From bc3dcee1979e322035b3e0ee0c556a644fff5400 Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Mon, 8 Sep 2025 12:34:52 +0100
Subject: [PATCH 01/41] Refactoring min-dep tests

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/pythonapp-min.yml | 283 ++++++++++++++++++----------
 1 file changed, 179 insertions(+), 104 deletions(-)

diff --git a/.github/workflows/pythonapp-min.yml b/.github/workflows/pythonapp-min.yml
index 0d147ca264..87b991c532 100644
--- a/.github/workflows/pythonapp-min.yml
+++ b/.github/workflows/pythonapp-min.yml
@@ -18,23 +18,45 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  # caching of these jobs:
-  #   - docker-py3-pip- (shared)
-  #   - ubuntu py37 pip-
-  #   - os-latest-pip- (shared)
-  min-dep-os:  # min dependencies installed tests for different OS
+  min-dep:  # min dependencies installed tests for different OS
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [windows-latest, macOS-latest, ubuntu-latest]
+        python-version: ['3.9']
+        pytorch-version: ['2.5.1']
+        include:
+        # Test Python versions under Ubuntu with lowest PyTorch version supported
+        - os: ubuntu-latest
+          pytorch-version: '2.5.1'
+          python-version: '3.10'
+        - os: ubuntu-latest
+          pytorch-version: '2.5.1'
+          python-version: '3.11'
+        - os: ubuntu-latest
+          pytorch-version: '2.5.1'
+          python-version: '3.12'
+
+        # test PyTorch versions under Ubuntu and lowest Python version supported
+        - os: ubuntu-latest
+          python-version: '3.9'
+          pytorch-version: '2.6.0'
+        - os: ubuntu-latest
+          python-version: '3.9'
+          pytorch-version: '2.7.1'
+        - os: ubuntu-latest
+          python-version: '3.9'
+          pytorch-version: '2.8.0'
+
+
     timeout-minutes: 40
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python 3.9
+    - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:
-        python-version: '3.9'
+        python-version: ${{ matrix.python-version }}
     - name: Prepare pip wheel
       run: |
         which python
@@ -51,10 +73,10 @@ jobs:
       with:
         path: ${{ steps.pip-cache.outputs.dir }}
         key: ${{ matrix.os }}-latest-pip-${{ steps.pip-cache.outputs.datew }}
-    - name: Install the dependencies
+    - name: Install the dependencies with PyTorch ${{ matrix.pytorch-version }}
       run: |
         # min. requirements
-        python -m pip install torch --index-url https://download.pytorch.org/whl/cpu
+        python -m pip install torch==${{ matrix.pytorch-version }}
         python -m pip install -r requirements-min.txt
         python -m pip list
         BUILD_MONAI=0 python setup.py develop  # no compile of extensions
@@ -63,7 +85,7 @@ jobs:
       run: |
         python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
         python -c "import monai; monai.config.print_config()"
-        ./runtests.sh --min
+        # ./runtests.sh --min
       shell: bash
       env:
         QUICKTEST: True
@@ -71,98 +93,151 @@ jobs:
         NGC_ORG: ${{ secrets.NGC_ORG }}
         NGC_TEAM: ${{ secrets.NGC_TEAM }}
 
-  min-dep-py3:  # min dependencies installed tests for different python
-    runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      matrix:
-        python-version: ['3.9', '3.10', '3.11', '3.12']
-    timeout-minutes: 40
-    steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Prepare pip wheel
-      run: |
-        which python
-        python -m pip install --user --upgrade pip setuptools wheel
-    - name: cache weekly timestamp
-      id: pip-cache
-      run: |
-        echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
-        echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
-      shell: bash
-    - name: cache for pip
-      uses: actions/cache@v4
-      id: cache
-      with:
-        path: ${{ steps.pip-cache.outputs.dir }}
-        key: ubuntu-latest-latest-pip-${{ steps.pip-cache.outputs.datew }}
-    - name: Install the dependencies
-      run: |
-        # min. requirements
-        python -m pip install torch --extra-index-url https://download.pytorch.org/whl/cpu
-        python -m pip install -r requirements-min.txt
-        python -m pip list
-        BUILD_MONAI=0 python setup.py develop  # no compile of extensions
-      shell: bash
-    - name: Run quick tests (CPU ${{ runner.os }})
-      run: |
-        python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
-        python -c "import monai; monai.config.print_config()"
-        ./runtests.sh --min
-      env:
-        QUICKTEST: True
-        NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
-        NGC_ORG: ${{ secrets.NGC_ORG }}
-        NGC_TEAM: ${{ secrets.NGC_TEAM }}
+  # # caching of these jobs:
+  # #   - docker-py3-pip- (shared)
+  # #   - ubuntu py37 pip-
+  # #   - os-latest-pip- (shared)
+  # min-dep-os:  # min dependencies installed tests for different OS
+  #   runs-on: ${{ matrix.os }}
+  #   strategy:
+  #     fail-fast: false
+  #     matrix:
+  #       os: [windows-latest, macOS-latest, ubuntu-latest]
+  #   timeout-minutes: 40
+  #   steps:
+  #   - uses: actions/checkout@v4
+  #   - name: Set up Python 3.9
+  #     uses: actions/setup-python@v5
+  #     with:
+  #       python-version: '3.9'
+  #   - name: Prepare pip wheel
+  #     run: |
+  #       which python
+  #       python -m pip install --upgrade pip wheel
+  #   - name: cache weekly timestamp
+  #     id: pip-cache
+  #     run: |
+  #       echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
+  #       echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
+  #     shell: bash
+  #   - name: cache for pip
+  #     uses: actions/cache@v4
+  #     id: cache
+  #     with:
+  #       path: ${{ steps.pip-cache.outputs.dir }}
+  #       key: ${{ matrix.os }}-latest-pip-${{ steps.pip-cache.outputs.datew }}
+  #   - name: Install the dependencies
+  #     run: |
+  #       # min. requirements
+  #       python -m pip install torch --index-url https://download.pytorch.org/whl/cpu
+  #       python -m pip install -r requirements-min.txt
+  #       python -m pip list
+  #       BUILD_MONAI=0 python setup.py develop  # no compile of extensions
+  #     shell: bash
+  #   - name: Run quick tests (CPU ${{ runner.os }})
+  #     run: |
+  #       python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
+  #       python -c "import monai; monai.config.print_config()"
+  #       ./runtests.sh --min
+  #     shell: bash
+  #     env:
+  #       QUICKTEST: True
+  #       NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
+  #       NGC_ORG: ${{ secrets.NGC_ORG }}
+  #       NGC_TEAM: ${{ secrets.NGC_TEAM }}
 
-  min-dep-pytorch:  # min dependencies installed tests for different pytorch
-    runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      matrix:
-        pytorch-version: ['2.5.1', '2.6.0', '2.7.1', '2.8.0']
-    timeout-minutes: 40
-    steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v5
-      with:
-        python-version: '3.9'
-    - name: Prepare pip wheel
-      run: |
-        which python
-        python -m pip install --user --upgrade pip setuptools wheel
-    - name: cache weekly timestamp
-      id: pip-cache
-      run: |
-        echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
-        echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
-      shell: bash
-    - name: cache for pip
-      uses: actions/cache@v4
-      id: cache
-      with:
-        path: ${{ steps.pip-cache.outputs.dir }}
-        key: ubuntu-latest-latest-pip-${{ steps.pip-cache.outputs.datew }}
-    - name: Install the dependencies
-      run: |
-        # min. requirements
-        python -m pip install torch==${{ matrix.pytorch-version }}
-        python -m pip install -r requirements-min.txt
-        python -m pip list
-        BUILD_MONAI=0 python setup.py develop  # no compile of extensions
-      shell: bash
-    - name: Run quick tests (pytorch ${{ matrix.pytorch-version }})
-      run: |
-        python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
-        python -c "import monai; monai.config.print_config()"
-        ./runtests.sh --min
-      env:
-        QUICKTEST: True
-        NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
-        NGC_ORG: ${{ secrets.NGC_ORG }}
-        NGC_TEAM: ${{ secrets.NGC_TEAM }}
+  # min-dep-py3:  # min dependencies installed tests for different python
+  #   runs-on: ubuntu-latest
+  #   strategy:
+  #     fail-fast: false
+  #     matrix:
+  #       python-version: ['3.9', '3.10', '3.11', '3.12']
+  #   timeout-minutes: 40
+  #   steps:
+  #   - uses: actions/checkout@v4
+  #   - name: Set up Python ${{ matrix.python-version }}
+  #     uses: actions/setup-python@v5
+  #     with:
+  #       python-version: ${{ matrix.python-version }}
+  #   - name: Prepare pip wheel
+  #     run: |
+  #       which python
+  #       python -m pip install --user --upgrade pip setuptools wheel
+  #   - name: cache weekly timestamp
+  #     id: pip-cache
+  #     run: |
+  #       echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
+  #       echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
+  #     shell: bash
+  #   - name: cache for pip
+  #     uses: actions/cache@v4
+  #     id: cache
+  #     with:
+  #       path: ${{ steps.pip-cache.outputs.dir }}
+  #       key: ubuntu-latest-latest-pip-${{ steps.pip-cache.outputs.datew }}
+  #   - name: Install the dependencies
+  #     run: |
+  #       # min. requirements
+  #       python -m pip install torch --extra-index-url https://download.pytorch.org/whl/cpu
+  #       python -m pip install -r requirements-min.txt
+  #       python -m pip list
+  #       BUILD_MONAI=0 python setup.py develop  # no compile of extensions
+  #     shell: bash
+  #   - name: Run quick tests (CPU ${{ runner.os }})
+  #     run: |
+  #       python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
+  #       python -c "import monai; monai.config.print_config()"
+  #       ./runtests.sh --min
+  #     env:
+  #       QUICKTEST: True
+  #       NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
+  #       NGC_ORG: ${{ secrets.NGC_ORG }}
+  #       NGC_TEAM: ${{ secrets.NGC_TEAM }}
+
+  # min-dep-pytorch:  # min dependencies installed tests for different pytorch
+  #   runs-on: ubuntu-latest
+  #   strategy:
+  #     fail-fast: false
+  #     matrix:
+  #       pytorch-version: ['2.5.1', '2.6.0', '2.7.1', '2.8.0']
+  #   timeout-minutes: 40
+  #   steps:
+  #   - uses: actions/checkout@v4
+  #   - name: Set up Python 3.9
+  #     uses: actions/setup-python@v5
+  #     with:
+  #       python-version: '3.9'
+  #   - name: Prepare pip wheel
+  #     run: |
+  #       which python
+  #       python -m pip install --user --upgrade pip setuptools wheel
+  #   - name: cache weekly timestamp
+  #     id: pip-cache
+  #     run: |
+  #       echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
+  #       echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
+  #     shell: bash
+  #   - name: cache for pip
+  #     uses: actions/cache@v4
+  #     id: cache
+  #     with:
+  #       path: ${{ steps.pip-cache.outputs.dir }}
+  #       key: ubuntu-latest-latest-pip-${{ steps.pip-cache.outputs.datew }}
+  #   - name: Install the dependencies
+  #     run: |
+  #       # min. requirements
+  #       python -m pip install torch==${{ matrix.pytorch-version }}
+  #       python -m pip install -r requirements-min.txt
+  #       python -m pip list
+  #       BUILD_MONAI=0 python setup.py develop  # no compile of extensions
+  #     shell: bash
+  #   - name: Run quick tests (pytorch ${{ matrix.pytorch-version }})
+  #     run: |
+  #       python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
+  #       python -c "import monai; monai.config.print_config()"
+  #       ./runtests.sh --min
+  #     env:
+  #       QUICKTEST: True
+  #       NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
+  #       NGC_ORG: ${{ secrets.NGC_ORG }}
+  #       NGC_TEAM: ${{ secrets.NGC_TEAM }}

From 2b9a9924d0ea66f272158cd451e477f58edbbb14 Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Mon, 8 Sep 2025 12:39:52 +0100
Subject: [PATCH 02/41] Update test

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/pythonapp-min.yml | 10 +---------
 1 file changed, 1 insertion(+), 9 deletions(-)

diff --git a/.github/workflows/pythonapp-min.yml b/.github/workflows/pythonapp-min.yml
index 87b991c532..3b70fb100b 100644
--- a/.github/workflows/pythonapp-min.yml
+++ b/.github/workflows/pythonapp-min.yml
@@ -1,4 +1,3 @@
-# Jenkinsfile.monai-premerge
 name: premerge-min
 
 on:
@@ -29,27 +28,20 @@ jobs:
         include:
         # Test Python versions under Ubuntu with lowest PyTorch version supported
         - os: ubuntu-latest
-          pytorch-version: '2.5.1'
           python-version: '3.10'
         - os: ubuntu-latest
-          pytorch-version: '2.5.1'
           python-version: '3.11'
         - os: ubuntu-latest
-          pytorch-version: '2.5.1'
           python-version: '3.12'
 
-        # test PyTorch versions under Ubuntu and lowest Python version supported
+        # Test PyTorch versions under Ubuntu with lowest Python version supported
         - os: ubuntu-latest
-          python-version: '3.9'
           pytorch-version: '2.6.0'
         - os: ubuntu-latest
-          python-version: '3.9'
           pytorch-version: '2.7.1'
         - os: ubuntu-latest
-          python-version: '3.9'
           pytorch-version: '2.8.0'
 
-
     timeout-minutes: 40
     steps:
     - uses: actions/checkout@v4

From 44bc1aedc282140cdc09abe32a1f2879ff7c7814 Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Mon, 8 Sep 2025 12:43:34 +0100
Subject: [PATCH 03/41] Update test

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/pythonapp-min.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pythonapp-min.yml b/.github/workflows/pythonapp-min.yml
index 3b70fb100b..8f019e1f54 100644
--- a/.github/workflows/pythonapp-min.yml
+++ b/.github/workflows/pythonapp-min.yml
@@ -23,8 +23,8 @@ jobs:
       fail-fast: false
       matrix:
         os: [windows-latest, macOS-latest, ubuntu-latest]
-        python-version: ['3.9']
-        pytorch-version: ['2.5.1']
+        python-version: '3.9'
+        pytorch-version: '2.5.1'
         include:
         # Test Python versions under Ubuntu with lowest PyTorch version supported
         - os: ubuntu-latest

From 0c8c868577549356c8298d5fcc91223142c620e9 Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Mon, 8 Sep 2025 12:45:13 +0100
Subject: [PATCH 04/41] Restoring include that worked

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/pythonapp-min.yml | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pythonapp-min.yml b/.github/workflows/pythonapp-min.yml
index 8f019e1f54..48f422af26 100644
--- a/.github/workflows/pythonapp-min.yml
+++ b/.github/workflows/pythonapp-min.yml
@@ -23,23 +23,29 @@ jobs:
       fail-fast: false
       matrix:
         os: [windows-latest, macOS-latest, ubuntu-latest]
-        python-version: '3.9'
-        pytorch-version: '2.5.1'
+        python-version: ['3.9']
+        pytorch-version: ['2.5.1']
         include:
         # Test Python versions under Ubuntu with lowest PyTorch version supported
         - os: ubuntu-latest
+          pytorch-version: '2.5.1'
           python-version: '3.10'
         - os: ubuntu-latest
+          pytorch-version: '2.5.1'
           python-version: '3.11'
         - os: ubuntu-latest
+          pytorch-version: '2.5.1'
           python-version: '3.12'
 
         # Test PyTorch versions under Ubuntu with lowest Python version supported
         - os: ubuntu-latest
+          python-version: '3.9'
           pytorch-version: '2.6.0'
         - os: ubuntu-latest
+          python-version: '3.9'
           pytorch-version: '2.7.1'
         - os: ubuntu-latest
+          python-version: '3.9'
           pytorch-version: '2.8.0'
 
     timeout-minutes: 40

From e3616e4e262437f24ddfd260f89c0309b228c8d0 Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Mon, 8 Sep 2025 12:57:07 +0100
Subject: [PATCH 05/41] Renaming file

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/{pythonapp-min.yml => cicd_tests.yml} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename .github/workflows/{pythonapp-min.yml => cicd_tests.yml} (100%)

diff --git a/.github/workflows/pythonapp-min.yml b/.github/workflows/cicd_tests.yml
similarity index 100%
rename from .github/workflows/pythonapp-min.yml
rename to .github/workflows/cicd_tests.yml

From 53cb0a4f31ec054c57b0a0d59cb1f0dce5ac8a56 Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Mon, 8 Sep 2025 13:05:26 +0100
Subject: [PATCH 06/41] Combining tests

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/cicd_tests.yml | 367 ++++++++++++++++++-------------
 1 file changed, 220 insertions(+), 147 deletions(-)

diff --git a/.github/workflows/cicd_tests.yml b/.github/workflows/cicd_tests.yml
index 48f422af26..a8ccc110ec 100644
--- a/.github/workflows/cicd_tests.yml
+++ b/.github/workflows/cicd_tests.yml
@@ -1,4 +1,4 @@
-name: premerge-min
+name: tests
 
 on:
   # quick tests for pull requests and the releasing branches
@@ -17,6 +17,39 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
+  static-checks:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        opt: ["codeformat", "pytype", "mypy"]
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.9'
+    - name: cache weekly timestamp
+      id: pip-cache
+      run: |
+        echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
+    - name: cache for pip
+      uses: actions/cache@v4
+      id: cache
+      with:
+        path: ~/.cache/pip
+        key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
+    - 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
+    - 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
+        
   min-dep:  # min dependencies installed tests for different OS
     runs-on: ${{ matrix.os }}
     strategy:
@@ -91,151 +124,191 @@ jobs:
         NGC_ORG: ${{ secrets.NGC_ORG }}
         NGC_TEAM: ${{ secrets.NGC_TEAM }}
 
-  # # caching of these jobs:
-  # #   - docker-py3-pip- (shared)
-  # #   - ubuntu py37 pip-
-  # #   - os-latest-pip- (shared)
-  # min-dep-os:  # min dependencies installed tests for different OS
-  #   runs-on: ${{ matrix.os }}
-  #   strategy:
-  #     fail-fast: false
-  #     matrix:
-  #       os: [windows-latest, macOS-latest, ubuntu-latest]
-  #   timeout-minutes: 40
-  #   steps:
-  #   - uses: actions/checkout@v4
-  #   - name: Set up Python 3.9
-  #     uses: actions/setup-python@v5
-  #     with:
-  #       python-version: '3.9'
-  #   - name: Prepare pip wheel
-  #     run: |
-  #       which python
-  #       python -m pip install --upgrade pip wheel
-  #   - name: cache weekly timestamp
-  #     id: pip-cache
-  #     run: |
-  #       echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
-  #       echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
-  #     shell: bash
-  #   - name: cache for pip
-  #     uses: actions/cache@v4
-  #     id: cache
-  #     with:
-  #       path: ${{ steps.pip-cache.outputs.dir }}
-  #       key: ${{ matrix.os }}-latest-pip-${{ steps.pip-cache.outputs.datew }}
-  #   - name: Install the dependencies
-  #     run: |
-  #       # min. requirements
-  #       python -m pip install torch --index-url https://download.pytorch.org/whl/cpu
-  #       python -m pip install -r requirements-min.txt
-  #       python -m pip list
-  #       BUILD_MONAI=0 python setup.py develop  # no compile of extensions
-  #     shell: bash
-  #   - name: Run quick tests (CPU ${{ runner.os }})
-  #     run: |
-  #       python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
-  #       python -c "import monai; monai.config.print_config()"
-  #       ./runtests.sh --min
-  #     shell: bash
-  #     env:
-  #       QUICKTEST: True
-  #       NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
-  #       NGC_ORG: ${{ secrets.NGC_ORG }}
-  #       NGC_TEAM: ${{ secrets.NGC_TEAM }}
+  full-dep:  # full dependencies installed tests for different OS
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [windows-latest, macOS-latest, ubuntu-latest]
+    timeout-minutes: 120
+    steps:
+    - if: runner.os == 'windows'
+      name: Config pagefile (Windows only)
+      uses: al-cheb/configure-pagefile-action@v1.4
+      with:
+        minimum-size: 8GB
+        maximum-size: 16GB
+        disk-root: "D:"
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.9'
+    - name: Prepare pip wheel
+      run: |
+        which python
+        python -m pip install --upgrade pip wheel
+    - name: cache weekly timestamp
+      id: pip-cache
+      run: |
+        echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
+        echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
+      shell: bash
+    - name: cache for pip
+      uses: actions/cache@v4
+      id: cache
+      with:
+        path: ${{ steps.pip-cache.outputs.dir }}
+        key: ${{ matrix.os }}-latest-pip-${{ steps.pip-cache.outputs.datew }}
+    - if: runner.os == 'windows'
+      name: Install torch cpu from pytorch.org (Windows only)
+      run: |
+        python -m pip install torch==2.5.1 torchvision==0.20.1+cpu --index-url https://download.pytorch.org/whl/cpu
+    - if: runner.os == 'Linux'
+      name: Install itk pre-release (Linux only)
+      run: |
+        python -m pip install --pre -U itk
+        find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
+    - name: Install the dependencies
+      run: |
+        python -m pip install --user --upgrade pip wheel
+        python -m pip install torch==2.5.1 torchvision==0.20.1
+        cat "requirements-dev.txt"
+        python -m pip install -r requirements-dev.txt
+        python -m pip list
+        python setup.py develop  # test no compile installation
+      shell: bash
+    - name: Run compiled (${{ runner.os }})
+      run: |
+        python setup.py develop --uninstall
+        BUILD_MONAI=1 python setup.py develop  # compile the cpp extensions
+      shell: bash
+    - name: Run quick tests (CPU ${{ runner.os }})
+      run: |
+        python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
+        python -c "import monai; monai.config.print_config()"
+        # python -m unittest -v
+      env:
+        QUICKTEST: True
+        PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python  # https://github.com/Project-MONAI/MONAI/issues/4354
+
+  packaging:
+    runs-on: ubuntu-latest
+    env:
+      QUICKTEST: True
+      shell: bash
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.9'
+    - name: cache weekly timestamp
+      id: pip-cache
+      run: |
+        echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
+    - name: cache for pip
+      uses: actions/cache@v4
+      id: cache
+      with:
+        path: |
+          ~/.cache/pip
+          ~/.cache/torch
+        key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
+    - name: Install dependencies
+      run: |
+        find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
+        python -m pip install --user --upgrade pip setuptools wheel twine packaging
+        # install the latest pytorch for testing
+        # however, "pip install monai*.tar.gz" will build cpp/cuda with an isolated
+        # fresh torch installation according to pyproject.toml
+        python -m pip install torch>=2.5.1 torchvision
+    - name: Check packages
+      run: |
+        pip uninstall monai
+        pip list | grep -iv monai
+        git fetch --depth=1 origin +refs/tags/*:refs/tags/*
+        set -e
 
-  # min-dep-py3:  # min dependencies installed tests for different python
-  #   runs-on: ubuntu-latest
-  #   strategy:
-  #     fail-fast: false
-  #     matrix:
-  #       python-version: ['3.9', '3.10', '3.11', '3.12']
-  #   timeout-minutes: 40
-  #   steps:
-  #   - uses: actions/checkout@v4
-  #   - name: Set up Python ${{ matrix.python-version }}
-  #     uses: actions/setup-python@v5
-  #     with:
-  #       python-version: ${{ matrix.python-version }}
-  #   - name: Prepare pip wheel
-  #     run: |
-  #       which python
-  #       python -m pip install --user --upgrade pip setuptools wheel
-  #   - name: cache weekly timestamp
-  #     id: pip-cache
-  #     run: |
-  #       echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
-  #       echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
-  #     shell: bash
-  #   - name: cache for pip
-  #     uses: actions/cache@v4
-  #     id: cache
-  #     with:
-  #       path: ${{ steps.pip-cache.outputs.dir }}
-  #       key: ubuntu-latest-latest-pip-${{ steps.pip-cache.outputs.datew }}
-  #   - name: Install the dependencies
-  #     run: |
-  #       # min. requirements
-  #       python -m pip install torch --extra-index-url https://download.pytorch.org/whl/cpu
-  #       python -m pip install -r requirements-min.txt
-  #       python -m pip list
-  #       BUILD_MONAI=0 python setup.py develop  # no compile of extensions
-  #     shell: bash
-  #   - name: Run quick tests (CPU ${{ runner.os }})
-  #     run: |
-  #       python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
-  #       python -c "import monai; monai.config.print_config()"
-  #       ./runtests.sh --min
-  #     env:
-  #       QUICKTEST: True
-  #       NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
-  #       NGC_ORG: ${{ secrets.NGC_ORG }}
-  #       NGC_TEAM: ${{ secrets.NGC_TEAM }}
+        # build tar.gz and wheel
+        python setup.py check -m -s
+        python setup.py sdist bdist_wheel
+        python -m twine check dist/*
+    - run: echo "pwd=$PWD" >> $GITHUB_OUTPUT
+      id: root
+    - run: echo "tmp_dir=$(mktemp -d)" >> $GITHUB_OUTPUT
+      id: mktemp
+    - name: Move packages
+      run: |
+        printf ${{ steps.root.outputs.pwd }}
+        printf ${{ steps.mktemp.outputs.tmp_dir }}
+        # move packages to a temp dir
+        cp dist/monai* "${{ steps.mktemp.outputs.tmp_dir }}"
+        rm -r build dist monai.egg-info
+        cd "${{ steps.mktemp.outputs.tmp_dir }}"
+        ls -al
+    - name: Install wheel file
+      working-directory: ${{ steps.mktemp.outputs.tmp_dir }}
+      run: |
+        # install from wheel
+        python -m pip install monai*.whl
+        python -c 'import monai; monai.config.print_config()' 2>&1 | grep -iv "unknown"
+        python -c 'import monai; print(monai.__file__)'
+        python -m pip uninstall -y monai
+        rm monai*.whl
+    - name: Install source archive
+      working-directory: ${{ steps.mktemp.outputs.tmp_dir }}
+      run: |
+        # install from tar.gz
+        name=$(ls *.tar.gz | head -n1)
+        echo $name
+        python -m pip install $name[all]
+        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 -r requirements-dev.txt
+        python -m unittest -v
+      env:
+        PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python  # https://github.com/Project-MONAI/MONAI/issues/4354
 
-  # min-dep-pytorch:  # min dependencies installed tests for different pytorch
-  #   runs-on: ubuntu-latest
-  #   strategy:
-  #     fail-fast: false
-  #     matrix:
-  #       pytorch-version: ['2.5.1', '2.6.0', '2.7.1', '2.8.0']
-  #   timeout-minutes: 40
-  #   steps:
-  #   - uses: actions/checkout@v4
-  #   - name: Set up Python 3.9
-  #     uses: actions/setup-python@v5
-  #     with:
-  #       python-version: '3.9'
-  #   - name: Prepare pip wheel
-  #     run: |
-  #       which python
-  #       python -m pip install --user --upgrade pip setuptools wheel
-  #   - name: cache weekly timestamp
-  #     id: pip-cache
-  #     run: |
-  #       echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
-  #       echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
-  #     shell: bash
-  #   - name: cache for pip
-  #     uses: actions/cache@v4
-  #     id: cache
-  #     with:
-  #       path: ${{ steps.pip-cache.outputs.dir }}
-  #       key: ubuntu-latest-latest-pip-${{ steps.pip-cache.outputs.datew }}
-  #   - name: Install the dependencies
-  #     run: |
-  #       # min. requirements
-  #       python -m pip install torch==${{ matrix.pytorch-version }}
-  #       python -m pip install -r requirements-min.txt
-  #       python -m pip list
-  #       BUILD_MONAI=0 python setup.py develop  # no compile of extensions
-  #     shell: bash
-  #   - name: Run quick tests (pytorch ${{ matrix.pytorch-version }})
-  #     run: |
-  #       python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
-  #       python -c "import monai; monai.config.print_config()"
-  #       ./runtests.sh --min
-  #     env:
-  #       QUICKTEST: True
-  #       NGC_API_KEY: ${{ secrets.NGC_API_KEY }}
-  #       NGC_ORG: ${{ secrets.NGC_ORG }}
-  #       NGC_TEAM: ${{ secrets.NGC_TEAM }}
+  build-docs:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.9'
+    - name: cache weekly timestamp
+      id: pip-cache
+      run: |
+        echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
+    - name: cache for pip
+      uses: actions/cache@v4
+      id: cache
+      with:
+        path: |
+          ~/.cache/pip
+          ~/.cache/torch
+        key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip wheel
+        python -m pip install -r docs/requirements.txt
+    - name: Make html
+      run: |
+        cd docs/
+        make clean
+        make html 2>&1 | tee tmp_log
+        if [[ $(grep -c "ERROR:" tmp_log) != 0 ]]; then echo "found errors"; grep "ERROR:" tmp_log; exit 1; fi
+        sed '/WARNING.*pip/d' tmp_log > tmp_log1; mv tmp_log1 tmp_log  # monai#7133
+        if [[ $(grep -c "WARNING:" tmp_log) != 0 ]]; then echo "found warnings"; grep "WARNING:" tmp_log; exit 1; fi
+      shell: bash

From 28f06ff8e75b4c617ccd163f183c78f8cff5e618 Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Mon, 8 Sep 2025 13:06:16 +0100
Subject: [PATCH 07/41] Removing combined file

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/pythonapp.yml | 245 --------------------------------
 1 file changed, 245 deletions(-)
 delete mode 100644 .github/workflows/pythonapp.yml

diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml
deleted file mode 100644
index c68c879231..0000000000
--- a/.github/workflows/pythonapp.yml
+++ /dev/null
@@ -1,245 +0,0 @@
-# Jenkinsfile.monai-premerge
-name: premerge
-
-on:
-  # quick tests for pull requests and the releasing branches
-  push:
-    branches:
-      - dev
-      - main
-      - releasing/*
-  pull_request:
-    head_ref-ignore:
-      - dev
-
-concurrency:
-  # automatically cancel the previously triggered workflows when there's a newer version
-  group: build-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
-
-jobs:
-  # caching of these jobs:
-  #   - docker-py3-pip- (shared)
-  #   - ubuntu py37 pip-
-  #   - os-latest-pip- (shared)
-  flake8-py3:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        opt: ["codeformat", "pytype", "mypy"]
-    steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v5
-      with:
-        python-version: '3.9'
-    - name: cache weekly timestamp
-      id: pip-cache
-      run: |
-        echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
-    - name: cache for pip
-      uses: actions/cache@v4
-      id: cache
-      with:
-        path: ~/.cache/pip
-        key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
-    - 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
-    - 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
-
-  quick-py3:  # full dependencies installed tests for different OS
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [windows-latest, macOS-latest, ubuntu-latest]
-    timeout-minutes: 120
-    steps:
-    - if: runner.os == 'windows'
-      name: Config pagefile (Windows only)
-      uses: al-cheb/configure-pagefile-action@v1.4
-      with:
-        minimum-size: 8GB
-        maximum-size: 16GB
-        disk-root: "D:"
-    - uses: actions/checkout@v4
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v5
-      with:
-        python-version: '3.9'
-    - name: Prepare pip wheel
-      run: |
-        which python
-        python -m pip install --upgrade pip wheel
-    - name: cache weekly timestamp
-      id: pip-cache
-      run: |
-        echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
-        echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
-      shell: bash
-    - name: cache for pip
-      uses: actions/cache@v4
-      id: cache
-      with:
-        path: ${{ steps.pip-cache.outputs.dir }}
-        key: ${{ matrix.os }}-latest-pip-${{ steps.pip-cache.outputs.datew }}
-    - if: runner.os == 'windows'
-      name: Install torch cpu from pytorch.org (Windows only)
-      run: |
-        python -m pip install torch==2.5.1 torchvision==0.20.1+cpu --index-url https://download.pytorch.org/whl/cpu
-    - if: runner.os == 'Linux'
-      name: Install itk pre-release (Linux only)
-      run: |
-        python -m pip install --pre -U itk
-        find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
-    - name: Install the dependencies
-      run: |
-        python -m pip install --user --upgrade pip wheel
-        python -m pip install torch==2.5.1 torchvision==0.20.1
-        cat "requirements-dev.txt"
-        python -m pip install -r requirements-dev.txt
-        python -m pip list
-        python setup.py develop  # test no compile installation
-      shell: bash
-    - name: Run compiled (${{ runner.os }})
-      run: |
-        python setup.py develop --uninstall
-        BUILD_MONAI=1 python setup.py develop  # compile the cpp extensions
-      shell: bash
-    - name: Run quick tests (CPU ${{ runner.os }})
-      run: |
-        python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
-        python -c "import monai; monai.config.print_config()"
-        python -m unittest -v
-      env:
-        QUICKTEST: True
-        PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python  # https://github.com/Project-MONAI/MONAI/issues/4354
-
-  packaging:
-    runs-on: ubuntu-latest
-    env:
-      QUICKTEST: True
-      shell: bash
-    steps:
-    - uses: actions/checkout@v4
-      with:
-        fetch-depth: 0
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v5
-      with:
-        python-version: '3.9'
-    - name: cache weekly timestamp
-      id: pip-cache
-      run: |
-        echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
-    - name: cache for pip
-      uses: actions/cache@v4
-      id: cache
-      with:
-        path: |
-          ~/.cache/pip
-          ~/.cache/torch
-        key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
-    - name: Install dependencies
-      run: |
-        find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
-        python -m pip install --user --upgrade pip setuptools wheel twine packaging
-        # install the latest pytorch for testing
-        # however, "pip install monai*.tar.gz" will build cpp/cuda with an isolated
-        # fresh torch installation according to pyproject.toml
-        python -m pip install torch>=2.5.1 torchvision
-    - name: Check packages
-      run: |
-        pip uninstall monai
-        pip list | grep -iv monai
-        git fetch --depth=1 origin +refs/tags/*:refs/tags/*
-        set -e
-
-        # build tar.gz and wheel
-        python setup.py check -m -s
-        python setup.py sdist bdist_wheel
-        python -m twine check dist/*
-    - run: echo "pwd=$PWD" >> $GITHUB_OUTPUT
-      id: root
-    - run: echo "tmp_dir=$(mktemp -d)" >> $GITHUB_OUTPUT
-      id: mktemp
-    - name: Move packages
-      run: |
-        printf ${{ steps.root.outputs.pwd }}
-        printf ${{ steps.mktemp.outputs.tmp_dir }}
-        # move packages to a temp dir
-        cp dist/monai* "${{ steps.mktemp.outputs.tmp_dir }}"
-        rm -r build dist monai.egg-info
-        cd "${{ steps.mktemp.outputs.tmp_dir }}"
-        ls -al
-    - name: Install wheel file
-      working-directory: ${{ steps.mktemp.outputs.tmp_dir }}
-      run: |
-        # install from wheel
-        python -m pip install monai*.whl
-        python -c 'import monai; monai.config.print_config()' 2>&1 | grep -iv "unknown"
-        python -c 'import monai; print(monai.__file__)'
-        python -m pip uninstall -y monai
-        rm monai*.whl
-    - name: Install source archive
-      working-directory: ${{ steps.mktemp.outputs.tmp_dir }}
-      run: |
-        # install from tar.gz
-        name=$(ls *.tar.gz | head -n1)
-        echo $name
-        python -m pip install $name[all]
-        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 ${{ steps.root.outputs.pwd }}/tests .
-        ls -al
-        python -m pip install -r requirements-dev.txt
-        python -m unittest -v
-      env:
-        PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python  # https://github.com/Project-MONAI/MONAI/issues/4354
-
-  build-docs:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python 3.9
-      uses: actions/setup-python@v5
-      with:
-        python-version: '3.9'
-    - name: cache weekly timestamp
-      id: pip-cache
-      run: |
-        echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
-    - name: cache for pip
-      uses: actions/cache@v4
-      id: cache
-      with:
-        path: |
-          ~/.cache/pip
-          ~/.cache/torch
-        key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip wheel
-        python -m pip install -r docs/requirements.txt
-    - name: Make html
-      run: |
-        cd docs/
-        make clean
-        make html 2>&1 | tee tmp_log
-        if [[ $(grep -c "ERROR:" tmp_log) != 0 ]]; then echo "found errors"; grep "ERROR:" tmp_log; exit 1; fi
-        sed '/WARNING.*pip/d' tmp_log > tmp_log1; mv tmp_log1 tmp_log  # monai#7133
-        if [[ $(grep -c "WARNING:" tmp_log) != 0 ]]; then echo "found warnings"; grep "WARNING:" tmp_log; exit 1; fi
-      shell: bash

From 4d8807555e420f0aa4f1adfa52c599fb2913fb0f Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Mon, 8 Sep 2025 13:38:11 +0100
Subject: [PATCH 08/41] Script update

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/cicd_tests.yml | 28 ++++++++++++++++------------
 1 file changed, 16 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/cicd_tests.yml b/.github/workflows/cicd_tests.yml
index a8ccc110ec..25870c4e9a 100644
--- a/.github/workflows/cicd_tests.yml
+++ b/.github/workflows/cicd_tests.yml
@@ -13,11 +13,15 @@ on:
 
 concurrency:
   # automatically cancel the previously triggered workflows when there's a newer version
-  group: build-min-${{ github.event.pull_request.number || github.ref }}
+  group: cicd-tests-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
+# These jobs run the CICD tests, type checking, and testing packaging and documentation generation. These use the 
+# minimum supported versions of Python and PyTorch in many places hard-coded as literals, so when support is dropped
+# for a version it is important to go through all jobs and check the versions they use are correct.
+
 jobs:
-  static-checks:
+  static-checks:  # Perform static type and other checks using runtests.sh
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -43,14 +47,14 @@ jobs:
         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
-    - name: Lint and type check
+    - name: Lint and type check with "./runtests.sh --build --${{ matrix.opt }}"
       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
+        # Github actions have multiple cores, so parallelize pytype
+        $(pwd)/runtests.sh --build --${{ matrix.opt }} -j $(nproc --all)
         
-  min-dep:  # min dependencies installed tests for different OS
+  min-dep:  # Test with minumum dependencies installed for different OS, Python, and PyTorch combinations
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -124,7 +128,7 @@ jobs:
         NGC_ORG: ${{ secrets.NGC_ORG }}
         NGC_TEAM: ${{ secrets.NGC_TEAM }}
 
-  full-dep:  # full dependencies installed tests for different OS
+  full-dep:  # Test with full dependencies installed for different OS runners
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -192,7 +196,7 @@ jobs:
         QUICKTEST: True
         PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python  # https://github.com/Project-MONAI/MONAI/issues/4354
 
-  packaging:
+  packaging:  # Test package generation
     runs-on: ubuntu-latest
     env:
       QUICKTEST: True
@@ -279,7 +283,7 @@ jobs:
       env:
         PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python  # https://github.com/Project-MONAI/MONAI/issues/4354
 
-  build-docs:
+  build-docs:  # Test building documentation
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
@@ -308,7 +312,7 @@ jobs:
         cd docs/
         make clean
         make html 2>&1 | tee tmp_log
-        if [[ $(grep -c "ERROR:" tmp_log) != 0 ]]; then echo "found errors"; grep "ERROR:" tmp_log; exit 1; fi
+        if [[ $(grep -c "ERROR:" tmp_log) != 0 ]]; then echo "Found errors:"; grep "ERROR:" tmp_log; exit 1; fi
         sed '/WARNING.*pip/d' tmp_log > tmp_log1; mv tmp_log1 tmp_log  # monai#7133
-        if [[ $(grep -c "WARNING:" tmp_log) != 0 ]]; then echo "found warnings"; grep "WARNING:" tmp_log; exit 1; fi
-      shell: bash
+        if [[ $(grep -c "WARNING:" tmp_log) != 0 ]]; then echo "Found warnings:"; grep "WARNING:" tmp_log; exit 1; fi
+      shell: bash
\ No newline at end of file

From d7e1451086822cf4f39a0d6357621451d4926ca4 Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Mon, 8 Sep 2025 13:55:12 +0100
Subject: [PATCH 09/41] Fix

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/cicd_tests.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/cicd_tests.yml b/.github/workflows/cicd_tests.yml
index 25870c4e9a..2c47923beb 100644
--- a/.github/workflows/cicd_tests.yml
+++ b/.github/workflows/cicd_tests.yml
@@ -16,7 +16,7 @@ concurrency:
   group: cicd-tests-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
-# These jobs run the CICD tests, type checking, and testing packaging and documentation generation. These use the 
+# These jobs run the CICD tests, type checking, and testing packaging and documentation generation. These use the
 # minimum supported versions of Python and PyTorch in many places hard-coded as literals, so when support is dropped
 # for a version it is important to go through all jobs and check the versions they use are correct.
 
@@ -53,7 +53,7 @@ jobs:
         $(pwd)/runtests.sh --build --clean
         # Github actions have multiple cores, so parallelize pytype
         $(pwd)/runtests.sh --build --${{ matrix.opt }} -j $(nproc --all)
-        
+
   min-dep:  # Test with minumum dependencies installed for different OS, Python, and PyTorch combinations
     runs-on: ${{ matrix.os }}
     strategy:
@@ -315,4 +315,4 @@ jobs:
         if [[ $(grep -c "ERROR:" tmp_log) != 0 ]]; then echo "Found errors:"; grep "ERROR:" tmp_log; exit 1; fi
         sed '/WARNING.*pip/d' tmp_log > tmp_log1; mv tmp_log1 tmp_log  # monai#7133
         if [[ $(grep -c "WARNING:" tmp_log) != 0 ]]; then echo "Found warnings:"; grep "WARNING:" tmp_log; exit 1; fi
-      shell: bash
\ No newline at end of file
+      shell: bash

From 7fc61070bef6540afbd8de7a3034b87de3a1057d Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Tue, 9 Sep 2025 00:21:57 +0100
Subject: [PATCH 10/41] Update with GPU runner

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/cicd_tests.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/cicd_tests.yml b/.github/workflows/cicd_tests.yml
index 2c47923beb..1af6a783bd 100644
--- a/.github/workflows/cicd_tests.yml
+++ b/.github/workflows/cicd_tests.yml
@@ -59,7 +59,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [windows-latest, macOS-latest, ubuntu-latest]
+        os: [windows-latest, macOS-latest, ubuntu-latest, linux-gpu-runner]
         python-version: ['3.9']
         pytorch-version: ['2.5.1']
         include:
@@ -110,6 +110,7 @@ jobs:
         key: ${{ matrix.os }}-latest-pip-${{ steps.pip-cache.outputs.datew }}
     - name: Install the dependencies with PyTorch ${{ matrix.pytorch-version }}
       run: |
+        /usr/bin/env nvidia-smi &> /dev/null || echo "No nvidia-smi found"
         # min. requirements
         python -m pip install torch==${{ matrix.pytorch-version }}
         python -m pip install -r requirements-min.txt

From 3a2381c646bc526cddab79c52219fb69d525dc1a Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Tue, 9 Sep 2025 00:32:46 +0100
Subject: [PATCH 11/41] Whoops

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/cicd_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cicd_tests.yml b/.github/workflows/cicd_tests.yml
index 1af6a783bd..1fbc2e6376 100644
--- a/.github/workflows/cicd_tests.yml
+++ b/.github/workflows/cicd_tests.yml
@@ -110,7 +110,7 @@ jobs:
         key: ${{ matrix.os }}-latest-pip-${{ steps.pip-cache.outputs.datew }}
     - name: Install the dependencies with PyTorch ${{ matrix.pytorch-version }}
       run: |
-        /usr/bin/env nvidia-smi &> /dev/null || echo "No nvidia-smi found"
+        /usr/bin/env nvidia-smi 2> /dev/null || echo "No nvidia-smi found"
         # min. requirements
         python -m pip install torch==${{ matrix.pytorch-version }}
         python -m pip install -r requirements-min.txt

From 95b731071258c9e57d99fa3aaa279eb8dbcc6dbd Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Tue, 9 Sep 2025 00:42:02 +0100
Subject: [PATCH 12/41] Adding GPU check

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/cicd_tests.yml | 23 +++++++++++------------
 1 file changed, 11 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/cicd_tests.yml b/.github/workflows/cicd_tests.yml
index 1fbc2e6376..139a755261 100644
--- a/.github/workflows/cicd_tests.yml
+++ b/.github/workflows/cicd_tests.yml
@@ -66,13 +66,7 @@ jobs:
         # Test Python versions under Ubuntu with lowest PyTorch version supported
         - os: ubuntu-latest
           pytorch-version: '2.5.1'
-          python-version: '3.10'
-        - os: ubuntu-latest
-          pytorch-version: '2.5.1'
-          python-version: '3.11'
-        - os: ubuntu-latest
-          pytorch-version: '2.5.1'
-          python-version: '3.12'
+          python-version: ['3.10', '3.11', '3.12']
 
         # Test PyTorch versions under Ubuntu with lowest Python version supported
         - os: ubuntu-latest
@@ -108,16 +102,21 @@ jobs:
       with:
         path: ${{ steps.pip-cache.outputs.dir }}
         key: ${{ matrix.os }}-latest-pip-${{ steps.pip-cache.outputs.datew }}
-    - name: Install the dependencies with PyTorch ${{ matrix.pytorch-version }}
+    - name: Install the minimum dependencies
       run: |
-        /usr/bin/env nvidia-smi 2> /dev/null || echo "No nvidia-smi found"
         # min. requirements
         python -m pip install torch==${{ matrix.pytorch-version }}
         python -m pip install -r requirements-min.txt
         python -m pip list
         BUILD_MONAI=0 python setup.py develop  # no compile of extensions
       shell: bash
-    - name: Run quick tests (CPU ${{ runner.os }})
+    - if: matrix.os == 'linux-gpu-runner'
+      name: Print GPU Info
+      run: |
+        nvidia-smi
+        python -c 'import torch; print(torch.rand(2,2).to("cuda:0"))'
+      shell: bash
+    - name: Run quick tests
       run: |
         python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
         python -c "import monai; monai.config.print_config()"
@@ -174,7 +173,7 @@ jobs:
       run: |
         python -m pip install --pre -U itk
         find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
-    - name: Install the dependencies
+    - name: Install the complete dependencies
       run: |
         python -m pip install --user --upgrade pip wheel
         python -m pip install torch==2.5.1 torchvision==0.20.1
@@ -188,7 +187,7 @@ jobs:
         python setup.py develop --uninstall
         BUILD_MONAI=1 python setup.py develop  # compile the cpp extensions
       shell: bash
-    - name: Run quick tests (CPU ${{ runner.os }})
+    - name: Run quick tests
       run: |
         python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
         python -c "import monai; monai.config.print_config()"

From d8128f4b4208615bd981441acf8a06bfde8a8f58 Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Tue, 9 Sep 2025 00:43:20 +0100
Subject: [PATCH 13/41] Fix

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/cicd_tests.yml | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/cicd_tests.yml b/.github/workflows/cicd_tests.yml
index 139a755261..b48b8468f4 100644
--- a/.github/workflows/cicd_tests.yml
+++ b/.github/workflows/cicd_tests.yml
@@ -66,7 +66,13 @@ jobs:
         # Test Python versions under Ubuntu with lowest PyTorch version supported
         - os: ubuntu-latest
           pytorch-version: '2.5.1'
-          python-version: ['3.10', '3.11', '3.12']
+          python-version: '3.10'
+        - os: ubuntu-latest
+          pytorch-version: '2.5.1'
+          python-version: '3.11'
+        - os: ubuntu-latest
+          pytorch-version: '2.5.1'
+          python-version: '3.12'
 
         # Test PyTorch versions under Ubuntu with lowest Python version supported
         - os: ubuntu-latest

From 55c351cc5021d131b43b022fdd7c6bc65692c95b Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Wed, 12 Nov 2025 14:35:27 +0000
Subject: [PATCH 14/41] Update with merge

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/cicd_tests.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/cicd_tests.yml b/.github/workflows/cicd_tests.yml
index a8e1829520..3de13a2da2 100644
--- a/.github/workflows/cicd_tests.yml
+++ b/.github/workflows/cicd_tests.yml
@@ -87,15 +87,16 @@ jobs:
 
     timeout-minutes: 40
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
     - name: Prepare pip wheel
       run: |
         which python
         python -m pip install --upgrade pip wheel
+        python -m pip install --user more-itertools>=8.0
     - name: cache weekly timestamp
       id: pip-cache
       run: |
@@ -158,6 +159,7 @@ jobs:
       run: |
         which python
         python -m pip install --upgrade pip wheel
+        python -m pip install --user more-itertools>=8.0
     - name: cache weekly timestamp
       id: pip-cache
       run: |

From 4d58d5b759e993f4b67d71555e06197556dba931 Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Wed, 12 Nov 2025 14:45:35 +0000
Subject: [PATCH 15/41] Removing Python 3.9 tests, adding Python 3.13 and
 Pytorch 2.9 tests

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/cicd_tests.yml | 42 ++++++++++++++++----------------
 1 file changed, 21 insertions(+), 21 deletions(-)

diff --git a/.github/workflows/cicd_tests.yml b/.github/workflows/cicd_tests.yml
index 3de13a2da2..8eb70e2533 100644
--- a/.github/workflows/cicd_tests.yml
+++ b/.github/workflows/cicd_tests.yml
@@ -28,10 +28,10 @@ jobs:
         opt: ["codeformat", "pytype", "mypy"]
     steps:
     - uses: actions/checkout@v5
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10
       uses: actions/setup-python@v6
       with:
-        python-version: '3.9'
+        python-version: '3.10'
     - name: cache weekly timestamp
       id: pip-cache
       run: |
@@ -59,31 +59,31 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [windows-latest, macOS-latest, ubuntu-latest, linux-gpu-runner]
-        python-version: ['3.9']
-        pytorch-version: ['2.5.1']
+        os: [windows-latest, macOS-latest, ubuntu-latest]
+        python-version: ['3.10']
+        pytorch-version: ['2.6.0']
         include:
         # Test Python versions under Ubuntu with lowest PyTorch version supported
         - os: ubuntu-latest
-          pytorch-version: '2.5.1'
-          python-version: '3.10'
-        - os: ubuntu-latest
-          pytorch-version: '2.5.1'
+          pytorch-version: '2.6.0'
           python-version: '3.11'
         - os: ubuntu-latest
-          pytorch-version: '2.5.1'
+          pytorch-version: '2.6.0'
           python-version: '3.12'
-
-        # Test PyTorch versions under Ubuntu with lowest Python version supported
         - os: ubuntu-latest
-          python-version: '3.9'
           pytorch-version: '2.6.0'
+          python-version: '3.13'
+
+        # Test PyTorch versions under Ubuntu with lowest Python version supported
         - os: ubuntu-latest
-          python-version: '3.9'
+          python-version: '3.10'
           pytorch-version: '2.7.1'
         - os: ubuntu-latest
-          python-version: '3.9'
+          python-version: '3.10'
           pytorch-version: '2.8.0'
+        - os: ubuntu-latest
+          python-version: '3.10'
+          pytorch-version: '2.9.0'
 
     timeout-minutes: 40
     steps:
@@ -151,10 +151,10 @@ jobs:
         maximum-size: 16GB
         disk-root: "D:"
     - uses: actions/checkout@v5
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10
       uses: actions/setup-python@v6
       with:
-        python-version: '3.9'
+        python-version: '3.10'
     - name: Prepare pip wheel
       run: |
         which python
@@ -213,10 +213,10 @@ jobs:
     - uses: actions/checkout@v5
       with:
         fetch-depth: 0
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10
       uses: actions/setup-python@v6
       with:
-        python-version: '3.9'
+        python-version: '3.10'
     - name: cache weekly timestamp
       id: pip-cache
       run: |
@@ -295,10 +295,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v5
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10
       uses: actions/setup-python@v6
       with:
-        python-version: '3.9'
+        python-version: '3.10'
     - name: cache weekly timestamp
       id: pip-cache
       run: |

From 29a2ff67010b0108b8386320a7928b77a757a0e2 Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Wed, 12 Nov 2025 15:03:31 +0000
Subject: [PATCH 16/41] Further changes for 3.9 to 3.10

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/conda.yml           |  2 +-
 .github/workflows/cron-ngc-bundle.yml |  4 +-
 .github/workflows/docker.yml          |  4 +-
 .github/workflows/pythonapp-gpu.yml   |  2 +-
 .github/workflows/release.yml         | 12 +++---
 .github/workflows/setupapp.yml        |  6 +--
 .github/workflows/weekly-preview.yml  |  8 ++--
 docs/.readthedocs.yaml                |  2 +-
 docs/requirements.txt                 |  2 +-
 docs/source/installation.md           |  4 +-
 json_test.py                          | 55 +++++++++++++++++++++++++++
 monai/apps/auto3dseg/auto_runner.py   |  2 +-
 monai/auto3dseg/utils.py              |  3 +-
 requirements-dev.txt                  |  4 +-
 setup.cfg                             | 15 ++++----
 15 files changed, 91 insertions(+), 34 deletions(-)
 create mode 100644 json_test.py

diff --git a/.github/workflows/conda.yml b/.github/workflows/conda.yml
index fd680e14c8..bedbcec548 100644
--- a/.github/workflows/conda.yml
+++ b/.github/workflows/conda.yml
@@ -19,7 +19,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.9", "3.10"]
+        python-version: ["3.10", "3.11"]
     runs-on: ${{ matrix.os }}
     timeout-minutes: 46 # equal to max + 3*std over the last 600 successful runs
     env:
diff --git a/.github/workflows/cron-ngc-bundle.yml b/.github/workflows/cron-ngc-bundle.yml
index c9bebc7bff..141a0b9acc 100644
--- a/.github/workflows/cron-ngc-bundle.yml
+++ b/.github/workflows/cron-ngc-bundle.yml
@@ -18,10 +18,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v5
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10
       uses: actions/setup-python@v6
       with:
-        python-version: '3.9'
+        python-version: '3.10'
     - name: cache weekly timestamp
       id: pip-cache
       run: echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index 4741dca858..5dd6fbe9f6 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -26,10 +26,10 @@ jobs:
         with:
           ref: dev
           fetch-depth: 0
-      - name: Set up Python 3.9
+      - name: Set up Python 3.10
         uses: actions/setup-python@v6
         with:
-          python-version: '3.9'
+          python-version: '3.10'
       - shell: bash
         run: |
           git describe
diff --git a/.github/workflows/pythonapp-gpu.yml b/.github/workflows/pythonapp-gpu.yml
index 347b49bba3..8639127b4d 100644
--- a/.github/workflows/pythonapp-gpu.yml
+++ b/.github/workflows/pythonapp-gpu.yml
@@ -53,7 +53,7 @@ jobs:
 
         if [ ${{ matrix.environment }} = "PT230+CUDA124" ]
         then
-        PYVER=3.9 PYSFX=3 DISTUTILS=python3-distutils && \
+        PYVER=3.10 PYSFX=3 DISTUTILS=python3-distutils && \
         apt-get update && apt-get install -y --no-install-recommends \
           curl \
           pkg-config \
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 3a8e8ffdf6..cfc2d4b7a4 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9', '3.10', '3.11']
+        python-version: ['3.10', '3.11', '3.12']
     steps:
     - uses: actions/checkout@v5
       with:
@@ -64,14 +64,14 @@ jobs:
       env:
         QUICKTEST: True
 
-    - if: matrix.python-version == '3.9' && startsWith(github.ref, 'refs/tags/')
+    - if: matrix.python-version == '3.10' && startsWith(github.ref, 'refs/tags/')
       name: Upload artifacts
       uses: actions/upload-artifact@v5
       with:
         name: dist
         path: dist/
 
-    - if: matrix.python-version == '3.9' && startsWith(github.ref, 'refs/tags/')
+    - if: matrix.python-version == '3.10' && startsWith(github.ref, 'refs/tags/')
       name: Check artifacts
       run: |
         ls -al dist/
@@ -79,7 +79,7 @@ jobs:
         ls -al dist/
 
     # remove publishing to Test PyPI as it is moved to blossom
-    # - if: matrix.python-version == '3.9' && startsWith(github.ref, 'refs/tags/')
+    # - if: matrix.python-version == '3.10' && startsWith(github.ref, 'refs/tags/')
     #   name: Publish to Test PyPI
     #   uses: pypa/gh-action-pypi-publish@release/v1
     #   with:
@@ -97,10 +97,10 @@ jobs:
         # full history so that we can git describe
         with:
           fetch-depth: 0
-      - name: Set up Python 3.9
+      - name: Set up Python 3.10
         uses: actions/setup-python@v6
         with:
-          python-version: '3.9'
+          python-version: '3.10'
       - shell: bash
         run: |
           find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
diff --git a/.github/workflows/setupapp.yml b/.github/workflows/setupapp.yml
index acd72eaf6f..912d254334 100644
--- a/.github/workflows/setupapp.yml
+++ b/.github/workflows/setupapp.yml
@@ -81,7 +81,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9', '3.10', '3.11']
+        python-version: ['3.10', '3.11', '3.12']
     steps:
     - uses: actions/checkout@v5
       with:
@@ -127,10 +127,10 @@ jobs:
   install:  # pip install from github url, the default branch is dev
     runs-on: ubuntu-latest
     steps:
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10
       uses: actions/setup-python@v6
       with:
-        python-version: '3.9'
+        python-version: '3.10'
     - name: cache weekly timestamp
       id: pip-cache
       run: |
diff --git a/.github/workflows/weekly-preview.yml b/.github/workflows/weekly-preview.yml
index 93d6f67f09..67a712fe2d 100644
--- a/.github/workflows/weekly-preview.yml
+++ b/.github/workflows/weekly-preview.yml
@@ -12,10 +12,10 @@ jobs:
         opt: ["codeformat", "pytype", "mypy"]
     steps:
     - uses: actions/checkout@v5
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10
       uses: actions/setup-python@v6
       with:
-        python-version: '3.9'
+        python-version: '3.10'
     - name: cache weekly timestamp
       id: pip-cache
       run: |
@@ -46,10 +46,10 @@ jobs:
       with:
         ref: dev
         fetch-depth: 0
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10
       uses: actions/setup-python@v6
       with:
-        python-version: '3.9'
+        python-version: '3.10'
     - name: Install setuptools
       run: |
         python -m pip install --user --upgrade setuptools wheel packaging
diff --git a/docs/.readthedocs.yaml b/docs/.readthedocs.yaml
index d2e2ee74a5..0212e806e8 100644
--- a/docs/.readthedocs.yaml
+++ b/docs/.readthedocs.yaml
@@ -6,7 +6,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.9"
+    python: "3.10"
 sphinx:
    configuration: docs/source/conf.py
 python:
diff --git a/docs/requirements.txt b/docs/requirements.txt
index f44f41a6b2..7f4db0f704 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -6,7 +6,7 @@ itk>=5.2
 nibabel
 parameterized
 scikit-image>=0.19.0
-scipy>=1.12.0; python_version >= '3.9'
+scipy>=1.12.0
 tensorboard
 commonmark==0.9.1
 recommonmark==0.6.0
diff --git a/docs/source/installation.md b/docs/source/installation.md
index b8befc10b4..bf7fa56138 100644
--- a/docs/source/installation.md
+++ b/docs/source/installation.md
@@ -19,7 +19,7 @@
 
 ---
 
-MONAI's core functionality is written in Python 3 (>= 3.9) and only requires [Numpy](https://numpy.org/) and [Pytorch](https://pytorch.org/).
+MONAI's core functionality is written in Python 3 (>= 3.10) and only requires [Numpy](https://numpy.org/) and [Pytorch](https://pytorch.org/).
 
 The package is currently distributed via Github as the primary source code repository,
 and the Python package index (PyPI). The pre-built Docker images are made available on DockerHub.
@@ -245,7 +245,7 @@ this will install PyTorch as well as `pytorch-cuda`, please follow https://pytor
 ```bash
 git clone https://github.com/Project-MONAI/MONAI.git
 cd MONAI/
-conda create -n <name> python=<ver>  # eg 3.9
+conda create -n <name> python=<ver>  # eg 3.10
 conda env update -n <name> -f environment-dev.yml
 ```
 
diff --git a/json_test.py b/json_test.py
new file mode 100644
index 0000000000..7111a67223
--- /dev/null
+++ b/json_test.py
@@ -0,0 +1,55 @@
+from functools import partial
+import numpy as np
+import torch
+import json
+
+
+JSON_NUMPY_TYPE = "numpy"
+JSON_TORCH_TYPE = "torch"
+
+
+class SafeEncoder(json.JSONEncoder):
+    def default(self, obj):
+        if isinstance(obj, np.ndarray):
+            return {"__type__": JSON_NUMPY_TYPE, "dtype": str(obj.dtype), "data": obj.tolist()}
+
+        if isinstance(obj, torch.Tensor):
+            return {
+                "__type__": JSON_TORCH_TYPE,
+                "dtype": str(obj.dtype).replace("torch.", ""),
+                "data": obj.detach().cpu().numpy().tolist(),
+            }
+
+        return super().default(obj)
+
+
+def json_decode_hook(item):
+    datatype = item.get("__type__", "")
+    if datatype == JSON_NUMPY_TYPE:
+        return np.array(item["data"], dtype=np.dtype(item["dtype"]))
+    elif datatype == JSON_TORCH_TYPE:
+        return torch.tensor(item["data"], dtype=getattr(torch, item["dtype"]))
+    else:
+        return item
+
+
+json_dumps = partial(json.dumps, cls=SafeEncoder)
+json_loads = partial(json.loads, object_hook=json_decode_hook)
+
+item = {
+    "np": np.random.rand(5, 5),
+    "pt": torch.rand(4, 4),
+    "int": 123,
+    "list": [1, 2, 3],
+    "tuple": (1, 2, 3),
+    "dict": {"one": 1, "two": 2},
+}
+
+print(item)
+print()
+
+dump_item = json_dumps(item)
+
+loaded_item = json_loads(dump_item)
+
+print(loaded_item)
diff --git a/monai/apps/auto3dseg/auto_runner.py b/monai/apps/auto3dseg/auto_runner.py
index 28ba2a88f9..9acab5d441 100644
--- a/monai/apps/auto3dseg/auto_runner.py
+++ b/monai/apps/auto3dseg/auto_runner.py
@@ -560,7 +560,7 @@ def set_device_info(
             cmd_prefix: command line prefix for subprocess running in BundleAlgo and EnsembleRunner.
                 Default using env "CMD_PREFIX" or None, examples are:
 
-                    - single GPU/CPU or multinode bcprun: "python " or "/opt/conda/bin/python3.9 ",
+                    - single GPU/CPU or multinode bcprun: "python " or "/opt/conda/bin/python3.10",
                     - single node multi-GPU running "torchrun --nnodes=1 --nproc_per_node=2 "
 
                 If user define this prefix, please make sure --nproc_per_node matches cuda_visible_device or
diff --git a/monai/auto3dseg/utils.py b/monai/auto3dseg/utils.py
index 211f23c415..8b5dab75b5 100644
--- a/monai/auto3dseg/utils.py
+++ b/monai/auto3dseg/utils.py
@@ -407,7 +407,8 @@ def _prepare_cmd_default(cmd: str, cmd_prefix: str | None = None, **kwargs: Any)
 
     Args:
         cmd: the command or script to run in the distributed job.
-        cmd_prefix: the command prefix to run the script, e.g., "python", "python -m", "python3", "/opt/conda/bin/python3.9 ".
+        cmd_prefix: the command prefix to run the script, 
+            e.g., "python", "python -m", "python3", "/opt/conda/bin/python3.10".
         kwargs: the keyword arguments to be passed to the script.
 
     Returns:
diff --git a/requirements-dev.txt b/requirements-dev.txt
index ff234c856e..e1422ea8ce 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -2,7 +2,7 @@
 -r requirements-min.txt
 pytorch-ignite==0.4.11
 gdown>=4.7.3
-scipy>=1.12.0; python_version >= '3.9'
+scipy>=1.12.0
 itk>=5.2
 nibabel
 pillow!=8.3.0  # https://github.com/python-pillow/Pillow/issues/5571
@@ -27,7 +27,7 @@ ninja
 torchio
 torchvision
 psutil
-cucim-cu12; platform_system == "Linux" and python_version >= "3.9" and python_version <= "3.10"
+cucim-cu12; platform_system == "Linux" and python_version <= "3.10"
 openslide-python
 openslide-bin
 imagecodecs; platform_system == "Linux" or platform_system == "Darwin"
diff --git a/setup.cfg b/setup.cfg
index b3949213c2..5011b6382e 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -21,9 +21,10 @@ classifiers =
     Intended Audience :: Healthcare Industry
     Programming Language :: C++
     Programming Language :: Python :: 3
-    Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.11
+    Programming Language :: Python :: 3.12
+    Programming Language :: Python :: 3.13
     Topic :: Scientific/Engineering
     Topic :: Scientific/Engineering :: Artificial Intelligence
     Topic :: Scientific/Engineering :: Medical Science Apps.
@@ -33,7 +34,7 @@ classifiers =
     Typing :: Typed
 
 [options]
-python_requires = >= 3.9
+python_requires = >= 3.10
 # for compiling and develop setup only
 # no need to specify the versions so that we could
 # compile for multiple targeted versions.
@@ -42,7 +43,7 @@ setup_requires =
     ninja
     packaging
 install_requires =
-    torch>=2.4.1
+    torch>=2.6.0
     numpy>=1.24,<3.0
 
 [options.extras_require]
@@ -50,7 +51,7 @@ all =
     nibabel
     ninja
     scikit-image>=0.14.2
-    scipy>=1.12.0; python_version >= '3.9'
+    scipy>=1.12.0
     pillow
     tensorboard
     gdown>=4.7.3
@@ -61,7 +62,7 @@ all =
     tqdm>=4.47.0
     lmdb
     psutil
-    cucim-cu12; platform_system == "Linux" and python_version >= '3.9' and python_version <= '3.10'
+    cucim-cu12; platform_system == "Linux" and python_version <= '3.10'
     openslide-python
     openslide-bin
     tifffile; platform_system == "Linux" or platform_system == "Darwin"
@@ -95,7 +96,7 @@ ninja =
 skimage =
     scikit-image>=0.14.2
 scipy =
-    scipy>=1.12.0; python_version >= '3.9'
+    scipy>=1.12.0
 pillow =
     pillow!=8.3.0
 tensorboard =
@@ -117,7 +118,7 @@ lmdb =
 psutil =
     psutil
 cucim =
-    cucim-cu12; platform_system == "Linux" and python_version >= '3.9' and python_version <= '3.10'
+    cucim-cu12; platform_system == "Linux" and python_version <= '3.10'
 openslide =
     openslide-python
     openslide-bin

From d309fe9ce2ddbb58e8c04975632cffb4980049ac Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 12 Nov 2025 15:04:23 +0000
Subject: [PATCH 17/41] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 monai/auto3dseg/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/monai/auto3dseg/utils.py b/monai/auto3dseg/utils.py
index 8b5dab75b5..ff1be57629 100644
--- a/monai/auto3dseg/utils.py
+++ b/monai/auto3dseg/utils.py
@@ -407,7 +407,7 @@ def _prepare_cmd_default(cmd: str, cmd_prefix: str | None = None, **kwargs: Any)
 
     Args:
         cmd: the command or script to run in the distributed job.
-        cmd_prefix: the command prefix to run the script, 
+        cmd_prefix: the command prefix to run the script,
             e.g., "python", "python -m", "python3", "/opt/conda/bin/python3.10".
         kwargs: the keyword arguments to be passed to the script.
 

From aa3080be6df90ba2dd9972d997999702fd5f7063 Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Wed, 12 Nov 2025 15:18:35 +0000
Subject: [PATCH 18/41] Whoops

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 json_test.py | 55 ----------------------------------------------------
 1 file changed, 55 deletions(-)
 delete mode 100644 json_test.py

diff --git a/json_test.py b/json_test.py
deleted file mode 100644
index 7111a67223..0000000000
--- a/json_test.py
+++ /dev/null
@@ -1,55 +0,0 @@
-from functools import partial
-import numpy as np
-import torch
-import json
-
-
-JSON_NUMPY_TYPE = "numpy"
-JSON_TORCH_TYPE = "torch"
-
-
-class SafeEncoder(json.JSONEncoder):
-    def default(self, obj):
-        if isinstance(obj, np.ndarray):
-            return {"__type__": JSON_NUMPY_TYPE, "dtype": str(obj.dtype), "data": obj.tolist()}
-
-        if isinstance(obj, torch.Tensor):
-            return {
-                "__type__": JSON_TORCH_TYPE,
-                "dtype": str(obj.dtype).replace("torch.", ""),
-                "data": obj.detach().cpu().numpy().tolist(),
-            }
-
-        return super().default(obj)
-
-
-def json_decode_hook(item):
-    datatype = item.get("__type__", "")
-    if datatype == JSON_NUMPY_TYPE:
-        return np.array(item["data"], dtype=np.dtype(item["dtype"]))
-    elif datatype == JSON_TORCH_TYPE:
-        return torch.tensor(item["data"], dtype=getattr(torch, item["dtype"]))
-    else:
-        return item
-
-
-json_dumps = partial(json.dumps, cls=SafeEncoder)
-json_loads = partial(json.loads, object_hook=json_decode_hook)
-
-item = {
-    "np": np.random.rand(5, 5),
-    "pt": torch.rand(4, 4),
-    "int": 123,
-    "list": [1, 2, 3],
-    "tuple": (1, 2, 3),
-    "dict": {"one": 1, "two": 2},
-}
-
-print(item)
-print()
-
-dump_item = json_dumps(item)
-
-loaded_item = json_loads(dump_item)
-
-print(loaded_item)

From fabc53869b4f34c0dd7baa4c503d0098db53b52f Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Sun, 7 Dec 2025 18:21:06 +0000
Subject: [PATCH 19/41] Adding ignore paths to stop tests triggering when
 documentation changed

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/build_docs.yml | 55 ++++++++++++++++++++++++++++++++
 .github/workflows/cicd_tests.yml | 42 +++++-------------------
 2 files changed, 63 insertions(+), 34 deletions(-)
 create mode 100644 .github/workflows/build_docs.yml

diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml
new file mode 100644
index 0000000000..178ddb728d
--- /dev/null
+++ b/.github/workflows/build_docs.yml
@@ -0,0 +1,55 @@
+name: build_docs
+
+on:
+  # build docs test for pull requests and the releasing branches
+  push:
+    branches:
+      - dev
+      - main
+      - releasing/*
+  pull_request:
+    head_ref-ignore:
+      - dev
+
+concurrency:
+  # automatically cancel the previously triggered workflows when there's a newer version
+  group: cicd-tests-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+# This test is for building documentation on any relevant push or PR. This ensures that any changes to docs or source
+# files is tested for correct doc building, whereas functional tests can be deferred if only docs were modified.
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v5
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v6
+      with:
+        python-version: '3.10'
+    - name: cache weekly timestamp
+      id: pip-cache
+      run: |
+        echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
+    - name: cache for pip
+      uses: actions/cache@v4
+      id: cache
+      with:
+        path: |
+          ~/.cache/pip
+          ~/.cache/torch
+        key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip wheel
+        python -m pip install -r docs/requirements.txt
+    - name: Make html
+      run: |
+        cd docs/
+        make clean
+        make html 2>&1 | tee tmp_log
+        if [[ $(grep -c "ERROR:" tmp_log) != 0 ]]; then echo "Found errors:"; grep "ERROR:" tmp_log; exit 1; fi
+        sed '/WARNING.*pip/d' tmp_log > tmp_log1; mv tmp_log1 tmp_log  # monai#7133
+        if [[ $(grep -c "WARNING:" tmp_log) != 0 ]]; then echo "Found warnings:"; grep "WARNING:" tmp_log; exit 1; fi
+      shell: bash
diff --git a/.github/workflows/cicd_tests.yml b/.github/workflows/cicd_tests.yml
index 8eb70e2533..3a732cfedc 100644
--- a/.github/workflows/cicd_tests.yml
+++ b/.github/workflows/cicd_tests.yml
@@ -7,9 +7,17 @@ on:
       - dev
       - main
       - releasing/*
+    paths-ignore:  # skip if only docs are modified
+      - '**.md'
+      - '**.rst'
+      - 'docs/**'
   pull_request:
     head_ref-ignore:
       - dev
+    paths-ignore:  # skip if only docs are modified
+      - '**.md'
+      - '**.rst'
+      - 'docs/**'
 
 concurrency:
   # automatically cancel the previously triggered workflows when there's a newer version
@@ -290,37 +298,3 @@ jobs:
         python -m unittest -v
       env:
         PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python  # https://github.com/Project-MONAI/MONAI/issues/4354
-
-  build-docs:  # Test building documentation
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v5
-    - 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@v4
-      id: cache
-      with:
-        path: |
-          ~/.cache/pip
-          ~/.cache/torch
-        key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip wheel
-        python -m pip install -r docs/requirements.txt
-    - name: Make html
-      run: |
-        cd docs/
-        make clean
-        make html 2>&1 | tee tmp_log
-        if [[ $(grep -c "ERROR:" tmp_log) != 0 ]]; then echo "Found errors:"; grep "ERROR:" tmp_log; exit 1; fi
-        sed '/WARNING.*pip/d' tmp_log > tmp_log1; mv tmp_log1 tmp_log  # monai#7133
-        if [[ $(grep -c "WARNING:" tmp_log) != 0 ]]; then echo "Found warnings:"; grep "WARNING:" tmp_log; exit 1; fi
-      shell: bash

From 89087256803e0d10ac4aa845d2c01235a92f70b9 Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Sun, 7 Dec 2025 18:48:47 +0000
Subject: [PATCH 20/41] Experimental image cleaning

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/build_docs.yml | 13 +++++++++++++
 .github/workflows/cicd_tests.yml |  3 ++-
 2 files changed, 15 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml
index 178ddb728d..24346d7feb 100644
--- a/.github/workflows/build_docs.yml
+++ b/.github/workflows/build_docs.yml
@@ -23,15 +23,26 @@ jobs:
   build-docs:
     runs-on: ubuntu-latest
     steps:
+    - name: Clean unused tools
+      run: |
+        find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
+        rm -rf /usr/share/dotnet
+        rm -rf /usr/local/lib/android
+        rm -rf /opt/ghc /usr/local/.ghcup
+        docker system prune -f
+
     - uses: actions/checkout@v5
+
     - 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@v4
       id: cache
@@ -40,10 +51,12 @@ jobs:
           ~/.cache/pip
           ~/.cache/torch
         key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip wheel
         python -m pip install -r docs/requirements.txt
+        
     - name: Make html
       run: |
         cd docs/
diff --git a/.github/workflows/cicd_tests.yml b/.github/workflows/cicd_tests.yml
index ccf9335772..52c3339704 100644
--- a/.github/workflows/cicd_tests.yml
+++ b/.github/workflows/cicd_tests.yml
@@ -297,4 +297,5 @@ jobs:
         python -m pip install -r requirements-dev.txt
         python -m unittest -v
       env:
-        PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python  # https://github.com/Project-MONAI/MONAI/issues/4354
\ No newline at end of file
+        PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python  # https://github.com/Project-MONAI/MONAI/issues/4354
+        
\ No newline at end of file

From 18f640d3096a859e1a5d0dd65af12ea088fde543 Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Sun, 7 Dec 2025 18:55:53 +0000
Subject: [PATCH 21/41] Fix

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/build_docs.yml | 10 +++++-----
 .github/workflows/cicd_tests.yml |  1 -
 2 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml
index 24346d7feb..c0b597201d 100644
--- a/.github/workflows/build_docs.yml
+++ b/.github/workflows/build_docs.yml
@@ -26,10 +26,10 @@ jobs:
     - name: Clean unused tools
       run: |
         find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
-        rm -rf /usr/share/dotnet
-        rm -rf /usr/local/lib/android
-        rm -rf /opt/ghc /usr/local/.ghcup
-        docker system prune -f
+        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@v5
 
@@ -56,7 +56,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip wheel
         python -m pip install -r docs/requirements.txt
-        
+
     - name: Make html
       run: |
         cd docs/
diff --git a/.github/workflows/cicd_tests.yml b/.github/workflows/cicd_tests.yml
index 52c3339704..b9f7d6019c 100644
--- a/.github/workflows/cicd_tests.yml
+++ b/.github/workflows/cicd_tests.yml
@@ -298,4 +298,3 @@ jobs:
         python -m unittest -v
       env:
         PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python  # https://github.com/Project-MONAI/MONAI/issues/4354
-        
\ No newline at end of file

From 4ec28007765611e4b78f16e4021b717889ebc406 Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Sun, 7 Dec 2025 20:09:04 +0000
Subject: [PATCH 22/41] Always import npt

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 monai/metrics/average_precision.py | 6 ++----
 monai/metrics/rocauc.py            | 6 ++----
 2 files changed, 4 insertions(+), 8 deletions(-)

diff --git a/monai/metrics/average_precision.py b/monai/metrics/average_precision.py
index 53c41aeca5..ba0213953c 100644
--- a/monai/metrics/average_precision.py
+++ b/monai/metrics/average_precision.py
@@ -12,12 +12,10 @@
 from __future__ import annotations
 
 import warnings
-from typing import TYPE_CHECKING, cast
+from typing import cast
 
 import numpy as np
-
-if TYPE_CHECKING:
-    import numpy.typing as npt
+import numpy.typing as npt
 
 import torch
 
diff --git a/monai/metrics/rocauc.py b/monai/metrics/rocauc.py
index 57a8a072b4..16e4d6bb15 100644
--- a/monai/metrics/rocauc.py
+++ b/monai/metrics/rocauc.py
@@ -12,12 +12,10 @@
 from __future__ import annotations
 
 import warnings
-from typing import TYPE_CHECKING, cast
+from typing import cast
 
 import numpy as np
-
-if TYPE_CHECKING:
-    import numpy.typing as npt
+import numpy.typing as npt
 
 import torch
 

From 27cb347520690298fbb87ee6a0c5dd37cc7feacb Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Sun, 7 Dec 2025 22:27:31 +0000
Subject: [PATCH 23/41] Disk size optimisation

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/cicd_tests.yml | 41 +++++++++++++++++++++++++++-----
 1 file changed, 35 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/cicd_tests.yml b/.github/workflows/cicd_tests.yml
index b9f7d6019c..4dd0e071fa 100644
--- a/.github/workflows/cicd_tests.yml
+++ b/.github/workflows/cicd_tests.yml
@@ -24,9 +24,9 @@ concurrency:
   group: cicd-tests-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
-# These jobs run the CICD tests, type checking, and testing packaging and documentation generation. These use the
-# minimum supported versions of Python and PyTorch in many places hard-coded as literals, so when support is dropped
-# for a version it is important to go through all jobs and check the versions they use are correct.
+# These jobs run the CICD tests, type checking, and testing packaging. These use the minimum supported versions of 
+# Python and PyTorch in many places hard-coded as literals, so when support is dropped for a version it is important to 
+# go through all jobs and check the versions they use are correct.
 
 jobs:
   static-checks:  # Perform static type and other checks using runtests.sh
@@ -35,6 +35,14 @@ jobs:
       matrix:
         opt: ["codeformat", "pytype", "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
@@ -52,7 +60,6 @@ jobs:
         key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
     - 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
     - name: Lint and type check with "./runtests.sh --build --${{ matrix.opt }}"
@@ -95,6 +102,14 @@ jobs:
 
     timeout-minutes: 40
     steps:
+    - if: runner.os == 'Linux'
+      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@v5
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v6
@@ -151,6 +166,14 @@ jobs:
         os: [windows-latest, macOS-latest, ubuntu-latest]
     timeout-minutes: 120
     steps:
+    - if: runner.os == 'Linux'
+      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
     - if: runner.os == 'windows'
       name: Config pagefile (Windows only)
       uses: al-cheb/configure-pagefile-action@v1.5
@@ -188,7 +211,6 @@ jobs:
       name: Install itk pre-release (Linux only)
       run: |
         python -m pip install --pre -U itk
-        find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
     - name: Install the complete dependencies
       run: |
         python -m pip install --user --upgrade pip wheel
@@ -218,6 +240,14 @@ jobs:
       QUICKTEST: True
       shell: bash
     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
       with:
         fetch-depth: 0
@@ -239,7 +269,6 @@ jobs:
         key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
     - name: Install dependencies
       run: |
-        find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
         python -m pip install --user --upgrade pip setuptools wheel twine packaging
         # install the latest pytorch for testing
         # however, "pip install monai*.tar.gz" will build cpp/cuda with an isolated

From 3c5a3da8e0f29b6732f93c5dabba4f2b725a5f45 Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Sun, 7 Dec 2025 23:51:50 +0000
Subject: [PATCH 24/41] Fix

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/cicd_tests.yml   | 6 +++---
 monai/metrics/average_precision.py | 1 -
 monai/metrics/rocauc.py            | 1 -
 3 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/cicd_tests.yml b/.github/workflows/cicd_tests.yml
index 4dd0e071fa..2d634c0c43 100644
--- a/.github/workflows/cicd_tests.yml
+++ b/.github/workflows/cicd_tests.yml
@@ -24,8 +24,8 @@ concurrency:
   group: cicd-tests-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
-# These jobs run the CICD tests, type checking, and testing packaging. These use the minimum supported versions of 
-# Python and PyTorch in many places hard-coded as literals, so when support is dropped for a version it is important to 
+# These jobs run the CICD tests, type checking, and testing packaging. These use the minimum supported versions of
+# Python and PyTorch in many places hard-coded as literals, so when support is dropped for a version it is important to
 # go through all jobs and check the versions they use are correct.
 
 jobs:
@@ -273,7 +273,7 @@ jobs:
         # install the latest pytorch for testing
         # however, "pip install monai*.tar.gz" will build cpp/cuda with an isolated
         # fresh torch installation according to pyproject.toml
-        python -m pip install torch>=2.5.1 torchvision
+        python -m pip install torch\>=2.5.1 torchvision
     - name: Check packages
       run: |
         pip uninstall monai
diff --git a/monai/metrics/average_precision.py b/monai/metrics/average_precision.py
index ba0213953c..7dd277bde6 100644
--- a/monai/metrics/average_precision.py
+++ b/monai/metrics/average_precision.py
@@ -16,7 +16,6 @@
 
 import numpy as np
 import numpy.typing as npt
-
 import torch
 
 from monai.utils import Average, look_up_option
diff --git a/monai/metrics/rocauc.py b/monai/metrics/rocauc.py
index 16e4d6bb15..72f0b3730c 100644
--- a/monai/metrics/rocauc.py
+++ b/monai/metrics/rocauc.py
@@ -16,7 +16,6 @@
 
 import numpy as np
 import numpy.typing as npt
-
 import torch
 
 from monai.utils import Average, look_up_option

From ea2816a9f226369cf22ddd9219b75b3056f063f7 Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Fri, 3 Apr 2026 21:53:27 +0100
Subject: [PATCH 25/41] Updates with version bumps

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/build_docs.yml    |  2 +-
 .github/workflows/cicd_tests.yml    | 96 +++++++++++++++--------------
 .github/workflows/cron.yml          |  6 +-
 .github/workflows/docker.yml        |  2 +-
 .github/workflows/pythonapp-gpu.yml |  2 +-
 .github/workflows/release.yml       |  4 +-
 .github/workflows/setupapp.yml      |  4 +-
 pyproject.toml                      |  4 +-
 requirements-dev.txt                |  3 +-
 requirements.txt                    |  3 +-
 setup.cfg                           | 10 +--
 11 files changed, 71 insertions(+), 65 deletions(-)

diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml
index c0b597201d..130c5aa60e 100644
--- a/.github/workflows/build_docs.yml
+++ b/.github/workflows/build_docs.yml
@@ -31,7 +31,7 @@ jobs:
         sudo rm -rf /opt/ghc /usr/local/.ghcup
         sudo docker system prune -f
 
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
 
     - name: Set up Python 3.10
       uses: actions/setup-python@v6
diff --git a/.github/workflows/cicd_tests.yml b/.github/workflows/cicd_tests.yml
index f6fc240657..68857b6187 100644
--- a/.github/workflows/cicd_tests.yml
+++ b/.github/workflows/cicd_tests.yml
@@ -24,9 +24,24 @@ concurrency:
   group: cicd-tests-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
+env:
+  # supported versions of Python
+  PYTHON_VER1: '3.10'
+  PYTHON_VER2: '3.11'
+  PYTHON_VER3: '3.12'
+  PYTHON_VER4: '3.13'
+  PYTHON_VER5: '3.14'
+  # supported versions of PyTorch
+  PYTORCH_VER1: '2.8.0'
+  PYTORCH_VER2: '2.9.1'
+  PYTORCH_VER3: '2.10.0'
+  PYTORCH_VER4: '2.11.0'
+  TORCHVISION_VER: "0.23.0"  # used for testing with lowest PyTorch version
+  PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python  # https://github.com/Project-MONAI/MONAI/issues/4354
+
 # These jobs run the CICD tests, type checking, and testing packaging. These use the minimum supported versions of
-# Python and PyTorch in many places hard-coded as literals, so when support is dropped for a version it is important to
-# go through all jobs and check the versions they use are correct.
+# Python and PyTorch in many places using the above environment variables, when support is dropped for a version it is 
+# important to update these as appropriate.
 
 jobs:
   static-checks:  # Perform static type and other checks using runtests.sh
@@ -44,10 +59,10 @@ jobs:
         sudo docker system prune -f
 
     - uses: actions/checkout@v6
-    - name: Set up Python 3.10
+    - name: Set up Python {{ $PYTHON_VER1 }}
       uses: actions/setup-python@v6
       with:
-        python-version: '3.10'
+        python-version: {{ $PYTHON_VER1 }}
         cache: 'pip'
     - name: Install dependencies
       run: |
@@ -65,31 +80,36 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
+        # Base test cases are to test on all three OSes with the lowest versions of Python and PyTorch, other cases are
+        # added below as special cases to cover other Python and PyTorch versions under Ubuntu
         os: [windows-latest, macOS-latest, ubuntu-latest]
-        python-version: ['3.10']
-        pytorch-version: ['2.6.0']
+        python-version: [{{ $PYTHON_VER1 }}]
+        pytorch-version: [{{ $PYTORCH_VER1 }}]
         include:
         # Test Python versions under Ubuntu with lowest PyTorch version supported
         - os: ubuntu-latest
-          pytorch-version: '2.6.0'
-          python-version: '3.11'
+          pytorch-version: {{ $PYTORCH_VER1 }}
+          python-version: {{ $PYTHON_VER2 }}
+        - os: ubuntu-latest
+          pytorch-version: {{ $PYTORCH_VER1 }}
+          python-version: {{ $PYTHON_VER3 }}
         - os: ubuntu-latest
-          pytorch-version: '2.6.0'
-          python-version: '3.12'
+          pytorch-version: {{ $PYTORCH_VER1 }}
+          python-version: {{ $PYTHON_VER4 }}
         - os: ubuntu-latest
-          pytorch-version: '2.6.0'
-          python-version: '3.13'
+          pytorch-version: {{ $PYTORCH_VER1 }}
+          python-version: {{ $PYTHON_VER5 }}
 
         # Test PyTorch versions under Ubuntu with lowest Python version supported
         - os: ubuntu-latest
-          python-version: '3.10'
-          pytorch-version: '2.7.1'
+          python-version: {{ $PYTHON_VER1 }}
+          pytorch-version: {{ $PYTORCH_VER2 }}
         - os: ubuntu-latest
-          python-version: '3.10'
-          pytorch-version: '2.8.0'
+          python-version: {{ $PYTHON_VER1 }}
+          pytorch-version: {{ $PYTORCH_VER3 }}
         - os: ubuntu-latest
-          python-version: '3.10'
-          pytorch-version: '2.9.0'
+          python-version: {{ $PYTHON_VER1 }}
+          pytorch-version: {{ $PYTORCH_VER4 }}
 
     timeout-minutes: 40
     steps:
@@ -101,28 +121,17 @@ jobs:
         sudo rm -rf /usr/local/lib/android
         sudo rm -rf /opt/ghc /usr/local/.ghcup
         sudo docker system prune -f
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
+        cache: 'pip'
     - name: Prepare pip wheel
       run: |
         which python
         python -m pip install --upgrade pip wheel
         python -m pip install --user more-itertools>=8.0
-    - name: cache weekly timestamp
-      id: pip-cache
-      run: |
-        echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
-        echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
-      shell: bash
-    - name: cache for pip
-      uses: actions/cache@v4
-      id: cache
-      with:
-        path: ${{ steps.pip-cache.outputs.dir }}
-        key: ${{ matrix.os }}-latest-pip-${{ steps.pip-cache.outputs.datew }}
     - name: Install the minimum dependencies
       run: |
         # min. requirements
@@ -156,6 +165,8 @@ jobs:
       matrix:
         os: [windows-latest, macOS-latest, ubuntu-latest]
     timeout-minutes: 120
+    env:
+      QUICKTEST: True
     steps:
     - if: runner.os == 'Linux'
       name: Clean unused tools
@@ -173,10 +184,10 @@ jobs:
         maximum-size: 16GB
         disk-root: "D:"
     - uses: actions/checkout@v6
-    - name: Set up Python 3.10
+    - name: Set up Python {{ $PYTHON_VER1 }}
       uses: actions/setup-python@v6
       with:
-        python-version: '3.10'
+        python-version: {{ $PYTHON_VER1 }}
         cache: 'pip'
     - name: Prepare pip wheel
       run: |
@@ -185,7 +196,7 @@ jobs:
     - if: runner.os == 'windows'
       name: Install torch cpu from pytorch.org (Windows only)
       run: |
-        python -m pip install torch==2.5.1 torchvision==0.20.1+cpu --index-url https://download.pytorch.org/whl/cpu
+        python -m pip install torch==$PYTORCH_VER1 torchvision==$TORCHVISION_VER+cpu --index-url https://download.pytorch.org/whl/cpu
     - if: runner.os == 'Linux'
       name: Install itk pre-release (Linux only)
       run: |
@@ -193,7 +204,7 @@ jobs:
     - name: Install the complete dependencies
       run: |
         python -m pip install --user --upgrade pip wheel
-        python -m pip install torch==2.5.1 torchvision==0.20.1
+        python -m pip install torch==$PYTORCH_VER1 torchvision==$TORCHVISION_VER
         cat "requirements-dev.txt"
         python -m pip install --no-build-isolation -r requirements-dev.txt
         python -m pip list
@@ -209,9 +220,6 @@ jobs:
         python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
         python -c "import monai; monai.config.print_config()"
         # python -m unittest -v
-      env:
-        QUICKTEST: True
-        PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python  # https://github.com/Project-MONAI/MONAI/issues/4354
 
   packaging:  # Test package generation
     runs-on: ubuntu-latest
@@ -230,10 +238,10 @@ jobs:
     - uses: actions/checkout@v6
       with:
         fetch-depth: 0
-    - name: Set up Python 3.10
+    - name: Set up Python {{ $PYTHON_VER1 }}
       uses: actions/setup-python@v6
       with:
-        python-version: '3.10'
+        python-version: {{ $PYTHON_VER1 }}
         cache: 'pip'
     - name: Install dependencies
       run: |
@@ -241,7 +249,7 @@ jobs:
         # install the latest pytorch for testing
         # however, "pip install monai*.tar.gz" will build cpp/cuda with an isolated
         # fresh torch installation according to pyproject.toml
-        python -m pip install torch>=2.5.1 torchvision --extra-index-url https://download.pytorch.org/whl/cpu
+        python -m pip install torch==$PYTORCH_VER1 torchvision --extra-index-url https://download.pytorch.org/whl/cpu
     - name: Check packages
       run: |
         pip uninstall monai
@@ -293,17 +301,15 @@ jobs:
         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
-      env:
-        PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python  # https://github.com/Project-MONAI/MONAI/issues/4354
 
   build-docs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v6
-    - name: Set up Python 3.10
+    - name: Set up Python {{ $PYTHON_VER1 }}
       uses: actions/setup-python@v6
       with:
-        python-version: '3.10'
+        python-version: {{ $PYTHON_VER1 }}
         cache: 'pip'
     - name: Install dependencies
       run: |
diff --git a/.github/workflows/cron.yml b/.github/workflows/cron.yml
index dca48dd9c8..f1ff708a43 100644
--- a/.github/workflows/cron.yml
+++ b/.github/workflows/cron.yml
@@ -67,7 +67,7 @@ jobs:
         if pgrep python; then pkill python; fi
       shell: bash
     - name: Upload coverage
-      uses: codecov/codecov-action@v5
+      uses: codecov/codecov-action@v6
       with:
         fail_ci_if_error: false
         files: ./coverage.xml
@@ -115,7 +115,7 @@ jobs:
         if pgrep python; then pkill python; fi
       shell: bash
     - name: Upload coverage
-      uses: codecov/codecov-action@v5
+      uses: codecov/codecov-action@v6
       with:
         fail_ci_if_error: false
         files: ./coverage.xml
@@ -220,7 +220,7 @@ jobs:
         if pgrep python; then pkill python; fi
       shell: bash
     - name: Upload coverage
-      uses: codecov/codecov-action@v5
+      uses: codecov/codecov-action@v6
       with:
         fail_ci_if_error: false
         files: ./coverage.xml
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
index 8fb53bc64c..78b05c954c 100644
--- a/.github/workflows/docker.yml
+++ b/.github/workflows/docker.yml
@@ -37,7 +37,7 @@ jobs:
           python setup.py build
           cat build/lib/monai/_version.py
       - name: Upload version
-        uses: actions/upload-artifact@v6
+        uses: actions/upload-artifact@v7
         with:
           name: _version.py
           path: build/lib/monai/_version.py
diff --git a/.github/workflows/pythonapp-gpu.yml b/.github/workflows/pythonapp-gpu.yml
index 0381bbe35c..7de9936e9b 100644
--- a/.github/workflows/pythonapp-gpu.yml
+++ b/.github/workflows/pythonapp-gpu.yml
@@ -125,6 +125,6 @@ jobs:
       shell: bash
     - name: Upload coverage
       if: ${{ github.head_ref != 'dev' && github.event.pull_request.merged != true }}
-      uses: codecov/codecov-action@v5
+      uses: codecov/codecov-action@v6
       with:
         files: ./coverage.xml
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index c04f186ee9..d7df47ae19 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -66,7 +66,7 @@ jobs:
 
     - if: matrix.python-version == '3.10' && startsWith(github.ref, 'refs/tags/')
       name: Upload artifacts
-      uses: actions/upload-artifact@v6
+      uses: actions/upload-artifact@v7
       with:
         name: dist
         path: dist/
@@ -109,7 +109,7 @@ jobs:
           python setup.py build
           cat build/lib/monai/_version.py
       - name: Upload version
-        uses: actions/upload-artifact@v6
+        uses: actions/upload-artifact@v7
         with:
           name: _version.py
           path: build/lib/monai/_version.py
diff --git a/.github/workflows/setupapp.yml b/.github/workflows/setupapp.yml
index d0124a50a3..63162b2dac 100644
--- a/.github/workflows/setupapp.yml
+++ b/.github/workflows/setupapp.yml
@@ -72,7 +72,7 @@ jobs:
         if pgrep python; then pkill python; fi
       shell: bash
     - name: Upload coverage
-      uses: codecov/codecov-action@v5
+      uses: codecov/codecov-action@v6
       with:
         fail_ci_if_error: false
         files: ./coverage.xml
@@ -108,7 +108,7 @@ jobs:
         BUILD_MONAI=1 ./runtests.sh --build --coverage --quick --min
         coverage xml --ignore-errors
     - name: Upload coverage
-      uses: codecov/codecov-action@v5
+      uses: codecov/codecov-action@v6
       with:
         fail_ci_if_error: false
         files: ./coverage.xml
diff --git a/pyproject.toml b/pyproject.toml
index 3e63c38d3f..4a222c7d16 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -3,14 +3,14 @@ requires = [
   "wheel",
   "setuptools",
   "more-itertools>=8.0",
-  "torch>=2.4.1",
+  "torch>=2.8.0",
   "ninja",
   "packaging"
 ]
 
 [tool.black]
 line-length = 120
-target-version = ['py39', 'py310', 'py311', 'py312']
+target-version = ['py310', 'py311', 'py312', 'py313']
 include = '\.pyi?$'
 exclude = '''
 (
diff --git a/requirements-dev.txt b/requirements-dev.txt
index a1e79c9197..915d30ed24 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -14,7 +14,7 @@ mccabe
 pep8-naming
 pycodestyle
 pyflakes
-black>=25.1.0
+black>=26.3.1
 isort>=5.1, !=6.0.0
 ruff
 pytype>=2020.6.1, <=2024.4.11; platform_system != "Windows"
@@ -25,6 +25,7 @@ torchio
 torchvision
 psutil
 cucim-cu12; platform_system == "Linux" and python_version <= "3.10"
+cucim-cu13; platform_system == "Linux" and python_version >= '3.11'
 openslide-python
 openslide-bin
 imagecodecs; platform_system == "Linux" or platform_system == "Darwin"
diff --git a/requirements.txt b/requirements.txt
index c43fb21f92..7d283182a4 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,3 +1,2 @@
-torch>=2.4.1; platform_system != "Windows"
-torch>=2.4.1, !=2.7.0; platform_system == "Windows"
+torch>=2.8.0
 numpy>=1.24,<3.0
diff --git a/setup.cfg b/setup.cfg
index 95ea7f9c76..724d1eceb3 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -43,7 +43,7 @@ setup_requires =
     ninja
     packaging
 install_requires =
-    torch>=2.6.0
+    torch>=2.8.0
     numpy>=1.24,<3.0
 
 [options.extras_require]
@@ -62,7 +62,7 @@ all =
     tqdm>=4.47.0
     lmdb
     psutil
-    cucim-cu12; platform_system == "Linux" and python_version >= '3.9' and python_version <= '3.10'
+    cucim-cu12; platform_system == "Linux" and python_version <= '3.10'
     cucim-cu13; platform_system == "Linux" and python_version >= '3.11'
     openslide-python
     openslide-bin
@@ -70,7 +70,7 @@ all =
     imagecodecs; platform_system == "Linux" or platform_system == "Darwin"
     pandas
     einops
-    transformers>=4.36.0, <4.41.0; python_version <= '3.10'
+    transformers>=4.53.0
     mlflow>=2.12.2
     clearml>=1.10.0rc0
     matplotlib>=3.6.3
@@ -84,7 +84,7 @@ all =
     nni; platform_system == "Linux" and "arm" not in platform_machine and "aarch" not in platform_machine
     optuna
     onnx>=1.13.0
-    onnxruntime; python_version <= '3.10'
+    onnxruntime
     zarr
     lpips==0.1.4
     nvidia-ml-py
@@ -119,7 +119,7 @@ lmdb =
 psutil =
     psutil
 cucim =
-    cucim-cu12; platform_system == "Linux" and python_version >= '3.9' and python_version <= '3.10'
+    cucim-cu12; platform_system == "Linux" and python_version <= '3.10'
     cucim-cu13; platform_system == "Linux" and python_version >= '3.11'
 openslide =
     openslide-python

From 63a92bf7015629ff5d7574a0f1e8ca85ab007b09 Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Fri, 3 Apr 2026 22:06:34 +0100
Subject: [PATCH 26/41] Syntax fix

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/cicd_tests.yml | 50 ++++++++++++++++----------------
 1 file changed, 25 insertions(+), 25 deletions(-)

diff --git a/.github/workflows/cicd_tests.yml b/.github/workflows/cicd_tests.yml
index 68857b6187..c1487f4c82 100644
--- a/.github/workflows/cicd_tests.yml
+++ b/.github/workflows/cicd_tests.yml
@@ -36,7 +36,7 @@ env:
   PYTORCH_VER2: '2.9.1'
   PYTORCH_VER3: '2.10.0'
   PYTORCH_VER4: '2.11.0'
-  TORCHVISION_VER: "0.23.0"  # used for testing with lowest PyTorch version
+  TORCHVISION_VER: '0.23.0'  # used for testing with lowest PyTorch version
   PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python  # https://github.com/Project-MONAI/MONAI/issues/4354
 
 # These jobs run the CICD tests, type checking, and testing packaging. These use the minimum supported versions of
@@ -59,10 +59,10 @@ jobs:
         sudo docker system prune -f
 
     - uses: actions/checkout@v6
-    - name: Set up Python {{ $PYTHON_VER1 }}
+    - name: Set up Python ${{ env.PYTHON_VER1 }}
       uses: actions/setup-python@v6
       with:
-        python-version: {{ $PYTHON_VER1 }}
+        python-version: ${{ env.PYTHON_VER1 }}
         cache: 'pip'
     - name: Install dependencies
       run: |
@@ -83,33 +83,33 @@ jobs:
         # Base test cases are to test on all three OSes with the lowest versions of Python and PyTorch, other cases are
         # added below as special cases to cover other Python and PyTorch versions under Ubuntu
         os: [windows-latest, macOS-latest, ubuntu-latest]
-        python-version: [{{ $PYTHON_VER1 }}]
-        pytorch-version: [{{ $PYTORCH_VER1 }}]
+        python-version: [ ${{ env.PYTHON_VER1 }} ]
+        pytorch-version: [ ${{ env.PYTORCH_VER1 }} ]
         include:
         # Test Python versions under Ubuntu with lowest PyTorch version supported
         - os: ubuntu-latest
-          pytorch-version: {{ $PYTORCH_VER1 }}
-          python-version: {{ $PYTHON_VER2 }}
+          pytorch-version: ${{ env.PYTORCH_VER1 }}
+          python-version: ${{ env.PYTHON_VER2 }}
         - os: ubuntu-latest
-          pytorch-version: {{ $PYTORCH_VER1 }}
-          python-version: {{ $PYTHON_VER3 }}
+          pytorch-version: ${{ env.PYTORCH_VER1 }}
+          python-version: ${{ env.PYTHON_VER3 }}
         - os: ubuntu-latest
-          pytorch-version: {{ $PYTORCH_VER1 }}
-          python-version: {{ $PYTHON_VER4 }}
+          pytorch-version: ${{ env.PYTORCH_VER1 }}
+          python-version: ${{ env.PYTHON_VER4 }}
         - os: ubuntu-latest
-          pytorch-version: {{ $PYTORCH_VER1 }}
-          python-version: {{ $PYTHON_VER5 }}
+          pytorch-version: ${{ env.PYTORCH_VER1 }}
+          python-version: ${{ env.PYTHON_VER5 }}
 
         # Test PyTorch versions under Ubuntu with lowest Python version supported
         - os: ubuntu-latest
-          python-version: {{ $PYTHON_VER1 }}
-          pytorch-version: {{ $PYTORCH_VER2 }}
+          python-version: ${{ env.PYTHON_VER1 }}
+          pytorch-version: ${{ env.PYTORCH_VER2 }}
         - os: ubuntu-latest
-          python-version: {{ $PYTHON_VER1 }}
-          pytorch-version: {{ $PYTORCH_VER3 }}
+          python-version: ${{ env.PYTHON_VER1 }}
+          pytorch-version: ${{ env.PYTORCH_VER3 }}
         - os: ubuntu-latest
-          python-version: {{ $PYTHON_VER1 }}
-          pytorch-version: {{ $PYTORCH_VER4 }}
+          python-version: ${{ env.PYTHON_VER1 }}
+          pytorch-version: ${{ env.PYTORCH_VER4 }}
 
     timeout-minutes: 40
     steps:
@@ -184,10 +184,10 @@ jobs:
         maximum-size: 16GB
         disk-root: "D:"
     - uses: actions/checkout@v6
-    - name: Set up Python {{ $PYTHON_VER1 }}
+    - name: Set up Python ${{ env.PYTHON_VER1 }}
       uses: actions/setup-python@v6
       with:
-        python-version: {{ $PYTHON_VER1 }}
+        python-version: ${{ env.PYTHON_VER1 }}
         cache: 'pip'
     - name: Prepare pip wheel
       run: |
@@ -238,10 +238,10 @@ jobs:
     - uses: actions/checkout@v6
       with:
         fetch-depth: 0
-    - name: Set up Python {{ $PYTHON_VER1 }}
+    - name: Set up Python ${{ env.PYTHON_VER1 }}
       uses: actions/setup-python@v6
       with:
-        python-version: {{ $PYTHON_VER1 }}
+        python-version: ${{ env.PYTHON_VER1 }}
         cache: 'pip'
     - name: Install dependencies
       run: |
@@ -306,10 +306,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v6
-    - name: Set up Python {{ $PYTHON_VER1 }}
+    - name: Set up Python ${{ env.PYTHON_VER1 }}
       uses: actions/setup-python@v6
       with:
-        python-version: {{ $PYTHON_VER1 }}
+        python-version: ${{ env.PYTHON_VER1 }}
         cache: 'pip'
     - name: Install dependencies
       run: |

From b6695267eb1b7a5e9ec27dede29be7a124f2fa49 Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Fri, 3 Apr 2026 22:07:57 +0100
Subject: [PATCH 27/41] Syntax fix

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/cicd_tests.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/cicd_tests.yml b/.github/workflows/cicd_tests.yml
index c1487f4c82..1f791f7e08 100644
--- a/.github/workflows/cicd_tests.yml
+++ b/.github/workflows/cicd_tests.yml
@@ -83,8 +83,8 @@ jobs:
         # Base test cases are to test on all three OSes with the lowest versions of Python and PyTorch, other cases are
         # added below as special cases to cover other Python and PyTorch versions under Ubuntu
         os: [windows-latest, macOS-latest, ubuntu-latest]
-        python-version: [ ${{ env.PYTHON_VER1 }} ]
-        pytorch-version: [ ${{ env.PYTORCH_VER1 }} ]
+        python-version: ${{ env.PYTHON_VER1 }}
+        pytorch-version: ${{ env.PYTORCH_VER1 }}
         include:
         # Test Python versions under Ubuntu with lowest PyTorch version supported
         - os: ubuntu-latest

From 22fe6ca63c376f553aa9480c768e389dc1cd7286 Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Fri, 3 Apr 2026 22:16:03 +0100
Subject: [PATCH 28/41] Pre-commit fix

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/cicd_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cicd_tests.yml b/.github/workflows/cicd_tests.yml
index 1f791f7e08..fbbb9af07c 100644
--- a/.github/workflows/cicd_tests.yml
+++ b/.github/workflows/cicd_tests.yml
@@ -40,7 +40,7 @@ env:
   PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python  # https://github.com/Project-MONAI/MONAI/issues/4354
 
 # These jobs run the CICD tests, type checking, and testing packaging. These use the minimum supported versions of
-# Python and PyTorch in many places using the above environment variables, when support is dropped for a version it is 
+# Python and PyTorch in many places using the above environment variables, when support is dropped for a version it is
 # important to update these as appropriate.
 
 jobs:

From edcbffe781982a5fb93b6e2dd096ddb9c21ae4d3 Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Fri, 3 Apr 2026 22:18:50 +0100
Subject: [PATCH 29/41] Redundant file

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/build_docs.yml | 68 --------------------------------
 1 file changed, 68 deletions(-)
 delete mode 100644 .github/workflows/build_docs.yml

diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml
deleted file mode 100644
index 130c5aa60e..0000000000
--- a/.github/workflows/build_docs.yml
+++ /dev/null
@@ -1,68 +0,0 @@
-name: build_docs
-
-on:
-  # build docs test for pull requests and the releasing branches
-  push:
-    branches:
-      - dev
-      - main
-      - releasing/*
-  pull_request:
-    head_ref-ignore:
-      - dev
-
-concurrency:
-  # automatically cancel the previously triggered workflows when there's a newer version
-  group: cicd-tests-${{ github.event.pull_request.number || github.ref }}
-  cancel-in-progress: true
-
-# This test is for building documentation on any relevant push or PR. This ensures that any changes to docs or source
-# files is tested for correct doc building, whereas functional tests can be deferred if only docs were modified.
-
-jobs:
-  build-docs:
-    runs-on: ubuntu-latest
-    steps:
-    - name: Clean unused tools
-      run: |
-        find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
-        sudo rm -rf /usr/share/dotnet
-        sudo rm -rf /usr/local/lib/android
-        sudo rm -rf /opt/ghc /usr/local/.ghcup
-        sudo docker system prune -f
-
-    - uses: actions/checkout@v6
-
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v6
-      with:
-        python-version: '3.10'
-
-    - name: cache weekly timestamp
-      id: pip-cache
-      run: |
-        echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
-
-    - name: cache for pip
-      uses: actions/cache@v4
-      id: cache
-      with:
-        path: |
-          ~/.cache/pip
-          ~/.cache/torch
-        key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip wheel
-        python -m pip install -r docs/requirements.txt
-
-    - name: Make html
-      run: |
-        cd docs/
-        make clean
-        make html 2>&1 | tee tmp_log
-        if [[ $(grep -c "ERROR:" tmp_log) != 0 ]]; then echo "Found errors:"; grep "ERROR:" tmp_log; exit 1; fi
-        sed '/WARNING.*pip/d' tmp_log > tmp_log1; mv tmp_log1 tmp_log  # monai#7133
-        if [[ $(grep -c "WARNING:" tmp_log) != 0 ]]; then echo "Found warnings:"; grep "WARNING:" tmp_log; exit 1; fi
-      shell: bash

From 30616b109692342aba754b53aa97ffda1aafb675 Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Fri, 3 Apr 2026 22:27:16 +0100
Subject: [PATCH 30/41] Syntax fix

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/cicd_tests.yml | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/cicd_tests.yml b/.github/workflows/cicd_tests.yml
index fbbb9af07c..3ddec1d308 100644
--- a/.github/workflows/cicd_tests.yml
+++ b/.github/workflows/cicd_tests.yml
@@ -26,17 +26,17 @@ concurrency:
 
 env:
   # supported versions of Python
-  PYTHON_VER1: '3.10'
-  PYTHON_VER2: '3.11'
-  PYTHON_VER3: '3.12'
-  PYTHON_VER4: '3.13'
-  PYTHON_VER5: '3.14'
+  PYTHON_VER1: "3.10"
+  PYTHON_VER2: "3.11"
+  PYTHON_VER3: "3.12"
+  PYTHON_VER4: "3.13"
+  PYTHON_VER5: "3.14"
   # supported versions of PyTorch
-  PYTORCH_VER1: '2.8.0'
-  PYTORCH_VER2: '2.9.1'
-  PYTORCH_VER3: '2.10.0'
-  PYTORCH_VER4: '2.11.0'
-  TORCHVISION_VER: '0.23.0'  # used for testing with lowest PyTorch version
+  PYTORCH_VER1: "2.8.0"
+  PYTORCH_VER2: "2.9.1"
+  PYTORCH_VER3: "2.10.0"
+  PYTORCH_VER4: "2.11.0"
+  TORCHVISION_VER: "0.23.0"  # used for testing with lowest PyTorch version
   PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python  # https://github.com/Project-MONAI/MONAI/issues/4354
 
 # These jobs run the CICD tests, type checking, and testing packaging. These use the minimum supported versions of

From 0b6ec1cce84cbd5e4eddfa42b62d5795f39ba4d5 Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Fri, 3 Apr 2026 22:40:38 +0100
Subject: [PATCH 31/41] Matrix restrictions

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/cicd_tests.yml | 52 ++++++++++++++++----------------
 1 file changed, 26 insertions(+), 26 deletions(-)

diff --git a/.github/workflows/cicd_tests.yml b/.github/workflows/cicd_tests.yml
index 3ddec1d308..90f8a9e8b2 100644
--- a/.github/workflows/cicd_tests.yml
+++ b/.github/workflows/cicd_tests.yml
@@ -26,17 +26,17 @@ concurrency:
 
 env:
   # supported versions of Python
-  PYTHON_VER1: "3.10"
-  PYTHON_VER2: "3.11"
-  PYTHON_VER3: "3.12"
-  PYTHON_VER4: "3.13"
-  PYTHON_VER5: "3.14"
+  PYTHON_VER1: '3.10'
+  PYTHON_VER2: '3.11'
+  PYTHON_VER3: '3.12'
+  PYTHON_VER4: '3.13'
+  PYTHON_VER5: '3.14'
   # supported versions of PyTorch
-  PYTORCH_VER1: "2.8.0"
-  PYTORCH_VER2: "2.9.1"
-  PYTORCH_VER3: "2.10.0"
-  PYTORCH_VER4: "2.11.0"
-  TORCHVISION_VER: "0.23.0"  # used for testing with lowest PyTorch version
+  PYTORCH_VER1: '2.8.0'
+  PYTORCH_VER2: '2.9.1'
+  PYTORCH_VER3: '2.10.0'
+  PYTORCH_VER4: '2.11.0'
+  TORCHVISION_VER: '0.23.0'  # used for testing with lowest PyTorch version
   PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python  # https://github.com/Project-MONAI/MONAI/issues/4354
 
 # These jobs run the CICD tests, type checking, and testing packaging. These use the minimum supported versions of
@@ -83,33 +83,33 @@ jobs:
         # Base test cases are to test on all three OSes with the lowest versions of Python and PyTorch, other cases are
         # added below as special cases to cover other Python and PyTorch versions under Ubuntu
         os: [windows-latest, macOS-latest, ubuntu-latest]
-        python-version: ${{ env.PYTHON_VER1 }}
-        pytorch-version: ${{ env.PYTORCH_VER1 }}
+        python-version: ['3.10']
+        pytorch-version: ['2.8.0']
         include:
         # Test Python versions under Ubuntu with lowest PyTorch version supported
         - os: ubuntu-latest
-          pytorch-version: ${{ env.PYTORCH_VER1 }}
-          python-version: ${{ env.PYTHON_VER2 }}
+          pytorch-version: '2.8.0'
+          python-version: '3.11'
         - os: ubuntu-latest
-          pytorch-version: ${{ env.PYTORCH_VER1 }}
-          python-version: ${{ env.PYTHON_VER3 }}
+          pytorch-version: '2.8.0'
+          python-version: '3.12'
         - os: ubuntu-latest
-          pytorch-version: ${{ env.PYTORCH_VER1 }}
-          python-version: ${{ env.PYTHON_VER4 }}
+          pytorch-version: '2.8.0'
+          python-version: '3.13'
         - os: ubuntu-latest
-          pytorch-version: ${{ env.PYTORCH_VER1 }}
-          python-version: ${{ env.PYTHON_VER5 }}
+          pytorch-version: '2.8.0'
+          python-version: '3.14'
 
         # Test PyTorch versions under Ubuntu with lowest Python version supported
         - os: ubuntu-latest
-          python-version: ${{ env.PYTHON_VER1 }}
-          pytorch-version: ${{ env.PYTORCH_VER2 }}
+          python-version: '3.10'
+          pytorch-version: '2.9.1'
         - os: ubuntu-latest
-          python-version: ${{ env.PYTHON_VER1 }}
-          pytorch-version: ${{ env.PYTORCH_VER3 }}
+          python-version: '3.10'
+          pytorch-version: '2.10.0'
         - os: ubuntu-latest
-          python-version: ${{ env.PYTHON_VER1 }}
-          pytorch-version: ${{ env.PYTORCH_VER4 }}
+          python-version: '3.10'
+          pytorch-version: '2.11.0'
 
     timeout-minutes: 40
     steps:

From 6782838f430c6ee0da4ad0bd510601d91ef639ad Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Sat, 4 Apr 2026 23:49:33 +0100
Subject: [PATCH 32/41] Updates for new black formatting

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/cicd_tests.yml              | 13 ++++-----
 monai/apps/detection/transforms/dictionary.py | 27 ++++++++-----------
 monai/apps/detection/utils/anchor_utils.py    | 13 ++++-----
 monai/apps/reconstruction/transforms/array.py |  4 +--
 monai/bundle/utils.py                         |  6 ++---
 monai/losses/dice.py                          |  5 ++--
 monai/losses/focal_loss.py                    |  5 ++--
 pyproject.toml                                |  6 +++--
 runtests.sh                                   |  4 +--
 9 files changed, 37 insertions(+), 46 deletions(-)

diff --git a/.github/workflows/cicd_tests.yml b/.github/workflows/cicd_tests.yml
index 90f8a9e8b2..9efa9e92dd 100644
--- a/.github/workflows/cicd_tests.yml
+++ b/.github/workflows/cicd_tests.yml
@@ -24,6 +24,7 @@ concurrency:
   group: cicd-tests-${{ github.event.pull_request.number || github.ref }}
   cancel-in-progress: true
 
+# Supported versions of Python and PyTorch are listed here for use below and as documentation
 env:
   # supported versions of Python
   PYTHON_VER1: '3.10'
@@ -40,8 +41,8 @@ env:
   PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python  # https://github.com/Project-MONAI/MONAI/issues/4354
 
 # These jobs run the CICD tests, type checking, and testing packaging. These use the minimum supported versions of
-# Python and PyTorch in many places using the above environment variables, when support is dropped for a version it is
-# important to update these as appropriate.
+# Python and PyTorch in many places using the above environment variables but also hard coded where necessary.
+# When support is dropped for a version it is important to update these as appropriate.
 
 jobs:
   static-checks:  # Perform static type and other checks using runtests.sh
@@ -97,7 +98,7 @@ jobs:
           pytorch-version: '2.8.0'
           python-version: '3.13'
         - os: ubuntu-latest
-          pytorch-version: '2.8.0'
+          pytorch-version: '2.9.0'
           python-version: '3.14'
 
         # Test PyTorch versions under Ubuntu with lowest Python version supported
@@ -196,7 +197,7 @@ jobs:
     - if: runner.os == 'windows'
       name: Install torch cpu from pytorch.org (Windows only)
       run: |
-        python -m pip install torch==$PYTORCH_VER1 torchvision==$TORCHVISION_VER+cpu --index-url https://download.pytorch.org/whl/cpu
+        python -m pip install torch==${PYTORCH_VER1} torchvision==${TORCHVISION_VER}+cpu --index-url https://download.pytorch.org/whl/cpu
     - if: runner.os == 'Linux'
       name: Install itk pre-release (Linux only)
       run: |
@@ -204,7 +205,7 @@ jobs:
     - name: Install the complete dependencies
       run: |
         python -m pip install --user --upgrade pip wheel
-        python -m pip install torch==$PYTORCH_VER1 torchvision==$TORCHVISION_VER
+        python -m pip install torch==${PYTORCH_VER1} torchvision==${TORCHVISION_VER}
         cat "requirements-dev.txt"
         python -m pip install --no-build-isolation -r requirements-dev.txt
         python -m pip list
@@ -249,7 +250,7 @@ jobs:
         # install the latest pytorch for testing
         # however, "pip install monai*.tar.gz" will build cpp/cuda with an isolated
         # fresh torch installation according to pyproject.toml
-        python -m pip install torch==$PYTORCH_VER1 torchvision --extra-index-url https://download.pytorch.org/whl/cpu
+        python -m pip install torch==${PYTORCH_VER1} torchvision --extra-index-url https://download.pytorch.org/whl/cpu
     - name: Check packages
       run: |
         pip uninstall monai
diff --git a/monai/apps/detection/transforms/dictionary.py b/monai/apps/detection/transforms/dictionary.py
index f52ab53531..737ec70b36 100644
--- a/monai/apps/detection/transforms/dictionary.py
+++ b/monai/apps/detection/transforms/dictionary.py
@@ -125,10 +125,8 @@ def __init__(self, box_keys: KeysCollection, box_ref_image_keys: str, allow_miss
         super().__init__(box_keys, allow_missing_keys)
         box_ref_image_keys_tuple = ensure_tuple(box_ref_image_keys)
         if len(box_ref_image_keys_tuple) > 1:
-            raise ValueError(
-                "Please provide a single key for box_ref_image_keys.\
-                All boxes of box_keys are attached to box_ref_image_keys."
-            )
+            raise ValueError("Please provide a single key for box_ref_image_keys.\
+                All boxes of box_keys are attached to box_ref_image_keys.")
         self.box_ref_image_keys = box_ref_image_keys
 
     def __call__(self, data: Mapping[Hashable, NdarrayOrTensor]) -> dict[Hashable, NdarrayOrTensor]:
@@ -290,8 +288,8 @@ def __init__(
         box_ref_image_keys_tuple = ensure_tuple(box_ref_image_keys)
         if len(box_ref_image_keys_tuple) > 1:
             raise ValueError(
-                "Please provide a single key for box_ref_image_keys.\
-                All boxes of box_keys are attached to box_ref_image_keys."
+                "Please provide a single key for `box_ref_image_keys`. "
+                "All boxes of box_keys are attached to `box_ref_image_keys`."
             )
         self.box_ref_image_keys = box_ref_image_keys
         self.image_meta_key = image_meta_key or f"{box_ref_image_keys}_{image_meta_key_postfix}"
@@ -311,8 +309,7 @@ def extract_affine(self, data: Mapping[Hashable, torch.Tensor]) -> tuple[Ndarray
             raise ValueError(f"{meta_key} is not found. Please check whether it is the correct the image meta key.")
         if "affine" not in meta_dict:
             raise ValueError(
-                f"'affine' is not found in {meta_key}. \
-                Please check whether it is the correct the image meta key."
+                f"Key 'affine' not found in {meta_key}. Please check it is the correct the image meta key."
             )
         affine: NdarrayOrTensor = meta_dict["affine"]
 
@@ -816,15 +813,15 @@ def __init__(
         box_keys_tuple = ensure_tuple(box_keys)
         if len(box_keys_tuple) != 1:
             raise ValueError(
-                "Please provide a single key for box_keys.\
-                All label_keys are attached to this box_keys."
+                "Please provide at least one key for `box_keys`. All `label_keys` are attached to this `box_keys`."
             )
         box_ref_image_keys_tuple = ensure_tuple(box_ref_image_keys)
         if len(box_ref_image_keys_tuple) != 1:
             raise ValueError(
-                "Please provide a single key for box_ref_image_keys.\
-                All box_keys and label_keys are attached to this box_ref_image_keys."
+                "Please provide at least one key for `box_ref_image_keys`. "
+                "All box_keys and label_keys are attached to this `box_ref_image_keys`."
             )
+
         self.label_keys = ensure_tuple(label_keys)
         super().__init__(box_keys_tuple, allow_missing_keys)
 
@@ -1091,10 +1088,8 @@ def __init__(
 
         box_keys_tuple = ensure_tuple(box_keys)
         if len(box_keys_tuple) != 1:
-            raise ValueError(
-                "Please provide a single key for box_keys.\
-                All label_keys are attached to this box_keys."
-            )
+            raise ValueError("Please provide a single key for box_keys.\
+                All label_keys are attached to this box_keys.")
         self.box_keys = box_keys_tuple[0]
         self.label_keys = ensure_tuple(label_keys)
 
diff --git a/monai/apps/detection/utils/anchor_utils.py b/monai/apps/detection/utils/anchor_utils.py
index 20f6fc6025..9ee1964215 100644
--- a/monai/apps/detection/utils/anchor_utils.py
+++ b/monai/apps/detection/utils/anchor_utils.py
@@ -124,10 +124,7 @@ def __init__(
             aspect_ratios = (aspect_ratios,) * len(self.sizes)
 
         if len(self.sizes) != len(aspect_ratios):
-            raise ValueError(
-                "len(sizes) and len(aspect_ratios) should be equal. \
-                It represents the number of feature maps."
-            )
+            raise ValueError("The number of feature maps, `len(sizes)` and `len(aspect_ratios)`, should be equal.")
 
         spatial_dims = len(ensure_tuple(aspect_ratios[0][0])) + 1
         spatial_dims = look_up_option(spatial_dims, [2, 3])
@@ -173,14 +170,14 @@ def generate_anchors(
         aspect_ratios_t = torch.as_tensor(aspect_ratios, dtype=dtype, device=device)  # sized (M,) or (M,2)
         if (self.spatial_dims >= 3) and (len(aspect_ratios_t.shape) != 2):
             raise ValueError(
-                f"In {self.spatial_dims}-D image, aspect_ratios for each level should be \
-                {len(aspect_ratios_t.shape) - 1}-D. But got aspect_ratios with shape {aspect_ratios_t.shape}."
+                f"In {self.spatial_dims}-D image, aspect_ratios for each level should be "
+                f"{len(aspect_ratios_t.shape) - 1}-D. Got aspect_ratios with shape {aspect_ratios_t.shape}."
             )
 
         if (self.spatial_dims >= 3) and (aspect_ratios_t.shape[1] != self.spatial_dims - 1):
             raise ValueError(
-                f"In {self.spatial_dims}-D image, aspect_ratios for each level should has \
-                shape (_,{self.spatial_dims - 1}). But got aspect_ratios with shape {aspect_ratios_t.shape}."
+                f"In {self.spatial_dims}-D image, aspect_ratios for each level should have "
+                f"shape (_,{self.spatial_dims - 1}). Got aspect_ratios with shape {aspect_ratios_t.shape}."
             )
 
         # if 2d, w:h = 1:aspect_ratios
diff --git a/monai/apps/reconstruction/transforms/array.py b/monai/apps/reconstruction/transforms/array.py
index 911d7a06bb..64fc8cdd2d 100644
--- a/monai/apps/reconstruction/transforms/array.py
+++ b/monai/apps/reconstruction/transforms/array.py
@@ -62,8 +62,8 @@ def __init__(
         """
         if len(center_fractions) != len(accelerations):
             raise ValueError(
-                "Number of center fractions \
-                should match number of accelerations"
+                "Number of center fractions `len(center_fractions)` "
+                "should match number of accelerations `len(accelerations)`."
             )
 
         self.center_fractions = center_fractions
diff --git a/monai/bundle/utils.py b/monai/bundle/utils.py
index 53d619f234..d37d7f1c05 100644
--- a/monai/bundle/utils.py
+++ b/monai/bundle/utils.py
@@ -124,10 +124,8 @@
         "run_name": None,
         # may fill it at runtime
         "save_execute_config": True,
-        "is_not_rank0": (
-            "$torch.distributed.is_available() \
-                and torch.distributed.is_initialized() and torch.distributed.get_rank() > 0"
-        ),
+        "is_not_rank0": ("$torch.distributed.is_available() \
+                and torch.distributed.is_initialized() and torch.distributed.get_rank() > 0"),
         # MLFlowHandler config for the trainer
         "trainer": {
             "_target_": "MLFlowHandler",
diff --git a/monai/losses/dice.py b/monai/losses/dice.py
index cd76ec1323..b4558f930c 100644
--- a/monai/losses/dice.py
+++ b/monai/losses/dice.py
@@ -204,9 +204,8 @@ def forward(self, input: torch.Tensor, target: torch.Tensor) -> torch.Tensor:
             else:
                 if self.class_weight.shape[0] != num_of_classes:
                     raise ValueError(
-                        """the length of the `weight` sequence should be the same as the number of classes.
-                        If `include_background=False`, the weight should not include
-                        the background category class 0."""
+                        "The length of the `weight` sequence should be the same as the number of classes. "
+                        "If `include_background=False`, the weight should not include the background category class 0."
                     )
             if self.class_weight.min() < 0:
                 raise ValueError("the value/values of the `weight` should be no less than 0.")
diff --git a/monai/losses/focal_loss.py b/monai/losses/focal_loss.py
index caa237fca8..7773cbdc9a 100644
--- a/monai/losses/focal_loss.py
+++ b/monai/losses/focal_loss.py
@@ -184,9 +184,8 @@ def forward(self, input: torch.Tensor, target: torch.Tensor) -> torch.Tensor:
             else:
                 if self.class_weight.shape[0] != num_of_classes:
                     raise ValueError(
-                        """the length of the `weight` sequence should be the same as the number of classes.
-                        If `include_background=False`, the weight should not include
-                        the background category class 0."""
+                        "The length of the `weight` sequence should be the same as the number of classes. "
+                        "If `include_background=False`, the weight should not include the background category class 0."
                     )
             if self.class_weight.min() < 0:
                 raise ValueError("the value/values of the `weight` should be no less than 0.")
diff --git a/pyproject.toml b/pyproject.toml
index 4a222c7d16..325622b66a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,7 +10,8 @@ requires = [
 
 [tool.black]
 line-length = 120
-target-version = ['py310', 'py311', 'py312', 'py313']
+target-version = ['py310']
+skip-magic-trailing-comma = true
 include = '\.pyi?$'
 exclude = '''
 (
@@ -30,6 +31,7 @@ exclude = '''
     | dist
   )/
   # also separately exclude a file named versioneer.py
+  | versioneer.py
   | monai/_version.py
 )
 '''
@@ -40,7 +42,7 @@ exclude = "monai/bundle/__main__.py"
 
 [tool.ruff]
 line-length = 120
-target-version = "py39"
+target-version = "py310"
 
 [tool.ruff.lint]
 select = [
diff --git a/runtests.sh b/runtests.sh
index a1551fe8dd..01401af4d7 100755
--- a/runtests.sh
+++ b/runtests.sh
@@ -516,9 +516,9 @@ then
 
     if [ $doBlackFix = true ]
     then
-        ${cmdPrefix}"${PY_EXE}" -m black --skip-magic-trailing-comma "$homedir"
+        ${cmdPrefix}"${PY_EXE}" -m black "$homedir"
     else
-        ${cmdPrefix}"${PY_EXE}" -m black --skip-magic-trailing-comma --check "$homedir"
+        ${cmdPrefix}"${PY_EXE}" -m black --check "$homedir"
     fi
 
     black_status=$?

From 87c6fee5be41ea84461c78c01ddbb820872b8a98 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sat, 4 Apr 2026 22:50:25 +0000
Subject: [PATCH 33/41] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 monai/apps/pathology/inferers/inferer.py      |  3 ++-
 monai/apps/pathology/transforms/post/array.py |  2 +-
 monai/bundle/scripts.py                       |  3 ++-
 monai/engines/evaluator.py                    |  3 ++-
 monai/engines/trainer.py                      |  3 ++-
 monai/losses/hausdorff_loss.py                |  2 +-
 monai/losses/sure_loss.py                     |  2 +-
 monai/networks/layers/conjugate_gradient.py   |  2 +-
 monai/networks/nets/dynunet.py                | 23 +++++++++----------
 monai/networks/nets/vista3d.py                |  3 ++-
 monai/optimizers/lr_finder.py                 |  3 ++-
 monai/transforms/adaptors.py                  |  2 +-
 monai/transforms/intensity/dictionary.py      |  2 +-
 monai/transforms/io/array.py                  |  2 +-
 monai/transforms/io/dictionary.py             |  2 +-
 monai/transforms/spatial/array.py             |  4 ++--
 monai/transforms/utility/array.py             |  3 ++-
 monai/utils/component_store.py                |  3 ++-
 monai/utils/decorators.py                     |  2 +-
 monai/visualize/gradient_based.py             |  3 ++-
 tests/bundle/test_config_item.py              |  2 +-
 tests/test_utils.py                           |  3 ++-
 22 files changed, 43 insertions(+), 34 deletions(-)

diff --git a/monai/apps/pathology/inferers/inferer.py b/monai/apps/pathology/inferers/inferer.py
index 392cba221f..f4ba74adac 100644
--- a/monai/apps/pathology/inferers/inferer.py
+++ b/monai/apps/pathology/inferers/inferer.py
@@ -12,7 +12,8 @@
 from __future__ import annotations
 
 from collections.abc import Sequence
-from typing import Any, Callable
+from typing import Any
+from collections.abc import Callable
 
 import numpy as np
 import torch
diff --git a/monai/apps/pathology/transforms/post/array.py b/monai/apps/pathology/transforms/post/array.py
index 561ed3ae20..a3892049e1 100644
--- a/monai/apps/pathology/transforms/post/array.py
+++ b/monai/apps/pathology/transforms/post/array.py
@@ -13,7 +13,7 @@
 
 import warnings
 from collections.abc import Sequence
-from typing import Callable
+from collections.abc import Callable
 
 import numpy as np
 import torch
diff --git a/monai/bundle/scripts.py b/monai/bundle/scripts.py
index fa9ba27096..9be611313a 100644
--- a/monai/bundle/scripts.py
+++ b/monai/bundle/scripts.py
@@ -23,7 +23,8 @@
 from pydoc import locate
 from shutil import copyfile
 from textwrap import dedent
-from typing import Any, Callable
+from typing import Any
+from collections.abc import Callable
 
 import torch
 from torch.cuda import is_available
diff --git a/monai/engines/evaluator.py b/monai/engines/evaluator.py
index 836b407ac5..4178dad9b9 100644
--- a/monai/engines/evaluator.py
+++ b/monai/engines/evaluator.py
@@ -13,7 +13,8 @@
 
 import warnings
 from collections.abc import Iterable, Sequence
-from typing import TYPE_CHECKING, Any, Callable
+from typing import TYPE_CHECKING, Any
+from collections.abc import Callable
 
 import torch
 from torch.utils.data import DataLoader
diff --git a/monai/engines/trainer.py b/monai/engines/trainer.py
index 15033cabac..b958ca4ec2 100644
--- a/monai/engines/trainer.py
+++ b/monai/engines/trainer.py
@@ -13,7 +13,8 @@
 
 import warnings
 from collections.abc import Iterable, Sequence
-from typing import TYPE_CHECKING, Any, Callable
+from typing import TYPE_CHECKING, Any
+from collections.abc import Callable
 
 import torch
 from torch.optim.optimizer import Optimizer
diff --git a/monai/losses/hausdorff_loss.py b/monai/losses/hausdorff_loss.py
index b75433e1da..017606ac08 100644
--- a/monai/losses/hausdorff_loss.py
+++ b/monai/losses/hausdorff_loss.py
@@ -17,7 +17,7 @@
 from __future__ import annotations
 
 import warnings
-from typing import Callable
+from collections.abc import Callable
 
 import torch
 from torch.nn.modules.loss import _Loss
diff --git a/monai/losses/sure_loss.py b/monai/losses/sure_loss.py
index cc02317f72..53583b9051 100644
--- a/monai/losses/sure_loss.py
+++ b/monai/losses/sure_loss.py
@@ -11,7 +11,7 @@
 
 from __future__ import annotations
 
-from typing import Callable
+from collections.abc import Callable
 
 import torch
 import torch.nn as nn
diff --git a/monai/networks/layers/conjugate_gradient.py b/monai/networks/layers/conjugate_gradient.py
index 93a45930d7..9432f15b6c 100644
--- a/monai/networks/layers/conjugate_gradient.py
+++ b/monai/networks/layers/conjugate_gradient.py
@@ -11,7 +11,7 @@
 
 from __future__ import annotations
 
-from typing import Callable
+from collections.abc import Callable
 
 import torch
 from torch import nn
diff --git a/monai/networks/nets/dynunet.py b/monai/networks/nets/dynunet.py
index ec418469bb..d130b886a7 100644
--- a/monai/networks/nets/dynunet.py
+++ b/monai/networks/nets/dynunet.py
@@ -12,7 +12,6 @@
 # isort: dont-add-import: from __future__ import annotations
 
 from collections.abc import Sequence
-from typing import Optional, Union
 
 import torch
 import torch.nn as nn
@@ -33,7 +32,7 @@ class DynUNetSkipLayer(nn.Module):
     forward passes of the network.
     """
 
-    heads: Optional[list[torch.Tensor]]
+    heads: list[torch.Tensor] | None
 
     def __init__(self, index, downsample, upsample, next_layer, heads=None, super_head=None):
         super().__init__()
@@ -133,13 +132,13 @@ def __init__(
         spatial_dims: int,
         in_channels: int,
         out_channels: int,
-        kernel_size: Sequence[Union[Sequence[int], int]],
-        strides: Sequence[Union[Sequence[int], int]],
-        upsample_kernel_size: Sequence[Union[Sequence[int], int]],
-        filters: Optional[Sequence[int]] = None,
-        dropout: Optional[Union[tuple, str, float]] = None,
-        norm_name: Union[tuple, str] = ("INSTANCE", {"affine": True}),
-        act_name: Union[tuple, str] = ("leakyrelu", {"inplace": True, "negative_slope": 0.01}),
+        kernel_size: Sequence[Sequence[int] | int],
+        strides: Sequence[Sequence[int] | int],
+        upsample_kernel_size: Sequence[Sequence[int] | int],
+        filters: Sequence[int] | None = None,
+        dropout: tuple | str | float | None = None,
+        norm_name: tuple | str = ("INSTANCE", {"affine": True}),
+        act_name: tuple | str = ("leakyrelu", {"inplace": True, "negative_slope": 0.01}),
         deep_supervision: bool = False,
         deep_supr_num: int = 1,
         res_block: bool = False,
@@ -326,10 +325,10 @@ def get_module_list(
         self,
         in_channels: list[int],
         out_channels: list[int],
-        kernel_size: Sequence[Union[Sequence[int], int]],
-        strides: Sequence[Union[Sequence[int], int]],
+        kernel_size: Sequence[Sequence[int] | int],
+        strides: Sequence[Sequence[int] | int],
         conv_block: nn.Module,
-        upsample_kernel_size: Optional[Sequence[Union[Sequence[int], int]]] = None,
+        upsample_kernel_size: Sequence[Sequence[int] | int] | None = None,
         trans_bias: bool = False,
     ):
         layers = []
diff --git a/monai/networks/nets/vista3d.py b/monai/networks/nets/vista3d.py
index 5490931d8d..df5250dac0 100644
--- a/monai/networks/nets/vista3d.py
+++ b/monai/networks/nets/vista3d.py
@@ -13,7 +13,8 @@
 
 import math
 from collections.abc import Sequence
-from typing import Any, Callable
+from typing import Any
+from collections.abc import Callable
 
 import numpy as np
 import torch
diff --git a/monai/optimizers/lr_finder.py b/monai/optimizers/lr_finder.py
index aa2e4567b3..bae04efff8 100644
--- a/monai/optimizers/lr_finder.py
+++ b/monai/optimizers/lr_finder.py
@@ -15,7 +15,8 @@
 import types
 import warnings
 from functools import partial
-from typing import TYPE_CHECKING, Any, Callable
+from typing import TYPE_CHECKING, Any
+from collections.abc import Callable
 
 import numpy as np
 import torch
diff --git a/monai/transforms/adaptors.py b/monai/transforms/adaptors.py
index 5a0c24c7f6..b3c8b34f5c 100644
--- a/monai/transforms/adaptors.py
+++ b/monai/transforms/adaptors.py
@@ -123,7 +123,7 @@ def __call__(self, img, seg):
 
 from __future__ import annotations
 
-from typing import Callable
+from collections.abc import Callable
 
 __all__ = ["adaptor", "apply_alias", "to_kwargs", "FunctionSignature"]
 
diff --git a/monai/transforms/intensity/dictionary.py b/monai/transforms/intensity/dictionary.py
index fac46f2487..f0878c0c99 100644
--- a/monai/transforms/intensity/dictionary.py
+++ b/monai/transforms/intensity/dictionary.py
@@ -18,7 +18,7 @@
 from __future__ import annotations
 
 from collections.abc import Hashable, Mapping, Sequence
-from typing import Callable
+from collections.abc import Callable
 
 import numpy as np
 
diff --git a/monai/transforms/io/array.py b/monai/transforms/io/array.py
index f0c1d1949d..95beb5ae96 100644
--- a/monai/transforms/io/array.py
+++ b/monai/transforms/io/array.py
@@ -23,7 +23,7 @@
 from collections.abc import Sequence
 from pathlib import Path
 from pydoc import locate
-from typing import Callable
+from collections.abc import Callable
 
 import numpy as np
 import torch
diff --git a/monai/transforms/io/dictionary.py b/monai/transforms/io/dictionary.py
index be1e78db8a..fc634baa30 100644
--- a/monai/transforms/io/dictionary.py
+++ b/monai/transforms/io/dictionary.py
@@ -19,7 +19,7 @@
 
 from collections.abc import Hashable, Mapping
 from pathlib import Path
-from typing import Callable
+from collections.abc import Callable
 
 import numpy as np
 
diff --git a/monai/transforms/spatial/array.py b/monai/transforms/spatial/array.py
index 55dab79c3d..6aba71a0f6 100644
--- a/monai/transforms/spatial/array.py
+++ b/monai/transforms/spatial/array.py
@@ -18,7 +18,7 @@
 from collections.abc import Callable, Sequence
 from copy import deepcopy
 from itertools import zip_longest
-from typing import Any, Optional, Union, cast
+from typing import Any, Optional, cast
 
 import numpy as np
 import torch
@@ -118,7 +118,7 @@
     "RandSimulateLowResolution",
 ]
 
-RandRange = Optional[Union[Sequence[Union[tuple[float, float], float]], float]]
+RandRange = Optional[Sequence[tuple[float, float] | float] | float]
 
 
 class SpatialResample(InvertibleTransform, LazyTransform):
diff --git a/monai/transforms/utility/array.py b/monai/transforms/utility/array.py
index 7df6e2c5ef..1483441dc1 100644
--- a/monai/transforms/utility/array.py
+++ b/monai/transforms/utility/array.py
@@ -21,7 +21,8 @@
 from collections.abc import Hashable, Mapping, Sequence
 from copy import deepcopy
 from functools import partial
-from typing import Any, Callable
+from typing import Any
+from collections.abc import Callable
 
 import numpy as np
 import torch
diff --git a/monai/utils/component_store.py b/monai/utils/component_store.py
index bf0d632ddd..6713b61769 100644
--- a/monai/utils/component_store.py
+++ b/monai/utils/component_store.py
@@ -15,7 +15,8 @@
 from collections.abc import Iterable
 from keyword import iskeyword
 from textwrap import dedent, indent
-from typing import Any, Callable, TypeVar
+from typing import Any, TypeVar
+from collections.abc import Callable
 
 T = TypeVar("T")
 
diff --git a/monai/utils/decorators.py b/monai/utils/decorators.py
index a784510c64..b6cfbf2bf7 100644
--- a/monai/utils/decorators.py
+++ b/monai/utils/decorators.py
@@ -16,7 +16,7 @@
 __all__ = ["RestartGenerator", "MethodReplacer"]
 
 from collections.abc import Generator
-from typing import Callable
+from collections.abc import Callable
 
 
 class RestartGenerator:
diff --git a/monai/visualize/gradient_based.py b/monai/visualize/gradient_based.py
index c54c9cd4ca..d858a3dfce 100644
--- a/monai/visualize/gradient_based.py
+++ b/monai/visualize/gradient_based.py
@@ -12,7 +12,8 @@
 from __future__ import annotations
 
 from functools import partial
-from typing import Any, Callable
+from typing import Any
+from collections.abc import Callable
 
 import torch
 
diff --git a/tests/bundle/test_config_item.py b/tests/bundle/test_config_item.py
index 4909ecf6be..e9f9d5ef8d 100644
--- a/tests/bundle/test_config_item.py
+++ b/tests/bundle/test_config_item.py
@@ -13,7 +13,7 @@
 
 import unittest
 from functools import partial
-from typing import Callable
+from collections.abc import Callable
 
 import torch
 from parameterized import parameterized
diff --git a/tests/test_utils.py b/tests/test_utils.py
index e365237401..3e7d831b07 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -34,7 +34,8 @@
 from itertools import product
 from pathlib import Path
 from subprocess import PIPE, Popen
-from typing import Any, Callable
+from typing import Any
+from collections.abc import Callable
 from urllib.error import ContentTooShortError, HTTPError
 
 import numpy as np

From 9b385866e59dac7abecd6b90c9949a15912e7693 Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Sun, 5 Apr 2026 00:18:40 +0100
Subject: [PATCH 34/41] Format fixes and script fixes

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/cicd_tests.yml              |  1 +
 monai/_version.py                             |  9 +++++----
 monai/apps/pathology/inferers/inferer.py      |  3 +--
 monai/apps/pathology/transforms/post/array.py |  3 +--
 monai/bundle/scripts.py                       |  3 +--
 monai/config/type_definitions.py              | 14 +++++++-------
 monai/data/image_reader.py                    |  2 +-
 monai/engines/evaluator.py                    |  3 +--
 monai/engines/trainer.py                      |  3 +--
 monai/networks/nets/vista3d.py                |  3 +--
 monai/optimizers/lr_finder.py                 |  2 +-
 monai/transforms/intensity/dictionary.py      |  3 +--
 monai/transforms/io/array.py                  |  3 +--
 monai/transforms/io/dictionary.py             |  3 +--
 monai/transforms/spatial/array.py             |  2 +-
 monai/transforms/utility/array.py             |  3 +--
 monai/utils/component_store.py                |  3 +--
 monai/utils/decorators.py                     |  3 +--
 monai/visualize/gradient_based.py             |  2 +-
 requirements-dev.txt                          |  1 +
 tests/bundle/test_config_item.py              |  2 +-
 tests/test_utils.py                           |  3 +--
 22 files changed, 32 insertions(+), 42 deletions(-)

diff --git a/.github/workflows/cicd_tests.yml b/.github/workflows/cicd_tests.yml
index 9efa9e92dd..1dbb36d8f4 100644
--- a/.github/workflows/cicd_tests.yml
+++ b/.github/workflows/cicd_tests.yml
@@ -198,6 +198,7 @@ jobs:
       name: Install torch cpu from pytorch.org (Windows only)
       run: |
         python -m pip install torch==${PYTORCH_VER1} torchvision==${TORCHVISION_VER}+cpu --index-url https://download.pytorch.org/whl/cpu
+      shell: bash
     - if: runner.os == 'Linux'
       name: Install itk pre-release (Linux only)
       run: |
diff --git a/monai/_version.py b/monai/_version.py
index 256d3654d9..759cdb5b80 100644
--- a/monai/_version.py
+++ b/monai/_version.py
@@ -15,7 +15,8 @@
 import re
 import subprocess
 import sys
-from typing import Callable, Dict
+from typing import Dict
+from collections.abc import Callable
 import functools
 
 
@@ -54,8 +55,8 @@ class NotThisMethod(Exception):
     """Exception raised if a method is not valid for the current scenario."""
 
 
-LONG_VERSION_PY: Dict[str, str] = {}
-HANDLERS: Dict[str, Dict[str, Callable]] = {}
+LONG_VERSION_PY: dict[str, str] = {}
+HANDLERS: dict[str, dict[str, Callable]] = {}
 
 
 def register_vcs_handler(vcs, method):  # decorator
@@ -145,7 +146,7 @@ def git_get_keywords(versionfile_abs):
     # _version.py.
     keywords = {}
     try:
-        with open(versionfile_abs, "r") as fobj:
+        with open(versionfile_abs) as fobj:
             for line in fobj:
                 if line.strip().startswith("git_refnames ="):
                     mo = re.search(r'=\s*"(.*)"', line)
diff --git a/monai/apps/pathology/inferers/inferer.py b/monai/apps/pathology/inferers/inferer.py
index f4ba74adac..37be148d45 100644
--- a/monai/apps/pathology/inferers/inferer.py
+++ b/monai/apps/pathology/inferers/inferer.py
@@ -11,9 +11,8 @@
 
 from __future__ import annotations
 
-from collections.abc import Sequence
+from collections.abc import Callable, Sequence
 from typing import Any
-from collections.abc import Callable
 
 import numpy as np
 import torch
diff --git a/monai/apps/pathology/transforms/post/array.py b/monai/apps/pathology/transforms/post/array.py
index a3892049e1..5ab272f018 100644
--- a/monai/apps/pathology/transforms/post/array.py
+++ b/monai/apps/pathology/transforms/post/array.py
@@ -12,8 +12,7 @@
 from __future__ import annotations
 
 import warnings
-from collections.abc import Sequence
-from collections.abc import Callable
+from collections.abc import Callable, Sequence
 
 import numpy as np
 import torch
diff --git a/monai/bundle/scripts.py b/monai/bundle/scripts.py
index 9be611313a..ab02cd552e 100644
--- a/monai/bundle/scripts.py
+++ b/monai/bundle/scripts.py
@@ -17,14 +17,13 @@
 import re
 import urllib
 import warnings
-from collections.abc import Mapping, Sequence
+from collections.abc import Callable, Mapping, Sequence
 from functools import partial
 from pathlib import Path
 from pydoc import locate
 from shutil import copyfile
 from textwrap import dedent
 from typing import Any
-from collections.abc import Callable
 
 import torch
 from torch.cuda import is_available
diff --git a/monai/config/type_definitions.py b/monai/config/type_definitions.py
index 48c0547e31..fe2ec31e0e 100644
--- a/monai/config/type_definitions.py
+++ b/monai/config/type_definitions.py
@@ -53,7 +53,7 @@
 #        convenience to end-users.  All supplied values will be
 #        internally converted to a tuple of `Hashable`'s before
 #        use
-KeysCollection = Union[Collection[Hashable], Hashable]
+KeysCollection = Collection[Hashable] | Hashable
 
 #: IndexSelection
 #
@@ -61,13 +61,13 @@
 # that store a subset of indices to select items from a List or Array like objects.
 # The indices must be integers, and if a container of indices is specified, the
 # container must be iterable.
-IndexSelection = Union[Iterable[int], int]
+IndexSelection = Iterable[int] | int
 
 #: Type of datatypes: Adapted from https://github.com/numpy/numpy/blob/v1.21.4/numpy/typing/_dtype_like.py#L121
-DtypeLike = Union[np.dtype, type, str, None]
+DtypeLike = np.dtype | type | str | None
 
 #: NdarrayOrTensor: Union of numpy.ndarray and torch.Tensor to be used for typing
-NdarrayOrTensor = Union[np.ndarray, torch.Tensor]
+NdarrayOrTensor = np.ndarray | torch.Tensor
 
 #: NdarrayTensor
 #
@@ -76,11 +76,11 @@
 NdarrayTensor = TypeVar("NdarrayTensor", bound=NdarrayOrTensor)
 
 #: TensorOrList: The TensorOrList type is used for defining `batch-first Tensor` or `list of channel-first Tensor`.
-TensorOrList = Union[torch.Tensor, Sequence[torch.Tensor]]
+TensorOrList = torch.Tensor | Sequence[torch.Tensor]
 
 #: PathLike: The PathLike type is used for defining a file path.
-PathLike = Union[str, os.PathLike]
+PathLike = str | os.PathLike
 
 #: SequenceStr
 # string or a sequence of strings for `mode` types.
-SequenceStr = Union[Sequence[str], str]
+SequenceStr = Sequence[str] | str
diff --git a/monai/data/image_reader.py b/monai/data/image_reader.py
index c300476a6b..8d99ed79a0 100644
--- a/monai/data/image_reader.py
+++ b/monai/data/image_reader.py
@@ -60,7 +60,7 @@
 if TYPE_CHECKING:
     import cupy
 
-    NdarrayOrCupy = Union[np.ndarray, cupy.ndarray]
+    NdarrayOrCupy = np.ndarray | cupy.ndarray
 else:
     NdarrayOrCupy = Any
 
diff --git a/monai/engines/evaluator.py b/monai/engines/evaluator.py
index 4178dad9b9..62d5f83847 100644
--- a/monai/engines/evaluator.py
+++ b/monai/engines/evaluator.py
@@ -12,9 +12,8 @@
 from __future__ import annotations
 
 import warnings
-from collections.abc import Iterable, Sequence
+from collections.abc import Callable, Iterable, Sequence
 from typing import TYPE_CHECKING, Any
-from collections.abc import Callable
 
 import torch
 from torch.utils.data import DataLoader
diff --git a/monai/engines/trainer.py b/monai/engines/trainer.py
index b958ca4ec2..921d54a59c 100644
--- a/monai/engines/trainer.py
+++ b/monai/engines/trainer.py
@@ -12,9 +12,8 @@
 from __future__ import annotations
 
 import warnings
-from collections.abc import Iterable, Sequence
+from collections.abc import Callable, Iterable, Sequence
 from typing import TYPE_CHECKING, Any
-from collections.abc import Callable
 
 import torch
 from torch.optim.optimizer import Optimizer
diff --git a/monai/networks/nets/vista3d.py b/monai/networks/nets/vista3d.py
index df5250dac0..232b8c1c11 100644
--- a/monai/networks/nets/vista3d.py
+++ b/monai/networks/nets/vista3d.py
@@ -12,9 +12,8 @@
 from __future__ import annotations
 
 import math
-from collections.abc import Sequence
+from collections.abc import Callable, Sequence
 from typing import Any
-from collections.abc import Callable
 
 import numpy as np
 import torch
diff --git a/monai/optimizers/lr_finder.py b/monai/optimizers/lr_finder.py
index bae04efff8..8692d2622f 100644
--- a/monai/optimizers/lr_finder.py
+++ b/monai/optimizers/lr_finder.py
@@ -14,9 +14,9 @@
 import pickle
 import types
 import warnings
+from collections.abc import Callable
 from functools import partial
 from typing import TYPE_CHECKING, Any
-from collections.abc import Callable
 
 import numpy as np
 import torch
diff --git a/monai/transforms/intensity/dictionary.py b/monai/transforms/intensity/dictionary.py
index f0878c0c99..0c25d4ac99 100644
--- a/monai/transforms/intensity/dictionary.py
+++ b/monai/transforms/intensity/dictionary.py
@@ -17,8 +17,7 @@
 
 from __future__ import annotations
 
-from collections.abc import Hashable, Mapping, Sequence
-from collections.abc import Callable
+from collections.abc import Callable, Hashable, Mapping, Sequence
 
 import numpy as np
 
diff --git a/monai/transforms/io/array.py b/monai/transforms/io/array.py
index 95beb5ae96..049779f606 100644
--- a/monai/transforms/io/array.py
+++ b/monai/transforms/io/array.py
@@ -20,10 +20,9 @@
 import sys
 import traceback
 import warnings
-from collections.abc import Sequence
+from collections.abc import Callable, Sequence
 from pathlib import Path
 from pydoc import locate
-from collections.abc import Callable
 
 import numpy as np
 import torch
diff --git a/monai/transforms/io/dictionary.py b/monai/transforms/io/dictionary.py
index fc634baa30..4927450c7d 100644
--- a/monai/transforms/io/dictionary.py
+++ b/monai/transforms/io/dictionary.py
@@ -17,9 +17,8 @@
 
 from __future__ import annotations
 
-from collections.abc import Hashable, Mapping
+from collections.abc import Callable, Hashable, Mapping
 from pathlib import Path
-from collections.abc import Callable
 
 import numpy as np
 
diff --git a/monai/transforms/spatial/array.py b/monai/transforms/spatial/array.py
index 6aba71a0f6..db926bb938 100644
--- a/monai/transforms/spatial/array.py
+++ b/monai/transforms/spatial/array.py
@@ -118,7 +118,7 @@
     "RandSimulateLowResolution",
 ]
 
-RandRange = Optional[Sequence[tuple[float, float] | float] | float]
+RandRange = Sequence[tuple[float, float] | float] | float | None
 
 
 class SpatialResample(InvertibleTransform, LazyTransform):
diff --git a/monai/transforms/utility/array.py b/monai/transforms/utility/array.py
index 1483441dc1..b39dd93931 100644
--- a/monai/transforms/utility/array.py
+++ b/monai/transforms/utility/array.py
@@ -18,11 +18,10 @@
 import sys
 import time
 import warnings
-from collections.abc import Hashable, Mapping, Sequence
+from collections.abc import Callable, Hashable, Mapping, Sequence
 from copy import deepcopy
 from functools import partial
 from typing import Any
-from collections.abc import Callable
 
 import numpy as np
 import torch
diff --git a/monai/utils/component_store.py b/monai/utils/component_store.py
index 6713b61769..360cea8fe3 100644
--- a/monai/utils/component_store.py
+++ b/monai/utils/component_store.py
@@ -12,11 +12,10 @@
 from __future__ import annotations
 
 from collections import namedtuple
-from collections.abc import Iterable
+from collections.abc import Callable, Iterable
 from keyword import iskeyword
 from textwrap import dedent, indent
 from typing import Any, TypeVar
-from collections.abc import Callable
 
 T = TypeVar("T")
 
diff --git a/monai/utils/decorators.py b/monai/utils/decorators.py
index b6cfbf2bf7..4a8b098ce1 100644
--- a/monai/utils/decorators.py
+++ b/monai/utils/decorators.py
@@ -15,8 +15,7 @@
 
 __all__ = ["RestartGenerator", "MethodReplacer"]
 
-from collections.abc import Generator
-from collections.abc import Callable
+from collections.abc import Callable, Generator
 
 
 class RestartGenerator:
diff --git a/monai/visualize/gradient_based.py b/monai/visualize/gradient_based.py
index d858a3dfce..a8d81eb579 100644
--- a/monai/visualize/gradient_based.py
+++ b/monai/visualize/gradient_based.py
@@ -11,9 +11,9 @@
 
 from __future__ import annotations
 
+from collections.abc import Callable
 from functools import partial
 from typing import Any
-from collections.abc import Callable
 
 import torch
 
diff --git a/requirements-dev.txt b/requirements-dev.txt
index f7717c1510..a948de701c 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -62,3 +62,4 @@ pyamg>=5.0.0, <5.3.0
 git+https://github.com/facebookresearch/segment-anything.git@6fdee8f2727f4506cfbbe553e23b895e27956588
 onnx_graphsurgeon
 polygraphy
+pybind11
diff --git a/tests/bundle/test_config_item.py b/tests/bundle/test_config_item.py
index e9f9d5ef8d..e7becb66bc 100644
--- a/tests/bundle/test_config_item.py
+++ b/tests/bundle/test_config_item.py
@@ -12,8 +12,8 @@
 from __future__ import annotations
 
 import unittest
-from functools import partial
 from collections.abc import Callable
+from functools import partial
 
 import torch
 from parameterized import parameterized
diff --git a/tests/test_utils.py b/tests/test_utils.py
index 3e7d831b07..d040a10a51 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -28,14 +28,13 @@
 import traceback
 import unittest
 import warnings
-from collections.abc import Iterable
+from collections.abc import Callable, Iterable
 from contextlib import contextmanager
 from functools import partial, reduce
 from itertools import product
 from pathlib import Path
 from subprocess import PIPE, Popen
 from typing import Any
-from collections.abc import Callable
 from urllib.error import ContentTooShortError, HTTPError
 
 import numpy as np

From 6309f30b143197862adc2c3665eb03716d22f709 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sat, 4 Apr 2026 23:18:58 +0000
Subject: [PATCH 35/41] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 monai/_version.py                 | 1 -
 monai/config/type_definitions.py  | 2 +-
 monai/data/image_reader.py        | 2 +-
 monai/transforms/spatial/array.py | 2 +-
 4 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/monai/_version.py b/monai/_version.py
index 759cdb5b80..f234227104 100644
--- a/monai/_version.py
+++ b/monai/_version.py
@@ -15,7 +15,6 @@
 import re
 import subprocess
 import sys
-from typing import Dict
 from collections.abc import Callable
 import functools
 
diff --git a/monai/config/type_definitions.py b/monai/config/type_definitions.py
index fe2ec31e0e..afe13abf37 100644
--- a/monai/config/type_definitions.py
+++ b/monai/config/type_definitions.py
@@ -13,7 +13,7 @@
 
 import os
 from collections.abc import Collection, Hashable, Iterable, Sequence
-from typing import TypeVar, Union
+from typing import TypeVar
 
 import numpy as np
 import torch
diff --git a/monai/data/image_reader.py b/monai/data/image_reader.py
index 8d99ed79a0..08697c3fee 100644
--- a/monai/data/image_reader.py
+++ b/monai/data/image_reader.py
@@ -22,7 +22,7 @@
 from collections.abc import Callable, Iterable, Iterator, Sequence
 from dataclasses import dataclass
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, Union
+from typing import TYPE_CHECKING, Any
 
 import numpy as np
 from torch.utils.data._utils.collate import np_str_obj_array_pattern
diff --git a/monai/transforms/spatial/array.py b/monai/transforms/spatial/array.py
index db926bb938..d6b5ed8641 100644
--- a/monai/transforms/spatial/array.py
+++ b/monai/transforms/spatial/array.py
@@ -18,7 +18,7 @@
 from collections.abc import Callable, Sequence
 from copy import deepcopy
 from itertools import zip_longest
-from typing import Any, Optional, cast
+from typing import Any, cast
 
 import numpy as np
 import torch

From 8e54c6418e7652acbe620bd1d86ecfad4ba71c5c Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Sun, 5 Apr 2026 20:15:23 +0100
Subject: [PATCH 36/41] Adding pybind11 to test MacOS failure

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/cicd_tests.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/cicd_tests.yml b/.github/workflows/cicd_tests.yml
index 1dbb36d8f4..cfb5dce328 100644
--- a/.github/workflows/cicd_tests.yml
+++ b/.github/workflows/cicd_tests.yml
@@ -205,7 +205,7 @@ jobs:
         python -m pip install --pre -U itk
     - name: Install the complete dependencies
       run: |
-        python -m pip install --user --upgrade pip wheel
+        python -m pip install --user --upgrade pip wheel pybind11
         python -m pip install torch==${PYTORCH_VER1} torchvision==${TORCHVISION_VER}
         cat "requirements-dev.txt"
         python -m pip install --no-build-isolation -r requirements-dev.txt

From 20570f3289658c67d5020112afb32afe012060bb Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Sun, 5 Apr 2026 23:25:31 +0100
Subject: [PATCH 37/41] mypy fixes

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/cicd_tests.yml                    |  2 +-
 monai/apps/vista3d/inferer.py                       |  4 +++-
 monai/data/image_reader.py                          |  6 +++---
 monai/networks/layers/convutils.py                  | 13 +++++--------
 monai/networks/nets/daf3d.py                        |  1 +
 monai/networks/nets/dints.py                        |  8 ++++----
 monai/optimizers/lr_scheduler.py                    |  2 +-
 monai/transforms/intensity/array.py                 |  4 ++--
 monai/transforms/utils_pytorch_numpy_unification.py |  4 ++--
 monai/visualize/visualizer.py                       |  3 ++-
 10 files changed, 24 insertions(+), 23 deletions(-)

diff --git a/.github/workflows/cicd_tests.yml b/.github/workflows/cicd_tests.yml
index cfb5dce328..47376f760b 100644
--- a/.github/workflows/cicd_tests.yml
+++ b/.github/workflows/cicd_tests.yml
@@ -205,7 +205,7 @@ jobs:
         python -m pip install --pre -U itk
     - name: Install the complete dependencies
       run: |
-        python -m pip install --user --upgrade pip wheel pybind11
+        python -m pip install --user --upgrade pip wheel pybind11  # pybind11 added for macOS, may not be needed
         python -m pip install torch==${PYTORCH_VER1} torchvision==${TORCHVISION_VER}
         cat "requirements-dev.txt"
         python -m pip install --no-build-isolation -r requirements-dev.txt
diff --git a/monai/apps/vista3d/inferer.py b/monai/apps/vista3d/inferer.py
index bdd833af9d..aedeb5f347 100644
--- a/monai/apps/vista3d/inferer.py
+++ b/monai/apps/vista3d/inferer.py
@@ -77,7 +77,7 @@ def point_based_window_inferer(
     image, pad = _pad_previous_mask(copy.deepcopy(inputs), roi_size)
     point_coords = point_coords + torch.tensor([pad[-2], pad[-4], pad[-6]]).to(point_coords.device)
     prev_mask = _pad_previous_mask(copy.deepcopy(prev_mask), roi_size)[0] if prev_mask is not None else None
-    stitched_output = None
+    stitched_output: torch.Tensor | None = None
     for p in point_coords[0][point_start:]:
         lx_, rx_ = _get_window_idx(p[0], roi_size[0], image.shape[-3], center_only=center_only, margin=margin)
         ly_, ry_ = _get_window_idx(p[1], roi_size[1], image.shape[-2], center_only=center_only, margin=margin)
@@ -113,6 +113,8 @@ def point_based_window_inferer(
                         )
                     stitched_output[unravel_slice] += output.to("cpu")
                     stitched_mask[unravel_slice] = 1
+
+    assert stitched_output is not None  # needed for correct typing below
     # if stitched_mask is 0, then NaN value
     stitched_output = stitched_output / stitched_mask
     # revert padding
diff --git a/monai/data/image_reader.py b/monai/data/image_reader.py
index 08697c3fee..c281e4fc67 100644
--- a/monai/data/image_reader.py
+++ b/monai/data/image_reader.py
@@ -22,7 +22,7 @@
 from collections.abc import Callable, Iterable, Iterator, Sequence
 from dataclasses import dataclass
 from pathlib import Path
-from typing import TYPE_CHECKING, Any
+from typing import TYPE_CHECKING, Any, TypeAlias
 
 import numpy as np
 from torch.utils.data._utils.collate import np_str_obj_array_pattern
@@ -60,9 +60,9 @@
 if TYPE_CHECKING:
     import cupy
 
-    NdarrayOrCupy = np.ndarray | cupy.ndarray
+    NdarrayOrCupy: TypeAlias = np.ndarray | cupy.ndarray
 else:
-    NdarrayOrCupy = Any
+    NdarrayOrCupy: TypeAlias = Any
 
 __all__ = ["ImageReader", "ITKReader", "NibabelReader", "NumpyReader", "PILReader", "PydicomReader", "NrrdReader"]
 
diff --git a/monai/networks/layers/convutils.py b/monai/networks/layers/convutils.py
index fc8ea03809..6602bcbcd6 100644
--- a/monai/networks/layers/convutils.py
+++ b/monai/networks/layers/convutils.py
@@ -12,6 +12,7 @@
 from __future__ import annotations
 
 from collections.abc import Sequence
+from typing import cast
 
 import numpy as np
 import torch
@@ -118,14 +119,10 @@ def gaussian_1d(
             out = out / (2.5066282 * sigma)
     elif approx.lower() == "scalespace":
         sigma2 = sigma * sigma
-        out_pos: list[torch.Tensor | None] = [None] * (tail + 1)
-        out_pos[0] = _modified_bessel_0(sigma2)
-        out_pos[1] = _modified_bessel_1(sigma2)
-        for k in range(2, len(out_pos)):
-            out_pos[k] = _modified_bessel_i(k, sigma2)
-        out = out_pos[:0:-1]
-        out.extend(out_pos)
-        out = torch.stack(out) * torch.exp(-sigma2)
+        out_pos: list[torch.Tensor] = [_modified_bessel_0(sigma2), _modified_bessel_1(sigma2)]
+        out_pos += [_modified_bessel_i(k, sigma2) for k in range(2, tail + 1)]
+        out_pos_mirror = out_pos[:0:-1] + out_pos
+        out = torch.stack(out_pos_mirror) * torch.exp(-sigma2)
     else:
         raise NotImplementedError(f"Unsupported option: approx='{approx}'.")
     return out / out.sum() if normalize else out  # type: ignore
diff --git a/monai/networks/nets/daf3d.py b/monai/networks/nets/daf3d.py
index 02e5bb022a..4e47d79a2d 100644
--- a/monai/networks/nets/daf3d.py
+++ b/monai/networks/nets/daf3d.py
@@ -570,6 +570,7 @@ def forward(self, x):
 
         supervised_final = self.predict2(aspp)
 
+        output: list | torch.Tensor
         if self.training:
             output = supervised1 + supervised2 + [supervised_final]
             output = [F.interpolate(o, size=x.size()[2:], mode="trilinear") for o in output]
diff --git a/monai/networks/nets/dints.py b/monai/networks/nets/dints.py
index f87fcebea8..98f8de5772 100644
--- a/monai/networks/nets/dints.py
+++ b/monai/networks/nets/dints.py
@@ -923,8 +923,8 @@ def get_topology_entropy(self, probs):
                 for res_idx in range(len(self.arch_code2out)):
                     _node_out[self.arch_code2out[res_idx]] += self.child_list[child_idx][res_idx]
                     _node_in[self.arch_code2in[res_idx]] += self.child_list[child_idx][res_idx]
-                _node_in = (_node_in >= 1).astype(int)
-                _node_out = (_node_out >= 1).astype(int)
+                _node_in = (_node_in >= 1).astype(int)  # type: ignore
+                _node_out = (_node_out >= 1).astype(int)  # type: ignore
                 node2in[self.node_act_dict[str(_node_out)]].append(child_idx)
                 node2out[self.node_act_dict[str(_node_in)]].append(child_idx)
             self.node2in = node2in
@@ -976,7 +976,7 @@ def decode(self):
             _node_act = np.zeros(self.num_depths).astype(int)
             for path_idx in range(len(self.child_list[child_idx])):
                 _node_act[self.arch_code2out[path_idx]] += self.child_list[child_idx][path_idx]
-            _node_act = (_node_act >= 1).astype(int)
+            _node_act = (_node_act >= 1).astype(int)  # type: ignore
             for mtx in self.transfer_mtx[str(_node_act)]:
                 connect_child_idx = path2child[str(mtx.flatten()[self.tidx].astype(int))]
                 sub_amtx[child_idx, connect_child_idx] = 1
@@ -1014,7 +1014,7 @@ def decode(self):
             a_idx -= 1
         for res_idx in range(len(self.arch_code2out)):
             node_a[a_idx, self.arch_code2in[res_idx]] += arch_code_a[0, res_idx]
-        node_a = (node_a >= 1).astype(int)
+        node_a = (node_a >= 1).astype(int)  # type: ignore
         return node_a, arch_code_a, arch_code_c, arch_code_a_max
 
     def forward(self, x):
diff --git a/monai/optimizers/lr_scheduler.py b/monai/optimizers/lr_scheduler.py
index 8f89352158..96c1412fea 100644
--- a/monai/optimizers/lr_scheduler.py
+++ b/monai/optimizers/lr_scheduler.py
@@ -107,4 +107,4 @@ def get_lr(self):
         if self.last_epoch < self.warmup_steps:
             return current_lr
         else:
-            return [max(self.end_lr, _current_lr) for _current_lr in current_lr]
+            return [max(self.end_lr, _current_lr) for _current_lr in current_lr]  # type: ignore
diff --git a/monai/transforms/intensity/array.py b/monai/transforms/intensity/array.py
index 986a715c22..23a57ae9fb 100644
--- a/monai/transforms/intensity/array.py
+++ b/monai/transforms/intensity/array.py
@@ -17,7 +17,7 @@
 from abc import abstractmethod
 from collections.abc import Callable, Iterable, Sequence
 from functools import partial
-from typing import Any
+from typing import Any, cast
 from warnings import warn
 
 import numpy as np
@@ -1872,7 +1872,7 @@ def interp(self, x: NdarrayOrTensor, xp: NdarrayOrTensor, fp: NdarrayOrTensor) -
         ns = torch if isinstance(x, torch.Tensor) else np
         if isinstance(x, np.ndarray):
             # approx 2x faster than code below for ndarray
-            return np.interp(x, xp, fp)
+            return cast(np.ndarray, np.interp(x, xp, fp))
 
         m = (fp[1:] - fp[:-1]) / (xp[1:] - xp[:-1])
         b = fp[:-1] - (m * xp[:-1])
diff --git a/monai/transforms/utils_pytorch_numpy_unification.py b/monai/transforms/utils_pytorch_numpy_unification.py
index 66756f4476..1bc9c206d8 100644
--- a/monai/transforms/utils_pytorch_numpy_unification.py
+++ b/monai/transforms/utils_pytorch_numpy_unification.py
@@ -12,7 +12,7 @@
 from __future__ import annotations
 
 from collections.abc import Sequence
-from typing import TypeVar
+from typing import TypeVar, cast
 
 import numpy as np
 import torch
@@ -65,7 +65,7 @@ def softplus(x: NdarrayOrTensor) -> NdarrayOrTensor:
         Softplus of the input.
     """
     if isinstance(x, np.ndarray):
-        return np.logaddexp(np.zeros_like(x), x)
+        return cast(np.ndarray, np.logaddexp(np.zeros_like(x), x))
     return torch.logaddexp(torch.zeros_like(x), x)
 
 
diff --git a/monai/visualize/visualizer.py b/monai/visualize/visualizer.py
index e7f5d9bbbe..023e444406 100644
--- a/monai/visualize/visualizer.py
+++ b/monai/visualize/visualizer.py
@@ -31,6 +31,7 @@ def default_upsampler(spatial_size: Sized, align_corners: bool = False) -> Calla
     def up(x):
         linear_mode = [InterpolateMode.LINEAR, InterpolateMode.BILINEAR, InterpolateMode.TRILINEAR]
         interp_mode = linear_mode[len(spatial_size) - 1]
-        return F.interpolate(x, size=spatial_size, mode=str(interp_mode.value), align_corners=align_corners)
+        smode = str(interp_mode.value)
+        return F.interpolate(x, size=spatial_size, mode=smode, align_corners=align_corners)  # type: ignore
 
     return up

From 5f5482b7b8b44a772db95212f853169273bae98e Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sun, 5 Apr 2026 22:25:49 +0000
Subject: [PATCH 38/41] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 monai/networks/layers/convutils.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/monai/networks/layers/convutils.py b/monai/networks/layers/convutils.py
index 6602bcbcd6..f4d321ea1c 100644
--- a/monai/networks/layers/convutils.py
+++ b/monai/networks/layers/convutils.py
@@ -12,7 +12,6 @@
 from __future__ import annotations
 
 from collections.abc import Sequence
-from typing import cast
 
 import numpy as np
 import torch

From 8ffacc83d6f76c4706ecb0d6754a346e591954d6 Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Sun, 5 Apr 2026 23:49:54 +0100
Subject: [PATCH 39/41] Enable tests

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/cicd_tests.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/cicd_tests.yml b/.github/workflows/cicd_tests.yml
index 47376f760b..ce86f2ce73 100644
--- a/.github/workflows/cicd_tests.yml
+++ b/.github/workflows/cicd_tests.yml
@@ -151,7 +151,7 @@ jobs:
       run: |
         python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
         python -c "import monai; monai.config.print_config()"
-        # ./runtests.sh --min
+        ./runtests.sh --min
       shell: bash
       env:
         QUICKTEST: True
@@ -221,7 +221,7 @@ jobs:
       run: |
         python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
         python -c "import monai; monai.config.print_config()"
-        # python -m unittest -v
+        python -m unittest -v
 
   packaging:  # Test package generation
     runs-on: ubuntu-latest

From ed2847582e570d52a9a32ca67922f2576c7b10fe Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Mon, 6 Apr 2026 11:40:55 +0100
Subject: [PATCH 40/41] Test fixes

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/cicd_tests.yml |  4 ++--
 tests/test_utils.py              | 12 +++++++-----
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/cicd_tests.yml b/.github/workflows/cicd_tests.yml
index ce86f2ce73..ca1ecb6dc1 100644
--- a/.github/workflows/cicd_tests.yml
+++ b/.github/workflows/cicd_tests.yml
@@ -37,7 +37,7 @@ env:
   PYTORCH_VER2: '2.9.1'
   PYTORCH_VER3: '2.10.0'
   PYTORCH_VER4: '2.11.0'
-  TORCHVISION_VER: '0.23.0'  # used for testing with lowest PyTorch version
+  TORCHVISION_VER: '0.23.0'  # used for testing with lowest PyTorch version (PYTORCH_VER1), update as needed
   PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python  # https://github.com/Project-MONAI/MONAI/issues/4354
 
 # These jobs run the CICD tests, type checking, and testing packaging. These use the minimum supported versions of
@@ -98,7 +98,7 @@ jobs:
           pytorch-version: '2.8.0'
           python-version: '3.13'
         - os: ubuntu-latest
-          pytorch-version: '2.9.0'
+          pytorch-version: '2.9.1'
           python-version: '3.14'
 
         # Test PyTorch versions under Ubuntu with lowest Python version supported
diff --git a/tests/test_utils.py b/tests/test_utils.py
index d040a10a51..b1babe983d 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -533,7 +533,7 @@ def run_process(self, func, local_rank, args, kwargs, results):
                 time.sleep(0.1)
             results.put(True)
         except Exception as e:
-            results.put(False)
+            results.put(str(e))
             raise e
         finally:
             os.environ.clear()
@@ -562,15 +562,17 @@ def _wrapper(*args, **kwargs):
             results = tmp.Queue()
             func = _call_original_func
             args = [obj.__name__, obj.__module__] + list(args)
+
             for proc_rank in range(self.nproc_per_node):
-                p = tmp.Process(
-                    target=self.run_process, args=(func, proc_rank, args, kwargs, results), daemon=self.daemon
-                )
+                run_args = (func, proc_rank, args, kwargs, results)
+                p = tmp.Process(target=self.run_process, args=run_args, daemon=self.daemon)
                 p.start()
                 processes.append(p)
+
             for p in processes:
                 p.join()
-                assert results.get(), "Distributed call failed."
+                pr=results.get()
+                assert pr is True, f"Distributed call failed: {pr}"
             _del_original_func(obj)
 
         return _wrapper

From 7e3b15cec9bcfaefe2f166a8a0c499af887c9635 Mon Sep 17 00:00:00 2001
From: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Date: Mon, 6 Apr 2026 12:00:27 +0100
Subject: [PATCH 41/41] Test fixes

Signed-off-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
---
 .github/workflows/cicd_tests.yml | 8 ++++----
 tests/test_utils.py              | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/cicd_tests.yml b/.github/workflows/cicd_tests.yml
index ca1ecb6dc1..0993a87b62 100644
--- a/.github/workflows/cicd_tests.yml
+++ b/.github/workflows/cicd_tests.yml
@@ -31,7 +31,7 @@ env:
   PYTHON_VER2: '3.11'
   PYTHON_VER3: '3.12'
   PYTHON_VER4: '3.13'
-  PYTHON_VER5: '3.14'
+  # PYTHON_VER5: '3.14'  # TODO: not compatible with Torchscript, re-enable once Torchscript removed from MONAI
   # supported versions of PyTorch
   PYTORCH_VER1: '2.8.0'
   PYTORCH_VER2: '2.9.1'
@@ -97,9 +97,9 @@ jobs:
         - os: ubuntu-latest
           pytorch-version: '2.8.0'
           python-version: '3.13'
-        - os: ubuntu-latest
-          pytorch-version: '2.9.1'
-          python-version: '3.14'
+        # - os: ubuntu-latest
+        #   pytorch-version: '2.9.1'
+        #   python-version: '3.14'
 
         # Test PyTorch versions under Ubuntu with lowest Python version supported
         - os: ubuntu-latest
diff --git a/tests/test_utils.py b/tests/test_utils.py
index b1babe983d..8bdbf6423e 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -571,7 +571,7 @@ def _wrapper(*args, **kwargs):
 
             for p in processes:
                 p.join()
-                pr=results.get()
+                pr = results.get()
                 assert pr is True, f"Distributed call failed: {pr}"
             _del_original_func(obj)