upgrade requirements and drop 3.9 compatibility

Author: nickzoic

.github/workflows/mypy-and-pylint.yml

@@ -11,7 +11,7 @@ jobs:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
       with:
-        python-version: '3.10'
+        python-version: '3.12'
     - run: pip install --upgrade pip
     - run: pip install .[dev]
     - run: mypy $(git ls-files 'countess/*.py')
@@ -22,7 +22,7 @@ jobs:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
       with:
-        python-version: '3.10'
+        python-version: '3.12'
     - run: pip install --upgrade pip
     - run: pip install .[dev]
     - run: pylint $(git ls-files 'countess/*.py')

.github/workflows/run-tests-push.yml

@@ -3,20 +3,6 @@ on:
   push:
 
 jobs:
-  run-tests-ubuntu-22_04-python-3_9:
-    runs-on: ubuntu-22.04
-    name: Ubuntu 22.04, Python 3.9
-    steps:
-    - uses: actions/checkout@v4
-    - uses: actions/setup-python@v5
-      with:
-        python-version: "3.9"
-        cache: 'pip'
-    - run: sudo apt install xvfb
-    - run: pip install --upgrade pip
-    - run: pip install .[dev]
-    - run: xvfb-run pytest -v -rP --doctest-modules countess/ tests/
-
   run-tests-ubuntu-22_04-python-3_10:
     runs-on: ubuntu-22.04
     name: Ubuntu 22.04, Python 3.10

countess/core/parameters.py

@@ -1010,11 +1010,7 @@ def __getattr__(self, name):
         try:
             return self.params[name]
         except KeyError as exc:
-            try:
-                raise AttributeError(name=name, obj=self) from exc
-            except TypeError:  # pragma: no cover
-                # 3.9 doesn't have name and obj attributes
-                raise AttributeError() from exc
+            raise AttributeError(name=name, obj=self) from exc
 
     def __setattr__(self, name, value):
         """Intercepts attempts to set parameters to a value and turns them into parameter.set_value.

countess/core/plugins.py

@@ -47,12 +47,7 @@
 
 def get_plugin_classes() -> Iterable[Type["BasePlugin"]]:
     plugin_classes = set()
-    try:
-        # Python >= 3.10
-        entry_points = importlib.metadata.entry_points().select(group="countess_plugins")
-    except AttributeError:
-        # Python < 3.10
-        entry_points = importlib.metadata.entry_points()["countess_plugins"]
+    entry_points = importlib.metadata.entry_points().select(group="countess_plugins")
 
     for ep in entry_points:
         try:

countess/plugins/python.py

@@ -2,7 +2,7 @@
 import logging
 import math
 import re
-from types import BuiltinFunctionType, FunctionType, ModuleType
+from types import BuiltinFunctionType, FunctionType, ModuleType, NoneType
 from typing import Any, Optional
 
 import numpy as np
@@ -13,9 +13,6 @@
 
 logger = logging.getLogger(__name__)
 
-# For 3.9 compatibility
-NoneType = type(None)
-
 # XXX pretty sure this is a job for ast.parse rather than just
 # running compile() and exec() but that can wait.
 # Builtins are restricted but there's still plenty of things which

pyproject.toml

@@ -10,7 +10,7 @@ maintainers = [
     { name = "Nick Moore", email="nick@zoic.org" },
 ]
 description = "CountESS"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 classifiers = [
     'Development Status :: 3 - Alpha',
     'Intended Audience :: Science/Research',
@@ -19,37 +19,37 @@ classifiers = [
 ]
 dependencies = [
     'dnaio~=1.2.3',
-    'duckdb>=1.3.1',
+    'duckdb~=1.3.1',
     'fqfa~=1.3.1',
-    'more_itertools~=9.1.0',
-    'numpy~=1.26',
-    'pandas~=2.2.3',
-    'psutil~=5.9.5',
+    'more_itertools~=10.7.0',
+    'numpy~=2.3.1',
+    'pandas~=2.3.0',
+    'psutil~=7.0.0',
     'pyarrow~=20.0.0',
-    'rapidfuzz~=3.13',
-    'scipy~=1.15.3',
-    'tkinterweb~=3.23.5',
+    'rapidfuzz~=3.13.0',
+    'scipy~=1.16.0',
+    'tkinterweb~=4.3.1',
     'ttkthemes~=3.2.2',
-    'typing_extensions~=4.8.0',
+    'typing_extensions~=4.14.0',
 ]
 
 [project.optional-dependencies]
 dev = [
     'black<24',
-    'build==1.2.2',
-    'coverage==7.3.2',
-    'mypy~=1.0.1',
-    'pylint~=3.2.3',
+    'build~=1.2.2',
+    'coverage~=7.9.1',
+    'mypy~=1.16.1',
+    'pylint~=3.3.7',
     'semver~=3.0.2',
-    'types-psutil~=5.9.5',
-    'types-ttkthemes~=3.2',
+    'types-psutil~=7.0.0',
+    'types-ttkthemes~=3.2.4',
     'twine~=6.1.0',
     'packaging~=25.0',
-    'pandas-stubs~=2.1.0',
+    'pandas-stubs~=2.2.3',
     'pyarrow-stubs~=20.0.0',
-    'pytest~=7.2',
-    'pytest-socket~=0.6.0',
-    'requests-mock~=1.11.0',
+    'pytest~=8.4.1',
+    'pytest-socket~=0.7.0',
+    'requests-mock~=1.12.1',
 ]
 
 [project.entry-points.countess_plugins]
@@ -133,6 +133,6 @@ markers = [ "slow", "gui" ]
 
 [tool.mypy]
 plugins = [
-    "numpy.typing.mypy_plugin",
+#    "numpy.typing.mypy_plugin",
 ]
 mypy_path = "mypy_stubs"

tests/test_plugins.py

@@ -3,30 +3,29 @@
 
 from countess.core.plugins import get_plugin_classes
 
-empty_entry_points_dict = {"countess_plugins": []}
-
-invalid_entry_points_dict = {
-    "countess_plugins": [importlib.metadata.EntryPoint(name="test", value="mockplugin", group="countess_plugins")]
-}
+empty_entry_points = importlib.metadata.EntryPoints()
 
+invalid_entry_points = importlib.metadata.EntryPoints((
+    importlib.metadata.EntryPoint(name="test", value="mockplugin", group="countess_plugins"),
+))
 
 class NoParentPlugin:
     pass
 
 
-noparent_entry_points_dict = {
-    "countess_plugins": [importlib.metadata.EntryPoint(name="test", value="NoParentPlugin", group="countess_plugins")]
-}
+noparent_entry_points = importlib.metadata.EntryPoints((
+    importlib.metadata.EntryPoint(name="test", value="NoParentPlugin", group="countess_plugins"),
+))
 
 
 def test_get_plugin_classes_invalid(caplog):
-    with patch("importlib.metadata.entry_points", lambda: invalid_entry_points_dict):
+    with patch("importlib.metadata.entry_points", lambda: invalid_entry_points):
         get_plugin_classes()
         assert "could not be loaded" in caplog.text
 
 
 def test_get_plugin_classes_wrongparent(caplog):
-    with patch("importlib.metadata.entry_points", lambda: noparent_entry_points_dict):
+    with patch("importlib.metadata.entry_points", lambda: noparent_entry_points):
         with patch("importlib.metadata.EntryPoint.load", lambda x: NoParentPlugin):
             get_plugin_classes()
             assert "not a valid CountESS plugin" in caplog.text