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Update test.yml
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‎.github/workflows/test.yml‎

Lines changed: 105 additions & 75 deletions
Original file line numberDiff line numberDiff line change
@@ -13,82 +13,112 @@ jobs:
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linux:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python 3.10
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uses: actions/setup-python@v5
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with:
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python-version: 3.10
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install wheel pytest
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pip install .[deepcell,astir]
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- name: Test with pytest
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run: |
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# Test package
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python -m pytest imc/
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# Run pipeline
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mkdir -p imctest
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cd imctest
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imc process https://zenodo.org/record/5018260/files/COVID19_brain_Patient03_ROI3_COVID19_olfactorybulb.txt?download=1
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# List output files
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ls -l processed/
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ls -l processed/${SAMPLE}
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ls -l results/phenotyping
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- name: Cache resources
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id: cache-resources
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uses: actions/cache@v4
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with:
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path: /home/$USER/.imc
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key: imc-resources-linux
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- uses: actions/checkout@v4
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- name: Set up Python 3.10
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uses: actions/setup-python@v5
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with:
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python-version: '3.10'
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- name: Cache pip packages
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uses: actions/cache@v4
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with:
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path: ~/.cache/pip
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key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip setuptools wheel
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# Core scientific stack (pin to stable, binary-available builds)
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pip install "numpy<2.0" "scipy>=1.11,<1.16" "pandas>=2.0,<3.0" "matplotlib>=3.7,<3.11" \
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"scikit-image==0.19.3" "tifffile==2021.11.2" "networkx>=2.6,<3.0" \
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"seaborn>=0.13,<0.14" "fastcluster==1.2.6"
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# Core dependencies for IMC and ecosystem
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pip install "imctools>=2.1.8" "joblib>=1.2,<1.6" "leidenalg>=0.10.2" \
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"python-louvain>=0.16" "scanpy>=1.9,<1.12" "bbknn>=1.6" \
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"numpy-groupies>=0.9,<0.12" "parmap>=1.6,<2.0" \
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"seaborn-extensions>=0.2.1" "outdated>=0.2.2" "ordered-set>=4.1.0" "urlpath>=1.2.0" "PyYAML>=6.0"
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# Optional backends used in your environment
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pip install "astir==0.1.5" "DeepCell==0.12.6"
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# Finally install your package
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pip install -e .
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- name: Test with pytest
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run: |
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# Test package
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python -m pytest imc/
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# Run pipeline
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mkdir -p imctest
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cd imctest
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imc process https://zenodo.org/record/5018260/files/COVID19_brain_Patient03_ROI3_COVID19_olfactorybulb.txt?download=1
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# List output files
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ls -l processed/
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ls -l results/phenotyping
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- name: Cache resources
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id: cache-resources
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uses: actions/cache@v4
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with:
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path: /home/$USER/.imc
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key: imc-resources-linux
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osx:
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runs-on: macos-latest
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python 3.10
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uses: actions/setup-python@v5
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with:
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python-version: 3.10
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip setuptools wheel
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# Core scientific stack (pin to stable, binary-available builds)
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pip install "numpy<2.0" "scipy>=1.11,<1.16" "pandas>=2.0,<3.0" "matplotlib>=3.7,<3.11" \
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"scikit-image==0.19.3" "tifffile==2021.11.2" "networkx>=2.6,<3.0" \
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"seaborn>=0.13,<0.14" "fastcluster==1.2.6"
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# Core dependencies for IMC and ecosystem
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pip install "imctools>=2.1.8" "joblib>=1.2,<1.6" "leidenalg>=0.10.2" \
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"python-louvain>=0.16" "scanpy>=1.9,<1.12" "bbknn>=1.6" \
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"numpy-groupies>=0.9,<0.12" "parmap>=1.6,<2.0" \
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"seaborn-extensions>=0.2.1" "outdated>=0.2.2" "ordered-set>=4.1.0" "urlpath>=1.2.0" "PyYAML>=6.0"
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# Optional backends used in your environment
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pip install "astir==0.1.5" "DeepCell==0.12.6"
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# Finally install your package
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pip install -e .
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- name: Test with pytest
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run: |
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# Test package
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python -m pytest imc/
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# Run example processing pipeline
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mkdir -p imctest
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cd imctest
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imc process https://zenodo.org/record/5018260/files/COVID19_brain_Patient03_ROI3_COVID19_olfactorybulb.txt?download=1
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# List output files
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ls -l processed/
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ls -l processed/${SAMPLE}
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ls -l results/phenotyping
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- name: Cache resources
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id: cache-resources
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uses: actions/cache@v4
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with:
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path: /home/$USER/.imc
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key: imc-resources-osx
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- uses: actions/checkout@v4
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- name: Set up Python 3.10
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uses: actions/setup-python@v5
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with:
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python-version: '3.10'
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- name: Cache pip packages
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uses: actions/cache@v4
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with:
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path: ~/Library/Caches/pip
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key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip setuptools wheel
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# Core scientific stack
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pip install "numpy<2.0" "scipy>=1.11,<1.16" "pandas>=2.0,<3.0" "matplotlib>=3.7,<3.11" \
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"scikit-image==0.19.3" "tifffile==2021.11.2" "networkx>=2.6,<3.0" \
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"seaborn>=0.13,<0.14" "fastcluster==1.2.6"
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# Core dependencies for IMC and ecosystem
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pip install "imctools>=2.1.8" "joblib>=1.2,<1.6" "leidenalg>=0.10.2" \
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"python-louvain>=0.16" "scanpy>=1.9,<1.12" "bbknn>=1.6" \
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"numpy-groupies>=0.9,<0.12" "parmap>=1.6,<2.0" \
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"seaborn-extensions>=0.2.1" "outdated>=0.2.2" "ordered-set>=4.1.0" "urlpath>=1.2.0" "PyYAML>=6.0"
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pip install "astir==0.1.5" "DeepCell==0.12.6"
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pip install -e .
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- name: Test with pytest
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run: |
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# Test package
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python -m pytest imc/
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# Run example processing pipeline
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mkdir -p imctest
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cd imctest
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imc process https://zenodo.org/record/5018260/files/COVID19_brain_Patient03_ROI3_COVID19_olfactorybulb.txt?download=1
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# List output files
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ls -l processed/
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ls -l results/phenotyping
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- name: Cache resources
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id: cache-resources
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uses: actions/cache@v4
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with:
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path: /Users/runner/.imc
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key: imc-resources-osx

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