Drop Python 3.9 support and fix Python 3.12 compatibility #1890

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Copilot wants to merge 8 commits into main from copilot/fix-build-issues-drop-python-3-9

.github/workflows/pythonapp.yml

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -32,7 +32,7 @@ jobs:
  
        strategy:

          matrix:

            os: [windows-latest, ubuntu-latest]

            python-version: ["3.9", "3.10", "3.11", "3.12"]

            python-version: ["3.10", "3.11", "3.12"]

        steps:

          - uses: actions/checkout@v6

          - name: Set up Python

    @@ -54,7 +54,7 @@ jobs:
  
          MONAI_ZOO_AUTH_TOKEN: ${{ github.token }}

        strategy:

          matrix:

            python-version: ["3.9", "3.10", "3.11", "3.12"]

            python-version: ["3.10", "3.11", "3.12"]

        steps:

          - uses: actions/checkout@v6

          - name: Set up Python

    @@ -88,7 +88,7 @@ jobs:
  
          MONAI_ZOO_AUTH_TOKEN: ${{ github.token }}

        strategy:

          matrix:

            python-version: ["3.9", "3.10", "3.11", "3.12"]

            python-version: ["3.10", "3.11", "3.12"]

        steps:

          - uses: actions/checkout@v6

            with:

monailabel/config.py

-Original file line number
+Diff line change
@@ Expand Up / @@ -9,13 +9,14 @@ @@
     # See the License for the specific language governing permissions and
     # limitations under the License.
     import os
-    from distutils.util import strtobool
     from importlib.metadata import distributions
     from typing import Any, Dict, List, Optional
     from pydantic import AnyHttpUrl
     from pydantic_settings import BaseSettings, SettingsConfigDict
+    from monailabel.utils.others.strtobool import strtobool
     def is_package_installed(name):
         return name in (x.metadata.get("Name") for x in distributions() if x.metadata is not None)
@@ Expand Down @@

monailabel/utils/others/class_utils.py

-Original file line number
+Diff line change
@@ Expand Up / @@ -15,10 +15,10 @@ @@
     import logging
     import os
     import sys
-    from distutils.util import strtobool
     from typing import List
     from monailabel.interfaces.exception import MONAILabelError, MONAILabelException
+    from monailabel.utils.others.strtobool import strtobool
     logger = logging.getLogger(__name__)
@@ Expand Down @@

monailabel/utils/others/generic.py

-Original file line number
+Diff line change
@@ Expand Up / @@ -9,7 +9,6 @@ @@
     # See the License for the specific language governing permissions and
     # limitations under the License.
-    import distutils.util
     import hashlib
     import json
     import logging
@@ Expand All / @@ -31,6 +30,7 @@ @@
     from monailabel.config import settings
     from monailabel.utils.others.modelzoo_list import MAINTAINED_BUNDLES
+    from monailabel.utils.others.strtobool import strtobool  # noqa: F401
     logger = logging.getLogger(__name__)
@@ Expand Down Expand Up / @@ -241,10 +241,6 @@ def _list_files(d, ext): @@
         ]
-    def strtobool(s):
-        return False if s is None else s if isinstance(s, bool) else bool(distutils.util.strtobool(s))
     def is_openslide_supported(name):
         ext = file_ext(name)
         supported_ext = (".bif", ".mrxs", ".ndpi", ".scn", ".svs", ".svslide", ".tif", ".tiff", ".vms", ".vmu")
@@ Expand Down @@

monailabel/utils/others/strtobool.py

-Original file line number
+Diff line change
@@ -0,0 +1,38 @@
+    # Copyright (c) MONAI Consortium
+    # Licensed under the Apache License, Version 2.0 (the "License");
+    # you may not use this file except in compliance with the License.
+    # You may obtain a copy of the License at
+    #     http://www.apache.org/licenses/LICENSE-2.0
+    # Unless required by applicable law or agreed to in writing, software
+    # distributed under the License is distributed on an "AS IS" BASIS,
+    # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+    # See the License for the specific language governing permissions and
+    # limitations under the License.
+    """Standalone utility function for string to boolean conversion.
+    This module exists separately to avoid circular import dependencies.
+    """
+    def strtobool(s):
+        """Convert a string representation of truth to true or false.
+        True values are 'y', 'yes', 't', 'true', 'on', and '1'; false values
+        are 'n', 'no', 'f', 'false', 'off', and '0'.  Returns the input if
+        already a bool. Returns False if None.
+        """
+        if s is None:
+            return False
+        if isinstance(s, bool):
+            return s
+        if not isinstance(s, str):
+            raise TypeError(f"strtobool expects a string or bool, got {type(s).__name__}: {s!r}")
+        val = s.lower()
+        if val in ('y', 'yes', 't', 'true', 'on', '1'):
+            return True
+        elif val in ('n', 'no', 'f', 'false', 'off', '0'):
+            return False
+        else:
+            raise ValueError(f"invalid truth value {s!r}")

plugins/cvat/endoscopy/deepedit.yaml

-Original file line number
+Diff line change
@@ Expand Up / @@ -23,7 +23,7 @@ metadata: @@
     spec:
       description: A pre-trained DeepEdit model for interactive model for Endoscopy
-      runtime: 'python:3.8'
+      runtime: 'python:3.10'
       handler: interactor:handler
       eventTimeout: 30s
@@ Expand Down @@

plugins/cvat/endoscopy/inbody.yaml

-Original file line number
+Diff line change
@@ Expand Up / @@ -24,7 +24,7 @@ metadata: @@
     spec:
       description: A pre-trained classification model for Endoscopy to flag if image follows InBody or OutBody
-      runtime: 'python:3.8'
+      runtime: 'python:3.10'
       handler: detector:handler
       eventTimeout: 30s
@@ Expand Down @@

plugins/cvat/endoscopy/tooltracking.yaml

-Original file line number
+Diff line change
@@ Expand Up / @@ -23,7 +23,7 @@ metadata: @@
     spec:
       description: A pre-trained tool tracking model for Endoscopy
-      runtime: 'python:3.8'
+      runtime: 'python:3.10'
       handler: detector:handler
       eventTimeout: 30s
@@ Expand Down @@

plugins/cvat/pathology/deepedit_nuclei.yaml

-Original file line number
+Diff line change
@@ Expand Up / @@ -23,7 +23,7 @@ metadata: @@
     spec:
       description: A pre-trained interaction/deepedit model for Pathology
-      runtime: 'python:3.8'
+      runtime: 'python:3.10'
       handler: detector:handler
       eventTimeout: 30s
@@ Expand Down @@

plugins/cvat/pathology/nuclick.yaml

-Original file line number
+Diff line change
@@ Expand Up / @@ -25,7 +25,7 @@ metadata: @@
     spec:
       description: A pre-trained NuClick model for interactive cell segmentation for Pathology
-      runtime: 'python:3.8'
+      runtime: 'python:3.10'
       handler: interactor:handler
       eventTimeout: 30s
@@ Expand Down @@

plugins/cvat/pathology/segmentation_nuclei.yaml

-Original file line number
+Diff line change
@@ Expand Up / @@ -27,7 +27,7 @@ metadata: @@
     spec:
       description: A pre-trained semantic segmentation model for Pathology
-      runtime: 'python:3.8'
+      runtime: 'python:3.10'
       handler: detector:handler
       eventTimeout: 30s
@@ Expand Down @@

plugins/cvat/sam2/interactor.yaml

-Original file line number
+Diff line change
@@ Expand Up / @@ -24,7 +24,7 @@ metadata: @@
     spec:
       description: A pre-trained SAM2 model for interactive model
-      runtime: 'python:3.8'
+      runtime: 'python:3.10'
       handler: interactor:handler
       eventTimeout: 30s
@@ Expand Down @@

plugins/cvat/sam2/tracker.yaml

-Original file line number
+Diff line change
@@ Expand Up / @@ -19,7 +19,7 @@ metadata: @@
     spec:
       description: A pre-trained SAM2 model for tracking model
-      runtime: 'python:3.8'
+      runtime: 'python:3.10'
       handler: tracker:handler
       eventTimeout: 30s
@@ Expand Down @@

pyproject.toml

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -19,7 +19,7 @@ requires = [
  
    [tool.black]

    line-length = 120

    target-version = ['py36', 'py37', 'py38']

    target-version = ['py310', 'py311', 'py312']

    include = '\.pyi?$'

    exclude = '''

    (

requirements.txt

-Original file line number
+Diff line change
@@ Expand Up / @@ -46,6 +46,7 @@ urllib3==2.6.0 @@
     scikit-learn
     scipy
     google-auth==2.29.0
+    SimpleITK>=2.2.0
     SAM-2 @ git+https://github.com/facebookresearch/sam2.git@c2ec8e14a185632b0a5d8b161928ceb50197eddc ; python_version >= '3.10'
     #sam2>=0.4.1; python_version >= '3.10'
@@ Expand Down @@

setup.cfg

-Original file line number
+Diff line change
@@ Expand Up / @@ -70,6 +70,7 @@ install_requires = @@
         scikit-learn
         scipy
         google-auth>=2.29.0
+        SimpleITK>=2.2.0
         sam2>=0.4.1; python_version >= '3.10'
         #SAM-2 @ git+https://github.com/facebookresearch/sam2.git@c2ec8e14a185632b0a5d8b161928ceb50197eddc ; python_version >= '3.10'
@@ Expand Down @@

setup.py

-Original file line number
+Diff line change
@@ Expand Up / @@ -14,13 +14,30 @@ @@
     import os
     import platform
     import subprocess
-    from distutils.util import strtobool
     from setuptools import find_packages, setup
     import versioneer
+    def strtobool(val):
+        """Convert a string representation of truth to true (1) or false (0).
+        True values are 'y', 'yes', 't', 'true', 'on', and '1'; false values
+        are 'n', 'no', 'f', 'false', 'off', and '0'.  Raises ValueError if
+        'val' is anything else.
+        """
+        if not isinstance(val, str):
+            raise TypeError(f"strtobool expects a string, got {type(val).__name__}")
+        val = val.lower()
+        if val in ('y', 'yes', 't', 'true', 'on', '1'):
+            return 1
+        elif val in ('n', 'no', 'f', 'false', 'off', '0'):
+            return 0
+        else:
+            raise ValueError(f"invalid truth value {val!r}")
     def recursive_files(directory, prefix):
         paths = []
         for path, _, filenames in os.walk(directory):
@@ Expand Down @@

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