Merge branch 'develop' into multichannel-reading

Author: shaneahmed

.github/workflows/conda-env-create.yml

@@ -33,7 +33,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     timeout-minutes: 20
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Copy requirements files
         shell: bash
         run: |
@@ -48,3 +48,4 @@ jobs:
         run: |
           micromamba info
           micromamba list
+          python -c "import torch, numpy; print(torch.__version__, numpy.__version__)"

.github/workflows/mypy-type-check.yml

@@ -33,6 +33,7 @@ jobs:
         sudo apt update
         sudo apt-get install -y libopenslide-dev openslide-tools libopenjp2-7 libopenjp2-tools
         python -m pip install --upgrade pip
+        pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
         pip install -r requirements/requirements_dev.txt
 
     - name: Perform type checking

.github/workflows/pip-install.yml

@@ -55,6 +55,8 @@ jobs:
     - name: OpenJPEG Version Information
       continue-on-error: true  # This -h option has exit code 1 for some reason
       run: opj_dump -h
+    - name: Install CPU-only PyTorch
+      run: python -m pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
     - name: pip Install From GitHub Repo on Linux and macOS
       if: runner.os != 'Windows'
       run: python -m pip install git+https://github.com/TissueImageAnalytics/tiatoolbox@${GITHUB_SHA}

.github/workflows/python-package.yml

@@ -30,7 +30,8 @@ jobs:
         sudo apt update
         sudo apt-get install -y libopenjp2-7 libopenjp2-tools
         python -m pip install --upgrade pip
-        python -m pip install ruff==0.14.3 pytest pytest-cov pytest-runner
+        python -m pip install ruff==0.14.7 pytest pytest-cov pytest-runner
+        pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
         pip install -r requirements/requirements.txt
     - name: Cache tiatoolbox static assets
       uses: actions/cache@v4
@@ -107,6 +108,7 @@ jobs:
       run: |
         sudo apt-get install -y libopenslide-dev libopenjp2-7
         python -m pip install --upgrade pip
+        pip install torch torchvision --index-url https://download.pytorch.org/whl/cpu
         pip install -r requirements/requirements.txt
         pip install build
     - name: Build package

.pre-commit-config.yaml

@@ -60,7 +60,7 @@ repos:
       - id: rst-inline-touching-normal # Detect mistake of inline code touching normal text in rst.
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.14.3
+    rev: v0.14.7
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

requirements/requirements.txt

@@ -32,7 +32,7 @@ SimpleITK>=2.2.1
 sphinx>=5.3.0
 tifffile>=2022.10.10, <=2025.5.10
 timm>=1.0.3
-torch>=2.1.0
+torch>=2.5.0
 torchvision>=0.15.0
 tqdm>=4.64.1
 umap-learn>=0.5.3

requirements/requirements_dev.txt

@@ -10,7 +10,7 @@ pytest>=7.2.0
 pytest-cov>=4.0.0
 pytest-runner>=6.0
 pytest-xdist[psutil]
-ruff==0.14.3  # This will be updated by pre-commit bot to latest version
+ruff==0.14.7  # This will be updated by pre-commit bot to latest version
 toml>=0.10.2
 twine>=4.0.1
 wheel>=0.37.1