fix typo in help menu #57
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| name: Tests | |
| on: | |
| push: | |
| branches: [ main, master ] | |
| pull_request: | |
| branches: [ main, master ] | |
| workflow_dispatch: # Allows manual triggering | |
| # Limit concurrent runs of this workflow | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest] # Temporarily disable macOS due to mappy build issues | |
| python-version: ['3.9', '3.10', '3.11', '3.12', '3.13'] | |
| include: | |
| # Add one macOS test with conda-based installation | |
| - os: macos-latest | |
| python-version: '3.11' | |
| use_conda: true | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: 'pip' | |
| - name: Install system dependencies | |
| run: | | |
| if [[ "$RUNNER_OS" == "Linux" ]]; then | |
| sudo apt-get update | |
| sudo apt-get install -y build-essential zlib1g-dev | |
| fi | |
| - name: Setup conda (macOS only) | |
| if: matrix.use_conda == true | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-version: latest | |
| activate-environment: test | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| if [[ "${{ matrix.use_conda }}" == "true" ]]; then | |
| # Use conda for macOS to avoid mappy build issues | |
| conda install -c conda-forge -c bioconda mappy numpy pytest pytest-cov -y | |
| pip install natsort gfftk buscolite gapmm2 pyhmmer pyfastx requests gb-io json-repair pytantan | |
| pip install -e . --no-deps | |
| else | |
| # Linux - use pip as normal | |
| python -m pip install --upgrade pip | |
| python -m pip install pytest pytest-cov | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| python -m pip install -e . | |
| fi | |
| shell: bash -l {0} | |
| - name: Run unit tests | |
| run: | | |
| pytest tests/unit/ -v --cov=funannotate2 --cov-report=xml | |
| shell: bash -l {0} | |
| - name: Run integration tests without external dependencies | |
| run: | | |
| pytest tests/integration/test_funannotate_cli.py -v | |
| shell: bash -l {0} | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| slug: nextgenusfs/funannotate2 |