Find overrepresented sequences using fragments #149
Workflow file for this run
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| name: Continous integration | |
| on: | |
| pull_request: | |
| paths-ignore: | |
| - 'docs/**' | |
| - '*.rst' | |
| push: | |
| branches: | |
| - develop | |
| - main | |
| tags: | |
| - "*" | |
| jobs: | |
| lint: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v2.3.4 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v2.2.1 | |
| with: | |
| python-version: 3.8 | |
| - name: Install tox | |
| run: pip install tox | |
| - name: Lint | |
| run: tox -e lint | |
| package-checks: | |
| strategy: | |
| matrix: | |
| tox_env: | |
| - twine_check | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v2.3.4 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v2.2.1 | |
| with: | |
| python-version: 3.8 | |
| - name: Install tox and upgrade setuptools and pip | |
| run: pip install --upgrade tox setuptools pip | |
| - name: Run tox -e ${{ matrix.tox_env }} | |
| run: tox -e ${{ matrix.tox_env }} | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| python-version: | |
| - "3.8" | |
| - "3.9" | |
| - "3.10" | |
| - "3.11" | |
| os: ["ubuntu-latest"] | |
| include: | |
| - os: "macos-latest" | |
| python-version: 3.8 | |
| - os: "windows-latest" | |
| python-version: 3.8 | |
| steps: | |
| - uses: actions/checkout@v2.3.4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2.2.1 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install tox and upgrade setuptools | |
| run: pip install --upgrade tox setuptools | |
| - name: Run tests | |
| run: tox | |
| - name: Upload coverage report | |
| uses: codecov/codecov-action@v1 | |
| # test-arch: | |
| # if: startsWith(github.ref, 'refs/tags') || github.ref == 'refs/heads/develop' || github.ref == 'refs/heads/main' | |
| # runs-on: "ubuntu-latest" | |
| # needs: lint | |
| # strategy: | |
| # matrix: | |
| # distro: [ "ubuntu20.04" ] | |
| # arch: ["aarch64"] | |
| # steps: | |
| # - uses: actions/checkout@v2.3.4 | |
| # - uses: uraimo/run-on-arch-action@v2.0.9 | |
| # name: Build & run test | |
| # with: | |
| # arch: ${{ matrix.arch }} | |
| # distro: ${{ matrix.distro }} | |
| # install: | | |
| # apt-get update -q -y | |
| # apt-get install -q -y python3 python3-pip gcc | |
| # run: | | |
| # python3 -m pip install -U setuptools pip wheel tox | |
| # tox | |
| deploy: | |
| if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') | |
| runs-on: ${{ matrix.os }} | |
| needs: [lint, package-checks, test] | |
| strategy: | |
| matrix: | |
| os: | |
| - ubuntu-latest | |
| - macos-latest | |
| - windows-latest | |
| cibw_archs_linux: ["x86_64"] | |
| build_sdist: [true] | |
| # include: | |
| # - os: "ubuntu-latest" | |
| # cibw_archs_linux: "aarch64" | |
| steps: | |
| - uses: actions/checkout@v2.3.4 | |
| - uses: actions/setup-python@v2 | |
| name: Install Python | |
| - name: Install cibuildwheel twine wheel | |
| run: python -m pip install cibuildwheel twine wheel | |
| - name: Set up QEMU | |
| if: ${{runner.os == 'Linux' && matrix.cibw_archs_linux == 'aarch64'}} | |
| uses: docker/setup-qemu-action@v1.0.1 | |
| with: | |
| platforms: arm64 | |
| - name: Build wheels | |
| run: cibuildwheel --output-dir dist | |
| env: | |
| CIBW_SKIP: "*-win32 *-manylinux_i686 pp3*" # Skip 32 bit, pypy | |
| CIBW_ARCHS_LINUX: ${{ matrix.cibw_archs_linux }} | |
| # Fully test the build wheels again. | |
| CIBW_TEST_REQUIRES: "pytest" | |
| # Simple test that requires the project to be build correctly | |
| CIBW_TEST_COMMAND: >- | |
| pytest {project}/tests/ | |
| - name: Build sdist | |
| if: ${{runner.os == 'Linux' && matrix.cibw_archs_linux == 'x86_64'}} | |
| run: | | |
| pip install build | |
| python -m build --sdist | |
| - uses: actions/upload-artifact@v2 | |
| with: | |
| name: "dist" | |
| path: "dist/" | |
| - name: Publish package to TestPyPI | |
| # pypa/gh-action-pypi-publish@master does not work on OSX | |
| # Alpha, Beta and dev releases contain a - in the tag. | |
| if: contains(github.ref, '-') && startsWith(github.ref, 'refs/tags') | |
| run: twine upload --skip-existing --repository-url https://test.pypi.org/legacy/ dist/* | |
| env: | |
| TWINE_USERNAME: __token__ | |
| TWINE_PASSWORD: ${{ secrets.TEST_PYPI_API_TOKEN }} | |
| - name: Publish package to PyPI | |
| if: "!contains(github.ref, '-') && startsWith(github.ref, 'refs/tags')" | |
| run: twine upload --skip-existing dist/* | |
| env: | |
| TWINE_USERNAME: __token__ | |
| TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }} |