added fix #20
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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 | |