ci.yml

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
                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 ${{ matrix.python }} \
                  tox --with tox-uv --with tox-gh


        -   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