Bump minimum Python to 3.11 and support Python 3.14 (#479)

Author: cthoyt

.github/workflows/tests.yml

@@ -25,7 +25,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ "3.13", "3.10" ]
+        python-version: [ "3.14", "3.11" ]
         tox-command: [ "lint", "pyroma", "mypy" ]
     steps:
       - uses: actions/checkout@v4
@@ -48,7 +48,7 @@ jobs:
         # We only test documentation on the latest version
         # sphinx 8.0 / sphinx-rtd-theme 3.0 discontinued Python 3.9 support
         # a year early, which prompted re-thinking about this.
-        python-version: [ "3.13" ]
+        python-version: [ "3.14" ]
     steps:
       - uses: actions/checkout@v4
       - name: "Install uv"
@@ -76,7 +76,7 @@ jobs:
     strategy:
       matrix:
         os: [ ubuntu-latest ]
-        python-version: [ "3.13", "3.10" ]
+        python-version: [ "3.14", "3.11" ]
     steps:
       - uses: actions/checkout@v4
       - name: "Install uv"

pyproject.toml

@@ -27,10 +27,10 @@ classifiers = [
     "Framework :: Sphinx",
     "Natural Language :: English",
     "Programming Language :: Python",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
     "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
     "Programming Language :: Python :: 3 :: Only",
     "Typing :: Typed",
     "Topic :: Scientific/Engineering :: Bio-Informatics",
@@ -55,7 +55,7 @@ license-files = [
     "LICENSE",
 ]
 
-requires-python = ">=3.10"
+requires-python = ">=3.11"
 dependencies = [
     "obonet>=0.3.0",
     "click",
@@ -162,7 +162,9 @@ gilda-slim = [
     "ssslm[gilda-slim]",
 ]
 sources = [
-    "pyobo[drugcentral,pid]",
+    # keep as sum of all sources
+    "psycopg2-binary",
+    "protmapper"
 ]
 drugcentral =[
     "psycopg2-binary",

src/pyobo/api/hierarchy.py

@@ -4,11 +4,11 @@
 import warnings
 from collections.abc import Iterable
 from functools import lru_cache
-from typing import overload
+from typing import NotRequired, overload
 
 import networkx as nx
 from curies import ReferenceTuple
-from typing_extensions import NotRequired, Unpack
+from typing_extensions import Unpack
 
 from .edges import get_edges
 from .names import get_name, get_references

src/pyobo/constants.py

@@ -6,10 +6,10 @@
 import re
 from collections.abc import Callable
 from pathlib import Path
-from typing import Literal, NamedTuple, TypeAlias
+from typing import Literal, NamedTuple, NotRequired, TypeAlias
 
 import pystow
-from typing_extensions import NotRequired, TypedDict
+from typing_extensions import TypedDict
 
 __all__ = [
     "DATABASE_DIRECTORY",

src/pyobo/struct/struct.py

@@ -16,7 +16,7 @@
 from dataclasses import dataclass, field
 from pathlib import Path
 from textwrap import dedent
-from typing import Annotated, Any, ClassVar, TextIO
+from typing import Annotated, Any, ClassVar, Self, TextIO
 
 import bioregistry
 import click
@@ -29,7 +29,6 @@
 from more_click import force_option, verbose_option
 from pystow.utils import safe_open
 from tqdm.auto import tqdm
-from typing_extensions import Self
 
 from . import vocabulary as v
 from .reference import (

src/pyobo/struct/struct_utils.py

@@ -9,15 +9,14 @@
 from abc import ABC, abstractmethod
 from collections import defaultdict
 from collections.abc import Iterable, Mapping, Sequence
-from typing import TYPE_CHECKING, Literal, NamedTuple, TypeAlias, overload
+from typing import TYPE_CHECKING, Literal, NamedTuple, Self, TypeAlias, overload
 
 import curies
 from curies import ReferenceTuple
 from curies import vocabulary as _v
 from curies.vocabulary import SynonymScope
 from pydantic import BaseModel, ConfigDict
 from ssslm import LiteralMapping
-from typing_extensions import Self
 
 from . import vocabulary as v
 from .reference import (