Merge branch 'develop' into ai-fixes

shaneahmed · web-flow · commit 84c8c4d81fb5 · 2026-03-30T12:12:00.000+01:00
diff --git a/.github/workflows/docker-publish.yml b/.github/workflows/docker-publish.yml
@@ -15,10 +15,6 @@ jobs:
       fail-fast: true
       matrix:
         include:
-          - dockerfile: ./docker/3.10/Debian/Dockerfile
-            mtag: py3.10-debian
-          - dockerfile: ./docker/3.10/Ubuntu/Dockerfile
-            mtag: py3.10-ubuntu
           - dockerfile: ./docker/3.11/Debian/Dockerfile
             mtag: py3.11-debian
           - dockerfile: ./docker/3.11/Ubuntu/Dockerfile
diff --git a/.github/workflows/mypy-type-check.yml b/.github/workflows/mypy-type-check.yml
@@ -18,7 +18,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.11", "3.12", "3.13"]
 
     steps:
 
diff --git a/.github/workflows/pip-install.yml b/.github/workflows/pip-install.yml
@@ -31,7 +31,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.11", "3.12", "3.13"]
         os: [ubuntu-24.04, windows-latest, macos-latest]
 
     # Force UTF-8 everywhere (Windows is the one that really needs it)
diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
@@ -20,7 +20,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.11", "3.12", "3.13"]
 
     steps:
     - uses: actions/checkout@v4
@@ -101,10 +101,10 @@ jobs:
     steps:
     - uses: actions/checkout@v4
 
-    - name: Set up Python 3.10
+    - name: Set up Python 3.11
       uses: actions/setup-python@v4
       with:
-        python-version: '3.10'
+        python-version: '3.11'
         cache: 'pip'
 
     - name: Install dependencies
diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -98,7 +98,7 @@ Before you submit a pull request, check that it meets these guidelines:
 
 1. The pull request should include tests.
 2. If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring, and add the feature to the pull request description.
-3. The pull request should work for Python 3.10, 3.11, 3.12 and 3.13, and for PyPy. Check https://github.com/TissueImageAnalytics/tiatoolbox/actions/workflows/python-package.yml and make sure that the tests pass for all supported Python versions.
+3. The pull request should work for Python 3.11, 3.12, and 3.13 and for PyPy. Check https://github.com/TissueImageAnalytics/tiatoolbox/actions/workflows/python-package.yml and make sure that the tests pass for all supported Python versions.
 
 Tips
 ----
diff --git a/README.md b/README.md
@@ -106,7 +106,7 @@ Prepare a computer as a convenient platform for further development of the Pytho
 5. Create virtual environment for TIAToolbox using
 
 ```sh
-    $ conda create -n tiatoolbox-dev python=3.10 # select version of your choice
+    $ conda create -n tiatoolbox-dev python=3.11 # select version of your choice
     $ conda activate tiatoolbox-dev
     $ pip install -r requirements/requirements_dev.txt
 ```
diff --git a/docker/3.10/Debian/Dockerfile b/docker/3.10/Debian/Dockerfile
diff --git a/docker/3.10/Ubuntu/Dockerfile b/docker/3.10/Ubuntu/Dockerfile
diff --git a/docs/installation.rst b/docs/installation.rst
@@ -59,7 +59,7 @@ MacPorts
 Installing Stable Release
 =========================
 
-Please note that TIAToolbox is tested for Python versions 3.10, 3.11, 3.12 and 3.13.
+Please note that TIAToolbox is tested for Python versions 3.11, 3.12, and 3.13.
 
 Recommended
 -----------
diff --git a/pyproject.toml b/pyproject.toml
@@ -136,8 +136,8 @@ line-length = 88
 # Allow unused variables when underscore-prefixed.
 lint.dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
 
-# Minimum Python version 3.10.
-target-version = "py310"
+# Minimum Python version 3.11.
+target-version = "py311"
 
 [tool.ruff.lint.mccabe]
 # Unlike Flake8, default to a complexity level of 10.
@@ -174,4 +174,4 @@ skip-magic-trailing-comma = false
 
 [tool.mypy]
 ignore_missing_imports = true
-python_version = "3.10"
+python_version = "3.11"
diff --git a/requirements/requirements.conda.yml b/requirements/requirements.conda.yml
@@ -6,9 +6,8 @@ channels:
   - defaults
 dependencies:
   - cython
-  - openslide
   - pip>=20.0.2
   - pixman>=0.39.0
-  - python>=3.10, <=3.13
+  - python>=3.11, <=3.13
   - pip:
     - -r requirements.txt
diff --git a/requirements/requirements.dev.conda.yml b/requirements/requirements.dev.conda.yml
@@ -6,9 +6,8 @@ channels:
   - defaults
 dependencies:
   - cython
-  - openslide
   - pip>=20.0.2
   - pixman>=0.39.0
-  - python>=3.10, <=3.13
+  - python>=3.11, <=3.13
   - pip:
       - -r requirements_dev.txt
diff --git a/requirements/requirements.txt b/requirements/requirements.txt
@@ -29,7 +29,7 @@ scikit-learn>=1.2.0
 scipy>=1.8
 shapely>=2.0.0
 SimpleITK>=2.2.1
-sphinx>=5.3.0, <9.0
+sphinx>=5.3.0, <9.0.0
 tifffile>=2022.10.10, <=2025.5.10
 timm>=1.0.3
 torch>=2.5.0
diff --git a/requirements/requirements.win64.conda.yml b/requirements/requirements.win64.conda.yml
@@ -9,6 +9,6 @@ dependencies:
   - openjpeg>=2.4.0
   - pip>=20.0.2
   - pixman>=0.39.0
-  - python>=3.10, <=3.13
+  - python>=3.11, <=3.13
   - pip:
       - -r requirements.txt
diff --git a/requirements/requirements.win64.dev.conda.yml b/requirements/requirements.win64.dev.conda.yml
@@ -9,6 +9,6 @@ dependencies:
   - openjpeg>=2.4.0
   - pip>=20.0.2
   - pixman>=0.39.0
-  - python>=3.10, <=3.13
+  - python>=3.11, <=3.13
   - pip:
       - -r requirements_dev.txt
diff --git a/setup.py b/setup.py
@@ -34,13 +34,12 @@
 setup(
     author="TIA Centre",
     author_email="TIA@warwick.ac.uk",
-    python_requires=">=3.10, <3.14",
+    python_requires=">=3.11, <3.14",
     classifiers=[
         "Development Status :: 2 - Pre-Alpha",
         "Intended Audience :: Developers",
         "Natural Language :: English",
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
         "Programming Language :: Python :: 3.12",
         "Programming Language :: Python :: 3.13",
diff --git a/tests/test_annotation_stores.py b/tests/test_annotation_stores.py
@@ -1827,13 +1827,13 @@ def test_load_cases_error(
             store._load_cases(["foo"], lambda: None, lambda: None)
 
     @staticmethod
-    def test_py310_init(
+    def test_py311_init(
         fill_store: Callable,  # noqa: ARG004
         store_cls: type[AnnotationStore],
         monkeypatch: object,
     ) -> None:
-        """Test that __init__ is compatible with Python 3.10."""
-        py310_version = (3, 10, 0)
+        """Test that __init__ is compatible with Python 3.11."""
+        py311_version = (3, 11, 0)
 
         class Connection(sqlite3.Connection):
             """Mock SQLite connection."""
@@ -1847,7 +1847,7 @@ def create_function(
                 """Mock create_function without `deterministic` kwarg."""
                 return self.create_function(self, name, num_params)
 
-        monkeypatch.setattr(sys, "version_info", py310_version)
+        monkeypatch.setattr(sys, "version_info", py311_version)
         monkeypatch.setattr(sqlite3, "Connection", Connection)
         _ = store_cls()
 
diff --git a/tiatoolbox/annotation/storage.py b/tiatoolbox/annotation/storage.py
@@ -58,6 +58,7 @@
     TYPE_CHECKING,
     Any,
     ClassVar,
+    Self,
     TypeVar,
     cast,
     overload,
@@ -72,7 +73,6 @@
 from shapely.geometry import LineString, Point, Polygon
 from shapely.geometry import mapping as geometry2feature
 from shapely.geometry import shape as feature2geometry
-from typing_extensions import Self
 
 import tiatoolbox
 from tiatoolbox import DuplicateFilter, logger
diff --git a/tiatoolbox/wsicore/wsireader.py b/tiatoolbox/wsicore/wsireader.py
@@ -9,7 +9,7 @@
 import os
 import re
 from collections import defaultdict
-from datetime import datetime, timezone
+from datetime import UTC, datetime
 from numbers import Number
 from pathlib import Path
 from typing import TYPE_CHECKING
@@ -4681,14 +4681,14 @@ def us_date(string: str) -> datetime:
                 """Return datetime parsed according to US date format (UTC-aware)."""
                 # and we immediately attach UTC.
                 dt = datetime.strptime(string, r"%m/%d/%y")  # noqa: DTZ007
-                return dt.replace(tzinfo=timezone.utc)
+                return dt.replace(tzinfo=UTC)
 
             def time(string: str) -> datetime:
                 """Return datetime parsed according to HMS format (UTC-aware)."""
                 # parse to time first; although .time() is tz-agnostic
                 # DTZ007 is triggered by strptime
                 t = datetime.strptime(string, r"%H:%M:%S").time()  # noqa: DTZ007
-                today_utc = datetime.now(timezone.utc)
+                today_utc = datetime.now(UTC)
                 return today_utc.replace(
                     hour=t.hour, minute=t.minute, second=t.second, microsecond=0
                 )
@@ -4698,7 +4698,7 @@ def time(string: str) -> datetime:
             for cast in casting_precedence:
                 try:
                     value = cast(value_string)
-                except ValueError:  # noqa: PERF203
+                except ValueError:
                     continue
                 else:
                     return key, value
