votuderep/.github/workflows/test.yml at main · quadram-institute-bioscience/votuderep · 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
97
98
name: Test

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

jobs:
  lint:
    name: Lint
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.11"
          cache: 'pip'

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install black ruff

      - name: Check formatting with black
        run: black --check src/ tests/

      - name: Lint with ruff
        run: ruff check src/ tests/

  test:
    name: Test Python ${{ matrix.python-version }} on ${{ matrix.os }}
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest, macos-latest]
        python-version: ["3.10", "3.11", "3.12"]

    steps:
      - uses: actions/checkout@v4

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
          cache: 'pip'

      - name: Install BLAST+ (Ubuntu)
        if: runner.os == 'Linux'
        run: |
          sudo apt-get update
          sudo apt-get install -y ncbi-blast+
          blastn -version

      - name: Install BLAST+ (macOS)
        if: runner.os == 'macOS'
        run: |
          brew install blast
          blastn -version

      - name: Install package and dependencies
        run: |
          python -m pip install --upgrade pip
          pip install -e ".[dev]"

      - name: Run tests with coverage
        run: |
          pytest --cov=votuderep --cov-report=xml --cov-report=term

      - name: Upload coverage to Codecov
        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.11'
        uses: codecov/codecov-action@v4
        with:
          file: ./coverage.xml
          fail_ci_if_error: false
          verbose: true

  test-install:
    name: Test installation
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4

      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: "3.11"

      - name: Test installation
        run: |
          python -m pip install --upgrade pip
          pip install .
          votuderep --version
          votuderep --help