Merge pull request #464 from Dana-Farber-AIOS/pydicom_update

Pydicom update

Author: jamesgwen

.github/workflows/publish-to-pypi.yml

@@ -13,10 +13,10 @@ jobs:
       - name: Checkout Code
         uses: actions/checkout@v4
 
-      - name: Set Up Python 3.9
+      - name: Set Up Python 3.10
         uses: actions/setup-python@v5
         with:
-          python-version: '3.9'
+          python-version: '3.10'
 
       - name: Install Build Tool
         run: pip install --upgrade build

.github/workflows/tests-linux.yml

@@ -18,7 +18,7 @@ jobs:
       # Limit concurrency to reduce memory pressure
       max-parallel: 2
       matrix:
-        python-version: ["3.9", "3.10"]
+        python-version: ["3.10", "3.11", "3.12"]
     timeout-minutes: 60
 
     steps:
@@ -69,7 +69,7 @@ jobs:
 
       - name: Install lightweight torchvision
         shell: bash -l {0}
-        run: pip install torchvision==0.14.1 --no-cache-dir
+        run: pip install torchvision==0.23.0 --no-cache-dir
 
       - name: Aggressive disk cleanup
         run: |
@@ -85,7 +85,7 @@ jobs:
         shell: bash -l {0}
         run: |
           micromamba activate pathml
-          pip install "numpy==1.23.5" "coverage<7.3" "numba==0.59.1" --force-reinstall --no-cache-dir
+          pip install "numpy>=1.26,<2" "coverage>=7.4,<8" "numba>=0.60,<0.62" --force-reinstall --no-cache-dir
           python -m coverage --version
           python -c "import numba; print('Numba version:', numba.__version__)"
 

.github/workflows/tests-macos.yml

@@ -17,7 +17,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [macos-latest]
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
       - uses: actions/checkout@v2
@@ -57,15 +57,15 @@ jobs:
 
       - name: Install torchvision
         shell: bash -l {0}
-        run: pip install torchvision==0.14.1
+        run: pip install torchvision==0.23.0
 
       - name: Fix coverage-numba incompatibility
         shell: bash -l {0}
         run: |
-            micromamba activate pathml
-            pip install "numpy==1.23.5" "coverage<7.3" "numba==0.59.1" --force-reinstall
-            python -m coverage --version
-            python -c "import numba; print('Numba version:', numba.__version__)"           
+          micromamba activate pathml
+          pip install "numpy>=1.26,<2" "coverage>=7.4,<8" "numba>=0.60,<0.62" --force-reinstall --no-cache-dir
+          python -m coverage --version
+          python -c "import numba; print('Numba version:', numba.__version__)"        
 
       - name: Test other modules with pytest and generate coverage
         shell: bash -l {0}

.github/workflows/tests-windows.yml

@@ -17,7 +17,7 @@ jobs:
     strategy:
       max-parallel: 5
       matrix:
-        python-version: [ "3.9", "3.10"]
+        python-version: ["3.10", "3.11", "3.12"]
     timeout-minutes: 120
 
     steps:
@@ -101,7 +101,7 @@ jobs:
 
       - name: Install torchvision
         shell: bash -l {0}
-        run: pip install torchvision==0.14.1
+        run: pip install torchvision==0.23.0
 
       - name: Set OPENSLIDE_PATH
         run: echo "OPENSLIDE_PATH=D:\a\pathml\pathml\openslide-binaries\openslide-win64-20231011\bin" >> $GITHUB_ENV
@@ -110,8 +110,8 @@ jobs:
       - name: Fix coverage-numba incompatibility
         shell: bash -l {0}
         run: |
-          micromamba activate pathml 
-          pip install "numpy==1.23.5" "coverage<7.3" "numba==0.59.1" --force-reinstall
+          micromamba activate pathml
+          pip install "numpy>=1.26,<2" "coverage>=7.4,<8" "numba>=0.60,<0.62" --force-reinstall --no-cache-dir
           python -m coverage --version
           python -c "import numba; print('Numba version:', numba.__version__)"
 

environment.yml

@@ -5,35 +5,35 @@ channels:
     - pytorch
 
 dependencies:
-    - python<=3.10
+    - python>=3.10
     - pip==25.0.1
-    - numpy==1.23.5
-    - scipy<=1.11.4
+    - numpy>=1.26.4,<2
+    - scipy>=1.12,<2
     - scikit-image<=0.22.0
-    - matplotlib<=3.8.2
+    - matplotlib>=3.8.0
     - openjdk<=18.0.0
     - h5py==3.10.0
     - dask<=2023.12.1
-    - pydicom==2.4.4
+    - pydicom==3.0.2
     - pytest==7.4.3
     - pre-commit<=3.6.0
-    - coverage==7.2.7
+    - coverage==7.4.0
     - networkx<=3.2.1
     - pip:
         - -r requirements/requirements_torch.txt
         # - coverage==7.2.7
         - numba>=0.59
-        - python-bioformats==4.0.7
-        - python-javabridge==4.0.3
+        - python-bioformats==4.1.0
+        - python-javabridge==4.0.4
         - protobuf==3.20.3
         - onnx==1.17.0
-        - onnxruntime==1.16.3
+        - onnxruntime>=1.17.0,<1.18
         - opencv-contrib-python==4.8.1.78
         - openslide-python==1.3.1
         - scanpy==1.9.6
-        - anndata<=0.10.3
+        - anndata>=0.7.6,<=0.10.3,
         - tqdm==4.66.3
         - loguru==0.7.2
         - pandas<=2.1.4
         - torch-geometric==2.3.1
-        - jpype1==1.4.1
+        - jpype1>=1.5.0

pathml/_version.py

@@ -3,4 +3,4 @@
 License: GNU GPL 2.0
 """
 
-__version__ = "3.0.4"
+__version__ = "3.0.5"

pathml/datasets/datasets.py

@@ -132,21 +132,21 @@ def __getitem__(self, index):
 
         # Load cell graphs, tissue graphs and assignments if they are provided
         if self.cell_dir is not None:
-            cell_graph = torch.load(self.cell_graphs[index])
+            cell_graph = torch.load(self.cell_graphs[index], weights_only=False)
             if hasattr(cell_graph, "target"):
                 target = cell_graph["target"]
             else:
                 target = None
 
         if self.tissue_dir is not None:
-            tissue_graph = torch.load(self.tissue_graphs[index])
+            tissue_graph = torch.load(self.tissue_graphs[index], weights_only=False)
             if hasattr(tissue_graph, "target"):
                 target = tissue_graph["target"]
             else:
                 target = None
 
         if self.assign_dir is not None:
-            assignment = torch.load(self.assigns[index])
+            assignment = torch.load(self.assigns[index], weights_only=False)
 
         # Create pathml.graph.utils.HACTPairData object with prvided objects
         data = HACTPairData(

requirements/environment_docker.yml

@@ -5,34 +5,33 @@ channels:
     - pytorch
 
 dependencies:
-    - python>=3.9,<3.11
+    - python>=3.10,<=3.12
     - pip==25.0.1
-    - numpy==1.23.5
-    - scipy<=1.11.4
+    - numpy>=1.26.4,<2
+    - scipy>=1.12,<2
     - scikit-image<=0.22.0
-    - matplotlib<=3.8.2
+    - matplotlib>=3.8.0
     - openjdk<=18.0.0
     - h5py==3.10.0
     - dask<=2023.12.1
-    - pydicom==2.4.4
-    - coverage<7.3
+    - pydicom==3.0.2
     - pytest==7.4.3 
     - pre-commit<=3.6.0
-    - coverage==7.2.7
+    - coverage==7.4.0
     - networkx<=3.2.1
     - pip:
         - torch==2.6.0
-        - python-bioformats==4.0.7
-        - python-javabridge==4.0.3
+        - python-bioformats==4.1.0
+        - python-javabridge==4.0.4
         - protobuf==3.20.3
         - onnx==1.17.0
-        - onnxruntime==1.16.3
+        - onnxruntime>=1.17.0,<1.18
         - opencv-contrib-python==4.8.1.78
         - openslide-python==1.3.1
         - scanpy==1.9.6
-        - anndata<=0.10.3
+        - anndata>=0.7.6,<=0.10.3
         - tqdm==4.66.1
         - loguru==0.7.2
         - pandas<=2.1.4
         - torch-geometric==2.3.1
-        - jpype1==1.4.1
+        - jpype1>=1.5.0

requirements/environment_mac.yml

@@ -5,37 +5,37 @@ channels:
     - pytorch
 
 dependencies:
-    - python<=3.10
+    - python>=3.10
     - pip==23.3.2
-    - numpy==1.23.5
+    - numpy>=1.26.4,<2
     - python-javabridge==4.0.3
-    - scipy<=1.11.4
+    - scipy>=1.12,<2
     - scikit-image<=0.22.0
-    - matplotlib<=3.8.2
+    - matplotlib>=3.8.0
     - openjdk<=18.0.0
     - h5py==3.10.0
     - dask<=2023.12.1
-    - pydicom==2.4.4
+    - pydicom==3.0.2
     - pytest==7.4.3 
     - pre-commit<=3.6.0
-    - coverage==7.2.7
+    - coverage==7.4.0
     - networkx<=3.2.1
     - pip:
         # - coverage==7.2.7
         - numba>=0.59
         # - setuptools==58.2.0
         # - numpy==1.23.5
         - torch==2.8.0
-        - python-bioformats==4.0.7
+        - python-bioformats==4.1.0
         # - python-javabridge==4.0.3
         - protobuf==3.20.3
         - onnx==1.17.0
-        - onnxruntime==1.16.3
+        - onnxruntime>=1.17.0,<1.18
         - opencv-contrib-python==4.8.1.78
         - scanpy==1.9.6
-        - anndata<=0.10.3
+        - anndata>=0.7.6,<=0.10.3
         - tqdm==4.66.3
         - loguru==0.7.2
         - pandas<=2.1.4
         - torch-geometric==2.3.1
-        - jpype1==1.4.1
+        - jpype1>=1.5.0

requirements/environment_test.yml

@@ -5,36 +5,36 @@ channels:
     - pytorch
 
 dependencies:
-    - python<=3.10
+    - python>=3.10
     - pip==25.0.1
-    - numpy==1.23.5
-    - scipy<=1.11.4
+    - numpy>=1.26.4,<2
+    - scipy>=1.12,<2
     - scikit-image<=0.22.0
-    - matplotlib<=3.8.2
+    - matplotlib>=3.8.0
     - openjdk<=18.0.0
     # - pytorch==2.8.0
     - h5py==3.10.0
     - dask<=2023.12.1
-    - pydicom==2.4.4
+    - pydicom==3.0.2
     - pytest==7.4.3
     - pre-commit<=3.6.0
-    - coverage==7.2.7
+    - coverage==7.4.0
     - networkx<=3.2.1
     - pip:
         - -r ../requirements/requirements_torch.txt
         # - coverage==7.2.7
         - numba>=0.59
-        - python-bioformats==4.0.7
-        - python-javabridge==4.0.3
+        - python-bioformats==4.1.0
+        - python-javabridge==4.0.4
         - protobuf==3.20.3
         - onnx==1.17.0
-        - onnxruntime==1.16.3
+        - onnxruntime>=1.17.0,<1.18
         - opencv-contrib-python==4.8.1.78
         - openslide-python==1.3.1
         - scanpy==1.9.6
-        - anndata<=0.10.3
+        - anndata>=0.7.6,<=0.10.3
         - tqdm==4.66.3
         - loguru==0.7.2
         - pandas<=2.1.4
         - torch-geometric==2.3.1
-        - jpype1==1.4.1
+        - jpype1>=1.5.0