Pixi first

.github/workflows/cuda-image.yml

@@ -11,22 +11,41 @@ jobs:
     # For biggish images, github actions runs out of disk space.
       - name: cleanup disk space
         run: sudo rm -rf /usr/local/lib/android /usr/share/dotnet /opt/ghc
-      - uses: actions/checkout@v3
+      - name: Checkout code
+        uses: actions/checkout@v3
 
-      - name: Login to GitHub Container Registry
-        uses: docker/login-action@v1
+      - name: Login to Docker Hub
+        uses: docker/login-action@v2
         with:
-          registry: ghcr.io
-          username: ${{github.actor}}
-          password: ${{secrets.GITHUB_TOKEN}}
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
 
-      - name: Build the Docker image (torch)
-        run: docker build cuda --build-arg BASE=quay.io/jupyter/pytorch-notebook:cuda12-ubuntu-24.04 --tag ghcr.io/schmidtdse/cuda:latest
-      - name: Publish cuda (torch)
-        run: docker push ghcr.io/schmidtdse/cuda:latest
-
-      - name: Build the Docker image (tensorflow)
-        run: docker build cuda --build-arg BASE=quay.io/jupyter/tensorflow-notebook:cuda-latest --tag ghcr.io/schmidtdse/tensorflow:latest
-      - name: Publish tensorflow
-        run: docker push ghcr.io/schmidtdse/tensorflow:latest
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v4
+        with:
+          context: cuda
+          push: true
+          tags: ${{ github.ref }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract Docker metadata (tags, labels)
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.IMAGE_NAME }}
+          tags: |
+            type=raw,value=latest,enable=${{ github.ref == format('refs/heads/{0}', github.event.repository.default_branch) }}
+            type=ref,event=branch
+            type=semver,pattern=v{{version}}
+            type=sha,format=short
 
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: cuda
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max

R/Dockerfile

@@ -0,0 +1,14 @@
+FROM ghcr.io/schmidtdse/base
+
+# Install R, RStudio
+USER root
+
+RUN curl -s https://raw.githubusercontent.com/rocker-org/ml/refs/heads/master/install_r.sh | bash
+RUN curl -s https://raw.githubusercontent.com/rocker-org/ml/refs/heads/master/install_rstudio.sh | bash
+
+USER ${NB_USER}
+
+# We either must modify the official /workdir/pixi.toml, or we can use pixi add
+# We don't need to activate pixi env, just be in the correct workdir
+RUN cd ${DOCKER_WORKDIR} && pixi add jupyter-rsession-proxy
+

base/Dockerfile

@@ -41,22 +41,18 @@ RUN apt-get update -q && apt-get -y install curl && apt-get clean && rm -rf /var
 RUN mkdir -p ${CODE_EXTENSIONSDIR} && chown -R ${NB_USER}:users ${CODE_EXTENSIONSDIR}
 RUN curl -fsSL https://code-server.dev/install.sh | sh && rm -rf /home/${NB_USER}/.cache 
 
-# Install R, RStudio
-RUN curl -s https://raw.githubusercontent.com/rocker-org/ml/refs/heads/master/install_r.sh | bash
-RUN curl -s https://raw.githubusercontent.com/rocker-org/ml/refs/heads/master/install_rstudio.sh | bash
-
 # Build the environment
 USER ${NB_USER}
 
 COPY vscode-extensions.txt /tmp/vscode-extensions.txt
 RUN xargs -n 1 code-server --extensions-dir ${CODE_EXTENSIONSDIR} --install-extension < /tmp/vscode-extensions.txt
 
-COPY pixi.toml .
+COPY --chown=${NB_UID}:${NB_UID} pixi.toml .
 RUN pixi install \
  && rm -rf ~/.cache/rattler
 
 # Set up shell activation script
- RUN pixi shell-hook -s bash > ./shell-hook
+RUN pixi shell-hook -s bash > ./shell-hook
 USER root
 ENV ENTRYPOINT_SCRIPT="/entrypoint.sh"
 RUN echo "#!/bin/bash" > ${ENTRYPOINT_SCRIPT}
@@ -65,7 +61,6 @@ RUN echo 'exec "$@"' >> ${ENTRYPOINT_SCRIPT}
 RUN chmod +x ${ENTRYPOINT_SCRIPT}
 
 USER ${NB_USER}
-WORKDIR "/home/${NB_USER}"
 EXPOSE 8888
 ENTRYPOINT ["/entrypoint.sh"]
 CMD ["jupyter", "lab", "--no-browser", "--ip=0.0.0.0"]

base/pixi.toml

@@ -1,7 +1,7 @@
 [workspace]
 authors = ["Matt Fisher <mfisher87@gmail.com>"]
 channels = ["conda-forge", "nodefaults"]
-name = "geojupyter-pixi-docker-image"
+name = "schmidtdse"
 platforms = ["linux-64"]
 version = "0.1.0"
 
@@ -15,7 +15,6 @@ jupyterlab-favorites = "*"
 jupyter-collaboration = "*"
 jupyter-server-proxy = "*"
 jupyter-vscode-proxy = "*"
-jupyter-rsession-proxy = "*"
 jupyterlab-myst = "*"
 typst = "*"
 ruff = "*"

cuda/Dockerfile

@@ -1,38 +1,66 @@
-ARG BASE=quay.io/jupyter/minimal-notebook:ubuntu-24.04
+FROM ghcr.io/prefix-dev/pixi:noble AS build
+LABEL "org.opencontainers.image.description"="A pixi-based Docker image for a robust GeoJupyter environment"
 
-# cuda image uses:
-# ARG BASE=quay.io/jupyter/pytorch-notebook:cuda12-ubuntu-24.04
-FROM $BASE
+# Use bash as default shell instead of sh
+ENV SHELL=/bin/bash
+# Don't buffer Python stdout/stderr output
+ENV PYTHONBUFFERED=1
+# Don't prompt in apt commands
+ENV DEBIAN_FRONTEND=noninteractive
 
-# Make code-server extensions etc persist to container, not hub
-ENV XDG_DATA_HOME=/opt/share
-ENV PATH=/opt/share/pixi/bin:$PATH
-
-## Grant user sudoer privileges
-USER root
-RUN adduser "$NB_USER" sudo && echo '%sudo ALL=(ALL) NOPASSWD:ALL' >>/etc/sudoers
-RUN mkdir /opt/share && chown -R ${NB_USER}:users /opt/share
-
-USER ${NB_USER}
+# Set up JupyterLab user
+ENV NB_USER=jovyan
+ENV NB_UID=1000
+ENV USER="${NB_USER}"
+ENV HOME="/home/${NB_USER}"
+RUN userdel ubuntu \
+ && groupadd \
+  --gid ${NB_UID} \
+  ${NB_USER} \
+ && useradd \
+  --comment "Default Jupyter user" \
+  --create-home \
+  --no-log-init \
+  --uid ${NB_UID} \
+  --gid ${NB_UID} \
+  --shell ${SHELL} \
+  ${NB_USER}
 
+ENV DOCKER_WORKDIR=/workdir
+WORKDIR ${DOCKER_WORKDIR}
+RUN chown ${NB_UID}:${NB_UID} ${DOCKER_WORKDIR}
 
-## Create user-owned workspace
-RUN sudo mkdir /workspace && sudo chown -R ${NB_USER}:users /workspace
+# this env var is recognized by jupyter-vscode-proxy:
+ENV CODE_EXTENSIONSDIR=/opt/share/code-server
+# put quarto on the path too
+ENV PATH=$PATH:/usr/lib/rstudio-server/bin/quarto/bin
 
+USER root
 # code-server (VSCode)
-RUN sudo curl -fsSL https://code-server.dev/install.sh | sh && rm -rf .cache 
+RUN apt-get update -q && apt-get -y install curl && apt-get clean && rm -rf /var/lib/apt/lists/*
+RUN mkdir -p ${CODE_EXTENSIONSDIR} && chown -R ${NB_USER}:users ${CODE_EXTENSIONSDIR}
+RUN curl -fsSL https://code-server.dev/install.sh | sh && rm -rf /home/${NB_USER}/.cache 
 
-# apt utilities, code-server setup
-COPY install_utilities.sh /tmp/install_utilities.sh
-RUN sudo bash /tmp/install_utilities.sh
+# Build the environment
+USER ${NB_USER}
 
-# install pixi
-RUN curl -fsSL https://pixi.sh/install.sh | PIXI_HOME=/opt/share/pixi bash
+COPY vscode-extensions.txt /tmp/vscode-extensions.txt
+RUN xargs -n 1 code-server --extensions-dir ${CODE_EXTENSIONSDIR} --install-extension < /tmp/vscode-extensions.txt
 
-COPY vscode-extensions.txt vscode-extensions.txt
-RUN xargs -n 1 code-server --install-extension < vscode-extensions.txt
+COPY --chown=${NB_UID}:${NB_UID} pixi.toml .
+RUN pixi install \
+ && rm -rf ~/.cache/rattler
 
-COPY environment.yml environment.yml
-RUN conda update --all --solver=classic -n base -c conda-forge conda && \
-    conda env update --file environment.yml
+# Set up shell activation script
+RUN pixi shell-hook -s bash > ./shell-hook
+USER root
+ENV ENTRYPOINT_SCRIPT="/entrypoint.sh"
+RUN echo "#!/bin/bash" > ${ENTRYPOINT_SCRIPT}
+ RUN cat ${PWD}/shell-hook >> ${ENTRYPOINT_SCRIPT}
+RUN echo 'exec "$@"' >> ${ENTRYPOINT_SCRIPT}
+RUN chmod +x ${ENTRYPOINT_SCRIPT}
 
+USER ${NB_USER}
+EXPOSE 8888
+ENTRYPOINT ["/entrypoint.sh"]
+CMD ["jupyter", "lab", "--no-browser", "--ip=0.0.0.0"]

cuda/pixi.toml

@@ -0,0 +1,29 @@
+[workspace]
+authors = ["Matt Fisher <mfisher87@gmail.com>"]
+channels = ["conda-forge", "nodefaults"]
+name = "schmidtdse-cuda"
+platforms = ["linux-64"]
+version = "0.1.0"
+
+[tasks]
+
+[dependencies]
+python = ">=3.12"
+jupyterhub-singleuser = "*"
+jupyterlab = ">=4.4.2"
+jupyterlab-favorites = "*"
+jupyter-collaboration = "*"
+jupyter-server-proxy = "*"
+jupyter-vscode-proxy = "*"
+jupyterlab-myst = "*"
+typst = "*"
+ruff = "*"
+pre-commit = "*"
+gh = "*"
+gh-scoped-creds = "*"
+
+[system-requirements]
+cuda = "12.6"
+
+[dependencies]
+pytorch-gpu = "*"

cuda/vscode-extensions.txt

@@ -1,5 +1,10 @@
 ms-python.python
 ms-toolsai.jupyter
 ms-vscode.live-server
+quarto.quarto
+posit.shiny
+reditorsupport.r
 continue.continue
+alefragnani.project-manager
+saoudrizwan.claude-dev