Update Docker image

dockerfiles/r-stat-301-grading/Dockerfile

@@ -1,17 +1,15 @@
 # Copyright (c) UBC-DSCI Development Team.
 # Distributed under the terms of the Modified BSD License.
-FROM ubcdsci/r-stat-301:latest
 
-LABEL maintainer="Tiffany Timbers <[email protected]>"
+# TODO: For testing purposes only, change back to ubcdsci/r-stat-301:latest
+FROM ubcstatit/r-stat-301-student:latest
 
-# install the rise slides extension
-RUN mamba install --quiet --yes "rise"
+LABEL maintainer="Brian Kim <[email protected]>"
 
-# install nbgrader
-RUN mamba install --quiet --yes "nbgrader=0.7.1" \
-    && jupyter nbextension install --sys-prefix --py nbgrader --overwrite \
-    && jupyter nbextension enable --sys-prefix --py nbgrader \
-    && jupyter serverextension enable --sys-prefix --py nbgrader 
+# install rise slides extension, nbgrader, clean cache
+RUN mamba install --quiet --yes \
+    'nbgrader=0.8.2' && \
+    mamba clean --all -f -y
 
-# Clean the cache
-RUN mamba clean --all -f -y 
+# re-upgrade jupyter-server (mamba downgrades it)
+RUN pip install --upgrade jupyter-server

dockerfiles/r-stat-301/Dockerfile

@@ -1,67 +1,65 @@
 # Copyright (c) UBC-DSCI Development Team. 
 # Distributed under the terms of the Modified BSD License.
-FROM jupyter/r-notebook
+FROM jupyter/minimal-notebook
 
-LABEL maintainer="Tiffany Timbers <[email protected]>"
+LABEL maintainer="Brian Kim <[email protected]>"
+
+SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 
 USER root
 
-# install vim
-RUN apt-get update && apt-get install -y vim
+# R pre-requisites
+RUN apt-get update --yes && \
+    apt-get install --yes --no-install-recommends \
+    fonts-dejavu \
+    unixodbc \
+    unixodbc-dev \
+    r-cran-rodbc \
+    gfortran \
+    gcc \
+    vim && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
+USER ${NB_UID}
+
+# Change workdir to $HOME/work so config files are preserved when bind mounting
+WORKDIR "${HOME}/work"
+
+# disable warnings that pollute build logs; seems to be related to the update to python 3.11
+# 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
+
+COPY conda-linux-64.lock /tmp/conda-linux-64.lock
+
+RUN mamba update --quiet --file /tmp/conda-linux-64.lock && \
+  mamba clean --all -y -f && \
+  fix-permissions "${CONDA_DIR}" && \
+  fix-permissions "/home/${NB_USER}" && \
+  Rscript -e "install.packages('faux', repos='http://cran.us.r-project.org')" && \
+  Rscript -e "install.packages('moderndive', repos='http://cran.us.r-project.org')"
 
+# Install pexpect from main branch to fix asyncio issue with jupyterlab_git
+RUN pip install --ignore-installed git+https://github.com/pexpect/pexpect.git@master
+
+# Disable the cell toolbar (which ignores metadata and students often accidentally click + delete grading cells)
+RUN jupyter labextension disable @jupyterlab/cell-toolbar-extension
+
+# Disable announcement pop-up on start
+RUN jupyter labextension disable "@jupyterlab/apputils-extension:announcements"
+
+# Configure shortcuts-extension to remove Shift-M cell merge shortcut
+COPY config/shortcuts.jupyterlab-settings /home/${NB_USER}/.jupyter/lab/user-settings/\@jupyterlab/shortcuts-extension/shortcuts.jupyterlab-settings
+
+# Copy jupyter_server_config.py which allows students to see and delete hidden files
+COPY config/jupyter_server_config.py /home/${NB_USER}/.jupyter
+
+# Copy gitconfig that sets default pull strategy to rebase
+COPY config/.gitconfig /home/${NB_USER}/
+
+# Make sure everything in the home folder is owned by NB_USER for running docker image locally.
+USER root
+RUN chown -R ${NB_USER} /home/${NB_USER}
 USER ${NB_UID}
 
-WORKDIR "${HOME}"
-
-# remove the "work/" directory added in an earlier layer...
-RUN rm -rf work
-
-# Install R packages
-RUN mamba install --quiet --yes \
-    'r-cowplot' \
-    'r-ggally' \
-    'r-gridextra' \
-    'r-infer' \
-    'r-kknn' \
-    'r-testthat' \
-    'r-rpostgres' \
-    'r-janitor' \
-    'r-mltools' \
-    'r-leaps' \
-    'r-faraway' \
-    'r-glmnet' \
-    'r-titanic' \
-    'r-performance' \
-    'r-binom' \
-    'r-gridgraphics' \
-    'r-aer' \
-    'r-latex2exp' \
-    'r-gsdesign' \
-    'r-car' \
-    'r-cardata' \
-    'r-mlbench' \
-    'r-qqplotr' \
-    'r-see' \
-    'r-boot' \
-    'r-caret' \
-    && mamba clean --all -f -y \
-    && fix-permissions "${CONDA_DIR}" \
-    && fix-permissions "/home/${NB_USER}" \
-    && Rscript -e "remotes::install_github('allisonhorst/[email protected]')" \
-    && Rscript -e "install.packages('faux', repos='http://cran.us.r-project.org')" \
-    && Rscript -e "install.packages('contextual', repos='http://cran.us.r-project.org')" \
-    && Rscript -e "install.packages('ISLR', repos='http://cran.us.r-project.org')" \
-    && Rscript -e "install.packages('ISLR2', repos='http://cran.us.r-project.org')" \
-    && Rscript -e "install.packages('glmbb', repos='http://cran.us.r-project.org')"
-
-# Install nbgitpuller, jupytext, jlab-git
-RUN pip install git+https://github.com/data-8/nbgitpuller@c23461d4f7ce47ec4e0d2bcfc3b2fde4939b80f8 \
-  && jupyter serverextension enable --sys-prefix nbgitpuller \
-  && pip install jupyterlab-git \
-  && pip install jupytext --upgrade \
-  && jupyter labextension install @techrah/text-shortcuts \
-  && jupyter lab build
-
-# Install the extension to remove the shift+M merge shortcut
-RUN mkdir -p /home/${NB_USER}/.jupyter/lab/user-settings/\@jupyterlab/shortcuts-extension
-COPY rm-merge-shortcut.py /home/${NB_USER}/.jupyter/lab/user-settings/\@jupyterlab/shortcuts-extension/shortcuts.jupyterlab-settings
+# Disable HEALTHCHECK for performance reasons
+HEALTHCHECK NONE