Drop support for Python 3.11

.github/workflows/CI.yml

@@ -23,15 +23,13 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ["3.11", "3.12", "3.13"]
+        python-version: ["3.12", "3.13"]
         rdkit: [true, false]
         openeye: [true, false]
         nagl: [true, false]
         exclude:
           - rdkit: false
             openeye: false
-          - openeye: true
-            python-version: "3.12"
           - openeye: true
             python-version: "3.13"
           - rdkit: false
@@ -153,7 +151,7 @@ jobs:
 
       - name: Run notebooks in docs
         if: ${{ matrix.rdkit == true && matrix.openeye == true }}
-        run: python -m pytest -v --no-cov --nbval-lax docs/
+        run: python -m pytest -v --durations=10 --no-cov --nbval-lax docs/
 
       - name: Run examples in docstrings
         if: ${{ matrix.rdkit == true && matrix.openeye == true && matrix.nagl == true }}

.github/workflows/beta_rc.yaml

@@ -20,7 +20,7 @@ jobs:
           - ubuntu-latest
           - macos-latest
         python-version:
-          - "3.11"
+          - "3.12"
 
     env:
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt

.github/workflows/conda.yml

@@ -21,7 +21,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ["3.11"]
+        python-version: ["3.12"]
         openeye: ["true", "false"]
 
     env:

.github/workflows/examples.yml

@@ -24,7 +24,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ["3.11", "3.12"]
+        python-version: [ "3.12"]
         rdkit: [true, false]
         openeye: [true, false]
         nagl: [true, false]

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ ci:
 files: ^pyproject.toml|openff|(^examples/((?!deprecated).)*$)|^docs|(^utilities/((?!deprecated).)*$)
 repos:
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.15.9
+  rev: v0.15.12
   hooks:
     - id: ruff-format
     - id: ruff-check
@@ -14,6 +14,6 @@ repos:
     - id: blacken-docs
       files: ^docs/.*\.(rst|md)$
 - repo: https://github.com/tox-dev/pyproject-fmt
-  rev: v2.21.0
+  rev: v2.21.1
   hooks:
     - id: pyproject-fmt

README.md

@@ -2,7 +2,7 @@
 | :------ |:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
 | **Latest Release** | [![Last release tag](https://img.shields.io/github/release-pre/openforcefield/openff-toolkit.svg)](https://github.com/openforcefield/openff-toolkit/releases)  [![Commits since release](https://img.shields.io/github/commits-since/openforcefield/openff-toolkit/0.18.0.svg)](https://github.com/openforcefield/openff-toolkit/releases/tag/0.18.0)[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17525527.svg)](https://doi.org/10.5281/zenodo.17525527)
 | **Communication** | [![docs stable](https://img.shields.io/badge/docs-stable-5077AB.svg?logo=read%20the%20docs)](https://open-forcefield-toolkit.readthedocs.io/) [![user & dev discussions](https://img.shields.io/badge/user%20%26%20dev%20discussions-GitHub-red?logo=github)](https://github.com/openforcefield/discussions/discussions) |
-| **Foundation** | [![license](https://img.shields.io/github/license/openforcefield/openff-toolkit.svg)](https://opensource.org/licenses/MIT) [![platforms](https://img.shields.io/badge/Platforms-Linux%2C%20MacOS-orange.svg)](https://open-forcefield-toolkit.readthedocs.io/en/stable/installation.html) [![python](https://img.shields.io/badge/python-3.11%2C%203.12%2C%203.13-blue.svg)](https://open-forcefield-toolkit.readthedocs.io/en/stable/installation.html) [![Funding](https://img.shields.io/badge/Funding-Open%20Force%20Field%20Consortium-brightgreen.svg)](http://openforcefield.org)        |
+| **Foundation** | [![license](https://img.shields.io/github/license/openforcefield/openff-toolkit.svg)](https://opensource.org/licenses/MIT) [![platforms](https://img.shields.io/badge/Platforms-Linux%2C%20MacOS-orange.svg)](https://open-forcefield-toolkit.readthedocs.io/en/stable/installation.html) [![python](https://img.shields.io/badge/python-3.12%2C%203.13-blue.svg)](https://open-forcefield-toolkit.readthedocs.io/en/stable/installation.html) [![Funding](https://img.shields.io/badge/Funding-Open%20Force%20Field%20Consortium-brightgreen.svg)](http://openforcefield.org)        |
 | **Installation** | [![Releases](https://img.shields.io/badge/obtain-latest-green.svg)](https://github.com/openforcefield/openff-toolkit/releases) [![Conda](https://img.shields.io/conda/v/conda-forge/openff-toolkit.svg)](https://anaconda.org/conda-forge/openff-toolkit) [![Last updated](https://anaconda.org/conda-forge/openff-toolkit/badges/latest_release_relative_date.svg)](https://anaconda.org/conda-forge/openff-toolkit) [![Anaconda Cloud downloads](https://anaconda.org/conda-forge/openff-toolkit/badges/downloads.svg)](https://anaconda.org/conda-forge/openff-toolkit)          |
 
 # The Open Force Field toolkit

docs/environment.yml

@@ -13,7 +13,7 @@ dependencies:
     - sphinx-notfound-page
     - sphinx=6
     # conda build dependencies
-    - python <3.13
+    - python =3.12
     - setuptools
     - numpy
     - openmm

docs/releasehistory.md

@@ -16,6 +16,8 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
 
 ### Behavior changes
 
+- [PR #2174](https://github.com/openforcefield/openff-toolkit/pull/2174): Drop support for Python 3.11
+
 ### Bugfixes
 
 ### New features

docs/users/developing.md

@@ -427,7 +427,6 @@ Widget state can also be saved programmatically by executing the notebook with [
 ## Supported Python versions
 
 The OpenFF Toolkit roughly follows [NEP 29](https://numpy.org/neps/nep-0029-deprecation_policy.html).
-As of April 2023 this means Python 3.9-3.10 are officially supported (3.11 is missing some upstream dependencies).
 We develop, test, and distribute on macOS and Linux-based operating systems.
 We do not currently support Windows.
 Some CI builds run using only RDKit as a backend, some run using only OpenEye Toolkits, and some run using both installed at once.
@@ -440,14 +439,12 @@ The CI matrix is currently as follows:
 +-----------------------+------------+-----------+-------------+------------+-----------+-------------+
 |                       | RDKit      | OpenEye   | RDKit + OE  | RDKit      | OpenEye   | RDKit + OE  |
 +=======================+============+===========+=============+============+===========+=============+
-| Python 3.8 and older  | No support after April 2023                                                 |
+| Python 3.11 and older | No support after April 2026                                                 |
 +-----------------------+------------+-----------+-------------+------------+-----------+-------------+
-| Python 3.9            | **Test**   | **Test**  | **Test**    | **Test**   | **Test**  | **Test**    |
+| Python 3.12           | **Test**   | **Test**  | **Test**    | **Test**   | **Test**  | **Test**    |
 +-----------------------+------------+-----------+-------------+------------+-----------+-------------+
-| Python 3.10           | **Test**   | Skip      | Skip        | **Test**   | Skip      | Skip        |
+| Python 3.13           | **Test**   | Skip      | Skip        | **Test**   | Skip      | Skip        |
 +-----------------------+------------+-----------+-------------+------------+-----------+-------------+
-| Python 3.11           | **Test**   | Skip      | Skip        | **Test**   | Skip      | Skip        |
-+-----------------------+------------+-----------+-------------+------------+-----------+-------------+
-| Python 3.12 and newer | Pending official releases and upstream support                              | 
+| Python 3.14 and newer | Pending official releases and upstream support                              |
 +-----------------------+------------+-----------+-------------+------------+-----------+-------------+
 ```

openff/toolkit/topology/molecule.py

@@ -40,7 +40,6 @@
     Any,
     Literal,
     TextIO,
-    TypeAlias,
     TypeVar,
     Union,
     overload,
@@ -105,8 +104,8 @@
 
 # TODO: These aliases are duplicated in a few places, might make sense to consolidate them
 #       into a single location, but that'd weirdly nudge them towards first-class existence
-TKR: TypeAlias = ToolkitRegistry | ToolkitWrapper
-MoleculeLike: TypeAlias = Union["Molecule", "FrozenMolecule", "_SimpleMolecule"]
+type TKR = ToolkitRegistry | ToolkitWrapper
+type MoleculeLike = "Molecule" | "FrozenMolecule" | "_SimpleMolecule"
 FM = TypeVar("FM", bound="FrozenMolecule")
 P = TypeVar("P", bound="Particle")
 A = TypeVar("A", bound="Atom")

openff/toolkit/topology/topology.py

@@ -22,7 +22,6 @@
     TYPE_CHECKING,
     Literal,
     TextIO,
-    TypeAlias,
     Union,
 )
 
@@ -73,11 +72,10 @@
     from openff.toolkit.topology.molecule import Atom, Bond
     from openff.toolkit.utils import ToolkitRegistry, ToolkitWrapper
 
-TKR: TypeAlias = Union["ToolkitRegistry", "ToolkitWrapper"]
-
-AtomLike: TypeAlias = Union["Atom", "_SimpleAtom"]
-BondLike: TypeAlias = Union["Bond", "_SimpleBond"]
-MoleculeLike: TypeAlias = Union["Molecule", "FrozenMolecule", "_SimpleMolecule"]
+type TKR = ToolkitRegistry | ToolkitWrapper
+type AtomLike = "Atom" | "_SimpleAtom"
+type BondLike = "Bond" | "_SimpleBond"
+type MoleculeLike = "Molecule" | "FrozenMolecule" | "_SimpleMolecule"
 
 _DISTANCE_UNITS = set(
     [

openff/toolkit/typing/engines/smirnoff/parameters.py

@@ -273,7 +273,7 @@ class ParameterAttribute:
     >>> my_par.attr_required
     Traceback (most recent call last):
     ...
-    AttributeError: 'MyParameter' object has no attribute '_attr_required'
+    AttributeError: 'MyParameter' object has no attribute '_attr_required'. Did you mean: 'attr_required'?
 
     The attribute allow automatic conversion and validation of units.
 

openff/toolkit/utils/openeye_wrapper.py

@@ -19,7 +19,7 @@
 import warnings
 from collections import defaultdict
 from functools import wraps
-from typing import TYPE_CHECKING, Any, TypeAlias
+from typing import TYPE_CHECKING, Any
 
 import numpy as np
 from cachetools import LRUCache, cached
@@ -67,7 +67,7 @@
 logger = logging.getLogger(__name__)
 
 
-TTA: TypeAlias = tuple[tuple[Any, ...], ...]
+type TTA = tuple[tuple[Any, ...], ...]
 
 
 def get_oeformat(file_format: str) -> str:

openff/toolkit/utils/utils.py

@@ -61,7 +61,7 @@ def inherit_docstrings(cls):
 T = TypeVar("T")
 
 
-def all_subclasses(cls: type[T]) -> list[type[T]]:
+def all_subclasses[T](cls: type[T]) -> list[type[T]]:
     """Recursively retrieve all subclasses of the specified class"""
     return cls.__subclasses__() + [g for s in cls.__subclasses__() for g in all_subclasses(s)]
 

pyproject.toml

@@ -10,27 +10,25 @@ keywords = [ "force field", "molecular mechanics", "parameterization" ]
 license = "MIT"
 license-files = [ "LICENSE" ]
 authors = [ { name = "Open Force Field Consortium", email = "info@openforcefield.org" } ]
-requires-python = ">=3.11"
+requires-python = ">=3.12"
 classifiers = [
   "Development Status :: 3 - Alpha",
   "Programming Language :: Python :: 3 :: Only",
-  "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
   "Programming Language :: Python :: 3.13",
   "Programming Language :: Python :: 3.14",
   "Topic :: Utilities",
 ]
-
 dynamic = [ "version" ]
 urls = { Homepage = "https://github.com/openforcefield/openff-toolkit" }
 
-[tool.setuptools.packages.find]
-include = [ 'openff.toolkit*' ]
+[tool.setuptools]
+packages.find.include = [ "openff.toolkit*" ]
 
 [tool.ruff]
+target-version = "py312"
 line-length = 119
 exclude = [ "examples/deprecated/", "utilities/deprecated" ]
-
 lint.select = [ "E", "F", "I", "NPY", "RUF", "UP", "W" ]
 lint.ignore = [ "D105", "D107", "D200", "D203", "D212", "E721", "RUF012" ]
 lint.per-file-ignores."docs/users/molecule_cookbook.ipynb" = [ "E402", "F821" ]
@@ -44,19 +42,6 @@ lint.isort.known-first-party = [ "openff.toolkit" ]
 # https://docs.astral.sh/ruff/settings/#lint_isort_known-third-party
 lint.isort.known-third-party = [ "openff.interchange", "openff.utilities", "openff.units" ]
 
-[tool.coverage.run]
-omit = [
-  "*/*/_tests/*",
-]
-
-[tool.coverage.report]
-exclude_lines = [
-  "pragma: no cover",
-  "if TYPE_CHECKING:",
-  "raise NotImplementedError",
-  "@overload",
-]
-
 [tool.mypy]
 python_version = 3.12
 plugins = "numpy.typing.mypy_plugin"
@@ -92,4 +77,15 @@ module = [
 ]
 ignore_missing_imports = true
 
+[tool.coverage]
+run.omit = [
+  "*/*/_tests/*",
+]
+report.exclude_lines = [
+  "@overload",
+  "if TYPE_CHECKING:",
+  "pragma: no cover",
+  "raise NotImplementedError",
+]
+
 [tool.versioningit]