imc/.github/workflows/test.yml at main · ElementoLab/imc · 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
# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
# 10/31/2025 compatibility issue for MacOS: all DeepCell versions require TensorFlow 2.8.0, which is not available for macOS ARM64. Skipped optional deepcell backend for MacOS

name: Test imc package

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

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

      - name: Set up Python 3.10
        id: setup-python
        uses: actions/setup-python@v5
        with:
          python-version: '3.10'

      - name: Cache pip packages
        uses: actions/cache@v4
        with:
          path: ~/.cache/pip
          key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }}

      - name: Install dependencies
        run: |
          ${{ env.pythonLocation }}/bin/python -m pip install --upgrade pip setuptools wheel
          ${{ env.pythonLocation }}/bin/python -m pip install pytest pytest-cov
          ${{ env.pythonLocation }}/bin/pip install "numpy<2.0" "scipy>=1.11,<1.16" "pandas>=2.0,<3.0" "matplotlib>=3.7,<3.11" "scikit-image==0.19.3" "tifffile>=2025.5" "networkx>=2.6,<3.0" "seaborn>=0.13,<0.14" "fastcluster==1.2.6"
          ${{ env.pythonLocation }}/bin/pip install "imctools>=2.1.8" "joblib>=1.2,<1.6" "leidenalg>=0.10.2" "python-louvain>=0.16" "scanpy>=1.9,<1.12" "bbknn>=1.6" "numpy-groupies>=0.9,<0.12" "parmap>=1.6,<2.0" "seaborn-extensions>=0.2.0" "outdated>=0.2.2" "ordered-set>=4.1.0" "urlpath>=1.2.0" "PyYAML>=6.0"
          ${{ env.pythonLocation }}/bin/pip install "astir==0.1.5" "DeepCell==0.12.6"
          ${{ env.pythonLocation }}/bin/pip install -e .

      - name: Test with pytest
        run: |
          ${{ env.pythonLocation }}/bin/python -m pytest imc/
          mkdir -p imctest
          cd imctest
          imc process https://zenodo.org/record/5018260/files/COVID19_brain_Patient03_ROI3_COVID19_olfactorybulb.txt?download=1
          ls -l processed/
          ls -l results/phenotyping


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

      - name: Set up Python 3.10
        uses: actions/setup-python@v5
        with:
          python-version: '3.10'

      - name: Cache pip packages
        uses: actions/cache@v4
        with:
          path: ~\AppData\Local\pip\Cache
          key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }}

      - name: Install dependencies
        shell: bash
        run: |
          python -m pip install --upgrade pip setuptools wheel
          python -m pip install pytest pytest-cov
          pip install "numpy<2.0" "scipy>=1.11,<1.16" "pandas>=2.0,<3.0" "matplotlib>=3.7,<3.11"
          pip install "scikit-image==0.19.3" "tifffile>=2025.5" "networkx>=2.6,<3.0"
          pip install "seaborn>=0.13,<0.14" "fastcluster==1.2.6"
          pip install "imctools>=2.1.8" "joblib>=1.2,<1.6" "leidenalg>=0.10.2" "python-louvain>=0.16"
          pip install "scanpy>=1.9,<1.12" "bbknn>=1.6" "numpy-groupies>=0.9,<0.12" "parmap>=1.6,<2.0"
          pip install "seaborn-extensions>=0.2.0" "outdated>=0.2.2" "ordered-set>=4.1.0" "urlpath>=1.2.0" "PyYAML>=6.0"
          pip install "astir==0.1.5" "DeepCell==0.12.6"
          pip install -e .

      - name: Test with pytest
        shell: bash
        run: |
          python -m pytest imc/


  osx:
    runs-on: macos-latest
    steps:
      - uses: actions/checkout@v4

      - name: Set up Python 3.10
        id: setup-python
        uses: actions/setup-python@v5
        with:
          python-version: '3.10'

      - name: Install HDF5
        run: |
          brew install hdf5
          echo "HDF5_DIR=$(brew --prefix hdf5)" >> $GITHUB_ENV

      - name: Cache pip packages
        uses: actions/cache@v4
        with:
          path: ~/Library/Caches/pip
          key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }}

      - name: Install dependencies
        run: |
          ${{ env.pythonLocation }}/bin/python -m pip install --upgrade pip setuptools wheel
          ${{ env.pythonLocation }}/bin/python -m pip install pytest pytest-cov
          ${{ env.pythonLocation }}/bin/pip install "numpy<2.0" "scipy>=1.11,<1.16" "pandas>=2.0,<3.0" "matplotlib>=3.7,<3.11" "scikit-image==0.19.3" "tifffile>=2025.5" "networkx>=2.6,<3.0" "seaborn>=0.13,<0.14" "fastcluster==1.2.6"
          ${{ env.pythonLocation }}/bin/pip install "imctools>=2.1.8" "joblib>=1.2,<1.6" "leidenalg>=0.10.2" "python-louvain>=0.16" "scanpy>=1.9,<1.12" "bbknn>=1.6" "numpy-groupies>=0.9,<0.12" "parmap>=1.6,<2.0" "seaborn-extensions>=0.2.0" "outdated>=0.2.2" "ordered-set>=4.1.0" "urlpath>=1.2.0" "PyYAML>=6.0"
          ${{ env.pythonLocation }}/bin/pip install -e .

      - name: Test with pytest
        run: |
          ${{ env.pythonLocation }}/bin/python -m pytest imc/