Recent sphinx versions store the output directory as a PosixPath rath… #205
Workflow file for this run
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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 FEMlium 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: none | |
| container: ubuntu:rolling | |
| setup_container: | | |
| export DEBIAN_FRONTEND="noninteractive" | |
| apt -y -qq update | |
| apt install -y -qq git python3-mpi4py python3-numpy python3-pip xorg | |
| rm /usr/lib/python3.*/EXTERNALLY-MANAGED | |
| notebook_pattern: | | |
| "**/generate_mesh*.ipynb" | |
| "**/tutorial_*_meshio.ipynb" | |
| - backend: dolfin | |
| container: numericalpdes/base_images:fenics | |
| setup_container: | | |
| export DEBIAN_FRONTEND="noninteractive" | |
| apt -y -qq update | |
| apt install -y -qq xorg | |
| notebook_pattern: | | |
| "**/tutorial_*_dolfin.ipynb" | |
| - 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: FEMlium/FEMlium | |
| 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: ${{ matrix.setup_container }} | |
| - name: Install FEMlium | |
| run: python3 -m pip install .[tutorials] | |
| - name: Install nbconvert and configure plotly | |
| run: | | |
| python3 -m pip -q install nbconvert | |
| PLOTLY_INIT=$(python3 -c 'import plotly; print(plotly.__file__)') | |
| echo "import plotly.offline" >> ${PLOTLY_INIT} | |
| echo "plotly.offline.init_notebook_mode(connected=True)" >> ${PLOTLY_INIT} | |
| - name: Copy jupyter template from website repository | |
| run: | | |
| jupyter --paths --json > /tmp/jupyter-paths | |
| JUPYTER_SHARE=$(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/femlium ${JUPYTER_SHARE}/nbconvert/templates/ | |
| rm /tmp/jupyter-paths | |
| - name: Convert notebooks to html | |
| run: | | |
| NOTEBOOKS_TO_RUN=() | |
| while read -r PATTERN; do | |
| NOTEBOOKS_TO_RUN+=($(find tutorials -wholename $(echo ${PATTERN} | sed 's|\"||g'))) | |
| done <<< $(printf "%s" "${{ matrix.notebook_pattern }}") | |
| mkdir -p _converted | |
| 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=${GITHUB_WORKSPACE}/_converted/${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 femlium --execute --output-dir ${NOTEBOOK_OUTPUT_DIRNAME} ${NOTEBOOK_BASENAME} | |
| popd | |
| pushd ${NOTEBOOK_OUTPUT_DIRNAME} | |
| sed -i "s|\"https://colab.research.google.com\"|\"https://colab.research.google.com/github/FEMlium/femlium.github.io/blob/open-in-colab/${NOTEBOOK_DIRNAME}/${NOTEBOOK_BASENAME}\"|g" ${NOTEBOOK_OUTPUT_BASENAME} | |
| sed -i "s|\"https://kaggle.com\"|\"https://kaggle.com/kernels/welcome?src=https://github.com/FEMlium/femlium.github.io/blob/open-in-kaggle/${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: _converted | |
| retention-days: 1 | |
| website: | |
| runs-on: ubuntu-latest | |
| needs: [convert_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: Download converted notebooks from artifacts | |
| uses: actions/download-artifact@v3 | |
| with: | |
| path: _converted | |
| - name: Generate sphinx website | |
| run: | | |
| rm -rf _build/html/* | |
| rsync -avh --remove-source-files _converted/converted-notebooks-*/ _build/html/ | |
| rm -rf _converted | |
| make html | |
| - name: Fix permissions | |
| run: | | |
| sudo chown $USER _build -R | |
| - name: Clean up old Github pages branch | |
| if: github.repository == 'FEMlium/femlium.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 [[ $(git ls-files --deleted tutorials | wc -l) -gt 0 ]]; then | |
| echo "The following tutorials have been deleted:" | |
| git ls-files --deleted tutorials | |
| exit 1 | |
| fi | |
| popd | |
| - name: Deploy to GitHub pages | |
| if: github.repository == 'FEMlium/femlium.github.io' && github.ref == 'refs/heads/main' | |
| run: | | |
| SHA_SHORT=$(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: ${SHA_SHORT}" | |
| git push origin gh-pages | |
| popd | |
| shell: bash | |
| - name: Deploy to GitHub artifacts | |
| if: github.repository == 'FEMlium/femlium.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 == 'FEMlium/femlium.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 |