[WIP] Support DOT inputs (and multigraphs); much improved boundary node splitting in pattern identification; add back frayed rope support; lots of other improvements #37
Workflow file for this run
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| # Based on | |
| # https://github.com/fedarko/strainFlye/blob/main/.github/workflows/main.yml | |
| name: MgSc Python CI | |
| on: [push, pull_request] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| # Gotta specify 3.10 as a string to avoid it being converted to 3.1: | |
| # https://github.com/actions/setup-python/issues/160, | |
| # https://github.com/fedarko/pyfastg/blob/master/.github/workflows/main.yml | |
| python-version: [3.6, 3.7, 3.8, 3.9, "3.10"] | |
| steps: | |
| # https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python | |
| - name: Check out code | |
| uses: actions/checkout@v3 | |
| # https://github.com/conda-incubator/setup-miniconda#example-3-other-options | |
| - name: Install conda dependencies | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: mgsc | |
| environment-file: environment.yml | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install MetagenomeScope (and its pip dependencies) | |
| run: conda run -n mgsc pip install -e .[dev] | |
| # I think later versions of black (e.g. 23.1) changed things in ways that | |
| # will cause this to fail. Since not all black versions support all | |
| # python versions, the easiest solution is to just only do stylechecking | |
| # when we're working with python 3.6. | |
| # See https://stackoverflow.com/q/73598359 re: "if" expressions here. | |
| - name: Lint and stylecheck the Python code | |
| if: ${{ matrix.python-version == 3.6 }} | |
| run: conda run -n mgsc make pystylecheck | |
| - name: Run Python tests | |
| run: conda run -n mgsc make pytest | |
| - name: Upload Python code coverage information to Codecov | |
| uses: codecov/codecov-action@v2 |