9058 Update CI Versions

.github/workflows/build_docs.yml

@@ -25,7 +25,7 @@ jobs:
     runs-on: ubuntu-latest
     env:
       # minimum supported version of Python
-      PYTHON_VER1: '3.10'
+      PYTHON_VER1: '3.11'
       # force installation of CPU-only PyTorch
       PIP_EXTRA_INDEX_URL: 'https://download.pytorch.org/whl/cpu'
     steps:

.github/workflows/cicd_tests.yml → .github/workflows/ci_tests.yml

@@ -24,25 +24,25 @@ concurrency:
 # Supported versions of Python and PyTorch are listed here for use below and as documentation
 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'  # TODO: not compatible with Torchscript, re-enable once Torchscript removed from MONAI
+  PYTHON_VER1: '3.11'
+  PYTHON_VER2: '3.12'
+  PYTHON_VER3: '3.13'
+  PYTHON_VER4: '3.14'
+  # PYTHON_VER5: '3.15'  # 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'
-  PYTORCH_VER3: '2.10.0'
-  PYTORCH_VER4: '2.11.0'
-  TORCHVISION_VER1: '0.23.0'  # used for testing with lowest PyTorch version (PYTORCH_VER1), update as needed
+  PYTORCH_VER1: '2.12.1'
+  PYTORCH_VER2: '2.13.0'
+  PYTORCH_VER3: '2.14.1'
+  PYTORCH_VER4: '2.15.0'
+  TORCHVISION_VER1: '0.27.1'  # used for testing with lowest PyTorch version (PYTORCH_VER1), update as needed
 
-  # versions of PyTorch/Torchvision to use for full-dep Windows tests, needed to get around a gloo bug
-  WIN_FULLDEP_VER: '2.11.0'
-  WIN_FULLDEP_VISION_VER: '0.26.0'
+  TQDM_DISABLE: 1  # squelch TQDM output to reduce log file size
 
   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
+  PIP_EXTRA_INDEX_URL: "https://download.pytorch.org/whl/cpu"  # forces CPU PyTorch installation, should be faster
+
+# These jobs run the CI tests, type checking, and testing packaging. These use the minimum supported versions of
 # 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.
 
@@ -133,33 +133,35 @@ 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: ['3.10']
-        pytorch-version: ['2.8.0']
+        python-version: ['3.11']
+        pytorch-version: ['2.12.1']
         include:
         # Test Python versions under Ubuntu with lowest PyTorch version supported
         - os: ubuntu-latest
-          pytorch-version: '2.8.0'
-          python-version: '3.11'
-        - os: ubuntu-latest
-          pytorch-version: '2.8.0'
+          pytorch-version: '2.12.1'
           python-version: '3.12'
         - os: ubuntu-latest
-          pytorch-version: '2.8.0'
+          pytorch-version: '2.12.1'
           python-version: '3.13'
-        # - os: ubuntu-latest
-        #   pytorch-version: '2.9.1'
-        #   python-version: '3.14'
+        - os: ubuntu-latest
+          pytorch-version: '2.12.1'
+          python-version: '3.14'
 
         # Test PyTorch versions under Ubuntu with lowest Python version supported
         - os: ubuntu-latest
-          python-version: '3.10'
-          pytorch-version: '2.9.1'
+          python-version: '3.11'
+          pytorch-version: '2.13.0'
+        - os: ubuntu-latest
+          python-version: '3.11'
+          pytorch-version: '2.14.1'
         - os: ubuntu-latest
-          python-version: '3.10'
-          pytorch-version: '2.10.0'
+          python-version: '3.11'
+          pytorch-version: '2.15.0'
+
+        # Test newer Python with latest PyTorch under Ubuntu
         - os: ubuntu-latest
-          python-version: '3.10'
-          pytorch-version: '2.11.0'
+          python-version: '3.12'
+          pytorch-version: '2.15.0'
 
     timeout-minutes: 40
     steps:
@@ -245,13 +247,8 @@ jobs:
       run: |
         which python
         python -m pip install --upgrade pip wheel
-    - if: runner.os == 'windows' && needs.test_skip.outputs.skip == 0
-      name: Install torch cpu from pytorch.org (Windows only)
-      run: |
-        python -m pip install torch==${WIN_FULLDEP_VER} torchvision==${WIN_FULLDEP_VISION_VER}+cpu --index-url https://download.pytorch.org/whl/cpu
-      shell: bash
-    - if: runner.os != 'windows' && needs.test_skip.outputs.skip == 0
-      name: Install torch gpu
+    - if: needs.test_skip.outputs.skip == 0
+      name: Install PyTorch
       run: |
         # install the lowest version of PyTorch supported
         python -m pip install torch==${PYTORCH_VER1} torchvision==${TORCHVISION_VER1}
@@ -324,7 +321,7 @@ jobs:
         python -m pip install --upgrade pip wheel tomli pytest
         # need a specific version of torch for nvsubquadratic
         python monai/config/print_dependencies.py build-system | \
-          xargs -d '\n' pip install --no-build-isolation torch==2.10.0 torchvision==0.25.0
+          xargs -d '\n' pip install --no-build-isolation
         # # nvsubquadratic runtime imports need only torch + einops + omegaconf; install
         # # the package itself without its core dependency tree (see job comment above).
         python -m pip install --no-build-isolation omegaconf

.github/workflows/conda.yml

@@ -22,7 +22,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.10", "3.11"]
+        python-version: ["3.11", "3.12"]
     runs-on: ${{ matrix.os }}
     timeout-minutes: 46 # equal to max + 3*std over the last 600 successful runs
     env:

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

@@ -21,10 +21,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v7
-    - name: Set up Python 3.10
+    - name: Set up Python 3.11
       uses: actions/setup-python@v6
       with:
-        python-version: '3.10'
+        python-version: '3.11'
         cache: pip
     - name: Install CPU PyTorch
       run: |

.github/workflows/docker.yml

@@ -29,10 +29,10 @@ jobs:
         with:
           ref: dev
           fetch-depth: 0
-      - name: Set up Python 3.10
+      - name: Set up Python 3.11
         uses: actions/setup-python@v6
         with:
-          python-version: '3.10'
+          python-version: '3.11'
       - shell: bash
         run: |
           git describe

.github/workflows/pythonapp-gpu.yml

@@ -58,7 +58,7 @@ jobs:
 
         if [ ${{ matrix.environment }} = "PT230+CUDA124" ]
         then
-        PYVER=3.10 PYSFX=3 DISTUTILS=python3-distutils && \
+        PYVER=3.11 PYSFX=3 DISTUTILS=python3-distutils && \
         apt-get update && apt-get install -y --no-install-recommends \
           curl \
           pkg-config \

.github/workflows/release.yml

@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.10', '3.11', '3.12', '3.13']
+        python-version: ['3.11', '3.12', '3.13', '3.14', '3.15']
     steps:
     - uses: actions/checkout@v7
       with:
@@ -67,22 +67,22 @@ jobs:
       env:
         QUICKTEST: True
 
-    - if: matrix.python-version == '3.10' && startsWith(github.ref, 'refs/tags/')
+    - if: matrix.python-version == '3.11' && startsWith(github.ref, 'refs/tags/')
       name: Upload artifacts
       uses: actions/upload-artifact@v7
       with:
         name: dist
         path: dist/
 
-    - if: matrix.python-version == '3.10' && startsWith(github.ref, 'refs/tags/')
+    - if: matrix.python-version == '3.11' && startsWith(github.ref, 'refs/tags/')
       name: Check artifacts
       run: |
         ls -al dist/
         rm dist/monai*.tar.gz
         ls -al dist/
 
     # remove publishing to Test PyPI as it is moved to blossom
-    # - if: matrix.python-version == '3.10' && startsWith(github.ref, 'refs/tags/')
+    # - if: matrix.python-version == '3.11' && startsWith(github.ref, 'refs/tags/')
     #   name: Publish to Test PyPI
     #   uses: pypa/gh-action-pypi-publish@release/v1
     #   with:
@@ -100,10 +100,10 @@ jobs:
         # full history so that we can git describe
         with:
           fetch-depth: 0
-      - name: Set up Python 3.10
+      - name: Set up Python 3.11
         uses: actions/setup-python@v6
         with:
-          python-version: '3.10'
+          python-version: '3.11'
       - shell: bash
         run: |
           find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;

.github/workflows/setupapp.yml

@@ -91,7 +91,7 @@ jobs:
   #   runs-on: ubuntu-latest
   #   strategy:
   #     matrix:
-  #       python-version: ['3.10', '3.11', '3.12']
+  #       python-version: ['3.11', '3.12']
   #   steps:
   #   - uses: actions/checkout@v7
   #     with:
@@ -136,10 +136,10 @@ jobs:
   install:  # pip install from github url, the default branch is dev
     runs-on: ubuntu-latest
     steps:
-    - name: Set up Python 3.10
+    - name: Set up Python 3.11
       uses: actions/setup-python@v6
       with:
-        python-version: '3.10'
+        python-version: '3.11'
     - name: Install CPU PyTorch
       run: |
         python -m pip install torch==2.8.0 torchvision --extra-index-url https://download.pytorch.org/whl/cpu

.github/workflows/weekly-preview.yml

@@ -12,8 +12,8 @@ on:
 
 
 env:
-  PYTHON_VER: '3.10'
-  PYTORCH_VER: '2.8.0'
+  PYTHON_VER: '3.11'
+  PYTORCH_VER: '2.12.1'
   PIP_EXTRA_INDEX_URL: "https://download.pytorch.org/whl/cpu"  # forces CPU PyTorch installation, should be faster
 
 jobs:

.gitignore

@@ -170,3 +170,5 @@ runs
 *.pth
 
 *zarr/*
+
+uv.lock

docs/.readthedocs.yaml

@@ -6,7 +6,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.10"
+    python: "3.11"
 sphinx:
    configuration: docs/source/conf.py
 python:

docs/source/installation.md

@@ -20,7 +20,7 @@
 
 ---
 
-MONAI's core functionality is written in Python 3 (>= 3.10) and only requires [Numpy](https://numpy.org/) and [PyTorch](https://pytorch.org/).
+MONAI's core functionality is written in Python 3 (>= 3.11) 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.
@@ -343,6 +343,6 @@ 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 3.10
+conda create -n <name> python=<ver>  # eg 3.11
 conda env update -n <name> -f environment-dev.yml
 ```

docs/source/whatsnew_1_6.md

@@ -14,7 +14,7 @@
 - `NumpyReader` has been updated with an `allow_pickle` boolean argument to enable/disable pickle loading from `.npy/.npz` files. This was previously hard-coded to be enabled, but is now defined by this argument and disabled by default. This addresses [GHSA-qxq5-qhx6-94qw](https://github.com/Project-MONAI/MONAI/security/advisories/GHSA-qxq5-qhx6-94qw).
 
 
-MONAI now tests for Python 3.10 onwards, having dropped version 3.9 which is now out of support. PyTorch 2.8 onwards is now supported only, older versions will likely continue to function.
+MONAI now tests for Python 3.11 onwards, having dropped version 3.9 which is now out of support. PyTorch 2.12 onwards is now supported only, older versions will likely continue to function.
 
 ## Nested Dot-Notation Access in ConfigParser
 

environment-dev.yml

@@ -2,7 +2,7 @@ name: monai
 channels:
   - defaults
 dependencies:
-  - python>=3.10
+  - python>=3.11
   - pip
   - pip:
     - -e .[all,testing]

monai/apps/auto3dseg/auto_runner.py

@@ -572,7 +572,7 @@ 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/python3.10",
+                    - single GPU/CPU or multinode bcprun: "python " or "/opt/conda/bin/python3.11",
                     - 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

monai/auto3dseg/utils.py

@@ -603,7 +603,7 @@ 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,
-            e.g., "python", "python -m", "python3", "/opt/conda/bin/python3.10".
+            e.g., "python", "python -m", "python3", "/opt/conda/bin/python3.11".
         kwargs: the keyword arguments to be passed to the script.
 
     Returns:

pyproject.toml

@@ -7,7 +7,7 @@ requires = [
   "more-itertools>=8.0",
   "ninja",
   "packaging",
-  "torch>=2.8.0",
+  "torch>=2.12.1",
   "numpy>=1.24,<3.0",
   "backports.tarfile"  # see https://github.com/Project-MONAI/MONAI/issues/8791
 ]
@@ -17,7 +17,7 @@ build-backend = "setuptools.build_meta"
 name = "monai"
 description = "AI Toolkit for Healthcare Imaging"
 readme = { file = "README.md", content-type = "text/markdown" }
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 license = { text = "Apache License 2.0" }
 authors = [{ name = "MONAI Consortium", email = "monai.contact@gmail.com" }]
 classifiers = [
@@ -27,10 +27,11 @@ classifiers = [
   "Intended Audience :: Healthcare Industry",
   "Programming Language :: C++",
   "Programming Language :: Python :: 3",
-  "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
+  "Programming Language :: Python :: 3.14",
+  "Programming Language :: Python :: 3.15",
   "Topic :: Scientific/Engineering",
   "Topic :: Scientific/Engineering :: Artificial Intelligence",
   "Topic :: Scientific/Engineering :: Medical Science Apps.",
@@ -40,7 +41,7 @@ classifiers = [
   "Typing :: Typed",
 ]
 dependencies = [
-  "torch>=2.8.0",
+  "torch>=2.12.1",
   "numpy>=1.24,<3.0"
 ]
 dynamic = ["version"]
@@ -78,7 +79,6 @@ all = [
   "nvidia-ml-py",
   "onnx_graphsurgeon",
   "onnx>=1.13.0",
-  "onnxruntime; python_version <= '3.10'",
   "onnxscript",
   "openslide-bin",
   "openslide-python",
@@ -141,7 +141,7 @@ nvimgcodec = [
   "cupy-cuda13x[ctk]!=14.1.0; platform_system == 'Linux'",
   "nvidia-nvimgcodec-cu13[all]>=0.8.0; platform_system == 'Linux'"
 ]
-onnx = ["onnx>=1.13.0", "onnxruntime; python_version <= '3.10'", "onnx_graphsurgeon", "onnxscript"]
+onnx = ["onnx>=1.13.0", "onnx_graphsurgeon", "onnxscript"]
 openslide = ["openslide-python", "openslide-bin"]
 optuna = ["optuna"]
 pandas = ["pandas"]
@@ -395,7 +395,7 @@ project-excludes = [
 ]
 
 # Match CI environment
-python-version = "3.10"
+python-version = "3.11"
 python-platform = "linux"
 
 # "legacy" preset provides a smooth migration from previous type checkers