Collect test coverage information #101
Workflow file for this run
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| # Copyright (C) 2024 Roberto Rossini <[email protected]> | |
| # | |
| # SPDX-License-Identifier: MIT | |
| name: CI | |
| on: | |
| push: | |
| branches: [main] | |
| paths: | |
| - ".github/workflows/ci.yml" | |
| - "src/**" | |
| - "test/**" | |
| - ".gitignore" | |
| - "pyproject.toml" | |
| pull_request: | |
| paths: | |
| - ".github/workflows/ci.yml" | |
| - "src/**" | |
| - "test/**" | |
| - ".gitignore" | |
| - "pyproject.toml" | |
| # https://stackoverflow.com/a/72408109 | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| shell: bash | |
| jobs: | |
| matrix-factory: | |
| name: Generate job matrix | |
| runs-on: ubuntu-latest | |
| outputs: | |
| matrix: ${{ steps.set-result.outputs.result }} | |
| steps: | |
| - name: Generate matrix | |
| uses: actions/github-script@v7 | |
| id: set-result | |
| with: | |
| script: | | |
| // Documentation | |
| // https://docs.github.com/en/actions/learn-github-actions/contexts#fromjson | |
| // https://github.com/actions/runner/issues/982#issuecomment-809360765 | |
| const platforms = ["windows-latest", "macos-latest", "ubuntu-latest"] | |
| var python_versions = ["3.9", "3.12"] | |
| if ("${{github.event_name}}" != "pull_request") { | |
| python_versions = python_versions.concat(["3.10", "3.11"]) | |
| } | |
| var includes = [] | |
| for (const plat of platforms) { | |
| for (const ver of python_versions) { | |
| includes.push({os: plat, python_version: ver}) | |
| } | |
| } | |
| return { include: includes } | |
| ci: | |
| name: CI | |
| needs: [matrix-factory] | |
| strategy: | |
| fail-fast: false | |
| matrix: ${{ fromJson(needs.matrix-factory.outputs.matrix) }} | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| TEST_DATASET_ID: 4DNFIOTPSS3L | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python_version }} | |
| cache: pip | |
| cache-dependency-path: pyproject.toml | |
| - name: Install package | |
| run: pip install --verbose '.[test]' | |
| - name: Run unit tests | |
| run: python -m pytest --cov -v --cov-report=xml . | |
| - name: Upload unit test coverage report to Codecov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| flags: "tests | unit | python-${{ matrix.python_version }}" | |
| disable_search: true | |
| files: coverage.xml | |
| fail_ci_if_error: true | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| verbose: true | |
| - name: Run simple CLI tests | |
| run: | | |
| stripepy --help | |
| stripepy --version | |
| - name: Cache test dataset | |
| id: cache-dset | |
| uses: actions/cache/restore@v4 | |
| with: | |
| key: ${{ env.TEST_DATASET_ID }} | |
| path: ${{ env.TEST_DATASET_ID }}.hic | |
| - name: Download test dataset | |
| if: steps.cache-dset.outputs.cache-hit != 'true' | |
| run: stripepy download --name ${{ env.TEST_DATASET_ID }} | |
| - name: Save test dataset | |
| if: steps.cache-dset.outputs.cache-hit != 'true' | |
| uses: actions/cache/save@v4 | |
| with: | |
| key: ${{ env.TEST_DATASET_ID }} | |
| path: ${{ env.TEST_DATASET_ID }}.hic | |
| - name: Test stripepy call | |
| run: | | |
| NPROC="$(python -c 'import multiprocessing as mp; print(mp.cpu_count())')" | |
| stripepy call \ | |
| ${{ env.TEST_DATASET_ID }}.hic \ | |
| 100000 \ | |
| -o stripepy/ \ | |
| --glob-pers-type constant \ | |
| --glob-pers-min 0.10 \ | |
| --loc-pers-min 0.33 \ | |
| --loc-trend-min 0.25 \ | |
| --roi middle \ | |
| --nproc "$NPROC" | |
| find stripepy/ -type f -exec ls -lah {} + | |
| if [ ! -f stripepy/*/*/results.hdf5 ]; then | |
| 1>&2 echo 'results.hdf5 is missing!' | |
| exit 1 | |
| fi | |
| ci-status-check: | |
| name: Status Check (CI) | |
| if: ${{ always() }} | |
| runs-on: ubuntu-latest | |
| needs: | |
| - ci | |
| steps: | |
| - name: Collect job results | |
| if: needs.ci.result != 'success' | |
| run: exit 1 |