Assorted updates

.github/workflows/ci.yaml

@@ -12,7 +12,7 @@ on:
 
 defaults:
   run:
-    shell: bash -l {0}
+    shell: bash -leo pipefail {0} {0}
 
 jobs:
   test:
@@ -24,7 +24,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [macOS-latest, ubuntu-latest]
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v4
@@ -37,23 +37,20 @@ jobs:
           python=${{ matrix.python-version }}
 
     - name: Install Package
-      run: |
-        python -m pip install -e .
+      run: python -m pip install -e .
 
     - name: Run Tests
-      run: |
-        pytest -v -nauto --cov=smirnoff_plugins --cov-report=xml --color=yes smirnoff_plugins/_tests/
+      run: pytest smirnoff_plugins/_tests/ \
+        -v -n logical \
+        --cov=smirnoff_plugins --cov-report=xml --color=yes
 
     - name: Run Example
       if: ${{ false }}
-      shell: bash -l {0}
-      run: |
-        python examples/buckingham-water.py
+      run: python examples/buckingham-water.py
 
     - name: Run mypy
       continue-on-error: true
-      run: |
-        mypy smirnoff_plugins/
+      run: mypy smirnoff_plugins/
 
     - name: CodeCov
       uses: codecov/codecov-action@v4

.pre-commit-config.yaml

@@ -2,19 +2,19 @@ ci:
   autoupdate_schedule: "quarterly"
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.5.0
   hooks:
   - id: check-yaml
   - id: debug-statements
 - repo: https://github.com/psf/black
-  rev: 23.7.0
+  rev: 24.2.0
   hooks:
   - id: black
 - repo: https://github.com/PyCQA/isort
-  rev: 5.12.0
+  rev: 5.13.2
   hooks:
   - id: isort
 - repo: https://github.com/PyCQA/flake8
-  rev: 6.1.0
+  rev: 7.0.0
   hooks:
   - id: flake8

devtools/conda-envs/test_env.yaml

@@ -1,6 +1,5 @@
 name: smirnoff-plugins-test
 channels:
-  - jaimergp/label/unsupported-cudatoolkit-shim
   - conda-forge
 
 dependencies:
@@ -10,8 +9,8 @@ dependencies:
     # Core dependencies
   - numpy
   - openmm
-  - openff-toolkit >=0.14.3
-  - openff-interchange >=0.3.18
+  - openff-toolkit =0.15
+  - openff-interchange
   - openff-utilities
   - openff-models
 
@@ -21,4 +20,4 @@ dependencies:
   - pytest-xdist
   - pytest-randomly
 
-  - mypy =1.2
+  - mypy

examples/buckingham-water.py

@@ -1,6 +1,7 @@
 """This script provides an example of how to construct a force field for a four site
 water model which uses a custom Buckingham potential to describe the non-bonded vdW
 interactions."""
+
 import math
 
 import numpy
@@ -107,7 +108,10 @@ def main():
     positions = openmm.unit.Quantity(
         numpy.vstack(
             [
-                (molecule.conformers[0].m_as(unit.angstrom) + numpy.array([[x, y, z]]) * 2.5)
+                (
+                    molecule.conformers[0].m_as(unit.angstrom)
+                    + numpy.array([[x, y, z]]) * 2.5
+                )
                 for x in range(math.ceil(n_molecules ** (1 / 3)))
                 for y in range(math.ceil(n_molecules ** (1 / 3)))
                 for z in range(math.ceil(n_molecules ** (1 / 3)))

setup.cfg

@@ -39,9 +39,6 @@ warn_unused_configs = True
 warn_unused_ignores = True
 warn_incomplete_stub = True
 show_error_codes = True
-# https://github.com/pydantic/pydantic/issues/5192
-disable_error_code = call-arg
-
 
 [mypy-openff.toolkit.*]
 ignore_missing_imports = True
@@ -58,8 +55,5 @@ ignore_missing_imports = True
 [mypy-openmm.app]
 ignore_missing_imports = True
 
-[mypy-openmm.app.element]
-ignore_missing_imports = True
-
 [mypy-openmm.unit]
 ignore_missing_imports = True

setup.py

@@ -2,6 +2,7 @@
 smirnoff-plugins
 Custom parameter handlers for extending SMIRNOFF force fields.
 """
+
 import sys
 
 from setuptools import find_packages, setup

smirnoff_plugins/_tests/conftest.py

@@ -2,9 +2,8 @@
 
 import numpy
 import pytest
-from openff.toolkit.topology import Molecule, Topology
-from openff.toolkit.typing.engines.smirnoff import ForceField, ParameterList
-from openff.units import unit
+from openff.toolkit import ForceField, Molecule, Topology, unit
+from openff.toolkit.typing.engines.smirnoff.parameters import ParameterList
 
 
 @pytest.fixture()

smirnoff_plugins/_tests/handlers/test_nonbonded.py

@@ -2,12 +2,10 @@
 import openmm.unit
 import pytest
 from openff.interchange import Interchange
-from openff.toolkit import Topology
-from openff.toolkit.topology import Molecule
-from openff.toolkit.typing.engines.smirnoff import ForceField
-from openff.units import unit
+from openff.toolkit import ForceField, Molecule, Topology, unit
 from openff.units.openmm import from_openmm, to_openmm
 from openff.utilities import get_data_file_path
+
 from smirnoff_plugins.utilities.openmm import (
     evaluate_energy,
     evaluate_water_energy_at_distances,
@@ -429,7 +427,8 @@ def mock_modify_openmm_forces(
 
     de = ForceField(
         get_data_file_path("_tests/data/de-force-1.0.1.offxml", "smirnoff_plugins"),
-        load_plugins=True)
+        load_plugins=True,
+    )
 
     combined_energies = get_openmm_energies(
         interchange=de.create_interchange(ligand.to_topology()),
@@ -764,7 +763,7 @@ def test_multipole_energies():
         {"smirks": "[#10:1]", "polarity": "1 * angstrom**3"}
     )
 
-    hf = Molecule.from_smiles("[F:1][H:2]")
+    hf = Molecule.from_mapped_smiles("[F:1][H:2]")
     hf.generate_conformers(n_conformers=1)
     off_top = hf.to_topology()
     neon = Molecule.from_smiles("[Ne]")

smirnoff_plugins/collections/nonbonded.py

@@ -11,10 +11,9 @@
     _SMIRNOFFNonbondedCollection,
 )
 from openff.models.types import FloatQuantity
-from openff.toolkit import Topology
+from openff.toolkit import Quantity, Topology, unit
 from openff.toolkit.topology import Atom
 from openff.toolkit.typing.engines.smirnoff.parameters import ParameterHandler
-from openff.units import Quantity, unit
 from openmm import CustomManyParticleForce, openmm
 
 from smirnoff_plugins.handlers.nonbonded import (
@@ -363,10 +362,10 @@ class SMIRNOFFDampedExp6810Collection(_NonbondedPlugin):
         "rho = 0.5*(rho1+rho2);"
     )
 
-    force_at_zero: FloatQuantity[
-        "kilojoules_per_mole * nanometer**-1"  # noqa
-    ] = unit.Quantity(
-        49.6144931952, unit.kilojoules_per_mole * unit.nanometer**-1  # noqa
+    force_at_zero: FloatQuantity["kilojoules_per_mole * nanometer**-1"] = (  # noqa
+        unit.Quantity(
+            49.6144931952, unit.kilojoules_per_mole * unit.nanometer**-1  # noqa
+        )
     )
 
     @classmethod

smirnoff_plugins/handlers/nonbonded.py

@@ -1,7 +1,9 @@
 import abc
 
+from openff.toolkit import unit
 from openff.toolkit.typing.engines.smirnoff.parameters import (
     ElectrostaticsHandler,
+    IncompatibleParameterError,
     LibraryChargeHandler,
     ParameterAttribute,
     ParameterHandler,
@@ -11,8 +13,6 @@
     _allow_only,
     vdWHandler,
 )
-from openff.toolkit.utils.exceptions import IncompatibleParameterError
-from openff.units import unit
 
 
 class _CustomNonbondedHandler(ParameterHandler, abc.ABC):

smirnoff_plugins/utilities/openmm.py

@@ -10,8 +10,7 @@
 import openmm.unit
 from openff.interchange import Interchange
 from openff.interchange.interop.openmm._positions import to_openmm_positions
-from openff.toolkit import ForceField, Molecule, Topology
-from openff.units import unit
+from openff.toolkit import ForceField, Molecule, Topology, unit
 from openff.units.openmm import ensure_quantity
 from openff.utilities import temporary_cd