update from test

.dockerignore

@@ -0,0 +1,12 @@
+# Ignore documentation
+book/
+docs/
+
+# Ignore version control folder
+.git/
+.gitignore
+
+# Ignore R stuff
+.Rhistory
+.Rproj.user
+py-rocket-base.Rproj

.github/workflows/test-build.yml

@@ -0,0 +1,37 @@
+name: Docker Image test
+on:
+  workflow_dispatch: null
+  push:
+    branches: test
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions: write-all
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          ref: test
+      - name: Login to GitHub Container Registry
+        if: github.repository == 'nmfs-opensci/py-rocket-base'
+        uses: docker/login-action@v1
+        with:
+          registry: ghcr.io
+          username: ${{github.actor}}
+          password: ${{secrets.GITHUB_TOKEN}}
+      - name: Create short_sha tag
+        shell: bash
+        run: |
+          short_sha=$(echo "${{ github.sha }}" | cut -c1-7)
+          echo "tag=${short_sha}" >> $GITHUB_ENV
+      - name: Build the Docker image
+        if: github.repository == 'nmfs-opensci/py-rocket-base'
+        run: |
+          docker build . -f Dockerfile \
+            --tag ghcr.io/nmfs-opensci/py-rocket-base/test:latest \
+            --tag ghcr.io/nmfs-opensci/py-rocket-base/test:${{ env.tag }}
+      - name: Publish
+        if: github.repository == 'nmfs-opensci/py-rocket-base'
+        run: |
+          docker push ghcr.io/nmfs-opensci/py-rocket-base/test:latest
+          docker push ghcr.io/nmfs-opensci/py-rocket-base/test:${{ env.tag }}

Dockerfile

@@ -0,0 +1,62 @@
+FROM ghcr.io/nmfs-opensci/py-rocket-base/base-image:latest
+
+USER root
+
+# Define environment variables
+# DISPLAY Tell applications where to open desktop apps - this allows notebooks to pop open GUIs
+ENV REPO_DIR="/srv/repo" \
+    DISPLAY=":1.0" \
+    R_VERSION="4.4.1"
+
+# Add NB_USER to staff group (required for rocker script)
+# Ensure the staff group exists first
+RUN groupadd -f staff && usermod -a -G staff "${NB_USER}"
+
+COPY --chown=${NB_USER}:${NB_USER} . ${REPO_DIR}
+RUN chgrp -R staff ${REPO_DIR} && \
+    chmod -R g+rwx ${REPO_DIR} && \
+    rm -rf ${REPO_DIR}/book ${REPO_DIR}/docs
+
+# Copy scripts to /pyrocket_scripts and set permissions
+RUN mkdir -p /pyrocket_scripts && \
+    cp -r ${REPO_DIR}/scripts/* /pyrocket_scripts/ && \
+    chown -R root:staff /pyrocket_scripts && \
+    chmod -R 775 /pyrocket_scripts
+
+# Install extra conda packages
+RUN /pyrocket_scripts/install-conda-packages.sh ${REPO_DIR}/environment.yml
+
+# Install R, RStudio via Rocker scripts
+ENV R_DOCKERFILE="verse_${R_VERSION}"
+RUN PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin && \
+    chmod +x ${REPO_DIR}/rocker.sh && \
+    ${REPO_DIR}/rocker.sh
+
+# Install extra apt packages
+# Install linux packages after R installation since the R install scripts get rid of packages
+RUN /pyrocket_scripts/install-apt-packages.sh ${REPO_DIR}/apt.txt
+
+# Re-enable man pages disabled in Ubuntu 18 minimal image
+# https://wiki.ubuntu.com/Minimal
+RUN yes | unminimize
+# NOTE: $NB_PYTHON_PREFIX is the same as $CONDA_PREFIX at run-time.
+# $CONDA_PREFIX isn't available in this context.
+# NOTE: Prepending ensures a working path; if $MANPATH was previously empty,
+# the trailing colon ensures that system paths are searched.
+ENV MANPATH="${NB_PYTHON_PREFIX}/share/man:${MANPATH}"
+RUN mandb
+
+# Add custom Jupyter server configurations
+RUN mkdir -p ${NB_PYTHON_PREFIX}/etc/jupyter/jupyter_server_config.d/ && \
+    mkdir -p ${NB_PYTHON_PREFIX}/etc/jupyter/jupyter_notebook_config.d/ && \
+    cp ${REPO_DIR}/custom_jupyter_server_config.json ${NB_PYTHON_PREFIX}/etc/jupyter/jupyter_server_config.d/ && \
+    cp ${REPO_DIR}/custom_jupyter_server_config.json ${NB_PYTHON_PREFIX}/etc/jupyter/jupyter_notebook_config.d/
+
+# Set up the start command 
+USER ${NB_USER}
+RUN chmod +x ${REPO_DIR}/start \
+    && cp ${REPO_DIR}/start /srv/start
+
+# Revert to default user and home as pwd
+USER ${NB_USER}
+WORKDIR ${HOME}

environment.yml

@@ -5,11 +5,11 @@ channels:
   - nodefaults
 
 dependencies:
-  - python~=3.11.0
-  - jupyterlab>=4.0
+  # Core JupyterHub packages
+  - python=3.12
+  - pangeo-notebook=2024.11.11
+  - pip
   - jupyter-resource-usage
-  - jupyterlab-git
-  # gh-scoped-creds allows users to securely push to GitHub from their repo.
   - gh-scoped-creds==4.1
 
   # R/RStudio Support
@@ -25,8 +25,7 @@ dependencies:
   #- syncthing~=1.22.1
 
   # Extra Jupyter tools
-  - ipython
-  - ipywidgets
+  - jupyterlab-git
   - jupyter-ai
   - jupyter-book
   - jupyter-offlinenotebook
@@ -35,21 +34,15 @@ dependencies:
   - jupyterlab-geojson
   - jupyterlab-h5web
   - jupyterlab-myst
-  - jupyterlab_pygments>=0.3.0
   - jupytext
   - nbdime
+
   # JupyterBook Addons
   - sphinx
   - sphinxcontrib-bibtex
-  # Interactive apps
-  - itables
-  - voila
-  # nbgitpuller is very helpful when distributing user content
-  - nbgitpuller
+
   # More git tools from github-cli
   - gh
-  # conda-lock
-  - conda-lock
 
   # Resolves warning "No ICDs were found": https://github.com/CryoInTheCloud/hub-image/issues/50
   - ocl-icd-system

scripts/install-conda-packages.sh

@@ -4,50 +4,68 @@
 # Check if a filename argument is provided
 if [ -z "$1" ]; then
     echo "Error: install-conda-packages.sh requires a file name (either conda-lock.yml or environment.yml)." >&2
-    echo "Usage: RUN /pyrocket_scripts/install-conda-packages.sh <filename.yml>" >&2
+    echo "Usage: RUN /pyrocket_scripts/install-conda-packages.sh <filename.yml> [env_name]" >&2
     exit 1
 fi
 
+# Set the environment name, defaulting to ${CONDA_ENV} if not provided
+ENV_FILE="$1"
+ENV_NAME="${2:-${CONDA_ENV}}"
+
 # Check if running as root and switch to NB_USER if needed
 if [[ $(id -u) -eq 0 ]]; then
     echo "Switching to ${NB_USER} to run install-conda-packages.sh"
-    exec su "${NB_USER}" -c "/bin/bash $0 $1"  # Pass along the filename argument
+    exec su "${NB_USER}" -c "/bin/bash $0 $ENV_FILE $ENV_NAME"
 fi
 
 # Main script execution as NB_USER
 echo "Running install-conda-packages.sh as ${NB_USER}"
-
-# Set the file variable to the provided argument
-ENV_FILE="$1"
+echo "  Using environment file: $ENV_FILE"
+echo "  Target environment: $ENV_NAME"
 
 # Verify the file exists and is readable
 if [ ! -f "$ENV_FILE" ]; then
     echo "  Error: File '$ENV_FILE' not found. Please provide a valid file path." >&2
-    echo "  Usage: RUN /pyrocket_scripts/install-conda-packages.sh <filename.yml>" >&2
     exit 1
 fi
 
-echo "  Found file: $ENV_FILE"
-
-# Determine file type based on content
-if grep -q "lock_set" "$ENV_FILE"; then
-    echo "  Detected conda-lock.yml file."
-    ${NB_PYTHON_PREFIX}/bin/conda-lock install --name ${CONDA_ENV} -f "$ENV_FILE"
-    INSTALLATION_HAPPENED=true
-elif grep -q "name:" "$ENV_FILE"; then
-    echo "  Detected environment.yml file."
-    ${CONDA_DIR}/condabin/mamba env update --name ${CONDA_ENV} -f "$ENV_FILE"
-    INSTALLATION_HAPPENED=true
+# Check if the Conda environment exists
+if ! ${CONDA_DIR}/condabin/conda env list | grep -q "^$ENV_NAME "; then
+    echo "  Environment '$ENV_NAME' not found. Creating it."
+
+    # Create environment based on file type
+    if grep -q "lock_set" "$ENV_FILE"; then
+        echo "  Detected conda-lock.yml file."
+        ${NB_PYTHON_PREFIX}/bin/conda-lock install --name $ENV_NAME -f "$ENV_FILE"
+    elif grep -q "name:" "$ENV_FILE"; then
+        echo "  Detected environment.yml file."
+        ${CONDA_DIR}/condabin/mamba env create -f "$ENV_FILE" --name $ENV_NAME
+        INSTALLATION_HAPPENED=true
+    else
+        echo "  Error: Unrecognized file format in '$ENV_FILE'."
+        exit 1
+    fi
 else
-    # If neither condition matches, output a helpful error message
-    echo "Error: Unrecognized file format in '${env_file}'."
-    echo "  - For an environment.yml file, ensure it includes a 'name:' entry. Any name is acceptable."
-    echo "  - For a conda-lock.yml file, ensure it includes a 'lock_set:' entry."
-    exit 1
+    echo "  Environment '$ENV_NAME' exists. Updating it."
+
+    # Update environment based on file type
+    if grep -q "lock_set" "$ENV_FILE"; then
+        echo "  Detected conda-lock.yml file."
+        ${NB_PYTHON_PREFIX}/bin/conda-lock install --name $ENV_NAME -f "$ENV_FILE"
+    elif grep -q "name:" "$ENV_FILE"; then
+        echo "  Detected environment.yml file."
+        ${CONDA_DIR}/condabin/mamba env update --name $ENV_NAME -f "$ENV_FILE"
+    else
+        echo "  Error: Unrecognized file format in '${ENV_FILE}'."
+        echo "    - For an environment.yml file, ensure it includes a 'name:' entry. Any name is acceptable."
+        echo "    - For a conda-lock.yml file, ensure it includes a 'lock_set:' entry."
+        exit 1
+    fi
 fi
 
 # Run cleanup if installation occurred
 if [ "$INSTALLATION_HAPPENED" = true ]; then
+    echo "  Installation clean-up."
     ${CONDA_DIR}/condabin/mamba clean -yaf
     find ${CONDA_DIR} -follow -type f -name '*.a' -delete
     find ${CONDA_DIR} -follow -type f -name '*.js.map' -delete

test.yml

@@ -0,0 +1,9 @@
+name: test
+
+channels:
+  - conda-forge
+  - nodefaults
+
+dependencies:
+  - cmocean
+