Raise minimum Python to 3.10 (#207)

* Raise minimum Python to 3.10

Python 3.9 reached end-of-life in October 2025. This bumps the floor to
3.10 and extends CI coverage through 3.14 to match the currently
supported CPython versions.

* Apply ruff upgrades

* Leave off 3.14 for now

* Remove `target-version` from Ruff

Ruff will infer a missing target-version from the requires-python field
in a pyproject.toml

* Remove Ruff format config

Redundant with defaults.

Author: manzt

.github/workflows/ci.yml

@@ -30,7 +30,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v6
       - uses: astral-sh/setup-uv@v7

examples/Plugin.ipynb

@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "74b20970",
+   "id": "ea68ab39",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -13,7 +13,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4b1a1665",
+   "id": "22ce47f6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -62,7 +62,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "06263c4c",
+   "id": "019c7c7e",
    "metadata": {},
    "source": [
     "The above config contains an unknown track type to `hg`, so we get a validation error because we don't know how to render the track!"
@@ -71,7 +71,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8c4a4b38",
+   "id": "8f5f4294",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -82,7 +82,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "d20a1b24",
+   "id": "5cc74c65",
    "metadata": {},
    "source": [
     "# `hg.PluginTrack`\n",
@@ -93,13 +93,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4d6149f1",
+   "id": "26813410",
    "metadata": {},
    "outputs": [],
    "source": [
-    "from typing import ClassVar, Union\n",
-    "\n",
-    "from typing_extensions import Literal\n",
+    "from typing import ClassVar, Literal\n",
     "\n",
     "\n",
     "class PileupTrack(hg.PluginTrack):\n",
@@ -109,17 +107,17 @@
     "    )\n",
     "\n",
     "\n",
-    "hg.Viewconf[Union[PileupTrack, hg.Track]](**config)  # works!"
+    "hg.Viewconf[PileupTrack | hg.Track](**config)  # works!"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "66e046ce",
+   "id": "ec287f3e",
    "metadata": {},
    "source": [
     "How does this work? The `hg.Viewconf` is a `pydantic.GenericModel` which is _generic_ over the track type. By default, only HiGlass's builtin track types are recognized, so `hg.Viewconf(**data)` will throw an error when a configuration contains an unknown track.\n",
     "\n",
-    "By supplying a our plugin track as a type parameter explicity, `hg.Viewconf[Union[PileupTrack, hg.Track]]`, we extend the model to recognize the `PileupTrack` in our config.\n",
+    "By supplying a our plugin track as a type parameter explicity, `hg.Viewconf[PileupTrack | hg.Track]`, we extend the model to recognize the `PileupTrack` in our config.\n",
     "\n",
     "This can seem a bit verbose, but supplying the type parameter explicitly is only necessary when deserializing an unknown config, e.g.\n",
     "\n",
@@ -134,21 +132,19 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4fde003f",
+   "id": "736146c8",
    "metadata": {},
    "outputs": [],
    "source": [
-    "from typing import ClassVar\n",
-    "\n",
-    "from typing_extensions import Literal\n",
+    "from typing import ClassVar, Literal\n",
     "\n",
     "import higlass as hg"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1210c425",
+   "id": "c178a248",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -166,13 +162,11 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "76a67f86",
+   "id": "d86e35fc",
    "metadata": {},
    "outputs": [],
    "source": [
-    "from typing import ClassVar\n",
-    "\n",
-    "from typing_extensions import Literal\n",
+    "from typing import ClassVar, Literal\n",
     "\n",
     "import higlass as hg\n",
     "\n",
@@ -218,7 +212,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "bb20c39e",
+   "id": "0a28bebf",
    "metadata": {},
    "source": [
     "## Extending plugins with `pydantic`\n",
@@ -231,12 +225,10 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "35355968",
+   "id": "6e397bed",
    "metadata": {},
    "outputs": [],
    "source": [
-    "from typing import Optional\n",
-    "\n",
     "from pydantic import BaseModel\n",
     "\n",
     "\n",
@@ -252,7 +244,7 @@
     "\n",
     "class SequenceTrack(hg.PluginTrack):\n",
     "    type: Literal[\"horizontal-sequence\"]\n",
-    "    data: Optional[SeqeuenceTrackData] = None\n",
+    "    data: SeqeuenceTrackData | None = None\n",
     "    plugin_url: ClassVar[str] = (\n",
     "        \"https://unpkg.com/higlass-sequence/dist/higlass-sequence.js\"\n",
     "    )\n",
@@ -279,7 +271,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1328f1d6",
+   "id": "98794dcf",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -289,7 +281,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "27f99ea4",
+   "id": "9776449b",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -298,7 +290,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "35965609",
+   "id": "93fb6b03",
    "metadata": {},
    "source": [
     "And the track is faithfully rendered by HiGlass"
@@ -307,7 +299,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7948b163",
+   "id": "aa4d7519",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -317,7 +309,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ad082d7f",
+   "id": "62543d11",
    "metadata": {},
    "outputs": [],
    "source": []
@@ -344,4 +336,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}

pyproject.toml

@@ -16,21 +16,19 @@ classifiers = [
     "Intended Audience :: Developers",
     "Programming Language :: Python",
     "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",
+    "Programming Language :: Python :: 3.13",
     "Operating System :: OS Independent",
 ]
-license = { text = "MIT" }
 dynamic = ["version"]
 readme = "README.md"
 dependencies = [
     "higlass-schema>=0.2.0",
     "anywidget>=0.9.0",
-    "typing-extensions ; python_version<'3.9'",
 ]
-requires-python = ">=3.8"
+requires-python = ">=3.10"
 urls = { homepage = "https://github.com/higlass/higlass-python" }
 
 [dependency-groups]
@@ -50,10 +48,6 @@ packages = ["src/higlass"]
 [tool.hatch.version]
 source = "vcs"
 
-[tool.ruff]
-line-length = 88
-target-version = "py38"
-
 [tool.ruff.lint]
 extend-select = [
     "E", # style errors

src/higlass/_scale.py

@@ -2,9 +2,9 @@
 
 import itertools
 from bisect import bisect_right
-from typing import Iterable, Tuple
+from collections.abc import Iterable
 
-GenomicPosition = Tuple[str, int]
+GenomicPosition = tuple[str, int]
 
 
 class Scale:

src/higlass/_utils.py

@@ -1,12 +1,12 @@
 from __future__ import annotations
 
 import uuid
-from typing import Literal, TypeVar, Union
+from typing import Literal, TypeVar
 
 import higlass_schema as hgs
 from pydantic import BaseModel
 
-TrackType = Union[hgs.EnumTrackType, Literal["heatmap"]]
+TrackType = hgs.EnumTrackType | Literal["heatmap"]
 TrackPosition = Literal["center", "top", "left", "bottom", "center", "whole", "gallery"]
 
 track_default_position: dict[str, TrackPosition] = {

src/higlass/api.py

@@ -7,7 +7,6 @@
     Generic,
     Literal,
     TypeVar,
-    Union,
     cast,
     overload,
 )
@@ -158,13 +157,13 @@ class PluginTrack(hgs.BaseTrack, _OptionsMixin, _PropertiesMixin):
     plugin_url: ClassVar[str]
 
 
-Track = Union[
-    HeatmapTrack,
-    IndependentViewportProjectionTrack,
-    EnumTrack,
-    CombinedTrack,
-    PluginTrack,
-]
+Track = (
+    HeatmapTrack
+    | IndependentViewportProjectionTrack
+    | EnumTrack
+    | CombinedTrack
+    | PluginTrack
+)
 
 TrackT = TypeVar("TrackT", bound=Track)
 
@@ -588,7 +587,7 @@ def mapper(view):
                 getattr(a, lockattr).locksByViewUid.update(locks.locksByViewUid)
                 getattr(a, lockattr).locksDict.update(locks.locksDict)
 
-    return cast(Viewconf[Union[TrackTA, TrackTB]], a)
+    return cast(Viewconf[TrackTA | TrackTB], a)
 
 
 hconcat = functools.partial(concat, "horizontal")
@@ -787,7 +786,7 @@ def combine(t1: Track, t2: Track, uid: str | None = None, **kwargs) -> CombinedT
     )
 
 
-T = TypeVar("T", bound=Union[EnumTrack, HeatmapTrack])
+T = TypeVar("T", bound=EnumTrack | HeatmapTrack)
 
 
 def divide(t1: T, t2: T, **kwargs) -> T: