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uc-cdis · Oct 15, 2024 · 3a63975 · 3a63975
1 parent a9e6401
commit 3a63975
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Showing 4 changed files with 20 additions and 12 deletions.
diff --git a/jupyter-superslim-rkernel/Dockerfile b/jupyter-superslim-rkernel/Dockerfile
@@ -59,7 +59,7 @@ ENV CONDA_DIR=/opt/conda \
     LC_ALL=en_US.UTF-8 \
     LANG=en_US.UTF-8 \
     LANGUAGE=en_US.UTF-8 \
-    R_BASE_VERSION=4.4.1
+    R_BASE_VERSION=4.3.3
 
 ENV PATH="${CONDA_DIR}/bin:${PATH}" \
     HOME="/home/${NB_USER}" \
@@ -70,11 +70,6 @@ ENV PATH="${CONDA_DIR}/bin:${PATH}" \
 COPY resources/scripts/fix-permissions /usr/local/bin/fix-permissions
 RUN chmod a+rx /usr/local/bin/fix-permissions
 
-# Use overrides.json file to change the default settings
-RUN mkdir -p /opt/conda/share/jupyter/lab/settings
-COPY resources/overrides.json /opt/conda/share/jupyter/lab/settings
-
-
 # Enable prompt color in the skeleton .bashrc before creating the default NB_USER
 # hadolint ignore=SC2016
 RUN sed -i 's/^#force_color_prompt=yes/force_color_prompt=yes/' /etc/skel/.bashrc && \
@@ -130,6 +125,10 @@ RUN set -x && \
     fix-permissions "${CONDA_DIR}" && \
     fix-permissions "/home/${NB_USER}"
 
+# Use overrides.json file to change the default settings
+RUN mkdir -p /opt/conda/share/jupyter/lab/settings
+COPY resources/overrides.json /opt/conda/share/jupyter/lab/settings
+
 # Install Jupyter Notebook, Lab, Hub and R packages
 # R packages including IRKernel which gets installed globally.
 # See https://github.com/rocker-org/rocker/blob/master/r-base/Dockerfile
@@ -138,7 +137,7 @@ RUN set -x && \
 # Correct permissions
 # Do all this in a single RUN command to avoid duplicating all of the
 # files across image layers when the permissions change
-RUN conda install --quiet --yes python="${PYTHON_VERSION}"\
+RUN conda install --quiet --yes python="${PYTHON_VERSION}" \
     'notebook' \
     'jupyterhub' \
     'jupyterlab' \

diff --git a/jupyter-superslim-rkernel/requirements.txt b/jupyter-superslim-rkernel/requirements.txt
@@ -1,6 +1,15 @@
-gen3>=4.25.1
+gen3>=4.25.0
 cdiserrors
 pandas
 numpy
-jupyter_server_ydoc
 tornado>=6.3.3 # not directly required, pinned by Snyk to avoid a vulnerability
+# begin jupyter plugins and utilities section
+# jupyterlab-lsp # not installing this now since it will cause some dependency conflicts for the latest version of gen3sdk and jupyterlab
+jupyterlab-search-replace
+jupyterlab-git
+jupyter_server_ydoc
+altair[all]
+lckr_jupyterlab_variableinspector
+ripgrep
+frictionless
+# end jupyter plugins and utilities section
diff --git a/jupyter-superslim/Dockerfile b/jupyter-superslim/Dockerfile
@@ -138,6 +138,7 @@ COPY resources/overrides.json /opt/conda/share/jupyter/lab/settings
 RUN conda install --quiet --yes python="${PYTHON_VERSION}" \
     'notebook' \
     'jupyterhub' \
+    'jupyterlab' \
     'jupyterhub-base' \
     'jupyter_server' \
     && conda clean --all -f -y && \

diff --git a/jupyter-superslim/requirements.txt b/jupyter-superslim/requirements.txt
@@ -1,16 +1,15 @@
-gen3
+gen3>=4.25.0
 cdiserrors
 pandas
 numpy
 tornado>=6.3.3 # not directly required, pinned by Snyk to avoid a vulnerability
 zipp>=3.19.1 # not directly required, pinned by Snyk to avoid a vulnerability
 # begin jupyter plugins and utilities section
-jupyterlab-lsp
+# jupyterlab-lsp # not installing this now since it will cause some dependency conflicts for the latest version of gen3sdk and jupyterlab
 jupyterlab-search-replace
 jupyterlab-git
 altair[all]
 lckr_jupyterlab_variableinspector
 ripgrep
 frictionless
 # end jupyter plugins and utilities section
-jupyterlab>=4.2.0 # install jupyterlab here to make sure it doesn't get downgraded