test.yml

name: Test
on: [push, pull_request]

jobs:
  test:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2

      - name: Set up Python
        uses: actions/setup-python@v2
        with:
          python-version: '3.x'

      - name: Install R
        run: |
          sudo apt-get update
          sudo apt-get install -y r-base r-base-dev

      - name: Cache pip dependencies
        uses: actions/cache@v2
        with:
          path: ~/.cache/pip
          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
          restore-keys: |
            ${{ runner.os }}-pip-

      - name: Install Python dependencies
        run: |
          python -m pip install --upgrade pip
          pip install numpy scipy pandas pytest bitarray duckdb pyarrow rpy2

      - name: Download and install plink
        run: |
          PLINK_URL="https://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20231211.zip"
          wget -q $PLINK_URL -O plink_linux_x86_64.zip
          unzip plink_linux_x86_64.zip -d plink
          sudo mv plink/plink /usr/local/bin/
          rm -rf plink_linux_x86_64.zip plink

      - name: Run unit tests
        run: pytest tests/unit_tests_mr_link_2.py

      - name: Run integration tests
        run: pytest tests/integration_tests_mr_link_2.py