From 47be4b3e61e3b8652e203fa30b85b2e6c2aa975a Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 4 Feb 2026 16:23:12 +0000
Subject: [PATCH 1/8] Initial plan


From 0798db3276513092e6db390c921e1fec30ea47a0 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 4 Feb 2026 16:24:55 +0000
Subject: [PATCH 2/8] Remove Python 3.9 support from CI workflows and update
 target versions

Co-authored-by: bhashemian <3968947+bhashemian@users.noreply.github.com>
---
 .github/workflows/pythonapp.yml | 6 +++---
 pyproject.toml                  | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml
index 52eff10fa..5400e13b4 100644
--- a/.github/workflows/pythonapp.yml
+++ b/.github/workflows/pythonapp.yml
@@ -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:
diff --git a/pyproject.toml b/pyproject.toml
index 2e0b24c58..b9adf875c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,7 +19,7 @@ requires = [
 
 [tool.black]
 line-length = 120
-target-version = ['py36', 'py37', 'py38']
+target-version = ['py310', 'py311', 'py312']
 include = '\.pyi?$'
 exclude = '''
 (

From b088ae0b54c0d6d9637aac91c32bf5cfe064b75e Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 4 Feb 2026 16:30:42 +0000
Subject: [PATCH 3/8] Remove deprecated distutils usage for Python 3.12+
 compatibility

Co-authored-by: bhashemian <3968947+bhashemian@users.noreply.github.com>
---
 monailabel/config.py                   |  3 ++-
 monailabel/utils/others/class_utils.py |  2 +-
 monailabel/utils/others/generic.py     | 20 ++++++++++++++++++--
 setup.py                               | 17 ++++++++++++++++-
 4 files changed, 37 insertions(+), 5 deletions(-)

diff --git a/monailabel/config.py b/monailabel/config.py
index ea8d1c37e..583bdf142 100644
--- a/monailabel/config.py
+++ b/monailabel/config.py
@@ -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.generic import strtobool
+
 
 def is_package_installed(name):
     return name in (x.metadata.get("Name") for x in distributions() if x.metadata is not None)
diff --git a/monailabel/utils/others/class_utils.py b/monailabel/utils/others/class_utils.py
index 0b92f5568..eb0f9c146 100644
--- a/monailabel/utils/others/class_utils.py
+++ b/monailabel/utils/others/class_utils.py
@@ -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.generic import strtobool
 
 logger = logging.getLogger(__name__)
 
diff --git a/monailabel/utils/others/generic.py b/monailabel/utils/others/generic.py
index a26edec63..5abb90220 100644
--- a/monailabel/utils/others/generic.py
+++ b/monailabel/utils/others/generic.py
@@ -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
@@ -242,7 +241,24 @@ 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))
+    """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
+    
+    val = str(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}")
 
 
 def is_openslide_supported(name):
diff --git a/setup.py b/setup.py
index aa4af4408..844d6fb20 100755
--- a/setup.py
+++ b/setup.py
@@ -14,13 +14,28 @@
 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.
+    """
+    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):

From c85e8027352c740be8a2454d7c78a1cd7dc9760e Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 4 Feb 2026 16:31:56 +0000
Subject: [PATCH 4/8] Fix flake8 whitespace issues in docstrings

Co-authored-by: bhashemian <3968947+bhashemian@users.noreply.github.com>
---
 monailabel/utils/others/generic.py | 4 ++--
 setup.py                           | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/monailabel/utils/others/generic.py b/monailabel/utils/others/generic.py
index 5abb90220..caa906bd0 100644
--- a/monailabel/utils/others/generic.py
+++ b/monailabel/utils/others/generic.py
@@ -242,7 +242,7 @@ def _list_files(d, ext):
 
 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.
@@ -251,7 +251,7 @@ def strtobool(s):
         return False
     if isinstance(s, bool):
         return s
-    
+
     val = str(s).lower()
     if val in ('y', 'yes', 't', 'true', 'on', '1'):
         return True
diff --git a/setup.py b/setup.py
index 844d6fb20..7bffe291f 100755
--- a/setup.py
+++ b/setup.py
@@ -22,7 +22,7 @@
 
 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.

From 6b0e3bedf65caf333a59e7bd0fff226a56ff3b79 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 4 Feb 2026 16:33:22 +0000
Subject: [PATCH 5/8] Update CVAT plugin runtime to Python 3.10

Co-authored-by: bhashemian <3968947+bhashemian@users.noreply.github.com>
---
 plugins/cvat/endoscopy/deepedit.yaml            | 2 +-
 plugins/cvat/endoscopy/inbody.yaml              | 2 +-
 plugins/cvat/endoscopy/tooltracking.yaml        | 2 +-
 plugins/cvat/pathology/deepedit_nuclei.yaml     | 2 +-
 plugins/cvat/pathology/nuclick.yaml             | 2 +-
 plugins/cvat/pathology/segmentation_nuclei.yaml | 2 +-
 plugins/cvat/sam2/interactor.yaml               | 2 +-
 plugins/cvat/sam2/tracker.yaml                  | 2 +-
 8 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/plugins/cvat/endoscopy/deepedit.yaml b/plugins/cvat/endoscopy/deepedit.yaml
index 494e8a37a..37c95e186 100644
--- a/plugins/cvat/endoscopy/deepedit.yaml
+++ b/plugins/cvat/endoscopy/deepedit.yaml
@@ -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
 
diff --git a/plugins/cvat/endoscopy/inbody.yaml b/plugins/cvat/endoscopy/inbody.yaml
index 48586b49c..20e33661b 100644
--- a/plugins/cvat/endoscopy/inbody.yaml
+++ b/plugins/cvat/endoscopy/inbody.yaml
@@ -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
 
diff --git a/plugins/cvat/endoscopy/tooltracking.yaml b/plugins/cvat/endoscopy/tooltracking.yaml
index 1cac8673e..f890aecd0 100644
--- a/plugins/cvat/endoscopy/tooltracking.yaml
+++ b/plugins/cvat/endoscopy/tooltracking.yaml
@@ -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
 
diff --git a/plugins/cvat/pathology/deepedit_nuclei.yaml b/plugins/cvat/pathology/deepedit_nuclei.yaml
index 3084c67e2..dc0260a86 100644
--- a/plugins/cvat/pathology/deepedit_nuclei.yaml
+++ b/plugins/cvat/pathology/deepedit_nuclei.yaml
@@ -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
 
diff --git a/plugins/cvat/pathology/nuclick.yaml b/plugins/cvat/pathology/nuclick.yaml
index 82976e241..242c7997c 100644
--- a/plugins/cvat/pathology/nuclick.yaml
+++ b/plugins/cvat/pathology/nuclick.yaml
@@ -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
 
diff --git a/plugins/cvat/pathology/segmentation_nuclei.yaml b/plugins/cvat/pathology/segmentation_nuclei.yaml
index f42a8a661..3a92a2866 100644
--- a/plugins/cvat/pathology/segmentation_nuclei.yaml
+++ b/plugins/cvat/pathology/segmentation_nuclei.yaml
@@ -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
 
diff --git a/plugins/cvat/sam2/interactor.yaml b/plugins/cvat/sam2/interactor.yaml
index 6787c300e..b1dc7c9a6 100644
--- a/plugins/cvat/sam2/interactor.yaml
+++ b/plugins/cvat/sam2/interactor.yaml
@@ -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
 
diff --git a/plugins/cvat/sam2/tracker.yaml b/plugins/cvat/sam2/tracker.yaml
index c6842f9bf..1ebba9d77 100644
--- a/plugins/cvat/sam2/tracker.yaml
+++ b/plugins/cvat/sam2/tracker.yaml
@@ -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
 

From 5bc06c623957459776114a1f19571035e9b1c005 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 4 Feb 2026 16:35:25 +0000
Subject: [PATCH 6/8] Improve strtobool type safety with proper error handling

Co-authored-by: bhashemian <3968947+bhashemian@users.noreply.github.com>
---
 monailabel/utils/others/generic.py | 4 +++-
 setup.py                           | 2 ++
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/monailabel/utils/others/generic.py b/monailabel/utils/others/generic.py
index caa906bd0..2c5e076a0 100644
--- a/monailabel/utils/others/generic.py
+++ b/monailabel/utils/others/generic.py
@@ -251,8 +251,10 @@ def strtobool(s):
         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 = str(s).lower()
+    val = s.lower()
     if val in ('y', 'yes', 't', 'true', 'on', '1'):
         return True
     elif val in ('n', 'no', 'f', 'false', 'off', '0'):
diff --git a/setup.py b/setup.py
index 7bffe291f..e5ae765a5 100755
--- a/setup.py
+++ b/setup.py
@@ -27,6 +27,8 @@ def strtobool(val):
     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

From ec0d5c8390011ec62539a979c44be6e7b57409de Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 4 Feb 2026 18:17:59 +0000
Subject: [PATCH 7/8] Add SimpleITK as explicit dependency to fix CI test
 failures

Co-authored-by: bhashemian <3968947+bhashemian@users.noreply.github.com>
---
 requirements.txt | 1 +
 setup.cfg        | 1 +
 2 files changed, 2 insertions(+)

diff --git a/requirements.txt b/requirements.txt
index d57ae0d0c..3d36bcecd 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -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'
 
diff --git a/setup.cfg b/setup.cfg
index 8f81210c1..e18b674b2 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -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'
 

From 6843287377cdcdc7ec7b16c68f84bf1ea36c18da Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 4 Feb 2026 20:05:34 +0000
Subject: [PATCH 8/8] Fix circular import by moving strtobool to standalone
 module

Co-authored-by: bhashemian <3968947+bhashemian@users.noreply.github.com>
---
 monailabel/config.py                   |  2 +-
 monailabel/utils/others/class_utils.py |  2 +-
 monailabel/utils/others/generic.py     | 24 +---------------
 monailabel/utils/others/strtobool.py   | 38 ++++++++++++++++++++++++++
 4 files changed, 41 insertions(+), 25 deletions(-)
 create mode 100644 monailabel/utils/others/strtobool.py

diff --git a/monailabel/config.py b/monailabel/config.py
index 583bdf142..18518c144 100644
--- a/monailabel/config.py
+++ b/monailabel/config.py
@@ -15,7 +15,7 @@
 from pydantic import AnyHttpUrl
 from pydantic_settings import BaseSettings, SettingsConfigDict
 
-from monailabel.utils.others.generic import strtobool
+from monailabel.utils.others.strtobool import strtobool
 
 
 def is_package_installed(name):
diff --git a/monailabel/utils/others/class_utils.py b/monailabel/utils/others/class_utils.py
index eb0f9c146..19747f800 100644
--- a/monailabel/utils/others/class_utils.py
+++ b/monailabel/utils/others/class_utils.py
@@ -18,7 +18,7 @@
 from typing import List
 
 from monailabel.interfaces.exception import MONAILabelError, MONAILabelException
-from monailabel.utils.others.generic import strtobool
+from monailabel.utils.others.strtobool import strtobool
 
 logger = logging.getLogger(__name__)
 
diff --git a/monailabel/utils/others/generic.py b/monailabel/utils/others/generic.py
index 2c5e076a0..def82a554 100644
--- a/monailabel/utils/others/generic.py
+++ b/monailabel/utils/others/generic.py
@@ -30,6 +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__)
 
@@ -240,29 +241,6 @@ def _list_files(d, ext):
     ]
 
 
-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}")
-
-
 def is_openslide_supported(name):
     ext = file_ext(name)
     supported_ext = (".bif", ".mrxs", ".ndpi", ".scn", ".svs", ".svslide", ".tif", ".tiff", ".vms", ".vmu")
diff --git a/monailabel/utils/others/strtobool.py b/monailabel/utils/others/strtobool.py
new file mode 100644
index 000000000..2741bf638
--- /dev/null
+++ b/monailabel/utils/others/strtobool.py
@@ -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}")