Rename package from stripepy to stripepy-hic #188
Workflow file for this run
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| # Copyright (C) 2024 Roberto Rossini <roberros@uio.no> | |
| # | |
| # SPDX-License-Identifier: MIT | |
| name: CI | |
| on: | |
| push: | |
| branches: [main] | |
| paths: | |
| - ".github/workflows/cache-test-datasets.yml" | |
| - ".github/workflows/ci.yml" | |
| - "src/**" | |
| - "test/**" | |
| - ".gitignore" | |
| - "pyproject.toml" | |
| pull_request: | |
| paths: | |
| - ".github/workflows/cache-test-datasets.yml" | |
| - ".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: ${{ steps.set-result.outputs.result }} | |
| steps: | |
| - name: Generate matrix | |
| uses: actions/github-script@v7 | |
| id: set-result | |
| with: | |
| script: | | |
| // Documentation | |
| // https://docs.github.com/en/actions/learn-github-actions/contexts#fromjson | |
| // https://github.com/actions/runner/issues/982#issuecomment-809360765 | |
| const platforms = ["windows-latest", "macos-latest", "ubuntu-latest"] | |
| var python_versions = ["3.9", "3.13"] | |
| if ("${{github.event_name}}" != "pull_request") { | |
| python_versions = python_versions.concat(["3.10", "3.11", "3.12"]) | |
| } | |
| var includes = [] | |
| for (const plat of platforms) { | |
| for (const ver of python_versions) { | |
| includes.push({os: plat, python_version: ver}) | |
| } | |
| } | |
| return { include: includes } | |
| cache-test-datasets: | |
| name: Cache test datasets | |
| uses: paulsengroup/StripePy/.github/workflows/cache-test-datasets.yml@main | |
| ci: | |
| name: CI | |
| needs: [cache-test-datasets, matrix-factory] | |
| strategy: | |
| fail-fast: false | |
| matrix: ${{ fromJson(needs.matrix-factory.outputs.matrix) }} | |
| runs-on: ${{ matrix.os }} | |
| 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 simple CLI tests | |
| run: | | |
| stripepy --help | |
| stripepy --version | |
| - name: Restore test dataset | |
| uses: actions/cache/restore@v4 | |
| with: | |
| key: ${{ needs.cache-test-datasets.outputs.cache-key }} | |
| path: test/data/ | |
| fail-on-cache-miss: true | |
| enableCrossOsArchive: true | |
| - name: Run unit tests | |
| run: | | |
| python -m pytest \ | |
| --cov=stripepy \ | |
| --verbose \ | |
| --cov-report=xml \ | |
| --cov-report=term \ | |
| test/ \ | |
| -m unit | |
| - name: Upload unit test coverage report to Codecov | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| flags: "tests | unit | python-${{ matrix.python_version }}" | |
| disable_search: true | |
| files: coverage.xml | |
| fail_ci_if_error: true | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| verbose: true | |
| - name: Run integration tests | |
| run: | | |
| rm -f coverage.xml | |
| python -m pytest \ | |
| --cov=stripepy \ | |
| --verbose \ | |
| --cov-report=xml \ | |
| --cov-report=term \ | |
| test/ \ | |
| -m end2end | |
| - name: Upload end2end test coverage report to Codecov | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| flags: "tests | integration | python-${{ matrix.python_version }}" | |
| disable_search: true | |
| files: coverage.xml | |
| fail_ci_if_error: true | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| verbose: true | |
| 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 |