ci.yml

name: CI

on: [push, pull_request]

defaults:
  run:
    shell: bash  # For -o pipefail

jobs:
  lint:
    # Run for PRs only if they come from a forked repo (avoids duplicate runs)
    if: >-
      github.event_name != 'pull_request' ||
      github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - name: Check for tab characters
        run: "! grep -P -R '\\t' src/ tests/*.{cpp,py}"

  build:
    if: >-
      github.event_name != 'pull_request' ||
      github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest, macos-latest]
    steps:
      - uses: actions/checkout@v4
      - name: Build
        run: |
          cmake -B build -DCMAKE_BUILD_TYPE=RelWithDebInfo
          cd build
          make -j3
          make install
      - name: Install Linux dependencies
        if: runner.os == 'Linux'
        run: sudo apt-get install samtools
      - name: Install macOS dependencies
        if: runner.os == 'macOS'
        run: brew install samtools
      - name: Run
        run: tests/run.sh

  pythonbindings:
    if: >-
      github.event_name != 'pull_request' ||
      github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: "3.10"
      - name: Install Python dependencies
        run: pip install pytest
      - name: Install Python bindings
        run: pip install .
      - name: Run tests
        run: pytest tests

  compare:
    if: >-
      github.event_name != 'pull_request' ||
      github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0  # Baseline comparison needs older commits
      - name: Install Linux dependencies
        if: runner.os == 'Linux'
        run: sudo apt-get install samtools python3-pysam picard-tools
      - name: Install macOS dependencies
        if: runner.os == 'macOS'
        run: brew install samtools pysam picard-tools
      - name: Cache test dataset
        uses: actions/cache@v4
        with:
          key: test-data-${{ hashFiles('tests/download.sh') }}
          path: tests/drosophila/
      - name: Cache baseline BAM
        id: cache-baseline-bam
        uses: actions/cache@v4
        with:
          key: baseline-bam-${{ hashFiles('tests/baseline-commit.txt') }}
          path: baseline/bam/
      - name: Compare to baseline
        run: tests/compare-baseline.sh
      - name: Validate with Picard
        run: |
          PicardCommandLine ValidateSamFile IGNORE=RECORD_MISSING_READ_GROUP IGNORE=MISSING_READ_GROUP I=head.bam