adding all missing files #35
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| name: Run Notebooks and Save Outputs | |
| on: | |
| push: | |
| branches: | |
| - main # Trigger the action on the main branch | |
| jobs: | |
| # First job: Clear outputs with nbstripout | |
| clear-outputs: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout Repository | |
| uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| - name: Install nbstripout | |
| run: | | |
| pip install nbstripout | |
| nbstripout --install | |
| - name: Strip notebook outputs | |
| run: | | |
| find . -name "*.ipynb" -exec nbstripout --force --keep-count {} + | |
| - name: Check for changes | |
| run: git status | |
| - name: Commit cleaned notebooks if needed | |
| run: | | |
| git config --global user.email "[email protected]" | |
| git config --global user.name "GitHub Action" | |
| git add . | |
| git commit -m "Auto-strip notebook outputs" || echo "No changes to commit" | |
| git push || echo "Nothing to push" | |
| # Second job: Run the notebooks | |
| run-notebooks: | |
| runs-on: ubuntu-latest | |
| needs: clear-outputs # Ensure this job runs after 'clear-outputs' | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - name: Clear GitHub Action Caches | |
| run: | | |
| echo "Clearing caches..." | |
| sudo rm -rf ~/.cache/pip | |
| sudo rm -rf executed_notebooks | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.10' | |
| - name: Install Python dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt | |
| - name: Install SCT | |
| run: | | |
| git clone --depth 1 https://github.com/spinalcordtoolbox/spinalcordtoolbox.git | |
| yes | spinalcordtoolbox/install_sct | |
| # NB: install_sct edits ~/.bashrc, but those environment changes don't get passed to subsequent steps in GH Actions. | |
| # So, we filter through the .bashrc and pass the values to $GITHUB_ENV and $GITHUB_PATH. | |
| # Relevant documentation: https://docs.github.com/en/actions/reference/workflow-commands-for-github-actions#environment-files | |
| # This workaround should be replaced by https://github.com/spinalcordtoolbox/spinalcordtoolbox/pull/3198#discussion_r568225392 | |
| cat ~/.bashrc | grep "export SCT_DIR" | cut -d " " -f 2 >> $GITHUB_ENV | |
| cat ~/.bashrc | grep "export PATH" | grep -o "/.*" | cut -d ':' -f 1 >> $GITHUB_PATH | |
| - name: Verify SCT installation | |
| run: | | |
| # Make sure SCT can be called from within the environment | |
| sct_check_dependencies | |
| - name: Run Jupyter Notebooks | |
| continue-on-error: true # Allow workflow to continue even if notebook execution fails | |
| run: | | |
| echo $PATH | |
| mkdir -p executed_notebooks | |
| for notebook in $(find . -name "*.ipynb"); do | |
| echo "Executing $notebook" | |
| jupyter nbconvert --to notebook --execute --allow-errors --inplace \ | |
| --output executed_notebooks/$(basename $notebook) $notebook \ | |
| 2>&1 | tee -a notebook_execution.log || exit 1 | |
| done | |
| - name: Check Execution Log | |
| run: cat notebook_execution.log | |
| - name: Upload Executed Notebooks | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: executed-notebooks | |
| path: executed_notebooks/ | |
| # Third job: Deploy to GitHub Pages (depends on run-notebooks) | |
| deploy: | |
| runs-on: ubuntu-latest | |
| needs: run-notebooks # Ensure this job runs after 'run-notebooks' | |
| steps: | |
| - name: Checkout Repository | |
| uses: actions/checkout@v3 | |
| - name: Download Executed Notebooks | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: executed-notebooks | |
| path: executed_notebooks/ | |
| - name: Copy Executed Notebooks to Pages Directory | |
| run: | | |
| COMMIT_SHA=$(git rev-parse --short HEAD) | |
| mkdir -p gh-pages/$COMMIT_SHA | |
| cp executed_notebooks/*.ipynb gh-pages/$COMMIT_SHA/ | |
| - name: Deploy to GitHub Pages | |
| uses: peaceiris/actions-gh-pages@v3 | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| publish_dir: gh-pages | |
| publish_branch: gh-pages |