[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -10,7 +10,7 @@ ci:
 repos:
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
-  rev: v0.15.22
+  rev: v0.16.6
   hooks:
     # Run the linter.
     - id: ruff
@@ -25,7 +25,7 @@ repos:
     - id: trailing-whitespace
 
 - repo: https://github.com/pycqa/isort
-  rev: 9.0.0b1
+  rev: 9.0.1
   hooks:
     - id: isort
       name: isort (python)

docs/conf.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 #
 # mbuild documentation build configuration file, created by
 # sphinx-quickstart on Wed Oct  1 08:59:12 2014.
@@ -14,8 +13,8 @@
 
 import os
 import sys
+from unittest import mock
 
-import mock
 import sphinx_rtd_theme
 
 # If extensions (or modules to document with autodoc) are in another directory,

docs/sphinxext/notebook_sphinxext.py

@@ -1,6 +1,5 @@
 # Copied from the mdtraj project, commit 3fddb5d  (Mar 10, 2016)
 
-from __future__ import print_function
 
 import os
 import shutil
@@ -12,7 +11,7 @@
 
 
 def _read(wd, name):
-    with open("{}/{}.ipynb".format(wd, name)) as f:
+    with open(f"{wd}/{name}.ipynb") as f:
         notebook = nbformat.read(f, as_version=4)
     return notebook
 
@@ -37,7 +36,7 @@ def export_html(wd, name):
         body, resources = exporter.from_notebook_node(nb)
 
         for fn, data in resources["outputs"].items():
-            with open("{}/{}".format(wd, fn), "wb") as f:
+            with open(f"{wd}/{fn}", "wb") as f:
                 f.write(data)
         return body
     except Exception as e:
@@ -48,7 +47,7 @@ def export_python(wd, name):
     nb = _read(wd, name)
     exporter = PythonExporter()
     body, resources = exporter.from_notebook_node(nb)
-    with open("{}/{}.py".format(wd, name), "w") as f:
+    with open(f"{wd}/{name}.py", "w") as f:
         f.write(body)
 
 
@@ -67,11 +66,11 @@ def run(self):
 
         # get path to notebook
         nb_rel_path = self.arguments[0]
-        nb_abs_path = "{}/../{}".format(setup.confdir, nb_rel_path)
+        nb_abs_path = f"{setup.confdir}/../{nb_rel_path}"
         nb_abs_path = os.path.abspath(nb_abs_path)
         nb_name = os.path.basename(nb_rel_path).split(".")[0]
-        dest_dir = "{}/{}/{}".format(
-            setup.app.builder.outdir, os.path.dirname(nb_rel_path), nb_name
+        dest_dir = (
+            f"{setup.app.builder.outdir}/{os.path.dirname(nb_rel_path)}/{nb_name}"
         )
         fmt = {"wd": dest_dir, "name": nb_name}
 

mbuild/__init__.py

@@ -1,5 +1,4 @@
 # ruff: noqa: F401
-# ruff: noqa: F403
 """mBuild: a hierarchical, component based molecule builder."""
 
 import logging

mbuild/box.py

@@ -11,7 +11,7 @@
 logger = logging.getLogger(__name__)
 
 
-class Box(object):
+class Box:
     """A box representing the bounds of the system.
 
     Parameters

mbuild/coarse_graining.py

@@ -32,7 +32,7 @@ def __init__(self, compound):
             name = "G"
         else:
             name = compound.name + "_PROXY"
-        super(Proxy, self).__init__(name=name)
+        super().__init__(name=name)
 
         self.wrapped = compound
         self.children = None

mbuild/compound.py

@@ -5,9 +5,8 @@
 import os
 import tempfile
 from collections import OrderedDict
-from collections.abc import Iterable
+from collections.abc import Iterable, Sequence
 from copy import deepcopy
-from typing import Sequence
 
 import ele
 import networkx as nx
@@ -26,7 +25,7 @@
 from mbuild.utils.io import import_, run_from_ipython
 from mbuild.utils.jsutils import overwrite_nglview_default
 
-__all__ = ["clone", "Compound", "Particle"]
+__all__ = ["Compound", "Particle", "clone"]
 
 logger = logging.getLogger(__name__)
 
@@ -62,7 +61,7 @@ def clone(existing_compound, clone_of=None, root_container=None):
     return newone
 
 
-class Compound(object):
+class Compound:
     """A building block in the mBuild hierarchy.
 
     Compound is the superclass of all composite building blocks in the mBuild
@@ -157,7 +156,7 @@ def __init__(
         element=None,
         port_particle=False,
     ):
-        super(Compound, self).__init__()
+        super().__init__()
 
         if name:
             if not isinstance(name, str):
@@ -358,13 +357,7 @@ def print_hierarchy(self, print_full=False, index=None, show_tree=True):
             if h["level"] == 0:
                 count = count + 1
             if print_full:
-                if index is None:
-                    tree.create_node(
-                        f"[{h['comp'].name}]: {h['comp'].n_particles} particles, {n_bonds} bonds, {len(h['comp'].children)} children",
-                        f"{h['comp_id']}",
-                        f"{h['parent_id']}",
-                    )
-                elif count == index:
+                if index is None or count == index:
                     tree.create_node(
                         f"[{h['comp'].name}]: {h['comp'].n_particles} particles, {n_bonds} bonds, {len(h['comp'].children)} children",
                         f"{h['comp_id']}",
@@ -1318,7 +1311,7 @@ def box(self, box):
             raise ValueError("Ports cannot have a box")
         # Make sure the box is bigger than the bounding box
         if box is not None:
-            if np.asarray((box.lengths < self.get_boundingbox().lengths)).any():
+            if np.asarray(box.lengths < self.get_boundingbox().lengths).any():
                 logger.warning(
                     "Compound.box.lengths < Compound.boundingbox.lengths. "
                     "There may be particles outside of the defined "

mbuild/conversion.py

@@ -241,7 +241,7 @@ def load_pybel_smiles(
         mymol = pybel.readstring("smi", smiles_or_filename)
         mymolGen = [mymol]
     # Now we treat it as a filename
-    except (OSError, IOError):
+    except OSError:
         mymolGen = pybel.readfile("smi", smiles_or_filename)
 
     for mymol in mymolGen:
@@ -996,7 +996,7 @@ def save(
     formats.json_formats.compound_to_json : Write to a json file
     """
     if os.path.exists(filename) and not overwrite:
-        raise IOError(f"{filename} exists; not overwriting")
+        raise OSError(f"{filename} exists; not overwriting")
     if compound.charge:
         if round(compound.charge, 4) != 0.0:
             logger.info(
@@ -1588,7 +1588,7 @@ def _to_topology(compound, atom_list, chains=None, residues=None):
         # Ensure that both atoms are part of the compound. This becomes an
         # issue if you try to convert a sub-compound to a topology which is
         # bonded to a different subcompound.
-        if all(a in atom_mapping.keys() for a in [atom1, atom2]):
+        if all(a in atom_mapping for a in [atom1, atom2]):
             top.add_bond(atom_mapping[atom1], atom_mapping[atom2])
     return top
 
@@ -1848,7 +1848,7 @@ def _iterate_children(compound, nodes, edges, names_only=False):
     for child in compound.children:
         if names_only:
             unique_name = child.name + "_" + str(id(child))
-            unique_name_parent = child.parent.name + "_" + str((id(child.parent)))
+            unique_name_parent = child.parent.name + "_" + str(id(child.parent))
             nodes.append(unique_name)
             edges.append([unique_name_parent, unique_name])
         else:

mbuild/coordinate_transform.py

@@ -76,7 +76,7 @@ def force_overlap(
                 )
 
 
-class CoordinateTransform(object):
+class CoordinateTransform:
     """Coordinate transforms."""
 
     def __init__(self, T=None):
@@ -105,7 +105,7 @@ def __init__(self, P):
         T[0, 3] = P[0]
         T[1, 3] = P[1]
         T[2, 3] = P[2]
-        super(Translation, self).__init__(T)
+        super().__init__(T)
 
 
 class RotationAroundZ(CoordinateTransform):
@@ -117,7 +117,7 @@ def __init__(self, theta):
         T[0, 1] = -np.sin(theta)
         T[1, 0] = np.sin(theta)
         T[1, 1] = np.cos(theta)
-        super(RotationAroundZ, self).__init__(T)
+        super().__init__(T)
 
 
 class RotationAroundY(CoordinateTransform):
@@ -129,7 +129,7 @@ def __init__(self, theta):
         T[0, 2] = np.sin(theta)
         T[2, 0] = -np.sin(theta)
         T[2, 2] = np.cos(theta)
-        super(RotationAroundY, self).__init__(T)
+        super().__init__(T)
 
 
 class RotationAroundX(CoordinateTransform):
@@ -141,7 +141,7 @@ def __init__(self, theta):
         T[1, 2] = -np.sin(theta)
         T[2, 1] = np.sin(theta)
         T[2, 2] = np.cos(theta)
-        super(RotationAroundX, self).__init__(T)
+        super().__init__(T)
 
 
 class Rotation(CoordinateTransform):
@@ -169,7 +169,7 @@ def __init__(self, theta, around):
             ]
         )
         T[0:3, 0:3] = m
-        super(Rotation, self).__init__(T)
+        super().__init__(T)
 
 
 class ChangeOfBasis(CoordinateTransform):
@@ -186,7 +186,7 @@ def __init__(self, basis, origin=None):
         T = inv(T)
 
         T[0:3, 3:4] = -np.array([origin]).transpose()
-        super(ChangeOfBasis, self).__init__(T)
+        super().__init__(T)
 
 
 class AxisTransform(CoordinateTransform):
@@ -223,7 +223,7 @@ def __init__(self, new_origin=None, point_on_x_axis=None, point_on_xy_plane=None
         # The concatentaion of translation and rotation.
         B_tr = np.dot(B, T_tr)
 
-        super(AxisTransform, self).__init__(B_tr)
+        super().__init__(B_tr)
 
 
 class RigidTransform(CoordinateTransform):
@@ -250,7 +250,7 @@ def __init__(self, A, B):
         H = np.zeros((3, 3), dtype=float)
 
         for i in range(rows):
-            H = H + np.transpose(A[i, :] - centroid_A).dot((B[i, :] - centroid_B))
+            H = H + np.transpose(A[i, :] - centroid_A).dot(B[i, :] - centroid_B)
 
         U, _, V = svd(H)
         V = np.transpose(V)
@@ -275,7 +275,7 @@ def __init__(self, A, B):
 
         T = C_B.dot(R_new).dot(C_A)
 
-        super(RigidTransform, self).__init__(T)
+        super().__init__(T)
 
 
 def unit_vector(v):