DEP/BLD: try to install skbio via conda, not pip #518
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| # Based roughly on the main.yml and standalone.yml workflows in | |
| # https://github.com/biocore/empress/blob/master/.github/workflows/, | |
| # and on https://docs.github.com/en/actions/quickstart | |
| name: strainFlye CI | |
| on: [push, pull_request] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| # For now (https://github.com/alimanfoo/pysamstats/blob/master/setup.py), | |
| # it seems like pysamstats + pysam only works with Python 3.7 and lower. | |
| # Ideally we could un-pin this eventually -- I suspect pysamstats being | |
| # able to work with pysam 0.16 and up will remove this restriction. | |
| strategy: | |
| matrix: | |
| python-version: [3.6, 3.7] | |
| steps: | |
| # Updating from v2 to v3 to match, as of writing, | |
| # 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: strainflye | |
| environment-file: environment.yml | |
| python-version: ${{ matrix.python-version }} | |
| # We need to keep saying "run this command from within the 'strainflye' | |
| # conda environment", and we can do this easily by prefixing commands | |
| # with "conda run -n" (as done in EMPress' main.yml file, linked above). | |
| # I don't know of a more elegant way to do this; I do know that | |
| # installing everything into the "base" environment (as done in, e.g., | |
| # https://autobencoder.com/2020-08-24-conda-actions) would remove the | |
| # need to keep re-activating the strainflye environment, but it'd have | |
| # the effect of polluting the base environment (which is not ideal | |
| # practice, according to | |
| # https://github.com/marketplace/actions/setup-miniconda#environment-activation). | |
| - name: Install strainFlye (and pip dependencies) | |
| run: conda run -n strainflye pip install -e .[dev] | |
| - name: Run tests | |
| run: conda run -n strainflye make test | |
| - name: Check that the strainFlye CLI seems good | |
| run: conda run -n strainflye strainFlye | |
| - name: Lint and stylecheck | |
| run: conda run -n strainflye make stylecheck | |
| - name: Upload code coverage information to Codecov | |
| uses: codecov/codecov-action@v2 |