Chore/add build for jupyterlab generic

.github/workflows/build_push_jupyterlab_generic.yml

@@ -0,0 +1,44 @@
+name: Push Jupyterlab Generic Image to quay
+
+on:
+  push:
+    paths:
+      - jupyterlab-generic/**
+      - .github/workflows/build_push_jupyterlab_generic.yml
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Extract branch name
+        id: extract_branch
+        run: |
+          echo "IMAGE_TAG=$(echo ${GITHUB_REF#refs/*/} | tr / _)"
+          echo "IMAGE_TAG=$(echo ${GITHUB_REF#refs/*/} | tr / _)" >> $GITHUB_ENV
+
+      - name: Login to Quay.io
+        id: login
+        uses: docker/login-action@v3
+        with:
+          registry: quay.io
+          username: ${{ secrets.QUAY_USERNAME }}
+          password: ${{ secrets.QUAY_ROBOT_TOKEN }}
+
+      - name: Extract metadata
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: |
+            quay.io/cdis/jupyterlab-generic:${{ env.IMAGE_TAG }}
+
+      - name: Build and Push Image
+        uses: docker/build-push-action@v6
+        with:
+          context: ./jupyterlab-generic
+          file: "./jupyterlab-generic/Dockerfile"
+          push: true
+          tags: |
+            quay.io/cdis/jupyterlab-generic:${{ env.IMAGE_TAG }}
+          labels: ${{ steps.meta.outputs.labels }}

jupyterlab-generic/Dockerfile

@@ -1,30 +1,22 @@
 # Generic Gen3 JupyterLab workspace
 
-FROM public.ecr.aws/amazonlinux/amazonlinux:2023-minimal AS builder-image
+FROM public.ecr.aws/amazonlinux/amazonlinux:2023-minimal
+LABEL maintainer="Center for Translational Data Science (CTDS)"
+LABEL name="jupyterlab-generic"
 
 # TODO: git, nodejs, and build are all required only to build jupyterlmod;
 #       these can be dropped once jupyterlmod fix is available in PyPI.
 RUN dnf upgrade --refresh && \
-    dnf install -y python3.13 python3.13-pip git nodejs && \
+    dnf install -y python3.13 python3.13-pip git nodejs shadow-utils which && \
     python3.13 -m venv /usr/local/python-venv && \
     source /usr/local/python-venv/bin/activate && \
     pip install --upgrade pip && \
     pip install jupyterlab && \
     pip install build && \
     pip install jupyterlmod git+https://github.com/pschumm/jupyter-lmod@pschumm/fix_hidden && \
-    pip install jupyterlab-git &&\
+    pip install jupyterlab-git && \
     pip install jupyterlab-search-replace
 
-
-FROM public.ecr.aws/amazonlinux/amazonlinux:2023-minimal AS runner-image
-LABEL maintainer="Center for Translational Data Science (CTDS)"
-LABEL name="jupyterlab-generic"
-
-RUN dnf upgrade --refresh && \
-    dnf install -y shadow-utils which python3.13 && \
-    python3.13 -m venv /usr/local/python-venv
-
-COPY --from=builder-image /usr/local/python-venv /usr/local/python-venv
 RUN /usr/local/python-venv/bin/jupyter kernelspec remove -y python3
 
 COPY jupyterlab-start.sh .

jupyterlab-generic/jupyterlab-start.sh

@@ -1,21 +1,18 @@
 #!/usr/bin/env bash
 
-# Symlink config files for persistence
-test -f ./pd/.bash_profile || touch ./pd/.bash_profile
-test -f ./pd/.bashrc || touch ./pd/.bashrc
-test -d ./pd/.jupyter || mkdir ./pd/.jupyter
-test -d ./pd/.ipython || mkdir ./pd/.ipython
-test -d ./pd/.config || mkdir ./pd/.config
-test -d ./pd/.local || mkdir ./pd/.local
-ln -s ./pd/.bash_profile .
-ln -s ./pd/.bashrc .
-ln -s ./pd/.jupyter .
-ln -s ./pd/.ipython .
-ln -s ./pd/.config .
-ln -s ./pd/.local .
-
-# Symlink data directory mounted at root
-ln -s /data .
+# # Symlink config files for persistence
+# test -f ./pd/.bash_profile || touch ./pd/.bash_profile
+# test -f ./pd/.bashrc || touch ./pd/.bashrc
+# test -d ./pd/.jupyter || mkdir ./pd/.jupyter
+# test -d ./pd/.ipython || mkdir ./pd/.ipython
+# test -d ./pd/.config || mkdir ./pd/.config
+# test -d ./pd/.local || mkdir ./pd/.local
+# ln -s ./pd/.bash_profile .
+# ln -s ./pd/.bashrc .
+# ln -s ./pd/.jupyter .
+# ln -s ./pd/.ipython .
+# ln -s ./pd/.config .
+# ln -s ./pd/.local .
 
 # Load JupyterLab extension dependencies
 source /apps/lmod/lmod/init/profile
@@ -24,7 +21,8 @@ module load git ripgrep
 module load py-pandas py-scipy
 
 /usr/local/python-venv/bin/jupyter lab \
-    --ip=0.0.0.0 \
+    --ServerApp.ip=0.0.0.0 \
     --KernelSpecManager.ensure_native_kernel=False \
     --ServerApp.quit_button=False \
-    --IdentityProvider.token=""
+    --IdentityProvider.token="" \
+    "$@"