pytorch_connectomics/.github/workflows/tests.yml at master · zhangdjr/pytorch_connectomics · 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
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
name: Tests

on:
  push:
    branches: [ main, master, v2.0 ]
  pull_request:
    branches: [ main, master, v2.0 ]

jobs:
  test:
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest, macos-latest, windows-latest]
        python-version: ['3.11']

    steps:
    - uses: actions/checkout@v3

    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v4
      with:
        python-version: ${{ matrix.python-version }}

    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip
        pip install pytest pytest-cov
        pip install -e .

    - name: Validate tutorial configs
      run: |
        python scripts/validate_tutorial_configs.py

    - name: Run tests
      run: |
        pytest tests/ -v --cov=connectomics --cov-report=xml

    - name: Upload coverage to Codecov
      uses: codecov/codecov-action@v3
      with:
        file: ./coverage.xml
        flags: unittests
        name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}

  lint:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v3
      with:
        fetch-depth: 0

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

    - name: Install linters
      run: |
        python -m pip install --upgrade pip
        pip install black flake8 isort mypy

    - name: Collect changed Python files
      id: changed-py
      shell: bash
      run: |
        if [[ "${{ github.event_name }}" == "pull_request" ]]; then
          git fetch --no-tags --depth=1 origin "${{ github.base_ref }}"
          files=$(git diff --name-only --diff-filter=ACMRT "origin/${{ github.base_ref }}...HEAD" -- 'connectomics/**/*.py')
        else
          if git rev-parse --verify HEAD~1 >/dev/null 2>&1; then
            files=$(git diff --name-only --diff-filter=ACMRT HEAD~1..HEAD -- 'connectomics/**/*.py')
          else
            files=$(git ls-files 'connectomics/**/*.py')
          fi
        fi

        echo "files<<EOF" >> "$GITHUB_OUTPUT"
        echo "$files" >> "$GITHUB_OUTPUT"
        echo "EOF" >> "$GITHUB_OUTPUT"

    - name: Run black
      env:
        CHANGED_FILES: ${{ steps.changed-py.outputs.files }}
      run: |
        python - <<'PY'
        import os
        import subprocess
        import sys

        files = [f for f in os.environ.get("CHANGED_FILES", "").splitlines() if f]
        if not files:
            print("No changed Python files under connectomics/. Skipping black.")
            sys.exit(0)

        subprocess.check_call(["black", "--check", *files])
        PY

    - name: Run flake8
      env:
        CHANGED_FILES: ${{ steps.changed-py.outputs.files }}
      run: |
        python - <<'PY'
        import os
        import subprocess
        import sys

        files = [f for f in os.environ.get("CHANGED_FILES", "").splitlines() if f]
        if not files:
            print("No changed Python files under connectomics/. Skipping flake8.")
            sys.exit(0)

        subprocess.check_call(["flake8", "--max-line-length=100", *files])
        PY

    - name: Run isort
      env:
        CHANGED_FILES: ${{ steps.changed-py.outputs.files }}
      run: |
        python - <<'PY'
        import os
        import subprocess
        import sys

        files = [f for f in os.environ.get("CHANGED_FILES", "").splitlines() if f]
        if not files:
            print("No changed Python files under connectomics/. Skipping isort.")
            sys.exit(0)

        subprocess.check_call(["isort", "--check", *files])
        PY

    - name: Run mypy
      env:
        CHANGED_FILES: ${{ steps.changed-py.outputs.files }}
      run: |
        python - <<'PY'
        import os
        import subprocess
        import sys

        files = [f for f in os.environ.get("CHANGED_FILES", "").splitlines() if f]
        if not files:
            print("No changed Python files under connectomics/. Skipping mypy.")
            sys.exit(0)

        subprocess.check_call(["mypy", "--config-file", ".github/mypy_changed.ini", *files])
        PY