adjusted github actions to uv + updated Py versions
#236
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| name: CI | |
| on: | |
| schedule: | |
| - cron: 00 00 * * 1 # run every Monday at 00:00 | |
| push: | |
| branches: [main] | |
| tags: [v*] | |
| pull_request: | |
| branches: [main] | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| timeout-minutes: 10 | |
| strategy: | |
| fail-fast: false | |
| max-parallel: 4 | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| python: ['3.9', '3.10', '3.11', '3.12', '3.13'] | |
| test_server: [false] | |
| include: | |
| - os: macos-latest | |
| python: 3.9 | |
| env: | |
| OS: ${{ matrix.os }} | |
| PYTHON: ${{ matrix.python }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Install uv | |
| uses: astral-sh/setup-uv@v5 | |
| with: | |
| enable-cache: true | |
| - name: Set up Python ${{ matrix.python }} | |
| run: uv python install ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| uv sync --all-extras | |
| uv pip install tox-gh-actions codecov | |
| - name: Install R | |
| if: matrix.test_server | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: 4.4.1 | |
| - name: Get R cache dir | |
| uses: actions/cache@v4 | |
| if: matrix.test_server | |
| with: | |
| path: ~/.local/share/renv | |
| key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }} | |
| - name: Install OmnipathR | |
| if: matrix.test_server | |
| run: | | |
| sudo apt-get install libcurl4-openssl-dev | |
| sudo Rscript --vanilla -e "if (!(requireNamespace('BiocManager', quietly=TRUE))) { install.packages(c('BiocManager', 'curl'), repos='https://cloud.r-project.org/') }; BiocManager::install('OmnipathR')" | |
| Rscript --vanilla -e "packageVersion('OmnipathR')" | |
| - name: Test | |
| env: | |
| PLATFORM: ${{ matrix.platform }} | |
| run: | | |
| uv run tox -vv | |
| - name: Upload coverage to Codecov | |
| if: success() | |
| env: | |
| CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }} | |
| run: | | |
| uv run codecov --no-color --required --flags unittests | |
| deploy: | |
| if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') | |
| needs: build | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Build a binary wheel and a source tarball | |
| run: uv build | |
| - name: Publish package on PyPI | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_PASSWORD }} | |
| skip_existing: true | |
| verbose: true |