📌 Update minimum Python version to 3.9

Signed-off-by: Shan E Ahmed Raza <13048456+shaneahmed@users.noreply.github.com>

.github/workflows/mypy-type-check.yml

@@ -16,7 +16,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
 

.github/workflows/pip-install.yml

@@ -12,7 +12,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
         os: [ubuntu-22.04, windows-latest, macos-latest]
     steps:
     - name: Set up Python ${{ matrix.python-version }}

.github/workflows/python-package.yml

@@ -17,7 +17,7 @@ jobs:
     strategy:
       fail-fast: true
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v3

README.md

@@ -115,7 +115,7 @@ 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=3.8 # select version of your choice
+    $ conda create -n tiatoolbox-dev python=3.9 # select version of your choice
     $ conda activate tiatoolbox-dev
     $ pip install -r requirements/requirements_dev.txt
 ```

pyproject.toml

@@ -157,8 +157,8 @@ line-length = 88
 # Allow unused variables when underscore-prefixed.
 lint.dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
 
-# Minimum Python version 3.8.
-target-version = "py38"
+# Minimum Python version 3.9.
+target-version = "py39"
 
 [tool.ruff.lint.mccabe]
 # Unlike Flake8, default to a complexity level of 10.
@@ -174,4 +174,4 @@ max-args = 10
 
 [tool.mypy]
 ignore_missing_imports = true
-python_version = 3.8
+python_version = 3.9

requirements/requirements.conda.yml

@@ -9,6 +9,6 @@ dependencies:
   - openslide
   - pip>=20.0.2
   - pixman>=0.39.0
-  - python>=3.8, <=3.11
+  - python>=3.9, <=3.12
   - pip:
     - -r requirements.txt

requirements/requirements.dev.conda.yml

@@ -9,6 +9,6 @@ dependencies:
   - openslide
   - pip>=20.0.2
   - pixman>=0.39.0
-  - python>=3.8, <=3.11
+  - python>=3.9, <=3.12
   - pip:
       - -r requirements_dev.txt

requirements/requirements.win64.conda.yml

@@ -9,6 +9,6 @@ dependencies:
   - openjpeg>=2.4.0
   - pip>=20.0.2
   - pixman>=0.39.0
-  - python>=3.8, <=3.11
+  - python>=3.9, <=3.12
   - pip:
       - -r requirements.txt

requirements/requirements.win64.dev.conda.yml

@@ -9,6 +9,6 @@ dependencies:
   - openjpeg>=2.4.0
   - pip>=20.0.2
   - pixman>=0.39.0
-  - python>=3.8, <=3.11
+  - python>=3.9, <=3.12
   - pip:
       - -r requirements_dev.txt

setup.py

@@ -34,16 +34,16 @@
 setup(
     author="TIA Centre",
     author_email="tia@dcs.warwick.ac.uk",
-    python_requires=">=3.8, <3.12",
+    python_requires=">=3.9, <3.13",
     classifiers=[
         "Development Status :: 2 - Pre-Alpha",
         "Intended Audience :: Developers",
         "Natural Language :: English",
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
     ],
     description="Computational pathology toolbox developed by TIA Centre.",
     dependency_links=dependency_links,

tests/test_annotation_stores.py

@@ -6,10 +6,11 @@
 import pickle
 import sqlite3
 import sys
+from collections.abc import Generator
 from itertools import repeat, zip_longest
 from pathlib import Path
 from timeit import timeit
-from typing import TYPE_CHECKING, Callable, ClassVar, Generator
+from typing import TYPE_CHECKING, Callable, ClassVar
 
 import numpy as np
 import pandas as pd
@@ -1806,8 +1807,8 @@ def test_py38_init(
         store_cls: type[AnnotationStore],
         monkeypatch: object,
     ) -> None:
-        """Test that __init__ is compatible with Python 3.8."""
-        py38_version = (3, 8, 0)
+        """Test that __init__ is compatible with Python 3.9."""
+        py38_version = (3, 9, 0)
 
         class Connection(sqlite3.Connection):
             """Mock SQLite connection."""

tests/test_app_bokeh.py

@@ -2,24 +2,19 @@
 
 from __future__ import annotations
 
+import importlib.resources as importlib_resources
 import io
 import json
 import multiprocessing
 import re
-import sys
 import time
+from collections.abc import Generator
 from pathlib import Path
-from typing import TYPE_CHECKING, Generator
+from typing import TYPE_CHECKING
 
 import bokeh.models as bkmodels
 import matplotlib.pyplot as plt
 import numpy as np
-
-if sys.version_info >= (3, 9):  # pragma: no cover
-    import importlib.resources as importlib_resources
-else:  # pragma: no cover
-    # To support Python 3.8
-    import importlib_resources  # type: ignore[import-not-found]
 import pytest
 import requests
 from bokeh.application import Application

tiatoolbox/__init__.py

@@ -2,17 +2,12 @@
 
 from __future__ import annotations
 
+import importlib.resources as importlib_resources
 import importlib.util
 import sys
 from pathlib import Path
 from typing import TYPE_CHECKING, Dict, TypedDict
 
-if sys.version_info >= (3, 9):  # pragma: no cover
-    import importlib.resources as importlib_resources
-else:  # pragma: no cover
-    # To support Python 3.8
-    import importlib_resources  # type: ignore[import-not-found]
-
 import yaml
 
 if TYPE_CHECKING:  # pragma: no cover
@@ -92,7 +87,6 @@ def read_registry_files(path_to_registry: str | Path) -> dict:
 
 
     """
-    path_to_registry = str(path_to_registry)  # To pass tests with Python 3.8
     pretrained_files_registry_path = importlib_resources.as_file(
         importlib_resources.files("tiatoolbox") / path_to_registry,
     )

tiatoolbox/annotation/storage.py

@@ -40,7 +40,7 @@
 import zlib
 from abc import ABC, abstractmethod
 from collections import defaultdict
-from collections.abc import MutableMapping
+from collections.abc import Generator, Iterable, Iterator, MutableMapping
 from dataclasses import dataclass, field
 from functools import lru_cache
 from pathlib import Path
@@ -50,9 +50,6 @@
     Any,
     Callable,
     ClassVar,
-    Generator,
-    Iterable,
-    Iterator,
 )
 
 import numpy as np
@@ -2278,7 +2275,7 @@ def register_custom_function(
             ) -> None:
                 """Register a custom SQLite function.
 
-                Only Python >= 3.8 supports deterministic functions,
+                Only Python >= 3.9 supports deterministic functions,
                 fallback to without this argument if not available.
 
                 Args:

tiatoolbox/cli/visualize.py

@@ -2,19 +2,13 @@
 
 from __future__ import annotations
 
+import importlib.resources as importlib_resources
 import os
 import subprocess
-import sys
 from pathlib import Path
 from threading import Thread
 
 import click
-
-if sys.version_info >= (3, 9):  # pragma: no cover
-    import importlib.resources as importlib_resources
-else:  # pragma: no cover
-    # To support Python 3.8
-    import importlib_resources  # type: ignore[import-not-found]
 from flask_cors import CORS
 
 from tiatoolbox.cli.common import tiatoolbox_cli

tiatoolbox/data/__init__.py

@@ -2,18 +2,14 @@
 """Package to define datasets available to download via TIAToolbox."""
 from __future__ import annotations
 
+import importlib.resources as importlib_resources
 import sys
 import tempfile
 import zipfile
 from pathlib import Path
 from typing import TYPE_CHECKING
 from urllib.parse import urlparse
 
-if sys.version_info >= (3, 9):  # pragma: no cover
-    import importlib.resources as importlib_resources
-else:  # pragma: no cover
-    import importlib_resources  # To support Python 3.8
-
 from tiatoolbox import logger, read_registry_files
 
 if TYPE_CHECKING:  # pragma: no cover

tiatoolbox/tools/stainextract.py

@@ -11,12 +11,8 @@
 from tiatoolbox.utils.transforms import rgb2od
 
 if TYPE_CHECKING:  # pragma: no cover
-    import sys
 
-    if sys.version_info >= (3, 9):
-        from typing import Self
-    else:  # pragma: no cover
-        from typing_extensions import Self  # To support Python 3.8
+    from typing import Self
 
 
 def vectors_in_correct_direction(e_vectors: np.ndarray) -> np.ndarray: