Merge pull request #15 from felder/felder_DH-418

[DH-418] updating single user image

Author: felder

apt.txt

@@ -1,10 +1,8 @@
 # Some linux packages for basic terminal work, particularly
 # oriented at users new to Unix/cmd line environments.
 
-# installing less as more just isn't enough
-less
-
 # Basic unix tools
+less
 man
 man-db
 manpages-posix
@@ -14,6 +12,7 @@ manpages-posix-dev
 # Download tools
 curl
 wget
+rsync
 
 # Core text editors on a *nix box: vim
 vim
@@ -27,11 +26,6 @@ jed-extra
 # powerful terminal-based file manager, better than the one in JLab
 mc
 
-# for easily managing multiple repositories with one command (perl-doc
-# is needed for its help pages to work)
-mr
-perl-doc
-
 # Regular build tools for compiling common stuff
 build-essential
 gfortran
@@ -48,9 +42,6 @@ lmodern
 pandoc
 latexdiff
 
-# Some useful git utilities use basic Ruby
-ruby
-
 # Other niceties for command-line work and life
 ack   # powerful grep-like tool
 pydf  # colorized disk usage
@@ -63,11 +54,6 @@ rsync
 tig  # console UI for git
 multitail
 
-# For later, these are not available in 18.04
-#browsh # text-based web browser, occasionally handy
-#dasel  # json/yml/csv/etc data wrangling at the terminal
-#fzf   # fuzzy file finder
-
 ## This section adds tools for desktop environment usage
 dbus-x11
 xorg

environment.yml

@@ -4,109 +4,122 @@ channels:
 - conda-forge
 
 dependencies:
-- python==3.11.*
-- syncthing==1.20.4
-- git==2.47.1
-- altair==5.0.1
-- beautifulsoup4==4.11.1
-- black==22.6.0
-- bokeh==2.4.3
-- bqplot==0.12.34
-- cartopy==0.21.0
-- coverage==7.2.2
-- cython==0.29.32
-- distributed==2023.6.0
-- fortran-magic==0.7
-- graphviz==8.0.3
-- python-graphviz==0.20.1
-- h5netcdf==1.0.2
-- h5py==3.7.0
-- hdf4==4.2.15
-- hdf5==1.12.2
-- intake==0.6.5
-- intake-esm==2021.8.17
-- intake-xarray==0.6.0
-- ipycanvas==0.12.1
-- ipydatagrid==1.1.12
-- ipympl==0.9.2
-- ipyparallel==8.4.1
-- ipython-sql==0.3.9
-- jsonschema==4.17.3
-- jupyter-archive==3.4.0
-- jupyter-book==0.15.1
-- jupyter-resource-usage==1.0.0
-- jupyter-server-proxy==4.2.0
-- jupyter_bokeh
-- jupyterhub==5.2.1
-- jupyterlab==4.0.11
-- jupyterlab-favorites==3.0.0
-- jupyterlab-geojson==3.2.0
-- jupyterlab-variableinspector==3.0.9
-- jupyterlab_pygments==0.2.2
-- jupyterlab_server==2.23.0
-- jupyterlab_widgets==3.0.8
-- jupyter_server==2.7.0
-- matplotlib==3.7.1
-- matplotlib-inline==0.1.6
-- mock==4.0.3
-# https://jira-secure.berkeley.edu/browse/DH-165
-- mongo-tools==4.0.4
-- nbclassic==1.0.0
-- nbdime==3.1.1
-- nbgitpuller==1.2.1
-- networkx==2.8.6
-- notebook==7.0.7
-- numba==0.57.0
-- numpy==1.24.2
-- pandas==2.0.3
-- pandoc==2.12
-- pandocfilters==1.5.0
-- pep8==1.7.1
-- pgspecial==1.13.1
-- pillow==10.0.1 # sknapp 2024-09-05 had to unpin this version to fix build ==9.2.0
-- plotly==5.13.1
-- pooch==1.6.0
-- prettytable==3.4.1
-- psycopg==3.1.11
-- pyarrow==9.0.0
-- pypdf2==2.10.4
-- pytables==3.7.0
-- pytest==8.3.2 # sknapp 2024-09-05 had to unpin this version to fix build ==7.1.2
-- pytest-cov==3.0.0
-- python-pdfkit==1.0.0
-- requests==2.28.2
-- scikit-image==0.19.3
-- scikit-learn==1.2.2
-- scipy==1.10.1
-- seaborn==0.12.2
-- sphinx-jupyterbook-latex==0.5.2
-- sqlparse==0.4.3
-- statsmodels==0.14.0
-- sympy==1.13.2 # sknapp 2024-09-05 had to unpin this version to fix build ==1.10.1
-- tornado==6.2.0
-- tqdm==4.64.0
-- xarray==2023.5.0
-- xlrd==2.0.1
-- micro==2.0.8
-- websockify==0.11.0
-- folium==0.14.0
-- sqlalchemy==2.0.32
-- pip
-- pip:
-  - jupyter-desktop-server
-  - otter-grader==5.1.3
-  - jupysql==0.10.0
-  - geopandas==0.12.1
-  - iwut==0.0.4
-  - tensorflow-cpu==2.12.0
-  - ipywidgets==8.0.7
-  # disable until fixed (probably this:  https://github.com/jupyterlab/jupyter-collaboration/issues/162)
-  # - jupyter_collaboration==1.0.1
-  - nbconvert[webpdf]==7.16.4
-  - pytest-notebook==0.8.1
-  - pymongo==4.4.1
-  - dbt-postgres==1.6.0
-  # - git+https://github.com/shaneknapp/python-popularity-contest.git@add-error-handling
-  # pulled in by ottr, if not pinned to 1.16.2, 1.16.3 causes DH-323
-  - jupytext==1.16.2
-  - jupyterlab-a11y-checker==0.1.2 # Adding a11y-checker for Data 101 staff's exploration
+  # Items required for basic level functionality
+  - gh-scoped-creds==4.1
+  - git==2.47.1
+  - jupyter-archive==3.4.0
+  - jupyter-resource-usage==1.1.0  
+  - jupyter-server-proxy==4.4.0
+  - jupyter_server==2.15.0 
+  - jupyterhub==5.2.1
+  - jupyterlab==4.3.4
+  - jupyterlab-git==0.50.2
+  - jupyterlab_rise==0.43.1
+  - jupytext==1.16.6
+  - nbgitpuller==1.2.1
+  - notebook==7.3.2
+  - pip==24.3.1  
+  - python==3.11.*
+
+  # other stuff
+  - altair==5.0.1
+  - beautifulsoup4==4.11.1
+  - black==22.6.0
+  - bokeh==2.4.3
+  - bqplot==0.12.34
+  - cartopy==0.24.0
+  - coverage==7.2.2
+  - cython==0.29.32
+  - dbt-postgres==1.9.0
+  - distributed==2023.6.0
+  - folium==0.14.0
+  - fortran-magic==0.7
+  - graphviz==9.0.0
+  - h5netcdf==1.0.2
+  - h5py==3.7.0
+  - hdf4==4.2.15
+  - hdf5==1.12.2
+  - intake==0.6.5
+  - intake-esm==2021.8.17
+  - intake-xarray==0.6.0
+  - ipycanvas==0.12.1
+  - ipydatagrid==1.4.0
+  - ipympl==0.9.2
+  - ipyparallel==8.4.1
+  - ipython-sql==0.3.9
+  - ipywidgets==8.1.5
+  - jsonschema==4.23.0
+  - jupysql==0.10.17
+  - jupyter-book==0.15.1
+  - jupyter_bokeh==2.0.4
+  - jupyterlab-favorites==3.0.0
+  - jupyterlab-geojson==3.2.0
+  - jupyterlab-variableinspector==3.0.9
+  - jupyterlab_pygments==0.2.2
+  - jupyterlab_server==2.27.3
+  - jupyterlab_widgets==3.0.13
+  - matplotlib==3.7.1
+  - matplotlib-inline==0.1.6
+  - micro==2.0.8
+  - mock==4.0.3
+  - mongo-tools==4.0.4
+  - nbclassic==1.0.0
+  - nbdime==4.0.2
+  - networkx==2.8.6
+  - numba==0.57.0
+  - numpy==1.24.2
+  - pandas==2.0.3
+  - pandoc==2.12
+  - pandocfilters==1.5.0
+  - pep8==1.7.1
+  - pgspecial==1.13.1
+  - pillow==10.0.1 # sknapp 2024-09-05 had to unpin this version to fix build ==9.2.0
+  - plotly==5.13.1
+  - pooch==1.6.0
+  - prettytable==3.12.0
+  - psycopg==3.1.11
+  - pyarrow==9.0.0
+  - pymongo==4.10.1
+  - pypdf2==2.10.4
+  - pytables==3.7.0
+  - pytest==8.3.2 # sknapp 2024-09-05 had to unpin this version to fix build ==7.1.2
+  - pytest-cov==3.0.0
+  - pytest-notebook==0.10.0
+  - python-graphviz==0.20.1
+  - python-pdfkit==1.0.0
+  - requests==2.32.3
+  - scikit-image==0.19.3
+  - scikit-learn==1.2.2
+  - scipy==1.10.1
+  - seaborn==0.13.2
+  - sphinx-jupyterbook-latex==0.5.2
+  - sqlalchemy==2.0.32
+  - sqlparse==0.5.3
+  - statsmodels==0.14.0
+  - sympy==1.13.2 # sknapp 2024-09-05 had to unpin this version to fix build ==1.10.1
+  - syncthing==1.20.4
+  - tornado==6.2.0
+  - tqdm==4.64.0
+  - xarray==2023.5.0
+  - xlrd==2.0.1
+  - websockify==0.11.0
+
+  - pip:
+    # items required for basic functionality
+    - nbconvert[webpdf]==7.16.5
+    - git-credential-helpers==0.2
+    - otter-grader==6.0.4
+
+    # other stuff
+    - jupyter-desktop-server==0.1.3
+    - iwut==0.0.4
+    # [DH-418] cannot get mamba to install this
+    - tensorflow-cpu==2.18.0
+    # [DH-418] cannot get mamba to install this
+    - geopandas==0.12.1
+    # disable until fixed (probably this:  https://github.com/jupyterlab/jupyter-collaboration/issues/162)
+    # DH-418, 2024-01-16, above issue still not fixed.  Also this package is available in condaforge
+    # https://anaconda.org/conda-forge/jupyter-collaboration
+    # - jupyter_collaboration==1.0.1
+    # - git+https://github.com/shaneknapp/python-popularity-contest.git@add-error-handling
+    - jupyterlab-a11y-checker==0.1.3 # Adding a11y-checker for Data 101 staff's exploration