diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8a76ac31..590354b1 100644 --- a/.pre-commit-config.yaml +++ b/.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 ] diff --git a/flowermd/__init__.py b/flowermd/__init__.py index 4c63ec18..e0995a2c 100644 --- a/flowermd/__init__.py +++ b/flowermd/__init__.py @@ -1,4 +1,5 @@ """flowerMD package.""" + from .base import ( CoPolymer, Lattice, diff --git a/flowermd/assets/__init__.py b/flowermd/assets/__init__.py index 6207ffe4..7a63aa3f 100644 --- a/flowermd/assets/__init__.py +++ b/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 diff --git a/flowermd/assets/forcefields/__init__.py b/flowermd/assets/forcefields/__init__.py index d28d9e6c..b571d989 100644 --- a/flowermd/assets/forcefields/__init__.py +++ b/flowermd/assets/forcefields/__init__.py @@ -1,4 +1,5 @@ """Forcefield files for flowerMD.""" + import os FF_DIR = os.path.abspath(os.path.dirname(__file__)) diff --git a/flowermd/assets/molecule_files/__init__.py b/flowermd/assets/molecule_files/__init__.py index 20a8f1fc..5c31c97f 100644 --- a/flowermd/assets/molecule_files/__init__.py +++ b/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__)) diff --git a/flowermd/base/__init__.py b/flowermd/base/__init__.py index 02a615cc..4376da88 100644 --- a/flowermd/base/__init__.py +++ b/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 diff --git a/flowermd/base/forcefield.py b/flowermd/base/forcefield.py index c416ea4c..532669d4 100644 --- a/flowermd/base/forcefield.py +++ b/flowermd/base/forcefield.py @@ -1,4 +1,5 @@ """Base forcefield classes.""" + import forcefield_utilities as ffutils import foyer diff --git a/flowermd/base/molecule.py b/flowermd/base/molecule.py index de0ce675..f4fd6a6f 100644 --- a/flowermd/base/molecule.py +++ b/flowermd/base/molecule.py @@ -1,4 +1,5 @@ """Base class for all flowerMD molecules, Polymers, and CoPolymers.""" + import itertools import os.path import random diff --git a/flowermd/base/simulation.py b/flowermd/base/simulation.py index 46f92f33..b8a7d247 100644 --- a/flowermd/base/simulation.py +++ b/flowermd/base/simulation.py @@ -1,4 +1,5 @@ """Base simulation class for flowerMD.""" + import inspect import pickle import warnings diff --git a/flowermd/base/system.py b/flowermd/base/system.py index 5b7154e2..7bc08545 100644 --- a/flowermd/base/system.py +++ b/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 diff --git a/flowermd/library/__init__.py b/flowermd/library/__init__.py index 9c28597b..7fa65b37 100644 --- a/flowermd/library/__init__.py +++ b/flowermd/library/__init__.py @@ -1,4 +1,5 @@ """Library of predefined molecules, recipes and forcefields.""" + from .forcefields import ( GAFF, OPLS_AA, diff --git a/flowermd/library/forcefields.py b/flowermd/library/forcefields.py index 4210c9a9..8f071f25 100644 --- a/flowermd/library/forcefields.py +++ b/flowermd/library/forcefields.py @@ -1,4 +1,5 @@ """All pre-defined forcefield classes for use in flowerMD.""" + import itertools import os diff --git a/flowermd/library/polymers.py b/flowermd/library/polymers.py index c3f7b96d..f287b12c 100644 --- a/flowermd/library/polymers.py +++ b/flowermd/library/polymers.py @@ -1,4 +1,5 @@ """Polymer and CoPolymer example classes.""" + import os import mbuild as mb diff --git a/flowermd/library/simulations/tensile.py b/flowermd/library/simulations/tensile.py index af5e2fba..7b2b37ea 100644 --- a/flowermd/library/simulations/tensile.py +++ b/flowermd/library/simulations/tensile.py @@ -1,4 +1,5 @@ """Tensile simulation class.""" + import hoomd import numpy as np diff --git a/flowermd/modules/surface_wetting/__init__.py b/flowermd/modules/surface_wetting/__init__.py index 67f5f6d6..b5a838ef 100644 --- a/flowermd/modules/surface_wetting/__init__.py +++ b/flowermd/modules/surface_wetting/__init__.py @@ -1,4 +1,5 @@ """Surface wetting module for FlowerMD.""" + from .surface_wetting import ( DropletSimulation, InterfaceBuilder, diff --git a/flowermd/modules/surface_wetting/surface_wetting.py b/flowermd/modules/surface_wetting/surface_wetting.py index a79d06d3..3f35383e 100644 --- a/flowermd/modules/surface_wetting/surface_wetting.py +++ b/flowermd/modules/surface_wetting/surface_wetting.py @@ -1,4 +1,5 @@ """Module for simulating surface wetting.""" + import warnings import gsd.hoomd diff --git a/flowermd/modules/welding/__init__.py b/flowermd/modules/welding/__init__.py index bb073947..d927c0a6 100644 --- a/flowermd/modules/welding/__init__.py +++ b/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 diff --git a/flowermd/modules/welding/utils.py b/flowermd/modules/welding/utils.py index 532acaad..470fb5ab 100644 --- a/flowermd/modules/welding/utils.py +++ b/flowermd/modules/welding/utils.py @@ -1,4 +1,5 @@ """Utility functions for the Welding module.""" + import hoomd import numpy as np diff --git a/flowermd/modules/welding/welding.py b/flowermd/modules/welding/welding.py index 0b486e53..c294d613 100644 --- a/flowermd/modules/welding/welding.py +++ b/flowermd/modules/welding/welding.py @@ -1,4 +1,5 @@ """Module for simulating interfaces and welding.""" + import gsd.hoomd import hoomd import numpy as np