Add opt-in support for chimeric ProForma parsing #739
Workflow file for this run
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| name: tests | |
| on: | |
| push: | |
| paths: | |
| - '**.py' | |
| - '.github/workflows/pythonpackage.yml' | |
| - 'test-requirements.txt' | |
| pull_request: | |
| paths: | |
| - '**.py' | |
| - '.github/workflows/pythonpackage.yml' | |
| - 'test-requirements.txt' | |
| jobs: | |
| build: | |
| if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name | |
| runs-on: 'ubuntu-latest' | |
| services: | |
| postgres: | |
| image: postgres:16 | |
| env: | |
| POSTGRES_USER: postgres | |
| POSTGRES_PASSWORD: postgres | |
| POSTGRES_DB: pyteomics_test | |
| options: >- | |
| --health-cmd "pg_isready -U postgres -d pyteomics_test" | |
| --health-interval 10s | |
| --health-timeout 5s | |
| --health-retries 5 | |
| ports: | |
| - 5432:5432 | |
| strategy: | |
| matrix: | |
| python-version: ['3.10', '3.11', '3.12', '3.13', '3.14'] | |
| steps: | |
| - uses: actions/checkout@v6 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v6 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install libhdf5-serial-dev | |
| python -m pip install --upgrade pip | |
| pip install numpy | |
| pip install -r test-requirements.txt | |
| pip install . | |
| - name: Run live PostgreSQL Unimod test | |
| env: | |
| PYTEOMICS_TEST_POSTGRES_URL: postgresql+psycopg://postgres:postgres@localhost:5432/pyteomics_test | |
| run: | | |
| cd tests; python -m unittest test_unimod.UnimodCompatibilityTests.test_live_postgresql_loader | |
| - name: Run the tests | |
| run: | | |
| cd tests; find . -name 'test_*.py' -print0 | xargs -0 -n1 python | |
| tests-multiplatform: | |
| if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name | |
| strategy: | |
| matrix: | |
| python-version: ['3.10', '3.11', '3.12', '3.13', '3.14'] | |
| os: ['macos-latest', 'windows-latest'] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v6 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v6 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install . | |
| - name: Run the tests | |
| run: | | |
| cd tests; python -m unittest test_util.UtilTest |