Merge pull request #114 from cmelab/pre-commit-ci-update-config

[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -18,7 +18,7 @@ repos:
       - id: trailing-whitespace
         exclude: 'flowermd/tests/assets/.* | flowermd/assets/.*'
   - repo: https://github.com/psf/black
-    rev: 23.12.1
+    rev: 24.1.1
     hooks:
       - id: black
         args: [ --line-length=80 ]

flowermd/__init__.py

@@ -1,4 +1,5 @@
 """flowerMD package."""
+
 from .base import (
     CoPolymer,
     Lattice,

flowermd/assets/__init__.py

@@ -1,3 +1,4 @@
 """Paths to the assets used by flowerMD."""
+
 from .forcefields import FF_DIR
 from .molecule_files import MON_DIR

flowermd/assets/forcefields/__init__.py

@@ -1,4 +1,5 @@
 """Forcefield files for flowerMD."""
+
 import os
 
 FF_DIR = os.path.abspath(os.path.dirname(__file__))

flowermd/assets/molecule_files/__init__.py

@@ -1,4 +1,5 @@
 """Molecule files for flowerMD."""
+
 import os
 
 MON_DIR = os.path.abspath(os.path.dirname(__file__))

flowermd/base/__init__.py

@@ -1,4 +1,5 @@
 """Base classes for flowerMD."""
+
 from .forcefield import BaseHOOMDForcefield, BaseXMLForcefield
 from .molecule import CoPolymer, Molecule, Polymer
 from .simulation import Simulation

flowermd/base/forcefield.py

@@ -1,4 +1,5 @@
 """Base forcefield classes."""
+
 import forcefield_utilities as ffutils
 import foyer
 

flowermd/base/molecule.py

@@ -1,4 +1,5 @@
 """Base class for all flowerMD molecules, Polymers, and CoPolymers."""
+
 import itertools
 import os.path
 import random

flowermd/base/simulation.py

@@ -1,4 +1,5 @@
 """Base simulation class for flowerMD."""
+
 import inspect
 import pickle
 import warnings

flowermd/base/system.py

@@ -1,4 +1,5 @@
 """System class for arranging Molecules into a box."""
+
 import pickle
 import warnings
 from abc import ABC, abstractmethod
@@ -99,9 +100,9 @@ def __init__(
                             mol_item.force_field.hoomd_forces
                         )
                     elif isinstance(mol_item.force_field, BaseXMLForcefield):
-                        self._gmso_forcefields_dict[
-                            str(self.n_mol_types)
-                        ] = mol_item.force_field.gmso_ff
+                        self._gmso_forcefields_dict[str(self.n_mol_types)] = (
+                            mol_item.force_field.gmso_ff
+                        )
                     elif isinstance(mol_item.force_field, list):
                         self._hoomd_forcefield.extend(mol_item.force_field)
                 self.n_mol_types += 1
@@ -418,9 +419,9 @@ def _create_hoomd_forcefield(self, r_cut, nlist_buffer, pppm_kwargs):
             nlist_buffer=nlist_buffer,
             pppm_kwargs=pppm_kwargs,
             auto_scale=False,
-            base_units=self._reference_values
-            if self._reference_values
-            else None,
+            base_units=(
+                self._reference_values if self._reference_values else None
+            ),
         )
         for force in ff:
             force_list.extend(ff[force])
@@ -432,9 +433,9 @@ def _create_hoomd_snapshot(self):
         snap, refs = to_gsd_snapshot(
             top=self.gmso_system,
             auto_scale=False,
-            base_units=self._reference_values
-            if self._reference_values
-            else None,
+            base_units=(
+                self._reference_values if self._reference_values else None
+            ),
         )
         self._snap_refs = self._reference_values.copy()
         return snap

flowermd/library/__init__.py

@@ -1,4 +1,5 @@
 """Library of predefined molecules, recipes and forcefields."""
+
 from .forcefields import (
     GAFF,
     OPLS_AA,

flowermd/library/forcefields.py

@@ -1,4 +1,5 @@
 """All pre-defined forcefield classes for use in flowerMD."""
+
 import itertools
 import os
 

flowermd/library/polymers.py

@@ -1,4 +1,5 @@
 """Polymer and CoPolymer example classes."""
+
 import os
 
 import mbuild as mb

flowermd/library/simulations/tensile.py

@@ -1,4 +1,5 @@
 """Tensile simulation class."""
+
 import hoomd
 import numpy as np
 

flowermd/modules/surface_wetting/__init__.py

@@ -1,4 +1,5 @@
 """Surface wetting module for FlowerMD."""
+
 from .surface_wetting import (
     DropletSimulation,
     InterfaceBuilder,

flowermd/modules/surface_wetting/surface_wetting.py

@@ -1,4 +1,5 @@
 """Module for simulating surface wetting."""
+
 import warnings
 
 import gsd.hoomd

flowermd/modules/welding/__init__.py

@@ -1,3 +1,4 @@
 """Welding module for FlowerMD."""
+
 from .utils import add_void_particles
 from .welding import Interface, SlabSimulation, WeldSimulation

flowermd/modules/welding/utils.py

@@ -1,4 +1,5 @@
 """Utility functions for the Welding module."""
+
 import hoomd
 import numpy as np
 

flowermd/modules/welding/welding.py

@@ -1,4 +1,5 @@
 """Module for simulating interfaces and welding."""
+
 import gsd.hoomd
 import hoomd
 import numpy as np