fix test db files #181
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| name: CI | |
| on: [push,pull_request] | |
| jobs: | |
| tests: | |
| name: "Python ${{ matrix.python-version }}" | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash -el {0} | |
| strategy: | |
| matrix: | |
| os: [macos-latest, ubuntu-latest] | |
| python-version: ["3.8", "3.9"] | |
| steps: | |
| - uses: "actions/checkout@v3" | |
| with: | |
| fetch-depth: 0 | |
| # Setup env | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: plassembler | |
| environment-file: build/environment.yaml | |
| python-version: ${{ matrix.python-version }} | |
| auto-activate-base: false | |
| miniforge-variant: Mambaforge | |
| channels: conda-forge,bioconda,defaults | |
| channel-priority: strict | |
| auto-update-conda: true | |
| - name: Install project | |
| shell: bash -l {0} | |
| run: | | |
| mamba install python=${{ matrix.python-version }} | |
| just install | |
| python -m pip install --upgrade pip | |
| pip3 install git+https://github.com/rrwick/Unicycler.git | |
| unicycler --help | |
| - name: Check formatting | |
| shell: bash -l {0} | |
| run: just check-fmt | |
| - name: Test and generate coverage report with pytest | |
| shell: bash -l {0} | |
| # need to set TERM to linux for some reason,kept getting a nasty error that was breaking unicycler | |
| # https://github.com/cypress-io/cypress/issues/15679 | |
| run: | | |
| export TERM=linux | |
| unicycler --version | |
| just test-ci | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/codecov-action@v3 | |