Merge pull request #44 from UBC-DSCI/dockerfile-updates-2024W1

Dockerfile updates 2024 w1

docker/py-dsci-100-grading/Dockerfile

@@ -3,7 +3,12 @@
 FROM ubcdsci/py-dsci-100:latest
 
 # install nbgrader and the rise slides extension
-RUN pip install jupyterlab-rise nbgrader
+# RUN pip install jupyterlab-rise nbgrader
+RUN pip install nbgrader
+
+# install rise from fork wheel with fixed CSS
+COPY jupyterlab_rise-0.42.0-py3-none-any.whl ./
+RUN pip install wheel && pip install jupyterlab_rise-0.42.0-py3-none-any.whl && rm -f jupyterlab_rise-0.42.0-py3-none-any.whl
 
 # Allow all shortcuts
 RUN rm -f /home/${NB_USER}/.jupyter/lab/user-settings/\@jupyterlab/shortcuts-extension/shortcuts.jupyterlab-settings

docker/py-dsci-100/Dockerfile

@@ -1,6 +1,6 @@
 # Copyright (c) UBC-DSCI Development Team.
 # Distributed under the terms of the Modified BSD License.
-FROM jupyter/scipy-notebook
+FROM quay.io/jupyter/scipy-notebook
 
 USER root
 
@@ -17,23 +17,22 @@ ENV PYDEVD_DISABLE_FILE_VALIDATION=1
 
 # Install Python packages
 RUN mamba install --quiet --yes \
-        'numpy' \
-        'jinja2' \
-        'click' \
-        'ghp-import' \
-        'ibis-framework' \
-        'nodejs' \
-        'psycopg2' \
-        'jupyter-resource-usage' \
-        'altair-all' \
-        'pandas' \
-    && mamba clean --all -f -y \
-    && fix-permissions "${CONDA_DIR}" \
-    && fix-permissions "/home/${NB_USER}" 
+  'numpy' \
+  'jinja2' \
+  'click' \
+  'ghp-import' \
+  'ibis-framework' \
+  'nodejs' \
+  'psycopg2' \
+  'jupyter-resource-usage' \
+  'altair-all' \
+  'pandas' \
+  && mamba clean --all -f -y \
+  && fix-permissions "${CONDA_DIR}" \
+  && fix-permissions "/home/${NB_USER}" 
 
 # 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  
+RUN pip install nbgitpuller jupyterlab-git pexpect==4.9.0
 
 # Disable announcement pop-up on start
 RUN jupyter labextension disable "@jupyterlab/apputils-extension:announcements"

docker/r-dsci-100-grading/Dockerfile

@@ -3,7 +3,12 @@
 FROM ubcdsci/r-dsci-100:latest
 
 # install nbgrader and the rise slides extension
-RUN pip install jupyterlab-rise nbgrader
+# RUN pip install jupyterlab-rise nbgrader
+RUN pip install nbgrader
+
+# install rise from fork wheel with fixed CSS
+COPY jupyterlab_rise-0.42.0-py3-none-any.whl ./
+RUN pip install wheel && pip install jupyterlab_rise-0.42.0-py3-none-any.whl && rm -f jupyterlab_rise-0.42.0-py3-none-any.whl
 
 # Allow all shortcuts
 RUN rm -f /home/${NB_USER}/.jupyter/lab/user-settings/\@jupyterlab/shortcuts-extension/shortcuts.jupyterlab-settings

docker/r-dsci-100/Dockerfile

@@ -1,11 +1,11 @@
 # Copyright (c) UBC-DSCI Development Team.
 # Distributed under the terms of the Modified BSD License.
-FROM jupyter/r-notebook:lab-4.0.5
+FROM quay.io/jupyter/r-notebook
 
 USER root
 
 # install vim and libgsl (for tidyclust)
-RUN apt-get update && apt-get install -y vim libgsl27 libgsl-dev build-essential
+RUN apt-get update && apt-get install -y vim libgsl-dev build-essential
 
 USER ${NB_UID}
 
@@ -15,29 +15,31 @@ 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
 
-# Install R packages
+# Install mamba packages
 RUN mamba install --quiet --yes \
-    'r-cowplot' \
-    'r-ggally' \
-	'r-gridextra' \
-	'r-infer' \
-	'r-kknn' \
-	'r-testthat' \
-	'r-rpostgres' \
+  'r-cowplot' \
+  'r-ggally' \
+  'r-gridextra' \
+  'r-infer' \
+  'r-kknn' \
+  'r-testthat' \
+  'r-rpostgres' \
   'r-themis' \
   'jupyter-resource-usage' \
-    && 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('ISLR', repos='http://cran.us.r-project.org')" \
-    && Rscript -e "install.packages('scales', repos='http://cran.us.r-project.org')" \
-    && Rscript -e "install.packages('tidyclust', repos='http://cran.us.r-project.org')" \
-    && Rscript -e "install.packages('janitor', repos='http://cran.us.r-project.org')"
+  && mamba clean --all -f -y \
+  && fix-permissions "${CONDA_DIR}" \
+  && fix-permissions "/home/${NB_USER}"
+
+# Install CRAN packages
+RUN Rscript -e "lib <- 'palmerpenguins'; remotes::install_github('allisonhorst/[email protected]'); if ( ! library('palmerpenguins',character.only=TRUE,logical.return=TRUE)){quit(status=1,save='no')}" \
+  && Rscript -e "lib <- 'tidyclust'; install.packages(lib, repos='http://cran.us.r-project.org'); if ( ! library(lib,character.only=TRUE,logical.return=TRUE)){quit(status=1,save='no')}" \
+  && Rscript -e "lib <- 'ISLR'; install.packages(lib, repos='http://cran.us.r-project.org'); if ( ! library(lib,character.only=TRUE,logical.return=TRUE)){quit(status=1,save='no')}" \
+  && Rscript -e "lib <- 'scales'; install.packages(lib, repos='http://cran.us.r-project.org'); if ( ! library(lib,character.only=TRUE,logical.return=TRUE)){quit(status=1,save='no')}" \
+  && Rscript -e "lib <- 'janitor'; install.packages(lib, repos='http://cran.us.r-project.org'); if ( ! library(lib,character.only=TRUE,logical.return=TRUE)){quit(status=1,save='no')}" \
+  && Rscript -e "lib <- 'withr'; install.packages('https://cran.r-project.org/src/contrib/Archive/withr/withr_2.5.0.tar.gz', repos=NULL, type='source'); if ( ! library(lib,character.only=TRUE,logical.return=TRUE)){quit(status=1,save='no')}"
 
 # Install nbgitpuller, jlab-git, newest pexpect 4.9.0
-RUN pip install nbgitpuller jupyterlab-git pexpect==4.9.0 \
-  && jupyter lab build  
+RUN pip install nbgitpuller jupyterlab-git pexpect==4.9.0
 
 # Disable the cell toolbar (which ignores metadata and students often accidentally click + delete grading cells)
 RUN jupyter labextension disable @jupyterlab/cell-toolbar-extension