[pre-commit.ci] pre-commit autoupdate (#1165)

pre-commit-ci[bot] · daico007 · web-flow · commit 9d20e3de94f9 · 2024-02-01T10:36:34.000-06:00
* [pre-commit.ci] pre-commit autoupdate updates: - [github.com/psf/black: 23.12.1 → 24.1.1](psf/black@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>
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -1,4 +1,5 @@
 """JSON format."""
+
 import json
 from collections import OrderedDict
 
diff --git 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
@@ -1,4 +1,5 @@
 """CHARMM Par format."""
+
 import warnings
 
 __all__ = ["write_par"]
diff --git 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
@@ -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
@@ -1,4 +1,5 @@
 """XYZ format."""
+
 from warnings import warn
 
 import numpy as np
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -1,4 +1,5 @@
 """CH2 moiety."""
+
 import mbuild as mb
 
 
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -1,4 +1,5 @@
 """Beta-cristobalite surface."""
+
 import mbuild as mb
 
 
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -1,4 +1,5 @@
 """Ordered set module."""
+
 from collections.abc import MutableSet
 
 
diff --git a/mbuild/utils/sorting.py b/mbuild/utils/sorting.py
@@ -1,4 +1,5 @@
 """mBuild sorting utilities."""
+
 import re
 
 

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,5 @@`
`1`	`1`	`"""mBuild: a hierarchical, component based molecule builder."""`
	`2`	`+`
`2`	`3`	`from mbuild.box import Box`
`3`	`4`	`from mbuild.coarse_graining import coarse_grain`
`4`	`5`	`from mbuild.compound import *`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,5 @@`
`1`	`1`	`"""mBuild box module."""`
	`2`	`+`
`2`	`3`	`from warnings import warn`
`3`	`4`
`4`	`5`	`import numpy as np`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,5 @@`
`1`	`1`	`"""Tools for coarse-grained systems."""`
	`2`	`+`
`2`	`3`	`from collections import OrderedDict`
`3`	`4`	`from copy import deepcopy`
`4`	`5`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,5 @@`
`1`	`1`	`"""Module for working with mBuild Compounds."""`
	`2`	`+`
`2`	`3`	`__all__ = ["clone", "Compound", "Particle"]`
`3`	`4`
`4`	`5`	`import itertools`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,5 @@`
`1`	`1`	`"""Module for handling conversions in mBuild."""`
	`2`	`+`
`2`	`3`	`import os`
`3`	`4`	`import sys`
`4`	`5`	`from collections import defaultdict`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,5 @@`
`1`	`1`	`"""Coordinate transformation functions."""`
	`2`	`+`
`2`	`3`	`from warnings import simplefilter, warn`
`3`	`4`
`4`	`5`	`simplefilter("always", DeprecationWarning)`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,5 @@`
`1`	`1`	`"""HOOMD v3 forcefield format."""`
	`2`	`+`
`2`	`3`	`import itertools`
`3`	`4`	`import operator`
`4`	`5`	`import warnings`