Add JOSS paper and citations #71
Workflow file for this run
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| name: Run code coverage | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| workflow_dispatch: | |
| jobs: | |
| run-coverage: | |
| name: ${{ matrix.os }}, opt reqs ${{ matrix.opt_req }} | |
| runs-on: ${{ matrix.os }} | |
| # TODO handle forks | |
| # run pipeline on either a push event or a PR event on a fork | |
| # if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name | |
| defaults: | |
| run: | |
| shell: bash | |
| strategy: | |
| matrix: | |
| include: | |
| - { os: ubuntu-latest , opt_req: true } | |
| - { os: windows-latest, opt_req: false } | |
| - { os: macos-latest , opt_req: false } | |
| env: # used by codecov-action | |
| OS: ${{ matrix.os }} | |
| PYTHON: '3.11' | |
| steps: | |
| - name: Cancel non-latest runs | |
| uses: styfle/[email protected] | |
| with: | |
| all_but_latest: true | |
| access_token: ${{ github.token }} | |
| - uses: actions/checkout@v3 | |
| with: | |
| submodules: 'recursive' | |
| fetch-depth: 0 # tags are required for versioneer to determine the version | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ env.PYTHON }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install -r requirements-dev.txt -r requirements.txt | |
| - name: Install package | |
| run: | | |
| python -m pip install -e . # must install in editable mode for coverage to find sources | |
| python -m pip list | |
| - name: Run tests and generate coverage report | |
| run: | | |
| pytest --cov | |
| gtnet predict data/small.fna > data/small.raw.test.csv | |
| gtnet filter --fpr 0.05 data/small.raw.csv > data/small.tax.test.csv | |
| gtnet classify --fpr 0.05 data/small.fna > data/small.tax.test.csv | |
| python -m coverage xml # codecov uploader requires xml format | |
| python -m coverage report -m | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| fail_ci_if_error: true |