Alternative ways to get genomic positions (#150) #369
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| 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 }} | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.r }} | |
| use-public-rspm: true | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@v5 | |
| - name: Install the project | |
| run: uv sync --extra dev --extra test --extra gtf --extra copykat | |
| - name: Install R dependencies | |
| run: | | |
| install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$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: | | |
| uv run coverage run -m pytest -v --color=yes | |
| - name: Report coverage | |
| run: | | |
| uv run coverage report | |
| - name: Upload coverage | |
| uses: codecov/codecov-action@v3 |