NeonTreeClassification/.github/workflows/ci.yml at main · GatorSense/NeonTreeClassification · 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
name: CI

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

jobs:
  test:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-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@v4
      with:
        python-version: ${{ matrix.python-version }}

    - name: Install uv
      run: pip install uv

    - name: Install dependencies
      run: |
        uv sync --extra dev --extra logging

    - name: Test imports
      run: |
        uv run python -c "
        import neon_tree_classification
        from neon_tree_classification import NeonCrownDataset
        from scripts.get_dataloaders import get_dataloaders
        print('All imports successful!')
        "

    - name: Run tests
      run: uv run pytest tests/ -v --tb=short

  test-with-processing:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4

    - name: Set up Python
      uses: actions/setup-python@v4
      with:
        python-version: '3.11'

    - name: Install R and development dependencies
      run: |
        sudo apt-get update
        sudo apt-get install -y r-base r-base-dev libtirpc-dev

    - name: Install uv
      run: pip install uv

    - name: Install all dependencies including processing
      run: |
        uv sync --all-extras

    - name: Test processing imports
      run: |
        uv run python -c "
        import neon_tree_classification
        from neon_tree_classification import NeonCrownDataset
        print('Core imports successful!')
        try:
          import rpy2
          print('Processing dependencies (rpy2) available!')
        except ImportError as e:
          print(f'Processing dependencies not available: {e}')
        "

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

    - name: Set up Python
      uses: actions/setup-python@v4
      with:
        python-version: '3.11'

    - name: Install uv
      run: pip install uv

    - name: Install dependencies
      run: |
        uv sync --extra dev

    - name: Check code formatting
      run: uv run black --check neon_tree_classification/ examples/ scripts/ tests/