kalign/.github/workflows/cmake.yml at main · TimoLassmann/kalign · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
name: CMake

on:
  push:
    branches: [ "main", "python" ]
    paths:
      - 'lib/**'
      - 'src/**'
      - 'tests/**'
      - 'CMakeLists.txt'
      - '.github/workflows/cmake.yml'
  pull_request:
    branches: [ "main" ]
    paths:
      - 'lib/**'
      - 'src/**'
      - 'tests/**'
      - 'CMakeLists.txt'
      - '.github/workflows/cmake.yml'

jobs:
  build:
    name: Build C/C++ on ${{ matrix.os }}
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest, macos-latest]
        build_type: [Release, Debug]

    steps:
    - uses: actions/checkout@v4

    - name: Install dependencies (Ubuntu)
      if: runner.os == 'Linux'
      run: |
        sudo apt-get update
        sudo apt-get install -y libomp-dev cmake

    - name: Install dependencies (macOS)
      if: runner.os == 'macOS'
      run: |
        brew install --formula libomp cmake

    - name: Configure CMake
      run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{ matrix.build_type }}

    - name: Build
      run: cmake --build ${{github.workspace}}/build --config ${{ matrix.build_type }} --parallel 2

    - name: Test
      working-directory: ${{github.workspace}}/build
      run: ctest -C ${{ matrix.build_type }} --output-on-failure

    - name: Test kalign executable
      run: |
        # Create test input
        echo ">seq1" > test.fasta
        echo "ATCGATCGATCG" >> test.fasta
        echo ">seq2" >> test.fasta
        echo "ATCGTCGATCG" >> test.fasta
        echo ">seq3" >> test.fasta
        echo "ATCGATCATCG" >> test.fasta

        # Test kalign executable
        ./build/src/kalign -i test.fasta -o test_output.fasta

        # Verify output exists and is not empty
        if [ -f test_output.fasta ] && [ -s test_output.fasta ]; then
          echo "✓ kalign executable test passed"
        else
          echo "✗ kalign executable test failed"
          exit 1
        fi

  address-sanitizer:
    name: Address Sanitizer
    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v4

    - name: Install dependencies
      run: |
        sudo apt-get update
        sudo apt-get install -y libomp-dev cmake

    - name: Configure CMake with ASAN
      run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=ASAN

    - name: Build
      run: cmake --build ${{github.workspace}}/build --config ASAN --parallel 2

    - name: Test with ASAN
      working-directory: ${{github.workspace}}/build
      run: ctest -C ASAN --output-on-failure