Merge branch 'main' of github.com:saezlab/omnipath #257
Workflow file for this run
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: 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] | |
| exclude: | |
| - os: macos-latest | |
| include: | |
| - os: macos-latest | |
| python: '3.13' | |
| 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 | |
| python-version: ${{ matrix.python }} | |
| - name: Install Python | |
| run: uv python install --python-preference only-managed ${{ matrix.python }} | |
| - name: Install dependencies | |
| run: | | |
| uv sync --all-extras | |
| uv pip install codecov | |
| uv tool install \ | |
| --python-preference only-managed \ | |
| --python ${{ matrix.python }} \ | |
| --with tox-uv \ | |
| --with tox-gh \ | |
| tox | |
| - 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: Set up test suite | |
| env: | |
| TOX_GH_MAJOR_MINOR: ${{ matrix.python }} | |
| run: | | |
| tox run -vv --notest --skip-missing-interpreters true | |
| - name: Run tests | |
| env: | |
| TOX_GH_MAJOR_MINOR: ${{ matrix.python }} | |
| run: | | |
| tox run -vv --skip-pkg-install | |
| - name: Upload coverage to Codecov | |
| if: success() | |
| env: | |
| CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }} | |
| run: | | |
| uv run codecovcli --verbose upload-process -t ${{ secrets.CODECOV_TOKEN }} -n $CODECOV_NAME -F 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 |