Add Visium breast-cancer tutorial #3
Workflow file for this run
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| name: Execute notebooks | |
| on: | |
| schedule: | |
| # Weekly: Mondays 04:00 UTC — re-executes ALL notebooks against latest releases. | |
| - cron: "0 4 * * 1" | |
| pull_request: | |
| branches: [main] | |
| paths: | |
| - "**/*.ipynb" | |
| - "pyproject.toml" | |
| - ".github/workflows/execute.yaml" | |
| workflow_dispatch: | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| execute: | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 60 | |
| steps: | |
| - uses: actions/checkout@v5 | |
| with: | |
| # Need full history so we can diff PR HEAD against the merge base. | |
| fetch-depth: 0 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.13" | |
| - name: Cache pooch datasets | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.cache/pooch | |
| key: pooch-${{ runner.os }}-${{ hashFiles('**/*.ipynb') }} | |
| restore-keys: | | |
| pooch-${{ runner.os }}- | |
| - name: Install execution environment | |
| run: | | |
| pip install --upgrade pip | |
| pip install -e ".[exec]" nbdime | |
| - name: Determine notebooks to execute | |
| id: pick | |
| run: | | |
| # On the weekly schedule and manual dispatch, run all notebooks. | |
| # On PR, run only notebooks the PR touched, to keep CI fast as the | |
| # gallery grows. (sklearn does the same.) | |
| if [ "${{ github.event_name }}" = "pull_request" ]; then | |
| base="${{ github.event.pull_request.base.sha }}" | |
| nbs=$(git diff --name-only --diff-filter=AMR "$base"...HEAD -- '*.ipynb' | grep -E '^(tutorials|examples)/' || true) | |
| else | |
| nbs=$(find tutorials examples -name "*.ipynb" -not -path "*/.ipynb_checkpoints/*" 2>/dev/null || true) | |
| fi | |
| if [ -z "$nbs" ]; then | |
| echo "No notebooks to execute." | |
| else | |
| echo "Will execute:" | |
| echo "$nbs" | |
| fi | |
| { | |
| echo 'files<<EOF' | |
| echo "$nbs" | |
| echo 'EOF' | |
| } >> "$GITHUB_OUTPUT" | |
| - name: Re-execute selected notebooks | |
| if: steps.pick.outputs.files != '' | |
| run: | | |
| while IFS= read -r nb; do | |
| [ -z "$nb" ] && continue | |
| echo "Executing $nb" | |
| jupyter nbconvert --to notebook --execute --inplace "$nb" | |
| done <<< "${{ steps.pick.outputs.files }}" | |
| - name: Strip widget metadata | |
| if: steps.pick.outputs.files != '' | |
| # `pooch` and other libs spawn `tqdm.notebook` widgets when running | |
| # in a Jupyter kernel; widget UUIDs regenerate on every execution and | |
| # would cause spurious diff failures below. Same hook runs locally | |
| # via .pre-commit-config.yaml so committed and re-executed notebooks | |
| # stay symmetric. | |
| run: | | |
| while IFS= read -r nb; do | |
| [ -z "$nb" ] && continue | |
| python scripts/strip_widget_metadata.py "$nb" || true | |
| done <<< "${{ steps.pick.outputs.files }}" | |
| - name: Diff outputs against committed | |
| if: steps.pick.outputs.files != '' | |
| run: | | |
| # If outputs drift from what's committed, fail the job. Authors are | |
| # expected to commit re-executed notebooks; CI catches drift between | |
| # commits (e.g., upstream lib changes). | |
| if ! git diff --quiet -- '*.ipynb'; then | |
| echo "Notebook outputs drifted from committed state:" | |
| nbdime diff | |
| exit 1 | |
| fi |