Add colab badge to notebooks #1900
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| name: Sphinx Docs | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| permissions: | |
| contents: write | |
| defaults: | |
| run: | |
| shell: bash | |
| jobs: | |
| convert_scripts: | |
| name: Translate scripts to notebooks | |
| runs-on: ubuntu-latest | |
| permissions: | |
| pull-requests: write | |
| contents: write | |
| outputs: | |
| commit_hash: ${{ steps.add-commit-push.outputs.commit_hash }} | |
| container: | |
| image: ghcr.io/ptb-mr/mrpro_py311:latest | |
| options: --user runner | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| with: | |
| token: ${{ secrets.commit }} | |
| ref: ${{ github.event.pull_request.head.ref }} | |
| fetch-depth: 0 | |
| - name: Install mrpro and dependencies | |
| run: pip install --upgrade --upgrade-strategy "eager" .[notebook] | |
| - name: Translate scripts to notebooks and add colab info | |
| run: | | |
| scripts=$(ls ./examples/*.py) | |
| for script in $scripts | |
| do jupytext --set-kernel "python3" --update --output ${script//.py/.ipynb} $script | |
| done | |
| - name: Add info for colab to notebooks | |
| run: | | |
| for script in $scripts | |
| do python .github/workflows/add_colab_info_to_notebooks.py ${script//.py/.ipynb} | |
| done | |
| - name: Add/Update badges | |
| id: badges | |
| uses: trsvchn/colab-badge-action@v4 | |
| with: | |
| check: "all" | |
| update: true | |
| - name: Check if any notebooks have been changed | |
| uses: tj-actions/verify-changed-files@v20 | |
| id: verify-changed-notebooks | |
| with: | |
| files: ./examples/*.ipynb | |
| - name: Commit notebooks | |
| if: steps.verify-changed-notebooks.outputs.files_changed == 'true' | |
| uses: actions4git/add-commit-push@v1 | |
| with: | |
| commit-message: Notebooks updated | |
| - name: Get hash of last commit | |
| id: add-commit-push | |
| run: echo "commit_hash=$(git rev-parse HEAD)" >> $GITHUB_OUTPUT | |
| get_notebooks: | |
| name: Get list of notebooks | |
| needs: convert_scripts | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout mrpro repo | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ needs.convert_scripts.outputs.commit_hash }} | |
| - id: set-matrix | |
| run: | | |
| cd ./examples/ | |
| ls | |
| echo "notebooks=$(ls *.ipynb | jq -R -s -c 'split("\n")[:-1]')" >> $GITHUB_OUTPUT | |
| - name: Notebook overview | |
| run: | | |
| echo "jupyter-notebooks: ${{ steps.set-matrix.outputs.notebooks }}" | |
| outputs: | |
| notebooks: ${{ steps.set-matrix.outputs.notebooks }} | |
| run_notebook: | |
| name: Run notebook | |
| needs: [convert_scripts, get_notebooks] | |
| runs-on: ubuntu-latest | |
| permissions: | |
| pull-requests: write | |
| contents: write | |
| container: | |
| image: ghcr.io/ptb-mr/mrpro_py311:latest | |
| options: --user root | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| notebook: ${{ fromJson(needs.get_notebooks.outputs.notebooks) }} | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ needs.convert_scripts.outputs.commit_hash }} | |
| - name: Install mrpro and dependencies | |
| run: pip install --upgrade --upgrade-strategy "eager" .[notebook] | |
| - name: Notebook name | |
| run: | | |
| echo "current jupyter-notebook: ${{ matrix.notebook }}" | |
| - name: Run notebook | |
| uses: fzimmermann89/run-notebook@v3 | |
| env: | |
| RUNNER: ${{ toJson(runner) }} | |
| with: | |
| notebook: ./examples/${{ matrix.notebook }} | |
| - name: Get artifact names | |
| id: artifact_names | |
| run: | | |
| notebook=${{ matrix.notebook }} | |
| echo "ARTIFACT_NAME=${notebook/.ipynb/}" >> $GITHUB_OUTPUT | |
| echo "HTML_RESULT=${notebook/.ipynb/.html}" >> $GITHUB_OUTPUT | |
| - name: Upload notebook | |
| uses: actions/upload-artifact@v4 | |
| if: always() | |
| with: | |
| name: ${{ steps.artifact_names.outputs.ARTIFACT_NAME }} | |
| path: ${{ github.workspace }}/nb-runner.out/${{ steps.artifact_names.outputs.HTML_RESULT }} | |
| env: | |
| RUNNER: ${{ toJson(runner) }} | |
| create_documentation: | |
| name: Build and deploy documentation | |
| needs: [convert_scripts, run_notebook] | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ghcr.io/ptb-mr/mrpro_py311:latest | |
| options: --user runner | |
| permissions: | |
| pull-requests: write | |
| contents: write | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ needs.convert_scripts.outputs.commit_hash }} | |
| - name: Install mrpro and dependencies | |
| run: pip install --upgrade --upgrade-strategy "eager" .[docs] | |
| - name: Download notebook html files | |
| id: download | |
| uses: actions/download-artifact@v4 | |
| with: | |
| path: ./docs/source/notebook_artifact/ | |
| - name: Copy notebook html files | |
| run: | | |
| mkdir ./docs/source/_notebooks | |
| cd ./docs/source/notebook_artifact/ | |
| notebooks=$(grep -rl --include='*' './') | |
| for nb in $notebooks | |
| do | |
| echo "current jupyter-notebook: $nb" | |
| cp ./$nb ../_notebooks/ | |
| done | |
| - name: List of notebooks | |
| run: | | |
| cd ./docs/source/_notebooks/ | |
| notebooks=$(grep -rl --include='*.html' './') | |
| cd ../ | |
| echo "" >> examples.rst | |
| for nb in $notebooks | |
| do | |
| echo " notebook_${nb/.html/.rst}" >> examples.rst | |
| notebook_description=$(grep '<h1 id=' ./_notebooks/$nb | sed 's/.*">\(.*\)<a class=.*/\1/') | |
| echo $notebook_description | |
| echo $notebook_description > "notebook_${nb/.html/.rst}" | |
| echo "========" >> "notebook_${nb/.html/.rst}" | |
| echo ".. raw:: html" >> "notebook_${nb/.html/.rst}" | |
| echo " :file: ./_notebooks/$nb" >> "notebook_${nb/.html/.rst}" | |
| done | |
| - name: Build docs | |
| run: | | |
| sphinx-build -b html ./docs/source ./docs/build/html | |
| rm -rf ./docs/build/html/.doctrees | |
| - name: Save Documentation | |
| id: save_docu | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: Documentation | |
| path: docs/build/html/ | |
| - run: echo 'Artifact url ${{ steps.save_docu.outputs.artifact-url }}' | |
| - run: echo 'Event number ${{ github.event.number }}' | |
| - run: echo 'Event name ${{github.event_name}}' | |
| - name: Update PR with link to summary | |
| if: github.event_name == 'pull_request' | |
| uses: edumserrano/find-create-or-update-comment@v3 | |
| with: | |
| issue-number: ${{ github.event.pull_request.number }} | |
| body-includes: '<!-- documentation build ${{ github.event.number }} -->' | |
| comment-author: 'github-actions[bot]' | |
| body: | | |
| <!-- documentation build ${{ github.event.number }} --> | |
| ### :books: Documentation | |
| :file_folder: [Download as zip](${{ steps.save_docu.outputs.artifact-url }}) | |
| :mag: [View online](https://zimf.de/zipserve/${{ steps.save_docu.outputs.artifact-url }}/) | |
| edit-mode: replace | |
| - name: Upload pages | |
| uses: actions/upload-pages-artifact@v3 | |
| with: | |
| path: docs/build/html/ | |
| if: github.event_name != 'pull_request' | |
| deploy: | |
| if: github.ref == 'refs/heads/main' | |
| permissions: | |
| pages: write | |
| id-token: write | |
| environment: | |
| name: github-pages | |
| url: ${{ steps.deployment.outputs.page_url }} | |
| runs-on: ubuntu-latest | |
| needs: create_documentation | |
| steps: | |
| - name: Deploy to GitHub Pages | |
| id: deployment | |
| uses: actions/deploy-pages@v4 | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| # Cancel in-progress runs when a new workflow with the same group name is triggered | |
| cancel-in-progress: true |