created R=2 figure for axial g-factor #75
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| name: Run Notebooks and Save Outputs | |
| on: | |
| push: | |
| branches: | |
| - main # Trigger the action on the main branch | |
| - mb/jb | |
| permissions: | |
| id-token: write | |
| pages: write | |
| jobs: | |
| # Run the notebooks | |
| run-notebooks: | |
| runs-on: ubuntu-latest | |
| 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 and build book | |
| continue-on-error: true # Allow workflow to continue even if notebook execution fails | |
| run: jupyter-book build . | |
| - name: Upload artifact | |
| uses: actions/upload-pages-artifact@v3 | |
| with: | |
| path: './_build/html' | |
| - name: Deploy to GitHub Pages | |
| id: deployment | |
| uses: actions/deploy-pages@v4 |