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Handle missing $FUNANNOTATE2_DB in install command #149
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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: | |
| version-consistency: | |
| name: Version consistency check | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Check pyproject.toml, CITATION.cff, and pixi.lock agree on version | |
| run: | | |
| set -euo pipefail | |
| PYPROJECT_VERSION=$(grep -E '^[[:space:]]*version[[:space:]]*=' pyproject.toml \ | |
| | head -1 \ | |
| | sed -E 's/.*version[[:space:]]*=[[:space:]]*"([^"]+)".*/\1/') | |
| if [ -z "$PYPROJECT_VERSION" ]; then | |
| echo "::error file=pyproject.toml::Could not extract version" | |
| exit 1 | |
| fi | |
| CFF_VERSION=$(grep -E '^version: ' CITATION.cff | head -1 | sed -E 's/^version: //') | |
| LOCK_VERSION=$(awk ' | |
| /^ name: funannotate2$/ { found = 1; next } | |
| found && /^ version:/ { print $2; exit } | |
| ' pixi.lock) | |
| printf 'pyproject.toml: %s\nCITATION.cff: %s\npixi.lock: %s\n' \ | |
| "$PYPROJECT_VERSION" "$CFF_VERSION" "$LOCK_VERSION" | |
| status=0 | |
| if [ "$PYPROJECT_VERSION" != "$CFF_VERSION" ]; then | |
| echo "::error file=CITATION.cff::CITATION.cff version ($CFF_VERSION) does not match pyproject.toml ($PYPROJECT_VERSION). Update CITATION.cff (the .githooks/pre-commit hook will do this automatically when pyproject.toml changes)." | |
| status=1 | |
| fi | |
| if [ "$PYPROJECT_VERSION" != "$LOCK_VERSION" ]; then | |
| echo "::error file=pixi.lock::pixi.lock pins funannotate2 ($LOCK_VERSION) but pyproject.toml is $PYPROJECT_VERSION. Run 'pixi install' locally and commit the refreshed pixi.lock; otherwise the Docker build will fail on 'pixi install --locked'." | |
| status=1 | |
| fi | |
| exit $status | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest] # Temporarily disable macOS due to mappy build issues | |
| python-version: ['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 cmake 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: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| env: | |
| # Force pytantan to build from sdist so all Python versions get the | |
| # same AVX2-off baseline. The published cp3x wheels have caused | |
| # import-time failures on 3.10/3.11 in this matrix. | |
| PIP_NO_BINARY: pytantan | |
| run: | | |
| if [[ "${{ 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 cmake -y | |
| # Install funannotate2 in editable mode - this will install all dependencies from pyproject.toml | |
| pip install -e . | |
| 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 |