From 9d20e3de94f9dac18374602cb616b1fac9355509 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 1 Feb 2024 10:36:34 -0600
Subject: [PATCH] [pre-commit.ci] pre-commit autoupdate (#1165)
MIME-Version: 1.0
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Content-Transfer-Encoding: 8bit

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/psf/black: 23.12.1 → 24.1.1](https://github.com/psf/black/compare/23.12.1...24.1.1)

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com>
---
 .pre-commit-config.yaml                            | 2 +-
 mbuild/__init__.py                                 | 1 +
 mbuild/box.py                                      | 1 +
 mbuild/coarse_graining.py                          | 1 +
 mbuild/compound.py                                 | 1 +
 mbuild/conversion.py                               | 1 +
 mbuild/coordinate_transform.py                     | 1 +
 mbuild/formats/cassandramcf.py                     | 1 +
 mbuild/formats/gsdwriter.py                        | 1 +
 mbuild/formats/hoomd_forcefield.py                 | 1 +
 mbuild/formats/hoomd_simulation.py                 | 1 +
 mbuild/formats/hoomd_snapshot.py                   | 1 +
 mbuild/formats/hoomdxml.py                         | 1 +
 mbuild/formats/json_formats.py                     | 1 +
 mbuild/formats/lammpsdata.py                       | 5 ++---
 mbuild/formats/par_writer.py                       | 1 +
 mbuild/formats/protobuf.py                         | 1 +
 mbuild/formats/vasp.py                             | 1 +
 mbuild/formats/xyz.py                              | 1 +
 mbuild/lattice.py                                  | 7 ++++---
 mbuild/lib/atoms/__init__.py                       | 1 +
 mbuild/lib/atoms/c3.py                             | 1 +
 mbuild/lib/atoms/h.py                              | 1 +
 mbuild/lib/atoms/n4.py                             | 1 +
 mbuild/lib/bulk_materials/__init__.py              | 1 +
 mbuild/lib/bulk_materials/amorphous_silica_bulk.py | 1 +
 mbuild/lib/moieties/__init__.py                    | 1 +
 mbuild/lib/moieties/ch2.py                         | 1 +
 mbuild/lib/moieties/ch3.py                         | 1 +
 mbuild/lib/moieties/ester.py                       | 1 +
 mbuild/lib/moieties/h2o.py                         | 1 +
 mbuild/lib/moieties/peg.py                         | 1 +
 mbuild/lib/moieties/silane.py                      | 1 +
 mbuild/lib/molecules/__init__.py                   | 1 +
 mbuild/lib/molecules/ethane.py                     | 1 +
 mbuild/lib/molecules/methane.py                    | 1 +
 mbuild/lib/molecules/water.py                      | 1 +
 mbuild/lib/recipes/__init__.py                     | 1 +
 mbuild/lib/recipes/alkane.py                       | 1 +
 mbuild/lib/recipes/monolayer.py                    | 1 +
 mbuild/lib/recipes/polymer.py                      | 1 +
 mbuild/lib/recipes/silica_interface.py             | 1 +
 mbuild/lib/recipes/tiled_compound.py               | 1 +
 mbuild/lib/recipes/water_box.py                    | 1 +
 mbuild/lib/surfaces/__init__.py                    | 1 +
 mbuild/lib/surfaces/amorphous_silica_surface.py    | 1 +
 mbuild/lib/surfaces/betacristobalite.py            | 1 +
 mbuild/packing.py                                  | 1 +
 mbuild/pattern.py                                  | 1 +
 mbuild/port.py                                     | 1 +
 mbuild/utils/conversion.py                         | 1 +
 mbuild/utils/decorators.py                         | 1 +
 mbuild/utils/geometry.py                           | 1 +
 mbuild/utils/io.py                                 | 1 +
 mbuild/utils/jsutils.py                            | 1 +
 mbuild/utils/orderedset.py                         | 1 +
 mbuild/utils/sorting.py                            | 1 +
 57 files changed, 61 insertions(+), 7 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 679bcf068..2f267be9d 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -17,7 +17,7 @@ repos:
     - id: trailing-whitespace
       exclude: setup.cfg
 - repo: https://github.com/psf/black
-  rev: 23.12.1
+  rev: 24.1.1
   hooks:
     - id: black
       args: [--line-length=80]
diff --git a/mbuild/__init__.py b/mbuild/__init__.py
index 02d471c49..67279916d 100644
--- a/mbuild/__init__.py
+++ b/mbuild/__init__.py
@@ -1,4 +1,5 @@
 """mBuild: a hierarchical, component based molecule builder."""
+
 from mbuild.box import Box
 from mbuild.coarse_graining import coarse_grain
 from mbuild.compound import *
diff --git a/mbuild/box.py b/mbuild/box.py
index 2b04dcda4..8a739db62 100644
--- a/mbuild/box.py
+++ b/mbuild/box.py
@@ -1,4 +1,5 @@
 """mBuild box module."""
+
 from warnings import warn
 
 import numpy as np
diff --git a/mbuild/coarse_graining.py b/mbuild/coarse_graining.py
index 732fb1f47..2e619afbf 100644
--- a/mbuild/coarse_graining.py
+++ b/mbuild/coarse_graining.py
@@ -1,4 +1,5 @@
 """Tools for coarse-grained systems."""
+
 from collections import OrderedDict
 from copy import deepcopy
 
diff --git a/mbuild/compound.py b/mbuild/compound.py
index 5ca296d9d..b53d7fbdc 100644
--- a/mbuild/compound.py
+++ b/mbuild/compound.py
@@ -1,4 +1,5 @@
 """Module for working with mBuild Compounds."""
+
 __all__ = ["clone", "Compound", "Particle"]
 
 import itertools
diff --git a/mbuild/conversion.py b/mbuild/conversion.py
index 25ce152b7..bca251d1b 100644
--- a/mbuild/conversion.py
+++ b/mbuild/conversion.py
@@ -1,4 +1,5 @@
 """Module for handling conversions in mBuild."""
+
 import os
 import sys
 from collections import defaultdict
diff --git a/mbuild/coordinate_transform.py b/mbuild/coordinate_transform.py
index 30c723d22..1edf2d609 100644
--- a/mbuild/coordinate_transform.py
+++ b/mbuild/coordinate_transform.py
@@ -1,4 +1,5 @@
 """Coordinate transformation functions."""
+
 from warnings import simplefilter, warn
 
 simplefilter("always", DeprecationWarning)
diff --git a/mbuild/formats/cassandramcf.py b/mbuild/formats/cassandramcf.py
index 8a6b4e890..14d92cb1f 100644
--- a/mbuild/formats/cassandramcf.py
+++ b/mbuild/formats/cassandramcf.py
@@ -2,6 +2,7 @@
 
 https://cassandra-mc.readthedocs.io/en/latest/guides/input_files.html#molecular-connectivity-file
 """
+
 from __future__ import division
 
 import warnings
diff --git a/mbuild/formats/gsdwriter.py b/mbuild/formats/gsdwriter.py
index 3ab4b5c03..2de3d5cd3 100644
--- a/mbuild/formats/gsdwriter.py
+++ b/mbuild/formats/gsdwriter.py
@@ -2,6 +2,7 @@
 
 https://gsd.readthedocs.io/en/stable/
 """
+
 import numpy as np
 
 from mbuild.utils.geometry import coord_shift
diff --git a/mbuild/formats/hoomd_forcefield.py b/mbuild/formats/hoomd_forcefield.py
index 8090991cd..8cd4b39c0 100644
--- a/mbuild/formats/hoomd_forcefield.py
+++ b/mbuild/formats/hoomd_forcefield.py
@@ -1,4 +1,5 @@
 """HOOMD v3 forcefield format."""
+
 import itertools
 import operator
 import warnings
diff --git a/mbuild/formats/hoomd_simulation.py b/mbuild/formats/hoomd_simulation.py
index 38452bb47..d1c847cbb 100644
--- a/mbuild/formats/hoomd_simulation.py
+++ b/mbuild/formats/hoomd_simulation.py
@@ -1,4 +1,5 @@
 """HOOMD simulation format."""
+
 import itertools
 import operator
 import warnings
diff --git a/mbuild/formats/hoomd_snapshot.py b/mbuild/formats/hoomd_snapshot.py
index 673e0415b..b52b9db72 100644
--- a/mbuild/formats/hoomd_snapshot.py
+++ b/mbuild/formats/hoomd_snapshot.py
@@ -1,4 +1,5 @@
 """HOOMD snapshot format."""
+
 import operator
 from collections import namedtuple
 
diff --git a/mbuild/formats/hoomdxml.py b/mbuild/formats/hoomdxml.py
index bd1efd120..6a564c804 100644
--- a/mbuild/formats/hoomdxml.py
+++ b/mbuild/formats/hoomdxml.py
@@ -1,4 +1,5 @@
 """HOOMD xml format."""
+
 import operator
 from collections import namedtuple
 from math import radians
diff --git a/mbuild/formats/json_formats.py b/mbuild/formats/json_formats.py
index 00f377ba7..6d549830e 100644
--- a/mbuild/formats/json_formats.py
+++ b/mbuild/formats/json_formats.py
@@ -1,4 +1,5 @@
 """JSON format."""
+
 import json
 from collections import OrderedDict
 
diff --git a/mbuild/formats/lammpsdata.py b/mbuild/formats/lammpsdata.py
index 46e434ec7..bf6fb6d5d 100644
--- a/mbuild/formats/lammpsdata.py
+++ b/mbuild/formats/lammpsdata.py
@@ -1,4 +1,5 @@
 """LAMMPS data format."""
+
 import itertools as it
 from collections import OrderedDict
 from warnings import warn
@@ -708,9 +709,7 @@ def _get_bond_types(
             (
                 round(
                     bond.type.k
-                    * (
-                        sigma_conversion_factor**2 / epsilon_conversion_factor
-                    ),
+                    * (sigma_conversion_factor**2 / epsilon_conversion_factor),
                     bond_precision,
                 ),
                 round(bond.type.req / sigma_conversion_factor, bond_precision),
diff --git a/mbuild/formats/par_writer.py b/mbuild/formats/par_writer.py
index db8d368d8..26410efa9 100644
--- a/mbuild/formats/par_writer.py
+++ b/mbuild/formats/par_writer.py
@@ -1,4 +1,5 @@
 """CHARMM Par format."""
+
 import warnings
 
 __all__ = ["write_par"]
diff --git a/mbuild/formats/protobuf.py b/mbuild/formats/protobuf.py
index b3fdec61b..1c8c8f1c2 100644
--- a/mbuild/formats/protobuf.py
+++ b/mbuild/formats/protobuf.py
@@ -3,6 +3,7 @@
 A language-agnostic data serialization format developed by Google
 https://developers.google.com/protocol-buffers
 """
+
 import ele
 import numpy as np
 from google.protobuf.text_format import Merge, PrintMessage
diff --git a/mbuild/formats/vasp.py b/mbuild/formats/vasp.py
index 5b0ee8e7e..2d2b1d7c0 100644
--- a/mbuild/formats/vasp.py
+++ b/mbuild/formats/vasp.py
@@ -1,4 +1,5 @@
 """VASP POSCAR format."""
+
 import warnings
 from itertools import chain
 
diff --git a/mbuild/formats/xyz.py b/mbuild/formats/xyz.py
index 53a4090ad..f4def4843 100644
--- a/mbuild/formats/xyz.py
+++ b/mbuild/formats/xyz.py
@@ -1,4 +1,5 @@
 """XYZ format."""
+
 from warnings import warn
 
 import numpy as np
diff --git a/mbuild/lattice.py b/mbuild/lattice.py
index df7252250..df81c5cab 100644
--- a/mbuild/lattice.py
+++ b/mbuild/lattice.py
@@ -1,4 +1,5 @@
 """mBuild lattice module for working with crystalline systems."""
+
 import itertools as it
 import pathlib
 import warnings
@@ -679,8 +680,8 @@ def populate(self, compound_dict=None, x=1, y=1, z=1):
 
         # if coordinates are below a certain threshold, set to 0
         tolerance = 1e-12
-        ret_lattice.xyz_with_ports[
-            ret_lattice.xyz_with_ports <= tolerance
-        ] = 0.0
+        ret_lattice.xyz_with_ports[ret_lattice.xyz_with_ports <= tolerance] = (
+            0.0
+        )
 
         return ret_lattice
diff --git a/mbuild/lib/atoms/__init__.py b/mbuild/lib/atoms/__init__.py
index 0f8bda678..fb9d8cbc1 100644
--- a/mbuild/lib/atoms/__init__.py
+++ b/mbuild/lib/atoms/__init__.py
@@ -1,4 +1,5 @@
 """mBuild library of atoms."""
+
 from mbuild.lib.atoms.c3 import C3
 from mbuild.lib.atoms.h import H
 from mbuild.lib.atoms.n4 import N4
diff --git a/mbuild/lib/atoms/c3.py b/mbuild/lib/atoms/c3.py
index ebf6863aa..09f84c7e4 100644
--- a/mbuild/lib/atoms/c3.py
+++ b/mbuild/lib/atoms/c3.py
@@ -1,4 +1,5 @@
 """A tri-valent, planar carbon atom."""
+
 import numpy as np
 
 import mbuild as mb
diff --git a/mbuild/lib/atoms/h.py b/mbuild/lib/atoms/h.py
index 6e8d667d8..a96e658e6 100644
--- a/mbuild/lib/atoms/h.py
+++ b/mbuild/lib/atoms/h.py
@@ -1,4 +1,5 @@
 """An H atom."""
+
 import numpy as np
 
 import mbuild as mb
diff --git a/mbuild/lib/atoms/n4.py b/mbuild/lib/atoms/n4.py
index 79b80e694..7f4103400 100644
--- a/mbuild/lib/atoms/n4.py
+++ b/mbuild/lib/atoms/n4.py
@@ -1,4 +1,5 @@
 """mBuild atom library for tetravalent nitrogen."""
+
 import numpy as np
 
 import mbuild as mb
diff --git a/mbuild/lib/bulk_materials/__init__.py b/mbuild/lib/bulk_materials/__init__.py
index 79fd5c1e6..9417b96a3 100644
--- a/mbuild/lib/bulk_materials/__init__.py
+++ b/mbuild/lib/bulk_materials/__init__.py
@@ -1,2 +1,3 @@
 """mBuild bulk materials library."""
+
 from mbuild.lib.bulk_materials.amorphous_silica_bulk import AmorphousSilicaBulk
diff --git a/mbuild/lib/bulk_materials/amorphous_silica_bulk.py b/mbuild/lib/bulk_materials/amorphous_silica_bulk.py
index 427eba32d..0b13c7d2d 100644
--- a/mbuild/lib/bulk_materials/amorphous_silica_bulk.py
+++ b/mbuild/lib/bulk_materials/amorphous_silica_bulk.py
@@ -1,4 +1,5 @@
 """A bulk structure of amorphous silica."""
+
 import mbuild as mb
 
 
diff --git a/mbuild/lib/moieties/__init__.py b/mbuild/lib/moieties/__init__.py
index b437b5575..a1978ef0b 100644
--- a/mbuild/lib/moieties/__init__.py
+++ b/mbuild/lib/moieties/__init__.py
@@ -1,4 +1,5 @@
 """mBuild library of common chemical moieties."""
+
 from mbuild.lib.moieties.ch2 import CH2
 from mbuild.lib.moieties.ch3 import CH3
 from mbuild.lib.moieties.ester import Ester
diff --git a/mbuild/lib/moieties/ch2.py b/mbuild/lib/moieties/ch2.py
index 390d4a2af..216610d83 100644
--- a/mbuild/lib/moieties/ch2.py
+++ b/mbuild/lib/moieties/ch2.py
@@ -1,4 +1,5 @@
 """CH2 moiety."""
+
 import mbuild as mb
 
 
diff --git a/mbuild/lib/moieties/ch3.py b/mbuild/lib/moieties/ch3.py
index 6bec892ce..9cb50c1d8 100644
--- a/mbuild/lib/moieties/ch3.py
+++ b/mbuild/lib/moieties/ch3.py
@@ -1,4 +1,5 @@
 """mBuild CH3 moiety."""
+
 import mbuild as mb
 
 
diff --git a/mbuild/lib/moieties/ester.py b/mbuild/lib/moieties/ester.py
index 18d90c709..d25d560db 100644
--- a/mbuild/lib/moieties/ester.py
+++ b/mbuild/lib/moieties/ester.py
@@ -1,4 +1,5 @@
 """Ester moiety."""
+
 import numpy as np
 
 import mbuild as mb
diff --git a/mbuild/lib/moieties/h2o.py b/mbuild/lib/moieties/h2o.py
index a07092693..337fd7532 100644
--- a/mbuild/lib/moieties/h2o.py
+++ b/mbuild/lib/moieties/h2o.py
@@ -1,4 +1,5 @@
 """A water molecule."""
+
 import mbuild as mb
 
 
diff --git a/mbuild/lib/moieties/peg.py b/mbuild/lib/moieties/peg.py
index dbf9a1431..47db0a676 100644
--- a/mbuild/lib/moieties/peg.py
+++ b/mbuild/lib/moieties/peg.py
@@ -1,4 +1,5 @@
 """mBuild polyethylene glycol (PEG) monomer moiety."""
+
 __author__ = "jonestj1"
 
 import mbuild as mb
diff --git a/mbuild/lib/moieties/silane.py b/mbuild/lib/moieties/silane.py
index 4d94eae1d..e444d86cb 100644
--- a/mbuild/lib/moieties/silane.py
+++ b/mbuild/lib/moieties/silane.py
@@ -1,4 +1,5 @@
 """A Silane (Si(OH)2) moiety."""
+
 import numpy as np
 
 import mbuild as mb
diff --git a/mbuild/lib/molecules/__init__.py b/mbuild/lib/molecules/__init__.py
index 9f2b8111a..f39893047 100644
--- a/mbuild/lib/molecules/__init__.py
+++ b/mbuild/lib/molecules/__init__.py
@@ -1,4 +1,5 @@
 """Library of molecules for mBuild."""
+
 from mbuild.lib.molecules.ethane import Ethane
 from mbuild.lib.molecules.methane import Methane
 from mbuild.lib.molecules.water import (
diff --git a/mbuild/lib/molecules/ethane.py b/mbuild/lib/molecules/ethane.py
index 733475713..0722208d2 100644
--- a/mbuild/lib/molecules/ethane.py
+++ b/mbuild/lib/molecules/ethane.py
@@ -1,4 +1,5 @@
 """An ethane molecule."""
+
 import mbuild as mb
 from mbuild.lib.moieties import CH3
 
diff --git a/mbuild/lib/molecules/methane.py b/mbuild/lib/molecules/methane.py
index 2e4c688e8..869433858 100644
--- a/mbuild/lib/molecules/methane.py
+++ b/mbuild/lib/molecules/methane.py
@@ -1,4 +1,5 @@
 """A methane molecule."""
+
 import mbuild as mb
 
 
diff --git a/mbuild/lib/molecules/water.py b/mbuild/lib/molecules/water.py
index ff12d2513..071c0e4bb 100644
--- a/mbuild/lib/molecules/water.py
+++ b/mbuild/lib/molecules/water.py
@@ -1,4 +1,5 @@
 """Water molecules with geometries from different models."""
+
 import numpy as np
 
 import mbuild as mb
diff --git a/mbuild/lib/recipes/__init__.py b/mbuild/lib/recipes/__init__.py
index 82ee28ffa..9d4fc9b3a 100644
--- a/mbuild/lib/recipes/__init__.py
+++ b/mbuild/lib/recipes/__init__.py
@@ -1,4 +1,5 @@
 """Library of recipes for mBuild."""
+
 from mbuild.lib.recipes.alkane import Alkane
 from mbuild.lib.recipes.monolayer import Monolayer
 from mbuild.lib.recipes.polymer import Polymer
diff --git a/mbuild/lib/recipes/alkane.py b/mbuild/lib/recipes/alkane.py
index 33509e01b..b0e908403 100644
--- a/mbuild/lib/recipes/alkane.py
+++ b/mbuild/lib/recipes/alkane.py
@@ -1,4 +1,5 @@
 """mBuild recipe for a generic alkane chain."""
+
 import mbuild as mb
 from mbuild.lib.moieties import CH2, CH3
 from mbuild.lib.molecules import Ethane, Methane
diff --git a/mbuild/lib/recipes/monolayer.py b/mbuild/lib/recipes/monolayer.py
index a475d36e3..25ab4a7f3 100644
--- a/mbuild/lib/recipes/monolayer.py
+++ b/mbuild/lib/recipes/monolayer.py
@@ -1,4 +1,5 @@
 """mBuild monolayer recipe."""
+
 from copy import deepcopy
 from warnings import warn
 
diff --git a/mbuild/lib/recipes/polymer.py b/mbuild/lib/recipes/polymer.py
index abf2b34ac..3b1eb623b 100644
--- a/mbuild/lib/recipes/polymer.py
+++ b/mbuild/lib/recipes/polymer.py
@@ -1,4 +1,5 @@
 """Recipe for an mBuild polymer."""
+
 import itertools as it
 
 import numpy as np
diff --git a/mbuild/lib/recipes/silica_interface.py b/mbuild/lib/recipes/silica_interface.py
index b1365c391..4f0149563 100644
--- a/mbuild/lib/recipes/silica_interface.py
+++ b/mbuild/lib/recipes/silica_interface.py
@@ -1,4 +1,5 @@
 """mBuild recipe for a silica interface."""
+
 import math
 import random
 
diff --git a/mbuild/lib/recipes/tiled_compound.py b/mbuild/lib/recipes/tiled_compound.py
index 3f6864b9d..4c228ca69 100644
--- a/mbuild/lib/recipes/tiled_compound.py
+++ b/mbuild/lib/recipes/tiled_compound.py
@@ -1,4 +1,5 @@
 """Module for creating TiledCompounds."""
+
 __all__ = ["TiledCompound"]
 
 import itertools as it
diff --git a/mbuild/lib/recipes/water_box.py b/mbuild/lib/recipes/water_box.py
index 0bec3b4ba..6e15b4940 100644
--- a/mbuild/lib/recipes/water_box.py
+++ b/mbuild/lib/recipes/water_box.py
@@ -1,4 +1,5 @@
 """mBuild recipe for building a water box."""
+
 import itertools
 import math as math
 from collections.abc import Iterable
diff --git a/mbuild/lib/surfaces/__init__.py b/mbuild/lib/surfaces/__init__.py
index 13e26df3c..b7e40474b 100644
--- a/mbuild/lib/surfaces/__init__.py
+++ b/mbuild/lib/surfaces/__init__.py
@@ -1,3 +1,4 @@
 """mBuild surface library."""
+
 from mbuild.lib.surfaces.amorphous_silica_surface import AmorphousSilicaSurface
 from mbuild.lib.surfaces.betacristobalite import Betacristobalite
diff --git a/mbuild/lib/surfaces/amorphous_silica_surface.py b/mbuild/lib/surfaces/amorphous_silica_surface.py
index 7076517fa..646229f3c 100644
--- a/mbuild/lib/surfaces/amorphous_silica_surface.py
+++ b/mbuild/lib/surfaces/amorphous_silica_surface.py
@@ -1,4 +1,5 @@
 """Amorphous silica surface."""
+
 import mbuild as mb
 
 
diff --git a/mbuild/lib/surfaces/betacristobalite.py b/mbuild/lib/surfaces/betacristobalite.py
index c97b11f3c..d78c7246b 100644
--- a/mbuild/lib/surfaces/betacristobalite.py
+++ b/mbuild/lib/surfaces/betacristobalite.py
@@ -1,4 +1,5 @@
 """Beta-cristobalite surface."""
+
 import mbuild as mb
 
 
diff --git a/mbuild/packing.py b/mbuild/packing.py
index 71dd98e4e..0e7e06316 100644
--- a/mbuild/packing.py
+++ b/mbuild/packing.py
@@ -2,6 +2,7 @@
 
 http://leandro.iqm.unicamp.br/m3g/packmol/home.shtml
 """
+
 import os
 import sys
 import tempfile
diff --git a/mbuild/pattern.py b/mbuild/pattern.py
index b5a58181d..8173c0e1a 100644
--- a/mbuild/pattern.py
+++ b/mbuild/pattern.py
@@ -1,4 +1,5 @@
 """mBuild pattern module."""
+
 from itertools import product
 
 import numpy as np
diff --git a/mbuild/port.py b/mbuild/port.py
index fcc77d4dd..31be5ef98 100644
--- a/mbuild/port.py
+++ b/mbuild/port.py
@@ -1,4 +1,5 @@
 """Ports used to facilitate bond formation."""
+
 import itertools
 from warnings import warn
 
diff --git a/mbuild/utils/conversion.py b/mbuild/utils/conversion.py
index cde18c540..bd3c47a97 100644
--- a/mbuild/utils/conversion.py
+++ b/mbuild/utils/conversion.py
@@ -1,4 +1,5 @@
 """mBuild conversion utilities."""
+
 from warnings import warn
 
 import numpy as np
diff --git a/mbuild/utils/decorators.py b/mbuild/utils/decorators.py
index 7da2a3671..b7a75f16f 100644
--- a/mbuild/utils/decorators.py
+++ b/mbuild/utils/decorators.py
@@ -1,4 +1,5 @@
 """Some helpful decorators."""
+
 from functools import wraps
 from warnings import warn
 
diff --git a/mbuild/utils/geometry.py b/mbuild/utils/geometry.py
index 8b558273a..972fd1e3b 100644
--- a/mbuild/utils/geometry.py
+++ b/mbuild/utils/geometry.py
@@ -1,4 +1,5 @@
 """mBuild utilites for geometrical operations."""
+
 import numpy as np
 
 import mbuild as mb
diff --git a/mbuild/utils/io.py b/mbuild/utils/io.py
index 80558a83b..8b233cbf1 100644
--- a/mbuild/utils/io.py
+++ b/mbuild/utils/io.py
@@ -18,6 +18,7 @@
 # License along with MDTraj. If not, see <http://www.gnu.org/licenses/>.
 ##############################################################################
 """
+
 import importlib
 import inspect
 import os
diff --git a/mbuild/utils/jsutils.py b/mbuild/utils/jsutils.py
index 403241b0f..5eeb1066b 100644
--- a/mbuild/utils/jsutils.py
+++ b/mbuild/utils/jsutils.py
@@ -4,6 +4,7 @@
 underlying 'js' libraries by the various notebook visualization libraries used
 by mBuild.
 """
+
 from .io import import_
 
 
diff --git a/mbuild/utils/orderedset.py b/mbuild/utils/orderedset.py
index c83227d56..6ca17aab4 100644
--- a/mbuild/utils/orderedset.py
+++ b/mbuild/utils/orderedset.py
@@ -1,4 +1,5 @@
 """Ordered set module."""
+
 from collections.abc import MutableSet
 
 
diff --git a/mbuild/utils/sorting.py b/mbuild/utils/sorting.py
index c33a45fce..6f775da39 100644
--- a/mbuild/utils/sorting.py
+++ b/mbuild/utils/sorting.py
@@ -1,4 +1,5 @@
 """mBuild sorting utilities."""
+
 import re