test.yml

name: Test

on:
    push:
        branches: [main]
    pull_request:
        branches: [main]

jobs:
    lint:
        runs-on: ubuntu-latest
        steps:
        -   uses: actions/checkout@v3
        -   name: Set up Python
            uses: actions/setup-python@v4
            with:
                python-version: '3.10'

        -   uses: actions/cache@v3
            with:
                path: ~/.cache/pre-commit
                key: precommit-${{ env.pythonLocation }}-${{ hashFiles('**/.pre-commit-config.yaml') }}
        -   name: Install dependencies
            run: |
                python -m pip install --upgrade pre-commit

        -   name: Run pre-commit
            run: |
                pre-commit run --color=always --show-diff-on-failure --all-files

    metrics:
        runs-on: ${{ matrix.os }}
        strategy:
            matrix:
                python: ['3.9', '3.11']
                os: [ubuntu-latest, macos-latest]

        steps:
        -   uses: actions/checkout@v3
        -   name: Set up Python ${{ matrix.python }}
            uses: actions/setup-python@v4
            with:
                python-version: ${{ matrix.python }}

        -   name: Install build dependencies
            run: |
                python -m pip install --upgrade pip
                pip install build twine

        -   name: Build a binary wheel and a source tarball
            run: |
                python -m build --sdist --wheel --outdir dist/
                twine check dist/*

        -   name: Install package with test dependencies
            run: |
                pip install dist/*.whl
                pip install '.[test,louvain]'

        -   name: Test with pytest
            if: ${{ matrix.os != 'macos-latest'}}
            run: |
                pytest --cov=scib --cov-report=xml -vv --ignore=tests/integration/ --ignore=tests/metrics/rpy2 -vv
                mv coverage.xml "$(echo 'coverage_metrics_${{ matrix.os }}_${{ matrix.python }}.xml' | sed 's/[^a-z0-9\.\/]/_/g')"

        -   name: Upload coverage to GitHub Actions
            uses: actions/upload-artifact@v3
            with:
                name: metrics
                path: coverage_*.xml

    rpy2:
        runs-on: ${{ matrix.os }}
        strategy:
            matrix:
                r: ['4.2']
                python: ['3.10']
                os: [ubuntu-latest]
        steps:
        -   uses: actions/checkout@v3
        -   name: Set up Python ${{ matrix.python }}
            uses: actions/setup-python@v4
            with:
                python-version: ${{ matrix.python }}
        -   name: Set up R
            uses: r-lib/actions/setup-r@v2
            with:
                r-version: ${{ matrix.r }}

        -   name: Install dependencies
            env:
                GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
            run: |
                python -m pip install --upgrade pip
                pip install '.[test,rpy2]'
                Rscript -e "install.packages('remotes')"
                Rscript -e "remotes::install_github('theislab/kBET')"

        -   name: Test with pytest
            run: |
                pytest --cov=scib --cov-report=xml -vv --tb=native -k rpy2
                mv coverage.xml "$(echo 'coverage_rpy2_${{ matrix.os }}_${{ matrix.python }}.xml' | sed 's/[^a-z0-9\.\/]/_/g')"

        -   name: Upload coverage to GitHub Actions
            uses: actions/upload-artifact@v3
            with:
                name: rpy2
                path: coverage_*.xml


    integration:
        runs-on: ${{ matrix.os }}
        strategy:
            matrix:
                python: ['3.9', '3.11']
                os: [ubuntu-latest]

        steps:
        -   uses: actions/checkout@v3
        -   name: Set up Python ${{ matrix.python }}
            uses: actions/setup-python@v4
            with:
                python-version: ${{ matrix.python }}

        -   name: Install dependencies
            run: |
                python -m pip install --upgrade pip
                pip install '.[test,scanorama,scvi,harmony]'

        -   name: Test with pytest
            run: |
                pytest --cov=scib --cov-report=xml -vv --tb=native -k integration
                mv coverage.xml "$(echo 'coverage_integration_${{ matrix.os }}_${{ matrix.python }}.xml' | sed 's/[^a-z0-9\.\/]/_/g')"

        -   name: Upload coverage to GitHub Actions
            uses: actions/upload-artifact@v3
            with:
                name: integration
                path: coverage_*.xml


    upload-codecov:
        needs: [metrics, rpy2]
        runs-on: ubuntu-latest

        steps:
        -   uses: actions/checkout@v3
            with:
                fetch-depth: 0

        -   name: Download coverage from GitHub Actions
            uses: actions/download-artifact@v3

        -   name: Upload coverage
            uses: codecov/codecov-action@v4
            with:
                token: ${{ secrets.CODECOV_TOKEN }}
                flags: unittests
                fail_ci_if_error: ${{ github.repository == 'theislab/scib' }}
                verbose: true

        -   name: Delete coverage artifacts
            uses: geekyeggo/delete-artifact@v4