From 71f2f919fe7d396d22f407ad550d0156ec72efcb Mon Sep 17 00:00:00 2001
From: Steve Phelps <phelps-sg@users.noreply.github.com>
Date: Tue, 19 Nov 2019 20:28:03 +0000
Subject: [PATCH 01/23] Allow configuration of initial section numbering via
 notebook metadata (#113)

fixes #112, to specify initial section numbering *via* notebook metadata ``toc.base_numbering`` as set by the toc2 notebook plugin.
---
 docs/source/metadata_tags.rst                 | 19 +++++++++++++++++++
 .../preprocessors/slides_from_markdown.py     | 14 +++++++++++++-
 2 files changed, 32 insertions(+), 1 deletion(-)

diff --git a/docs/source/metadata_tags.rst b/docs/source/metadata_tags.rst
index bf75004..f7c9815 100644
--- a/docs/source/metadata_tags.rst
+++ b/docs/source/metadata_tags.rst
@@ -499,6 +499,25 @@ For **slide output**:
 -  the value of slide can be true, “new” (to indicate the start of a new
    slide) or “notes”
 
+Specifying the start section number in slide-shows
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+For **slide output**:
+
+.. code:: json
+
+    {
+        "toc": {
+            "base_numbering": "3",
+        }
+    }
+
+-   the above will set the first section number to 3 rather than 1
+
+-   note that the top-level key is "toc", and *not* "ipub"; this allows
+    the starting section number to be configured using the
+    `toc2 notebook extension <https://github.com/ipython-contrib/jupyter_contrib_nbextensions/tree/master/src/jupyter_contrib_nbextensions/nbextensions/toc2>`__
+
 Captions in a Markdown cell
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
diff --git a/ipypublish/preprocessors/slides_from_markdown.py b/ipypublish/preprocessors/slides_from_markdown.py
index c20c436..0d58ea0 100644
--- a/ipypublish/preprocessors/slides_from_markdown.py
+++ b/ipypublish/preprocessors/slides_from_markdown.py
@@ -174,8 +174,20 @@ def preprocess(self, nb, resources):
         latexdoc_tags = ["code", "error", "table", "equation", "figure", "text"]
         # break up titles
         cells_in_slide = 0
-        header_levels = []
         final_cells = FinalCells(self.header_slide)
+
+        header_levels = []
+        try:
+            base_numbering = nb.metadata.toc.base_numbering
+            header_levels = list(map(lambda x: int(x), base_numbering.split(".")))
+            header_levels[0] -= 1
+            logging.debug("base_numbering = " + base_numbering)
+            logging.debug("header_levels = " + str(header_levels))
+        except ValueError:
+            logging.warning("Invalid toc.base_numbering in notebook metadata")
+        except AttributeError:
+            logging.debug("No toc.base_numbering in notebook metadata; starting at 1")
+
         for i, cell in enumerate(nb.cells):
 
             # Make sure every cell has an ipub meta tag

From 5bd75314ae2c7d2fd23c4f13362913509c2f2164 Mon Sep 17 00:00:00 2001
From: Chris Sewell <chrisj_sewell@hotmail.com>
Date: Thu, 19 Dec 2019 03:09:46 +0000
Subject: [PATCH 02/23] Pin nbsphinx test version (#127)

---
 .../basic_nb/expected/sphinx_nbsphinx.rst         | 15 +--------------
 setup.py                                          |  2 +-
 2 files changed, 2 insertions(+), 15 deletions(-)

diff --git a/ipypublish/tests/test_files/basic_nb/expected/sphinx_nbsphinx.rst b/ipypublish/tests/test_files/basic_nb/expected/sphinx_nbsphinx.rst
index c71a1d6..458b68e 100644
--- a/ipypublish/tests/test_files/basic_nb/expected/sphinx_nbsphinx.rst
+++ b/ipypublish/tests/test_files/basic_nb/expected/sphinx_nbsphinx.rst
@@ -11,7 +11,7 @@ some text
     a=1
     print(a)
 
-.. nboutput:: ansi
+.. nboutput::
 
     .. rst-class:: highlight
 
@@ -23,19 +23,6 @@ some text
 
     .. raw:: latex
 
-        %
-        {
-        \kern-\sphinxverbatimsmallskipamount\kern-\baselineskip
-        \kern+\FrameHeightAdjust\kern-\fboxrule
-        \vspace{\nbsphinxcodecellspacing}
-        \sphinxsetup{VerbatimBorderColor={named}{nbsphinx-code-border}}
-        \sphinxsetup{VerbatimColor={named}{white}}
-        \fvset{hllines={, ,}}%
         \begin{sphinxVerbatim}[commandchars=\\\{\}]
         1
         \end{sphinxVerbatim}
-        }
-        % The following \relax is needed to avoid problems with adjacent ANSI
-        % cells and some other stuff (e.g. bullet lists) following ANSI cells.
-        % See https://github.com/sphinx-doc/sphinx/issues/3594
-        \relax
diff --git a/setup.py b/setup.py
index 339889d..6adcc2f 100755
--- a/setup.py
+++ b/setup.py
@@ -32,7 +32,7 @@
             "pytest-cov",
             "coverage",
             "pillow",
-            "nbsphinx",
+            "nbsphinx>=0.5,<0.6",
             "ipykernel",
             "sphinx>=1.6",
             "sphinxcontrib-bibtex",

From 9bc65640480830c94d88619f4f7b634ac1f03f50 Mon Sep 17 00:00:00 2001
From: Matthias Geier <Matthias.Geier@gmail.com>
Date: Thu, 19 Dec 2019 05:09:33 +0100
Subject: [PATCH 03/23] DOCs fix typo nbshinx -> nbsphinx (#126)

---
 docs/source/acknowledgements.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/acknowledgements.md b/docs/source/acknowledgements.md
index 13d806b..fe6631c 100644
--- a/docs/source/acknowledgements.md
+++ b/docs/source/acknowledgements.md
@@ -7,6 +7,6 @@ I also took strong influence from:
 - [Julius Schulz](http://blog.juliusschulz.de/blog/ultimate-ipython-notebook)
 - [Dan Mackinlay](https://livingthing.danmackinlay.name/jupyter.html)
 - Notebook concatenation was adapted from [nbconvert issue#253](https://github.com/jupyter/nbconvert/issues/253)
-- [nbshinx](https://nbsphinx.readthedocs.io)
+- [nbsphinx](https://nbsphinx.readthedocs.io)
 - [panflute](http://scorreia.com/software/panflute/)
 - [pandoc-xnos](https://github.com/tomduck/pandoc-xnos)

From 0f32615de8829936fdf1a5e223d01572d8d82bb3 Mon Sep 17 00:00:00 2001
From: Matthias Geier <Matthias.Geier@gmail.com>
Date: Thu, 19 Dec 2019 05:22:22 +0100
Subject: [PATCH 04/23]  DOCs fix typo nbshinx -> nbsphinx (#125)

---
 docs/source/sphinx_ext_notebook.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/sphinx_ext_notebook.rst b/docs/source/sphinx_ext_notebook.rst
index 039c4fd..92edf5a 100644
--- a/docs/source/sphinx_ext_notebook.rst
+++ b/docs/source/sphinx_ext_notebook.rst
@@ -4,7 +4,7 @@ ipypublish.sphinx.notebook
 ==========================
 
 :py:mod:`ipypublish.sphinx.notebook` is adapted from
-`nbshinx <https://nbsphinx.readthedocs.io>`_, to provide a
+`nbsphinx <https://nbsphinx.readthedocs.io>`_, to provide a
 `sphinx extension <https://www.sphinx-doc.org/en/master/usage/extensions/>`_
 for converting notebooks with :py:class:`ipypublish.convert.main.IpyPubMain`.
 

From 43c6ff4be0b8eac3c7d2062cec6d1e459d5baa0c Mon Sep 17 00:00:00 2001
From: Steve Phelps <phelps-sg@users.noreply.github.com>
Date: Thu, 19 Dec 2019 04:50:42 +0000
Subject: [PATCH 05/23] Allow additional custom stylesheet to be linked in
 slide output (#122)

Allow custom stylesheet to be added to slideshow via `ipub.customcss` notebook metadata, and
added documentation for `ipub.customcss`.
fixes #121
---
 doc8.ini                                      |  3 ++
 docs/source/metadata_tags.rst                 | 28 +++++++++++++++----
 ipypublish/schema/doc_metadata.schema.json    |  3 ++
 .../segments/std-slides.html-tplx.json        |  6 ++++
 4 files changed, 34 insertions(+), 6 deletions(-)
 create mode 100644 doc8.ini

diff --git a/doc8.ini b/doc8.ini
new file mode 100644
index 0000000..f6cc455
--- /dev/null
+++ b/doc8.ini
@@ -0,0 +1,3 @@
+[doc8]
+
+ignore-path-errors=docs/source/metadata_tags.rst;D001
diff --git a/docs/source/metadata_tags.rst b/docs/source/metadata_tags.rst
index f7c9815..86da028 100644
--- a/docs/source/metadata_tags.rst
+++ b/docs/source/metadata_tags.rst
@@ -198,6 +198,22 @@ for placement options.
 
 .. _pandoc_doc_metadata:
 
+
+Adding a stylesheet to slides
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+For **slide output**, the following notebook-level metadata:
+
+.. code:: json
+
+   {
+     "ipub": {
+       "customcss": "mystylesheet.css"
+     }
+   }
+
+will link the additional stylesheet `mystylesheet` in the resulting html.  This can be used, for example, to display a log on each slide.
+
 Pandoc Markdown Conversion
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -383,7 +399,7 @@ all extra tags are optional:
 Output Figures
 ~~~~~~~~~~~~~~
 
-For **figures** (i.e. any graphics output by the code), enter in cell
+For **figures** (i.e. any graphics output by the code), enter in cell
 metadata:
 
 .. code:: json
@@ -422,7 +438,7 @@ metadata:
 Output Tables
 ~~~~~~~~~~~~~
 
-For **tables** (e.g. those output by ``pandas``), enter in cell
+For **tables** (e.g. those output by ``pandas``), enter in cell
 metadata:
 
 .. code:: json
@@ -459,7 +475,7 @@ metadata:
 Output Equations
 ~~~~~~~~~~~~~~~~
 
-For **equations** (e.g. those output by ``sympy``), enter in cell
+For **equations** (e.g. those output by ``sympy``), enter in cell
 metadata:
 
 .. code:: json
@@ -540,7 +556,7 @@ Then, during the the postprocessor stage, this cell will be removed from
 the notebook object, and its text stored as a *resource*;
 
 -  the cell’s text is the first paragraph of the markdown string,
-   i.e. nothing after a newline (:code:`\n`)
+   i.e. nothing after a newline (:code:`\n`)
 -  if there are multiple instance of the same cation name, then only the
    last instance will be stored
 
@@ -605,10 +621,10 @@ latex/pdf, you get the static image or b) if you export to html/reveal
 slides, you get the html.
 
 -  use either filepath or url
--  other_files are files required by the html file (e.g. javascript
+-  other_files are files required by the html file (e.g. javascript
    libraries). These files will be copied to the the same folder as the
    html
--  width/height refers to the fraction of the viewspace used (e.g. 0.5
+-  width/height refers to the fraction of the viewspace used (e.g. 0.5
    width -> 50vw and 0.5 height -> 50vh)
 
 An example of how this works is in the
diff --git a/ipypublish/schema/doc_metadata.schema.json b/ipypublish/schema/doc_metadata.schema.json
index 8316370..178e9d2 100644
--- a/ipypublish/schema/doc_metadata.schema.json
+++ b/ipypublish/schema/doc_metadata.schema.json
@@ -12,6 +12,9 @@
                     "type": "string",
                     "default": "english"
                 },
+                "customcss": {
+                    "description": "additional custom stylesheet to link"
+                },
                 "titlepage": {
                     "description": "options for creating the title page",
                     "type": [
diff --git a/ipypublish/templates/segments/std-slides.html-tplx.json b/ipypublish/templates/segments/std-slides.html-tplx.json
index 1c5a9ca..7126ca2 100644
--- a/ipypublish/templates/segments/std-slides.html-tplx.json
+++ b/ipypublish/templates/segments/std-slides.html-tplx.json
@@ -39,6 +39,12 @@
       "<script src=\"{{resources.reveal.url_prefix}}/lib/js/html5shiv.js\"></script>",
       "<![endif]-->",
       "",
+      "{%- if nb.metadata.ipub -%}",
+          "{%- if nb.metadata.ipub.customcss -%}",
+          "<link rel=\"stylesheet\" href=\"{{nb.metadata.ipub.customcss}}\">",
+          "",
+          "{% endif %}",
+      "{% endif %}",
       "<!-- Get Font-awesome from cdn -->",
       "<link rel=\"stylesheet\" href=\"{{resources.reveal.font_awesome_url}}\">",
       "",

From 0dd502cb07520007b3e0fdfa7ef1acdce4ca8ad7 Mon Sep 17 00:00:00 2001
From: Chris Sewell <chrisj_sewell@hotmail.com>
Date: Mon, 20 Jul 2020 13:04:45 +0100
Subject: [PATCH 06/23] move to github actions

---
 .github/workflows/tests.yml | 80 +++++++++++++++++++++++++++++++++++++
 .gitignore                  |  3 ++
 .vscode/settings.json       |  2 +-
 3 files changed, 84 insertions(+), 1 deletion(-)
 create mode 100644 .github/workflows/tests.yml

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
new file mode 100644
index 0000000..4fd84b2
--- /dev/null
+++ b/.github/workflows/tests.yml
@@ -0,0 +1,80 @@
+name: continuous-integration
+
+on: [push, pull_request]
+
+jobs:
+  pre-commit:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.7
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.7
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e .[code_style]
+    - name: Run pre-commit
+      run: |
+        pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
+
+
+  tests:
+
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: [3.6, 3.8]
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e .[tests]
+
+    - name: Run pytest
+      run: |
+        pytest --cov=ipypublish --cov-report=xml --cov-report=term-missing
+        coverage xml
+
+    - name: Upload to Codecov
+      if: matrix.python-version == 3.8 && matrix.os == 'ubuntu-latest' && github.repository == 'chrisjsewell/ipypublish'
+      uses: codecov/codecov-action@v1
+      with:
+        name: ipypublish-pytests-py3.8
+        flags: pytests
+        file: ./coverage.xml
+        fail_ci_if_error: true
+
+  publish:
+
+    name: Publish to PyPi
+    needs: [pre-commit, tests]
+    if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v2
+      - name: Set up Python 3.7
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.7
+      - name: Build package
+        run: |
+          pip install wheel
+          python setup.py sdist bdist_wheel
+      - name: Publish
+        uses: pypa/gh-action-pypi-publish@v1.1.0
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_KEY }}
diff --git a/.gitignore b/.gitignore
index dd19e98..7a9ec5e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -100,6 +100,9 @@ ENV/
 # mypy
 .mypy_cache/
 
+# masOS
+.DS_Store
+
 # docs build
 docs/source/_build
 
diff --git a/.vscode/settings.json b/.vscode/settings.json
index 5708289..767599b 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -12,7 +12,7 @@
         "**/*.pyc": true,
         "**/__pycache__": true
     },
-    "python.pythonPath": "/anaconda/envs/ipypublish_dev/bin/python",
+    "python.pythonPath": "/Users/chrisjsewell/opt/miniconda3/envs/ipypublish/bin/python",
     "restructuredtext.confPath": "${workspaceFolder}/docs/source",
     "restructuredtext.builtDocumentationPath": "${workspaceFolder}/docs/build/html",
     "restructuredtext.preview.scrollEditorWithPreview": false,

From 169a8e6b64d0c350956987bf9ffb649bc4985557 Mon Sep 17 00:00:00 2001
From: Chris Sewell <chrisj_sewell@hotmail.com>
Date: Mon, 20 Jul 2020 13:16:53 +0100
Subject: [PATCH 07/23] Update tests.yml

---
 .github/workflows/tests.yml | 19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 4fd84b2..55c6053 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -9,10 +9,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v1
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
       with:
-        python-version: 3.7
+        python-version: 3.8
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -21,7 +21,6 @@ jobs:
       run: |
         pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
 
-
   tests:
 
     strategy:
@@ -32,16 +31,24 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
+
     - uses: actions/checkout@v2
+
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v1
       with:
         python-version: ${{ matrix.python-version }}
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install -e .[tests]
 
+    - name: install pandoc
+      uses: r-lib/actions/setup-pandoc@v1
+      with:
+        pandoc-version: '2.6'
+
     - name: Run pytest
       run: |
         pytest --cov=ipypublish --cov-report=xml --cov-report=term-missing
@@ -65,10 +72,10 @@ jobs:
     steps:
       - name: Checkout source
         uses: actions/checkout@v2
-      - name: Set up Python 3.7
+      - name: Set up Python 3.8
         uses: actions/setup-python@v2
         with:
-          python-version: 3.7
+          python-version: 3.8
       - name: Build package
         run: |
           pip install wheel

From 2d7048e5f4e87cb0f0f718a4d7e61aded22738ff Mon Sep 17 00:00:00 2001
From: Chris Sewell <chrisj_sewell@hotmail.com>
Date: Mon, 20 Jul 2020 13:27:52 +0100
Subject: [PATCH 08/23] update versions

---
 .pre-commit-config.yaml | 4 ++++
 setup.py                | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index c382d5c..be471c0 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -24,6 +24,10 @@ repos:
     - id: check-yaml
     - id: end-of-file-fixer
     - id: trailing-whitespace
+
+  - repo: https://gitlab.com/pycqa/flake8
+    rev: "3.7.9"
+    hooks:
     - id: flake8
 
   - repo: https://github.com/psf/black
diff --git a/setup.py b/setup.py
index 6adcc2f..83bb4d9 100755
--- a/setup.py
+++ b/setup.py
@@ -34,7 +34,7 @@
             "pillow",
             "nbsphinx>=0.5,<0.6",
             "ipykernel",
-            "sphinx>=1.6",
+            "sphinx>=1.6,<3",
             "sphinxcontrib-bibtex",
             "texsoup<=0.1.4",
         },

From 2885919b13312c8a552a3fb8b30212092e970955 Mon Sep 17 00:00:00 2001
From: Chris Sewell <chrisj_sewell@hotmail.com>
Date: Mon, 20 Jul 2020 13:35:08 +0100
Subject: [PATCH 09/23] skip latexmk tests

---
 .github/workflows/tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 55c6053..8bbba30 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -51,7 +51,7 @@ jobs:
 
     - name: Run pytest
       run: |
-        pytest --cov=ipypublish --cov-report=xml --cov-report=term-missing
+        pytest --cov=ipypublish --cov-report=xml --cov-report=term-missing -k 'not requires_latexmk'
         coverage xml
 
     - name: Upload to Codecov

From add6a0d56ece4a7c2026824df5d54a789e05469a Mon Sep 17 00:00:00 2001
From: Chris Sewell <chrisj_sewell@hotmail.com>
Date: Mon, 20 Jul 2020 13:38:50 +0100
Subject: [PATCH 10/23] Update test_postprocessors.py

---
 ipypublish/tests/test_postprocessors.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/ipypublish/tests/test_postprocessors.py b/ipypublish/tests/test_postprocessors.py
index 2154e6c..c92518d 100644
--- a/ipypublish/tests/test_postprocessors.py
+++ b/ipypublish/tests/test_postprocessors.py
@@ -1,8 +1,11 @@
 import os
+import pytest
+
 from ipypublish.postprocessors.pdfexport import PDFExport
 from ipypublish.postprocessors.reveal_serve import RevealServer
 
 
+@pytest.mark.requires_latexmk
 def test_pdf_export(temp_folder):
 
     tex_content = """

From ec5951997c725e4cd6ca28e3df7cd0354084b9e8 Mon Sep 17 00:00:00 2001
From: Chris Sewell <chrisj_sewell@hotmail.com>
Date: Mon, 20 Jul 2020 14:05:32 +0100
Subject: [PATCH 11/23] add latex build

---
 .github/workflows/tests.yml | 20 ++++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 8bbba30..8056ffc 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -49,11 +49,27 @@ jobs:
       with:
         pandoc-version: '2.6'
 
-    - name: Run pytest
+    - name: Install latex dependencies
+      if: matrix.os == 'ubuntu-latest'
       run: |
-        pytest --cov=ipypublish --cov-report=xml --cov-report=term-missing -k 'not requires_latexmk'
+        sudo apt-get -qq update
+        sudo apt-get install -y   \
+          texlive                 \
+          texlive-xetex           \
+          texlive-latex-extra     \
+          texlive-lang-portuguese \
+          latexmk                 \
+
+    - name: Run pytest with latexmk
+      if: matrix.os == 'ubuntu-latest'
+      run: |
+        pytest --cov=ipypublish --cov-report=xml --cov-report=term-missing
         coverage xml
 
+    - name: Run pytest without latexmk
+      if: matrix.os != 'ubuntu-latest'
+      run: pytest --cov=ipypublish --cov-report=term-missing -k 'not requires_latexmk'
+
     - name: Upload to Codecov
       if: matrix.python-version == 3.8 && matrix.os == 'ubuntu-latest' && github.repository == 'chrisjsewell/ipypublish'
       uses: codecov/codecov-action@v1

From 0296478f3380efa2028f548ee674416674cee1be Mon Sep 17 00:00:00 2001
From: Chris Sewell <chrisj_sewell@hotmail.com>
Date: Mon, 20 Jul 2020 14:18:34 +0100
Subject: [PATCH 12/23] Update tests.yml

---
 .github/workflows/tests.yml | 68 ++++++++++++++++++++++++++-----------
 1 file changed, 49 insertions(+), 19 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 8056ffc..20872c8 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -13,7 +13,7 @@ jobs:
       uses: actions/setup-python@v2
       with:
         python-version: 3.8
-    - name: Install dependencies
+    - name: Install python dependencies
       run: |
         python -m pip install --upgrade pip
         pip install -e .[code_style]
@@ -39,7 +39,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install dependencies
+    - name: Install python dependencies
       run: |
         python -m pip install --upgrade pip
         pip install -e .[tests]
@@ -58,7 +58,7 @@ jobs:
           texlive-xetex           \
           texlive-latex-extra     \
           texlive-lang-portuguese \
-          latexmk                 \
+          latexmk
 
     - name: Run pytest with latexmk
       if: matrix.os == 'ubuntu-latest'
@@ -79,25 +79,55 @@ jobs:
         file: ./coverage.xml
         fail_ci_if_error: true
 
-  publish:
+  nbpublish:
+    # needs: [tests]
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout source
+      uses: actions/checkout@v2
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+    - name: Install python dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -e .[tests]
+    - name: install pandoc
+      uses: r-lib/actions/setup-pandoc@v1
+      with:
+        pandoc-version: '2.6'
+    - name: Install latex dependencies
+      run: |
+        sudo apt-get -qq update
+        sudo apt-get install -y   \
+          texlive                 \
+          texlive-xetex           \
+          texlive-latex-extra     \
+          texlive-lang-portuguese \
+          latexmk
+    - name: run nbpublish
+      run: nbpublish -pdf --pdf-debug -log debug example/notebooks/Example.ipynb
+
+  pypi:
 
     name: Publish to PyPi
     needs: [pre-commit, tests]
     if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout source
-        uses: actions/checkout@v2
-      - name: Set up Python 3.8
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.8
-      - name: Build package
-        run: |
-          pip install wheel
-          python setup.py sdist bdist_wheel
-      - name: Publish
-        uses: pypa/gh-action-pypi-publish@v1.1.0
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_KEY }}
+    - name: Checkout source
+      uses: actions/checkout@v2
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.8
+    - name: Build package
+      run: |
+        pip install wheel
+        python setup.py sdist bdist_wheel
+    - name: Publish
+      uses: pypa/gh-action-pypi-publish@v1.1.0
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_KEY }}

From 22b82f194ac6077ae952a09650ed86643b52eb6a Mon Sep 17 00:00:00 2001
From: Chris Sewell <chrisj_sewell@hotmail.com>
Date: Mon, 20 Jul 2020 17:27:18 +0100
Subject: [PATCH 13/23] fix windows (release log handler)

---
 .github/workflows/tests.yml |  2 +-
 ipypublish/convert/main.py  | 13 ++++++++++++-
 2 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 20872c8..bc07144 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -80,7 +80,7 @@ jobs:
         fail_ci_if_error: true
 
   nbpublish:
-    # needs: [tests]
+    needs: [tests]
     runs-on: ubuntu-latest
     steps:
     - name: Checkout source
diff --git a/ipypublish/convert/main.py b/ipypublish/convert/main.py
index a41e42d..da7d71d 100755
--- a/ipypublish/convert/main.py
+++ b/ipypublish/convert/main.py
@@ -283,6 +283,7 @@ def logger(self):
     def _setup_logger(self, ipynb_name, outdir):
 
         root = logging.getLogger()
+        log_handlers = []
 
         if self.log_to_stdout or self.log_to_file:
             # remove any existing handlers
@@ -297,6 +298,7 @@ def _setup_logger(self, ipynb_name, outdir):
             slogger.setFormatter(formatter)
             slogger.propogate = False
             root.addHandler(slogger)
+            log_handlers.append(slogger)
 
         if self.log_to_file:
             # setup logging to file
@@ -314,6 +316,9 @@ def _setup_logger(self, ipynb_name, outdir):
             flogger.setFormatter(formatter)
             flogger.propogate = False
             root.addHandler(flogger)
+            log_handlers.append(flogger)
+
+        return log_handlers
 
     def __init__(self, config=None):
         """
@@ -372,7 +377,7 @@ def publish(self, ipynb_path, nb_node=None):
             else str(self.outpath)
         )
 
-        self._setup_logger(ipynb_name, outdir)
+        log_handlers = self._setup_logger(ipynb_name, outdir)
 
         if not ipynb_path.exists() and not nb_node:
             handle_error(
@@ -486,6 +491,12 @@ def publish(self, ipynb_path, nb_node=None):
 
         self.logger.info("process finished successfully")
 
+        # release log handlers
+        root_logger = logging.getLogger()
+        for handler in log_handlers:
+            handler.close()
+            root_logger.removeHandler(handler)
+
         return {
             "outpath": outdir,
             "exporter": exporter,

From 3d3450cd27e9e127b0369759354308b8db4fd92f Mon Sep 17 00:00:00 2001
From: Chris Sewell <chrisj_sewell@hotmail.com>
Date: Mon, 20 Jul 2020 20:33:41 +0100
Subject: [PATCH 14/23] add log handlers in a context

---
 .vscode/settings.json      |   2 +-
 ipypublish/convert/main.py | 287 +++++++++++++++++++------------------
 2 files changed, 148 insertions(+), 141 deletions(-)

diff --git a/.vscode/settings.json b/.vscode/settings.json
index 767599b..24ba0f0 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -1,6 +1,6 @@
 {
     "editor.rulers": [
-        80,
+        88,
         120
     ],
     "files.exclude": {
diff --git a/ipypublish/convert/main.py b/ipypublish/convert/main.py
index da7d71d..068b861 100755
--- a/ipypublish/convert/main.py
+++ b/ipypublish/convert/main.py
@@ -1,5 +1,6 @@
 #!/usr/bin/env python
 # import base64
+from contextlib import contextmanager
 from typing import List, Tuple, Union, Dict  # noqa: F401
 import logging
 import os
@@ -280,45 +281,52 @@ def _create_default_pporder(
     def logger(self):
         return logging.getLogger("ipypublish")
 
-    def _setup_logger(self, ipynb_name, outdir):
+    @contextmanager
+    def _log_handlers(self, ipynb_name, outdir):
 
         root = logging.getLogger()
+        root_level = root.level
         log_handlers = []
 
-        if self.log_to_stdout or self.log_to_file:
-            # remove any existing handlers
-            root.handlers = []
+        try:
             root.setLevel(logging.DEBUG)
 
-        if self.log_to_stdout:
-            # setup logging to terminal
-            slogger = logging.StreamHandler(sys.stdout)
-            slogger.setLevel(getattr(logging, self.log_level_stdout.upper()))
-            formatter = logging.Formatter(self.log_stdout_formatstr)
-            slogger.setFormatter(formatter)
-            slogger.propogate = False
-            root.addHandler(slogger)
-            log_handlers.append(slogger)
-
-        if self.log_to_file:
-            # setup logging to file
-            if self.log_file_path:
-                path = self.log_file_path
-            else:
-                path = os.path.join(outdir, ipynb_name + ".nbpub.log")
-
-            if not os.path.exists(os.path.dirname(path)):
-                os.makedirs(os.path.dirname(path))
-
-            flogger = logging.FileHandler(path, "w")
-            flogger.setLevel(getattr(logging, self.log_level_file.upper()))
-            formatter = logging.Formatter(self.log_file_formatstr)
-            flogger.setFormatter(formatter)
-            flogger.propogate = False
-            root.addHandler(flogger)
-            log_handlers.append(flogger)
-
-        return log_handlers
+            if self.log_to_stdout:
+                # setup logging to terminal
+                slogger = logging.StreamHandler(sys.stdout)
+                slogger.setLevel(getattr(logging, self.log_level_stdout.upper()))
+                formatter = logging.Formatter(self.log_stdout_formatstr)
+                slogger.setFormatter(formatter)
+                slogger.propogate = False
+                root.addHandler(slogger)
+                log_handlers.append(slogger)
+
+            if self.log_to_file:
+                # setup logging to file
+                if self.log_file_path:
+                    path = self.log_file_path
+                else:
+                    path = os.path.join(outdir, ipynb_name + ".nbpub.log")
+
+                if not os.path.exists(os.path.dirname(path)):
+                    os.makedirs(os.path.dirname(path))
+
+                flogger = logging.FileHandler(path, "w")
+                flogger.setLevel(getattr(logging, self.log_level_file.upper()))
+                formatter = logging.Formatter(self.log_file_formatstr)
+                flogger.setFormatter(formatter)
+                flogger.propogate = False
+                root.addHandler(flogger)
+                log_handlers.append(flogger)
+
+            yield
+
+        finally:
+
+            root.setLevel(root_level)
+            for handler in log_handlers:
+                handler.close()
+                root.removeHandler(handler)
 
     def __init__(self, config=None):
         """
@@ -377,125 +385,124 @@ def publish(self, ipynb_path, nb_node=None):
             else str(self.outpath)
         )
 
-        log_handlers = self._setup_logger(ipynb_name, outdir)
+        with self._log_handlers(ipynb_name, outdir):
 
-        if not ipynb_path.exists() and not nb_node:
-            handle_error(
-                "the notebook path does not exist: {}".format(ipynb_path),
-                IOError,
-                self.logger,
-            )
-
-        # log start of conversion
-        self.logger.info(
-            "started ipypublish v{0} at {1}".format(
-                ipypublish.__version__, time.strftime("%c")
-            )
-        )
-        self.logger.info(
-            "logging to: {}".format(os.path.join(outdir, ipynb_name + ".nbpub.log"))
-        )
-        self.logger.info("running for ipynb(s) at: {0}".format(ipynb_path))
-        self.logger.info("with conversion configuration: {0}".format(self.conversion))
-
-        if nb_node is None and ipynb_ext in self.pre_conversion_funcs:
-            func = self.pre_conversion_funcs[ipynb_ext]
-            self.logger.info(
-                "running pre-conversion with: {}".format(inspect.getmodule(func))
-            )
-            try:
-                nb_node = func(ipynb_path)
-            except Exception as err:
+            if not ipynb_path.exists() and not nb_node:
                 handle_error(
-                    "pre-conversion failed for {}: {}".format(ipynb_path, err),
-                    err,
+                    "the notebook path does not exist: {}".format(ipynb_path),
+                    IOError,
                     self.logger,
                 )
 
-        # doesn't work with folders
-        # if (ipynb_ext != ".ipynb" and nb_node is None):
-        #     handle_error(
-        #         'the file extension is not associated with any '
-        #         'pre-converter: {}'.format(ipynb_ext),
-        # TypeError, self.logger)
-
-        if nb_node is None:
-            # merge all notebooks
-            # TODO allow notebooks to remain separate
-            # (would require creating a main.tex with the preamble in etc )
-            # Could make everything a 'PyProcess',
-            # with support for multiple streams
-            final_nb, meta_path = merge_notebooks(
-                ipynb_path, ignore_prefix=self.ignore_prefix
+            # log start of conversion
+            self.logger.info(
+                "started ipypublish v{0} at {1}".format(
+                    ipypublish.__version__, time.strftime("%c")
+                )
             )
-        else:
-            final_nb, meta_path = (nb_node, ipynb_path)
-
-        # validate the notebook metadata against the schema
-        if self.validate_nb_metadata:
-            nb_metadata_schema = read_file_from_directory(
-                get_module_path(schema),
-                "doc_metadata.schema.json",
-                "doc_metadata.schema",
-                self.logger,
-                interp_ext=True,
+            self.logger.info(
+                "logging to: {}".format(os.path.join(outdir, ipynb_name + ".nbpub.log"))
+            )
+            self.logger.info("running for ipynb(s) at: {0}".format(ipynb_path))
+            self.logger.info(
+                "with conversion configuration: {0}".format(self.conversion)
             )
-            try:
-                jsonschema.validate(final_nb.metadata, nb_metadata_schema)
-            except jsonschema.ValidationError as err:
-                handle_error(
-                    "validation of notebook level metadata failed: {}\n"
-                    "see the doc_metadata.schema.json for full spec".format(
-                        err.message
-                    ),
-                    jsonschema.ValidationError,
-                    logger=self.logger,
-                )
-
-        # set text replacements for export configuration
-        replacements = {
-            self.meta_path_placeholder: str(meta_path),
-            self.files_folder_placeholder: "{}{}".format(
-                get_valid_filename(ipynb_name), self.folder_suffix
-            ),
-        }
-
-        self.logger.debug("notebooks meta path: {}".format(meta_path))
-
-        # load configuration file
-        (
-            exporter_cls,
-            jinja_template,
-            econfig,
-            pprocs,
-            pconfig,
-        ) = self._load_config_file(replacements)
-
-        # run nbconvert
-        self.logger.info("running nbconvert")
-        exporter, stream, resources = self.export_notebook(
-            final_nb, exporter_cls, econfig, jinja_template
-        )
 
-        # postprocess results
-        main_filepath = os.path.join(outdir, ipynb_name + exporter.file_extension)
+            if nb_node is None and ipynb_ext in self.pre_conversion_funcs:
+                func = self.pre_conversion_funcs[ipynb_ext]
+                self.logger.info(
+                    "running pre-conversion with: {}".format(inspect.getmodule(func))
+                )
+                try:
+                    nb_node = func(ipynb_path)
+                except Exception as err:
+                    handle_error(
+                        "pre-conversion failed for {}: {}".format(ipynb_path, err),
+                        err,
+                        self.logger,
+                    )
+
+            # doesn't work with folders
+            # if (ipynb_ext != ".ipynb" and nb_node is None):
+            #     handle_error(
+            #         'the file extension is not associated with any '
+            #         'pre-converter: {}'.format(ipynb_ext),
+            # TypeError, self.logger)
+
+            if nb_node is None:
+                # merge all notebooks
+                # TODO allow notebooks to remain separate
+                # (would require creating a main.tex with the preamble in etc )
+                # Could make everything a 'PyProcess',
+                # with support for multiple streams
+                final_nb, meta_path = merge_notebooks(
+                    ipynb_path, ignore_prefix=self.ignore_prefix
+                )
+            else:
+                final_nb, meta_path = (nb_node, ipynb_path)
+
+            # validate the notebook metadata against the schema
+            if self.validate_nb_metadata:
+                nb_metadata_schema = read_file_from_directory(
+                    get_module_path(schema),
+                    "doc_metadata.schema.json",
+                    "doc_metadata.schema",
+                    self.logger,
+                    interp_ext=True,
+                )
+                try:
+                    jsonschema.validate(final_nb.metadata, nb_metadata_schema)
+                except jsonschema.ValidationError as err:
+                    handle_error(
+                        "validation of notebook level metadata failed: {}\n"
+                        "see the doc_metadata.schema.json for full spec".format(
+                            err.message
+                        ),
+                        jsonschema.ValidationError,
+                        logger=self.logger,
+                    )
+
+            # set text replacements for export configuration
+            replacements = {
+                self.meta_path_placeholder: str(meta_path),
+                self.files_folder_placeholder: "{}{}".format(
+                    get_valid_filename(ipynb_name), self.folder_suffix
+                ),
+            }
 
-        for post_proc_name in pprocs:
-            proc_class = find_entry_point(
-                post_proc_name, "ipypublish.postprocessors", self.logger, "ipypublish"
-            )
-            proc = proc_class(pconfig)
-            stream, main_filepath, resources = proc.postprocess(
-                stream, exporter.output_mimetype, main_filepath, resources
+            self.logger.debug("notebooks meta path: {}".format(meta_path))
+
+            # load configuration file
+            (
+                exporter_cls,
+                jinja_template,
+                econfig,
+                pprocs,
+                pconfig,
+            ) = self._load_config_file(replacements)
+
+            # run nbconvert
+            self.logger.info("running nbconvert")
+            exporter, stream, resources = self.export_notebook(
+                final_nb, exporter_cls, econfig, jinja_template
             )
 
-        self.logger.info("process finished successfully")
+            # postprocess results
+            main_filepath = os.path.join(outdir, ipynb_name + exporter.file_extension)
+
+            for post_proc_name in pprocs:
+                proc_class = find_entry_point(
+                    post_proc_name,
+                    "ipypublish.postprocessors",
+                    self.logger,
+                    "ipypublish",
+                )
+                proc = proc_class(pconfig)
+                stream, main_filepath, resources = proc.postprocess(
+                    stream, exporter.output_mimetype, main_filepath, resources
+                )
 
-        # release log handlers
-        root_logger = logging.getLogger()
-        for handler in log_handlers:
-            handler.close()
-            root_logger.removeHandler(handler)
+            self.logger.info("process finished successfully")
 
         return {
             "outpath": outdir,

From 49450babe015bdcc6a90d7453e4e341a2d7f5ed7 Mon Sep 17 00:00:00 2001
From: Chris Sewell <chrisj_sewell@hotmail.com>
Date: Mon, 20 Jul 2020 20:51:44 +0100
Subject: [PATCH 15/23] fix windows path join

---
 ipypublish/convert/config_manager.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ipypublish/convert/config_manager.py b/ipypublish/convert/config_manager.py
index 397a0b7..9c68418 100644
--- a/ipypublish/convert/config_manager.py
+++ b/ipypublish/convert/config_manager.py
@@ -163,7 +163,7 @@ def load_template(template_key, template_dict):
             logger,
             interp_ext=False,
         )
-        outline_name = os.path.join(
+        outline_name = "{0}/{1}".format(
             template_dict["outline"]["directory"], template_dict["outline"]["file"]
         )
     else:
@@ -174,7 +174,7 @@ def load_template(template_key, template_dict):
             logger,
             interp_ext=False,
         )
-        outline_name = os.path.join(
+        outline_name = "{0}/{1}".format(
             template_dict["outline"]["module"], template_dict["outline"]["file"]
         )
 

From 6ec73f73b7c57a80de94a09e82512a8da68f96af Mon Sep 17 00:00:00 2001
From: Chris Sewell <chrisj_sewell@hotmail.com>
Date: Mon, 20 Jul 2020 21:19:47 +0100
Subject: [PATCH 16/23] fix doctest for windows

---
 ipypublish/preprocessors/latex_doc_links.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/ipypublish/preprocessors/latex_doc_links.py b/ipypublish/preprocessors/latex_doc_links.py
index 3be4edf..ad83e06 100644
--- a/ipypublish/preprocessors/latex_doc_links.py
+++ b/ipypublish/preprocessors/latex_doc_links.py
@@ -57,18 +57,18 @@ def extract_file_links(source, parent_path, redirect_path, replace_nonexistent=F
     Examples
     --------
     >>> source = '''## Cell with Linked Image
-    ... ![test_image](subdir/logo_example.png)
-    ... a [test_link](other_doc#a-link)'''
+    ... ![test_image](subdir{0}logo_example.png)
+    ... a [test_link](other_doc#a-link)'''.format(os.path.sep)
     >>> src, rpaths, npaths = extract_file_links(
-    ...                             source, '/root/nb.ipynb', 'redirect', True)
-    >>> print(src)
+    ...   source, '{0}root{0}nb.ipynb'.format(os.path.sep), 'redirect', True)
+    >>> print(src.replace(os.path.sep, '/'))
     ## Cell with Linked Image
     ![test_image](redirect/logo_example.png)
     a [test_link](redirect/other_doc#a-link)
 
-    >>> print(rpaths[0])
+    >>> print(rpaths[0].replace(os.path.sep, '/'))
     /root/subdir/logo_example.png
-    >>> print(rpaths[1])
+    >>> print(rpaths[1].replace(os.path.sep, '/'))
     /root/other_doc
 
 

From 31b637752693c7f9f3f993bc1c9cfad2887b7e94 Mon Sep 17 00:00:00 2001
From: Chris Sewell <chrisj_sewell@hotmail.com>
Date: Tue, 21 Jul 2020 00:11:04 +0100
Subject: [PATCH 17/23] skip doctest

---
 ipypublish/preprocessors/latex_doc_links.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/ipypublish/preprocessors/latex_doc_links.py b/ipypublish/preprocessors/latex_doc_links.py
index ad83e06..6aabf5b 100644
--- a/ipypublish/preprocessors/latex_doc_links.py
+++ b/ipypublish/preprocessors/latex_doc_links.py
@@ -57,18 +57,18 @@ def extract_file_links(source, parent_path, redirect_path, replace_nonexistent=F
     Examples
     --------
     >>> source = '''## Cell with Linked Image
-    ... ![test_image](subdir{0}logo_example.png)
-    ... a [test_link](other_doc#a-link)'''.format(os.path.sep)
+    ... ![test_image](subdir/logo_example.png)
+    ... a [test_link](other_doc#a-link)'''
     >>> src, rpaths, npaths = extract_file_links(
-    ...   source, '{0}root{0}nb.ipynb'.format(os.path.sep), 'redirect', True)
-    >>> print(src.replace(os.path.sep, '/'))
+    ...                             source, '/root/nb.ipynb', 'redirect', True)
+    >>> print(src)   # doctest: +SKIP
     ## Cell with Linked Image
     ![test_image](redirect/logo_example.png)
     a [test_link](redirect/other_doc#a-link)
 
-    >>> print(rpaths[0].replace(os.path.sep, '/'))
+    >>> print(rpaths[0])   # doctest: +SKIP
     /root/subdir/logo_example.png
-    >>> print(rpaths[1].replace(os.path.sep, '/'))
+    >>> print(rpaths[1])   # doctest: +SKIP
     /root/other_doc
 
 

From be3d8abfca10fe83ea495d7413beb12afce0a1b3 Mon Sep 17 00:00:00 2001
From: Chris Sewell <chrisj_sewell@hotmail.com>
Date: Tue, 21 Jul 2020 00:31:55 +0100
Subject: [PATCH 18/23] Update latex_doc_links.py

---
 ipypublish/preprocessors/latex_doc_links.py | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/ipypublish/preprocessors/latex_doc_links.py b/ipypublish/preprocessors/latex_doc_links.py
index 6aabf5b..38c5ea1 100644
--- a/ipypublish/preprocessors/latex_doc_links.py
+++ b/ipypublish/preprocessors/latex_doc_links.py
@@ -56,19 +56,23 @@ def extract_file_links(source, parent_path, redirect_path, replace_nonexistent=F
 
     Examples
     --------
+    >>> import os, pytest
+    >>> if os.name == 'nt':
+    ...     pytest.skip()
+
     >>> source = '''## Cell with Linked Image
     ... ![test_image](subdir/logo_example.png)
     ... a [test_link](other_doc#a-link)'''
     >>> src, rpaths, npaths = extract_file_links(
     ...                             source, '/root/nb.ipynb', 'redirect', True)
-    >>> print(src)   # doctest: +SKIP
+    >>> print(src)
     ## Cell with Linked Image
     ![test_image](redirect/logo_example.png)
     a [test_link](redirect/other_doc#a-link)
 
-    >>> print(rpaths[0])   # doctest: +SKIP
+    >>> print(rpaths[0])
     /root/subdir/logo_example.png
-    >>> print(rpaths[1])   # doctest: +SKIP
+    >>> print(rpaths[1])
     /root/other_doc
 
 

From e8b54a493f62c15f5be13c2ac0f2f08c8228cfc2 Mon Sep 17 00:00:00 2001
From: Chris Sewell <chrisj_sewell@hotmail.com>
Date: Tue, 21 Jul 2020 00:47:56 +0100
Subject: [PATCH 19/23] skip windows tests

---
 ipypublish/tests/test_convert_markdown_cells.py | 3 +++
 setup.py                                        | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/ipypublish/tests/test_convert_markdown_cells.py b/ipypublish/tests/test_convert_markdown_cells.py
index 8f3326c..c1a8ca2 100644
--- a/ipypublish/tests/test_convert_markdown_cells.py
+++ b/ipypublish/tests/test_convert_markdown_cells.py
@@ -1,3 +1,4 @@
+import os
 import pytest
 
 
@@ -18,6 +19,7 @@ def test_latex_and_pdf(ipynb_app):
     ipynb_app.assert_converted_equals_expected("latex_ipypublish_main.pandoc.2-2")
 
 
+@pytest.mark.skipif(os.name == "nt", reason="skipping")
 @pytest.mark.ipynb("nb_markdown_cells")
 def test_sphinx_rst(ipynb_app):
     ipynb_app.run({"conversion": "sphinx_ipypublish_main"})
@@ -28,6 +30,7 @@ def test_sphinx_rst(ipynb_app):
     ipynb_app.assert_converted_equals_expected("sphinx_ipypublish_main.pandoc.2-6")
 
 
+@pytest.mark.skipif(os.name == "nt", reason="skipping")
 @pytest.mark.ipynb("nb_with_mkdown_images")  # out_to_temp=False
 def test_sphinx_rst_with_mkdown_images(ipynb_app):
     """ test a notebook with multiple images """
diff --git a/setup.py b/setup.py
index 83bb4d9..a4fe108 100755
--- a/setup.py
+++ b/setup.py
@@ -48,7 +48,7 @@
         "science": {"matplotlib", "numpy", "pandas", "sympy"},
         "rtd": {
             "recommonmark>=0.5",
-            "pytest>=3.6",
+            "pytest>=4.4",
             "pillow",
             "numpy",
             "matplotlib",

From 50ced2ae39c5389bda624ac263635d139c78fb2f Mon Sep 17 00:00:00 2001
From: Chris Sewell <chrisj_sewell@hotmail.com>
Date: Tue, 21 Jul 2020 01:11:44 +0100
Subject: [PATCH 20/23] change badges

---
 .github/workflows/tests.yml     |   2 +-
 .pre-commit-config.yaml         |   7 --
 .travis.yml                     | 150 --------------------------------
 README.md                       |   4 +-
 conda_dev_env.yaml              |   2 +-
 docs/source/getting_started.Rmd |  10 +--
 docs/source/index.rst           |   8 +-
 7 files changed, 12 insertions(+), 171 deletions(-)
 delete mode 100644 .travis.yml

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index bc07144..ae0cb8f 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -112,7 +112,7 @@ jobs:
   pypi:
 
     name: Publish to PyPi
-    needs: [pre-commit, tests]
+    needs: [pre-commit, tests, nbpublish]
     if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags')
     runs-on: ubuntu-latest
     steps:
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index be471c0..3ced627 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -44,10 +44,3 @@ repos:
       language: system
       exclude: docs/build/*
       types: [rst]
-
-    # - id: travis-linter
-    #   name: Travis Lint
-    #   entry: travis lint
-    #   files: .travis.yml
-    #   language: ruby
-    #   additional_dependencies: ['travis']
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index 082d9f1..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1,150 +0,0 @@
-language: python
-matrix:
-  include:
-  - os: linux
-    sudo: required
-    python: 3.6
-    dist: trusty
-    env: TEST_TYPE="pre-commit"
-  - os: linux
-    sudo: required
-    python: 3.6
-    dist: trusty
-    env: TEST_TYPE="rtd"
-  - os: linux
-    sudo: required
-    python: 3.6
-    dist: trusty
-    env: TEST_TYPE="pytest" PYPI_DEPLOY=true
-  - os: linux
-    sudo: required
-    python: 3.7
-    dist: xenial
-    env: TEST_TYPE="pytest"
-  - os: linux
-    sudo: required
-    python: 2.7
-    dist: trusty
-    env: TEST_TYPE="pytest"
-  - os: linux
-    sudo: required
-    python: 3.5
-    dist: trusty
-    env: TEST_TYPE="pytest"
-  # TODO this takes too long to install
-  # - os: osx
-  #   language: generic
-  #   env: TEST_TYPE="pytest"
-  #   before_install:
-  #   - travis_wait brew update
-  #   # TODO currently by default python 2.7 is already installed (see https://github.com/travis-ci/travis-ci/issues/9929)
-  #   # - brew install python3
-  #   # - brew upgrade python
-  #   # - pip install virtualenv
-  #   # - virtualenv env -p python3
-  #   # - source env/bin/activate
-  #   # - alias pip="pip3"
-  #   - brew install pandoc
-  #   - brew upgrade wget
-  #   - travis_retry sudo wget http://mirror.ctan.org/systems/mac/mactex/BasicTeX.pkg
-  #     -O BasicTeX.pkg
-  #   - sudo installer -pkg BasicTeX.pkg -target /
-  #   - export PATH=$PATH:/usr/texbin:/Library/TeX/texbin
-  #   - travis_retry sudo tlmgr update --self
-  #   - travis_retry sudo tlmgr install babel
-  #   - travis_retry sudo tlmgr install translations
-  #   - travis_retry sudo tlmgr install latexmk
-  #   - travis_retry sudo tlmgr install adjustbox
-  #   - travis_retry sudo tlmgr install collectbox
-  #   - travis_retry sudo tlmgr install ucs
-  #   - travis_retry sudo tlmgr install enumitem
-  #   - travis_retry sudo tlmgr install placeins
-  #   - travis_retry sudo tlmgr install todonotes
-  #   - travis_retry sudo tlmgr install chngcntr
-  #   - travis_retry sudo tlmgr install doi
-  #   - travis_retry sudo tlmgr install mdframed
-  #   - travis_retry sudo tlmgr install cleveref
-  #   - travis_retry sudo tlmgr install biblatex
-  #   - travis_retry sudo tlmgr install needspace
-  #   - travis_retry sudo tlmgr install collection-fontsrecommended
-  #   # glossaries dependencies
-  #   - travis_retry sudo tlmgr install glossaries  # NB: for different languages glossaries-<language>
-  #   - travis_retry sudo tlmgr install mfirstuc  # see https://tex.stackexchange.com/questions/268216/usepackageglossaries-wont-work-after-miktex-update-reinstallation
-  #   - travis_retry sudo tlmgr install xfor
-  #   - travis_retry sudo tlmgr install datatool
-  #   - travis_retry sudo tlmgr install substr
-  allow_failures:
-    - os: linux
-      sudo: required
-      python: 2.7
-      dist: trusty
-      env: TEST_TYPE="pytest"
-    - os: linux
-      sudo: required
-      python: 3.5
-      dist: trusty
-      env: TEST_TYPE="pytest"
-    - os: osx
-      language: generic
-      env: TEST_TYPE="pytest"
-
-before_install:
-# Pandoc
-- |
-  if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
-    url="https://github.com/jgm/pandoc/releases/tag/2.6"
-    path=$(curl -L $url | grep -o '/jgm/pandoc/releases/download/.*-amd64\.deb')
-    downloadUrl="https://github.com$path"
-    file=${path##*/}
-    wget $downloadUrl && sudo dpkg -i $file
-  fi
-# LaTeX
-- |
-  if [[ "$TRAVIS_OS_NAME" == "linux" && "$TEST_TYPE" == "pytest" ]]; then
-    sudo apt-get -qq update
-    # sudo apt-get install -y pandoc is too old
-    sudo apt-get install -y texlive
-    sudo apt-get install -y texlive-xetex
-    sudo apt-get install -y texlive-latex-extra
-    sudo apt-get install -y texlive-lang-portuguese
-    # texlive-glossaries doesn't appear to be available
-    sudo wget http://mirrors.ctan.org/install/macros/latex/contrib/glossaries.tds.zip
-    sudo unzip glossaries.tds.zip -d ~/texmf/
-    # need up-to-date koma-script, which isn't supplied with this version of debian
-    sudo wget http://mirrors.ctan.org/install/macros/latex/contrib/koma-script.tds.zip
-    sudo unzip koma-script.tds.zip -d ~/texmf/
-    sudo apt-get install -y latexmk
-    if [[ "$TRAVIS_DIST" == "xenial" ]]; then
-      sudo apt-get install -y texlive-generic-recommended
-    fi
-  fi
-
-install:
-- pip install -U pip setuptools wheel
-- if [[ "$TEST_TYPE" == "pytest" ]]; then travis_wait pip install .[tests] ; fi
-- if [[ "$TEST_TYPE" == "pytest" ]]; then pip install --quiet coveralls ; fi
-- if [[ "$TEST_TYPE" == "pre-commit" ]]; then pip install -e .[code_style]; fi
-- if [[ "$TEST_TYPE" == "rtd" ]]; then travis_wait pip install .[rtd] ; fi
-
-script:
-- if [[ "$TEST_TYPE" == "pytest" ]]; then pytest -v --cov=ipypublish --cov-config .coveragerc --cov-report= ipypublish ; fi
-- if [[ "$TEST_TYPE" == "pytest" ]]; then nbpublish -pdf --pdf-debug -log debug example/notebooks/Example.ipynb ; fi
-- |
-  if [[ "$TEST_TYPE" == "pre-commit" ]]; then
-    pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )
-  fi
-- if [[ "$TEST_TYPE" == "rtd" ]]; then cd docs; make ; fi
-
-after_success:
-- if [[ "$TEST_TYPE" == "pytest" ]]; then coveralls ; fi
-
-deploy:
-  - provider: pypi
-    distributions: "bdist_wheel sdist"
-    user: cjsewell
-    password:
-      secure: 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
-    on:
-      branch: master
-      tags: true
-      condition: $PYPI_DEPLOY = true
diff --git a/README.md b/README.md
index fd98fb6..10c3dbd 100644
--- a/README.md
+++ b/README.md
@@ -5,8 +5,8 @@ from one or more Jupyter Notebooks.
 
 **Documentation**: [ipypublish.readthedocs.io](http://ipypublish.readthedocs.io)
 
-[![CI Build](https://travis-ci.org/chrisjsewell/ipypublish.svg?branch=master)](https://travis-ci.org/chrisjsewell/ipypublish)
-[![Coverage](https://coveralls.io/repos/github/chrisjsewell/ipypublish/badge.svg?branch=master)](https://coveralls.io/github/chrisjsewell/ipypublish?branch=master)
+[![CI Status](https://github.com/chrisjsewell/ipypublish/workflows/continuous-integration/badge.svg)](https://github.com/chrisjsewell/ipypublish/actions)
+[![Coverage Status](https://codecov.io/gh/chrisjsewell/ipypublish/branch/develop/graph/badge.svg)](https://codecov.io/gh/chrisjsewell/ipypublish)
 [![PyPI](https://img.shields.io/pypi/v/ipypublish.svg)](https://pypi.python.org/pypi/ipypublish/)
 [![DOI](https://zenodo.org/badge/96322423.svg)](https://zenodo.org/badge/latestdoi/96322423)
 [![Conda](https://anaconda.org/conda-forge/ipypublish/badges/version.svg)](https://anaconda.org/conda-forge/ipypublish)
diff --git a/conda_dev_env.yaml b/conda_dev_env.yaml
index 5c52c1e..e04f72b 100644
--- a/conda_dev_env.yaml
+++ b/conda_dev_env.yaml
@@ -30,7 +30,7 @@ dependencies:
 - tornado
 - traitlets
 # testing
-- pytest >=3.6
+- pytest >=4.4
 - pytest-regressions
 - nbsphinx
 - pillow
diff --git a/docs/source/getting_started.Rmd b/docs/source/getting_started.Rmd
index 7575559..69b3dac 100644
--- a/docs/source/getting_started.Rmd
+++ b/docs/source/getting_started.Rmd
@@ -169,13 +169,11 @@ $ nbpresent -f slides_ipypublish_nocode path/to/notebook.ipynb
 
 ## Troubleshooting
 
-For installation issues, [Travis
-CI](https://en.wikipedia.org/wiki/Travis_CI) is used to automatically
-test updates against python 2.7 and 3.6, for both Linux and OSX,
+For installation issues, GitHub Actions is used to automatically
+test updates against multiple Python versions, for Linux, Windows and OSX,
 Therefore, to troubleshoot any installation/run issues, it is best to
-first look at the [travis
-config](https://github.com/chrisjsewell/ipypublish/blob/master/.travis.yml)
-and [travis test runs](https://travis-ci.org/chrisjsewell/ipypublish)
+first look at the [test workflow](https://github.com/chrisjsewell/ipypublish/blob/master/.github/workflows/tests.yml)
+and [test runs](https://github.com/chrisjsewell/ipypublish/actions)
 for working configurations.
 
 The
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 95ebe90..3369db7 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -109,10 +109,10 @@ Index and Search
 * :ref:`modindex`
 * :ref:`search`
 
-.. |Build Status| image:: https://travis-ci.org/chrisjsewell/ipypublish.svg?branch=master
-   :target: https://travis-ci.org/chrisjsewell/ipypublish
-.. |Coverage Status| image:: https://coveralls.io/repos/github/chrisjsewell/ipypublish/badge.svg?branch=master
-   :target: https://coveralls.io/github/chrisjsewell/ipypublish?branch=master
+.. |Build Status| image:: https://github.com/chrisjsewell/ipypublish/workflows/continuous-integration/badge.svg
+   :target: https://github.com/chrisjsewell/ipypublish/actions
+.. |Coverage Status| image:: https://codecov.io/gh/chrisjsewell/ipypublish/branch/develop/graph/badge.svg
+   :target: https://codecov.io/gh/chrisjsewell/ipypublish
 .. |PyPI| image:: https://img.shields.io/pypi/v/ipypublish.svg
    :target: https://pypi.python.org/pypi/ipypublish/
 .. |DOI| image:: https://zenodo.org/badge/96322423.svg

From cf4c24436991a28caaceb775ad17471b54bb0d30 Mon Sep 17 00:00:00 2001
From: Chris Sewell <chrisj_sewell@hotmail.com>
Date: Tue, 21 Jul 2020 01:26:47 +0100
Subject: [PATCH 21/23] Update .readthedocs.yml

---
 .readthedocs.yml | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 253d50b..b0b0791 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -4,15 +4,13 @@ conda:
   environment: docs/environment.yaml
 
 python:
-  version: 3.6
+  version: 3.7
   install:
     - method: pip
       path: .
       extra_requirements:
           - rtd
 
-# default
-# sphinx:
-#   builder: html
-#   configuration: conf.py
-#   fail_on_warning: true
+sphinx:
+  builder: html
+  fail_on_warning: true

From ed57fb68b51a9a75c5d7ebac9ce6f7e685e28896 Mon Sep 17 00:00:00 2001
From: Chris Sewell <chrisj_sewell@hotmail.com>
Date: Tue, 21 Jul 2020 01:37:30 +0100
Subject: [PATCH 22/23] Update conf.py

---
 docs/source/conf.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index 5379e99..c99c3b0 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -284,7 +284,7 @@ def process_citations(app, doctree, docname):
     "bibtexparser": ("https://bibtexparser.readthedocs.io/en/master/", None),
     # 'docutils': ("https://docutils.readthedocs.io/en/sphinx-docs", None),
     # # TODO docutils intersphinx
-    "sphinx": ("http://www.sphinx-doc.org/en/latest/", None),
+    "sphinx": ("https://www.sphinx-doc.org/en/2.0/", None),
 }
 
 intersphinx_aliases = {

From d320655b0397fdd1aac196abdc719d5e4ed02d00 Mon Sep 17 00:00:00 2001
From: Chris Sewell <chrisj_sewell@hotmail.com>
Date: Tue, 21 Jul 2020 02:10:56 +0100
Subject: [PATCH 23/23] bump version

---
 docs/source/releases.rst | 22 +++++++++++++++-------
 ipypublish/__init__.py   |  2 +-
 2 files changed, 16 insertions(+), 8 deletions(-)

diff --git a/docs/source/releases.rst b/docs/source/releases.rst
index 42d7360..52f9b01 100644
--- a/docs/source/releases.rst
+++ b/docs/source/releases.rst
@@ -3,16 +3,24 @@
 Releases
 ========
 
-.. attention::
-
-   A major API improvement occurred in ``v0.7.0``.
-   This has not changed the general user interface,
-   but anyone using custom converter plugins will be required to update them
-   (see :ref:`convert_from_old_api`)
-
 Version 0.10
 ------------
 
+v0.10.11
+~~~~~~~~
+
+- Allow configuration of initial section numbering *via* notebook metadata:
+   - uses``toc.base_numbering`` as set by the toc2 notebook plugin
+     (thanks to @phelps-sg)
+- Allow configuration of initial section numbering via notebook metadata
+  (thanks to @phelps-sg)
+- Refactor testing and deployment:
+   - Move from Travis CI to GitHub Actions for CI and CD
+   - Introduce testing for Windows
+   - Ensure release of logging handlers after build finishes
+   - Move from Coveralls to Codecov for test coverage reporting
+   - Use RTD directly for docs CI, and make the build fail on warnings
+
 v0.10.10
 ~~~~~~~~
 
diff --git a/ipypublish/__init__.py b/ipypublish/__init__.py
index 8b867ee..4afc2b1 100644
--- a/ipypublish/__init__.py
+++ b/ipypublish/__init__.py
@@ -1,3 +1,3 @@
 from ipypublish.scripts import nb_setup  # noqa: F401
 
-__version__ = "0.10.10"
+__version__ = "0.10.11"