Update files for Binder

sagemath · Apr 18, 2024 · 45d8b2b · 45d8b2b
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diff --git a/.github/Dockerfile b/.github/Dockerfile
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+# Multi-stage Dockerfile for slim Sage
+# https://docs.docker.com/build/building/multi-stage
+
+FROM ghcr.io/sagemath/sage/sage-ubuntu-focal-standard-with-targets:10.3 AS target
+
+# Resolve symbolic links to recreate them later
+RUN readlink /sage/prefix >> /sage/prefix_link
+RUN readlink /sage/venv >> /sage/venv_link
+
+WORKDIR /sage
+
+# Strip executables in /sage
+RUN LC_ALL=C find local src pkgs -executable -type f -exec strip '{}' ';' 2>&1 | grep -v "file format not recognized" || true
+
+# To exclude doc directory in the next stage
+RUN rm -rf local/share/doc
+
+FROM ghcr.io/sagemath/sage/sage-ubuntu-focal-standard-with-system-packages:10.3
+
+USER root
+
+# Remove warnings
+ENV DEBIAN_FRONTEND noninteractive
+ENV DEBCONF_NOWARNINGS="yes"
+
+# Install JupyterLab to the system
+RUN apt-get update
+RUN apt-get install -y python3-pip
+RUN python3 -m pip install --no-warn-script-location notebook jupyterlab ipywidgets
+
+# Disable annoying pupup for Jupyter news
+RUN jupyter labextension disable "@jupyterlab/apputils-extension:announcements"
+
+# Install /sage from target
+COPY --from=target /sage/local /sage/local
+COPY --from=target /sage/src/bin /sage/src/bin
+COPY --from=target /sage/src/sage /sage/src/sage
+COPY --from=target /sage/sage /sage/sage
+COPY --from=target /sage/pkgs/sage-conf /sage/pkgs/sage-conf
+
+# Recreate symbolic links
+COPY --from=target /sage/prefix_link /sage/prefix_link
+COPY --from=target /sage/venv_link /sage/venv_link
+RUN ln -s $(cat /sage/prefix_link) /sage/prefix && rm /sage/prefix_link
+RUN ln -s $(cat /sage/venv_link) /sage/venv && rm /sage/venv_link
+
+# Configure Sage library
+RUN /sage/sage -pip install --root-user-action=ignore /sage/pkgs/sage-conf
+
+# Remove problematic lines!
+RUN sed -i '/^__requires__/d' /sage/venv/bin/sage-venv-config
+RUN sed -i '/^__import__/d' /sage/venv/bin/sage-venv-config
diff --git a/.github/workflows/update-dockerfile-dev.yml b/.github/workflows/update-dockerfile-dev.yml
@@ -0,0 +1,82 @@
+name: Update dev image
+
+on:
+  schedule:
+    - cron: '0 1 * * *'  # Run every day
+  workflow_dispatch:
+
+env:
+  SAGE_TARGET: ghcr.io/sagemath/sage/sage-ubuntu-focal-standard-with-targets
+  SAGE_SYSTEM: ghcr.io/sagemath/sage/sage-ubuntu-focal-standard-with-system-packages
+  TAG: dev
+  BRANCH: dev
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      packages: write
+    steps:
+
+    # Prepare .github/Dockerfile for slim Sage image
+
+    - name: Checkout code
+      uses: actions/checkout@v4
+      with:
+        ref: ${{ env.BRANCH }}
+    - name: Prepare .github/Dockerfile
+      run: |
+        SAGE_VERSION=$(docker run --rm ${SAGE_TARGET}:$TAG /sage/sage --version | grep -oP 'SageMath version \K[0-9.]+(?:beta\d+)?(?:rc\d+)?')
+        SAGE_TARGET_ESCAPED=$(echo "${SAGE_TARGET}" | sed 's/\//\\\//g' | sed 's/\./\\\./g')
+        SAGE_TARGET_VERSION_ESCAPED=$(echo "${SAGE_TARGET}:${SAGE_VERSION}" | sed 's/\//\\\//g' | sed 's/\./\\\./g')
+        sed -i "s/FROM ${SAGE_TARGET_ESCAPED}:\S*/FROM ${SAGE_TARGET_VERSION_ESCAPED}/g" .github/Dockerfile
+        SAGE_SYSTEM_ESCAPED=$(echo "${SAGE_SYSTEM}" | sed 's/\//\\\//g' | sed 's/\./\\\./g')
+        SAGE_SYSTEM_VERSION_ESCAPED=$(echo "${SAGE_SYSTEM}:${SAGE_VERSION}" | sed 's/\//\\\//g' | sed 's/\./\\\./g')
+        sed -i "s/FROM ${SAGE_SYSTEM_ESCAPED}:\S*/FROM ${SAGE_SYSTEM_VERSION_ESCAPED}/g" .github/Dockerfile
+        PACKAGE_NAME=ghcr.io/${{ github.repository }}:${SAGE_VERSION}
+        echo "PACKAGE_NAME=$PACKAGE_NAME" >> $GITHUB_ENV
+        git config --global user.email alice@wonderland
+        git config --global user.name alice
+        git commit -a --amend -m "Dockerfile for Sage ${SAGE_VERSION}"
+        git push -f origin $BRANCH
+
+    # Build and publish the slim Sage image to github package registry (ghpr)
+
+    - name: Log in to the Container registry
+      uses: docker/login-action@v3
+      with:
+        registry: ghcr.io
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+    - name: Build and push Docker image
+      uses: docker/build-push-action@v5
+      with:
+        context: .github
+        push: true
+        tags: ${{ env.PACKAGE_NAME }}
+
+    # Update files for Binder
+
+    - name: Checkout code
+      uses: actions/checkout@v4
+      with:
+        ref: ${{ env.BRANCH }}
+    - name: Update files for Binder
+      run: |
+        PACKAGE_NAME=${{ env.PACKAGE_NAME }}
+        PACKAGE_NAME_ESCAPED=$(echo "${PACKAGE_NAME}" | sed 's/\//\\\//g')
+        sed -i "s/FROM \S*/FROM ${PACKAGE_NAME_ESCAPED}/g" Dockerfile
+        sed -i "s/FROM \S*/FROM ${PACKAGE_NAME_ESCAPED}/g" README.rst
+        git config --global user.email alice@wonderland
+        git config --global user.name alice
+        git commit -a --amend -m "Update files for Binder"
+        git push -f origin $BRANCH
+
+    # Build docker image for Binder from Dockerfile at root
+
+    - name: Binder build
+      timeout-minutes: 30
+      continue-on-error: true
+      run: |
+        curl --keepalive-time 600 -L https://mybinder.org/build/gh/sagemath/sage-binder-env/$BRANCH
diff --git a/.github/workflows/update-dockerfile-master.yml b/.github/workflows/update-dockerfile-master.yml
@@ -0,0 +1,82 @@
+name: Update master image
+
+on:
+  schedule:
+    - cron: '0 0 * * *'  # Run every day
+  workflow_dispatch:
+
+env:
+  SAGE_TARGET: ghcr.io/sagemath/sage/sage-ubuntu-focal-standard-with-targets
+  SAGE_SYSTEM: ghcr.io/sagemath/sage/sage-ubuntu-focal-standard-with-system-packages
+  TAG: latest
+  BRANCH: master
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      packages: write
+    steps:
+
+    # Prepare .github/Dockerfile for slim Sage image
+
+    - name: Checkout code
+      uses: actions/checkout@v4
+      with:
+        ref: ${{ env.BRANCH }}
+    - name: Prepare .github/Dockerfile
+      run: |
+        SAGE_VERSION=$(docker run --rm ${SAGE_TARGET}:$TAG /sage/sage --version | grep -oP 'SageMath version \K[0-9.]+(?:beta\d+)?(?:rc\d+)?')
+        SAGE_TARGET_ESCAPED=$(echo "${SAGE_TARGET}" | sed 's/\//\\\//g' | sed 's/\./\\\./g')
+        SAGE_TARGET_VERSION_ESCAPED=$(echo "${SAGE_TARGET}:${SAGE_VERSION}" | sed 's/\//\\\//g' | sed 's/\./\\\./g')
+        sed -i "s/FROM ${SAGE_TARGET_ESCAPED}:\S*/FROM ${SAGE_TARGET_VERSION_ESCAPED}/g" .github/Dockerfile
+        SAGE_SYSTEM_ESCAPED=$(echo "${SAGE_SYSTEM}" | sed 's/\//\\\//g' | sed 's/\./\\\./g')
+        SAGE_SYSTEM_VERSION_ESCAPED=$(echo "${SAGE_SYSTEM}:${SAGE_VERSION}" | sed 's/\//\\\//g' | sed 's/\./\\\./g')
+        sed -i "s/FROM ${SAGE_SYSTEM_ESCAPED}:\S*/FROM ${SAGE_SYSTEM_VERSION_ESCAPED}/g" .github/Dockerfile
+        PACKAGE_NAME=ghcr.io/${{ github.repository }}:${SAGE_VERSION}
+        echo "PACKAGE_NAME=$PACKAGE_NAME" >> $GITHUB_ENV
+        git config --global user.email alice@wonderland
+        git config --global user.name alice
+        git commit -a --amend -m "Dockerfile for Sage ${SAGE_VERSION}"
+        git push -f origin $BRANCH
+
+    # Build and publish the slim Sage image to github package registry (ghpr)
+
+    - name: Log in to the Container registry
+      uses: docker/login-action@v3
+      with:
+        registry: ghcr.io
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+    - name: Build and push Docker image
+      uses: docker/build-push-action@v5
+      with:
+        context: .github
+        push: true
+        tags: ${{ env.PACKAGE_NAME }}
+
+    # Update files for Binder
+
+    - name: Checkout code
+      uses: actions/checkout@v4
+      with:
+        ref: ${{ env.BRANCH }}
+    - name: Update files for Binder
+      run: |
+        PACKAGE_NAME=${{ env.PACKAGE_NAME }}
+        PACKAGE_NAME_ESCAPED=$(echo "${PACKAGE_NAME}" | sed 's/\//\\\//g')
+        sed -i "s/FROM \S*/FROM ${PACKAGE_NAME_ESCAPED}/g" Dockerfile
+        sed -i "s/FROM \S*/FROM ${PACKAGE_NAME_ESCAPED}/g" README.rst
+        git config --global user.email alice@wonderland
+        git config --global user.name alice
+        git commit -a --amend -m "Update files for Binder"
+        git push -f origin $BRANCH
+
+    # Build docker image for Binder from Dockerfile at root
+
+    - name: Binder build
+      timeout-minutes: 30
+      continue-on-error: true
+      run: |
+        curl --keepalive-time 600 -L https://mybinder.org/build/gh/sagemath/sage-binder-env/$BRANCH
diff --git a/.gitignore b/.gitignore
diff --git a/Dockerfile b/Dockerfile
@@ -0,0 +1,28 @@
+# Dockerfile for binder
+# Reference: https://mybinder.readthedocs.io/en/latest/tutorials/dockerfile.html
+
+FROM ghcr.io/sagemath/sage-binder-env:10.3
+
+USER root
+
+# Create user alice with uid 1000
+ARG NB_USER=alice
+ARG NB_UID=1000
+ENV NB_USER alice
+ENV NB_UID 1000
+ENV HOME /home/${NB_USER}
+RUN adduser --disabled-password --gecos "Default user" --uid ${NB_UID} ${NB_USER}
+
+# Make sure the contents of the notebooks directory are in ${HOME}
+COPY notebooks/* ${HOME}/
+RUN chown -R ${NB_USER}:${NB_USER} ${HOME}
+
+# Switch to the user
+USER ${NB_USER}
+
+# Install Sage kernel to Jupyter
+RUN mkdir -p $(jupyter --data-dir)/kernels
+RUN ln -s /sage/venv/share/jupyter/kernels/sagemath $(jupyter --data-dir)/kernels
+
+# Start in the home directory of the user
+WORKDIR /home/${NB_USER}