Bump aligntools version #755
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| name: main | |
| on: | |
| push: | |
| branches: [ "master", "devel" ] | |
| pull_request: | |
| branches: [ "master", "devel" ] | |
| schedule: | |
| - cron: "0 14 * * 1" | |
| jobs: | |
| quicktest: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install dependencies | |
| run: sudo apt-get update && sudo apt-get install -y python3 python3-pip mafft ncbi-blast+ | |
| - name: Run build | |
| run: pip3 install .[test] | |
| - name: Run tests and collect coverage | |
| run: pytest -v -m "not slow" --cov=./src | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v3 | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| slowtest: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| testcase: ["tests/test_end_to_end.py::test_large", "tests/test_end_to_end.py::test_large_csv", "tests/test_end_to_end.py::test_large_hxb2"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install dependencies | |
| run: sudo apt-get update && sudo apt-get install -y python3 python3-pip mafft ncbi-blast+ | |
| - name: Run build | |
| run: pip3 install .[test] | |
| - name: Run tests and collect coverage | |
| run: pytest -v ${{ matrix.testcase }} | |
| installtest: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, ubuntu-20.04, ubuntu-22.04] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Install dependencies | |
| run: sudo apt-get update && sudo apt-get install -y python3 python3-pip mafft ncbi-blast+ | |
| - name: Run build | |
| run: pip3 install . | |
| - name: Check installed version | |
| run: test "$(git describe --tags --abbrev=0)" == "v$(cfeintact version)" | |
| - name: Run test | |
| run: cfeintact check --subtype B tests/data-small.fasta && test -f "defects.csv" | |
| dockerinstall: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Build the Docker image | |
| run: docker build . --tag cfeintact | |
| - name: Run test | |
| run: docker run cfeintact sh -c 'cfeintact check --subtype B tests/data-small.fasta && test -f "defects.csv"' | |
| linter: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install dependencies | |
| run: sudo apt-get update && sudo apt-get install -y python3 python3-pip | |
| - name: Run build | |
| run: pip3 install .[dev] | |
| - name: Run linter | |
| run: flake8 | |
| typechecker: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install dependencies | |
| run: sudo apt-get update && sudo apt-get install -y python3 python3-pip | |
| - name: Run build | |
| run: pip3 install .[dev] | |
| - name: Run typechecker | |
| run: mypy |