feat: add vscodium images for new amalthea

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

@@ -42,6 +42,10 @@ jobs:
           - docker/julia/Dockerfile
           - docker/batch/Dockerfile
           - docker/qgis/Dockerfile
+          - docker/vscode/base.Dockerfile
+          - docker/vscode/conda.Dockerfile
+          - docker/vscode/poetry.Dockerfile
+          - docker/vscode/R.Dockerfile
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -414,7 +418,7 @@ jobs:
             PYTHON_VERSION: "3.11"
     steps:
       - name: Docker Login
-        uses: Azure/docker-login@v1
+        uses: docker/login-action@v3
         with:
           username: ${{ secrets.RENKU_DOCKER_USERNAME }}
           password: ${{ secrets.RENKU_DOCKER_PASSWORD }}
@@ -698,3 +702,229 @@ jobs:
           tags: ${{ steps.meta.outputs.tags }}
           cache-from: type=gha
           provenance: false
+
+  build-vscode-base:
+    needs: lint
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: true
+      matrix:
+        include:
+          - BASE_IMAGE: debian:bookworm
+            BASE_IMAGE_TAG: debian
+            LATEST: true
+    steps:
+      - name: Docker Login
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.RENKU_DOCKER_USERNAME }}
+          password: ${{ secrets.RENKU_DOCKER_PASSWORD }}
+      - uses: actions/checkout@v4
+      - name: Set up QEMU
+        uses: docker/[email protected]
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      - name: Docker meta
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.DOCKER_PREFIX }}-vscode
+          tags: |
+            type=sha,prefix=${{ matrix.BASE_IMAGE_TAG }}-
+            type=semver,pattern={{version}},prefix=${{ matrix.BASE_IMAGE_TAG }}-
+            type=raw,value=latest,enable=${{ github.ref == 'refs/heads/main' && matrix.LATEST }}
+      - name: Build and export
+        uses: docker/build-push-action@v6
+        with:
+          build-args: |
+            BASE_IMAGE=${{ matrix.BASE_IMAGE }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+          context: docker/vscode
+          file: docker/vscode/base.Dockerfile
+          labels: ${{ steps.meta.outputs.labels }}
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          provenance: false
+
+  build-vscode-conda:
+    needs: build-vscode-base
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: true
+      matrix:
+        include:
+          - PYTHON_VERSION: 3.12.7
+            BASE_IMAGE_TAG: debian
+            LATEST: true
+          - PYTHON_VERSION: 3.11.10
+            BASE_IMAGE_TAG: debian
+            LATEST: true
+          - PYTHON_VERSION: 3.10.15
+            BASE_IMAGE_TAG: debian
+            LATEST: true
+    steps:
+      - name: Docker Login
+        uses: docker/login-action@v3
+        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" >> $GITHUB_OUTPUT
+          echo "renku_base=${DOCKER_PREFIX}-vscode:${{ matrix.BASE_IMAGE_TAG }}-${sha_short}" >> $GITHUB_OUTPUT
+      - name: Set up QEMU
+        uses: docker/[email protected]
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      - name: Docker meta
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.DOCKER_PREFIX }}-vscode-python
+          tags: |
+            type=sha,prefix=py-${{ matrix.PYTHON_VERSION }}-
+            type=semver,pattern={{version}},prefix=py-${{ matrix.PYTHON_VERSION }}-
+            type=raw,value=latest,enable=${{ github.ref == 'refs/heads/main' && matrix.LATEST }}
+      - name: Build and export
+        uses: docker/build-push-action@v6
+        with:
+          build-args: |
+            BASE_IMAGE=${{ steps.vars.outputs.renku_base }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+          context: docker/vscode
+          file: docker/vscode/conda.Dockerfile
+          labels: ${{ steps.meta.outputs.labels }}
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          provenance: false
+
+  build-vscode-poetry:
+    needs: build-vscode-base
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: true
+      matrix:
+        include:
+          - PYTHON_VERSION: 3.12.7
+            BASE_IMAGE_TAG: debian
+            PYENV_VERSION: v2.4.17
+            POETRY_VERSION: 1.8.4
+            LATEST: true
+          - PYTHON_VERSION: 3.11.10
+            BASE_IMAGE_TAG: debian
+            PYENV_VERSION: v2.4.17
+            POETRY_VERSION: 1.8.4
+            LATEST: false
+          - PYTHON_VERSION: 3.10.15
+            BASE_IMAGE_TAG: debian
+            PYENV_VERSION: v2.4.17
+            POETRY_VERSION: 1.8.4
+            LATEST: false
+    steps:
+      - name: Docker Login
+        uses: docker/login-action@v3
+        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" >> $GITHUB_OUTPUT
+          echo "renku_base=${DOCKER_PREFIX}-vscode:${{ matrix.BASE_IMAGE_TAG }}-${sha_short}" >> $GITHUB_OUTPUT
+      - name: Set up QEMU
+        uses: docker/[email protected]
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      - name: Docker meta
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.DOCKER_PREFIX }}-vscode-poetry
+          tags: |
+            type=sha,prefix=py-${{ matrix.PYTHON_VERSION }}-
+            type=semver,pattern={{version}},prefix=py-${{ matrix.PYTHON_VERSION }}-
+            type=raw,value=latest,enable=${{ github.ref == 'refs/heads/main' && matrix.LATEST }}
+      - name: Build and export
+        uses: docker/build-push-action@v6
+        with:
+          build-args: |
+            BASE_IMAGE=${{ steps.vars.outputs.renku_base }}
+            PYTHON_VERSION=${{ matrix.PYTHON_VERSION }}
+            POETRY_VERSION=${{ matrix.POETRY_VERSION }}
+            PYENV_VERSION=${{ matrix.PYENV_VERSION }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+          context: docker/vscode
+          file: docker/vscode/poetry.Dockerfile
+          labels: ${{ steps.meta.outputs.labels }}
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          provenance: false
+
+  build-vscode-r:
+    needs: build-vscode-base
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: true
+      matrix:
+        include:
+          - R_VERSION: 4.4.2
+            BASE_IMAGE_TAG: debian
+            LATEST: true
+          - R_VERSION: 4.3.3
+            BASE_IMAGE_TAG: debian
+            LATEST: false
+          - R_VERSION: 4.2.3
+            BASE_IMAGE_TAG: debian
+            LATEST: false
+    steps:
+      - name: Docker Login
+        uses: docker/login-action@v3
+        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" >> $GITHUB_OUTPUT
+          echo "renku_base=${DOCKER_PREFIX}-vscode:${{ matrix.BASE_IMAGE_TAG }}-${sha_short}" >> $GITHUB_OUTPUT
+      - name: Set up QEMU
+        uses: docker/[email protected]
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      - name: Docker meta
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.DOCKER_PREFIX }}-vscode-r
+          tags: |
+            type=sha,prefix=r-${{ matrix.R_VERSION }}-
+            type=semver,pattern={{version}},prefix=r-${{ matrix.R_VERSION }}-
+            type=raw,value=latest,enable=${{ github.ref == 'refs/heads/main' && matrix.LATEST }}
+      - name: Build and export
+        uses: docker/build-push-action@v6
+        with:
+          build-args: |
+            BASE_IMAGE=${{ steps.vars.outputs.renku_base }}
+            R_VERSION=${{ matrix.R_VERSION }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max
+          context: docker/vscode
+          file: docker/vscode/R.Dockerfile
+          labels: ${{ steps.meta.outputs.labels }}
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          provenance: false

docker/py/entrypoint.sh

@@ -57,7 +57,8 @@ jupyter() {
 if [[ -v RENKU_BASE_URL_PATH ]]; then
     "$@" --ServerApp.port=8888 --ServerApp.base_url="$RENKU_BASE_URL_PATH" \
         --ServerApp.token="" --ServerApp.password="" --ServerApp.allow_remote_access=true \
-        --ContentsManager.allow_hidden=true --ServerApp.allow_origin=*
+        --ContentsManager.allow_hidden=true --ServerApp.allow_origin=* \
+        --ServerApp.root_dir="${HOME}/work"
 fi
 
 # run the command

docker/vscode/R.Dockerfile

@@ -0,0 +1,29 @@
+ARG BASE_IMAGE=renku/renkulab-vscode:latest
+FROM $BASE_IMAGE
+ARG R_VERSION=4.4.2
+ARG SESSION_USER=vscode
+ARG WORKDIR=/home/${SESSION_USER}
+ARG MOUNTDIR=${WORKDIR}/work
+
+SHELL [ "/bin/bash", "-c", "-o", "pipefail" ]
+USER root
+# From https://docs.posit.co/resources/install-r.html
+RUN curl -O https://cdn.rstudio.com/r/debian-12/pkgs/r-${R_VERSION}_1_amd64.deb \
+	&& apt-get update \
+	&& apt-get install -y --no-install-recommends ./r-${R_VERSION}_1_amd64.deb \
+	&& rm -rf /var/lib/apt/lists/* \
+	&& rm -rf ./r-${R_VERSION}_1_amd64.deb \
+	&& ln -s /opt/R/${R_VERSION}/bin/R /usr/local/bin/R \
+	&& ln -s /opt/R/${R_VERSION}/bin/Rscript /usr/local/bin/Rscript
+
+USER ${SESSION_USER}
+ENV __MOUNTDIR__=${MOUNTDIR}
+WORKDIR ${WORKDIR}
+# The .Renviron changes allow R to install packages in the work directory
+# See https://www.r-bloggers.com/2020/10/customizing-your-package-library-location/
+# The .Rprofile changes allow R to be able to use precompiled packages
+# See https://packagemanager.posit.co/client/#/repos/cran/setup
+RUN printf "\nR_LIBS_SITE=\"%s/.rlibs\"\n" "${MOUNTDIR}" >> /home/${SESSION_USER}/.Renviron \
+	&& printf "\noptions(repos = c(CRAN = \"https://packagemanager.posit.co/cran/__linux__/bookworm/latest\"))\n" >> /home/${SESSION_USER}/.Rprofile
+ENTRYPOINT ["tini", "--", "sh", "-c"]
+CMD ["mkdir -p ${__MOUNTDIR__}/.rlibs && bash /entrypoint.sh"]

docker/vscode/README.md

@@ -0,0 +1,8 @@
+# Images with VSCodium
+
+The devcontainer images here are a great base for this:
+https://hub.docker.com/r/microsoft/vscode-devcontainers
+
+They do not contain vscode in them. They contain an executable
+that is called `code` but that is just a shell script that
+prints a message that VSCode is not installed.

docker/vscode/base.Dockerfile

@@ -0,0 +1,23 @@
+ARG BASE_IMAGE=debian:bookworm
+FROM $BASE_IMAGE
+ARG VSCODIUM_VERSION=1.95.2.24313
+ARG SESSION_USER=vscode
+ARG WORKDIR=/home/${SESSION_USER}
+ARG MOUNTDIR=${WORKDIR}/work
+SHELL [ "/bin/bash", "-c", "-o", "pipefail" ]
+RUN apt-get update && \
+	apt-get install -y --no-install-recommends ca-certificates curl tini build-essential git git-lfs && \
+	mkdir -p /codium-server && \
+	curl -L https://github.com/VSCodium/vscodium/releases/download/${VSCODIUM_VERSION}/vscodium-reh-web-linux-x64-${VSCODIUM_VERSION}.tar.gz | tar -xz -C /codium-server && \
+	rm -rf /var/lib/apt/lists/*
+RUN useradd -m -s /bin/bash ${SESSION_USER}
+ENV LANG=C.UTF-8
+ENV LC_ALL=C.UTF-8
+
+USER ${SESSION_USER}
+COPY entrypoint.sh /entrypoint.sh
+WORKDIR ${WORKDIR}
+# We are setting this to a weird double underscore name to avoid collisions with user-set vars
+ENV __MOUNTDIR__=${MOUNTDIR}
+RUN mkdir -p ${MOUNTDIR}
+ENTRYPOINT ["tini", "--", "/bin/bash", "/entrypoint.sh"]

docker/vscode/conda.Dockerfile

@@ -0,0 +1,29 @@
+ARG BASE_IMAGE=renku/renkulab-vscode:latest
+FROM $BASE_IMAGE
+ARG MICROMAMBA_VERSION=2.0.2-2
+ARG MAMBA_VERSION=1.5.9
+ARG CONDA_VERSION=24.9.2
+ARG PYTHON_VERSION=3.12.7
+ARG OS=linux
+ARG ARCH=64
+ARG SESSION_USER=vscode
+ARG WORKDIR=/home/${SESSION_USER}
+ARG MOUNTDIR=${WORKDIR}/work
+ARG VENVS_PATH=${MOUNTDIR}/.venvs
+ENV __VENVS_PATH__=${VENVS_PATH}
+ENV __PYTHON_VERSION__=${PYTHON_VERSION}
+ENV __MAMBA_VERSION__=${MAMBA_VERSION}
+ENV __CONDA_VERSION__=${CONDA_VERSION}
+SHELL [ "/bin/bash", "-c", "-o", "pipefail" ]
+USER root
+RUN apt-get update && \
+	apt-get install -y curl --no-install-recommends && \
+	curl -L "https://github.com/mamba-org/micromamba-releases/releases/download/${MICROMAMBA_VERSION}/micromamba-${OS}-${ARCH}" -o /usr/local/bin/micromamba && \
+	chmod a+x /usr/local/bin/micromamba && \
+	rm -rf /var/lib/apt/lists/*
+
+USER ${SESSION_USER}
+WORKDIR ${WORKDIR}
+ENV __MOUNTDIR__=${MOUNTDIR}
+ENTRYPOINT ["tini", "--", "sh", "-c"]
+CMD ["set -ex && micromamba install --yes --root-prefix=${__VENVS_PATH__} --prefix=${__VENVS_PATH__} python=${__PYTHON_VERSION__} mamba=${__MAMBA_VERSION__} conda=${__CONDA_VERSION__} && ${__VENVS_PATH__}/bin/mamba init && ${__VENVS_PATH__}/bin/conda config --add channels conda-forge && ${__VENVS_PATH__}/bin/conda config --set channel_priority strict && ${__VENVS_PATH__}/bin/conda config --remove channels defaults && bash /entrypoint.sh"]

docker/vscode/entrypoint.sh

@@ -0,0 +1,12 @@
+set -ex
+MOUNTDIR=${__MOUNTDIR__}
+mkdir -p "${MOUNTDIR}/.vscode/extensions"
+/codium-server/bin/codium-server \
+	--server-base-path "$RENKU_BASE_URL_PATH/" \
+	--without-connection-token \
+	--host 0.0.0.0 \
+	--port 8888 \
+	--extensions-dir "${MOUNTDIR}/.vscode/extensions" \
+	--accept-server-license-terms \
+	--telemetry-level off \
+	--server-data-dir "${MOUNTDIR}/.vscode"

docker/vscode/poetry.Dockerfile

@@ -0,0 +1,26 @@
+ARG BASE_IMAGE=renku/renkulab-vscode:latest
+FROM $BASE_IMAGE
+ARG PYENV_VERSION=v2.4.17
+ARG PYTHON_VERSION=3.12.7
+# Empty string for poetry version means the latest version
+ARG POETRY_VERSION=""
+ARG SESSION_USER=vscode
+ARG WORKDIR=/home/${SESSION_USER}
+ARG MOUNTDIR=${WORKDIR}/work
+ARG VENVS_PATH=${MOUNTDIR}/.venvs
+SHELL [ "/bin/bash", "-c", "-o", "pipefail" ]
+USER root
+RUN apt-get update && \
+	apt-get install -y --no-install-recommends curl libz-dev libreadline-dev libncurses-dev libsqlite3-dev libssl-dev liblzma-dev libgdbm-dev libbz2-dev libffi-dev && \
+	mkdir -p /python-build && \
+	curl -L https://github.com/pyenv/pyenv/archive/refs/tags/${PYENV_VERSION}.tar.gz | tar -xz -C /python-build && \
+	/bin/sh /python-build/*/plugins/python-build/install.sh && \
+	python-build ${PYTHON_VERSION} /usr/local && \
+	rm -rf /python-build && \
+	rm -rf /var/lib/apt/lists/*
+
+USER ${SESSION_USER}
+ENV __MOUNTDIR__=${MOUNTDIR}
+RUN curl -sSL https://install.python-poetry.org | python3 - --version=${POETRY_VERSION} && \
+	/home/${SESSION_USER}/.local/bin/poetry config virtualenvs.path ${VENVS_PATH}
+WORKDIR ${WORKDIR}