Further CICD Cleanup

.github/workflows/cicd_tests.yml

@@ -56,7 +56,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        opt: ["codeformat", "pytype", "mypy"]
+        opt: ["codeformat", "mypy"]  #  "pytype" omitted for being essentially deprecated, see #8865
     steps:
     - name: Clean unused tools
       run: |
@@ -171,7 +171,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [windows-latest, macOS-latest, ubuntu-latest]
+        os: [windows-latest, ubuntu-latest]  # macOS-latest omitted for now for being very slow, see #8864
     timeout-minutes: 120
     env:
       QUICKTEST: True
@@ -220,7 +220,6 @@ jobs:
     - name: Install the complete dependencies
       run: |
         python -m pip install --user --upgrade pip wheel pybind11  # TODO: pybind11 added for macOS, may not be needed
-        #python -m pip install torch==${PYTORCH_VER1} torchvision==${TORCHVISION_VER1}
         cat "requirements-dev.txt"
         python -m pip install --no-build-isolation -r requirements-dev.txt
         python -m pip list
@@ -267,8 +266,8 @@ jobs:
         python -m pip install torch==${PYTORCH_VER1} torchvision --extra-index-url https://download.pytorch.org/whl/cpu
     - name: Check packages
       run: |
-        pip uninstall monai
-        pip list | grep -iv monai
+        python -m pip uninstall -y monai
+        python -m pip list | grep -iv monai
         git fetch --depth=1 origin +refs/tags/*:refs/tags/*
         set -e
 
@@ -306,12 +305,3 @@ jobs:
         python -m pip install ${name}[all] --extra-index-url https://download.pytorch.org/whl/cpu
         python -c 'import monai; monai.config.print_config()' 2>&1 | grep -iv "unknown"
         python -c 'import monai; print(monai.__file__)'
-    - name: Quick test
-      working-directory: ${{ steps.mktemp.outputs.tmp_dir }}
-      run: |
-        # run min tests
-        cp ${{ steps.root.outputs.pwd }}/requirements*.txt .
-        cp -r ${{ steps.root.outputs.pwd }}/tests .
-        ls -al
-        python -m pip install --no-build-isolation -r requirements-dev.txt --extra-index-url https://download.pytorch.org/whl/cpu
-        python -m unittest -v

.github/workflows/cron-ngc-bundle.yml

@@ -2,6 +2,9 @@
 name: cron-ngc-bundle
 
 on:
+  pull_request:
+    branches:
+      - dev  # temporary for testing in the PR
   schedule:
     - cron: "0 2 * * *"  # at 02:00 UTC
   # Allows you to run this workflow manually from the Actions tab
@@ -22,20 +25,15 @@ jobs:
       uses: actions/setup-python@v6
       with:
         python-version: '3.10'
-    - name: cache weekly timestamp
-      id: pip-cache
-      run: echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
-    - name: cache for pip
-      uses: actions/cache@v5
-      id: cache
-      with:
-        path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
+        cache: pip
+    - name: Install CPU PyTorch
+      run: |
+        python -m pip install torch==2.8.0 torchvision --extra-index-url https://download.pytorch.org/whl/cpu
     - name: Install dependencies
       run: |
         rm -rf /github/home/.cache/torch/hub/bundle/
-        python -m pip install --upgrade pip wheel
-        python -m pip install -r requirements-dev.txt
+        python -m pip install --no-build-isolation --upgrade pip wheel wheel-stub
+        python -m pip install --no-build-isolation -r requirements-dev.txt
     - name: Loading Bundles
       run: |
         # clean up temporary files

.github/workflows/release.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.11', '3.12', '3.13']
     steps:
     - uses: actions/checkout@v6
       with:

.github/workflows/setupapp.yml

@@ -45,7 +45,7 @@ jobs:
     - name: Install the dependencies
       run: |
         which python
-        python -m pip install --upgrade pip wheel
+        python -m pip install --upgrade pip wheel wheel-stub
         python -m pip install --upgrade torch torchvision
         python -m pip install -r requirements-dev.txt
     - name: Run unit tests report coverage
@@ -91,10 +91,13 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
         cache: pip
+    - name: Install CPU PyTorch
+      run: |
+        python -m pip install torch==2.8.0 torchvision --extra-index-url https://download.pytorch.org/whl/cpu
     - name: Install the dependencies
       run: |
         find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
-        python -m pip install --upgrade pip wheel
+        python -m pip install --no-build-isolation --upgrade pip wheel wheel-stub
         python -m pip install --no-build-isolation -r requirements-dev.txt
     - name: Run quick tests CPU ubuntu
       env:
@@ -120,18 +123,10 @@ jobs:
       uses: actions/setup-python@v6
       with:
         python-version: '3.10'
-    - name: cache weekly timestamp
-      id: pip-cache
+        cache: pip
+    - name: Install CPU PyTorch
       run: |
-        echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
-    - name: cache for pip
-      uses: actions/cache@v5
-      id: cache
-      with:
-        path: |
-          ~/.cache/pip
-          ~/.cache/torch
-        key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
+        python -m pip install torch==2.8.0 torchvision --extra-index-url https://download.pytorch.org/whl/cpu
     - name: Install the default branch no build (dev branch only)
       if: github.ref == 'refs/heads/dev'
       run: |

.github/workflows/weekly-preview.yml

@@ -5,38 +5,35 @@ on:
   - cron: "0 2 * * 0"  # 02:00 of every Sunday
 
 jobs:
-  flake8-py3:
+  static-checks:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        opt: ["codeformat", "pytype", "mypy"]
+        opt: ["codeformat", "mypy"]
     steps:
+    - name: Clean unused tools
+      run: |
+        find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
+        sudo rm -rf /usr/share/dotnet
+        sudo rm -rf /usr/local/lib/android
+        sudo rm -rf /opt/ghc /usr/local/.ghcup
+        sudo docker system prune -f
+
     - uses: actions/checkout@v6
     - name: Set up Python 3.10
       uses: actions/setup-python@v6
       with:
         python-version: '3.10'
-    - name: cache weekly timestamp
-      id: pip-cache
-      run: |
-        echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
-    - name: cache for pip
-      uses: actions/cache@v5
-      id: cache
-      with:
-        path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
+        cache: 'pip'
     - name: Install dependencies
       run: |
-        find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
         python -m pip install --upgrade pip wheel
-        python -m pip install -r requirements-dev.txt
+        python -m pip install --no-build-isolation -r requirements-dev.txt
     - name: Lint and type check
       run: |
         # clean up temporary files
         $(pwd)/runtests.sh --build --clean
-        # Github actions have 2 cores, so parallelize pytype
-        $(pwd)/runtests.sh --build --${{ matrix.opt }} -j 2
+        $(pwd)/runtests.sh --build --${{ matrix.opt }}
 
   packaging:
     if: github.repository == 'Project-MONAI/MONAI'

environment-dev.yml

@@ -6,7 +6,7 @@ channels:
   - conda-forge
 dependencies:
   - numpy>=1.24,<3.0
-  - pytorch>=2.3.0
+  - pytorch>=2.8.0
   - torchio
   - torchvision
   - pytorch-cuda>=11.6