scilpy/.github/workflows/test.yml at master · scilus/scilpy · 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
name: Scilpy test suite

on:
  push:
    branches:
      - master
  pull_request:
    branches:
      - master
  merge_group:

concurrency:
  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true

env:
  MPLBACKEND: agg
  OPENBLAS_NUM_THREADS: 1
  PYTEST_XDIST_AUTO_NUM_WORKERS: 8

jobs:
  test:
    runs-on: scilus-large
    if: github.repository == 'scilus/scilpy'

    steps:
      - name: Checkout repository at merge
        uses: actions/checkout@v7

      - name: Fetch python version from repository
        id: python-selector
        run: |
          echo "python-version=$(head -1 .python-version)" >> $GITHUB_OUTPUT
          echo "C_INCLUDE_PATH=$pythonLocation/include/python$(head -1 .python-version):$C_INCLUDE_PATH" >> $GITHUB_ENV

      - name: Set up Python and uv for Scilpy
        uses: astral-sh/setup-uv@v8.2.0
        with:
          python-version: ${{ steps.python-selector.outputs.python-version }}
          activate-environment: true
          enable-cache: true

      - name: Install non-python dependencies
        run: |
          sudo apt-get update
          sudo apt-get install -y \
            build-essential \
            curl \
            git \
            libblas-dev \
            liblapack-dev \
            libfreetype6-dev \
            libdrm-dev \
            libgl1-mesa-dev \
            libosmesa6-dev \
            python3-dev \

      - name: stdlib checkout
        if: ${{ !contains(steps.python-selector.outputs.python-version, '3.12') }}
        run: |
          echo "SETUPTOOLS_USE_DISTUTILS=stdlib" >> "$GITHUB_ENV"

      - name: Install Scilpy
        run: |
          uv pip install --upgrade pip wheel
          uv pip install --upgrade "setuptools<71.0.0"
          uv pip install -e .
          # TODO: to adapt once Scilpy passes to VTK 9.4.0, which selects OSMesa at runtime
          # https://discourse.vtk.org/t/status-update-runtime-opengl-render-window-selection-in-vtk/14583
          VTK_VERSION=$(cat pyproject.toml | grep 'vtk==' | sed 's/vtk==//g' | sed 's/\"//g' )
          pip install --extra-index-url https://wheels.vtk.org vtk-osmesa==$VTK_VERSION
          uv pip install pytest-xdist pytest-cov
          scil_data_download
          scil_search_keywords test --regenerate_help_files --processes 8

      - name: Run unit tests
        run: |
          uv run --active pytest src/scilpy --cov-report term-missing:skip-covered --dist=loadgroup --ignore=src/scilpy/cli
          mv .test_reports unit_test_reports

      - name: Run smoke tests
        run: |
          uv run --active pytest src/scilpy/cli --cov-report term-missing:skip-covered --dist=loadgroup
          mv .coverage .coverage.smoke
          mv .test_reports smoke_test_reports

      - name: Save test results and coverage
        uses: actions/upload-artifact@v7
        id: test-coverage-results
        with:
          name: test-coverage-${{ github.run_id }}
          retention-days: 1
          include-hidden-files: true
          path: |
            unit_test_reports/
            smoke_test_reports/

  coverage:
    runs-on: ubuntu-latest
    if: github.repository == 'scilus/scilpy'
    needs: test

    steps:
      - name: Checkout repository at merge
        uses: actions/checkout@v7

      - name: Download test results and coverage
        uses: actions/download-artifact@v8
        with:
          name: test-coverage-${{ github.run_id }}

      - name: Upload coverage reports to Codecov
        uses: codecov/codecov-action@v7.0.0
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          files: unit_test_reports/*
          disable_search: true
          flags: unittests
          name: scilpy-tests-${{ github.run_id }}-${{ github.run_attempt }}
          verbose: true
          fail_ci_if_error: true

      - name: Upload coverage reports to Codecov
        uses: codecov/codecov-action@v7.0.0
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          files: smoke_test_reports/*
          disable_search: true
          flags: smoketests
          name: scilpy-tests-${{ github.run_id }}-${{ github.run_attempt }}
          verbose: true
          fail_ci_if_error: true