main.yml

name: CI
on:
  push:
  pull_request:

jobs:
    ci:
        strategy:
          fail-fast: true
          matrix:
            python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
            os: [ubuntu-22.04] #, macos-latest, windows-latest]
        runs-on: ${{ matrix.os }}
        steps:
        - uses: actions/checkout@v3
        - uses: actions/setup-python@v4
          with:
            python-version: ${{ matrix.python-version }}
        - name: Test
          run: |
            PYTHONPATH=$(pwd) python example/filter_dp.py \
              --input_vcf tests/hc_subset.vcf.gz \
              --output_vcf tests/hc_subset_dp.vcf.gz
            if [ ! -f tests/hc_subset_dp.vcf.gz ]; then  exit 1; fi
            if [ ! -f tests/hc_subset_dp.vcf.gz.tbi ]; then   exit 1; fi
        - name: Test csi
          run: |
            rm tests/hc_subset.vcf.gz.tbi
            PYTHONPATH=$(pwd) VCF_INDEX_TYPE=2 python example/filter_dp.py \
              --input_vcf tests/hc_subset.vcf.gz \
              --output_vcf tests/hc_subset_dp.vcf.gz
            if [ ! -f tests/hc_subset_dp.vcf.gz ]; then   exit 1; fi
            if [ ! -f tests/hc_subset_dp.vcf.gz.csi ]; then   exit 1; fi