python-test.yml

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]

    steps:
      - uses: actions/checkout@v2
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v2
        with:
          python-version: ${{ matrix.python-version }}
      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install ./taxoniumtools
      - name: Download files
        run: |
          wget https://github.com/theosanderson/taxonium/raw/master/taxoniumtools/test_data/tfci.meta.tsv.gz
          wget https://raw.githubusercontent.com/theosanderson/taxonium/master/taxoniumtools/test_data/hu1.gb
          wget https://github.com/theosanderson/taxonium/raw/master/taxoniumtools/test_data/tfci.pb
          wget https://github.com/theosanderson/taxonium/raw/master/taxoniumtools/test_data/test_config.json
          wget 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
      - uses: actions/upload-artifact@v3
        with:
          name: tfci-taxonium
          path: tfci-taxonium.jsonl.gz
      - 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
      - uses: actions/upload-artifact@v3
        with:
          name: tfci-taxonium-chron
          path: tfci-taxonium-chron.jsonl.gz
      - 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
      - uses: actions/upload-artifact@v3
        with:
          name: tfci-taxonium-config
          path: tfci-taxonium-config.jsonl.gz
      - name: Test no genbank, no metadata
        run: |
          usher_to_taxonium --input tfci.pb --output tfci-bare.jsonl.gz
      - name: Test only varaible 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
      - uses: actions/upload-artifact@v3
        with:
          name: tfci-var
          path: tfci-var.jsonl.gz
      - name: Basic test, nwk
        run: |
          newick_to_taxonium --input test.nwk --output nwk.jsonl.gz
      - uses: LouisBrunner/checks-action@v1.1.1
        if: always()
        with:
          token: ${{ secrets.GITHUB_TOKEN }}
          name: Python tests
          conclusion: ${{ job.status }}