Initial draft of the website

.github/workflows/open_in_cloud.yml

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+name: "Update notebooks for cloud environments"
+
+on:
+  push:
+    branches:
+      - "**"
+      - "!gh-pages"
+      - "!open-in-colab"
+      - "!open-in-kaggle"
+  pull_request:
+    branches:
+      - main
+  schedule:
+    - cron: "0 4 * * MON"
+  workflow_dispatch:
+    inputs:
+      branch:
+        description: "Branch on viskex repository"
+        type: string
+
+jobs:
+  open_in_colab:
+    strategy:
+      matrix:
+        include:
+          - backend: dolfinx
+            fem_on_colab_packages: |
+              gmsh@current%dolfinx.io
+              fenicsx==real@current$dolfinx
+            notebook_pattern: |
+              "**/tutorial_*_dolfinx.ipynb"
+          - backend: firedrake
+            fem_on_colab_packages: |
+              firedrake==real@current
+            notebook_pattern: |
+              "**/tutorial_*_firedrake.ipynb"
+      fail-fast: false
+    uses: fem-on-colab/open-in-colab-workflow/.github/workflows/workflow_call.yml@main
+    with:
+      work_directory: open_in_colab
+      notebook_pattern: ${{ matrix.notebook_pattern }}
+      notebook_preparation: |
+        python3 -m pip install --no-dependencies git+https://github.com/multiphenics/nbvalx.git
+        git clone https://github.com/viskex/viskex.git
+        cd viskex
+        if [ -n "${{ (inputs || github.event.inputs).branch }}" ]; then
+          git checkout "${{ (inputs || github.event.inputs).branch }}"
+        fi
+        NO_TESTS_COLLECTED=5
+        python3 -m pytest --ipynb-action=create-notebooks --tag-collapse --work-dir=.ipynb_colab tutorials || (($?==$NO_TESTS_COLLECTED))
+        find tutorials -type d -name .ipynb_colab -exec rsync -avz --remove-source-files --include="*.ipynb" --exclude="*" {}/ {}/.. \;
+        NOTEBOOKS_TO_INCLUDE=""
+        while read -r PATTERN; do
+          NOTEBOOKS_TO_INCLUDE="${NOTEBOOKS_TO_INCLUDE} --include=$(echo ${PATTERN} | sed 's|\"||g')"
+        done <<< $(printf "%s" "${{ matrix.notebook_pattern }}")
+        rsync -avz --delete --include "*/" ${NOTEBOOKS_TO_INCLUDE} --exclude="*" tutorials ../open_in_colab/
+      fem_on_colab_packages: ${{ matrix.fem_on_colab_packages }}
+      pip_packages: |
+        viskex@https://github.com/viskex/viskex.git@current
+      test_script: |
+        apt install -y -qq libgl1-mesa-glx xvfb
+        export DISPLAY=":99"
+        Xvfb $DISPLAY -screen 0 1024x768x24 > /dev/null 2>&1 &
+        NOTEBOOKS_TO_TEST=""
+        while read -r PATTERN; do
+          NOTEBOOKS_TO_TEST="${NOTEBOOKS_TO_TEST} $(find open_in_colab -wholename $(echo ${PATTERN} | sed 's|\"||g'))"
+        done <<< $(printf "%s" "${{ matrix.notebook_pattern }}")
+        python3 -m pytest --nbval ${NOTEBOOKS_TO_TEST}
+      publish_on: github@viskex/viskex.github.io@open-in-colab
+      publish_if_repository: viskex/viskex.github.io
+
+  open_in_kaggle:
+    strategy:
+      matrix:
+        include:
+          - backend: dolfinx
+            fem_on_kaggle_packages: |
+              gmsh@current%dolfinx.io
+              fenicsx==real@current$dolfinx
+            notebook_pattern: |
+              "**/tutorial_*_dolfinx.ipynb"
+          - backend: firedrake
+            fem_on_kaggle_packages: |
+              firedrake==real@current
+            notebook_pattern: |
+              "**/tutorial_*_firedrake.ipynb"
+      fail-fast: false
+    uses: fem-on-kaggle/open-in-kaggle-workflow/.github/workflows/workflow_call.yml@main
+    with:
+      work_directory: open_in_kaggle
+      notebook_pattern: ${{ matrix.notebook_pattern }}
+      notebook_preparation: |
+        python3 -m pip install --no-dependencies git+https://github.com/multiphenics/nbvalx.git
+        git clone https://github.com/viskex/viskex.git
+        cd viskex
+        if [ -n "${{ (inputs || github.event.inputs).branch }}" ]; then
+          git checkout "${{ (inputs || github.event.inputs).branch }}"
+        fi
+        NO_TESTS_COLLECTED=5
+        python3 -m pytest --ipynb-action=create-notebooks --tag-collapse --work-dir=.ipynb_kaggle tutorials || (($?==$NO_TESTS_COLLECTED))
+        find tutorials -type d -name .ipynb_kaggle -exec rsync -avz --remove-source-files --include="*.ipynb" --exclude="*" {}/ {}/.. \;
+        NOTEBOOKS_TO_INCLUDE=""
+        while read -r PATTERN; do
+          NOTEBOOKS_TO_INCLUDE="${NOTEBOOKS_TO_INCLUDE} --include=$(echo ${PATTERN} | sed 's|\"||g')"
+        done <<< $(printf "%s" "${{ matrix.notebook_pattern }}")
+        rsync -avz --delete --include "*/" ${NOTEBOOKS_TO_INCLUDE} --exclude="*" tutorials ../open_in_kaggle/
+      fem_on_kaggle_packages: ${{ matrix.fem_on_kaggle_packages }}
+      pip_packages: |
+        viskex@https://github.com/viskex/viskex.git@current
+      test_script: |
+        apt install -y -qq libgl1-mesa-glx xvfb
+        export DISPLAY=":99"
+        Xvfb $DISPLAY -screen 0 1024x768x24 > /dev/null 2>&1 &
+        NOTEBOOKS_TO_TEST=""
+        while read -r PATTERN; do
+          NOTEBOOKS_TO_TEST="${NOTEBOOKS_TO_TEST} $(find open_in_kaggle -wholename $(echo ${PATTERN} | sed 's|\"||g'))"
+        done <<< $(printf "%s" "${{ matrix.notebook_pattern }}")
+        python3 -m pytest --nbval ${NOTEBOOKS_TO_TEST}
+      publish_on: github@viskex/viskex.github.io@open-in-kaggle
+      publish_if_repository: viskex/viskex.github.io
+
+  warn:
+    runs-on: ubuntu-latest
+    if: github.repository == 'viskex/viskex.github.io' && github.ref == 'refs/heads/main' && github.event_name == 'schedule'
+    steps:
+    - name: Warn if scheduled workflow is about to be disabled
+      uses: fem-on-colab/warn-workflow-about-to-be-disabled-action@main
+      with:
+        workflow-filename: open_in_cloud.yml
+        days-elapsed: 50

.github/workflows/website.yml

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+name: "Website update"
+
+on:
+  push:
+    branches:
+      - "**"
+      - "!gh-pages"
+  pull_request:
+    branches:
+      - main
+  schedule:
+    - cron: "0 3 * * MON"
+  workflow_dispatch:
+    inputs:
+      branch:
+        description: "Branch on viskex repository"
+        type: string
+      reset_github_pages:
+        description: "Reset the gh-pages branch (yes or no; default: no). Remember to set the gh-pages branch back in Settings -> Pages!"
+        type: string
+
+jobs:
+  convert_notebooks:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        include:
+          - backend: dolfinx
+            container: dolfinx/dolfinx:nightly
+            setup_container: |
+              export DEBIAN_FRONTEND="noninteractive"
+              apt -y -qq update
+              apt install -y -qq libgl1-mesa-glx xvfb
+            notebook_pattern: |
+              "**/tutorial_*_dolfinx.ipynb"
+          - backend: firedrake
+            container: firedrakeproject/firedrake
+            setup_container: |
+              export DEBIAN_FRONTEND="noninteractive"
+              apt -y -qq update
+              apt install -y -qq libgl1-mesa-glx xorg xvfb
+              echo "/home/firedrake/firedrake/bin" >> $GITHUB_PATH
+            notebook_pattern: |
+              "**/tutorial_*_firedrake.ipynb"
+      fail-fast: false
+    container:
+      image: ${{ matrix.container }}
+      options: --user root
+    steps:
+      - name: Determine which branch to checkout when cloning source repository
+        id: source_branch
+        run: |
+          if [ -n "${{ (inputs || github.event.inputs).branch }}" ]; then
+            echo "branch=${{ (inputs || github.event.inputs).branch }}" >> ${GITHUB_OUTPUT}
+          else
+            echo "branch=main" >> ${GITHUB_OUTPUT}
+          fi
+        shell: bash
+      - name: Clone source repository on the previously computed branch
+        uses: actions/checkout@v3
+        with:
+          repository: viskex/viskex
+          ref: ${{ steps.source_branch.outputs.branch }}
+          fetch-depth: 0
+      - name: Clone website repository on current branch
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+          path: _website
+      - name: Setup container
+        run: |
+          ${{ matrix.setup_container }}
+          python3 -m pip -q install nbconvert
+      - name: Install viskex
+        run: python3 -m pip install .[tutorials]
+      - name: Install nbconvert
+        run: python3 -m pip -q install nbconvert
+      - name: Copy jupyter template from website repository
+        run: |
+          jupyter --paths --json > /tmp/jupyter-paths
+          JUPYTER_SHARE=$(python3 -c 'import json; data = json.loads(open("/tmp/jupyter-paths", "r").read()); print(data["data"][-1])')
+          mkdir -p ${JUPYTER_SHARE}/nbconvert/templates
+          cp -rf _website/share/jupyter/nbconvert/templates/html/viskex ${JUPYTER_SHARE}/nbconvert/templates/
+          rm /tmp/jupyter-paths
+      - name: Convert notebooks to html
+        run: |
+          NOTEBOOKS_TO_RUN=()
+          while read -r PATTERN; do
+            NOTEBOOKS_TO_RUN+=($(find tutorials -wholename $(echo ${PATTERN} | sed 's|\"||g')))
+          done <<< $(printf "%s" "${{ matrix.notebook_pattern }}")
+          mkdir -p _build/html
+          export DISPLAY=":99"
+          Xvfb $DISPLAY -screen 0 1024x768x24 > /dev/null 2>&1 &
+          for NOTEBOOK in "${NOTEBOOKS_TO_RUN[@]}"; do
+            NOTEBOOK_DIRNAME=$(dirname "${NOTEBOOK}")
+            NOTEBOOK_OUTPUT_DIRNAME=${GITHUB_WORKSPACE}/_build/html/${NOTEBOOK_DIRNAME}
+            NOTEBOOK_BASENAME=$(basename "${NOTEBOOK}")
+            NOTEBOOK_OUTPUT_BASENAME=${NOTEBOOK_BASENAME/.ipynb/.html}
+            pushd ${NOTEBOOK_DIRNAME}
+            VISKEX_PYVISTA_BACKEND="panel" jupyter nbconvert --to html --template viskex --execute --output-dir ${NOTEBOOK_OUTPUT_DIRNAME} ${NOTEBOOK_BASENAME}
+            popd
+            pushd ${NOTEBOOK_OUTPUT_DIRNAME}
+            sed -i "s|\"https://colab.research.google.com\"|\"https://colab.research.google.com/github/viskex/viskex.github.io/blob/open-in-colab/${NOTEBOOK_DIRNAME}/${NOTEBOOK_BASENAME}\"|g" ${NOTEBOOK_OUTPUT_BASENAME}
+            sed -i "s|\"https://kaggle.com\"|\"https://kaggle.com/kernels/welcome?src=https://github.com/viskex/viskex.github.io/blob/open-in-kaggle/${NOTEBOOK_DIRNAME}/${NOTEBOOK_BASENAME}\"|g" ${NOTEBOOK_OUTPUT_BASENAME}
+            popd
+          done
+        shell: bash
+      - name: Store converted notebooks as artifacts
+        uses: actions/upload-artifact@v3
+        with:
+          name: converted-notebooks-${{ matrix.backend }}
+          path: _build/html
+          retention-days: 1
+
+  publish_notebooks:
+    runs-on: ubuntu-latest
+    needs: [convert_notebooks]
+    steps:
+      - name: Clone website repository on current branch
+        uses: actions/checkout@v3
+      - name: Clone website repository on gh-pages branch
+        uses: actions/checkout@v3
+        with:
+          ref: gh-pages
+          fetch-depth: 0
+          path: _build/html
+      - name: Download converted notebooks from artifacts
+        uses: actions/download-artifact@v3
+        with:
+          path: _build/html
+      - name: Flatten the artifacts hierarchy
+        run: |
+          rsync -avh --remove-source-files _build/html/converted-notebooks-*/ _build/html/
+          find _build/html/ -type d -empty -delete
+      - name: Upload release file to website
+        if: github.repository == 'viskex/viskex.github.io' && github.ref == 'refs/heads/main'
+        run: |
+          SHA_SHORT=$(git rev-parse --short HEAD)
+          pushd _build/html
+          git config user.name "GitHub Actions"
+          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git add .
+          git pull origin gh-pages
+          [ -n "$(git status --porcelain=v1 2>/dev/null)" ] && git commit -m "deploy notebooks: ${SHA_SHORT}"
+          git push origin gh-pages
+          popd
+        shell: bash
+
+  website:
+    runs-on: ubuntu-latest
+    needs: [publish_notebooks]
+    steps:
+      - name: Clone website repository on current branch
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: Clone website repository on gh-pages branch
+        uses: actions/checkout@v3
+        with:
+          ref: gh-pages
+          fetch-depth: 0
+          path: _build/html
+      - name: Install dependencies
+        run: |
+          pip3 -q install sphinx-material
+      - name: Generate sphinx website
+        run: |
+          rm -rf _build/html/* && make html
+      - name: Fix permissions
+        run: |
+          sudo chown $USER _build -R
+      - name: Clean up old Github pages branch
+        if: github.repository == 'viskex/viskex.github.io' && github.event.inputs.reset_github_pages == 'yes'
+        run: |
+          if git ls-remote origin | grep -sw gh-pages 2>&1 >/dev/null; then git push origin --delete gh-pages; fi
+      - name: Check that no tutorials have been deleted
+        run: |
+          pushd _build/html
+          if [[ $(git ls-files --deleted tutorials | wc -l) -gt 0 ]]; then
+            echo "The following tutorials have been deleted:"
+            git ls-files --deleted tutorials
+            exit 1
+          fi
+          popd
+      - name: Deploy to GitHub pages
+        if: github.repository == 'viskex/viskex.github.io' && github.ref == 'refs/heads/main'
+        run: |
+          SHA_SHORT=$(git rev-parse --short HEAD)
+          pushd _build/html
+          git config user.name "GitHub Actions"
+          git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+          git add .
+          git pull origin gh-pages
+          [ -n "$(git status --porcelain=v1 2>/dev/null)" ] && git commit -m "deploy website: ${SHA_SHORT}"
+          git push origin gh-pages
+          popd
+        shell: bash
+      - name: Deploy to GitHub artifacts
+        if: github.repository == 'viskex/viskex.github.io' && github.ref != 'refs/heads/main'
+        uses: actions/upload-artifact@v3
+        with:
+          name: website
+          path: _build/html
+          retention-days: 1
+
+  warn:
+    runs-on: ubuntu-latest
+    if: github.repository == 'viskex/viskex.github.io' && github.ref == 'refs/heads/main' && github.event_name == 'schedule'
+    steps:
+      - uses: actions/checkout@v3
+      - name: Warn if scheduled workflow is about to be disabled
+        uses: fem-on-colab/warn-workflow-about-to-be-disabled-action@main
+        with:
+          workflow-filename: website.yml
+          days-elapsed: 50

Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)