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 01/18] 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 02/18] 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 03/18] 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 04/18] 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 05/18] 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 06/18] 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 07/18] 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 08/18] 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 09/18] 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 10/18] 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 11/18] 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 12/18] 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 13/18] 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 14/18] 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 15/18] 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 16/18] 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 17/18] [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 18/18] 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)