Merge branch 'main' into dependabot/pip/docker/py/pip-24.1

.github/workflows/build-and-push-to-docker.yml

@@ -38,6 +38,7 @@ jobs:
           - docker/cuda/Dockerfile
           - docker/vnc/Dockerfile
           - docker/matlab/Dockerfile
+          - docker/matlab-jupyter/Dockerfile
           - docker/julia/Dockerfile
           - docker/batch/Dockerfile
           - docker/qgis/Dockerfile
@@ -347,7 +348,6 @@ jobs:
   build-py-ext:
     needs: build-py
     runs-on: ubuntu-latest
-
     strategy:
       fail-fast: true
       matrix:
@@ -396,6 +396,55 @@ jobs:
           provenance: false
           platforms: linux/amd64,linux/arm64
 
+  build-matlab-ext:
+    needs: build-py
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: true
+      matrix:
+        include:
+          - EXTENSION: matlab-jupyter
+            PYTHON_VERSION: "3.10"
+          - EXTENSION: matlab-jupyter
+            PYTHON_VERSION: "3.11"
+    steps:
+      - name: Docker Login
+        uses: Azure/docker-login@v1
+        with:
+          username: ${{ secrets.RENKU_DOCKER_USERNAME }}
+          password: ${{ secrets.RENKU_DOCKER_PASSWORD }}
+      - uses: actions/checkout@v4
+      - name: Set outputs
+        id: vars
+        run: |
+          sha_short=$(git rev-parse --short HEAD)
+          echo "sha_short=$sha_short" >> $GITHUB_OUTPUT
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3.0.0
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      - name: Docker meta
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.DOCKER_PREFIX }}-${{ matrix.EXTENSION }}
+          tags: |
+            type=sha,prefix=${{ matrix.PYTHON_VERSION }}-
+            type=semver,pattern={{version}},prefix=${{ matrix.PYTHON_VERSION }}-
+            type=raw,value=latest,enable=${{ github.ref == 'refs/heads/main' }},prefix=${{ matrix.PYTHON_VERSION }}-
+      - name: Build and push
+        uses: docker/build-push-action@v5
+        with:
+          build-args: |
+            RENKU_BASE=${{ env.DOCKER_PREFIX }}-py:${{ matrix.PYTHON_VERSION }}-${{ steps.vars.outputs.sha_short }}
+          context: docker/${{ matrix.EXTENSION }}
+          labels: ${{ steps.meta.outputs.labels }}
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          cache-from: type=gha
+          provenance: false
+          platforms: linux/amd64
+
   build-vnc-ext:
     needs: build-py-ext
     runs-on: ubuntu-latest

Makefile

@@ -167,6 +167,13 @@ batch: py
 		-t $(DOCKER_PREFIX)-batch:$(EXTRA_DOCKER_LABEL) \
 		$(BUILDX_EXTRA_FLAGS)
 
+matlab-jupyter: py
+	docker $(BUILD_CMD) docker/matlab-jupyter \
+		--build-arg RENKU_BASE="$(RENKU_BASE)" \
+		--build-arg BASE_IMAGE=mathworks/matlab:r2024a \
+		-t $(DOCKER_PREFIX)-matlab-jupyter:$(EXTRA_DOCKER_LABEL) \
+		$(BUILDX_EXTRA_FLAGS)
+
 bioc: py
 	docker $(BUILD_CMD) docker/r \
 		--build-arg RENKU_BASE="$(RENKU_BASE)" \

docker/matlab-jupyter/Dockerfile

@@ -0,0 +1,76 @@
+# define build arguments
+ARG RENKU_BASE=renku/renkulab-py:latest
+ARG BASE_IMAGE=mathworks/matlab:r2024a
+
+# define base images
+FROM $RENKU_BASE as renku_base
+FROM $BASE_IMAGE
+
+LABEL maintainer="Swiss Data Science Center <info@datascience.ch>"
+
+USER root
+
+ENV NB_USER matlab
+ENV NB_UID 1000
+ENV NB_GID 100
+ENV VENV_DIR /srv/venv
+ENV HOME /home/${NB_USER}
+ENV SHELL bash
+ENV CONDA_PATH /opt/conda
+SHELL [ "/bin/bash", "-c", "-o", "pipefail" ]
+
+# prepend conda and local/bin to PATH
+ENV PATH ${HOME}/.local/bin:${CONDA_PATH}/bin:${HOME}/.renku/bin:$PATH
+
+# Add Tini
+ENV TINI_VERSION v0.18.0
+ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /tini
+RUN chmod +x /tini && ln -s /tini /usr/bin/
+
+# install dependencies
+RUN apt-get update --fix-missing && \
+    apt-get install -yq --no-install-recommends \
+    bzip2 \
+    ca-certificates \
+    curl \
+    git \
+    gpg-agent \
+    rclone \
+    vim && \
+    apt-get purge && \
+    apt-get clean && \
+    apt-get autoremove --yes && \
+    rm -rf /var/lib/apt/lists/* && \
+    curl -L -s https://github.com/git-lfs/git-lfs/releases/download/v3.3.0/git-lfs-linux-"$(dpkg --print-architecture)"-v3.3.0.tar.gz -o /tmp/git-lfs-linux-"$(dpkg --print-architecture)"-v3.3.0.tar.gz && \
+    tar -zxvf /tmp/git-lfs-linux-"$(dpkg --print-architecture)"-v3.3.0.tar.gz -C /tmp && \
+    /tmp/git-lfs-3.3.0/install.sh && \
+    rm -rf /tmp/git-lfs* && \
+    curl -L -o /usr/bin/mpm -s https://www.mathworks.com/mpm/glnxa64/mpm && \
+    chmod a+x /usr/bin/mpm
+
+# inject the renku-jupyter stack
+COPY --from=renku_base /opt/conda /opt/conda
+COPY --from=renku_base --chown=matlab:matlab /usr/local/bin/ /usr/local/bin/
+COPY --from=renku_base --chown=matlab:matlab /home/jovyan/ /home/matlab/
+COPY --from=renku_base /entrypoint.sh /entrypoint.sh
+COPY --from=renku_base /renku/bashrc /renku/bashrc
+
+# set permissions of the R library directory to be editable by NB_USER
+RUN chown 1000:100 /opt/conda && \
+    chown -R 1000:1000 /opt/matlab/R2024a && \
+    # this hack lets some of the setup from the base renku image work here
+    ln -s /home/${NB_USER} /home/jovyan
+
+USER ${NB_USER}
+
+# set up conda in the NB_USER environment
+RUN echo ". ${CONDA_PATH}/etc/profile.d/conda.sh" >> ~/.bashrc && \
+    echo "conda activate base" >> ~/.bashrc && \
+    cat /renku/bashrc >> $HOME/.bashrc && \
+    echo "source ~/.bashrc" >> ~/.bash_profile && \
+    pip install --no-cache-dir "jupyter-matlab-proxy"
+
+ENTRYPOINT [ "/tini", "--", "/entrypoint.sh" ]
+CMD [ "jupyter", "server", "--ip", "0.0.0.0" ]
+
+WORKDIR ${HOME}

docker/matlab/Dockerfile

@@ -10,7 +10,7 @@ ARG BASE_IMAGE=renku/renkulab-vnc:latest
 
 # Replace "mathworks/matlab" with any Docker image that contains MATLAB
 # MATLAB should be available on the path in the Docker image
-FROM mathworks/matlab:r2021b AS matlab-install-stage
+FROM mathworks/matlab:r2023b AS matlab-install-stage
 ARG BASE_ML_INSTALL_LOC
 
 # Run code to locate a MATLAB install in the base image and softlink