Update test.yml #102
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| # 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 | |
| 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 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.10 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install wheel pytest | |
| pip install .[deepcell,astir] | |
| - name: Test with pytest | |
| run: | | |
| # Test package | |
| python -m pytest imc/ | |
| # Run pipeline | |
| mkdir -p imctest | |
| cd imctest | |
| imc process https://zenodo.org/record/5018260/files/COVID19_brain_Patient03_ROI3_COVID19_olfactorybulb.txt?download=1 | |
| # List output files | |
| ls -l processed/ | |
| ls -l processed/${SAMPLE} | |
| ls -l results/phenotyping | |
| - name: Cache resources | |
| id: cache-resources | |
| uses: actions/cache@v4 | |
| with: | |
| path: /home/$USER/.imc | |
| key: imc-resources-linux | |
| osx: | |
| runs-on: macos-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.10 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip setuptools wheel | |
| # Core scientific stack (pin to stable, binary-available builds) | |
| 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==2021.11.2" "networkx>=2.6,<3.0" \ | |
| "seaborn>=0.13,<0.14" "fastcluster==1.2.6" | |
| # Core dependencies for IMC and ecosystem | |
| 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>=0.2.1" "outdated>=0.2.2" "ordered-set>=4.1.0" "urlpath>=1.2.0" "PyYAML>=6.0" | |
| # Optional backends used in your environment | |
| pip install "astir==0.1.5" "DeepCell==0.12.6" | |
| # Finally install your package | |
| pip install -e . | |
| - name: Test with pytest | |
| run: | | |
| # Test package | |
| python -m pytest imc/ | |
| # Run example processing pipeline | |
| mkdir -p imctest | |
| cd imctest | |
| imc process https://zenodo.org/record/5018260/files/COVID19_brain_Patient03_ROI3_COVID19_olfactorybulb.txt?download=1 | |
| # List output files | |
| ls -l processed/ | |
| ls -l processed/${SAMPLE} | |
| ls -l results/phenotyping | |
| - name: Cache resources | |
| id: cache-resources | |
| uses: actions/cache@v4 | |
| with: | |
| path: /home/$USER/.imc | |
| key: imc-resources-osx |