Replace yapf with ruff format.

.pre-commit-config.yaml

@@ -64,22 +64,18 @@ repos:
     - --keep-before=#!
     - --keep-after=.. include
 - repo: https://github.com/kynan/nbstripout
-  rev: 0.7.1
+  rev: 0.8.1
   hooks:
     - id: nbstripout
-- repo: https://github.com/google/yapf
-  rev: 'v0.40.2'
-  hooks:
-  - id: yapf
 - repo: https://github.com/astral-sh/ruff-pre-commit
   rev: 'v0.8.0'
   hooks:
-  # - id: ruff-format  # TODO: enable formatting after all other v5 PRs are merged
-  #   types_or: [python]
+  - id: ruff-format
+    types_or: [python]
   - id: ruff
     types_or: [python]
 - repo: https://github.com/pre-commit/mirrors-clang-format
-  rev: v19.1.1
+  rev: v19.1.4
   hooks:
   - id: clang-format
     types_or: [c, c++, cuda, inc]

example_plugins/pair_plugin/__init__.py

@@ -5,4 +5,4 @@
 
 from hoomd.pair_plugin import pair
 
-__all__ = ['pair']
+__all__ = ["pair"]

example_plugins/pair_plugin/pair.py

@@ -20,9 +20,11 @@ class ExamplePair(pair.Pair):
     _cpp_class_name = "PotentialPairExample"
     _accepted_modes = ("none", "shift", "xplor")
 
-    def __init__(self, nlist, default_r_cut=None, default_r_on=0., mode='none'):
+    def __init__(self, nlist, default_r_cut=None, default_r_on=0.0, mode="none"):
         super().__init__(nlist, default_r_cut, default_r_on, mode)
         params = TypeParameter(
-            'params', 'particle_types',
-            TypeParameterDict(k=float, sigma=float, len_keys=2))
+            "params",
+            "particle_types",
+            TypeParameterDict(k=float, sigma=float, len_keys=2),
+        )
         self._add_typeparam(params)

example_plugins/pair_plugin/pytest/test_example_pair.py

@@ -14,16 +14,15 @@
 
 # Python implementation of the pair force and energy.
 def harm_force_and_energy(dx, k, sigma, r_cut, shift=False):
-
     dr = np.linalg.norm(dx)
 
     if dr >= r_cut:
         return np.array([0.0, 0.0, 0.0], dtype=np.float64), 0.0
 
     f = k * (sigma - dr) * np.array(dx, dtype=np.float64) / dr
-    e = 0.5 * k * (sigma - dr)**2
+    e = 0.5 * k * (sigma - dr) ** 2
     if shift:
-        e -= 0.5 * k * (r_cut - sigma)**2
+        e -= 0.5 * k * (r_cut - sigma) ** 2
 
     return f, e
 
@@ -39,10 +38,9 @@ def harm_force_and_energy(dx, k, sigma, r_cut, shift=False):
 
 
 @pytest.mark.parametrize("distance, k, sigma, mode", testdata)
-def test_force_and_energy_eval(simulation_factory,
-                               two_particle_snapshot_factory, distance, k,
-                               sigma, mode):
-
+def test_force_and_energy_eval(
+    simulation_factory, two_particle_snapshot_factory, distance, k, sigma, mode
+):
     # Build the simulation from the factory fixtures defined in
     # hoomd/conftest.py.
     sim = simulation_factory(two_particle_snapshot_factory(d=distance))
@@ -53,7 +51,8 @@ def test_force_and_energy_eval(simulation_factory,
 
     cell = hoomd.md.nlist.Cell(buffer=0.4)
     example_pair: hoomd.md.pair.Pair = pair_plugin.pair.ExamplePair(
-        cell, default_r_cut=sigma, mode=mode)
+        cell, default_r_cut=sigma, mode=mode
+    )
     example_pair.params[("A", "A")] = dict(k=k, sigma=sigma)
     integrator.forces = [example_pair]
     integrator.methods = [nve]

example_plugins/shape_plugin/__init__.py

@@ -5,4 +5,4 @@
 
 from . import integrate
 
-__all__ = ['integrate']
+__all__ = ["integrate"]

example_plugins/shape_plugin/integrate.py

@@ -20,26 +20,29 @@ class MySphere(hpmc.integrate.HPMCIntegrator):
     _ext_module = _shape_plugin
     _cpp_cls = "IntegratorHPMCMonoMySphere"
 
-    def __init__(self,
-                 default_d=0.1,
-                 default_a=0.1,
-                 translation_move_probability=0.5,
-                 nselect=4,
-                 kT=1.0):
+    def __init__(
+        self,
+        default_d=0.1,
+        default_a=0.1,
+        translation_move_probability=0.5,
+        nselect=4,
+        kT=1.0,
+    ):
         # initialize base class
-        super().__init__(default_d, default_a, translation_move_probability,
-                         nselect, kT)
-
-        typeparam_shape = TypeParameter('shape',
-                                        type_kind='particle_types',
-                                        param_dict=TypeParameterDict(
-                                            radius=float,
-                                            ignore_statistics=False,
-                                            orientable=False,
-                                            len_keys=1))
+        super().__init__(
+            default_d, default_a, translation_move_probability, nselect, kT
+        )
+
+        typeparam_shape = TypeParameter(
+            "shape",
+            type_kind="particle_types",
+            param_dict=TypeParameterDict(
+                radius=float, ignore_statistics=False, orientable=False, len_keys=1
+            ),
+        )
         self._add_typeparam(typeparam_shape)
 
-    @log(category='object', requires_run=True)
+    @log(category="object", requires_run=True)
     def type_shapes(self):
         """list[dict]: Description of shapes in ``type_shapes`` format."""
         return super()._return_type_shapes()

example_plugins/updater_plugin/__init__.py

@@ -5,4 +5,4 @@
 
 from hoomd.updater_plugin import update
 
-__all__ = ['update']
+__all__ = ["update"]

example_plugins/updater_plugin/pytest/test_example_updater.py

@@ -23,7 +23,6 @@
 # Use pytest decorator to automate testing over the sequence of parameters.
 @pytest.mark.parametrize("vel", velocities)
 def test_updater(simulation_factory, one_particle_snapshot_factory, vel):
-
     # `one_particle_snapshot_factory` and `simulation_factory` are pytest
     # fixtures defined in hoomd/conftest.py. These factories automatically
     # handle iterating tests over different CPU and GPU devices.
@@ -34,7 +33,8 @@ def test_updater(simulation_factory, one_particle_snapshot_factory, vel):
 
     # Add our plugin to the simulation.
     updater: operation.Updater = updater_plugin.update.ExampleUpdater(
-        hoomd.trigger.On(sim.timestep))
+        hoomd.trigger.On(sim.timestep)
+    )
     sim.operations.updaters.append(updater)
 
     # Test that the initial velocity matches our input.
@@ -49,6 +49,6 @@ def test_updater(simulation_factory, one_particle_snapshot_factory, vel):
     snap = sim.state.get_snapshot()
     if snap.communicator.rank == 0:
         velocity = snap.particles.velocity[0]
-        np.testing.assert_array_almost_equal(velocity,
-                                             np.array([0.0, 0.0, 0.0]),
-                                             decimal=6)
+        np.testing.assert_array_almost_equal(
+            velocity, np.array([0.0, 0.0, 0.0]), decimal=6
+        )

example_plugins/updater_plugin/update.py

@@ -22,7 +22,9 @@ def _attach_hook(self):
         # initialize the reflected c++ class
         if isinstance(self._simulation.device, hoomd.device.CPU):
             self._cpp_obj = _updater_plugin.ExampleUpdater(
-                self._simulation.state._cpp_sys_def, self.trigger)
+                self._simulation.state._cpp_sys_def, self.trigger
+            )
         else:
             self._cpp_obj = _updater_plugin.ExampleUpdaterGPU(
-                self._simulation.state._cpp_sys_def, self.trigger)
+                self._simulation.state._cpp_sys_def, self.trigger
+            )