change max line length back to 80

.pre-commit-config.yaml

@@ -12,8 +12,9 @@ repos:
     rev: v0.4.2 # Ruff version
     hooks:
       - id: ruff
-        args: [--line-length=80, --fix, --extend-ignore=E203]
+        args: [--fix, --extend-ignore=E203]
       - id: ruff-format
+        args: [ --line-length=80 ]
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.6.0
     hooks:

docs/source/conf.py

@@ -10,7 +10,9 @@
 import sys
 
 project = "flowerMD"
-copyright = "2023, Chris Jones, Marjan Albooyeh, Rainier Barrett, Eric Jankowski"
+copyright = (
+    "2023, Chris Jones, Marjan Albooyeh, Rainier Barrett, Eric Jankowski"
+)
 author = "Chris Jones, Marjan Albooyeh, Rainier Barrett, Eric Jankowski"
 
 sys.path.insert(0, os.path.abspath("../.."))

flowermd/base/forcefield.py

@@ -11,7 +11,9 @@ def __init__(self, forcefield_files=None, name=None):
         super(BaseXMLForcefield, self).__init__(
             forcefield_files=forcefield_files, name=name
         )
-        self.gmso_ff = ffutils.FoyerFFs().load(forcefield_files or name).to_gmso_ff()
+        self.gmso_ff = (
+            ffutils.FoyerFFs().load(forcefield_files or name).to_gmso_ff()
+        )
 
 
 class BaseHOOMDForcefield:
@@ -20,6 +22,8 @@ class BaseHOOMDForcefield:
     def __init__(self, hoomd_forces):
         self.hoomd_forces = hoomd_forces
         if hoomd_forces is None:
-            raise NotImplementedError("`hoomd_forces` must be defined in the subclass.")
+            raise NotImplementedError(
+                "`hoomd_forces` must be defined in the subclass."
+            )
         if not isinstance(hoomd_forces, list):
             raise TypeError("`hoomd_forces` must be a list.")

flowermd/base/molecule.py

@@ -204,7 +204,8 @@ def _load(self):
                 return mb.load(self.smiles, smiles=True)
             else:
                 raise MoleculeLoadError(
-                    msg=f"Unable to load the molecule from smiles " f"{self.smiles}."
+                    msg=f"Unable to load the molecule from smiles "
+                    f"{self.smiles}."
                 )
 
     def _align_backbones_z_axis(self, heavy_atoms_only=False):
@@ -213,7 +214,11 @@ def _align_backbones_z_axis(self, heavy_atoms_only=False):
             if heavy_atoms_only:
                 try:
                     positions = np.array(
-                        [p.xyz[0] for p in mol.particles() if p.element.symbol != "H"]
+                        [
+                            p.xyz[0]
+                            for p in mol.particles()
+                            if p.element.symbol != "H"
+                        ]
                     )
                 except AttributeError:
                     positions = mol.xyz
@@ -272,7 +277,9 @@ def _identify_particle_information(self, gmso_molecule):
             ):
                 self.hydrogen_types.append(p_name)
             self.particle_typeid.append(self.particle_types.index(p_name))
-            self.particle_charge.append(site.charge.to_value() if site.charge else 0)
+            self.particle_charge.append(
+                site.charge.to_value() if site.charge else 0
+            )
 
     def _identify_pairs(self, particle_types):
         """Identify all unique particle pairs from the particle types.
@@ -283,7 +290,9 @@ def _identify_pairs(self, particle_types):
             List of all particle types.
 
         """
-        self.pairs = set(itertools.combinations_with_replacement(particle_types, 2))
+        self.pairs = set(
+            itertools.combinations_with_replacement(particle_types, 2)
+        )
 
     def _identify_bond_types(self, gmso_molecule):
         """Identify all unique bond types from the GMSO topology.
@@ -426,7 +435,9 @@ def _validate_force_field(self):
             # Update topology information from typed gmso after applying ff.
             self._identify_topology_information(self.gmso_molecule)
         elif isinstance(self.force_field, BaseHOOMDForcefield):
-            _validate_hoomd_ff(self.force_field.hoomd_forces, self.topology_information)
+            _validate_hoomd_ff(
+                self.force_field.hoomd_forces, self.topology_information
+            )
         elif isinstance(self.force_field, List):
             _validate_hoomd_ff(self.force_field, self.topology_information)
         else:

flowermd/base/simulation.py

@@ -71,7 +71,8 @@ def __init__(
     ):
         if not isinstance(forcefield, Iterable) or isinstance(forcefield, str):
             raise ValueError(
-                "forcefield must be a sequence of " "hoomd.md.force.Force objects."
+                "forcefield must be a sequence of "
+                "hoomd.md.force.Force objects."
             )
         else:
             for obj in forcefield:
@@ -86,7 +87,9 @@ def __init__(
         self.gsd_write_freq = int(gsd_write_freq)
         self.maximum_write_buffer_size = gsd_max_buffer_size
         self.log_write_freq = int(log_write_freq)
-        self._std_out_freq = int((self.gsd_write_freq + self.log_write_freq) / 2)
+        self._std_out_freq = int(
+            (self.gsd_write_freq + self.log_write_freq) / 2
+        )
         self.gsd_file_name = gsd_file_name
         self.log_file_name = log_file_name
         self.log_quantities = [
@@ -433,7 +436,9 @@ def thermostat(self, thermostat):
         thermostat : flowermd.utils.HOOMDThermostats, required
             The type of thermostat to use.
         """
-        if not issubclass(self._thermostat, hoomd.md.methods.thermostats.Thermostat):
+        if not issubclass(
+            self._thermostat, hoomd.md.methods.thermostats.Thermostat
+        ):
             raise ValueError(
                 f"Invalid thermostat. Please choose from: {HOOMDThermostats}"
             )
@@ -522,7 +527,9 @@ def _initialize_thermostat(self, thermostat_kwargs):
         required_thermostat_kwargs = {}
         for k in inspect.signature(self.thermostat).parameters:
             if k not in thermostat_kwargs.keys():
-                raise ValueError(f"Missing required parameter {k} for thermostat.")
+                raise ValueError(
+                    f"Missing required parameter {k} for thermostat."
+                )
             required_thermostat_kwargs[k] = thermostat_kwargs[k]
         return self.thermostat(**required_thermostat_kwargs)
 
@@ -544,7 +551,9 @@ def set_integrator_method(self, integrator_method, method_kwargs):
         if not self.integrator:  # Integrator and method not yet created
             self.integrator = hoomd.md.Integrator(
                 dt=self.dt,
-                integrate_rotational_dof=(True if self._rigid_constraint else False),
+                integrate_rotational_dof=(
+                    True if self._rigid_constraint else False
+                ),
             )
             if self._rigid_constraint:
                 self.integrator.rigid = self._rigid_constraint
@@ -706,7 +715,9 @@ def run_update_volume(
         self.set_integrator_method(
             integrator_method=hoomd.md.methods.ConstantVolume,
             method_kwargs={
-                "thermostat": self._initialize_thermostat({"kT": kT, "tau": tau_kt}),
+                "thermostat": self._initialize_thermostat(
+                    {"kT": kT, "tau": tau_kt}
+                ),
                 "filter": self.integrate_group,
             },
         )
@@ -838,7 +849,9 @@ def run_NPT(
                 "rescale_all": rescale_all,
                 "gamma": gamma,
                 "filter": self.integrate_group,
-                "thermostat": self._initialize_thermostat({"kT": kT, "tau": tau_kt}),
+                "thermostat": self._initialize_thermostat(
+                    {"kT": kT, "tau": tau_kt}
+                ),
             },
         )
         if thermalize_particles:
@@ -881,7 +894,9 @@ def run_NVT(
         self.set_integrator_method(
             integrator_method=hoomd.md.methods.ConstantVolume,
             method_kwargs={
-                "thermostat": self._initialize_thermostat({"kT": kT, "tau": tau_kt}),
+                "thermostat": self._initialize_thermostat(
+                    {"kT": kT, "tau": tau_kt}
+                ),
                 "filter": self.integrate_group,
             },
         )
@@ -1090,13 +1105,17 @@ def _thermalize_system(self, kT):
                 filter=self.integrate_group, kT=kT.range[0]
             )
         else:
-            self.state.thermalize_particle_momenta(filter=self.integrate_group, kT=kT)
+            self.state.thermalize_particle_momenta(
+                filter=self.integrate_group, kT=kT
+            )
 
     def _lj_force(self):
         """Return the Lennard-Jones pair force."""
         if not self.integrator:
             lj_force = [
-                f for f in self._forcefield if isinstance(f, hoomd.md.pair.pair.LJ)
+                f
+                for f in self._forcefield
+                if isinstance(f, hoomd.md.pair.pair.LJ)
             ][0]
         else:
             lj_force = [
@@ -1122,15 +1141,19 @@ def _create_state(self, initial_state):
             print("Initializing simulation state from a GSD file.")
             self.create_state_from_gsd(initial_state)
         elif isinstance(initial_state, hoomd.snapshot.Snapshot):
-            print("Initializing simulation state from a hoomd.snapshot.Snapshot")
+            print(
+                "Initializing simulation state from a hoomd.snapshot.Snapshot"
+            )
             self.create_state_from_snapshot(initial_state)
         elif isinstance(initial_state, gsd.hoomd.Frame):
             print("Initializing simulation state from a gsd.hoomd.Frame.")
             self.create_state_from_snapshot(initial_state)
 
     def _add_hoomd_writers(self):
         """Create gsd and log writers."""
-        gsd_logger = hoomd.logging.Logger(categories=["scalar", "string", "sequence"])
+        gsd_logger = hoomd.logging.Logger(
+            categories=["scalar", "string", "sequence"]
+        )
         logger = hoomd.logging.Logger(categories=["scalar", "string"])
         gsd_logger.add(self, quantities=["timestep", "tps"])
         logger.add(self, quantities=["timestep", "tps"])