Test Python 3.14

.github/workflows/CI.yml

@@ -23,15 +23,13 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ["3.12", "3.13"]
+        python-version: ["3.12", "3.13", "3.14"]
         rdkit: [true, false]
-        openeye: [true, false]
+        openeye: [false]
         nagl: [true, false]
         exclude:
           - rdkit: false
             openeye: false
-          - openeye: true
-            python-version: "3.13"
           - rdkit: false
             nagl: true
 

devtools/conda-envs/rdkit-examples.yaml

@@ -6,7 +6,7 @@ dependencies:
   - python
   - versioningit
   - packaging
-  - numpy <2.3
+  - numpy
   - networkx
   - cachetools
   # https://github.com/openforcefield/openff-toolkit/issues/2150
@@ -23,7 +23,6 @@ dependencies:
   - typing_extensions
   - nglview
     # Toolkit-specific
-  - ambertools
     # https://github.com/rdkit/rdkit/issues/7221 and https://github.com/rdkit/rdkit/issues/7583
   - rdkit =2024
     # Test-only/optional/dev/typing/examples

devtools/conda-envs/rdkit.yaml

@@ -6,7 +6,7 @@ dependencies:
   - python
   - versioningit
   - packaging
-  - numpy <2.3
+  - numpy
   - networkx
   - cachetools
   # https://github.com/openforcefield/openff-toolkit/issues/2150
@@ -22,7 +22,6 @@ dependencies:
   - openff-nagl-models >=0.3.0
   - typing_extensions
     # Toolkit-specific
-  - ambertools >=22
     # https://github.com/rdkit/rdkit/issues/7221 and https://github.com/rdkit/rdkit/issues/7583
   - rdkit !=2024.03.6,!=2024.03.5
     # Test-only/optional/dev/typing

devtools/conda-envs/test_env.yaml

@@ -7,7 +7,7 @@ dependencies:
   - python
   - versioningit
   - packaging
-  - numpy <2.3
+  - numpy
   - networkx
   - cachetools
   # https://github.com/openforcefield/openff-toolkit/issues/2150
@@ -23,7 +23,6 @@ dependencies:
   - openff-nagl-models >=0.3.0
   - typing_extensions
     # Toolkit-specific
-  - ambertools >=22
     # rdkit 2024.03.6 and 2024.09.1 packages fail when run natively on osx-arm64 macs
     # https://github.com/rdkit/rdkit/issues/7583
   - rdkit !=2024.03.6,!=2024.09.1

devtools/scripts/build_cookiecutter_json.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import json
 import sys
 

docs/conf.py

@@ -16,6 +16,8 @@
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 #
+from __future__ import annotations
+
 import os
 import sys
 from importlib.util import find_spec as find_import_spec

docs/conftest.py

@@ -6,6 +6,8 @@
 The nbval-sanitize.cfg file is also for use with nbval.
 """
 
+from __future__ import annotations
+
 
 def pytest_collectstart(collector):
     """

docs/users/molecule_cookbook.ipynb

@@ -56,6 +56,8 @@
    ],
    "source": [
     "# Workaround for https://github.com/conda-forge/qcfractal-feedstock/issues/43\n",
+    "from __future__ import annotations\n",
+    "\n",
     "try:\n",
     "    import qcportal  # noqa: RUF100\n",
     "except ImportError:\n",

docs/users/pdb_cookbook/index.ipynb

@@ -66,6 +66,8 @@
    },
    "outputs": [],
    "source": [
+    "from __future__ import annotations\n",
+    "\n",
     "import sys\n",
     "import warnings\n",
     "\n",

examples/QCArchive_interface/QCarchive_interface.ipynb

@@ -256,6 +256,8 @@
     }
    ],
    "source": [
+    "from __future__ import annotations\n",
+    "\n",
     "import qcportal\n",
     "\n",
     "from openff.toolkit import Molecule\n",

examples/SMIRNOFF_simulation/run_simulation.ipynb

@@ -28,6 +28,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "from __future__ import annotations\n",
+    "\n",
     "from openff.toolkit.utils import get_data_file_path"
    ]
   },

examples/conformer_energies/conformer_energies.ipynb

@@ -23,6 +23,8 @@
    },
    "outputs": [],
    "source": [
+    "from __future__ import annotations\n",
+    "\n",
     "from openff.interchange.drivers.openmm import get_openmm_energies\n",
     "from rdkit.Chem import rdMolAlign\n",
     "\n",

examples/conformer_energies/conformer_energies.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import argparse
 
 from openff.interchange.drivers.openmm import get_openmm_energies

examples/examples_helper.py

@@ -1,6 +1,8 @@
 #!/usr/bin/env python3
 """Copy the openff-toolkit examples suite to a local directory"""
 
+from __future__ import annotations
+
 import argparse
 from os import environ
 from pathlib import Path

examples/forcefield_modification/forcefield_modification.ipynb

@@ -15,6 +15,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "from __future__ import annotations\n",
+    "\n",
     "from copy import deepcopy\n",
     "\n",
     "from openff.units import unit\n",

examples/inspect_assigned_parameters/inspect_assigned_parameters.ipynb

@@ -118,6 +118,8 @@
     }
    ],
    "source": [
+    "from __future__ import annotations\n",
+    "\n",
     "from openff.toolkit import ForceField, Molecule, Topology\n",
     "\n",
     "# Create a simple molecule from SMILES and turn it into a topology.\n",

examples/toolkit_showcase/toolkit_showcase.ipynb

@@ -43,6 +43,8 @@
    ],
    "source": [
     "# Imports from the comp chem ecosystem\n",
+    "from __future__ import annotations\n",
+    "\n",
     "import mdtraj\n",
     "import nglview\n",
     "import numpy as np\n",

examples/using_smirnoff_in_amber_or_gromacs/export_with_interchange.ipynb

@@ -28,6 +28,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "from __future__ import annotations\n",
+    "\n",
     "from pprint import pprint\n",
     "from shutil import which\n",
     "\n",

examples/using_smirnoff_with_amber_protein_forcefield/BRD4_inhibitor_benchmark.ipynb

@@ -19,6 +19,8 @@
    "source": [
     "# Retrieve protein and ligand files for BRD4 and a docked inhibitor from the benchmark systems GitHub repository\n",
     "# https://github.com/MobleyLab/benchmarksets\n",
+    "from __future__ import annotations\n",
+    "\n",
     "import requests\n",
     "\n",
     "repo_url = \"https://raw.githubusercontent.com/MobleyLab/benchmarksets/master/input_files/\"\n",

examples/virtual_sites/vsite_showcase.ipynb

@@ -44,6 +44,8 @@
     }
    ],
    "source": [
+    "from __future__ import annotations\n",
+    "\n",
     "import time\n",
     "\n",
     "import numpy\n",

examples/visualization/visualization.ipynb

@@ -66,6 +66,8 @@
    },
    "outputs": [],
    "source": [
+    "from __future__ import annotations\n",
+    "\n",
     "from openff.toolkit import Molecule, Topology\n",
     "from openff.toolkit.utils import get_data_file_path"
    ]

openff/toolkit/__init__.py

@@ -3,6 +3,8 @@
 A modern, extensible library for molecular mechanics force field science from the Open Force Field Consortium.
 """
 
+from __future__ import annotations
+
 import importlib
 from importlib.metadata import version
 from typing import TYPE_CHECKING

openff/toolkit/_tests/_stale_tests.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import pytest
 
 from openff.toolkit import ForceField

openff/toolkit/_tests/conftest.py

@@ -2,6 +2,8 @@
 Configuration file for pytest.
 """
 
+from __future__ import annotations
+
 import logging
 
 import pytest

openff/toolkit/_tests/create_molecules.py

@@ -5,6 +5,8 @@
 
 """
 
+from __future__ import annotations
+
 import numpy as np
 
 from openff.toolkit import unit

openff/toolkit/_tests/mocking.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import numpy
 
 from openff.toolkit import Quantity, unit

openff/toolkit/_tests/molecule/test_state_enumeration.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import pytest
 
 from openff.toolkit import Molecule

openff/toolkit/_tests/test_energies.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import json
 
 import numpy as np

openff/toolkit/_tests/test_examples.py

@@ -2,6 +2,8 @@
 Test that the examples in the repo run without errors.
 """
 
+from __future__ import annotations
+
 import pathlib
 import re
 import subprocess

openff/toolkit/_tests/test_forcefield.py

@@ -3,6 +3,8 @@
 
 """
 
+from __future__ import annotations
+
 import copy
 import itertools
 import os

openff/toolkit/_tests/test_interchange.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import pytest
 from openff.utilities import requires_package as requires_pkg
 

openff/toolkit/_tests/test_io.py

@@ -3,6 +3,8 @@
 
 """
 
+from __future__ import annotations
+
 import pytest
 
 from openff.toolkit.typing.engines.smirnoff.io import XMLParameterIOHandler

openff/toolkit/_tests/test_links.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import pathlib
 import re
 from urllib.request import Request, urlopen

openff/toolkit/_tests/test_mm_molecule.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import copy
 
 import numpy as np

openff/toolkit/_tests/test_molecule.py

@@ -13,6 +13,8 @@
 
 """
 
+from __future__ import annotations
+
 import copy
 import os
 import pathlib

openff/toolkit/_tests/test_nagl.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import pathlib
 import re
 

openff/toolkit/_tests/test_parameter_plugins.py

@@ -2,6 +2,8 @@
 Test classes and function in module openff.toolkit.typing.engines.smirnoff.plugins
 """
 
+from __future__ import annotations
+
 import pytest
 
 from openff.toolkit import ForceField, Quantity

openff/toolkit/_tests/test_parameters.py

@@ -3,6 +3,8 @@
 
 """
 
+from __future__ import annotations
+
 from collections import defaultdict
 from inspect import isabstract, isclass
 

openff/toolkit/_tests/test_toolkit_io.py

@@ -3,6 +3,8 @@
 
 """
 
+from __future__ import annotations
+
 import pathlib
 import sys
 import tempfile

openff/toolkit/_tests/test_toolkits.py

@@ -3,6 +3,8 @@
 
 """
 
+from __future__ import annotations
+
 import logging
 import os
 import pathlib

openff/toolkit/_tests/test_topology.py

@@ -3,6 +3,8 @@
 
 """
 
+from __future__ import annotations
+
 import itertools
 import re
 from copy import deepcopy

openff/toolkit/_tests/test_utils.py

@@ -3,6 +3,8 @@
 
 """
 
+from __future__ import annotations
+
 import os
 
 import pytest

openff/toolkit/_tests/test_utils_callback.py

@@ -3,6 +3,8 @@
 
 """
 
+from __future__ import annotations
+
 import pytest
 
 from openff.toolkit.utils.callback import Callbackable, callback_method

openff/toolkit/_tests/test_utils_collections.py

@@ -3,6 +3,8 @@
 
 """
 
+from __future__ import annotations
+
 import copy
 
 import pytest