[pre-commit.ci] auto fixes from pre-commit.com hooks #568
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| name: Testing Python | |
| on: | |
| workflow_call: | |
| pull_request: | |
| push: | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: [3.8, 3.9, "3.10", 3.11, 3.12] | |
| fail-fast: false | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: "pip" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install ./taxoniumtools | |
| - name: Download test files | |
| run: | | |
| wget -q https://github.com/theosanderson/taxonium/raw/master/taxoniumtools/test_data/tfci.meta.tsv.gz | |
| wget -q https://raw.githubusercontent.com/theosanderson/taxonium/master/taxoniumtools/test_data/hu1.gb | |
| wget -q https://github.com/theosanderson/taxonium/raw/master/taxoniumtools/test_data/tfci.pb | |
| wget -q https://github.com/theosanderson/taxonium/raw/master/taxoniumtools/test_data/test_config.json | |
| wget -q https://github.com/theosanderson/taxonium/raw/master/taxoniumtools/test_data/test.nwk | |
| - name: Basic test | |
| run: | | |
| usher_to_taxonium \ | |
| --input tfci.pb \ | |
| --output tfci-taxonium.jsonl.gz \ | |
| --metadata tfci.meta.tsv.gz \ | |
| --genbank hu1.gb \ | |
| --columns genbank_accession,country,date,pangolin_lineage \ | |
| --clade_types nextstrain,pango | |
| - name: Upload basic test artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: tfci-taxonium-${{ matrix.python-version }} | |
| path: tfci-taxonium.jsonl.gz | |
| compression-level: 9 | |
| overwrite: true | |
| retention-days: 5 | |
| - name: Test with chronumental | |
| run: | | |
| pip install chronumental | |
| usher_to_taxonium \ | |
| --input tfci.pb \ | |
| --output tfci-taxonium-chron.jsonl.gz \ | |
| --metadata tfci.meta.tsv.gz \ | |
| --genbank hu1.gb \ | |
| --columns genbank_accession,country,date,pangolin_lineage \ | |
| --chronumental \ | |
| --chronumental_steps 300 \ | |
| --clade_types nextstrain,pango | |
| - name: Upload chronumental test artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: tfci-taxonium-chron-${{ matrix.python-version }} | |
| path: tfci-taxonium-chron.jsonl.gz | |
| compression-level: 9 | |
| overwrite: true | |
| retention-days: 5 | |
| - name: Test with config | |
| run: | | |
| usher_to_taxonium \ | |
| --input tfci.pb \ | |
| --output tfci-taxonium-config.jsonl.gz \ | |
| --metadata tfci.meta.tsv.gz \ | |
| --genbank hu1.gb \ | |
| --columns genbank_accession,country,date,pangolin_lineage \ | |
| --config_json test_config.json \ | |
| --name_internal_nodes | |
| - name: Upload config test artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: tfci-taxonium-config-${{ matrix.python-version }} | |
| path: tfci-taxonium-config.jsonl.gz | |
| compression-level: 9 | |
| overwrite: true | |
| retention-days: 5 | |
| - name: Test no genbank, no metadata | |
| run: | | |
| usher_to_taxonium \ | |
| --input tfci.pb \ | |
| --output tfci-bare.jsonl.gz | |
| - name: Test only variable sites | |
| run: | | |
| usher_to_taxonium \ | |
| --input tfci.pb \ | |
| --output tfci-var.jsonl.gz \ | |
| --only_variable_sites \ | |
| --metadata tfci.meta.tsv.gz \ | |
| --genbank hu1.gb \ | |
| --columns genbank_accession,country,date,pangolin_lineage | |
| - name: Upload variable sites test artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: tfci-var-${{ matrix.python-version }} | |
| path: tfci-var.jsonl.gz | |
| compression-level: 9 | |
| overwrite: true | |
| retention-days: 5 | |
| - name: Basic test, nwk | |
| run: | | |
| newick_to_taxonium \ | |
| --input test.nwk \ | |
| --output nwk.jsonl.gz | |
| - name: Upload newick test artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: nwk-${{ matrix.python-version }} | |
| path: nwk.jsonl.gz | |
| compression-level: 9 | |
| overwrite: true | |
| retention-days: 5 | |
| - name: Report test status | |
| uses: LouisBrunner/[email protected] | |
| if: always() | |
| with: | |
| token: ${{ secrets.GITHUB_TOKEN }} | |
| name: Python ${{ matrix.python-version }} tests | |
| conclusion: ${{ job.status }} |