scanpy/.github/workflows/ci.yml at 4d3580f7aca26e05a6632515ee020268fda75f45 · scverse/scanpy · 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
name: CI

on:
  push:
    branches:
      - main
      - "[0-9]+.[0-9]+.x"
  pull_request:

env:
  PYTEST_ADDOPTS: "-v --color=yes -n auto --internet-tests --junitxml=test-data/test-results.xml"
  PYTHONTRACEMALLOC: "20"
  FORCE_COLOR: "1"
  MPLBACKEND: agg
  UV_CONSTRAINT: ci/constraints.txt

defaults:
  run:
    shell: bash -e {0} # -e to fail on error

jobs:
  get-environments:
    runs-on: ubuntu-latest
    outputs:
      envs: ${{ steps.get-envs.outputs.envs }}
    steps:
      - uses: actions/checkout@v4
        with:
          filter: blob:none
          fetch-depth: 0
      - uses: astral-sh/setup-uv@v5
        with:
          enable-cache: false
      - id: get-envs
        run: |
          ENVS_JSON=$(NO_COLOR=1 uvx hatch env show --json | jq -c 'to_entries
            | map(
              select(.key | startswith("hatch-test"))
              | {
                name: .key,
                "test-type": (if (.key | test("pre|min")) then "coverage" else null end),
                python: .value.python | sub("3[.]13"; "3.13.3"),  # https://github.com/numba/numba/issues/10101
              }
            )')
          echo "envs=${ENVS_JSON}" | tee $GITHUB_OUTPUT

  test:
    needs: get-environments
    runs-on: ubuntu-latest
    strategy:
      matrix:
        env: ${{ fromJSON(needs.get-environments.outputs.envs) }}
    env:  # environment variable for use in codecov’s env_vars tagging
      ENV_NAME: ${{ matrix.env.name }}
    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0
          filter: blob:none

      - uses: astral-sh/setup-uv@v5
        with:
          enable-cache: true
          python-version: ${{ matrix.env.python }}
          cache-dependency-glob: pyproject.toml

      - name: Cache downloaded data
        uses: actions/cache@v4
        with:
          path: .pytest_cache/d/scanpy-data
          key: pytest

      - name: Install dependencies
        run: uvx hatch -v env create ${{ matrix.env.name }}

      - name: Run tests
        if: matrix.env.test-type == null
        run: uvx hatch run ${{ matrix.env.name }}:run
      - name: Run tests (coverage)
        if: matrix.env.test-type == 'coverage'
        run: uvx hatch run ${{ matrix.env.name }}:run-cov --cov --cov-report=xml

      - name: Upload coverage data
        uses: codecov/codecov-action@v5
        if: matrix.env.test-type == 'coverage'
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          env_vars: ENV_NAME
          fail_ci_if_error: true
          files: test-data/coverage.xml

      - name: Upload test results
        # yaml strings can’t start with “!”, so using explicit substitution
        if: ${{ !cancelled() }}
        uses: codecov/test-results-action@v1
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          env_vars: ENV_NAME
          fail_ci_if_error: true
          file: test-data/test-results.xml

      - name: Publish debug artifacts
        if: matrix.env.test-type == 'coverage'
        uses: actions/upload-artifact@v4
        with:
          name: debug-data-${{ matrix.env.name }}
          path: .pytest_cache/d/debug

  build:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0
          filter: blob:none
      - uses: actions/setup-python@v5
        with:
          python-version: "3.13"
      - uses: astral-sh/setup-uv@v5
        with:
          enable-cache: false
      - run: uvx --from build pyproject-build --sdist --wheel .
      - run: uvx twine check dist/*

  check:
    if: always()
    needs:
      - get-environments
      - test
      - build
    runs-on: ubuntu-latest
    steps:
        - uses: re-actors/alls-green@release/v1
          with:
            jobs: ${{ toJSON(needs) }}