Speed up (using mamba) and fix the CI; better installation documentation #525
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| # Based roughly on the main.yml and standalone.yml workflows in | |
| # https://github.com/biocore/empress/blob/master/.github/workflows/, | |
| # https://docs.github.com/en/actions/quickstart, and | |
| # https://github.com/fedarko/wotplot/blob/ce702b63bf790c41d02b0493e3a7eebda6fcec70/.github/workflows/main.yml | |
| # (which i based off of this file originally, so it's an ouroboros of me | |
| # copying code from myself because i can never remember how yaml works) | |
| 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/mamba-org/setup-micromamba | |
| - name: Install conda dependencies with mamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: environment.yml | |
| create-args: python=${{ matrix.python-version }} | |
| init-shell: bash | |
| - name: Install strainFlye (and pip dependencies) | |
| run: pip install -e .[dev] | |
| shell: bash -el {0} | |
| - name: Lint and stylecheck | |
| run: make stylecheck | |
| shell: bash -el {0} | |
| - name: Run tests | |
| run: make test | |
| shell: bash -el {0} | |
| - name: Check that the strainFlye CLI seems good | |
| run: strainFlye | |
| shell: bash -el {0} | |
| - name: Upload code coverage information to Codecov | |
| uses: codecov/codecov-action@v2 |