Merge pull request #1216 from mosdef-hub/pre-commit-ci-update-config

[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: v0.8.4
+  rev: v0.9.1
   hooks:
     # Run the linter.
     - id: ruff

mbuild/compound.py

@@ -521,7 +521,7 @@ def _particle_mass(particle):
     def mass(self, value):
         if self._contains_only_ports() is False:
             raise MBuildError(
-                "Cannot set the mass of a Compound containing " "children compounds"
+                "Cannot set the mass of a Compound containing children compounds"
             )
 
         value = float(value)
@@ -1081,7 +1081,7 @@ def add_bond(self, particle_pair, bond_order=None):
                 "unspecified",
             ]:
                 raise ValueError(
-                    "Invalid bond_order given. Available bond orders are: " "single",
+                    "Invalid bond_order given. Available bond orders are: single",
                     "double",
                     "triple",
                     "aromatic",
@@ -1239,7 +1239,7 @@ def remove_bond(self, particle_pair):
         bond_vector = particle_pair[0].pos - particle_pair[1].pos
         if np.allclose(bond_vector, np.zeros(3)):
             warn(
-                "Particles {} and {} overlap! Ports will not be added." "".format(
+                "Particles {} and {} overlap! Ports will not be added.".format(
                     *particle_pair
                 )
             )

mbuild/conversion.py

@@ -1782,9 +1782,7 @@ def to_smiles(compound, backend="pybel"):
     if backend == "pybel":
         mol = to_pybel(compound)
 
-        warn(
-            "The bond orders will be guessed using pybel" "OBMol.PerceviedBondOrders()"
-        )
+        warn("The bond orders will be guessed using pybelOBMol.PerceviedBondOrders()")
         mol.OBMol.PerceiveBondOrders()
         smiles_string = mol.write("smi").replace("\t", " ").split(" ")[0]
 

mbuild/formats/cassandramcf.py

@@ -53,7 +53,7 @@ def write_mcf(structure, filename, angle_style, dihedral_style, lj14=None, coul1
     # Only will write MCF for Cassandra-supported options
     if angle_style.casefold() != "fixed" and angle_style.casefold() != "harmonic":
         raise ValueError(
-            "Invalid selection for angle_style. Please choose 'fixed' or " "'harmonic'"
+            "Invalid selection for angle_style. Please choose 'fixed' or 'harmonic'"
         )
 
     if len(structure.urey_bradleys) > 0:
@@ -75,7 +75,7 @@ def write_mcf(structure, filename, angle_style, dihedral_style, lj14=None, coul1
     if dihedral_style.casefold() != "none":
         if len(structure.rb_torsions) > 0 and dihedral_style.casefold() != "opls":
             raise ValueError(
-                "Dihedral style declared as {} but RB torsions " "found.".format(
+                "Dihedral style declared as {} but RB torsions found.".format(
                     dihedral_style
                 )
             )
@@ -131,15 +131,17 @@ def write_mcf(structure, filename, angle_style, dihedral_style, lj14=None, coul1
             else:
                 lj14 = 0.0
                 warnings.warn(
-                    "Unable to infer LJ 1-4 scaling factor. Setting to "
-                    "{:.1f}".format(lj14)
+                    "Unable to infer LJ 1-4 scaling factor. Setting to {:.1f}".format(
+                        lj14
+                    )
                 )
         else:
             lj14 = 0.0
             if len(structure.dihedrals) > 0 or len(structure.rb_torsions) > 0:
                 warnings.warn(
-                    "Unable to infer LJ 1-4 scaling factor. Setting to "
-                    "{:.1f}".format(lj14)
+                    "Unable to infer LJ 1-4 scaling factor. Setting to {:.1f}".format(
+                        lj14
+                    )
                 )
 
     if coul14 < 0.0 or coul14 > 1.0:
@@ -353,8 +355,7 @@ def _write_atom_information(mcf_file, structure, in_ring, IG_CONSTANT_KCAL):
     mcf_file.write("{:d}\n".format(len(structure.atoms)))
     for i in range(len(structure.atoms)):
         mcf_file.write(
-            "{:<4d}  {:<6s}  {:<2s}  {:7.3f}  {:12.8f}  "
-            "{:3s}  {:8.5f}  {:8.5f}".format(
+            "{:<4d}  {:<6s}  {:<2s}  {:7.3f}  {:12.8f}  {:3s}  {:8.5f}  {:8.5f}".format(
                 i + 1,
                 types[i],
                 elements[i],
@@ -422,7 +423,7 @@ def _write_angle_information(mcf_file, structure, angle_style, IG_CONSTANT_KCAL)
         ]
     else:
         raise ValueError(
-            "Only 'fixed' and 'harmonic' angle styles are supported by " "Cassandra"
+            "Only 'fixed' and 'harmonic' angle styles are supported by Cassandra"
         )
 
     header = (
@@ -529,7 +530,7 @@ def _write_dihedral_information(mcf_file, structure, dihedral_style, KCAL_TO_KJ)
                 dihedral_parms = ["" for dihedral in dihedrals]
         else:
             raise ValueError(
-                "Only 'OPLS', 'CHARMM', and 'none' dihedral styles are " "supported."
+                "Only 'OPLS', 'CHARMM', and 'none' dihedral styles are supported."
             )
 
         mcf_file.write("{:d}\n".format(len(dihedrals)))
@@ -539,7 +540,7 @@ def _write_dihedral_information(mcf_file, structure, dihedral_style, KCAL_TO_KJ)
             # The atom order provided in the parmed.Structure
             # is written to the MCF file.
             mcf_file.write(
-                "{:<4d}  {:<4d}  {:<4d}  {:<4d}  {:<4d}" "  {:s}  {:s}\n".format(
+                "{:<4d}  {:<4d}  {:<4d}  {:<4d}  {:<4d}  {:s}  {:s}\n".format(
                     i + 1,
                     dihedral.atom1.idx + 1,
                     dihedral.atom2.idx + 1,
@@ -578,8 +579,7 @@ def _write_improper_information(mcf_file, structure, KCAL_TO_KJ):
     improper_type = "harmonic"
     for i, improper in enumerate(structure.impropers):
         mcf_file.write(
-            "{:<4d}  {:<4d}  {:<4d}  {:<4d}  {:<4d}"
-            "  {:s}  {:8.3f}  {:8.3f}\n".format(
+            "{:<4d}  {:<4d}  {:<4d}  {:<4d}  {:<4d}  {:s}  {:8.3f}  {:8.3f}\n".format(
                 i + 1,
                 improper.atom1.idx + 1,
                 improper.atom2.idx + 1,

mbuild/lib/recipes/polymer.py

@@ -95,8 +95,7 @@ def __init__(self, monomers=None, end_groups=None):
             )
         elif len(self._end_groups) != 2:
             raise ValueError(
-                "Please provide two end groups; "
-                f"you provided {len(self._end_groups)}"
+                f"Please provide two end groups; you provided {len(self._end_groups)}"
             )
         self._port_labels = ["up", "down"]
         self._headtail = [None, None]

mbuild/packing.py

@@ -281,7 +281,7 @@ def fill_box(
                     )
                 if len(compound) != len(compound_ratio):
                     raise ValueError(
-                        "Length of `compound_ratio` must equal length of " "`compound`"
+                        "Length of `compound_ratio` must equal length of `compound`"
                     )
                 prototype_mass = 0
                 for c, r in zip(compound, compound_ratio):
@@ -747,7 +747,7 @@ def fill_sphere(
                     )
                 if len(compound) != len(compound_ratio):
                     raise ValueError(
-                        "Length of `compound_ratio` must equal length of " "`compound`"
+                        "Length of `compound_ratio` must equal length of `compound`"
                     )
                 prototype_mass = 0
                 for c, r in zip(compound, compound_ratio):

mbuild/utils/decorators.py

@@ -96,8 +96,7 @@ def deleter(self, fdel):
             def show_warning_msg(self):
                 if self.warning_msg is not None:
                     warn(
-                        f"Property {fcn.__name__} is deprecated. "
-                        f"{self.warning_msg}",
+                        f"Property {fcn.__name__} is deprecated. {self.warning_msg}",
                         DeprecationWarning,
                     )
                     if not self.always_show:

mbuild/utils/io.py

@@ -208,7 +208,8 @@ def import_(module):
             message = MESSAGES[module]
         except KeyError:
             message = (
-                "The code at {filename}:{line_number} requires the " f"{module} package"
+                "The code at {filename}:{line_number} requires the "
+                f"{module} package"
             )
             raise ImportError(f"No module named {module}")