Add Brainweb phantom #3057
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| name: Sphinx Docs | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| permissions: | |
| contents: write | |
| defaults: | |
| run: | |
| shell: bash | |
| jobs: | |
| get_notebooks: | |
| name: Get list of notebooks | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout mrpro repo | |
| uses: actions/checkout@v4 | |
| - id: set-matrix | |
| run: | | |
| echo "notebook_paths=$(find examples/notebooks -type f -name '*.ipynb' | jq -R -s -c 'split("\n")[:-1]')" >> $GITHUB_OUTPUT | |
| - name: Notebook overview | |
| run: | | |
| echo "jupyter-notebooks: ${{ steps.set-matrix.outputs.notebook_paths }}" | |
| outputs: | |
| notebook_paths: ${{ steps.set-matrix.outputs.notebook_paths }} | |
| run_notebook: | |
| name: Run notebook | |
| needs: 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_path: ${{ fromJson(needs.get_notebooks.outputs.notebook_paths) }} | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| - name: Install mrpro and dependencies | |
| run: pip install --index-url=https://download.pytorch.org/whl/cpu --extra-index-url https://pypi.org/simple/ --upgrade --upgrade-strategy "eager" -e .[notebook] | |
| - name: Notebook name | |
| run: | | |
| echo "current jupyter-notebook: ${{ matrix.notebook_path }}" | |
| - name: Add nb-myst download badge | |
| run: | | |
| notebook=${{ matrix.notebook_path }} | |
| notebook_name=$(basename $notebook) | |
| download_badge_md="[](path:$notebook_name)" | |
| python_command="import nbformat as nbf\n\ | |
| nb = nbf.read(open('$notebook'), as_version=4)\n\ | |
| # if the 1st cell is md and has colab text => add space after\n\ | |
| if nb['cells'][0]['cell_type'] == 'markdown' and 'colab' in nb['cells'][0]['source'].lower():\n\ | |
| nb['cells'][0]['source'] += ' '\n\ | |
| # if there is no md cell with colab => create empty md cell on top\n\ | |
| else:\n\ | |
| nb['cells'].insert(0, nbf.v4.new_markdown_cell())\n\ | |
| nb['cells'][0]['source'] += '$download_badge_md'\n\ | |
| nbf.write(nb, open('$notebook', 'w'))" | |
| python -c "exec (\"$python_command\")" | |
| - name: Run notebook | |
| uses: fzimmermann89/run-notebook@v3 | |
| env: | |
| RUNNER: ${{ toJson(runner) }} | |
| with: | |
| notebook: ${{ matrix.notebook_path }} | |
| - name: Get artifact names | |
| id: artifact_names | |
| run: | | |
| notebook=${{ matrix.notebook_path }} | |
| echo "ARTIFACT_NAME=$(basename ${notebook/.ipynb})" >> $GITHUB_OUTPUT | |
| echo "IPYNB_EXECUTED=$(basename $notebook)" >> $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.IPYNB_EXECUTED }} | |
| env: | |
| RUNNER: ${{ toJson(runner) }} | |
| create_documentation: | |
| name: Build and deploy documentation | |
| needs: run_notebook | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ghcr.io/ptb-mr/mrpro_py311:latest | |
| options: --user runner | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # fetch history for github links | |
| fetch-tags: true | |
| - name: Install mrpro and dependencies | |
| run: pip install --index-url=https://download.pytorch.org/whl/cpu --extra-index-url https://pypi.org/simple/ --upgrade --upgrade-strategy "eager" -e .[docs] | |
| - name: Download executed notebook ipynb files | |
| id: download | |
| uses: actions/download-artifact@v4 | |
| with: | |
| path: ./docs/source/_notebooks/ | |
| merge-multiple: true | |
| - name: Build docs | |
| run: | | |
| sphinx-build -b html ./docs/source ./docs/build/html | |
| rm -rf ./docs/build/html/.doctrees | |
| - name: Upload documentation artifact | |
| id: upload_docs | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: Documentation | |
| path: docs/build/html/ | |
| # if the one of above steps fails the "artifact-url" will be an empty string | |
| - name: Dump documentation info | |
| if: always() | |
| run: | | |
| echo "${{ steps.upload_docs.outputs.artifact-url }}" > artifact_url | |
| - name: Upload docs-metadata artifact | |
| if: always() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: artifact_url | |
| path: artifact_url | |
| 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 |