Further changes for 3.9 to 3.10

ericspod · ericspod · commit 29a2ff67010b · 2025-11-12T15:03:31.000Z
Signed-off-by: Eric Kerfoot &lt;17726042+ericspod@users.noreply.github.com&gt;
diff --git 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: ${{ matrix.os }}
     timeout-minutes: 46 # equal to max + 3*std over the last 600 successful runs
     env:
diff --git a/.github/workflows/cron-ngc-bundle.yml b/.github/workflows/cron-ngc-bundle.yml
@@ -18,10 +18,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v5
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10
       uses: actions/setup-python@v6
       with:
-        python-version: '3.9'
+        python-version: '3.10'
     - name: cache weekly timestamp
       id: pip-cache
       run: echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -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
@@ -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
@@ -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:
@@ -64,22 +64,22 @@ 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/
         rm dist/monai*.tar.gz
         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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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.
@@ -42,15 +43,15 @@ setup_requires =
     ninja
     packaging
 install_requires =
-    torch>=2.4.1
+    torch>=2.6.0
     numpy>=1.24,<3.0
 
 [options.extras_require]
 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
