Take into account that chromosomes may be removed when specifying man… #291
This file contains 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: Test | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| schedule: | |
| - cron: "0 5 1,15 * *" | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -e {0} # -e to fail on error | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - os: ubuntu-latest | |
| python: "3.10" | |
| r: release | |
| - os: ubuntu-latest | |
| python: "3.12" | |
| r: release | |
| - os: ubuntu-latest | |
| python: "3.12" | |
| r: release | |
| pip-flags: "--pre" | |
| env: | |
| OS: ${{ matrix.os }} | |
| PYTHON: ${{ matrix.python }} | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| cache: "pip" | |
| cache-dependency-path: "**/pyproject.toml" | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.r }} | |
| use-public-rspm: true | |
| - name: Install test dependencies | |
| run: | | |
| python -m pip install --upgrade pip wheel | |
| - name: Install dependencies | |
| run: | | |
| pip install ".[dev,test,copykat]" | |
| - name: Install R dependencies | |
| run: | | |
| install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch)) | |
| # TODO: use copykat version from february, latest version seens to have a bug... | |
| pak::pkg_install(c('stringr', 'navinlabcode/copykat@674e331cf12ce14b62eaf6459f7c84a82fc4c775')) | |
| shell: Rscript {0} | |
| - name: Test | |
| env: | |
| MPLBACKEND: agg | |
| PLATFORM: ${{ matrix.os }} | |
| DISPLAY: :42 | |
| run: | | |
| coverage run -m pytest -v --color=yes | |
| - name: Report coverage | |
| run: | | |
| coverage report | |
| - name: Upload coverage | |
| uses: codecov/codecov-action@v3 |