Update project.R #551
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Build app bundle | ||
|
Check failure on line 1 in .github/workflows/release.yml
|
||
| # Two triggers: a version tag publishes a Release with the bundle attached, and | ||
| # manual dispatch builds one without publishing, for checking a change before | ||
| # tagging. | ||
| on: | ||
| push: | ||
| tags: ['v*'] | ||
| workflow_dispatch: | ||
| inputs: | ||
| gene_universe: | ||
| description: 'Gene universe for the grid' | ||
| default: '^protein-coding$' | ||
| n_masks: | ||
| description: 'Masks per coverage level and loss mode' | ||
| default: '10' | ||
| # Read by default; the publishing job asks for write on its own. A | ||
| # workflow-level write token would be handed to every future job added here. | ||
| permissions: | ||
| contents: read | ||
| jobs: | ||
| bundle: | ||
| runs-on: ubuntu-latest | ||
| permissions: | ||
| contents: write | ||
| # The coverage calibration recomputes one GLS fingerprint per | ||
| # (sample, level, mode, mask); on two cores that is the long pole. | ||
| timeout-minutes: 180 | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| - uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| r-version: 'release' | ||
| - name: Tests must pass before anything is published | ||
| run: | | ||
| Rscript tests/test_labels.R | ||
| Rscript tests/test_spectrum.R | ||
| Rscript tests/test_condition_invariants.R | ||
| # GEO downloads are stable for a given accession, so cache them rather | ||
| # than hitting NCBI on every run. | ||
| - name: Cache GEO downloads | ||
| uses: actions/cache@v4 | ||
| with: | ||
| path: data | ||
| key: geo-${{ hashFiles('config/datasets/*.R') }} | ||
| - name: Fetch inputs | ||
| run: | | ||
| ./tsf fetch --geo-dir data | ||
| ./tsf check --geo-dir data | ||
| # The reference needs the common format, nothing further: fingerprints | ||
| # come from the expression matrices, so neither maxT nor the spectral | ||
| # stages are on this path. | ||
| - name: Ingest | ||
| run: | | ||
| ./tsf run --to ingest \ | ||
| --geo-dir data --interim-dir interim --results-dir results \ | ||
| --gene-universe '${{ github.event.inputs.gene_universe || ''^protein-coding$'' }}' | ||
| # n_masks is the cheap-trial-build knob: the coverage calibration | ||
| # recomputes one GLS fingerprint per (sample, level, mode, mask), so it is | ||
| # the long pole. A tag build takes the configured default; a manual | ||
| # dispatch can lower it. This input was declared and documented but never | ||
| # reached the CLI, so the knob silently did nothing. | ||
| # | ||
| # pipefail matters: without it the exit status is tee's, so a failing | ||
| # reference stage would still be published. | ||
| - name: Build reference and validate out of cohort | ||
| shell: bash | ||
| run: | | ||
| set -o pipefail | ||
| args=(--geo-dir data --interim-dir interim --results-dir results) | ||
| if [ -n "${{ github.event.inputs.n_masks }}" ]; then | ||
| args+=(--n-masks "${{ github.event.inputs.n_masks }}") | ||
| fi | ||
| ./tsf reference "${args[@]}" 2>&1 | tee reference.log | ||
| # The validation numbers are what tell a recipient how much a match is | ||
| # worth, so they go on the run's summary page rather than only into a log | ||
| # nobody opens. | ||
| - name: Report validation on the summary page | ||
| if: always() | ||
| run: | | ||
| { | ||
| echo '## Reference validation' | ||
| echo '```' | ||
| grep -E 'Out-of-cohort|coverage band|%:|USABLE|WEAK|NOT BETTER|Grid compatibility' reference.log || true | ||
| echo '```' | ||
| } >> "$GITHUB_STEP_SUMMARY" | ||
| - name: Refuse to publish a reference that does not beat its baseline | ||
| run: | | ||
| if grep -q 'NOT BETTER THAN GUESSING' reference.log; then | ||
| echo "The reference does not beat the majority-class baseline out of cohort." | ||
| echo "Publishing it would ship confident-looking output with no information." | ||
| exit 1 | ||
| fi | ||
| - name: Build the bundle | ||
| run: | | ||
| ./tsf bundle --results-dir results --interim-dir interim \ | ||
| --out TissueSpectF-app | ||
| sha256sum TissueSpectF-app.zip > TissueSpectF-app.zip.sha256 | ||
| cat TissueSpectF-app/REFERENCE.txt >> "$GITHUB_STEP_SUMMARY" | ||
| - uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: TissueSpectF-app | ||
| path: | | ||
| TissueSpectF-app.zip | ||
| TissueSpectF-app.zip.sha256 | ||
| retention-days: 30 | ||
| - name: Attach to the release | ||
| if: startsWith(github.ref, 'refs/tags/') | ||
| uses: softprops/action-gh-release@v2 | ||
| with: | ||
| files: | | ||
| TissueSpectF-app.zip | ||
| TissueSpectF-app.zip.sha256 | ||
| body_path: TissueSpectF-app/REFERENCE.txt | ||
| fail_on_unmatched_files: true | ||
