add ruff changes

.github/workflows/pytest.yml

@@ -2,7 +2,6 @@ name: pytest
 
 on:
   push:
-    # Action will run when any changes to these paths are pushed or pr'ed to master
     branches: [ main ]
     paths:
       - flowermd/**
@@ -26,6 +25,7 @@ on:
 
 jobs:
   pytest:
+    if: github.event.pull_request.draft == false
     strategy:
       fail-fast: false
       matrix:

.pre-commit-config.yaml

@@ -1,27 +1,26 @@
 ci:
   autofix_commit_msg: |
     [pre-commit.ci] auto fixes from pre-commit.com hooks
-
     for more information, see https://pre-commit.ci
   autofix_prs: true
   autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
   autoupdate_schedule: weekly
   skip: [ ]
   submodules: false
-
 repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.2 # Ruff version
+    hooks:
+      - id: ruff
+        args: [--line-length=80, --fix, --extend-ignore=E203]
+      - id: ruff-format
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.6.0
     hooks:
       - id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
         exclude: 'flowermd/tests/assets/.* | flowermd/assets/.*'
-  - repo: https://github.com/psf/black
-    rev: 24.4.2
-    hooks:
-      - id: black
-        args: [ --line-length=80 ]
   - repo: https://github.com/pycqa/isort
     rev: 5.13.2
     hooks:
@@ -30,19 +29,3 @@ repos:
         args:
           [ --profile=black, --line-length=80 ]
         exclude: 'flowermd/tests/assets/.* '
-
-  - repo: https://github.com/pycqa/flake8
-    rev: 7.0.0
-    hooks:
-      - id: flake8
-        args:
-          - --max-line-length=80
-          - --extend-ignore=E203
-        exclude: '__init__.py'
-
-  - repo: https://github.com/pycqa/pydocstyle
-    rev: '6.3.0'
-    hooks:
-      - id: pydocstyle
-        exclude: ^(flowermd/tests/|flowermd/internal/|flowermd/utils|setup.py|flowermd/__version__.py|docs/)
-        args: [ --convention=numpy ]

docs/source/conf.py

@@ -10,9 +10,7 @@
 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

@@ -11,9 +11,7 @@ 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:
@@ -22,8 +20,6 @@ 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

@@ -204,8 +204,7 @@ 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):
@@ -214,11 +213,7 @@ 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
@@ -277,9 +272,7 @@ 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.
@@ -290,9 +283,7 @@ 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.
@@ -314,7 +305,7 @@ def _identify_bond_types(self, gmso_molecule):
                 or bond.connection_members[1].name
             )
             bond_connections = [p1_name, p2_name]
-            if not tuple(bond_connections[::-1]) in self.bond_types:
+            if tuple(bond_connections[::-1]) not in self.bond_types:
                 self.bond_types.add(tuple(bond_connections))
 
     def _identify_angle_types(self, gmso_molecule):
@@ -341,7 +332,7 @@ def _identify_angle_types(self, gmso_molecule):
                 or angle.connection_members[2].name
             )
             angle_connections = [p1_name, p2_name, p3_name]
-            if not tuple(angle_connections[::-1]) in self.angle_types:
+            if tuple(angle_connections[::-1]) not in self.angle_types:
                 self.angle_types.add(tuple(angle_connections))
 
     def _identify_dihedral_types(self, gmso_molecule):
@@ -372,7 +363,7 @@ def _identify_dihedral_types(self, gmso_molecule):
                 or dihedral.connection_members[3].name
             )
             dihedral_connections = [p1_name, p2_name, p3_name, p4_name]
-            if not tuple(dihedral_connections[::-1]) in self.dihedral_types:
+            if tuple(dihedral_connections[::-1]) not in self.dihedral_types:
                 self.dihedral_types.add(tuple(dihedral_connections))
 
     def _identify_improper_types(self, gmso_molecule):
@@ -403,7 +394,7 @@ def _identify_improper_types(self, gmso_molecule):
                 or improper.connection_members[3].name
             )
             improper_connections = [p1_name, p2_name, p3_name, p4_name]
-            if not tuple(improper_connections[::-1]) in self.improper_types:
+            if tuple(improper_connections[::-1]) not in self.improper_types:
                 self.improper_types.add(tuple(improper_connections))
 
     def _identify_topology_information(self, gmso_molecule):
@@ -435,9 +426,7 @@ 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

@@ -71,8 +71,7 @@ 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:
@@ -87,9 +86,7 @@ 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 = [
@@ -436,9 +433,7 @@ 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}"
             )
@@ -527,9 +522,7 @@ 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)
 
@@ -551,9 +544,7 @@ 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
@@ -715,9 +706,7 @@ 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,
             },
         )
@@ -849,9 +838,7 @@ 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:
@@ -894,9 +881,7 @@ 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,
             },
         )
@@ -1105,17 +1090,13 @@ 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 = [
@@ -1141,19 +1122,15 @@ 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"])