Merge pull request #38 from briank-git/main

Update DSCI 100 R and Python Docker Images

docker/py-dsci-100/.gitconfig

@@ -0,0 +1,2 @@
+[pull]
+        rebase = false

docker/py-dsci-100/Dockerfile

@@ -15,11 +15,6 @@ WORKDIR "${HOME}/work"
 # https://discourse.jupyter.org/t/debugger-warning-it-seems-that-frozen-modules-are-being-used-python-3-11-0/16544/12
 ENV PYDEVD_DISABLE_FILE_VALIDATION=1
 
-# update scikit-learn to the current @main (July 20, 2023) 
-# to get this merged PR: https://github.com/scikit-learn/scikit-learn/pull/26772
-# which fixes this issue: https://github.com/scikit-learn/scikit-learn/issues/26768
-RUN pip install --upgrade git+https://github.com/scikit-learn/scikit-learn@7de59b2017f39048880a3858d32c8caef9308954
-
 # Install Python packages
 RUN mamba install --quiet --yes \
         'numpy' \
@@ -29,15 +24,16 @@ RUN mamba install --quiet --yes \
         'ibis-framework' \
         'nodejs' \
         'psycopg2' \
+        'jupyter-resource-usage' \
     && mamba clean --all -f -y \
     && fix-permissions "${CONDA_DIR}" \
     && fix-permissions "/home/${NB_USER}" 
 
 # Install some recent python package that might not be on conda yet
 RUN pip install pandas"<2.1" altair"==5.0.1" "vegafusion[embed]" vl-convert-python
 
-# Install nbgitpuller, jlab-git
-RUN pip install nbgitpuller jupyterlab-git \
+# Install nbgitpuller, jlab-git, newest pexpect 4.9.0
+RUN pip install nbgitpuller jupyterlab-git==0.50.0 pexpect==4.9.0 \
   && jupyter lab build  
 
 # Disable the cell toolbar (which ignores metadata and students often accidentally click + delete grading cells)
@@ -46,7 +42,20 @@ RUN jupyter labextension disable @jupyterlab/cell-toolbar-extension
 # Install the extension to remove the shift+M merge shortcut
 COPY shortcuts.jupyterlab-settings /home/${NB_USER}/.jupyter/lab/user-settings/\@jupyterlab/shortcuts-extension/shortcuts.jupyterlab-settings
 
-# Make sure everything in the home folder is owned by NB_USER
+# Copy jupyter_server_config.py which allows students to see and delete hidden files
+COPY jupyter_server_config.py /home/${NB_USER}/.jupyter
+
+# Copy gitconfig that sets global default pull strategy to merge
+COPY .gitconfig /home/${NB_USER}/
+
 USER root
+# Install zip package
+RUN apt install zip
+
+# Make sure everything in the home folder is owned by NB_USER
 RUN chown -R ${NB_USER} /home/${NB_USER}
+
 USER ${NB_UID}
+
+# Disable healthcheck for performance reasons
+HEALTHCHECK NONE

docker/py-dsci-100/jupyter_server_config.py

@@ -0,0 +1,49 @@
+# Configuration file for jupyter-server.
+
+c = get_config()  #noqa
+
+#------------------------------------------------------------------------------
+# ContentsManager(LoggingConfigurable) configuration
+#------------------------------------------------------------------------------
+## Base class for serving files and directories.
+#  
+#      This serves any text or binary file,
+#      as well as directories,
+#      with special handling for JSON notebook documents.
+#  
+#      Most APIs take a path argument,
+#      which is always an API-style unicode path,
+#      and always refers to a directory.
+#  
+#      - unicode, not url-escaped
+#      - '/'-separated
+#      - leading and trailing '/' will be stripped
+#      - if unspecified, path defaults to '',
+#        indicating the root path.
+
+## Allow access to hidden files
+#  Default: False
+c.ContentsManager.allow_hidden = True
+
+#------------------------------------------------------------------------------
+# FileContentsManager(FileManagerMixin, ContentsManager) configuration
+#------------------------------------------------------------------------------
+## Allow access to hidden files
+#  See also: ContentsManager.allow_hidden
+c.FileContentsManager.allow_hidden = True
+
+#------------------------------------------------------------------------------
+# AsyncContentsManager(ContentsManager) configuration
+#------------------------------------------------------------------------------
+## Base class for serving files and directories asynchronously.
+
+## Allow access to hidden files
+#  See also: ContentsManager.allow_hidden
+c.AsyncContentsManager.allow_hidden = True
+
+#------------------------------------------------------------------------------
+# AsyncFileContentsManager(FileContentsManager, AsyncFileManagerMixin, AsyncContentsManager) configuration
+#------------------------------------------------------------------------------
+## Allow access to hidden files
+#  See also: ContentsManager.allow_hidden
+c.AsyncFileContentsManager.allow_hidden = True

docker/r-dsci-100/.gitconfig

@@ -0,0 +1,2 @@
+[pull]
+        rebase = false

docker/r-dsci-100/Dockerfile

@@ -24,6 +24,7 @@ RUN mamba install --quiet --yes \
 	'r-kknn' \
 	'r-testthat' \
 	'r-rpostgres' \
+  'jupyter-resource-usage' \
     && mamba clean --all -f -y \
     && fix-permissions "${CONDA_DIR}" \
     && fix-permissions "/home/${NB_USER}" \
@@ -32,8 +33,8 @@ RUN mamba install --quiet --yes \
     && Rscript -e "install.packages('tidyclust', repos='http://cran.us.r-project.org')" \
     && Rscript -e "install.packages('janitor', repos='http://cran.us.r-project.org')"
 
-# Install nbgitpuller, jlab-git
-RUN pip install nbgitpuller jupyterlab-git \
+# Install nbgitpuller, jlab-git, newest pexpect 4.9.0
+RUN pip install nbgitpuller jupyterlab-git pexpect==4.9.0 \
   && jupyter lab build  
 
 # Disable the cell toolbar (which ignores metadata and students often accidentally click + delete grading cells)
@@ -42,8 +43,16 @@ RUN jupyter labextension disable @jupyterlab/cell-toolbar-extension
 # Install the extension to remove the shift+M merge shortcut
 COPY shortcuts.jupyterlab-settings /home/${NB_USER}/.jupyter/lab/user-settings/\@jupyterlab/shortcuts-extension/shortcuts.jupyterlab-settings
 
+# Copy jupyter_server_config.py which allows students to see and delete hidden files
+COPY jupyter_server_config.py /home/${NB_USER}/.jupyter
+
+# Copy gitconfig that sets global default pull strategy to merge
+COPY .gitconfig /home/${NB_USER}/
+
 # Make sure everything in the home folder is owned by NB_USER
 USER root
 RUN chown -R ${NB_USER} /home/${NB_USER}
 USER ${NB_UID}
 
+# Disable healthcheck for performance reasons
+HEALTHCHECK NONE

docker/r-dsci-100/jupyter_server_config.py

@@ -0,0 +1,49 @@
+# Configuration file for jupyter-server.
+
+c = get_config()  #noqa
+
+#------------------------------------------------------------------------------
+# ContentsManager(LoggingConfigurable) configuration
+#------------------------------------------------------------------------------
+## Base class for serving files and directories.
+#  
+#      This serves any text or binary file,
+#      as well as directories,
+#      with special handling for JSON notebook documents.
+#  
+#      Most APIs take a path argument,
+#      which is always an API-style unicode path,
+#      and always refers to a directory.
+#  
+#      - unicode, not url-escaped
+#      - '/'-separated
+#      - leading and trailing '/' will be stripped
+#      - if unspecified, path defaults to '',
+#        indicating the root path.
+
+## Allow access to hidden files
+#  Default: False
+c.ContentsManager.allow_hidden = True
+
+#------------------------------------------------------------------------------
+# FileContentsManager(FileManagerMixin, ContentsManager) configuration
+#------------------------------------------------------------------------------
+## Allow access to hidden files
+#  See also: ContentsManager.allow_hidden
+c.FileContentsManager.allow_hidden = True
+
+#------------------------------------------------------------------------------
+# AsyncContentsManager(ContentsManager) configuration
+#------------------------------------------------------------------------------
+## Base class for serving files and directories asynchronously.
+
+## Allow access to hidden files
+#  See also: ContentsManager.allow_hidden
+c.AsyncContentsManager.allow_hidden = True
+
+#------------------------------------------------------------------------------
+# AsyncFileContentsManager(FileContentsManager, AsyncFileManagerMixin, AsyncContentsManager) configuration
+#------------------------------------------------------------------------------
+## Allow access to hidden files
+#  See also: ContentsManager.allow_hidden
+c.AsyncFileContentsManager.allow_hidden = True