/import-from-nanopub: clone sibling repos + stage starter files #20
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| name: CI smoke run | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| workflow_dispatch: | |
| # Smoke test: runs the replication pipeline end-to-end via the Snakefile. | |
| # Large inputs should be cached via actions/cache@v4 — see data/README.md. | |
| jobs: | |
| run: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Skip CI if template has not been initialised or notebooks are scaffolds | |
| id: guard | |
| run: | | |
| if grep -rln '{{[A-Z_]\+}}' . --include='*.md' --include='*.yml' --include='*.yaml' --include='*.json' --include='*.cff' --include='*.py' 2>/dev/null | grep -v '^./.claude/skills/init-template/' | head -1 > /dev/null; then | |
| echo "::notice::Template placeholders detected ({{...}} tokens). Run /init-template inside Claude Code (or substitute manually) before CI runs meaningfully. Skipping the rest of this workflow." | |
| echo "skip=true" >> "$GITHUB_OUTPUT" | |
| elif grep -lE 'raise NotImplementedError|"<dataset-name>"|# Example skeleton — adapt' notebooks/*.py 2>/dev/null | head -1 > /dev/null; then | |
| echo "::notice::Notebooks are still in scaffold state — replace placeholders in notebooks/*.py with your actual replication code (Phase 2). The Snakefile rule outputs will not be produced until then. Skipping pipeline run." | |
| echo "skip=true" >> "$GITHUB_OUTPUT" | |
| else | |
| echo "skip=false" >> "$GITHUB_OUTPUT" | |
| fi | |
| - name: Set up Micromamba | |
| if: steps.guard.outputs.skip != 'true' | |
| uses: mamba-org/setup-micromamba@v3 | |
| with: | |
| environment-file: environment.yml | |
| environment-name: ${{ github.event.repository.name }} | |
| init-shell: bash | |
| cache-environment: true | |
| # ----- credentials (uncomment + add the matching GitHub secret) ----- | |
| # | |
| # - name: Set up Copernicus Marine credentials | |
| # if: ${{ secrets.COPERNICUS_CREDENTIALS_BASE64 != '' }} | |
| # run: | | |
| # mkdir -p ~/.copernicusmarine | |
| # echo "${{ secrets.COPERNICUS_CREDENTIALS_BASE64 }}" | base64 -d \ | |
| # > ~/.copernicusmarine/.copernicusmarine-credentials | |
| # | |
| # - name: Set up CDS credentials | |
| # if: ${{ secrets.CDSAPI_KEY != '' }} | |
| # run: | | |
| # echo "url: https://cds.climate.copernicus.eu/api/v2" > ~/.cdsapirc | |
| # echo "key: ${{ secrets.CDSAPI_KEY }}" >> ~/.cdsapirc | |
| # ----- data caching (uncomment + adjust path/key) ----- | |
| # | |
| # - name: Cache input data | |
| # id: cache_data | |
| # uses: actions/cache@v4 | |
| # with: | |
| # path: data/raw | |
| # key: input-data-v1 | |
| - name: Run pipeline | |
| if: steps.guard.outputs.skip != 'true' | |
| shell: micromamba-shell {0} | |
| run: snakemake --cores 1 | |
| - name: Upload results | |
| if: always() && steps.guard.outputs.skip != 'true' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ci-outputs | |
| path: | | |
| results/ | |
| figures/ |