training-resources/.github/workflows/test-python-scripts.yml at master · NEUBIAS/training-resources · 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
name: test-python-scripts

on:
  push:
    branches:
      - gh-pages
      - master
  pull_request:

jobs:
  test-python-all-platforms:
    strategy:
      fail-fast: false
      matrix:
        os: [macos-latest, ubuntu-latest]
    runs-on: ${{ matrix.os }}
    steps:
      - uses: actions/checkout@v4
      - name: install xvfb/deps
        if: matrix.os == 'ubuntu-latest'
        run: |
          sudo apt-get update
          sudo apt-get install -yy mesa-utils libgl1-mesa-dev xvfb curl
      - uses: conda-incubator/setup-miniconda@v3
        with:
          auto-update-conda: true
          activate-environment: test
          channel-priority: strict
          miniforge-version: latest
          conda-remove-defaults: "true"
      - name: install common conda dependencies
        run: conda install -n test -c conda-forge -c euro-bioimaging python=3.12 napari=0.6.6 pyqt pytest notebook matplotlib jupytext "scikit-image>=0.20" openijtiff -y
      - name: linux test
        if: matrix.os == 'ubuntu-latest'
        shell: bash -l {0}
        run: xvfb-run --server-args="-screen 0 1024x768x24" conda run -n test pytest -vv test_python/test_all_platforms.py
      - name: osx test
        if: matrix.os == 'macos-latest'
        shell: bash -l {0}
        run: conda run -n test pytest -vv test_python/test_all_platforms.py
      - name: windows test
        if: matrix.os == 'windows-latest'
        shell: cmd /C CALL {0}
        run: conda run -n test pytest -vv test_python/test_all_platforms.py

  test-python-unix: # Fails because lacking download capability
    # This will prevent it from running on any standard event
    if: github.event_name == 'none'
    strategy:
      fail-fast: false
      matrix:
        os: [macos-latest, ubuntu-latest]
    runs-on: ${{ matrix.os }}
    steps:
      - uses: actions/checkout@v4
      - name: install xvfb/deps
        if: matrix.os == 'ubuntu-latest'
        run: |
          sudo apt-get update
          sudo apt-get install -yy mesa-utils libgl1-mesa-dev xvfb curl
      - uses: conda-incubator/setup-miniconda@v3
        with:
          auto-update-conda: true
          activate-environment: test
          channel-priority: strict
          miniforge-version: latest
          environment-file: _includes/tool_installation/image_data_formats_conda_env.yml
          conda-remove-defaults: "true"
      - name: install common conda dependencies
        run: conda install -n test -c conda-forge pytest -y
      - name: linux test
        if: matrix.os == 'ubuntu-latest'
        shell: bash -l {0}
        run: xvfb-run --server-args="-screen 0 1024x768x24" conda run -n test pytest -v test_python/test_unix.py
      - name: osx test
        if: matrix.os == 'macos-latest'
        shell: bash -l {0}
        run: conda run -n test pytest -v test_python/test_unix.py