Add JOSS paper and citations #70
Workflow file for this run
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| name: Run tests | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| jobs: | |
| run-tests: | |
| name: Run tests on ${{ matrix.os }} | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| shell: bash | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - { os: ubuntu-latest , opt_req: true } | |
| - { os: windows-latest, opt_req: false } | |
| - { os: macos-latest , opt_req: true } | |
| steps: | |
| - name: Cancel non-latest runs | |
| uses: styfle/[email protected] | |
| with: | |
| all_but_latest: true | |
| access_token: ${{ github.token }} | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.11' | |
| - 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 . # must install in editable mode for coverage to find sources | |
| python -m pip list | |
| - name: Run tests | |
| run: | | |
| pytest | |
| - name: Run GTNet Predict on Bins | |
| run: | | |
| gtnet predict data/small.fna > data/small.raw.test.csv | |
| python -c 'import pandas as pd; pd.testing.assert_frame_equal(pd.read_csv("data/small.raw.csv"), pd.read_csv("data/small.raw.test.csv"), check_exact=False, atol=1e-4)' | |
| - name: Run GTNet Filter on Bins | |
| run: | | |
| gtnet filter --fpr 0.05 data/small.raw.csv > data/small.tax.test.csv | |
| python -c 'import pandas as pd; pd.testing.assert_frame_equal(pd.read_csv("data/small.tax.0.05.csv"), pd.read_csv("data/small.tax.test.csv"), check_exact=False, atol=1e-4)' | |
| - name: Run GTNet Classify on Bins | |
| run: | | |
| gtnet classify --fpr 0.05 data/small.fna > data/small.tax.test.csv | |
| python -c 'import pandas as pd; pd.testing.assert_frame_equal(pd.read_csv("data/small.tax.0.05.csv"), pd.read_csv("data/small.tax.test.csv"), check_exact=False, atol=1e-4)' | |
| - name: Run GTNet Predict on Contigs | |
| run: | | |
| gtnet predict --seqs data/small.fna > data/small.seqs.raw.test.csv | |
| python -c 'import pandas as pd; pd.testing.assert_frame_equal(pd.read_csv("data/small.seqs.raw.csv"), pd.read_csv("data/small.seqs.raw.test.csv"), check_exact=False, atol=1e-4)' | |
| - name: Run GTNet Filter on Contigs | |
| run: | | |
| gtnet filter --fpr 0.05 data/small.seqs.raw.csv > data/small.seqs.tax.test.csv | |
| python -c 'import pandas as pd; pd.testing.assert_frame_equal(pd.read_csv("data/small.seqs.tax.0.05.csv"), pd.read_csv("data/small.seqs.tax.test.csv"), check_exact=False, atol=1e-4)' | |
| - name: Run GTNet Classify on Bins | |
| run: | | |
| gtnet classify --seqs --fpr 0.05 data/small.fna > data/small.seqs.tax.test.csv | |
| python -c 'import pandas as pd; pd.testing.assert_frame_equal(pd.read_csv("data/small.seqs.tax.0.05.csv"), pd.read_csv("data/small.seqs.tax.test.csv"), check_exact=False, atol=1e-4)' | |