Merge pull request #39 from uc-cdis/feat/jupyter-nb7

HP-1589 Feat/jupyter nb7

README.md

@@ -5,10 +5,10 @@ A "slim" build of jupyter notebook images
 ## Run locally
 
 ```
-docker-compose -f ./jupytersuperslim.yaml up
+docker compose -f ./jupytersuperslim.yaml up
 ```
 
-Then connect to http://localhost:9880/lw-workspace/proxy/
+Then connect to http://localhost:9888/lw-workspace/proxy/
 
 ## Deploy to hatchery
 

jupyter-superslim-rkernel/Dockerfile

@@ -22,20 +22,18 @@ USER root
 # (ARGS are in lower case to distinguish them from ENV)
 # Check https://github.com/conda-forge/miniforge/releases
 # Conda version
-ARG conda_version="4.10.3"
+ARG conda_version="24.7.1"
 # Miniforge installer patch version
-ARG miniforge_patch_number="3"
+ARG miniforge_patch_number="2"
 # Package Manager and Python implementation to use (https://github.com/conda-forge/miniforge)
-# - conda only: either Miniforge3 to use Python or Miniforge-pypy3 to use PyPy
-# - conda + mamba: either Mambaforge to use Python or Mambaforge-pypy3 to use PyPy
-ARG miniforge_python="Mambaforge"
+ARG miniforge_python="Miniforge3"
 # Miniforge archive to install
 ARG miniforge_version="${conda_version}-${miniforge_patch_number}"
 
 
 # Install all OS dependencies for notebook server that starts but lacks all
 # features (e.g., download as all possible file formats)
-ENV DEBIAN_FRONTEND noninteractive
+ENV DEBIAN_FRONTEND=noninteractive
 RUN apt-get update --yes && \
     apt-get install --yes --no-install-recommends \
     tini \
@@ -61,7 +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=4.1.0
+    R_BASE_VERSION=4.3.3
 
 ENV PATH="${CONDA_DIR}/bin:${PATH}" \
     HOME="/home/${NB_USER}" \
@@ -72,11 +70,6 @@ ENV PATH="${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 && \
@@ -97,12 +90,12 @@ RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
     fix-permissions "${CONDA_DIR}"
 
 USER ${NB_UID}
-ARG PYTHON_VERSION=default
+ARG PYTHON_VERSION=3.9
 
 # Install conda as jovyan and check the sha256 sum provided on the download site
 WORKDIR /tmp
 
-# Prerequisites installation: conda, mamba, pip, tini
+# Prerequisites installation: conda, pip, tini
 RUN set -x && \
     # Miniforge installer
     miniforge_arch=$(uname -m) && \
@@ -117,19 +110,25 @@ RUN set -x && \
     rm "${miniforge_installer}" && \
     # Conda configuration see https://conda.io/projects/conda/en/latest/configuration.html
     echo "conda ${CONDA_VERSION}" >> "${CONDA_DIR}/conda-meta/pinned" && \
+    conda update -n base -c defaults conda && \
     conda config --system --set auto_update_conda false && \
     conda config --system --set show_channel_urls true && \
     if [[ "${PYTHON_VERSION}" != "default" ]]; then conda install --yes python="${PYTHON_VERSION}"; fi && \
     conda list python | grep '^python ' | tr -s ' ' | cut -d ' ' -f 1,2 >> "${CONDA_DIR}/conda-meta/pinned" && \
     conda install --quiet --yes \
     "conda=${CONDA_VERSION}" \
+    "python=${PYTHON_VERSION}" \
     'pip' && \
     conda update --all --quiet --yes && \
     conda clean --all -f -y && \
     rm -rf "/home/${NB_USER}/.cache/yarn" && \
     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 \
+RUN conda install --quiet --yes python="${PYTHON_VERSION}" \
     'notebook' \
     'jupyterhub' \
     'jupyterlab' \
@@ -162,9 +161,8 @@ RUN conda install --quiet --yes \
     'r-gplots' \
     'r-gtools' \
     'r-catools' \
-    'jupyterhub=2' \
-    'jupyterhub-base=2' \
-    'jupyter_server=1' \
+    'jupyterhub-base' \
+    'jupyter_server' \
     && conda clean --all -f -y && \
     npm cache clean --force && \
     jupyter notebook --generate-config && \

jupyter-superslim-rkernel/requirements.txt

@@ -1,6 +1,16 @@
-gen3==4.17.2
+gen3
 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
+jupyter-lsp
+jupyterlab-lsp
+jupyterlab-search-replace
+jupyterlab-git
+jupyter_server_ydoc
+altair[all]
+lckr_jupyterlab_variableinspector
+ripgrep
+frictionless
+# end jupyter plugins and utilities section

jupyter-superslim/Dockerfile

@@ -22,20 +22,18 @@ USER root
 # (ARGS are in lower case to distinguish them from ENV)
 # Check https://github.com/conda-forge/miniforge/releases
 # Conda version
-ARG conda_version="4.10.3"
+ARG conda_version="24.7.1"
 # Miniforge installer patch version
-ARG miniforge_patch_number="3"
+ARG miniforge_patch_number="2"
 # Package Manager and Python implementation to use (https://github.com/conda-forge/miniforge)
-# - conda only: either Miniforge3 to use Python or Miniforge-pypy3 to use PyPy
-# - conda + mamba: either Mambaforge to use Python or Mambaforge-pypy3 to use PyPy
-ARG miniforge_python="Mambaforge"
+ARG miniforge_python="Miniforge3"
 # Miniforge archive to install
 ARG miniforge_version="${conda_version}-${miniforge_patch_number}"
 
 
 # Install all OS dependencies for notebook server that starts but lacks all
 # features (e.g., download as all possible file formats)
-ENV DEBIAN_FRONTEND noninteractive
+ENV DEBIAN_FRONTEND=noninteractive
 RUN apt-get update --yes && \
     apt-get install --yes --no-install-recommends \
     tini \
@@ -91,13 +89,13 @@ RUN echo "auth requisite pam_deny.so" >> /etc/pam.d/su && \
     fix-permissions "${CONDA_DIR}"
 
 USER ${NB_UID}
-ARG PYTHON_VERSION=default
+ARG PYTHON_VERSION=3.9
 
 
 # Install conda as jovyan and check the sha256 sum provided on the download site
 WORKDIR /tmp
 
-# Prerequisites installation: conda, mamba, pip, tini
+# Prerequisites installation: conda, pip, tini
 RUN set -x && \
     # Miniforge installer
     miniforge_arch=$(uname -m) && \
@@ -112,12 +110,14 @@ RUN set -x && \
     rm "${miniforge_installer}" && \
     # Conda configuration see https://conda.io/projects/conda/en/latest/configuration.html
     echo "conda ${CONDA_VERSION}" >> "${CONDA_DIR}/conda-meta/pinned" && \
+    conda update -n base -c defaults conda && \
     conda config --system --set auto_update_conda false && \
     conda config --system --set show_channel_urls true && \
     if [[ "${PYTHON_VERSION}" != "default" ]]; then conda install --yes python="${PYTHON_VERSION}"; fi && \
     conda list python | grep '^python ' | tr -s ' ' | cut -d ' ' -f 1,2 >> "${CONDA_DIR}/conda-meta/pinned" && \
     conda install --quiet --yes \
     "conda=${CONDA_VERSION}" \
+    "python=${PYTHON_VERSION}" \
     'pip' && \
     conda update --all --quiet --yes && \
     conda clean --all -f -y && \
@@ -135,13 +135,12 @@ COPY resources/overrides.json /opt/conda/share/jupyter/lab/settings
 # Correct permissions
 # Do all this in a single RUN command to avoid duplicating all of the
 # files across image layers when the permissions change
-RUN conda install --quiet --yes \
+RUN conda install --quiet --yes python="${PYTHON_VERSION}" \
     'notebook' \
     'jupyterhub' \
     'jupyterlab' \
-    'jupyterhub=2' \
-    'jupyterhub-base=2' \
-    'jupyter_server=1' \
+    'jupyterhub-base' \
+    'jupyter_server' \
     && conda clean --all -f -y && \
     npm cache clean --force && \
     jupyter notebook --generate-config && \

jupyter-superslim/requirements.txt

@@ -1,7 +1,16 @@
-gen3==4.17.2
+gen3
 cdiserrors
 pandas
 numpy
-jupyter_server_ydoc
 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
+jupyter-lsp
+jupyterlab-lsp
+jupyterlab-search-replace
+jupyterlab-git
+altair[all]
+lckr_jupyterlab_variableinspector
+ripgrep
+frictionless
+# end jupyter plugins and utilities section