker/graphs/contributors?from=2021-03-12&to=2021-08-24&type=c)) - -[@akhmerov](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aakhmerov+updated%3A2021-03-12..2021-08-24&type=Issues) | [@aplamada](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aaplamada+updated%3A2021-03-12..2021-08-24&type=Issues) | [@betatim](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abetatim+updated%3A2021-03-12..2021-08-24&type=Issues) | [@choldgraf](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acholdgraf+updated%3A2021-03-12..2021-08-24&type=Issues) | [@civodul](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acivodul+updated%3A2021-03-12..2021-08-24&type=Issues) | [@consideRatio](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AconsideRatio+updated%3A2021-03-12..2021-08-24&type=Issues) | 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[@meeseeksmachine](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ameeseeksmachine+updated%3A2021-03-12..2021-08-24&type=Issues) | [@minrk](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aminrk+updated%3A2021-03-12..2021-08-24&type=Issues) | [@MridulS](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AMridulS+updated%3A2021-03-12..2021-08-24&type=Issues) | [@ocefpaf](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aocefpaf+updated%3A2021-03-12..2021-08-24&type=Issues) | [@paugier](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Apaugier+updated%3A2021-03-12..2021-08-24&type=Issues) | [@rnestler](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Arnestler+updated%3A2021-03-12..2021-08-24&type=Issues) | [@sgibson91](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Asgibson91+updated%3A2021-03-12..2021-08-24&type=Issues) | [@SylvainCorlay](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3ASylvainCorlay+updated%3A2021-03-12..2021-08-24&type=Issues) | [@tomyun](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Atomyun+updated%3A2021-03-12..2021-08-24&type=Issues) | [@welcome](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awelcome+updated%3A2021-03-12..2021-08-24&type=Issues) | [@willingc](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awillingc+updated%3A2021-03-12..2021-08-24&type=Issues) | [@xhochy](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Axhochy+updated%3A2021-03-12..2021-08-24&type=Issues) | [@yuvipanda](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayuvipanda+updated%3A2021-03-12..2021-08-24&type=Issues) - -## 2021.03.0 - -([full changelog](https://github.com/jupyterhub/repo2docker/compare/40f475f...71eb805)) - -### Merged PRs - -- [MRG] Cleanup install_requires including duplicates [#1020](https://github.com/jupyterhub/repo2docker/pull/1020) ([@manics](https://github.com/manics)) -- buildpacks.r: dont use apt-key directly to respect \*\_proxy env vars [#1019](https://github.com/jupyterhub/repo2docker/pull/1019) ([@g-braeunlich](https://github.com/g-braeunlich)) -- freeze with mamba, add 3.9 [#1017](https://github.com/jupyterhub/repo2docker/pull/1017) ([@minrk](https://github.com/minrk)) -- bump python in circleci test [#1013](https://github.com/jupyterhub/repo2docker/pull/1013) ([@minrk](https://github.com/minrk)) -- fix dataverse regression introduced in last release [#1011](https://github.com/jupyterhub/repo2docker/pull/1011) ([@MridulS](https://github.com/MridulS)) -- Add GH workflow to push releases to PYPi and introduce CalVer [#1004](https://github.com/jupyterhub/repo2docker/pull/1004) ([@betatim](https://github.com/betatim)) -- Add entrypoint script which automatically propagates \*\_PROXY env vars… [#1003](https://github.com/jupyterhub/repo2docker/pull/1003) ([@g-braeunlich](https://github.com/g-braeunlich)) -- Update to JupyterLab 3.0 [#996](https://github.com/jupyterhub/repo2docker/pull/996) ([@jtpio](https://github.com/jtpio)) -- Add a contentprovider for Software Heritage persistent ID (SWHID) [#988](https://github.com/jupyterhub/repo2docker/pull/988) ([@douardda](https://github.com/douardda)) -- [MRG] Stream jupyter server logs to a file [#987](https://github.com/jupyterhub/repo2docker/pull/987) ([@betatim](https://github.com/betatim)) -- [MRG] Experiment with different install mechanism to get code coverage stats again [#982](https://github.com/jupyterhub/repo2docker/pull/982) ([@betatim](https://github.com/betatim)) -- add 4.0, 4.0.2 to list of supported R versions [#960](https://github.com/jupyterhub/repo2docker/pull/960) ([@minrk](https://github.com/minrk)) - -### Contributors to this release - -([GitHub contributors page for this release](https://github.com/jupyterhub/repo2docker/graphs/contributors?from=2021-01-23&to=2021-03-12&type=c)) - -[@betatim](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abetatim+updated%3A2021-01-23..2021-03-12&type=Issues) | [@choldgraf](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acholdgraf+updated%3A2021-01-23..2021-03-12&type=Issues) | [@ctr26](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Actr26+updated%3A2021-01-23..2021-03-12&type=Issues) | [@douardda](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Adouardda+updated%3A2021-01-23..2021-03-12&type=Issues) | [@g-braeunlich](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ag-braeunlich+updated%3A2021-01-23..2021-03-12&type=Issues) | [@jabbera](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajabbera+updated%3A2021-01-23..2021-03-12&type=Issues) | 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[@welcome](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awelcome+updated%3A2021-01-23..2021-03-12&type=Issues) | [@yuvipanda](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayuvipanda+updated%3A2021-01-23..2021-03-12&type=Issues) - -## 2021.01.0 - -([full changelog](https://github.com/jupyterhub/repo2docker/compare/2e477dd...40f475f)) - -### Merged PRs - -- MRG: Fix figshare test [#1001](https://github.com/jupyterhub/repo2docker/pull/1001) ([@manics](https://github.com/manics)) -- [MRG] Weekly test of master to check for external failures [#998](https://github.com/jupyterhub/repo2docker/pull/998) ([@manics](https://github.com/manics)) -- Replace urllib by requests in contentproviders [#993](https://github.com/jupyterhub/repo2docker/pull/993) ([@douardda](https://github.com/douardda)) -- Use mambaforge instead of miniforge [#992](https://github.com/jupyterhub/repo2docker/pull/992) ([@SylvainCorlay](https://github.com/SylvainCorlay)) -- buildpacks/nix: 2.3 -> 2.3.9 [#991](https://github.com/jupyterhub/repo2docker/pull/991) ([@FRidh](https://github.com/FRidh)) -- buildpacks/nix: disable sandboxing (bugfix) [#990](https://github.com/jupyterhub/repo2docker/pull/990) ([@FRidh](https://github.com/FRidh)) -- Add Julia 1.5.3 support [#984](https://github.com/jupyterhub/repo2docker/pull/984) ([@tomyun](https://github.com/tomyun)) -- [MRG] Update to node 14 [#983](https://github.com/jupyterhub/repo2docker/pull/983) ([@jtpio](https://github.com/jtpio)) -- Mamba 0.6.1 [#979](https://github.com/jupyterhub/repo2docker/pull/979) ([@minrk](https://github.com/minrk)) -- [MRG] Remove reference to `master` branch from CLI doc [#977](https://github.com/jupyterhub/repo2docker/pull/977) ([@betatim](https://github.com/betatim)) -- [MRG] Ensure REPO_DIR owned by NB_USER [#975](https://github.com/jupyterhub/repo2docker/pull/975) ([@tomyun](https://github.com/tomyun)) -- add chown to COPY commands to reduce layer count [#969](https://github.com/jupyterhub/repo2docker/pull/969) ([@bollwyvl](https://github.com/bollwyvl)) -- MRG: set TIMEFORMAT for timed bash conda commands [#966](https://github.com/jupyterhub/repo2docker/pull/966) ([@manics](https://github.com/manics)) -- MRG: Disable jupyterlab extension build minimize [#963](https://github.com/jupyterhub/repo2docker/pull/963) ([@manics](https://github.com/manics)) -- Bump Black version to 20.8b1 and use --target-version=py36 [#955](https://github.com/jupyterhub/repo2docker/pull/955) ([@paugier](https://github.com/paugier)) -- MRG: Add workflow to build Docker image [#954](https://github.com/jupyterhub/repo2docker/pull/954) ([@manics](https://github.com/manics)) -- [MRG] Crosslink 'Configuring your repository' with usage [#952](https://github.com/jupyterhub/repo2docker/pull/952) ([@manics](https://github.com/manics)) -- [MRG] Bump Python requirement to 3.6 from 3.5 [#951](https://github.com/jupyterhub/repo2docker/pull/951) 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installs python x.y (& concise rewording) [#914](https://github.com/jupyterhub/repo2docker/pull/914) ([@mdeff](https://github.com/mdeff)) -- doc: environment.yml installs a conda env, not only python [#913](https://github.com/jupyterhub/repo2docker/pull/913) ([@mdeff](https://github.com/mdeff)) -- [MRG] Add gitpod.io config for docs [#908](https://github.com/jupyterhub/repo2docker/pull/908) ([@betatim](https://github.com/betatim)) -- [MRG] - fix repo2docker logo in Sphinx docs [#906](https://github.com/jupyterhub/repo2docker/pull/906) ([@trallard](https://github.com/trallard)) -- [MRG] Add nbresuse==0.3.3 (full freeze.py) [#904](https://github.com/jupyterhub/repo2docker/pull/904) ([@manics](https://github.com/manics)) -- Add missing “:” for R code [#900](https://github.com/jupyterhub/repo2docker/pull/900) ([@adamhsparks](https://github.com/adamhsparks)) -- Add Julia 1.4.2 support [#899](https://github.com/jupyterhub/repo2docker/pull/899) ([@davidanthoff](https://github.com/davidanthoff)) -- Update Dockerfile to add Docker [#896](https://github.com/jupyterhub/repo2docker/pull/896) ([@hamelsmu](https://github.com/hamelsmu)) -- [MRG] Fix RShiny proxy [#893](https://github.com/jupyterhub/repo2docker/pull/893) ([@betatim](https://github.com/betatim)) -- [MRG] Bump version of irkernel for R 4.0 [#892](https://github.com/jupyterhub/repo2docker/pull/892) ([@betatim](https://github.com/betatim)) -- [MRG] chmod start script from repo2docker-entrypoint [#886](https://github.com/jupyterhub/repo2docker/pull/886) ([@danlester](https://github.com/danlester)) -- [MRG] Workaround Docker issue impacting some tests on macOS [#882](https://github.com/jupyterhub/repo2docker/pull/882) ([@hwine](https://github.com/hwine)) -- [MRG] pypi jupyter-offlinenotebook==0.1.0 [#880](https://github.com/jupyterhub/repo2docker/pull/880) ([@manics](https://github.com/manics)) -- Work around a Julia bug 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[#862](https://github.com/jupyterhub/repo2docker/pull/862) ([@jtpio](https://github.com/jtpio)) -- Use miniforge instead of miniconda to get conda [#859](https://github.com/jupyterhub/repo2docker/pull/859) ([@yuvipanda](https://github.com/yuvipanda)) -- [MRG] If looking for latest MRAN URL try earlier snapshots too [#851](https://github.com/jupyterhub/repo2docker/pull/851) ([@manics](https://github.com/manics)) -- [MRG] Update black 19.10b0, target Python 3.5 [#849](https://github.com/jupyterhub/repo2docker/pull/849) ([@manics](https://github.com/manics)) -- [MRG] Add jupyter-offlinenotebook extension [#845](https://github.com/jupyterhub/repo2docker/pull/845) ([@betatim](https://github.com/betatim)) -- docs: postBuild warn about shell script errors being ignored [#844](https://github.com/jupyterhub/repo2docker/pull/844) ([@manics](https://github.com/manics)) -- [MRG] Update changelog for 0.11.0 [#842](https://github.com/jupyterhub/repo2docker/pull/842) ([@betatim](https://github.com/betatim)) - -### Contributors to this release - -([GitHub contributors page for this release](https://github.com/jupyterhub/repo2docker/graphs/contributors?from=2020-02-05&to=2021-01-23&type=c)) - -[@adamhsparks](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aadamhsparks+updated%3A2020-02-05..2021-01-23&type=Issues) | [@AliMirlou](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AAliMirlou+updated%3A2020-02-05..2021-01-23&type=Issues) | [@betatim](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abetatim+updated%3A2020-02-05..2021-01-23&type=Issues) | [@bitnik](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abitnik+updated%3A2020-02-05..2021-01-23&type=Issues) | [@blink1073](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ablink1073+updated%3A2020-02-05..2021-01-23&type=Issues) | 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[@welcome](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awelcome+updated%3A2020-02-05..2021-01-23&type=Issues) | [@westurner](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awesturner+updated%3A2020-02-05..2021-01-23&type=Issues) | [@willingc](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awillingc+updated%3A2020-02-05..2021-01-23&type=Issues) | [@xhochy](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Axhochy+updated%3A2020-02-05..2021-01-23&type=Issues) | [@yuvipanda](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayuvipanda+updated%3A2020-02-05..2021-01-23&type=Issues) - -## 0.11.0 - -([full changelog](https://github.com/jupyterhub/repo2docker/compare/69c09ae...2e477dd)) - -### Enhancements made - -- [MRG] Allow absolute paths in build_script_files [#681](https://github.com/jupyterhub/repo2docker/pull/681) ([@Xarthisius](https://github.com/Xarthisius)) - -### Maintenance and upkeep improvements - -- adduser: useradd --no-log-init to reduce lastlog size [#804](https://github.com/jupyterhub/repo2docker/pull/804) ([@manics](https://github.com/manics)) -- [MRG] Bumped conda version to 4.7.12 [#802](https://github.com/jupyterhub/repo2docker/pull/802) ([@davidrpugh](https://github.com/davidrpugh)) -- Use port 80 to download GPG keys to avoid firewall problems [#797](https://github.com/jupyterhub/repo2docker/pull/797) ([@betatim](https://github.com/betatim)) -- [MRG] Update nteract-on-jupyter to 2.1.3 [#794](https://github.com/jupyterhub/repo2docker/pull/794) ([@betatim](https://github.com/betatim)) -- use getpass.getuser instead of os.getlogin [#789](https://github.com/jupyterhub/repo2docker/pull/789) ([@minrk](https://github.com/minrk)) -- Add baseline infra for Azure Pipelines [#787](https://github.com/jupyterhub/repo2docker/pull/787) ([@willingc](https://github.com/willingc)) -- [MRG] Restore the hooks directory when building the docker image [#786](https://github.com/jupyterhub/repo2docker/pull/786) ([@betatim](https://github.com/betatim)) -- Add script to compare Dockerfiles generated by current and older… [#785](https://github.com/jupyterhub/repo2docker/pull/785) ([@nuest](https://github.com/nuest)) -- Print Dockerfile to stdout when --no-build [#784](https://github.com/jupyterhub/repo2docker/pull/784) ([@minrk](https://github.com/minrk)) -- add hooks to dockerignore [#782](https://github.com/jupyterhub/repo2docker/pull/782) ([@minrk](https://github.com/minrk)) -- add explicit log message on failing Docker connection [#779](https://github.com/jupyterhub/repo2docker/pull/779) ([@nuest](https://github.com/nuest)) -- [WIP] Upgrade IRKernel version to 1.0.2 [#770](https://github.com/jupyterhub/repo2docker/pull/770) ([@GeorgianaElena](https://github.com/GeorgianaElena)) -- Bump Miniconda from 4.6.14 to 4.7.10 [#769](https://github.com/jupyterhub/repo2docker/pull/769) ([@davidrpugh](https://github.com/davidrpugh)) -- Add support for Julia 1.2.0 [#768](https://github.com/jupyterhub/repo2docker/pull/768) ([@davidanthoff](https://github.com/davidanthoff)) -- include full docker progress events in push progress events [#727](https://github.com/jupyterhub/repo2docker/pull/727) ([@minrk](https://github.com/minrk)) +### New features -### Documentation improvements +- always unpack a single zenodo zip {pr}`1043` by {user}`akhmerov` +- Refreeze with conda-lock {pr}`1024` by {user}`minrk` +- Refine buffered output debugging {pr}`1016` by {user}`minrk` +- reimplement entrypoint in Python {pr}`1014` by {user}`minrk` +- Fetch available Julia versions from hosted json {pr}`994` by {user}`tomyun` +- Define an interface for Container engines {pr}`848` by {user}`manics` + +### API changes -- [MRG] Add docs for Figshare and Dataverse; update Dataverse installations file formatting [#796](https://github.com/jupyterhub/repo2docker/pull/796) ([@nuest](https://github.com/nuest)) -- Provide help text for commandline arguments [#517](https://github.com/jupyterhub/repo2docker/pull/517) ([@yuvipanda](https://github.com/yuvipanda)) +### Bug fixes + +- Workaround docker-py dependency's failure to import six {pr}`1066:` by {user}`consideratio` +- fix: add chardet, a not explicitly declared dependency {pr}`1064` by {user}`johnhoman` +- Add build-base to build stage of docker image {pr}`1051` by {user}`yuvipanda` +- Fix regression in hydroshare introduced after moving to requests {pr}`1034` by {user}`MridulS` ### Other merged PRs -- [MRG] Update changelog for 0.11.0 [#842](https://github.com/jupyterhub/repo2docker/pull/842) ([@betatim](https://github.com/betatim)) -- Merge pull request #840 from minrk/py38 [#840](https://github.com/jupyterhub/repo2docker/pull/840) ([@minrk](https://github.com/minrk)) -- [MRG] update base environment [#839](https://github.com/jupyterhub/repo2docker/pull/839) ([@minrk](https://github.com/minrk)) -- Start RStudio if R is installed via conda [#838](https://github.com/jupyterhub/repo2docker/pull/838) ([@xhochy](https://github.com/xhochy)) -- Merge pull request #834 from GeorgianaElena/new_badge [#834](https://github.com/jupyterhub/repo2docker/pull/834) ([@GeorgianaElena](https://github.com/GeorgianaElena)) -- Add support for Julia 1.3.1 [#831](https://github.com/jupyterhub/repo2docker/pull/831) ([@davidanthoff](https://github.com/davidanthoff)) -- [WIP] r build-pack: when using ppa install r-recommended [#830](https://github.com/jupyterhub/repo2docker/pull/830) ([@manics](https://github.com/manics)) -- [MRG] Deprecate legacy buildpack [#829](https://github.com/jupyterhub/repo2docker/pull/829) ([@betatim](https://github.com/betatim)) -- [MRG] Fix a broken link, update favicon [#826](https://github.com/jupyterhub/repo2docker/pull/826) ([@betatim](https://github.com/betatim)) -- adding instructions for contentprovider extension [#824](https://github.com/jupyterhub/repo2docker/pull/824) ([@choldgraf](https://github.com/choldgraf)) -- Add support for Julia 1.0.5 and 1.3.0 [#822](https://github.com/jupyterhub/repo2docker/pull/822) ([@davidanthoff](https://github.com/davidanthoff)) -- updating theme to pandas sphinx [#816](https://github.com/jupyterhub/repo2docker/pull/816) ([@choldgraf](https://github.com/choldgraf)) -- [MRG] Fixes link rendering [#811](https://github.com/jupyterhub/repo2docker/pull/811) ([@arokem](https://github.com/arokem)) -- [MRG] Remove explicit checkout when ref given [#810](https://github.com/jupyterhub/repo2docker/pull/810) ([@betatim](https://github.com/betatim)) -- [MRG] Fix submodule check out [#809](https://github.com/jupyterhub/repo2docker/pull/809) ([@davidbrochart](https://github.com/davidbrochart)) -- [MRG] add Hydroshare as a content provider [#800](https://github.com/jupyterhub/repo2docker/pull/800) ([@sblack-usu](https://github.com/sblack-usu)) -- [MRG] Add support for installing different versions of R [#772](https://github.com/jupyterhub/repo2docker/pull/772) ([@betatim](https://github.com/betatim)) -- Handle different file encodings [#771](https://github.com/jupyterhub/repo2docker/pull/771) ([@GeorgianaElena](https://github.com/GeorgianaElena)) -- Tiny typo in docs/source/index.rst [#760](https://github.com/jupyterhub/repo2docker/pull/760) ([@AartGoossens](https://github.com/AartGoossens)) -- [MRG] Dataverse content provider [#739](https://github.com/jupyterhub/repo2docker/pull/739) ([@Xarthisius](https://github.com/Xarthisius)) +- Update README quay.io URL, Add docker latest tag {pr}`1075` by {user}`manics` +- GitHub workflow build and push to Docker hub {pr}`1071` by {user}`manics` +- Rename master branch to main {pr}`1068` by {user}`manics` +- Remove Pipfile & Pipfile.lock {pr}`1054` by {user}`yuvipanda` +- Remove CircleCI docs build {pr}`1053` by {user}`yuvipanda` +- Pin doc requirements to avoid CI breakages {pr}`1052` by {user}`manics` +- Stop using deprecated add_stylesheet in sphinx {pr}`1050` by {user}`yuvipanda` +- Add study participation notice to readme {pr}`1046` by {user}`sgibson91` +- Bump urllib3 from 1.26.4 to 1.26.5 {pr}`1045` by {user}`dependabot` +- State newly used installation command {pr}`1040` by {user}`fkohrt` +- Bump pyyaml from 5.1.1 to 5.4 {pr}`1029` by {user}`dependabot` +- Set default Julia version to 1.6 {pr}`1028` by {user}`tomyun` +- Fix logo URL in README {pr}`1027` by {user}`betatim` -### Contributors to this release +## Version 2021.03.0 -([GitHub contributors page for this release](https://github.com/jupyterhub/repo2docker/graphs/contributors?from=2019-08-07&to=2020-02-05&type=c)) +[Full changelog](https://github.com/jupyterhub/repo2docker/compare/2021.01.0...2021.03.0) -[@AartGoossens](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AAartGoossens+updated%3A2019-08-07..2020-02-05&type=Issues) | 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[@trallard](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Atrallard+updated%3A2019-08-07..2020-02-05&type=Issues) | [@travigd](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Atravigd+updated%3A2019-08-07..2020-02-05&type=Issues) | [@willingc](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awillingc+updated%3A2019-08-07..2020-02-05&type=Issues) | [@Xarthisius](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AXarthisius+updated%3A2019-08-07..2020-02-05&type=Issues) | [@xhochy](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Axhochy+updated%3A2019-08-07..2020-02-05&type=Issues) | [@yuvipanda](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayuvipanda+updated%3A2019-08-07..2020-02-05&type=Issues) +### New features -## 0.10.0 +- freeze with mamba, add 3.9 {pr}`1017` by {user}`minrk` +- Add GH workflow to push releases to PYPi and introduce CalVer {pr}`1004` by {user}`betatim` +- Add entrypoint script which automatically propagates \*\_PROXY env vars… {pr}`1003` (\[@g-braeunlich\]()) +- Update to JupyterLab 3.0 {pr}`996` by {user}`jtpio` +- Fetch available Julia versions from hosted json {pr}`994` by {user}`tomyun` +- Add a contentprovider for Software Heritage persistent ID (SWHID) {pr}`988` by {user}`douardda` +- Stream jupyter server logs to a file {pr}`987` by {user}`betatim` +- add 4.0, 4.0.2 to list of supported R versions {pr}`960` by {user}`minrk` -([full changelog](https://github.com/jupyterhub/repo2docker/compare/734664a...69c09ae)) +### API changes -### Enhancements made +### Bug fixes -- [MRG/REVIEW] Support Pipfile / Pipfile.lock with pipenv [#649](https://github.com/jupyterhub/repo2docker/pull/649) ([@consideRatio](https://github.com/consideRatio)) +- fix dataverse regression introduced in last release {pr}`1011` by {user}`MridulS` +- buildpacks.r: dont use apt-key directly to respect \*\_proxy env vars {pr}`1019` (\[@g-braeunlich\]()) -### Maintenance and upkeep improvements +### Other merged PRs -- [MRG] Rewrite tests in test_semver.py #615 [#757](https://github.com/jupyterhub/repo2docker/pull/757) ([@Geektrovert](https://github.com/Geektrovert)) -- [MRG] switch pip packages to conda-forge in conda buildpack [#728](https://github.com/jupyterhub/repo2docker/pull/728) ([@scottyhq](https://github.com/scottyhq)) +- Cleanup install_requires including duplicates {pr}`1020` by {user}`manics` +- bump docker action version {pr}`1018` by {user}`minrk` +- bump python in circleci test {pr}`1013` by {user}`minrk` +- Investigating the missing logs {pr}`1008` by {user}`betatim` +- Experiment with different install mechanism to get code coverage stats again {pr}`982` by {user}`betatim` + +## Version 2021.01.0 + +[Full changelog](https://github.com/jupyterhub/repo2docker/compare/0.11.0...2021.01.0) + +### New features + +- Replace urllib by requests in contentproviders {pr}`993` by {user}`douardda` +- Use mambaforge instead of miniforge {pr}`992` by {user}`SylvainCorlay` +- buildpacks/nix: 2.3 -> 2.3.9 {pr}`991` by {user}`FRidh` +- Drop support for stencila {pr}`985` by {user}`minrk` +- Add Julia 1.5.3 support {pr}`984` by {user}`tomyun` +- Update to node 14 {pr}`983` by {user}`jtpio` +- Mamba 0.6.1 {pr}`979` by {user}`minrk` +- Ensure REPO_DIR owned by NB_USER {pr}`975` by {user}`tomyun` +- Add Julia 1.5.2 support {pr}`965` by {user}`tomyun` +- Mamba number three {pr}`962` by {user}`SylvainCorlay` +- Add a Mercurial contentprovider {pr}`950` by {user}`paugier` +- Add Julia 1.5.1 support {pr}`949` by {user}`tomyun` +- Handle requirements.txt with `--pre` lines {pr}`943` by {user}`betatim` +- Add Julia 1.5.0 support {pr}`938` by {user}`tomyun` +- Update JupyterLab to 2.2.0 {pr}`933` by {user}`manics` +- Bump nix version to 2.3 {pr}`915` by {user}`jboynyc` +- Add nbresuse==0.3.3 (full freeze.py) {pr}`904` by {user}`manics` +- Add Julia 1.4.2 support {pr}`899` by {user}`davidanthoff` +- Bump version of irkernel for R 4.0 {pr}`892` by {user}`betatim` +- chmod start script from repo2docker-entrypoint {pr}`886` by {user}`danlester` +- pypi jupyter-offlinenotebook==0.1.0 {pr}`880` by {user}`manics` +- Add support for Julia 1.4.1 {pr}`878` by {user}`davidanthoff` +- Change --env option to work like docker's {pr}`874` by {user}`hwine` +- Add support for Julia 1.4.0 {pr}`870` by {user}`davidanthoff` +- Update server proxy and rsession proxy {pr}`869` by {user}`betatim` +- Use miniforge instead of miniconda to get conda {pr}`859` by {user}`yuvipanda` +- If looking for latest MRAN URL try earlier snapshots too {pr}`851` by {user}`manics` +- Add jupyter-offlinenotebook extension {pr}`845` by {user}`betatim` + +### API changes + +- Bump Python requirement to 3.6 from 3.5 {pr}`951` by {user}`betatim` + +### Bug fixes + +- buildpacks/nix: disable sandboxing (bugfix) {pr}`990` by {user}`FRidh` +- avoid deprecated import of collections.abc {pr}`924` by {user}`minrk` +- Add missing “:” for R code {pr}`900` by {user}`adamhsparks` +- Fix RShiny proxy {pr}`893` by {user}`betatim` +- Work around a Julia bug {pr}`879` by {user}`davidanthoff` +- Fix typo {pr}`862` by {user}`jtpio` ### Other merged PRs -- [MRG] Call parent preassemble scripts methods [#752](https://github.com/jupyterhub/repo2docker/pull/752) ([@betatim](https://github.com/betatim)) -- parse pipfiles to determine Python version [#748](https://github.com/jupyterhub/repo2docker/pull/748) ([@minrk](https://github.com/minrk)) -- typo in doi regexp [#746](https://github.com/jupyterhub/repo2docker/pull/746) ([@minrk](https://github.com/minrk)) -- refreeze 2019-07-16 [#745](https://github.com/jupyterhub/repo2docker/pull/745) ([@minrk](https://github.com/minrk)) -- [MRG] preassembly for conda/python [#743](https://github.com/jupyterhub/repo2docker/pull/743) ([@minrk](https://github.com/minrk)) -- [MRG] Adding bash to Dockerfile to fix git-credential-env [#738](https://github.com/jupyterhub/repo2docker/pull/738) ([@eexwhyzee](https://github.com/eexwhyzee)) -- bump xeus-cling in tests [#735](https://github.com/jupyterhub/repo2docker/pull/735) ([@minrk](https://github.com/minrk)) -- [MRG] Switch to binder-examples/requirements for our tests [#732](https://github.com/jupyterhub/repo2docker/pull/732) ([@betatim](https://github.com/betatim)) -- [MRG] Remove print statement and unused import [#730](https://github.com/jupyterhub/repo2docker/pull/730) ([@betatim](https://github.com/betatim)) -- [MRG] Handle root user case more gracefully. Fixes #696 [#723](https://github.com/jupyterhub/repo2docker/pull/723) ([@Xarthisius](https://github.com/Xarthisius)) -- Update target_repo_dir docstring [#721](https://github.com/jupyterhub/repo2docker/pull/721) ([@fmaussion](https://github.com/fmaussion)) -- [WIP] Version bump Conda from 4.6.14 to 4.7.5 [#719](https://github.com/jupyterhub/repo2docker/pull/719) ([@davidrpugh](https://github.com/davidrpugh)) -- [MRG] Install APT packages before copying the repo contents [#716](https://github.com/jupyterhub/repo2docker/pull/716) ([@betatim](https://github.com/betatim)) -- updated link for the community edition of docker [#715](https://github.com/jupyterhub/repo2docker/pull/715) ([@johnjarmitage](https://github.com/johnjarmitage)) -- Revert "[MRG] Remove more files during the image build to slimdown the image" [#712](https://github.com/jupyterhub/repo2docker/pull/712) ([@betatim](https://github.com/betatim)) -- Add support for julia 1.0.4 and 1.1.1 [#710](https://github.com/jupyterhub/repo2docker/pull/710) ([@davidanthoff](https://github.com/davidanthoff)) -- [MRG] Remove more files during the image build to slimdown the image [#709](https://github.com/jupyterhub/repo2docker/pull/709) ([@betatim](https://github.com/betatim)) -- base docker image on alpine [#705](https://github.com/jupyterhub/repo2docker/pull/705) ([@minrk](https://github.com/minrk)) -- [MRG] Generalize Zenodo content provider to support other Invenio repositories [#704](https://github.com/jupyterhub/repo2docker/pull/704) ([@tmorrell](https://github.com/tmorrell)) -- add `git-lfs` to dockerfile used for the repo2docker image [#703](https://github.com/jupyterhub/repo2docker/pull/703) ([@minrk](https://github.com/minrk)) -- [MRG] Add auto-formatting setup [#699](https://github.com/jupyterhub/repo2docker/pull/699) ([@betatim](https://github.com/betatim)) -- [MRG] Update verification of Node install [#695](https://github.com/jupyterhub/repo2docker/pull/695) ([@betatim](https://github.com/betatim)) -- [MRG] Zenodo content provider [#693](https://github.com/jupyterhub/repo2docker/pull/693) ([@betatim](https://github.com/betatim)) -- Adding contentprovider documentation [#692](https://github.com/jupyterhub/repo2docker/pull/692) ([@choldgraf](https://github.com/choldgraf)) -- set CONDA_DEFAULT_ENV [#690](https://github.com/jupyterhub/repo2docker/pull/690) ([@minrk](https://github.com/minrk)) -- Switch Travis CI to Ubuntu Xenial 16.04 [#689](https://github.com/jupyterhub/repo2docker/pull/689) ([@jrbourbeau](https://github.com/jrbourbeau)) -- [MRG] Drop support for Python 3.4 [#684](https://github.com/jupyterhub/repo2docker/pull/684) ([@betatim](https://github.com/betatim)) -- [MRG] Use getpass instead of pwd to fetch username [#683](https://github.com/jupyterhub/repo2docker/pull/683) ([@betatim](https://github.com/betatim)) -- Do not try to build the image with root as the primary user [#679](https://github.com/jupyterhub/repo2docker/pull/679) ([@Xarthisius](https://github.com/Xarthisius)) -- Revert "[MRG] Do not try to build the image with root as the primary user." [#678](https://github.com/jupyterhub/repo2docker/pull/678) ([@betatim](https://github.com/betatim)) -- [MRG] Update base image used for memory limit checks [#677](https://github.com/jupyterhub/repo2docker/pull/677) ([@betatim](https://github.com/betatim)) -- [MRG] Do not try to build the image with root as the primary user. [#676](https://github.com/jupyterhub/repo2docker/pull/676) ([@Xarthisius](https://github.com/Xarthisius)) -- bumping release date [#669](https://github.com/jupyterhub/repo2docker/pull/669) ([@choldgraf](https://github.com/choldgraf)) -- [MRG] release info updates [#668](https://github.com/jupyterhub/repo2docker/pull/668) ([@choldgraf](https://github.com/choldgraf)) -- [MRG] Remove the conda package cache as we can't hardlink to it [#666](https://github.com/jupyterhub/repo2docker/pull/666) ([@betatim](https://github.com/betatim)) - -### Contributors to this release - -([GitHub contributors page for this release](https://github.com/jupyterhub/repo2docker/graphs/contributors?from=2019-05-05&to=2019-08-07&type=c)) - -[@AliMirlou](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AAliMirlou+updated%3A2019-05-05..2019-08-07&type=Issues) | [@arnavs](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aarnavs+updated%3A2019-05-05..2019-08-07&type=Issues) | 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an absolute path [#657](https://github.com/jupyterhub/repo2docker/pull/657) ([@yuvipanda](https://github.com/yuvipanda)) -- [MRG] Update contributing guidelines and issue templates [#655](https://github.com/jupyterhub/repo2docker/pull/655) ([@KirstieJane](https://github.com/KirstieJane)) -- [MRG] Update issue templates [#654](https://github.com/jupyterhub/repo2docker/pull/654) ([@betatim](https://github.com/betatim)) -- Support .binder directory [#653](https://github.com/jupyterhub/repo2docker/pull/653) ([@jhamman](https://github.com/jhamman)) -- [MRG] Fix handling of memory limit command line argument [#652](https://github.com/jupyterhub/repo2docker/pull/652) ([@betatim](https://github.com/betatim)) -- [MRG] install notebook in its own env [#651](https://github.com/jupyterhub/repo2docker/pull/651) ([@minrk](https://github.com/minrk)) -- [MRG] Bump nteract-on-jupyter to 2.0.12 and notebook to 5.7.8 [#650](https://github.com/jupyterhub/repo2docker/pull/650) ([@betatim](https://github.com/betatim)) -- [MRG] Unpin pip again [#647](https://github.com/jupyterhub/repo2docker/pull/647) ([@betatim](https://github.com/betatim)) -- [MRG] Fix up the server proxy package to get websockets back [#646](https://github.com/jupyterhub/repo2docker/pull/646) ([@betatim](https://github.com/betatim)) -- mentioning s2i in faq [#642](https://github.com/jupyterhub/repo2docker/pull/642) ([@choldgraf](https://github.com/choldgraf)) -- [MRG] Update change log [#641](https://github.com/jupyterhub/repo2docker/pull/641) ([@betatim](https://github.com/betatim)) -- [MRG] Fix sphinx deprecation for recommonmark [#640](https://github.com/jupyterhub/repo2docker/pull/640) ([@betatim](https://github.com/betatim)) -- [MRG] Ensure git submodules are updated and initialized [#639](https://github.com/jupyterhub/repo2docker/pull/639) ([@djhoese](https://github.com/djhoese)) -- [MRG] Remove conda package directory [#638](https://github.com/jupyterhub/repo2docker/pull/638) 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[#614](https://github.com/jupyterhub/repo2docker/pull/614) ([@drmowinckels](https://github.com/drmowinckels)) -- [MRG] Add tests for Julia semver matching [#613](https://github.com/jupyterhub/repo2docker/pull/613) ([@betatim](https://github.com/betatim)) -- Use JULIA_PROJECT env variable to activate julia env [#612](https://github.com/jupyterhub/repo2docker/pull/612) ([@davidanthoff](https://github.com/davidanthoff)) -- [MRG] Add PR template with links to contrib docs and less focus on code contributions [#607](https://github.com/jupyterhub/repo2docker/pull/607) ([@betatim](https://github.com/betatim)) -- [MRG] Reopen change log [#606](https://github.com/jupyterhub/repo2docker/pull/606) ([@betatim](https://github.com/betatim)) -- [MRG] Add FAQ entry and Howto on exporting conda environments [#598](https://github.com/jupyterhub/repo2docker/pull/598) ([@betatim](https://github.com/betatim)) -- [MRG] Add tests for setting Python version during freeze [#592](https://github.com/jupyterhub/repo2docker/pull/592) ([@betatim](https://github.com/betatim)) -- Fix release date of 0.8.0 [#590](https://github.com/jupyterhub/repo2docker/pull/590) ([@betatim](https://github.com/betatim)) - -### Contributors to this release - -([GitHub contributors page for this release](https://github.com/jupyterhub/repo2docker/graphs/contributors?from=2019-02-21&to=2019-05-05&type=c)) - -[@alimanfoo](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aalimanfoo+updated%3A2019-02-21..2019-05-05&type=Issues) | [@betatim](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abetatim+updated%3A2019-02-21..2019-05-05&type=Issues) | [@captainsafia](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acaptainsafia+updated%3A2019-02-21..2019-05-05&type=Issues) | [@cboettig](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acboettig+updated%3A2019-02-21..2019-05-05&type=Issues) | 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[@LucianaMarques](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3ALucianaMarques+updated%3A2019-02-21..2019-05-05&type=Issues) | [@manics](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Amanics+updated%3A2019-02-21..2019-05-05&type=Issues) | [@meeseeksmachine](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ameeseeksmachine+updated%3A2019-02-21..2019-05-05&type=Issues) | [@minrk](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aminrk+updated%3A2019-02-21..2019-05-05&type=Issues) | [@NHDaly](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3ANHDaly+updated%3A2019-02-21..2019-05-05&type=Issues) | [@nuest](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Anuest+updated%3A2019-02-21..2019-05-05&type=Issues) | [@pat-s](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Apat-s+updated%3A2019-02-21..2019-05-05&type=Issues) | 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docs [#588](https://github.com/jupyterhub/repo2docker/pull/588) ([@betatim](https://github.com/betatim)) -- fix "Possible nested set" warning [#587](https://github.com/jupyterhub/repo2docker/pull/587) ([@minrk](https://github.com/minrk)) -- regen Pipfile.lock [#586](https://github.com/jupyterhub/repo2docker/pull/586) ([@minrk](https://github.com/minrk)) -- [MRG] Update documentation with more cross references [#585](https://github.com/jupyterhub/repo2docker/pull/585) ([@betatim](https://github.com/betatim)) -- install: one-liner to install most recent upstream code [#583](https://github.com/jupyterhub/repo2docker/pull/583) ([@haraldschilly](https://github.com/haraldschilly)) -- pin conda during Python-switch step [#576](https://github.com/jupyterhub/repo2docker/pull/576) ([@minrk](https://github.com/minrk)) -- Check if '--debug' is set properly [#575](https://github.com/jupyterhub/repo2docker/pull/575) ([@yuvipanda](https://github.com/yuvipanda)) -- npm installation [#573](https://github.com/jupyterhub/repo2docker/pull/573) ([@GladysNalvarte](https://github.com/GladysNalvarte)) -- missing quotes in GIT_CREDENTIAL_ENV [#572](https://github.com/jupyterhub/repo2docker/pull/572) ([@minrk](https://github.com/minrk)) -- Update conf.py [#569](https://github.com/jupyterhub/repo2docker/pull/569) ([@lheagy](https://github.com/lheagy)) -- updating interfaces page and adding jupyterlab workspaces page [#568](https://github.com/jupyterhub/repo2docker/pull/568) ([@choldgraf](https://github.com/choldgraf)) -- fix docker commit tag [#562](https://github.com/jupyterhub/repo2docker/pull/562) ([@minrk](https://github.com/minrk)) -- Set JULIA_DEPOT_PATH [#555](https://github.com/jupyterhub/repo2docker/pull/555) ([@yuvipanda](https://github.com/yuvipanda)) -- Updated log info for local content provider [#551](https://github.com/jupyterhub/repo2docker/pull/551) ([@GladysNalvarte](https://github.com/GladysNalvarte)) -- Fixes Travis build errors related to pytest and Sphinx [#547](https://github.com/jupyterhub/repo2docker/pull/547) ([@craig-willis](https://github.com/craig-willis)) -- Spurious comment in `Dockerfile` #543 [#544](https://github.com/jupyterhub/repo2docker/pull/544) ([@benjaminr](https://github.com/benjaminr)) -- Bump default python version to 3.7 [#539](https://github.com/jupyterhub/repo2docker/pull/539) ([@yuvipanda](https://github.com/yuvipanda)) -- Use a minimal hand-crafted Dockerfile for speed [#536](https://github.com/jupyterhub/repo2docker/pull/536) ([@betatim](https://github.com/betatim)) -- [MRG] Add tests for port mapping conversion [#534](https://github.com/jupyterhub/repo2docker/pull/534) ([@betatim](https://github.com/betatim)) -- adding a roadmap link to the root [#532](https://github.com/jupyterhub/repo2docker/pull/532) ([@choldgraf](https://github.com/choldgraf)) -- Minor howto doc fixes [#531](https://github.com/jupyterhub/repo2docker/pull/531) ([@jrbourbeau](https://github.com/jrbourbeau)) -- fix commit hash truncation on docker images [#530](https://github.com/jupyterhub/repo2docker/pull/530) ([@minrk](https://github.com/minrk)) -- Run docker builds on docker hub [#527](https://github.com/jupyterhub/repo2docker/pull/527) ([@minrk](https://github.com/minrk)) -- Add tag command snippet [#526](https://github.com/jupyterhub/repo2docker/pull/526) ([@minrk](https://github.com/minrk)) -- Remove f-strings [#520](https://github.com/jupyterhub/repo2docker/pull/520) ([@jrbourbeau](https://github.com/jrbourbeau)) -- refreeze with notebook 5.7.4 [#519](https://github.com/jupyterhub/repo2docker/pull/519) ([@minrk](https://github.com/minrk)) -- Update RTD to install repo2docker [#518](https://github.com/jupyterhub/repo2docker/pull/518) ([@jrbourbeau](https://github.com/jrbourbeau)) -- Fix cache-busting when running tests locally [#509](https://github.com/jupyterhub/repo2docker/pull/509) ([@yuvipanda](https://github.com/yuvipanda)) -- Copy repo to ${REPO_DIR} rather than ${HOME} [#507](https://github.com/jupyterhub/repo2docker/pull/507) ([@yuvipanda](https://github.com/yuvipanda)) -- Fix typos and syntax errors in the documentation [#505](https://github.com/jupyterhub/repo2docker/pull/505) ([@betatim](https://github.com/betatim)) -- fix push-tags condition [#501](https://github.com/jupyterhub/repo2docker/pull/501) ([@minrk](https://github.com/minrk)) -- Add repo2docker Dockerfile labels [#500](https://github.com/jupyterhub/repo2docker/pull/500) ([@jrbourbeau](https://github.com/jrbourbeau)) -- push tagged images on travis [#499](https://github.com/jupyterhub/repo2docker/pull/499) ([@minrk](https://github.com/minrk)) -- Update changelog in preparation for releasing v0.7.0 [#498](https://github.com/jupyterhub/repo2docker/pull/498) ([@betatim](https://github.com/betatim)) -- Make repo2docker easier to use as a library - Part 1 [#496](https://github.com/jupyterhub/repo2docker/pull/496) ([@yuvipanda](https://github.com/yuvipanda)) -- Make apt-get install be quiet [#483](https://github.com/jupyterhub/repo2docker/pull/483) ([@yuvipanda](https://github.com/yuvipanda)) - -### Contributors to this release - -([GitHub contributors page for this release](https://github.com/jupyterhub/repo2docker/graphs/contributors?from=2018-12-12&to=2019-02-21&type=c)) - -[@alimanfoo](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aalimanfoo+updated%3A2018-12-12..2019-02-21&type=Issues) | [@annakrystalli](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aannakrystalli+updated%3A2018-12-12..2019-02-21&type=Issues) | [@benjaminr](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abenjaminr+updated%3A2018-12-12..2019-02-21&type=Issues) | [@betatim](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abetatim+updated%3A2018-12-12..2019-02-21&type=Issues) | 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[@VladimirVisnovsky](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AVladimirVisnovsky+updated%3A2018-12-12..2019-02-21&type=Issues) | [@WillKoehrsen](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AWillKoehrsen+updated%3A2018-12-12..2019-02-21&type=Issues) | [@yuvipanda](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayuvipanda+updated%3A2018-12-12..2019-02-21&type=Issues) - -## 0.7.0 - -([full changelog](https://github.com/jupyterhub/repo2docker/compare/1b8e16a...72d7634)) - -### Merged PRs - -- Update changelog in preparation for releasing v0.7.0 [#498](https://github.com/jupyterhub/repo2docker/pull/498) ([@betatim](https://github.com/betatim)) -- Remove duplicate codecov config [#495](https://github.com/jupyterhub/repo2docker/pull/495) ([@betatim](https://github.com/betatim)) -- Bump nbrsessionproxy version [#493](https://github.com/jupyterhub/repo2docker/pull/493) ([@yuvipanda](https://github.com/yuvipanda)) -- Add codecov configuration [#492](https://github.com/jupyterhub/repo2docker/pull/492) ([@betatim](https://github.com/betatim)) -- Update the roadmap [#491](https://github.com/jupyterhub/repo2docker/pull/491) ([@betatim](https://github.com/betatim)) -- Log a 'success' message when push is complete [#482](https://github.com/jupyterhub/repo2docker/pull/482) ([@yuvipanda](https://github.com/yuvipanda)) -- Revert "[MRG] Start reusing existing docker images if content hasn't changed" [#481](https://github.com/jupyterhub/repo2docker/pull/481) ([@yuvipanda](https://github.com/yuvipanda)) -- Make apt be quieter [#479](https://github.com/jupyterhub/repo2docker/pull/479) ([@yuvipanda](https://github.com/yuvipanda)) -- Allow specifying images to reuse cache from [#478](https://github.com/jupyterhub/repo2docker/pull/478) ([@yuvipanda](https://github.com/yuvipanda)) -- removing note that env.yml is needed for julia [#477](https://github.com/jupyterhub/repo2docker/pull/477) ([@choldgraf](https://github.com/choldgraf)) -- [MRG] Tweak docstring to make it more understandable [#474](https://github.com/jupyterhub/repo2docker/pull/474) ([@betatim](https://github.com/betatim)) -- Ensure Python3 before reading README with encoding arg [#472](https://github.com/jupyterhub/repo2docker/pull/472) ([@nokome](https://github.com/nokome)) -- Add space between logo and title in README [#468](https://github.com/jupyterhub/repo2docker/pull/468) ([@willingc](https://github.com/willingc)) -- Add jupyterhub to base environment [#467](https://github.com/jupyterhub/repo2docker/pull/467) ([@yuvipanda](https://github.com/yuvipanda)) -- [MRG] Add a first roadmap [#465](https://github.com/jupyterhub/repo2docker/pull/465) ([@betatim](https://github.com/betatim)) -- Update CHANGES.rst [#464](https://github.com/jupyterhub/repo2docker/pull/464) ([@betatim](https://github.com/betatim)) -- [MRG] Add and use new logo [#463](https://github.com/jupyterhub/repo2docker/pull/463) ([@betatim](https://github.com/betatim)) -- [MRG] Start reusing existing docker images if content hasn't changed [#461](https://github.com/jupyterhub/repo2docker/pull/461) ([@betatim](https://github.com/betatim)) -- Updates for Stencila [#457](https://github.com/jupyterhub/repo2docker/pull/457) ([@nuest](https://github.com/nuest)) -- Update changelog [#454](https://github.com/jupyterhub/repo2docker/pull/454) ([@betatim](https://github.com/betatim)) -- adding back sidebars [#451](https://github.com/jupyterhub/repo2docker/pull/451) ([@choldgraf](https://github.com/choldgraf)) -- [MRG] Switch to BaseImage for nix build pack [#448](https://github.com/jupyterhub/repo2docker/pull/448) ([@betatim](https://github.com/betatim)) -- [MRG] Pipfile for repo2Docker [#447](https://github.com/jupyterhub/repo2docker/pull/447) ([@trallard](https://github.com/trallard)) -- adding circleci preview and jupyterhub docs theme [#446](https://github.com/jupyterhub/repo2docker/pull/446) ([@choldgraf](https://github.com/choldgraf)) -- [MRG] Change back into main repository directory [#436](https://github.com/jupyterhub/repo2docker/pull/436) ([@betatim](https://github.com/betatim)) -- PEP8 styling [#435](https://github.com/jupyterhub/repo2docker/pull/435) ([@betatim](https://github.com/betatim)) -- [MRG] Switch to right sub-directory for coverage reports [#432](https://github.com/jupyterhub/repo2docker/pull/432) ([@betatim](https://github.com/betatim)) -- Add pip install doc-requirements.txt to setup of virtual environment instructions [#431](https://github.com/jupyterhub/repo2docker/pull/431) ([@matthewfeickert](https://github.com/matthewfeickert)) -- [MRG] Only check beginning of name of Python shared library [#429](https://github.com/jupyterhub/repo2docker/pull/429) ([@betatim](https://github.com/betatim)) -- Adjust css for header links [#428](https://github.com/jupyterhub/repo2docker/pull/428) ([@evertrol](https://github.com/evertrol)) -- [MRG] Update the contributing docs [#427](https://github.com/jupyterhub/repo2docker/pull/427) ([@betatim](https://github.com/betatim)) -- Add a change log [#426](https://github.com/jupyterhub/repo2docker/pull/426) ([@evertrol](https://github.com/evertrol)) -- Change faq to rst [#425](https://github.com/jupyterhub/repo2docker/pull/425) ([@evertrol](https://github.com/evertrol)) -- Fix documentation: avoid clashing markup [#422](https://github.com/jupyterhub/repo2docker/pull/422) ([@evertrol](https://github.com/evertrol)) -- Add an edit-mode option [#421](https://github.com/jupyterhub/repo2docker/pull/421) ([@evertrol](https://github.com/evertrol)) -- Speed up cloning by using a depth of 1 if there is no refspec [#420](https://github.com/jupyterhub/repo2docker/pull/420) ([@evertrol](https://github.com/evertrol)) -- fix my heading mistake in the docs for DESCRIPTION files [#418](https://github.com/jupyterhub/repo2docker/pull/418) ([@gedankenstuecke](https://github.com/gedankenstuecke)) -- Subdirectory support [#413](https://github.com/jupyterhub/repo2docker/pull/413) ([@dsludwig](https://github.com/dsludwig)) -- updating index, usage, and install docs [#409](https://github.com/jupyterhub/repo2docker/pull/409) ([@choldgraf](https://github.com/choldgraf)) -- Adding support for nix buildpack in repo2docker [#407](https://github.com/jupyterhub/repo2docker/pull/407) ([@costrouc](https://github.com/costrouc)) -- add R DESCRIPTION support [#406](https://github.com/jupyterhub/repo2docker/pull/406) ([@gedankenstuecke](https://github.com/gedankenstuecke)) -- Support python 3.7 [#405](https://github.com/jupyterhub/repo2docker/pull/405) ([@minrk](https://github.com/minrk)) -- [MRG] Make travis fail when pytest fails [#401](https://github.com/jupyterhub/repo2docker/pull/401) ([@betatim](https://github.com/betatim)) -- Fix relative location of the start script [#400](https://github.com/jupyterhub/repo2docker/pull/400) ([@giovannipizzi](https://github.com/giovannipizzi)) -- Add more details to our setup() command [#394](https://github.com/jupyterhub/repo2docker/pull/394) ([@betatim](https://github.com/betatim)) -- Julia v1.0 support: Add option to specify julia version in REQUIRE [#393](https://github.com/jupyterhub/repo2docker/pull/393) ([@NHDaly](https://github.com/NHDaly)) -- Bump nteract-on-jupyter version [#390](https://github.com/jupyterhub/repo2docker/pull/390) ([@yuvipanda](https://github.com/yuvipanda)) - -### Contributors to this release - -([GitHub contributors page for this release](https://github.com/jupyterhub/repo2docker/graphs/contributors?from=2018-09-09&to=2018-12-12&type=c)) - -[@agahkarakuzu](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aagahkarakuzu+updated%3A2018-09-09..2018-12-12&type=Issues) | [@betatim](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abetatim+updated%3A2018-09-09..2018-12-12&type=Issues) | [@blairhudson](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ablairhudson+updated%3A2018-09-09..2018-12-12&type=Issues) | [@cboettig](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acboettig+updated%3A2018-09-09..2018-12-12&type=Issues) | [@choldgraf](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acholdgraf+updated%3A2018-09-09..2018-12-12&type=Issues) | [@consideRatio](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AconsideRatio+updated%3A2018-09-09..2018-12-12&type=Issues) | [@costrouc](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acostrouc+updated%3A2018-09-09..2018-12-12&type=Issues) | [@craig-willis](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acraig-willis+updated%3A2018-09-09..2018-12-12&type=Issues) | [@ctr26](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Actr26+updated%3A2018-09-09..2018-12-12&type=Issues) | [@davidanthoff](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Adavidanthoff+updated%3A2018-09-09..2018-12-12&type=Issues) | [@dsludwig](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Adsludwig+updated%3A2018-09-09..2018-12-12&type=Issues) | [@evertrol](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aevertrol+updated%3A2018-09-09..2018-12-12&type=Issues) | [@gedankenstuecke](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Agedankenstuecke+updated%3A2018-09-09..2018-12-12&type=Issues) | [@giovannipizzi](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Agiovannipizzi+updated%3A2018-09-09..2018-12-12&type=Issues) | [@jhamman](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajhamman+updated%3A2018-09-09..2018-12-12&type=Issues) | [@jzf2101](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajzf2101+updated%3A2018-09-09..2018-12-12&type=Issues) | [@karthik](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Akarthik+updated%3A2018-09-09..2018-12-12&type=Issues) | [@KristofferC](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AKristofferC+updated%3A2018-09-09..2018-12-12&type=Issues) | [@ltalirz](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Altalirz+updated%3A2018-09-09..2018-12-12&type=Issues) | [@ltetrel](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Altetrel+updated%3A2018-09-09..2018-12-12&type=Issues) | [@manics](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Amanics+updated%3A2018-09-09..2018-12-12&type=Issues) | [@matthewfeickert](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Amatthewfeickert+updated%3A2018-09-09..2018-12-12&type=Issues) | [@minrk](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aminrk+updated%3A2018-09-09..2018-12-12&type=Issues) | [@NHDaly](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3ANHDaly+updated%3A2018-09-09..2018-12-12&type=Issues) | [@nokome](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Anokome+updated%3A2018-09-09..2018-12-12&type=Issues) | [@nuest](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Anuest+updated%3A2018-09-09..2018-12-12&type=Issues) | [@pdurbin](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Apdurbin+updated%3A2018-09-09..2018-12-12&type=Issues) | [@psychemedia](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Apsychemedia+updated%3A2018-09-09..2018-12-12&type=Issues) | [@rbavery](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Arbavery+updated%3A2018-09-09..2018-12-12&type=Issues) | [@rgbkrk](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Argbkrk+updated%3A2018-09-09..2018-12-12&type=Issues) | [@ryanlovett](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aryanlovett+updated%3A2018-09-09..2018-12-12&type=Issues) | [@spMohanty](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AspMohanty+updated%3A2018-09-09..2018-12-12&type=Issues) | [@tgeorgeux](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Atgeorgeux+updated%3A2018-09-09..2018-12-12&type=Issues) | [@trallard](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Atrallard+updated%3A2018-09-09..2018-12-12&type=Issues) | [@trybik](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Atrybik+updated%3A2018-09-09..2018-12-12&type=Issues) | [@willingc](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awillingc+updated%3A2018-09-09..2018-12-12&type=Issues) | [@WillKoehrsen](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AWillKoehrsen+updated%3A2018-09-09..2018-12-12&type=Issues) | [@yuvipanda](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayuvipanda+updated%3A2018-09-09..2018-12-12&type=Issues) - -## 0.6.0 - -([full changelog](https://github.com/jupyterhub/repo2docker/compare/d97eee9...1b8e16a)) +- Fix figshare test {pr}`1001` by {user}`manics` +- Weekly test of master to check for external failures {pr}`998` by {user}`manics` +- Remove reference to `master` branch from CLI doc {pr}`977` by {user}`betatim` +- add chown to COPY commands to reduce layer count {pr}`969` by {user}`bollwyvl` +- set TIMEFORMAT for timed bash conda commands {pr}`966` by {user}`manics` +- Disable jupyterlab extension build minimize {pr}`963` by {user}`manics` +- Bump Black version to 20.8b1 and use --target-version=py36 {pr}`955` by {user}`paugier` +- Add workflow to build Docker image {pr}`954` by {user}`manics` +- Crosslink 'Configuring your repository' with usage {pr}`952` by {user}`manics` +- Add `www-frame-origin=same` to /etc/rstudio/rserver.conf {pr}`944` (\[@rkevin-arch\]()) +- GitHub Actions {pr}`942` by {user}`minrk` +- stop running tests on travis {pr}`940` by {user}`minrk` +- update repo URLs for jupyterhub/repo2docker {pr}`939` by {user}`minrk` +- Upgrade custom test infrastructure for pytest 6.0.0 {pr}`936` by {user}`betatim` +- validate_image_name: mention lowercase, fix formatting {pr}`934` by {user}`manics` +- Update snapshot date for simple R test {pr}`930` by {user}`betatim` +- little improvement for testing binder_dir {pr}`928` by {user}`bitnik` +- update docs for config dirs {pr}`927` by {user}`bitnik` +- doc: runtime.txt installs python x.y (& concise rewording) {pr}`914` by {user}`mdeff` +- doc: environment.yml installs a conda env, not only python {pr}`913` by {user}`mdeff` +- Make the memory limit test simpler {pr}`912` by {user}`betatim` +- Add gitpod.io config for docs {pr}`908` by {user}`betatim` +- fix repo2docker logo in Sphinx docs {pr}`906` by {user}`trallard` +- Update Dockerfile to add Docker {pr}`896` by {user}`hamelsmu` +- Document test failure workarounds {pr}`890` by {user}`hwine` +- Workaround Docker issue impacting some tests on macOS {pr}`882` by {user}`hwine` +- \[docs\] fix grammatical error in section title {pr}`872` by {user}`jameslamb` +- Fix long form args requirements {pr}`866` by {user}`betatim` +- Adopt new Sphinx theme name {pr}`864` by {user}`xhochy` +- Document loose conda export with --from-history {pr}`863` by {user}`xhochy` +- utils.execute_cmd flush buffer if no EOL {pr}`850` by {user}`manics` +- Update black 19.10b0, target Python 3.5 {pr}`849` by {user}`manics` +- docs: postBuild warn about shell script errors being ignored {pr}`844` by {user}`manics` +- Update changelog for 0.11.0 {pr}`842` by {user}`betatim` + +## Version 0.11.0 + +Release date: 2020-02-05 + +### New features + +- Add support for Figshare in {pr}`788` by {user}`nuest`. +- Add support for Dataverse in {pr}`739` by {user}`Xarthisius`. +- Add support for configuring the version of R installed in {pr}`772` by + {user}`betatim`. +- Add support for Julia 1.2.0 in {pr}`768` by {user}`davidanthoff`. +- Add support for Julia 1.3.0 and 1.0.5 in {pr}`822` by {user}`davidanthoff`. +- Add support for Julia 1.3.1 in {pr}`831` by {user}`davidanthoff`. +- Update Miniconda to 4.7.10 in {pr}`769` by {user}`davidrpugh`. +- Update IRKernel to 1.0.2 in {pr}`770` by {user}`GeorgianaElena`. +- Update RStudio to 1.2 in {pr}`803` by {user}`pablobernabeu`. +- Switch to "pandas" sphinx theme for documentation in {pr}`816` by {user}`choldgraf`. +- Add content provider documentation in {pr}`824` by {user}`choldgraf`. +- Remove legacy buildpack in {pr}`829` by {user}`betatim`. +- Add support for automatic RStudio install when using R packages via conda + in {pr}`838` by {user}`xhochy`. +- Add support for Python 3.8 in {pr}`840` by {user}`minrk`. +- Add Hydroshare as content provider in {pr}`800` by {user}`sblack-usu`. +- Update to Jupyter Notebook 6 and Lab 1.2 in {pr}`839` by {user}`minrk`. + +### Bug fixes + +- Fix for submodule check out in {pr}`809` by {user}`davidbrochart`. +- Handle `requirements.txt` files with different encodings in {pr}`771` + by {user}`GeorgianaElena`. +- Update to nteract-on-jupyter 2.1.3 in {pr}`2.1.3 by :user:`betatim`. +- Use `useradd --no-log-init` to fix exhausting disk space in {pr}`804` by + {user}`manics.` +- Add help text for commandline arguments in {pr}`517` by {user}`yuvipanda`. +- Fix submodule checkout in {pr}`809` by {user}`davidbrochart`. + +## Version 0.10.0 + +Release date: 2019-08-07 + +### New features + +- Increased minimum Python version supported for running `repo2docker` itself + to Python 3.5 in {pr}`684` by {user}`betatim`. +- Support for `Pipfile` and `Pipfile.lock` implemented in {pr}`649` by + {user}`consideratio`. +- Use only conda packages for our base environments in {pr}`728` by + {user}`scottyhq`. +- Fast rebuilds when repo dependencies haven't changed by {user}`minrk` and + {user}`betatim` in {pr}`743`, {pr}`752`, {pr}`718` and {pr}`716`. +- Add support for Zenodo in {pr}`693` by {user}`betatim`. +- Add support for general Invenio repositories in {pr}`704` by {user}`tmorrell`. +- Add support for julia 1.0.4 and 1.1.1 in {pr}`710` by {user}`davidanthoff`. +- Bump Conda from 4.6.14 to 4.7.5 in {pr}`719` by {user}`davidrpugh`. + +### API changes + +### Bug fixes + +- Prevent building the image as root if --user-id and --user-name are not specified + in {pr}`676` by {user}`Xarthisius`. +- Add bash to Dockerfile to fix usage of private repos with git-crendential-env in + {pr}`738` by {user}`eexwhyzee`. +- Fix memory limit enforcement in {pr}`677` by {user}`betatim`. + +## Version 0.9.0 + +Release date: 2019-05-05 + +### New features + +- Support for julia `Project.toml`, `JuliaProject.toml` and `Manifest.toml` files in {pr}`595` by + {user}`davidanthoff` +- Set JULIA_PROJECT globally, so that every julia instance starts with the + julia environment activated in {pr}`612` by {user}`davidanthoff`. +- Update Miniconda version to 4.6.14 and Conda version to 4.6.14 in {pr}`637` by + {user}`jhamman` +- Install notebook into `notebook` env instead of `root`. + Activate conda environments and shell integration via ENTRYPOINT + in {pr}`651` by {user}`minrk` +- Support for `.binder` directory in addition to `binder` directory for location of + configuration files, in {pr}`653` by {user}`jhamman`. +- Updated contributor guide and issue templates for bugs, feature requests, + and support questions in {pr}`654` and {pr}`655` by {user}`KirstieJane` and + {user}`betatim`. +- Create a page naming and describing the "Reproducible Execution + Environment Specification" (the specification used by repo2docker) + in {pr}`662` by {user}`choldgraf`. + +### API changes + +### Bug fixes + +- Install IJulia kernel into \$\{NB_PYTHON_PREFIX}/share/jupyter in {pr}`622` by + {user}`davidanthoff`. +- Ensure git submodules are updated and initilized correctly in {pr}`639` by + {user}`djhoese`. +- Use archive.debian.org as source for the debian jessie based legacy + buildpack in {pr}`633` by {user}`betatim`. +- Update to version 5.7.6 of the `notebook` package used in all environments + in {pr}`628` by {user}`betatim`. +- Update to version 5.7.8 of the `notebook` package and version 2.0.12 of + `nteract-on-jupyter` in {pr}`650` by {user}`betatim`. +- Switch to newer version of jupyter-server-proxy to fix websocket handling + in {pr}`646` by {user}`betatim`. +- Update to pip version 19.0.3 in {pr}`647` by {user}`betatim`. +- Ensure ENTRYPOINT is an absolute path in {pr}`657` by {user}`yuvipanda`. +- Fix handling of `--build-memory-limit` values without a postfix in {pr}`652` + by {user}`betatim`. + +## Version 0.8.0 + +Release date: 2019-02-21 + +### New features + +- Add additional metadata to docker images about how they were built {pr}`500` by + {user}`jrbourbeau`. +- Allow users to install global NPM packages: {pr}`573` by {user}`GladysNalvarte`. +- Add documentation on switching the user interface presented by a + container. {pr}`568` by user:`choldgraf`. +- Increased test coverage to ~87% by {user}`betatim` and {user}`yuvipanda`. +- Documentation improvements and additions by {user}`lheagy`, {user}`choldgraf`. +- Remove f-strings from code base, repo2docker is compatible with Python 3.4+ + again by {user}`jrbourbeau` in {pr}`520`. +- Local caching of previously built repostories to speed up launch times + by {user}`betatim` in {pr}`511`. +- Make destination of repository content in the container image configurable + on the CLI via `--target-repo-dir`. By {user}`yuvipanda` in {pr}`507`. +- Expose CPU limit settings for building and running containers. By + {user}`GladysNalvarte` in {pr}`579`. +- Make Python 3.7 the default version. By {user}`yuvipanda` and {user}`minrk` in + {pr}`539`. + +### API changes + +### Bug fixes + +- In some cases the version of conda installed in images was not pinned and got + upgraded by user actions. Fixed in {pr}`576` by {user}`minrk`. +- Fix an error related to checking if debug output was enabled or not: + {pr}`575` by {user}`yuvipanda`. +- Update nteract frontend to version 2.0.0 by {user}`yuvipanda` in {pr}`571`. +- Fix quoting issue in `GIT_CREDENTIAL_ENV` environment variable by + {user}`minrk` in {pr}`572`. +- Change to using the first 8 characters of each Git commit, not the last 8, + to tag each built docker image of repo2docker itself. {user}`minrk` in {pr}`562`. +- Allow users to select the Julia when using a `requirements.txt` by + {user}`yuvipanda` in {pr}`557`. +- Set `JULIA_DEPOT_PATH` to install packages outside the home directory by + {user}`yuvipanda` in {pr}`555`. +- Update to Jupyter notebook 5.7.4 {pr}`519` by {user}`minrk`. + +## Version 0.7.0 + +Release date: 2018-12-12 + +### New features + +- Build from sub-directory: build the image based on a sub-directory of a + repository {pr}`413` by {user}`dsludwig`. +- Editable mode: allows editing a local repository from a live container + {pr}`421` by {user}`evertrol`. +- Change log added {pr}`426` by {user}`evertrol`. +- Documentation: improved the documentation for contributors {pr}`453` by + {user}`choldgraf`. +- Buildpack: added support for the nix package manager {pr}`407` by + {user}`costrouc`. +- Log a 'success' message when push is complete {pr}`482` by + {user}`yuvipanda`. +- Allow specifying images to reuse cache from {pr}`478` by + {user}`yuvipanda`. +- Add JupyterHub back to base environment {pr}`476` by {user}`yuvipanda`. +- Repo2docker has a logo! by {user}`agahkarakuzu` and {user}`blairhudson`. +- Improve support for Stencila, including identifying stencila runtime from + document context {pr}`457` by {user}`nuest`. + +### API changes + +- Add content provider abstraction {pr}`421` by {user}`betatim`. + +### Bug fixes + +- Update to Jupyter notebook 5.7 {pr}`475` by {user}`betatim` and {user}`minrk`. + +## Version 0.6 -### Documentation improvements +Released 2018-09-09 -- Add architecture document [#235](https://github.com/jupyterhub/repo2docker/pull/235) ([@yuvipanda](https://github.com/yuvipanda)) +## Version 0.5 -### Other merged PRs +Released 2018-02-07 + +## Version 0.4.1 + +Released 2018-09-06 + +## Version 0.2 + +Released 2018-05-25 + +## Version 0.1.1 + +Released 2017-04-19 + +## Version 0.1 -- Add more details to our setup() command [#394](https://github.com/jupyterhub/repo2docker/pull/394) ([@betatim](https://github.com/betatim)) -- Bump conda version to 4.5.11 [#391](https://github.com/jupyterhub/repo2docker/pull/391) ([@yuvipanda](https://github.com/yuvipanda)) -- Issue #388 - Use bash echo for git-credential-env [#389](https://github.com/jupyterhub/repo2docker/pull/389) ([@zymergen-luke](https://github.com/zymergen-luke)) -- Change PyPI deploy account to mybinderteam [#385](https://github.com/jupyterhub/repo2docker/pull/385) ([@betatim](https://github.com/betatim)) -- [MRG] Update contributing documentation [#384](https://github.com/jupyterhub/repo2docker/pull/384) ([@betatim](https://github.com/betatim)) -- Update to JupyterLab 0.34 [#378](https://github.com/jupyterhub/repo2docker/pull/378) ([@blink1073](https://github.com/blink1073)) -- [MRG] Escape environment variable when using Python string formatting [#377](https://github.com/jupyterhub/repo2docker/pull/377) ([@betatim](https://github.com/betatim)) -- Split out tests, tweak docs, and a style change [#375](https://github.com/jupyterhub/repo2docker/pull/375) ([@betatim](https://github.com/betatim)) -- remove conda-meta/history [#373](https://github.com/jupyterhub/repo2docker/pull/373) ([@minrk](https://github.com/minrk)) -- Fix warnings in the documentation build and add to CI [#372](https://github.com/jupyterhub/repo2docker/pull/372) ([@betatim](https://github.com/betatim)) -- adding message and changing header characters for config files [#370](https://github.com/jupyterhub/repo2docker/pull/370) ([@choldgraf](https://github.com/choldgraf)) -- Install nodejs/npm from nodesource [#364](https://github.com/jupyterhub/repo2docker/pull/364) ([@GladysNalvarte](https://github.com/GladysNalvarte)) -- Add launch script [#363](https://github.com/jupyterhub/repo2docker/pull/363) ([@jhamman](https://github.com/jhamman)) -- Specify custom_display_url argument [#358](https://github.com/jupyterhub/repo2docker/pull/358) ([@GladysNalvarte](https://github.com/GladysNalvarte)) -- Switch from PyDataScienceHandbook to Pytudes [#355](https://github.com/jupyterhub/repo2docker/pull/355) ([@betatim](https://github.com/betatim)) -- bump versions and refreeze [#354](https://github.com/jupyterhub/repo2docker/pull/354) ([@minrk](https://github.com/minrk)) -- [MRG] Add version argument [#352](https://github.com/jupyterhub/repo2docker/pull/352) ([@vsoch](https://github.com/vsoch)) -- Add CircleCI Deploy Option [#351](https://github.com/jupyterhub/repo2docker/pull/351) ([@vsoch](https://github.com/vsoch)) -- from traitlets import TraitError in utils.py [#348](https://github.com/jupyterhub/repo2docker/pull/348) ([@cclauss](https://github.com/cclauss)) -- scinece -> science [#347](https://github.com/jupyterhub/repo2docker/pull/347) ([@danielleberre](https://github.com/danielleberre)) -- Fix some rst weirdness in the uage docs [#346](https://github.com/jupyterhub/repo2docker/pull/346) ([@betatim](https://github.com/betatim)) -- Add DockerSpawner command in JupyterHub config [#344](https://github.com/jupyterhub/repo2docker/pull/344) ([@rprimet](https://github.com/rprimet)) -- Test that images can start notebook servers in all the builders [#343](https://github.com/jupyterhub/repo2docker/pull/343) ([@GladysNalvarte](https://github.com/GladysNalvarte)) -- Setup auto releasing on GitHub tagging [#342](https://github.com/jupyterhub/repo2docker/pull/342) ([@betatim](https://github.com/betatim)) -- documentation improvements based on reviews for walkthrough and configuration details [#338](https://github.com/jupyterhub/repo2docker/pull/338) ([@jzf2101](https://github.com/jzf2101)) -- Tweaking Docs for Readability [#335](https://github.com/jupyterhub/repo2docker/pull/335) ([@jzf2101](https://github.com/jzf2101)) -- Include LICENSE file in wheels [#327](https://github.com/jupyterhub/repo2docker/pull/327) ([@toddrme2178](https://github.com/toddrme2178)) -- Switch to miniconda v4.5.1 [#324](https://github.com/jupyterhub/repo2docker/pull/324) ([@betatim](https://github.com/betatim)) -- Support shiny apps [#320](https://github.com/jupyterhub/repo2docker/pull/320) ([@ryanlovett](https://github.com/ryanlovett)) -- prefer R to conda in buildpack order [#317](https://github.com/jupyterhub/repo2docker/pull/317) ([@minrk](https://github.com/minrk)) -- Use XDG standard ~/.local for user software installs [#313](https://github.com/jupyterhub/repo2docker/pull/313) ([@yuvipanda](https://github.com/yuvipanda)) -- To add the user bin folder to the path [#311](https://github.com/jupyterhub/repo2docker/pull/311) ([@aborruso](https://github.com/aborruso)) -- stencila support [#309](https://github.com/jupyterhub/repo2docker/pull/309) ([@minrk](https://github.com/minrk)) -- Add links to the front page and modify travis [#308](https://github.com/jupyterhub/repo2docker/pull/308) ([@betatim](https://github.com/betatim)) -- Bump nteract jupyter extension [#306](https://github.com/jupyterhub/repo2docker/pull/306) ([@yuvipanda](https://github.com/yuvipanda)) -- remove \_nb_ext_conf from legacy env [#303](https://github.com/jupyterhub/repo2docker/pull/303) ([@minrk](https://github.com/minrk)) -- bump base image to ubuntu 18.04 [#302](https://github.com/jupyterhub/repo2docker/pull/302) ([@minrk](https://github.com/minrk)) -- Documentation and warning improvements [#300](https://github.com/jupyterhub/repo2docker/pull/300) ([@choldgraf](https://github.com/choldgraf)) -- Fix two typos [#299](https://github.com/jupyterhub/repo2docker/pull/299) ([@darabos](https://github.com/darabos)) -- Always install Python with conda [#298](https://github.com/jupyterhub/repo2docker/pull/298) ([@minrk](https://github.com/minrk)) -- split post build script command in Docker file [#294](https://github.com/jupyterhub/repo2docker/pull/294) ([@bitnik](https://github.com/bitnik)) -- Add guidelines on merging work [#292](https://github.com/jupyterhub/repo2docker/pull/292) ([@betatim](https://github.com/betatim)) -- Support setup.py in Python buildpacks [#289](https://github.com/jupyterhub/repo2docker/pull/289) ([@GladysNalvarte](https://github.com/GladysNalvarte)) -- Use travis_retry to run tests [#288](https://github.com/jupyterhub/repo2docker/pull/288) ([@betatim](https://github.com/betatim)) -- Add a test to select Python 3 via runtime.txt [#287](https://github.com/jupyterhub/repo2docker/pull/287) ([@betatim](https://github.com/betatim)) -- Enables Python2 just with runtime.txt file [#284](https://github.com/jupyterhub/repo2docker/pull/284) ([@GladysNalvarte](https://github.com/GladysNalvarte)) -- Add note about os support and update example repo [#283](https://github.com/jupyterhub/repo2docker/pull/283) ([@willingc](https://github.com/willingc)) -- Add codecov configuration to enable PR comments [#279](https://github.com/jupyterhub/repo2docker/pull/279) ([@betatim](https://github.com/betatim)) -- fixing python2 search [#277](https://github.com/jupyterhub/repo2docker/pull/277) ([@choldgraf](https://github.com/choldgraf)) -- Freeze legacy environment [#276](https://github.com/jupyterhub/repo2docker/pull/276) ([@GladysNalvarte](https://github.com/GladysNalvarte)) -- Refreeze environments [#274](https://github.com/jupyterhub/repo2docker/pull/274) ([@willingc](https://github.com/willingc)) -- add docstrings to docker buildpack [#272](https://github.com/jupyterhub/repo2docker/pull/272) ([@willingc](https://github.com/willingc)) -- add docstrings for conda buildpack [#271](https://github.com/jupyterhub/repo2docker/pull/271) ([@willingc](https://github.com/willingc)) -- add docstrings for legacy buildpack [#270](https://github.com/jupyterhub/repo2docker/pull/270) ([@willingc](https://github.com/willingc)) -- Add docstrings to python3 and python2 buildpacks [#265](https://github.com/jupyterhub/repo2docker/pull/265) ([@willingc](https://github.com/willingc)) -- Add doc for new buildpacks [#264](https://github.com/jupyterhub/repo2docker/pull/264) ([@willingc](https://github.com/willingc)) -- Fix detecting dependency files in binder/ subidr [#261](https://github.com/jupyterhub/repo2docker/pull/261) ([@betatim](https://github.com/betatim)) -- refreeze environments [#260](https://github.com/jupyterhub/repo2docker/pull/260) ([@minrk](https://github.com/minrk)) -- Adding unzip to base packages [#259](https://github.com/jupyterhub/repo2docker/pull/259) ([@kmader](https://github.com/kmader)) -- Revert "Add shiny-server." [#258](https://github.com/jupyterhub/repo2docker/pull/258) ([@yuvipanda](https://github.com/yuvipanda)) -- make sure there's a newline before each 'File: ' heading [#255](https://github.com/jupyterhub/repo2docker/pull/255) ([@ctb](https://github.com/ctb)) -- [MRG] Setup R libraries path for RStudio [#254](https://github.com/jupyterhub/repo2docker/pull/254) ([@betatim](https://github.com/betatim)) -- upgrade nteract_on_jupyter to 1.5.0 [#252](https://github.com/jupyterhub/repo2docker/pull/252) ([@rgbkrk](https://github.com/rgbkrk)) -- remove -v from conda env update [#248](https://github.com/jupyterhub/repo2docker/pull/248) ([@minrk](https://github.com/minrk)) -- [WIP] Specify plans for stability in repo2docker dependency [#244](https://github.com/jupyterhub/repo2docker/pull/244) ([@betatim](https://github.com/betatim)) -- Do not require postBuild to be executable [#241](https://github.com/jupyterhub/repo2docker/pull/241) ([@yuvipanda](https://github.com/yuvipanda)) -- Add shiny-server. [#239](https://github.com/jupyterhub/repo2docker/pull/239) ([@ryanlovett](https://github.com/ryanlovett)) -- clone recursively [#233](https://github.com/jupyterhub/repo2docker/pull/233) ([@minrk](https://github.com/minrk)) -- instantiate Repo2Docker to run tests [#229](https://github.com/jupyterhub/repo2docker/pull/229) ([@minrk](https://github.com/minrk)) -- do not reuse BuildPack instances [#228](https://github.com/jupyterhub/repo2docker/pull/228) ([@minrk](https://github.com/minrk)) -- Bump jupyterlab and jupyter notebook to latest versions [#225](https://github.com/jupyterhub/repo2docker/pull/225) ([@betatim](https://github.com/betatim)) -- Add a CONTRIBUTING.md [#224](https://github.com/jupyterhub/repo2docker/pull/224) ([@yuvipanda](https://github.com/yuvipanda)) -- Install from wheel when testing in travis [#222](https://github.com/jupyterhub/repo2docker/pull/222) ([@yuvipanda](https://github.com/yuvipanda)) -- Bump version to v0.5 [#221](https://github.com/jupyterhub/repo2docker/pull/221) ([@yuvipanda](https://github.com/yuvipanda)) -- Switch freeze guidance to not be a directive [#220](https://github.com/jupyterhub/repo2docker/pull/220) ([@rgbkrk](https://github.com/rgbkrk)) -- pin nteract_on_jupyter to 1.4.0 [#219](https://github.com/jupyterhub/repo2docker/pull/219) ([@rgbkrk](https://github.com/rgbkrk)) -- Add docstrings and minor style fixes for application files and JuliaBuildPack [#213](https://github.com/jupyterhub/repo2docker/pull/213) ([@willingc](https://github.com/willingc)) -- Add native R + IRKernel + RStudio support [#210](https://github.com/jupyterhub/repo2docker/pull/210) ([@yuvipanda](https://github.com/yuvipanda)) -- Fix Python version detection for conda [#209](https://github.com/jupyterhub/repo2docker/pull/209) ([@minrk](https://github.com/minrk)) -- Clarify that --debug and --no-build are for debugging only [#205](https://github.com/jupyterhub/repo2docker/pull/205) ([@yuvipanda](https://github.com/yuvipanda)) -- Remove outdated builder info from docs [#204](https://github.com/jupyterhub/repo2docker/pull/204) ([@yuvipanda](https://github.com/yuvipanda)) -- Add nteract jupyter extension to requirements.txt based setups [#200](https://github.com/jupyterhub/repo2docker/pull/200) ([@yuvipanda](https://github.com/yuvipanda)) -- Emergency Bump to artful [#197](https://github.com/jupyterhub/repo2docker/pull/197) ([@yuvipanda](https://github.com/yuvipanda)) -- Refreeze conda environment [#193](https://github.com/jupyterhub/repo2docker/pull/193) ([@yuvipanda](https://github.com/yuvipanda)) -- refreeze conda environments [#187](https://github.com/jupyterhub/repo2docker/pull/187) ([@minrk](https://github.com/minrk)) -- Provide a flag to pass environment variables at runtime [#186](https://github.com/jupyterhub/repo2docker/pull/186) ([@rprimet](https://github.com/rprimet)) -- Stop using alpine base images [#183](https://github.com/jupyterhub/repo2docker/pull/183) ([@yuvipanda](https://github.com/yuvipanda)) -- Fix indentation causing only last line of apt.txt to be parsed [#181](https://github.com/jupyterhub/repo2docker/pull/181) ([@nmih](https://github.com/nmih)) -- Fixed run argument check for mounting volumes. [#179](https://github.com/jupyterhub/repo2docker/pull/179) ([@mukundans91](https://github.com/mukundans91)) -- Add default command to base Dockerfile template [#176](https://github.com/jupyterhub/repo2docker/pull/176) ([@AaronWatters](https://github.com/AaronWatters)) -- Added regex pattern based validation for image name argument [#175](https://github.com/jupyterhub/repo2docker/pull/175) ([@mukundans91](https://github.com/mukundans91)) -- Allow mounting arbitrary volumes into the repo2docker container [#172](https://github.com/jupyterhub/repo2docker/pull/172) ([@yuvipanda](https://github.com/yuvipanda)) -- adding runtime to preparing + improving config section [#168](https://github.com/jupyterhub/repo2docker/pull/168) ([@choldgraf](https://github.com/choldgraf)) -- improving docs [#165](https://github.com/jupyterhub/repo2docker/pull/165) ([@choldgraf](https://github.com/choldgraf)) -- Remove symlink & just copy postBuild file instead 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[#88](https://github.com/jupyterhub/repo2docker/pull/88) ([@yuvipanda](https://github.com/yuvipanda)) -- Switch base image to alpine + fix typo causing CI to fail [#87](https://github.com/jupyterhub/repo2docker/pull/87) ([@yuvipanda](https://github.com/yuvipanda)) -- make binder directory visible [#86](https://github.com/jupyterhub/repo2docker/pull/86) ([@minrk](https://github.com/minrk)) -- Look in .binder directory for files [#83](https://github.com/jupyterhub/repo2docker/pull/83) ([@minrk](https://github.com/minrk)) -- Update virtualenv base to use jupyterlab 0.27 [#81](https://github.com/jupyterhub/repo2docker/pull/81) ([@ellisonbg](https://github.com/ellisonbg)) -- Update JupyterLab to 0.27 [#80](https://github.com/jupyterhub/repo2docker/pull/80) ([@ellisonbg](https://github.com/ellisonbg)) -- document `--debug` [#79](https://github.com/jupyterhub/repo2docker/pull/79) ([@choldgraf](https://github.com/choldgraf)) -- make JUPYTERHUB_VERSION a build arg 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[@willingc](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awillingc+updated%3A2017-09-06..2018-09-09&type=Issues) | [@yuvipanda](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayuvipanda+updated%3A2017-09-06..2018-09-09&type=Issues) | [@zymergen-luke](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Azymergen-luke+updated%3A2017-09-06..2018-09-09&type=Issues) - -## v0.4.1 - -([full changelog](https://github.com/jupyterhub/repo2docker/compare/e7674ce...d97eee9)) - -### Merged PRs - -- Add --debug & --no-build options [#68](https://github.com/jupyterhub/repo2docker/pull/68) ([@yuvipanda](https://github.com/yuvipanda)) -- Moved old COPYING.md to LICENSE, and updated with current language. [#67](https://github.com/jupyterhub/repo2docker/pull/67) ([@tdalseide](https://github.com/tdalseide)) -- Add license - Issue #64 [#65](https://github.com/jupyterhub/repo2docker/pull/65) ([@sumalaika](https://github.com/sumalaika)) -- Include package_data in setup.py [#59](https://github.com/jupyterhub/repo2docker/pull/59) ([@yuvipanda](https://github.com/yuvipanda)) -- Include package_data in setup.py [#58](https://github.com/jupyterhub/repo2docker/pull/58) ([@yuvipanda](https://github.com/yuvipanda)) -- Add npm to base image [#57](https://github.com/jupyterhub/repo2docker/pull/57) ([@yuvipanda](https://github.com/yuvipanda)) -- config file for RTD [#56](https://github.com/jupyterhub/repo2docker/pull/56) ([@choldgraf](https://github.com/choldgraf)) -- fixing RTD build [#54](https://github.com/jupyterhub/repo2docker/pull/54) ([@choldgraf](https://github.com/choldgraf)) -- updating autogen examples [#53](https://github.com/jupyterhub/repo2docker/pull/53) ([@choldgraf](https://github.com/choldgraf)) -- adding doc generation from the tests [#51](https://github.com/jupyterhub/repo2docker/pull/51) ([@choldgraf](https://github.com/choldgraf)) -- Validate that Julia is using our pre-installed conda [#50](https://github.com/jupyterhub/repo2docker/pull/50) ([@yuvipanda](https://github.com/yuvipanda)) -- Cleanup conda [#49](https://github.com/jupyterhub/repo2docker/pull/49) ([@yuvipanda](https://github.com/yuvipanda)) -- Add back --no-clean support [#48](https://github.com/jupyterhub/repo2docker/pull/48) ([@yuvipanda](https://github.com/yuvipanda)) -- Add a little more info to README [#47](https://github.com/jupyterhub/repo2docker/pull/47) ([@yuvipanda](https://github.com/yuvipanda)) -- Print stdout for all the tests! [#46](https://github.com/jupyterhub/repo2docker/pull/46) ([@yuvipanda](https://github.com/yuvipanda)) -- Fix legacy dockerfile support and add tests [#43](https://github.com/jupyterhub/repo2docker/pull/43) ([@yuvipanda](https://github.com/yuvipanda)) -- Fix dockerfile builds and add tests for them [#42](https://github.com/jupyterhub/repo2docker/pull/42) ([@yuvipanda](https://github.com/yuvipanda)) -- fix the python2 kernelspec [#35](https://github.com/jupyterhub/repo2docker/pull/35) ([@minrk](https://github.com/minrk)) -- julia version bump [#30](https://github.com/jupyterhub/repo2docker/pull/30) ([@choldgraf](https://github.com/choldgraf)) -- Add support for Julia buildpack [#29](https://github.com/jupyterhub/repo2docker/pull/29) ([@yuvipanda](https://github.com/yuvipanda)) -- Add initial sphinx docs [#26](https://github.com/jupyterhub/repo2docker/pull/26) ([@willingc](https://github.com/willingc)) -- Add JupyterLab to the default environment for venv + conda builders [#22](https://github.com/jupyterhub/repo2docker/pull/22) ([@yuvipanda](https://github.com/yuvipanda)) -- Cleanup docker pull hack [#21](https://github.com/jupyterhub/repo2docker/pull/21) ([@yuvipanda](https://github.com/yuvipanda)) -- Add a default build pack [#20](https://github.com/jupyterhub/repo2docker/pull/20) ([@yuvipanda](https://github.com/yuvipanda)) -- add LegacyBinderDockerfile buildpack [#16](https://github.com/jupyterhub/repo2docker/pull/16) ([@minrk](https://github.com/minrk)) - -### Contributors to this release - -([GitHub contributors page for this release](https://github.com/jupyterhub/repo2docker/graphs/contributors?from=2017-05-25&to=2017-09-06&type=c)) - -[@arokem](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aarokem+updated%3A2017-05-25..2017-09-06&type=Issues) | [@betatim](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abetatim+updated%3A2017-05-25..2017-09-06&type=Issues) | [@cboettig](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acboettig+updated%3A2017-05-25..2017-09-06&type=Issues) | [@choldgraf](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acholdgraf+updated%3A2017-05-25..2017-09-06&type=Issues) | [@consideRatio](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AconsideRatio+updated%3A2017-05-25..2017-09-06&type=Issues) | [@dpsanders](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Adpsanders+updated%3A2017-05-25..2017-09-06&type=Issues) | [@jzf2101](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajzf2101+updated%3A2017-05-25..2017-09-06&type=Issues) | [@minrk](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aminrk+updated%3A2017-05-25..2017-09-06&type=Issues) | [@rprimet](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Arprimet+updated%3A2017-05-25..2017-09-06&type=Issues) | [@sje30](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Asje30+updated%3A2017-05-25..2017-09-06&type=Issues) | [@sumalaika](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Asumalaika+updated%3A2017-05-25..2017-09-06&type=Issues) | [@taylorreiter](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ataylorreiter+updated%3A2017-05-25..2017-09-06&type=Issues) | [@tdalseide](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Atdalseide+updated%3A2017-05-25..2017-09-06&type=Issues) | [@tkelman](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Atkelman+updated%3A2017-05-25..2017-09-06&type=Issues) | [@willingc](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awillingc+updated%3A2017-05-25..2017-09-06&type=Issues) | [@yuvipanda](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayuvipanda+updated%3A2017-05-25..2017-09-06&type=Issues) - -## 0.2.0 - -([full changelog](https://github.com/jupyterhub/repo2docker/compare/efd55a9...e7674ce)) - -### Merged PRs - -- line endings! [#14](https://github.com/jupyterhub/repo2docker/pull/14) ([@minrk](https://github.com/minrk)) -- bundle s2i in wheels [#12](https://github.com/jupyterhub/repo2docker/pull/12) ([@minrk](https://github.com/minrk)) -- Add builder creation doc [#11](https://github.com/jupyterhub/repo2docker/pull/11) ([@willingc](https://github.com/willingc)) -- Use same port in host and docker container [#10](https://github.com/jupyterhub/repo2docker/pull/10) ([@yuvipanda](https://github.com/yuvipanda)) -- support repo as positional arg [#8](https://github.com/jupyterhub/repo2docker/pull/8) ([@minrk](https://github.com/minrk)) -- further simplify s2i buildpacks [#7](https://github.com/jupyterhub/repo2docker/pull/7) ([@minrk](https://github.com/minrk)) -- add conda detector [#2](https://github.com/jupyterhub/repo2docker/pull/2) ([@minrk](https://github.com/minrk)) - -### Contributors to this release - -([GitHub contributors page for this release](https://github.com/jupyterhub/repo2docker/graphs/contributors?from=2017-04-19&to=2017-05-25&type=c)) - -[@choldgraf](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acholdgraf+updated%3A2017-04-19..2017-05-25&type=Issues) | [@minrk](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aminrk+updated%3A2017-04-19..2017-05-25&type=Issues) | [@willingc](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awillingc+updated%3A2017-04-19..2017-05-25&type=Issues) | [@yuvipanda](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayuvipanda+updated%3A2017-04-19..2017-05-25&type=Issues) +Released 2017-04-14 From 2775e14161a280434d2a81b8980b0b768713c6c5 Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Thu, 8 Jun 2023 07:20:42 +0200 Subject: [PATCH 152/171] Pin action to vX instead of vX.Y.Z to reduce automation noise --- .github/workflows/release.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml index 74c429441..3a1a4c9fc 100644 --- a/.github/workflows/release.yml +++ b/.github/workflows/release.yml @@ -57,7 +57,7 @@ jobs: # all previous steps always run in order to exercise them - name: Publish distribution to PyPI if: startsWith(github.ref, 'refs/tags') - uses: pypa/gh-action-pypi-publish@v1.8.6 + uses: pypa/gh-action-pypi-publish@release/v1 with: password: ${{ secrets.PYPI_PASSWORD }} From 1e31b117d864880dda9d580d1e868af9bcbbd15e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Collonval?= Date: Thu, 8 Jun 2023 09:00:03 +0200 Subject: [PATCH 153/171] Fix links to jupyterlab-demo postBuild file --- docs/source/config_files.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/config_files.rst b/docs/source/config_files.rst index 8d14f7a49..1c2cca45b 100644 --- a/docs/source/config_files.rst +++ b/docs/source/config_files.rst @@ -162,8 +162,8 @@ Note that by default the build will not be stopped if an error occurs inside a s You should include ``set -e`` or the equivalent at the start of the script to avoid errors being silently ignored. An example use-case of ``postBuild`` file is JupyterLab's demo on mybinder.org. -It uses a ``postBuild`` file in a folder called ``binder`` to `prepare -their demo for binder `_. +It uses a ``postBuild`` file in a folder called ``.binder`` to `prepare +their demo for binder `_. .. _start: From 07be88950ba57529edf27619994710eaa77cf326 Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Thu, 8 Jun 2023 09:11:16 +0200 Subject: [PATCH 154/171] Only pin to major versions as input to freeze --- repo2docker/buildpacks/conda/environment.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/repo2docker/buildpacks/conda/environment.yml b/repo2docker/buildpacks/conda/environment.yml index 538bdbbf5..8f844145c 100644 --- a/repo2docker/buildpacks/conda/environment.yml +++ b/repo2docker/buildpacks/conda/environment.yml @@ -4,9 +4,9 @@ dependencies: - python=3.10 - nodejs=18 - pip - - ipywidgets==8.0.2 - - jupyter-offlinenotebook==0.2.2 - - jupyter-resource-usage==0.7.0 - - jupyterlab==3.4.8 - - jupyterhub-singleuser==3.1.1 - - notebook==6.4.12 + - ipywidgets==8.* # https://github.com/jupyter-widgets/ipywidgets + - jupyter-offlinenotebook==0.2.* # https://github.com/manics/jupyter-offlinenotebook + - jupyter-resource-usage==0.7.* # https://github.com/jupyter-server/jupyter-resource-usage + - jupyterlab==3.* # https://github.com/jupyterlab/jupyterlab + - jupyterhub-singleuser==3.* # https://github.com/jupyterhub/jupyterhub + - notebook==6.* # https://github.com/jupyter/notebook From 90252fd30d858dcf46949ef36eda0226422c07e0 Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Thu, 8 Jun 2023 11:31:26 +0200 Subject: [PATCH 155/171] Pin jupyter-server, previously held back to v1 by jupyterlab 3.4.* --- repo2docker/buildpacks/conda/environment.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/repo2docker/buildpacks/conda/environment.yml b/repo2docker/buildpacks/conda/environment.yml index 8f844145c..156129bd1 100644 --- a/repo2docker/buildpacks/conda/environment.yml +++ b/repo2docker/buildpacks/conda/environment.yml @@ -7,6 +7,7 @@ dependencies: - ipywidgets==8.* # https://github.com/jupyter-widgets/ipywidgets - jupyter-offlinenotebook==0.2.* # https://github.com/manics/jupyter-offlinenotebook - jupyter-resource-usage==0.7.* # https://github.com/jupyter-server/jupyter-resource-usage - - jupyterlab==3.* # https://github.com/jupyterlab/jupyterlab + - jupyter_server==1.* # https://github.com/jupyter-server/jupyter_server - jupyterhub-singleuser==3.* # https://github.com/jupyterhub/jupyterhub + - jupyterlab==3.* # https://github.com/jupyterlab/jupyterlab - notebook==6.* # https://github.com/jupyter/notebook From 8bb242d40c85a537141d125661282a3a04da4583 Mon Sep 17 00:00:00 2001 From: Erik Sundell Date: Thu, 8 Jun 2023 11:36:22 +0200 Subject: [PATCH 156/171] Refreeze conda buildpack's dependencies --- .../conda/environment.py-3.10-linux-64.lock | 139 ++++++++++-------- .../environment.py-3.10-linux-aarch64.lock | 139 ++++++++++-------- .../buildpacks/conda/environment.py-3.10.yml | 15 +- .../conda/environment.py-3.11-linux-64.lock | 137 +++++++++-------- .../environment.py-3.11-linux-aarch64.lock | 137 +++++++++-------- .../buildpacks/conda/environment.py-3.11.yml | 15 +- .../conda/environment.py-3.7-linux-64.lock | 110 ++++++++------ .../environment.py-3.7-linux-aarch64.lock | 97 ++++++------ .../buildpacks/conda/environment.py-3.7.yml | 15 +- .../conda/environment.py-3.8-linux-64.lock | 137 +++++++++-------- .../environment.py-3.8-linux-aarch64.lock | 137 +++++++++-------- .../buildpacks/conda/environment.py-3.8.yml | 15 +- .../conda/environment.py-3.9-linux-64.lock | 137 +++++++++-------- .../environment.py-3.9-linux-aarch64.lock | 137 +++++++++-------- .../buildpacks/conda/environment.py-3.9.yml | 15 +- 15 files changed, 773 insertions(+), 609 deletions(-) diff --git a/repo2docker/buildpacks/conda/environment.py-3.10-linux-64.lock b/repo2docker/buildpacks/conda/environment.py-3.10-linux-64.lock index ecdeefec9..8b535800e 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.10-linux-64.lock +++ b/repo2docker/buildpacks/conda/environment.py-3.10-linux-64.lock @@ -1,150 +1,167 @@ # AUTO GENERATED FROM environment.py-3.10.yml, DO NOT MANUALLY MODIFY -# Frozen on 2023-04-09 15:23:40 UTC +# Frozen on 2023-06-08 09:35:19 UTC # Generated by conda-lock. # platform: linux-64 -# input_hash: 999dec5129d8880d536f4005b8c79138df000d64e6626932b69eee478a0c6c4e +# input_hash: 5e20d8617672faf1f048550dc6ffdcf6288c12f1faf23a9051314056a752d9f3 @EXPLICIT https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81 -https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.12.7-ha878542_0.conda#ff9f73d45c4a07d6f424495288a26080 +https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2023.5.7-hbcca054_0.conda#f5c65075fc34438d5b456c7f3f5ab695 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jupyter-offlinenotebook==0.2.* # https://github.com/manics/jupyter-offlinenotebook +- jupyter-resource-usage==0.7.* # https://github.com/jupyter-server/jupyter-resource-usage +- jupyter_server==1.* # https://github.com/jupyter-server/jupyter_server +- jupyterhub-singleuser==3.* # https://github.com/jupyterhub/jupyterhub +- jupyterlab==3.* # https://github.com/jupyterlab/jupyterlab +- notebook==6.* # https://github.com/jupyter/notebook diff --git a/repo2docker/buildpacks/conda/environment.py-3.11-linux-64.lock b/repo2docker/buildpacks/conda/environment.py-3.11-linux-64.lock index 07e932500..0f9849e4a 100644 --- a/repo2docker/buildpacks/conda/environment.py-3.11-linux-64.lock +++ b/repo2docker/buildpacks/conda/environment.py-3.11-linux-64.lock @@ -1,20 +1,21 @@ # AUTO GENERATED FROM environment.py-3.11.yml, DO NOT MANUALLY MODIFY -# Frozen on 2023-04-09 15:24:10 UTC +# Frozen on 2023-06-08 09:35:47 UTC # Generated by conda-lock. # platform: linux-64 -# input_hash: 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+1,15 @@ # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY -# Generated on 2023-04-09 15:24:10 UTC +# Generated on 2023-06-08 09:35:47 UTC channels: - conda-forge dependencies: - python=3.11.* - nodejs=18 - pip -- ipywidgets==8.0.2 -- jupyter-offlinenotebook==0.2.2 -- jupyter-resource-usage==0.7.0 -- jupyterlab==3.4.8 -- jupyterhub-singleuser==3.1.1 -- notebook==6.4.12 +- ipywidgets==8.* # https://github.com/jupyter-widgets/ipywidgets +- jupyter-offlinenotebook==0.2.* # https://github.com/manics/jupyter-offlinenotebook +- jupyter-resource-usage==0.7.* # https://github.com/jupyter-server/jupyter-resource-usage +- jupyter_server==1.* # https://github.com/jupyter-server/jupyter_server +- jupyterhub-singleuser==3.* # https://github.com/jupyterhub/jupyterhub +- jupyterlab==3.* # https://github.com/jupyterlab/jupyterlab +- notebook==6.* # https://github.com/jupyter/notebook diff --git a/repo2docker/buildpacks/conda/environment.py-3.7-linux-64.lock 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a/repo2docker/buildpacks/conda/environment.py-3.9.yml +++ b/repo2docker/buildpacks/conda/environment.py-3.9.yml @@ -1,14 +1,15 @@ # AUTO GENERATED FROM environment.yml, DO NOT MANUALLY MODIFY -# Generated on 2023-04-09 15:23:05 UTC +# Generated on 2023-06-08 09:34:51 UTC channels: - conda-forge dependencies: - python=3.9.* - nodejs=18 - pip -- ipywidgets==8.0.2 -- jupyter-offlinenotebook==0.2.2 -- jupyter-resource-usage==0.7.0 -- jupyterlab==3.4.8 -- jupyterhub-singleuser==3.1.1 -- notebook==6.4.12 +- ipywidgets==8.* # https://github.com/jupyter-widgets/ipywidgets +- jupyter-offlinenotebook==0.2.* # https://github.com/manics/jupyter-offlinenotebook +- jupyter-resource-usage==0.7.* # https://github.com/jupyter-server/jupyter-resource-usage +- jupyter_server==1.* # https://github.com/jupyter-server/jupyter_server +- jupyterhub-singleuser==3.* # https://github.com/jupyterhub/jupyterhub +- jupyterlab==3.* # https://github.com/jupyterlab/jupyterlab +- notebook==6.* # https://github.com/jupyter/notebook From 8500d479a53fdf9bca79136213a8c13fd9bd8dae Mon Sep 17 00:00:00 2001 From: Min RK Date: Fri, 9 Jun 2023 12:50:32 +0200 Subject: [PATCH 157/171] Stop using MRAN - remove cutoff for picking RSPM, always use it - remove now-redundant r4.0-mran test - shift base R 3.6 snapshot date to after October 2017, when rspm snapshots seem to have started - update docs to point to RSPM --- docs/source/config_files.rst | 4 ++-- docs/source/howto/languages.rst | 7 ++----- repo2docker/buildpacks/r.py | 22 +--------------------- tests/r/r3.6-mran/runtime.txt | 1 - tests/r/{r3.6-mran => r3.6-rspm}/install.R | 0 tests/r/r3.6-rspm/runtime.txt | 1 + tests/r/{r3.6-mran => r3.6-rspm}/verify | 4 ++-- tests/r/r4.0-mran/install.R | 1 - tests/r/r4.0-mran/runtime.txt | 1 - tests/r/r4.0-mran/verify | 13 ------------- tests/unit/test_r.py | 22 +--------------------- 11 files changed, 9 insertions(+), 67 deletions(-) delete mode 100644 tests/r/r3.6-mran/runtime.txt rename tests/r/{r3.6-mran => r3.6-rspm}/install.R (100%) create mode 100644 tests/r/r3.6-rspm/runtime.txt rename tests/r/{r3.6-mran => r3.6-rspm}/verify (63%) delete mode 100644 tests/r/r4.0-mran/install.R delete mode 100644 tests/r/r4.0-mran/runtime.txt delete mode 100755 tests/r/r4.0-mran/verify diff --git a/docs/source/config_files.rst b/docs/source/config_files.rst index 1c2cca45b..457bfa207 100644 --- a/docs/source/config_files.rst +++ b/docs/source/config_files.rst @@ -118,7 +118,7 @@ with ``REQUIRE`` and ``environment.yml``, visit ================================================ This is used to install R libraries pinned to a specific snapshot on -`MRAN `_. +`Posit Package Manager `_. To set the date of the snapshot add a runtime.txt_. For an example ``install.R`` file, visit our `example install.R file `_. @@ -207,7 +207,7 @@ For these cases, we have a special file, ``runtime.txt``. Have ``python-x.y`` in ``runtime.txt`` to run the repository with Python version x.y. See our `Python2 example repository `_. -Have ``r----
`` in ``runtime.txt`` to run the repository with R version RVERSION and libraries from a YYYY-MM-DD snapshot of `MRAN `_. +Have ``r----
`` in ``runtime.txt`` to run the repository with R version RVERSION and libraries from a YYYY-MM-DD snapshot of `Posit Package Manager `__. RVERSION can be set to 3.4, 3.5, 3.6, or to patch releases for the 3.5 and 3.6 series. If you do not specify a version, the latest release will be used (currently R 3.6). See our `R example repository `_. diff --git a/docs/source/howto/languages.rst b/docs/source/howto/languages.rst index 75ea7e537..af51a6fdf 100644 --- a/docs/source/howto/languages.rst +++ b/docs/source/howto/languages.rst @@ -65,17 +65,14 @@ to install libraries from on the given date. You can install more R packages fro by adding a :ref:`install.R` file to your repo. RStudio and IRKernel are installed by default for all R versions. -If you request R 4.1 or later, or specify a snapshot date newer than -``2022-01-01``, `packagemanager.posit.co `_ +`packagemanager.posit.co `_ will be used to provide much faster installations via `binary packages `_. For *some* packages, this might require you install underlying system libraries using :ref:`apt.txt` - look at the page for the CRAN package you are interested in at `packagemanager.posit.co `_ to find a list. -For older R versions with an older snapshot date, `MRAN `_ -is used as source of packages. This purely provides source packages, and you should -migrate away from this if possible. +repo2docker stopped using the Microsoft mirror MRAN for older R versions after its shutdown in July, 2023. Julia diff --git a/repo2docker/buildpacks/r.py b/repo2docker/buildpacks/r.py index 464587d6a..c02be42ea 100644 --- a/repo2docker/buildpacks/r.py +++ b/repo2docker/buildpacks/r.py @@ -229,30 +229,10 @@ def get_rspm_snapshot_url(self, snapshot_date, max_days_prior=7): ) ) - @lru_cache() - def get_mran_snapshot_url(self, snapshot_date, max_days_prior=7): - for i in range(max_days_prior): - try_date = snapshot_date - datetime.timedelta(days=i) - # Fall back to MRAN if packagemanager.posit.co doesn't have it - url = f"https://mran.microsoft.com/snapshot/{try_date.isoformat()}" - r = requests.head(url) - if r.ok: - return url - raise ValueError( - "No snapshot found for {} or {} days prior in mran.microsoft.com".format( - snapshot_date.strftime("%Y-%m-%d"), max_days_prior - ) - ) - @lru_cache() def get_cran_mirror_url(self, snapshot_date): # Date after which we will use rspm + binary packages instead of MRAN + source packages - rspm_cutoff_date = datetime.date(2022, 1, 1) - - if snapshot_date >= rspm_cutoff_date or self.r_version >= V("4.1"): - return self.get_rspm_snapshot_url(snapshot_date) - else: - return self.get_mran_snapshot_url(snapshot_date) + return self.get_rspm_snapshot_url(snapshot_date) @lru_cache() def get_devtools_snapshot_url(self): diff --git a/tests/r/r3.6-mran/runtime.txt b/tests/r/r3.6-mran/runtime.txt deleted file mode 100644 index 308424ab2..000000000 --- a/tests/r/r3.6-mran/runtime.txt +++ /dev/null @@ -1 +0,0 @@ -r-3.6-2016-01-03 diff --git a/tests/r/r3.6-mran/install.R b/tests/r/r3.6-rspm/install.R similarity index 100% rename from tests/r/r3.6-mran/install.R rename to tests/r/r3.6-rspm/install.R diff --git a/tests/r/r3.6-rspm/runtime.txt b/tests/r/r3.6-rspm/runtime.txt new file mode 100644 index 000000000..cc18726fd --- /dev/null +++ b/tests/r/r3.6-rspm/runtime.txt @@ -0,0 +1 @@ +r-3.6-2017-11-01 diff --git a/tests/r/r3.6-mran/verify b/tests/r/r3.6-rspm/verify similarity index 63% rename from tests/r/r3.6-mran/verify rename to tests/r/r3.6-rspm/verify index 26f561028..475dd91f8 100755 --- a/tests/r/r3.6-mran/verify +++ b/tests/r/r3.6-rspm/verify @@ -7,7 +7,7 @@ if (!(version$major == "3" && as.double(version$minor) >= 6 && as.double(version quit("yes", 1) } -# Fail if MRAN isn't the configured CRAN mirror -if (!(startsWith(options()$repos["CRAN"], "https://mran.microsoft.com"))) { +# Fail if RSPM isn't the configured CRAN mirror +if (!(startsWith(options()$repos["CRAN"], "https://packagemanager.posit.co"))) { quit("yes", 1) } diff --git a/tests/r/r4.0-mran/install.R b/tests/r/r4.0-mran/install.R deleted file mode 100644 index f609959ef..000000000 --- a/tests/r/r4.0-mran/install.R +++ /dev/null @@ -1 +0,0 @@ -install.packages("digest") diff --git a/tests/r/r4.0-mran/runtime.txt b/tests/r/r4.0-mran/runtime.txt deleted file mode 100644 index b051a4326..000000000 --- a/tests/r/r4.0-mran/runtime.txt +++ /dev/null @@ -1 +0,0 @@ -r-4.0-2021-07-07 diff --git a/tests/r/r4.0-mran/verify b/tests/r/r4.0-mran/verify deleted file mode 100755 index b821ec6cc..000000000 --- a/tests/r/r4.0-mran/verify +++ /dev/null @@ -1,13 +0,0 @@ -#!/usr/bin/env Rscript -library('digest') - -# Fail if version is not 4.0 -print(version) -if (!(version$major == "4" && as.double(version$minor) >= 0 && as.double(version$minor) < 1)) { - quit("yes", 1) -} - -# The date we have chosen should give us an MRAN mirror -if (!(startsWith(options()$repos["CRAN"], "https://mran.microsoft.com"))) { - quit("yes", 1) -} \ No newline at end of file diff --git a/tests/unit/test_r.py b/tests/unit/test_r.py index f30d542a8..b565e814a 100644 --- a/tests/unit/test_r.py +++ b/tests/unit/test_r.py @@ -40,7 +40,7 @@ def test_version_completion(tmpdir, base_image): ("r-3.5-2019-01-01", (2019, 1, 1)), ], ) -def test_mran_date(tmpdir, runtime, expected, base_image): +def test_cran_date(tmpdir, runtime, expected, base_image): tmpdir.chdir() with open("runtime.txt", "w") as f: @@ -72,23 +72,3 @@ def test_snapshot_rspm_date(base_image): with pytest.raises(ValueError): r.get_rspm_snapshot_url(date(1691, 9, 5)) - - -@pytest.mark.parametrize("expected", [date(2019, 12, 29), date(2019, 12, 26)]) -@pytest.mark.parametrize("requested", [date(2019, 12, 31)]) -def test_snapshot_mran_date(requested, expected, base_image): - def mock_request_head(url): - r = Response() - if url == "https://mran.microsoft.com/snapshot/" + expected.isoformat(): - r.status_code = 200 - else: - r.status_code = 404 - r.reason = "Mock MRAN no snapshot" - return r - - with patch("requests.head", side_effect=mock_request_head): - r = buildpacks.RBuildPack(base_image) - assert ( - r.get_mran_snapshot_url(requested) - == f"https://mran.microsoft.com/snapshot/{expected.isoformat()}" - ) From 12240843457ddabc44cebed8353472d4025ad327 Mon Sep 17 00:00:00 2001 From: YuviPanda Date: Fri, 9 Jun 2023 17:56:42 +0530 Subject: [PATCH 158/171] Bump 3.6-rspm snapshot to after IRkernel was introduced --- tests/r/r3.6-rspm/runtime.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/r/r3.6-rspm/runtime.txt b/tests/r/r3.6-rspm/runtime.txt index cc18726fd..009200f36 100644 --- a/tests/r/r3.6-rspm/runtime.txt +++ b/tests/r/r3.6-rspm/runtime.txt @@ -1 +1 @@ -r-3.6-2017-11-01 +r-3.6-2018-11-20 From 5572e37a7d94951c7ea47162915f1d4b856112a2 Mon Sep 17 00:00:00 2001 From: YuviPanda Date: Fri, 9 Jun 2023 18:27:37 +0530 Subject: [PATCH 159/171] Bump up the R snapshot date some more --- tests/r/r3.6-rspm/runtime.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/r/r3.6-rspm/runtime.txt b/tests/r/r3.6-rspm/runtime.txt index 009200f36..b43a0768c 100644 --- a/tests/r/r3.6-rspm/runtime.txt +++ b/tests/r/r3.6-rspm/runtime.txt @@ -1 +1 @@ -r-3.6-2018-11-20 +r-3.6-2018-12-20 From 0a756e72dd810403f7d5cbaf709ed5fc5ae19577 Mon Sep 17 00:00:00 2001 From: YuviPanda Date: Fri, 9 Jun 2023 19:54:19 +0530 Subject: [PATCH 160/171] Try a slightly older snapshot date --- tests/r/r3.6-rspm/runtime.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/r/r3.6-rspm/runtime.txt b/tests/r/r3.6-rspm/runtime.txt index b43a0768c..613f8971f 100644 --- a/tests/r/r3.6-rspm/runtime.txt +++ b/tests/r/r3.6-rspm/runtime.txt @@ -1 +1 @@ -r-3.6-2018-12-20 +r-3.6-2018-11-31 From 3fb91c7f56b86f0283d44928fdfed9f6d339ee9e Mon Sep 17 00:00:00 2001 From: YuviPanda Date: Fri, 9 Jun 2023 23:44:54 +0530 Subject: [PATCH 161/171] Try a slightly newer date --- tests/r/r3.6-rspm/runtime.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/r/r3.6-rspm/runtime.txt b/tests/r/r3.6-rspm/runtime.txt index 613f8971f..ef918a220 100644 --- a/tests/r/r3.6-rspm/runtime.txt +++ b/tests/r/r3.6-rspm/runtime.txt @@ -1 +1 @@ -r-3.6-2018-11-31 +r-3.6-2018-12-07 From 6c719bd6717b1e57e99e6c1937b4045523d2224c Mon Sep 17 00:00:00 2001 From: YuviPanda Date: Sun, 11 Jun 2023 12:55:34 +0530 Subject: [PATCH 162/171] Remove unnecessary method call --- repo2docker/buildpacks/r.py | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/repo2docker/buildpacks/r.py b/repo2docker/buildpacks/r.py index c02be42ea..3bbcb00a7 100644 --- a/repo2docker/buildpacks/r.py +++ b/repo2docker/buildpacks/r.py @@ -229,11 +229,6 @@ def get_rspm_snapshot_url(self, snapshot_date, max_days_prior=7): ) ) - @lru_cache() - def get_cran_mirror_url(self, snapshot_date): - # Date after which we will use rspm + binary packages instead of MRAN + source packages - return self.get_rspm_snapshot_url(snapshot_date) - @lru_cache() def get_devtools_snapshot_url(self): """ @@ -272,7 +267,7 @@ def get_build_scripts(self): contents of runtime.txt. """ - cran_mirror_url = self.get_cran_mirror_url(self.checkpoint_date) + cran_mirror_url = self.get_rspm_snapshot_url(self.checkpoint_date) if self.platform != "linux/amd64": raise RuntimeError( From a0fd8743b221b21a2fcb8e59ca56bbb366c4c44e Mon Sep 17 00:00:00 2001 From: YuviPanda Date: Sun, 11 Jun 2023 12:56:53 +0530 Subject: [PATCH 163/171] Remove mentions of MRAN --- docs/source/config_files.rst | 2 +- repo2docker/buildpacks/r.py | 3 +-- tests/r/README.md | 12 ------------ 3 files changed, 2 insertions(+), 15 deletions(-) diff --git a/docs/source/config_files.rst b/docs/source/config_files.rst index 457bfa207..eabbdb56b 100644 --- a/docs/source/config_files.rst +++ b/docs/source/config_files.rst @@ -118,7 +118,7 @@ with ``REQUIRE`` and ``environment.yml``, visit ================================================ This is used to install R libraries pinned to a specific snapshot on -`Posit Package Manager `_. +`Posit Package Manager `_. To set the date of the snapshot add a runtime.txt_. For an example ``install.R`` file, visit our `example install.R file `_. diff --git a/repo2docker/buildpacks/r.py b/repo2docker/buildpacks/r.py index 3bbcb00a7..73d08d77a 100644 --- a/repo2docker/buildpacks/r.py +++ b/repo2docker/buildpacks/r.py @@ -22,8 +22,7 @@ class RBuildPack(PythonBuildPack): Where 'year', 'month' and 'date' refer to a specific date whose CRAN snapshot we will use to fetch packages. - Uses https://packagemanager.posit.co, or MRAN if no snapshot - is found on packagemanager.posit.co + Uses https://packagemanager.posit.co. 2. A `DESCRIPTION` file signaling an R package diff --git a/tests/r/README.md b/tests/r/README.md index 61df6db48..51488e41f 100644 --- a/tests/r/README.md +++ b/tests/r/README.md @@ -24,18 +24,6 @@ `runtime.txt` is omitted and a recent enough snapshot date is assumed a RSPM snapshot of CRAN to be used. -### r3.6-mran - -- Test setup of a R 3.6 environment by specifying `r-3.6-...` in `runtime.txt`, - where the date provided in `runtime.txt` is old enough for a MRAN snapshot of - CRAN to be used. - -### r4.0-mran - -- Test setup of a R 4.0 environment by specifying `r-4.0-...` in `runtime.txt`, - where the date provided in `runtime.txt` is old enough for a MRAN snapshot of - CRAN to be used. - ### r4.0-rspm - Test setup of a R 4.0 environment by specifying `r-4.0-...` in `runtime.txt`, From 0dfce7677511785b9b4931bad44d814ea2baa569 Mon Sep 17 00:00:00 2001 From: YuviPanda Date: Sun, 11 Jun 2023 13:04:28 +0530 Subject: [PATCH 164/171] Throw a useful error message when snapshot is too old --- repo2docker/buildpacks/r.py | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/repo2docker/buildpacks/r.py b/repo2docker/buildpacks/r.py index 73d08d77a..5f44afe6e 100644 --- a/repo2docker/buildpacks/r.py +++ b/repo2docker/buildpacks/r.py @@ -9,6 +9,9 @@ from ._r_base import rstudio_base_scripts from .python import PythonBuildPack +# Aproximately the first snapshot on RSPM (Posit package manager) +# that seems to have a working IRKernel. +RSPM_CUTOFF_DATE = datetime.datetime(2018, 12, 7) class RBuildPack(PythonBuildPack): """ @@ -265,6 +268,12 @@ def get_build_scripts(self): We set the snapshot date used to install R libraries from based on the contents of runtime.txt. """ + if self.checkpoint_date < RSPM_CUTOFF_DATE: + raise RuntimeError( + f'Microsoft killed MRAN, the source of R package snapshots before {RSPM_CUTOFF_DATE.strptime("%Y-%m-%d")}. '\ + f'This repo has a snapshot date of {self.checkpoint_date.strftime("%Y-%m-%d")} specified in runtime.txt. '\ + 'Please use a newer snapshot date' + ) cran_mirror_url = self.get_rspm_snapshot_url(self.checkpoint_date) From 9f1a6406b69cbe402565dac156ab8cef7c710381 Mon Sep 17 00:00:00 2001 From: YuviPanda Date: Sun, 11 Jun 2023 13:09:40 +0530 Subject: [PATCH 165/171] Use correct type to represent cutoff date --- repo2docker/buildpacks/r.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/repo2docker/buildpacks/r.py b/repo2docker/buildpacks/r.py index 5f44afe6e..ff0336911 100644 --- a/repo2docker/buildpacks/r.py +++ b/repo2docker/buildpacks/r.py @@ -11,7 +11,7 @@ # Aproximately the first snapshot on RSPM (Posit package manager) # that seems to have a working IRKernel. -RSPM_CUTOFF_DATE = datetime.datetime(2018, 12, 7) +RSPM_CUTOFF_DATE = datetime.date(2018, 12, 7) class RBuildPack(PythonBuildPack): """ From 5947b756bab340d2b226df0a0ceed382358f24f1 Mon Sep 17 00:00:00 2001 From: YuviPanda Date: Sun, 11 Jun 2023 13:09:48 +0530 Subject: [PATCH 166/171] Use correct method to format datetime --- repo2docker/buildpacks/r.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/repo2docker/buildpacks/r.py b/repo2docker/buildpacks/r.py index ff0336911..8f92e0f01 100644 --- a/repo2docker/buildpacks/r.py +++ b/repo2docker/buildpacks/r.py @@ -270,7 +270,7 @@ def get_build_scripts(self): """ if self.checkpoint_date < RSPM_CUTOFF_DATE: raise RuntimeError( - f'Microsoft killed MRAN, the source of R package snapshots before {RSPM_CUTOFF_DATE.strptime("%Y-%m-%d")}. '\ + f'Microsoft killed MRAN, the source of R package snapshots before {RSPM_CUTOFF_DATE.strftime("%Y-%m-%d")}. '\ f'This repo has a snapshot date of {self.checkpoint_date.strftime("%Y-%m-%d")} specified in runtime.txt. '\ 'Please use a newer snapshot date' ) From 49bdc6c048079bd25c23f2600eed2d862490b305 Mon Sep 17 00:00:00 2001 From: YuviPanda Date: Sun, 11 Jun 2023 13:10:02 +0530 Subject: [PATCH 167/171] Add unit test for MRAN death --- tests/unit/test_r.py | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/tests/unit/test_r.py b/tests/unit/test_r.py index b565e814a..d50295951 100644 --- a/tests/unit/test_r.py +++ b/tests/unit/test_r.py @@ -72,3 +72,14 @@ def test_snapshot_rspm_date(base_image): with pytest.raises(ValueError): r.get_rspm_snapshot_url(date(1691, 9, 5)) + + +def test_mran_dead(tmpdir, base_image): + tmpdir.chdir() + + with open("runtime.txt", "w") as f: + f.write('r-3.6-2017-06-04') + + r = buildpacks.RBuildPack(base_image) + with pytest.raises(RuntimeError, match=r'^Microsoft killed MRAN, the source of R package snapshots before 2018-12-07.*'): + r.get_build_scripts() \ No newline at end of file From 18e76f9d38b141a4b328478f4eb6d1026e5576c8 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Sun, 11 Jun 2023 07:40:57 +0000 Subject: [PATCH 168/171] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- repo2docker/buildpacks/r.py | 7 ++++--- tests/unit/test_r.py | 9 ++++++--- 2 files changed, 10 insertions(+), 6 deletions(-) diff --git a/repo2docker/buildpacks/r.py b/repo2docker/buildpacks/r.py index 8f92e0f01..7dd724e04 100644 --- a/repo2docker/buildpacks/r.py +++ b/repo2docker/buildpacks/r.py @@ -13,6 +13,7 @@ # that seems to have a working IRKernel. RSPM_CUTOFF_DATE = datetime.date(2018, 12, 7) + class RBuildPack(PythonBuildPack): """ Setup R for use with a repository @@ -270,9 +271,9 @@ def get_build_scripts(self): """ if self.checkpoint_date < RSPM_CUTOFF_DATE: raise RuntimeError( - f'Microsoft killed MRAN, the source of R package snapshots before {RSPM_CUTOFF_DATE.strftime("%Y-%m-%d")}. '\ - f'This repo has a snapshot date of {self.checkpoint_date.strftime("%Y-%m-%d")} specified in runtime.txt. '\ - 'Please use a newer snapshot date' + f'Microsoft killed MRAN, the source of R package snapshots before {RSPM_CUTOFF_DATE.strftime("%Y-%m-%d")}. ' + f'This repo has a snapshot date of {self.checkpoint_date.strftime("%Y-%m-%d")} specified in runtime.txt. ' + "Please use a newer snapshot date" ) cran_mirror_url = self.get_rspm_snapshot_url(self.checkpoint_date) diff --git a/tests/unit/test_r.py b/tests/unit/test_r.py index d50295951..a7028d829 100644 --- a/tests/unit/test_r.py +++ b/tests/unit/test_r.py @@ -78,8 +78,11 @@ def test_mran_dead(tmpdir, base_image): tmpdir.chdir() with open("runtime.txt", "w") as f: - f.write('r-3.6-2017-06-04') + f.write("r-3.6-2017-06-04") r = buildpacks.RBuildPack(base_image) - with pytest.raises(RuntimeError, match=r'^Microsoft killed MRAN, the source of R package snapshots before 2018-12-07.*'): - r.get_build_scripts() \ No newline at end of file + with pytest.raises( + RuntimeError, + match=r"^Microsoft killed MRAN, the source of R package snapshots before 2018-12-07.*", + ): + r.get_build_scripts() From 119cff990f9960f746512cae657c8c4dd26030ce Mon Sep 17 00:00:00 2001 From: YuviPanda Date: Tue, 13 Jun 2023 11:20:18 +0530 Subject: [PATCH 169/171] Add changelog for 2023.06.0 --- docs/source/changelog.md | 96 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 96 insertions(+) diff --git a/docs/source/changelog.md b/docs/source/changelog.md index 6bd03fd64..660da1250 100644 --- a/docs/source/changelog.md +++ b/docs/source/changelog.md @@ -1,5 +1,101 @@ # Changelog +## Version 2023.06.0 + +([full changelog](https://github.com/jupyterhub/repo2docker/compare/2022.10.0...0ea6f7d85ed2adab17dae3ba2685a90df52c166d)) + +### Breaking changes + +- JupyterHub version installed by default upgraded from 1.5 to 3.1.1 +- Microsoft [killed MRAN](https://techcommunity.microsoft.com/t5/azure-sql-blog/microsoft-r-application-network-retirement/ba-p/3707161), so all package snapshots now come from [Posit Package Manager](https://packagemanager.posit.co/client/). Snapshots from before 2018-12-07 are now no longer available, so you might have to update the snapshot date in your `runtime.txt`. + +### New features added + +- Support Python 3.11 and upgrade jupyterhub from 1.5.0 to 3.1.1 [#1239](https://github.com/jupyterhub/repo2docker/pull/1239) ([@minrk](https://github.com/minrk)) +- allow user to specify a single port with default command [#918](https://github.com/jupyterhub/repo2docker/pull/918) ([@minrk](https://github.com/minrk)) +- Let `FROM ` in the Dockerfile template be configurable [#909](https://github.com/jupyterhub/repo2docker/pull/909) ([@yuvipanda](https://github.com/yuvipanda)) + +### Enhancements made + +- Update to mamba 1.4.0 [#1256](https://github.com/jupyterhub/repo2docker/pull/1256) ([@SylvainCorlay](https://github.com/SylvainCorlay)) +- [MRG] download original file formats from Dataverse #1242 [#1253](https://github.com/jupyterhub/repo2docker/pull/1253) ([@pdurbin](https://github.com/pdurbin)) +- Add optional registry credentials to push() [#1245](https://github.com/jupyterhub/repo2docker/pull/1245) ([@manics](https://github.com/manics)) +- Add ARM64 support where possible [#1228](https://github.com/jupyterhub/repo2docker/pull/1228) ([@manics](https://github.com/manics)) +- Switch default python to 3.10 [#1219](https://github.com/jupyterhub/repo2docker/pull/1219) ([@yuvipanda](https://github.com/yuvipanda)) + +### Bugs fixed + +- Microsoft killed MRAN, stop relying on it [#1285](https://github.com/jupyterhub/repo2docker/pull/1285) ([@minrk](https://github.com/minrk)) +- Update the location of R packagemanager [#1273](https://github.com/jupyterhub/repo2docker/pull/1273) ([@Xarthisius](https://github.com/Xarthisius)) +- missing `f` in julia fetch error f-string [#1264](https://github.com/jupyterhub/repo2docker/pull/1264) ([@minrk](https://github.com/minrk)) +- avoid duplicate log statements by memoizing getters [#1248](https://github.com/jupyterhub/repo2docker/pull/1248) ([@minrk](https://github.com/minrk)) +- Add Conda env library path to RStudio configuration [#1237](https://github.com/jupyterhub/repo2docker/pull/1237) ([@TimStewartJ](https://github.com/TimStewartJ)) +- Create Julia projects based on binder/Project.toml when found [#1216](https://github.com/jupyterhub/repo2docker/pull/1216) ([@frankier](https://github.com/frankier)) +- Allow REPO_DIR to be a non-existing folder by creating it and providing the user with permissions [#976](https://github.com/jupyterhub/repo2docker/pull/976) ([@bollwyvl](https://github.com/bollwyvl)) + +### Maintenance and upkeep improvements + +- Microsoft killed MRAN, stop relying on it [#1285](https://github.com/jupyterhub/repo2docker/pull/1285) ([@minrk](https://github.com/minrk)) +- Relax pins to major versions and refreeze, introduce explicit jupyter_server v1 pin [#1283](https://github.com/jupyterhub/repo2docker/pull/1283) ([@consideRatio](https://github.com/consideRatio)) +- fix github link templates [#1276](https://github.com/jupyterhub/repo2docker/pull/1276) ([@minrk](https://github.com/minrk)) +- dependabot: monthly updates of github actions [#1262](https://github.com/jupyterhub/repo2docker/pull/1262) ([@consideRatio](https://github.com/consideRatio)) +- Remove deprecated nteract_on_jupyter [#1259](https://github.com/jupyterhub/repo2docker/pull/1259) ([@yuvipanda](https://github.com/yuvipanda)) +- disable codecov failures [#1251](https://github.com/jupyterhub/repo2docker/pull/1251) ([@minrk](https://github.com/minrk)) +- Support Python 3.11 and upgrade jupyterhub from 1.5.0 to 3.1.1 [#1239](https://github.com/jupyterhub/repo2docker/pull/1239) ([@minrk](https://github.com/minrk)) +- pre-commit update to fix ci [#1238](https://github.com/jupyterhub/repo2docker/pull/1238) ([@minrk](https://github.com/minrk)) +- Upgrade to mamba 1.1 and enable rich SAT error messages [#1232](https://github.com/jupyterhub/repo2docker/pull/1232) ([@SylvainCorlay](https://github.com/SylvainCorlay)) +- Upgrade to mamba 1.0 [#1213](https://github.com/jupyterhub/repo2docker/pull/1213) ([@SylvainCorlay](https://github.com/SylvainCorlay)) +- docker image: update alpine to 3.16 [#1212](https://github.com/jupyterhub/repo2docker/pull/1212) ([@consideRatio](https://github.com/consideRatio)) +- reconcile CLI/config priority [#1211](https://github.com/jupyterhub/repo2docker/pull/1211) ([@minrk](https://github.com/minrk)) +- pipfile: pass --clear flag, and do it separetely to not be ignored [#1208](https://github.com/jupyterhub/repo2docker/pull/1208) ([@consideRatio](https://github.com/consideRatio)) +- run submodule test over https [#1204](https://github.com/jupyterhub/repo2docker/pull/1204) ([@minrk](https://github.com/minrk)) +- pre-commit: add pyupgrade, isort, and prettier for .md files [#1202](https://github.com/jupyterhub/repo2docker/pull/1202) ([@consideRatio](https://github.com/consideRatio)) +- Create wheels with the build package, stop calling setup.py directly [#1199](https://github.com/jupyterhub/repo2docker/pull/1199) ([@consideRatio](https://github.com/consideRatio)) +- Add check-tmp step to local repo tests [#1126](https://github.com/jupyterhub/repo2docker/pull/1126) ([@minrk](https://github.com/minrk)) +- Set default, type, and help method for engine in argparse [#1073](https://github.com/jupyterhub/repo2docker/pull/1073) ([@jgarte](https://github.com/jgarte)) + +### Documentation improvements + +- Fix links to jupyterlab-demo postBuild file [#1282](https://github.com/jupyterhub/repo2docker/pull/1282) ([@fcollonval](https://github.com/fcollonval)) +- Recreate changelog as markdown [#1281](https://github.com/jupyterhub/repo2docker/pull/1281) ([@yuvipanda](https://github.com/yuvipanda)) +- fix github link templates [#1276](https://github.com/jupyterhub/repo2docker/pull/1276) ([@minrk](https://github.com/minrk)) +- update docs for default and supported Python versions [#1250](https://github.com/jupyterhub/repo2docker/pull/1250) ([@minrk](https://github.com/minrk)) +- docs: add devenv, linkcheck, and refresh misc config etc [#1197](https://github.com/jupyterhub/repo2docker/pull/1197) ([@consideRatio](https://github.com/consideRatio)) + +### Other merged PRs + +- build(deps): bump pypa/gh-action-pypi-publish from 1.8.5 to (edit) release/v1 [#1279](https://github.com/jupyterhub/repo2docker/pull/1279) ([@dependabot](https://github.com/dependabot)) +- [pre-commit.ci] pre-commit autoupdate [#1270](https://github.com/jupyterhub/repo2docker/pull/1270) ([@pre-commit-ci](https://github.com/pre-commit-ci)) +- build(deps): bump pypa/gh-action-pypi-publish from 1.8.4 to 1.8.5 [#1263](https://github.com/jupyterhub/repo2docker/pull/1263) ([@dependabot](https://github.com/dependabot)) +- [pre-commit.ci] pre-commit autoupdate [#1261](https://github.com/jupyterhub/repo2docker/pull/1261) ([@pre-commit-ci](https://github.com/pre-commit-ci)) +- build(deps): bump pypa/gh-action-pypi-publish from 1.8.3 to 1.8.4 [#1260](https://github.com/jupyterhub/repo2docker/pull/1260) ([@dependabot](https://github.com/dependabot)) +- build(deps): bump pypa/gh-action-pypi-publish from 1.6.4 to 1.8.3 [#1257](https://github.com/jupyterhub/repo2docker/pull/1257) ([@dependabot](https://github.com/dependabot)) +- [pre-commit.ci] pre-commit autoupdate [#1252](https://github.com/jupyterhub/repo2docker/pull/1252) ([@pre-commit-ci](https://github.com/pre-commit-ci)) +- Ensure `BuildPack.python_version` is specified [#1249](https://github.com/jupyterhub/repo2docker/pull/1249) ([@minrk](https://github.com/minrk)) +- Update install-nix.bash [#1244](https://github.com/jupyterhub/repo2docker/pull/1244) ([@robertodr](https://github.com/robertodr)) +- build(deps): bump docker/build-push-action from 3 to 4 [#1241](https://github.com/jupyterhub/repo2docker/pull/1241) ([@dependabot](https://github.com/dependabot)) +- Update to `jupyter-resource-usage==0.7.0` [#1236](https://github.com/jupyterhub/repo2docker/pull/1236) ([@jtpio](https://github.com/jtpio)) +- Also install dev requirements on Gitpod [#1235](https://github.com/jupyterhub/repo2docker/pull/1235) ([@jtpio](https://github.com/jtpio)) +- Bump to Node 18 [#1234](https://github.com/jupyterhub/repo2docker/pull/1234) ([@jtpio](https://github.com/jtpio)) +- [pre-commit.ci] pre-commit autoupdate [#1229](https://github.com/jupyterhub/repo2docker/pull/1229) ([@pre-commit-ci](https://github.com/pre-commit-ci)) +- Quick-fix for Docker image build [#1227](https://github.com/jupyterhub/repo2docker/pull/1227) ([@manics](https://github.com/manics)) +- Fix tests/external/reproductions.repos.yaml [#1226](https://github.com/jupyterhub/repo2docker/pull/1226) ([@manics](https://github.com/manics)) +- Fix typo [#1224](https://github.com/jupyterhub/repo2docker/pull/1224) ([@fkohrt](https://github.com/fkohrt)) +- build(deps): bump pypa/gh-action-pypi-publish from 1.5.1 to 1.6.4 [#1223](https://github.com/jupyterhub/repo2docker/pull/1223) ([@dependabot](https://github.com/dependabot)) +- [pre-commit.ci] pre-commit autoupdate [#1222](https://github.com/jupyterhub/repo2docker/pull/1222) ([@pre-commit-ci](https://github.com/pre-commit-ci)) +- ci: cleanup no longer used test logic related to memlimit [#1218](https://github.com/jupyterhub/repo2docker/pull/1218) ([@consideRatio](https://github.com/consideRatio)) +- [pre-commit.ci] pre-commit autoupdate [#1217](https://github.com/jupyterhub/repo2docker/pull/1217) ([@pre-commit-ci](https://github.com/pre-commit-ci)) +- ci: use non-deprecated codecov uploader [#1209](https://github.com/jupyterhub/repo2docker/pull/1209) ([@consideRatio](https://github.com/consideRatio)) +- ci: stop running pre-commit in gha, rely on pre-commit.ci [#1200](https://github.com/jupyterhub/repo2docker/pull/1200) ([@consideRatio](https://github.com/consideRatio)) +- Initial changelog for 2022.10.0 [#1194](https://github.com/jupyterhub/repo2docker/pull/1194) ([@manics](https://github.com/manics)) + +### Contributors to this release + +([GitHub contributors page for this release](https://github.com/jupyterhub/repo2docker/graphs/contributors?from=2022-10-18&to=2023-06-13&type=c)) + +[@AliMirlou](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AAliMirlou+updated%3A2022-10-18..2023-06-13&type=Issues) | [@betatim](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abetatim+updated%3A2022-10-18..2023-06-13&type=Issues) | [@bollwyvl](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abollwyvl+updated%3A2022-10-18..2023-06-13&type=Issues) | [@choldgraf](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acholdgraf+updated%3A2022-10-18..2023-06-13&type=Issues) | [@consideRatio](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AconsideRatio+updated%3A2022-10-18..2023-06-13&type=Issues) | [@craig-willis](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acraig-willis+updated%3A2022-10-18..2023-06-13&type=Issues) | [@dependabot](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Adependabot+updated%3A2022-10-18..2023-06-13&type=Issues) | [@fcollonval](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Afcollonval+updated%3A2022-10-18..2023-06-13&type=Issues) | [@fkohrt](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Afkohrt+updated%3A2022-10-18..2023-06-13&type=Issues) | [@frankier](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Afrankier+updated%3A2022-10-18..2023-06-13&type=Issues) | [@jgarte](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajgarte+updated%3A2022-10-18..2023-06-13&type=Issues) | [@jhamman](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajhamman+updated%3A2022-10-18..2023-06-13&type=Issues) | [@jtpio](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajtpio+updated%3A2022-10-18..2023-06-13&type=Issues) | [@manics](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Amanics+updated%3A2022-10-18..2023-06-13&type=Issues) | [@meeseeksmachine](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ameeseeksmachine+updated%3A2022-10-18..2023-06-13&type=Issues) | [@minrk](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aminrk+updated%3A2022-10-18..2023-06-13&type=Issues) | [@nuest](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Anuest+updated%3A2022-10-18..2023-06-13&type=Issues) | [@pdurbin](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Apdurbin+updated%3A2022-10-18..2023-06-13&type=Issues) | [@pre-commit-ci](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Apre-commit-ci+updated%3A2022-10-18..2023-06-13&type=Issues) | [@robertodr](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Arobertodr+updated%3A2022-10-18..2023-06-13&type=Issues) | [@SylvainCorlay](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3ASylvainCorlay+updated%3A2022-10-18..2023-06-13&type=Issues) | [@TimStewartJ](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3ATimStewartJ+updated%3A2022-10-18..2023-06-13&type=Issues) | [@trybik](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Atrybik+updated%3A2022-10-18..2023-06-13&type=Issues) | [@welcome](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awelcome+updated%3A2022-10-18..2023-06-13&type=Issues) | [@westurner](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awesturner+updated%3A2022-10-18..2023-06-13&type=Issues) | [@Xarthisius](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AXarthisius+updated%3A2022-10-18..2023-06-13&type=Issues) | [@yamaton](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayamaton+updated%3A2022-10-18..2023-06-13&type=Issues) | [@yuvipanda](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayuvipanda+updated%3A2022-10-18..2023-06-13&type=Issues) + + ## Version 2022.10.0 [Full changelog](https://github.com/jupyterhub/repo2docker/compare/2022.02.0...2022.10.0) From fcdf7c424e9c229d952fe7dcc185d49cc8a4c20d Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 13 Jun 2023 05:51:13 +0000 Subject: [PATCH 170/171] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- docs/source/changelog.md | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/source/changelog.md b/docs/source/changelog.md index 660da1250..4ded350ec 100644 --- a/docs/source/changelog.md +++ b/docs/source/changelog.md @@ -95,7 +95,6 @@ [@AliMirlou](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AAliMirlou+updated%3A2022-10-18..2023-06-13&type=Issues) | [@betatim](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abetatim+updated%3A2022-10-18..2023-06-13&type=Issues) | [@bollwyvl](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Abollwyvl+updated%3A2022-10-18..2023-06-13&type=Issues) | [@choldgraf](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acholdgraf+updated%3A2022-10-18..2023-06-13&type=Issues) | [@consideRatio](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AconsideRatio+updated%3A2022-10-18..2023-06-13&type=Issues) | [@craig-willis](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Acraig-willis+updated%3A2022-10-18..2023-06-13&type=Issues) | [@dependabot](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Adependabot+updated%3A2022-10-18..2023-06-13&type=Issues) | [@fcollonval](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Afcollonval+updated%3A2022-10-18..2023-06-13&type=Issues) | [@fkohrt](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Afkohrt+updated%3A2022-10-18..2023-06-13&type=Issues) | [@frankier](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Afrankier+updated%3A2022-10-18..2023-06-13&type=Issues) | [@jgarte](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajgarte+updated%3A2022-10-18..2023-06-13&type=Issues) | [@jhamman](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajhamman+updated%3A2022-10-18..2023-06-13&type=Issues) | [@jtpio](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ajtpio+updated%3A2022-10-18..2023-06-13&type=Issues) | [@manics](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Amanics+updated%3A2022-10-18..2023-06-13&type=Issues) | [@meeseeksmachine](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ameeseeksmachine+updated%3A2022-10-18..2023-06-13&type=Issues) | [@minrk](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Aminrk+updated%3A2022-10-18..2023-06-13&type=Issues) | [@nuest](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Anuest+updated%3A2022-10-18..2023-06-13&type=Issues) | [@pdurbin](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Apdurbin+updated%3A2022-10-18..2023-06-13&type=Issues) | [@pre-commit-ci](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Apre-commit-ci+updated%3A2022-10-18..2023-06-13&type=Issues) | [@robertodr](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Arobertodr+updated%3A2022-10-18..2023-06-13&type=Issues) | [@SylvainCorlay](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3ASylvainCorlay+updated%3A2022-10-18..2023-06-13&type=Issues) | [@TimStewartJ](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3ATimStewartJ+updated%3A2022-10-18..2023-06-13&type=Issues) | [@trybik](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Atrybik+updated%3A2022-10-18..2023-06-13&type=Issues) | [@welcome](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awelcome+updated%3A2022-10-18..2023-06-13&type=Issues) | [@westurner](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Awesturner+updated%3A2022-10-18..2023-06-13&type=Issues) | [@Xarthisius](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3AXarthisius+updated%3A2022-10-18..2023-06-13&type=Issues) | [@yamaton](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayamaton+updated%3A2022-10-18..2023-06-13&type=Issues) | [@yuvipanda](https://github.com/search?q=repo%3Ajupyterhub%2Frepo2docker+involves%3Ayuvipanda+updated%3A2022-10-18..2023-06-13&type=Issues) - ## Version 2022.10.0 [Full changelog](https://github.com/jupyterhub/repo2docker/compare/2022.02.0...2022.10.0) From 5f12217705b69242e4def9c4eeced30fa04d1581 Mon Sep 17 00:00:00 2001 From: Yuvi Panda Date: Tue, 13 Jun 2023 12:51:33 +0530 Subject: [PATCH 171/171] Use correct tag Co-authored-by: Erik Sundell --- docs/source/changelog.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/changelog.md b/docs/source/changelog.md index 4ded350ec..772de23e9 100644 --- a/docs/source/changelog.md +++ b/docs/source/changelog.md @@ -2,7 +2,7 @@ ## Version 2023.06.0 -([full changelog](https://github.com/jupyterhub/repo2docker/compare/2022.10.0...0ea6f7d85ed2adab17dae3ba2685a90df52c166d)) +([full changelog](https://github.com/jupyterhub/repo2docker/compare/2022.10.0...2023.06.0)) ### Breaking changes