Repository navigation
Merge pull request #81 from peterjc/patch-1 #152
This file contains hidden or 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: 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 |