Update test.yml

Author: hangyinn

.github/workflows/test.yml

@@ -16,6 +16,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Set up Python 3.10
+        id: setup-python
         uses: actions/setup-python@v5
         with:
           python-version: '3.10'
@@ -28,41 +29,35 @@ jobs:
 
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip setuptools wheel
+          ${{ env.pythonLocation }}/bin/python -m pip install --upgrade pip setuptools wheel
+          ${{ env.pythonLocation }}/bin/python -m pip install pytest pytest-cov
 
-          # Core scientific stack (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 scientific stack
+          ${{ 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==2021.11.2 networkx>=2.6,<3.0 \
+              seaborn>=0.13,<0.14 fastcluster==1.2.6
 
-          # Core dependencies for IMC 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=0.2.1" "outdated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"
+          # Core dependencies
+          ${{ 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=0.2.0 outdated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
 
           # Optional backends
-          pip install "astir==0.1.5" "DeepCell==0.12.6"
+          ${{ env.pythonLocation }}/bin/pip install astir==0.1.5 DeepCell==0.12.6
 
-          # Install the local package
-          pip install -e .
+          ${{ env.pythonLocation }}/bin/pip install -e .
 
       - name: Test with pytest
         run: |
-          python -m pytest imc/
+          ${{ 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
 
-      - name: Cache resources
-        id: cache-resources
-        uses: actions/cache@v4
-        with:
-          path: /home/$USER/.imc
-          key: imc-resources-linux
 
   windows:
     runs-on: windows-latest
@@ -81,35 +76,38 @@ jobs:
           key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }}
 
       - name: Install dependencies
+        shell: bash
         run: |
           python -m pip install --upgrade pip setuptools wheel
-          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" \
-                "scikit-image==0.19.3" "tifffile==2021.11.2" "networkx>=2.6,<3.0" \
-                "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" "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"
-          pip install "astir==0.1.5" "DeepCell==0.12.6"
+          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==2021.11.2 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/
           mkdir imctest
           cd imctest
           imc process https://zenodo.org/record/5018260/files/COVID19_brain_Patient03_ROI3_COVID19_olfactorybulb.txt?download=1
-          dir processed
-          dir results\phenotyping
+          ls -l processed/
+          ls -l results/phenotyping
+
 
   osx:
     runs-on: macos-latest
     steps:
       - uses: actions/checkout@v4
 
       - name: Set up Python 3.9
+        id: setup-python
         uses: actions/setup-python@v5
         with:
           python-version: '3.9'
@@ -122,31 +120,26 @@ jobs:
 
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip setuptools wheel
-          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" \
-                "scikit-image==0.19.3" "tifffile==2021.11.2" "networkx>=2.6,<3.0" \
-                "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" "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"
-          pip install "astir==0.1.5" "DeepCell==0.12.6"
-          pip install -e .
+          ${{ 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==2021.11.2 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==0.1.1 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: |
-          python -m pytest imc/
+          ${{ 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
 
-      - name: Cache resources
-        id: cache-resources
-        uses: actions/cache@v4
-        with:
-          path: /Users/runner/.imc
-          key: imc-resources-osx