Update ipython and black minimum versions to fix security alerts #119
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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 | |
| # 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=0.2.0" "outdated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/ |