Himito/.github/workflows/ci.yml at d3b8e6b5481250949fc2b363fe80d573a576f461 · broadinstitute/Himito · GitHub

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name: CI

on:
  push:
    branches: [ main, master, develop ]
  pull_request:
    branches: [ main, master, develop ]
  workflow_dispatch:

permissions:
  contents: read

env:
  CARGO_TERM_COLOR: always
  RUST_BACKTRACE: 1

jobs:
  test:
    name: Test on ${{ matrix.os }}
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest, macos-latest]
        rust: [stable, beta]
        include:
          - os: ubuntu-latest
            rust: stable
            cache-key: linux-stable
          - os: macos-latest
            rust: stable
            cache-key: macos-stable

    steps:
      - name: Checkout code
        uses: actions/checkout@v4

      - name: Install system dependencies (Ubuntu)
        if: matrix.os == 'ubuntu-latest'
        run: |
          sudo apt-get update
          sudo apt-get install -y \
            libcurl4-openssl-dev \
            libssl-dev \
            zlib1g-dev \
            libbz2-dev \
            liblzma-dev \
            samtools \
            bcftools

      - name: Install system dependencies (macOS)
        if: matrix.os == 'macos-latest'
        run: |
          brew install samtools bcftools || true

      - name: Install Rust toolchain
        uses: dtolnay/rust-toolchain@stable
        with:
          toolchain: ${{ matrix.rust }}

      - name: Cache cargo registry
        uses: actions/cache@v4
        with:
          path: |
            ~/.cargo/bin/
            ~/.cargo/registry/index/
            ~/.cargo/registry/cache/
            ~/.cargo/git/db/
            target/
          key: ${{ runner.os }}-cargo-${{ matrix.cache-key }}-${{ hashFiles('**/Cargo.lock') }}
          restore-keys: |
            ${{ runner.os }}-cargo-${{ matrix.cache-key }}-

      - name: Build project
        run: cargo build --release --verbose

      - name: Test help command
        run: |
          cargo run --release -- --help || true
          cargo run --release -- quick-start --help || true
          cargo run --release -- filter --help || true
          cargo run --release -- build --help || true
          cargo run --release -- correct --help || true
          cargo run --release -- call --help || true
          cargo run --release -- asm --help || true
          cargo run --release -- methyl --help || true

  integration-test:
    name: Integration Test
    runs-on: ubuntu-latest
    needs: test

    steps:
      - name: Checkout code
        uses: actions/checkout@v4

      - name: Install system dependencies
        run: |
          sudo apt-get update
          sudo apt-get install -y \
            libcurl4-openssl-dev \
            libssl-dev \
            zlib1g-dev \
            libbz2-dev \
            liblzma-dev \
            samtools \
            bcftools

      - name: Install Rust toolchain
        uses: dtolnay/rust-toolchain@stable

      - name: Build project
        run: cargo build --release

      - name: Test Himito quick-start command
        run: |
          if [ -f "test_data/HG005_100x.bam" ] && [ -f "test_data/HG005_100x.bai" ]; then
            cargo run --release -- quick-start \
              -i test_data/HG005_100x.bam \
              -c "chrM" \
              -k 21 \
              --sampleid HG005 \
              -r test_data/rCRS.fasta \
              --output-prefix test_output/himito_test || echo "Himito test skipped - may require additional dependencies"
          else
            echo "Test data not available, skipping evaluate test"
          fi

      - name: Cleanup test outputs
        if: always()
        run: |
          rm -rf test_output test_data || true

  lint:
    name: Lint
    runs-on: ubuntu-latest

    steps:
      - name: Checkout code
        uses: actions/checkout@v4

      - name: Install Rust toolchain
        uses: dtolnay/rust-toolchain@stable

      - name: Check for common issues
        run: |
          # Check for unsafe code usage
          if grep -r "unsafe" src/ --include="*.rs" | grep -v "// SAFETY" | grep -v "unsafe {"; then
            echo "Warning: Found unsafe code without safety comments"
          fi