Update selfcheck.R #642
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| name: Tests | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| workflow_dispatch: | |
| jobs: | |
| tests: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: 'release' | |
| # The test suite is deliberately dependency-free: base R only, no | |
| # Bioconductor. That is what makes this job take a minute instead of | |
| # fifteen, and what lets the label and spectral cores be checked on any | |
| # machine without an install step. | |
| - name: Unit tests | |
| run: | | |
| Rscript tests/test_labels.R | |
| Rscript tests/test_spectrum.R | |
| Rscript tests/test_condition_invariants.R | |
| Rscript tests/test_differential.R | |
| # End-to-end run on synthetic data with a known injected peak: catches | |
| # regressions that unit tests cannot, such as a stage writing a schema the | |
| # next stage does not read. | |
| # Every stage is invoked through the real CLI, not through the test | |
| # harness: a module missing from the load path fails here and nowhere | |
| # else, because the unit tests source what they need explicitly. | |
| # Paths are supplied because config/project.R has no defaults and a dry | |
| # run's whole output is where it would read and write. This step used to | |
| # omit them and started failing the moment the defaults were removed -- | |
| # the workflow lagged the policy change, which is what CI is for. | |
| - name: CLI reaches every stage | |
| env: | |
| TSF_GEO_DIR: data | |
| TSF_INTERIM_DIR: interim | |
| TSF_RESULTS_DIR: results | |
| run: | | |
| ./tsf --help > /dev/null | |
| for s in ingest spectra maxt condition consensus clean stability peaks compare; do | |
| ./tsf run --to "$s" --dry-run > /dev/null || exit 1 | |
| done | |
| # Each command must ask only for the paths it uses. `fetch` downloads and | |
| # has no results tree; demanding one is a false requirement. | |
| - name: Path requirements are per command | |
| run: | | |
| # fetch needs geo_dir and nothing else. | |
| ./tsf fetch --geo-dir data --dry-run > /dev/null | |
| # run needs all three, and must say so rather than failing later. | |
| if ./tsf run --to ingest --dry-run > /dev/null 2>&1; then | |
| echo "run should require paths and did not"; exit 1 | |
| fi | |
| ./tsf run --to ingest --dry-run 2>&1 | grep -q -- "--interim-dir" \ | |
| || { echo "the error should name the missing flag"; exit 1; } | |
| - name: Self-check | |
| env: | |
| TSF_MAXT_B: '100' | |
| TSF_CONDITION_B: '500' | |
| run: ./tsf selfcheck |