linter

src/pontibus/components/extended_solvent_component.py

@@ -131,8 +131,8 @@ def from_keyed_dict(cls, dct: dict):
             dct,
             lambda d: registry[GufeKey(d[":gufe-key:"])],
             is_gufe_key_dict,
-            mode='decode',
-            top=True
+            mode="decode",
+            top=True,
         )
 
         return from_dict_depth_one(dct)
@@ -189,10 +189,7 @@ def _from_dict_depth_one(dct: dict) -> GufeTokenizable:
     new_dct = {}
 
     for entry in dct:
-        if (
-            isinstance(dct[entry], dict) and
-            '__qualname__' in dct[entry]
-        ):
+        if isinstance(dct[entry], dict) and "__qualname__" in dct[entry]:
             new_dct[entry] = _from_dict(dct[entry])
         else:
             new_dct[entry] = dct[entry]

src/pontibus/protocols/solvation/__init__.py

@@ -4,9 +4,7 @@
 Run absolute solvation free energy calculations using OpenMM and OpenMMTools.
 
 """
-from .settings import(
-    ASFESettings
-)
+from .settings import ASFESettings
 from .asfe_protocol import (
     ASFEProtocol,
     ASFEProtocolResult,

src/pontibus/protocols/solvation/asfe_protocol.py

@@ -1,10 +1,7 @@
 # This code is part of OpenFE and is licensed under the MIT license.
 # For details, see https://github.com/OpenFreeEnergy/openfe
 
-from typing import (
-    Union,
-    Optional
-)
+from typing import Union, Optional
 import uuid
 
 import numpy as np
@@ -200,8 +197,7 @@ def _validate_solvent(state: ChemicalSystem, nonbonded_method: str):
           * If there is a SolventComponent and the `nonbonded_method` is
             `nocutoff`.
         """
-        solv = [comp for comp in state.values()
-                if isinstance(comp, SolventComponent)]
+        solv = [comp for comp in state.values() if isinstance(comp, SolventComponent)]
 
         if len(solv) > 0 and nonbonded_method.lower() == "nocutoff":
             errmsg = "nocutoff cannot be used for solvent transformations"
@@ -238,12 +234,10 @@ def _create(
 
         # Validate the lambda schedule
         self._validate_lambda_schedule(
-            self.settings.lambda_settings,
-            self.settings.solvent_simulation_settings
+            self.settings.lambda_settings, self.settings.solvent_simulation_settings
         )
         self._validate_lambda_schedule(
-            self.settings.lambda_settings,
-            self.settings.vacuum_simulation_settings
+            self.settings.lambda_settings, self.settings.vacuum_simulation_settings
         )
 
         # Check nonbond & solvent compatibility
@@ -349,9 +343,7 @@ def _get_components(self):
         # (of stateA since we enforce only one disappearing ligand)
         return alchem_comps, None, prot_comp, off_comps
 
-    def _handle_settings(
-            self
-    ) -> dict[str, gufe.settings.SettingsBaseModel]:
+    def _handle_settings(self) -> dict[str, gufe.settings.SettingsBaseModel]:
         """
         Extract the relevant settings for a vacuum transformation.
 
@@ -433,9 +425,7 @@ def _get_components(self):
         # disallowed on create
         return alchem_comps, solv_comp, prot_comp, off_comps
 
-    def _handle_settings(
-        self
-    ) -> dict[str, gufe.settings.SettingsBaseModel]:
+    def _handle_settings(self) -> dict[str, gufe.settings.SettingsBaseModel]:
         """
         Extract the relevant settings for a vacuum transformation.
 

src/pontibus/protocols/solvation/base.py

@@ -2,11 +2,7 @@
 # For details, see https://github.com/OpenFreeEnergy/openfe
 
 import logging
-from typing import (
-    Any,
-    Optional,
-    Union
-)
+from typing import Any, Optional, Union
 import numpy.typing as npt
 from gufe import (
     SmallMoleculeComponent,
@@ -25,9 +21,7 @@
 from openmm import app
 import openmmtools
 from openfe.utils import log_system_probe
-from pontibus.components import (
-    ExtendedSolventComponent
-)
+from pontibus.components import ExtendedSolventComponent
 from pontibus.protocols.solvation.settings import (
     IntegratorSettings,
     OpenFFPartialChargeSettings,
@@ -132,10 +126,7 @@ def _get_omm_objects(
         solvent_component: Optional[SolventComponent],
         smc_components: dict[SmallMoleculeComponent, OFFMolecule],
     ) -> tuple[
-        app.Topology,
-        openmm.System,
-        openmm.unit.Quantity,
-        dict[str, npt.NDArray]
+        app.Topology, openmm.System, openmm.unit.Quantity, dict[str, npt.NDArray]
     ]:
         """
         Get the OpenMM Topology, Positions and System of the
@@ -311,9 +302,7 @@ def run(
             )
 
             # 15. Run simulation
-            unit_result_dict = self._run_simulation(
-                sampler, reporter, settings, dry
-            )
+            unit_result_dict = self._run_simulation(sampler, reporter, settings, dry)
 
         finally:
             # close reporter when you're done to prevent file handle clashes
@@ -355,10 +344,7 @@ def _execute(
     ) -> dict[str, Any]:
         log_system_probe(logging.INFO, paths=[ctx.scratch])
 
-        outputs = self.run(
-            scratch_basepath=ctx.scratch,
-            shared_basepath=ctx.shared
-        )
+        outputs = self.run(scratch_basepath=ctx.scratch, shared_basepath=ctx.shared)
 
         return {
             "repeat_id": self._inputs["repeat_id"],

src/pontibus/protocols/solvation/settings.py

@@ -81,8 +81,7 @@ def is_positive_distance(cls, v):
         # these are time units, not simulation steps
         if not v.is_compatible_with(unit.nanometer):
             raise ValueError(
-                "nonbonded_cutoff must be in distance units "
-                "(i.e. nanometers)"
+                "nonbonded_cutoff must be in distance units " "(i.e. nanometers)"
             )
         if v < 0:
             errmsg = "nonbonded_cutoff must be a positive value"

src/pontibus/tests/components/test_extendedsolvent.py

@@ -15,9 +15,9 @@
 def test_defaults():
     s = ExtendedSolventComponent()
 
-    assert s.smiles == '[H][O][H]'
-    assert s.positive_ion == 'Na+'
-    assert s.negative_ion == 'Cl-'
+    assert s.smiles == "[H][O][H]"
+    assert s.positive_ion == "Na+"
+    assert s.negative_ion == "Cl-"
     assert s.ion_concentration == 0.0 * unit.molar
     assert s.neutralize == False
     assert s.solvent_molecule == WATER
@@ -26,33 +26,31 @@ def test_defaults():
 def test_neq_different_smc():
     water_off = WATER.to_openff()
     # Create a water with partial charges
-    water_off.assign_partial_charges(partial_charge_method='gasteiger')
+    water_off.assign_partial_charges(partial_charge_method="gasteiger")
     WATER2 = SmallMoleculeComponent.from_openff(water_off)
     s1 = ExtendedSolventComponent(solvent_molecule=WATER)
     s2 = ExtendedSolventComponent(solvent_molecule=WATER2)
 
     assert s1 != s2
-    assert s1.smiles == '[H][O][H]' == s2.smiles
+    assert s1.smiles == "[H][O][H]" == s2.smiles
 
 
 def test_neq_different_solvent():
-    meth_off = Molecule.from_smiles('C')
+    meth_off = Molecule.from_smiles("C")
     meth_off.generate_conformers()
     METH = SmallMoleculeComponent.from_openff(meth_off)
     s1 = ExtendedSolventComponent()
     s2 = ExtendedSolventComponent(solvent_molecule=METH)
 
     assert s1 != s2
-    assert s1.smiles == '[H][O][H]'
-    assert s2.smiles == '[H][C]([H])([H])[H]'
+    assert s1.smiles == "[H][O][H]"
+    assert s2.smiles == "[H][C]([H])([H])[H]"
     assert s1.smiles != s2.smiles
 
 
 def test_dict_roundtrip_eq():
     s1 = ExtendedSolventComponent()
-    s2 = ExtendedSolventComponent.from_dict(
-        s1.to_dict()
-    )
+    s2 = ExtendedSolventComponent.from_dict(s1.to_dict())
     assert s1 == s2
     assert s1.solvent_molecule == s2.solvent_molecule
     # Smiles isn't a dict entry, so make sure it got preserved
@@ -61,9 +59,7 @@ def test_dict_roundtrip_eq():
 
 def test_keyed_dict_roundtrip_eq():
     s1 = ExtendedSolventComponent()
-    s2 = ExtendedSolventComponent.from_keyed_dict(
-        s1.to_keyed_dict()
-    )
+    s2 = ExtendedSolventComponent.from_keyed_dict(s1.to_keyed_dict())
     assert s1 == s2
     # Smiles isn't a dict entry, so make sure it got preserved
     assert s1.smiles == s2.smiles
@@ -74,9 +70,7 @@ def test_keyed_dict_roundtrip_eq():
 
 def test_shallow_dict_roundtrip_eq():
     s1 = ExtendedSolventComponent()
-    s2 = ExtendedSolventComponent.from_shallow_dict(
-        s1.to_shallow_dict()
-    )
+    s2 = ExtendedSolventComponent.from_shallow_dict(s1.to_shallow_dict())
     assert s1 == s2
     # Smiles isn't a dict entry, so make sure it got preserved
     assert s1.smiles == s2.smiles

src/pontibus/tests/conftest.py

@@ -43,33 +43,42 @@ class SlowTests:
     To run the `slow` tests, either use the `--runslow` flag when invoking
     pytest, or set the environment variable `PONTIBUS_SLOW_TESTS` to `true`
     """
+
     def __init__(self, config):
         self.config = config
 
     @staticmethod
     def _modify_slow(items, config):
-        msg = ("need --runslow pytest cli option or the environment variable "
-               "`PONTIBUS_SLOW_TESTS` set to `True` to run")
+        msg = (
+            "need --runslow pytest cli option or the environment variable "
+            "`PONTIBUS_SLOW_TESTS` set to `True` to run"
+        )
         skip_slow = pytest.mark.skip(reason=msg)
         for item in items:
             if "slow" in item.keywords:
                 item.add_marker(skip_slow)
 
     @staticmethod
     def _modify_integration(items, config):
-        msg = ("need --gpu pytest cli option or the environment "
-               "variable `PONTIBUS_GPU_TESTS` set to `True` to run")
+        msg = (
+            "need --gpu pytest cli option or the environment "
+            "variable `PONTIBUS_GPU_TESTS` set to `True` to run"
+        )
         skip_int = pytest.mark.skip(reason=msg)
         for item in items:
             if "gpu" in item.keywords:
                 item.add_marker(skip_int)
 
     def pytest_collection_modifyitems(self, items, config):
-        if (config.getoption('--gpu') or
-            os.getenv("PONTIBUS_GPU_TESTS", default="false").lower() == 'true'):
+        if (
+            config.getoption("--gpu")
+            or os.getenv("PONTIBUS_GPU_TESTS", default="false").lower() == "true"
+        ):
             return
-        elif (config.getoption('--runslow') or
-              os.getenv("PONTIBUS_SLOW_TESTS", default="false").lower() == 'true'):
+        elif (
+            config.getoption("--runslow")
+            or os.getenv("PONTIBUS_SLOW_TESTS", default="false").lower() == "true"
+        ):
             self._modify_integration(items, config)
         else:
             self._modify_integration(items, config)
@@ -83,26 +92,27 @@ def pytest_addoption(parser):
         "--runslow", action="store_true", default=False, help="run slow tests"
     )
     parser.addoption(
-        "--gpu", action="store_true", default=False,
+        "--gpu",
+        action="store_true",
+        default=False,
         help="run gpu tests",
     )
 
 
 def pytest_configure(config):
     config.pluginmanager.register(SlowTests(config), "slow")
     config.addinivalue_line("markers", "slow: mark test as slow")
-    config.addinivalue_line(
-            "markers", "gpu: mark test as long integration test")
+    config.addinivalue_line("markers", "gpu: mark test as long integration test")
 
 
-@pytest.fixture(scope='session')
+@pytest.fixture(scope="session")
 def benzene_modifications():
     files = {}
-    with importlib.resources.files('openfe.tests.data') as d:
-        fn = str(d / 'benzene_modifications.sdf')
+    with importlib.resources.files("openfe.tests.data") as d:
+        fn = str(d / "benzene_modifications.sdf")
         supp = Chem.SDMolSupplier(str(fn), removeHs=False)
         for rdmol in supp:
-            files[rdmol.GetProp('_Name')] = SmallMoleculeComponent(rdmol)
+            files[rdmol.GetProp("_Name")] = SmallMoleculeComponent(rdmol)
     return files
 
 
@@ -111,19 +121,19 @@ def CN_molecule():
     """
     A basic CH3NH2 molecule for quick testing.
     """
-    with resources.files('openfe.tests.data') as d:
-        fn = str(d / 'CN.sdf')
+    with resources.files("openfe.tests.data") as d:
+        fn = str(d / "CN.sdf")
         supp = Chem.SDMolSupplier(str(fn), removeHs=False)
 
         smc = [SmallMoleculeComponent(i) for i in supp][0]
 
     return smc
 
 
-@pytest.fixture(scope='session')
+@pytest.fixture(scope="session")
 def T4_protein_component():
-    with resources.files('openfe.tests.data') as d:
-        fn = str(d / '181l_only.pdb')
+    with resources.files("openfe.tests.data") as d:
+        fn = str(d / "181l_only.pdb")
         comp = gufe.ProteinComponent.from_pdb_file(fn, name="T4_protein")
 
     return comp