Limit line length in formatted documentation examples.

hoomd/data/typeconverter.py

@@ -624,7 +624,9 @@ def to_type_converter(value):
     Example::
 
         # list take a list of tuples of 3 floats each
-        validation = to_type_converter({"str": str, "list": [(float, float, float)]})
+        validation = to_type_converter(
+            {"str": str, "list": [(float, float, float)]}
+        )
     """
     if isinstance(value, tuple):
         return TypeConverterFixedLengthSequence(value)

hoomd/device.py

@@ -217,7 +217,9 @@ def message_filename(self):
 
                 communicator = hoomd.communicator.Communicator(ranks_per_partition=2)
                 filename = f"messages.{communicator.partition}"
-                device = hoomd.device.CPU(communicator=communicator, message_filename=filename)
+                device = hoomd.device.CPU(
+                    communicator=communicator, message_filename=filename
+                )
         """
         return self._message_filename
 

hoomd/filter/custom.py

@@ -48,7 +48,9 @@ def __eq__(self, other):
             def __call__(self, state):
                 with state.cpu_local_snapshot as snap:
                     masses = snap.particles.mass
-                    indices = (masses > self.min_mass) & (masses < self.max_mass)
+                    indices = (masses > self.min_mass) & (
+                        masses < self.max_mass
+                    )
                     return numpy.copy(snap.particles.tag[indices])
 
 

hoomd/hpmc/compute.py

@@ -85,7 +85,9 @@ class FreeVolume(Compute):
 
     Examples::
 
-        fv = hoomd.hpmc.compute.FreeVolume(test_particle_type="B", num_samples=1000)
+        fv = hoomd.hpmc.compute.FreeVolume(
+            test_particle_type="B", num_samples=1000
+        )
 
 
     {inherited}

hoomd/hpmc/integrate.py

@@ -922,7 +922,9 @@ class ConvexSpheropolygon(HPMCIntegrator):
 
     Examples::
 
-        mc = hoomd.hpmc.integrate.ConvexSpheropolygon(default_d=0.3, default_a=0.4)
+        mc = hoomd.hpmc.integrate.ConvexSpheropolygon(
+            default_d=0.3, default_a=0.4
+        )
         mc.shape["A"] = dict(
             vertices=[
                 (-0.5, -0.5),
@@ -1592,7 +1594,9 @@ class Sphinx(HPMCIntegrator):
     Example::
 
         mc = hpmc.integrate.Sphinx(default_d=0.3, default_a=0.4)
-        mc.shape["A"] = dict(centers=[(0, 0, 0), (1, 0, 0)], diameters=[1, 0.25])
+        mc.shape["A"] = dict(
+            centers=[(0, 0, 0), (1, 0, 0)], diameters=[1, 0.25]
+        )
         print("diameters = ", mc.shape["A"]["diameters"])
 
     {inherited}

hoomd/hpmc/pair/lj_gauss.py

@@ -42,7 +42,9 @@ class LJGauss(Pair):
     .. code-block:: python
 
         lj_gauss = hoomd.hpmc.pair.LJGauss()
-        lj_gauss.params[("A", "A")] = dict(epsilon=1.0, sigma=0.02, r0=1.6, r_cut=2.5)
+        lj_gauss.params[("A", "A")] = dict(
+            epsilon=1.0, sigma=0.02, r0=1.6, r_cut=2.5
+        )
         simulation.operations.integrator.pair_potentials = [lj_gauss]
 
     {inherited}

hoomd/md/methods/methods.py

@@ -823,7 +823,9 @@ class Langevin(Method):
 
             .. code-block:: python
 
-                langevin.kT = hoomd.variant.Ramp(A=2.0, B=1.0, t_start=0, t_ramp=1_000_000)
+                langevin.kT = hoomd.variant.Ramp(
+                    A=2.0, B=1.0, t_start=0, t_ramp=1_000_000
+                )
 
         tally_reservoir_energy (bool): When True, track the energy exchange
             between the thermal reservoir and the particles.
@@ -1050,7 +1052,9 @@ class Brownian(Method):
 
             .. code-block:: python
 
-                brownian.kT = hoomd.variant.Ramp(A=2.0, B=1.0, t_start=0, t_ramp=1_000_000)
+                brownian.kT = hoomd.variant.Ramp(
+                    A=2.0, B=1.0, t_start=0, t_ramp=1_000_000
+                )
 
         gamma (TypeParameter[ ``particle type``, `float` ]): The drag
             coefficient for each particle type
@@ -1193,7 +1197,9 @@ class OverdampedViscous(Method):
 
     .. code-block:: python
 
-        overdamped_viscous = hoomd.md.methods.OverdampedViscous(filter=hoomd.filter.All())
+        overdamped_viscous = hoomd.md.methods.OverdampedViscous(
+            filter=hoomd.filter.All()
+        )
         simulation.operations.integrator.methods = [overdamped_viscous]
 
     {inherited}

hoomd/md/methods/thermostats.py

@@ -23,7 +23,9 @@
 
     .. code-block:: python
 
-        simulation.state.thermalize_particle_momenta(filter=hoomd.filter.All(), kT=1.5)
+        simulation.state.thermalize_particle_momenta(
+            filter=hoomd.filter.All(), kT=1.5
+        )
 
 .. invisible-code-block: python
 
@@ -382,7 +384,9 @@ class Berendsen(Thermostat):
 
             .. code-block:: python
 
-                berendsen.kT = hoomd.variant.Ramp(A=1.0, B=2.0, t_start=0, t_ramp=1_000_000)
+                berendsen.kT = hoomd.variant.Ramp(
+                    A=1.0, B=2.0, t_start=0, t_ramp=1_000_000
+                )
 
         tau (float): Time constant of thermostat. :math:`[time]`
     """

hoomd/md/minimize/fire.py

@@ -125,7 +125,9 @@ class FIRE(_DynamicIntegrator):
 
         fire = md.minimize.FIRE(dt=0.05)
         fire.methods.append(
-            md.methods.ConstantPressure(hoomd.filter.All(), S=1, tauS=1, couple="none")
+            md.methods.ConstantPressure(
+                hoomd.filter.All(), S=1, tauS=1, couple="none"
+            )
         )
         sim.operations.integrator = fire
         while not (fire.converged):

hoomd/md/pair/aniso.py

@@ -809,7 +809,9 @@ class PatchyLJ(Patchy):
         lj_params = dict(epsilon=1, sigma=1)
         envelope_params = dict(alpha=math.pi / 2, omega=20)
 
-        patchylj = hoomd.md.pair.aniso.PatchyLJ(nlist=neighbor_list, default_r_cut=3.0)
+        patchylj = hoomd.md.pair.aniso.PatchyLJ(
+            nlist=neighbor_list, default_r_cut=3.0
+        )
         patchylj.params[("A", "A")] = dict(
             pair_params=lj_params,
             envelope_params=envelope_params,
@@ -925,7 +927,9 @@ class PatchyExpandedLJ(Patchy):
         lj_params = dict(epsilon=1, sigma=1)
         envelope_params = dict(alpha=math.pi / 2, omega=20)
 
-        patchylj = hoomd.md.pair.aniso.PatchyLJ(nlist=neighbor_list, default_r_cut=3.0)
+        patchylj = hoomd.md.pair.aniso.PatchyLJ(
+            nlist=neighbor_list, default_r_cut=3.0
+        )
         patchylj.params[("A", "A")] = dict(
             pair_params=lj_params,
             envelope_params=envelope_params,
@@ -1114,7 +1118,9 @@ class PatchyMie(Patchy):
         mie_params = dict(epsilon=1, sigma=1, n=15, m=10)
         envelope_params = dict(alpha=math.pi / 3, omega=20)
 
-        patchy_mie = hoomd.md.pair.aniso.PatchyMie(nlist=neighbor_list, default_r_cut=3.0)
+        patchy_mie = hoomd.md.pair.aniso.PatchyMie(
+            nlist=neighbor_list, default_r_cut=3.0
+        )
         patchy_mie.params[("A", "A")] = dict(
             pair_params=mie_params,
             envelope_params=envelope_params,

hoomd/md/pair/pair.py

@@ -353,7 +353,9 @@ class ExpandedGaussian(Pair):
 
         nl = nlist.Cell()
         expanded_gauss = pair.ExpandedGaussian(default_r_cut=3.0, nlist=nl)
-        expanded_gauss.params[("A", "A")] = dict(epsilon=1.0, sigma=1.0, delta=0.5)
+        expanded_gauss.params[("A", "A")] = dict(
+            epsilon=1.0, sigma=1.0, delta=0.5
+        )
         expanded_gauss.r_cut[("A", "B")] = 3.0
 
     {inherited}
@@ -417,7 +419,9 @@ class ExpandedLJ(Pair):
         nl = nlist.Cell()
         expanded_lj = pair.ExpandedLJ(default_r_cut=3.0, nlist=nl)
         expanded_lj.params[("A", "A")] = dict(epsilon=1.0, sigma=1.0, delta=1.0)
-        expanded_lj.params[("A", "B")] = dict(epsilon=2.0, sigma=1.0, delta=0.75)
+        expanded_lj.params[("A", "B")] = dict(
+            epsilon=2.0, sigma=1.0, delta=0.75
+        )
         expanded_lj.params[("B", "B")] = dict(epsilon=1.0, sigma=1.0, delta=0.5)
 
     {inherited}
@@ -1428,7 +1432,9 @@ class ReactionField(Pair):
         nl = nlist.Cell()
         reaction_field = pair.reaction_field(nl, default_r_cut=3.0)
         reaction_field.params[("A", "B")] = dict(epsilon=1.0, eps_rf=1.0)
-        reaction_field.params[("B", "B")] = dict(epsilon=1.0, eps_rf=0.0, use_charge=True)
+        reaction_field.params[("B", "B")] = dict(
+            epsilon=1.0, eps_rf=0.0, use_charge=True
+        )
 
     {inherited}
 

hoomd/md/update.py

@@ -41,7 +41,9 @@ class ZeroMomentum(Updater):
 
     Examples::
 
-        zero_momentum = hoomd.md.update.ZeroMomentum(hoomd.trigger.Periodic(100))
+        zero_momentum = hoomd.md.update.ZeroMomentum(
+            hoomd.trigger.Periodic(100)
+        )
     """
 
     __doc__ += Updater._doc_inherited

hoomd/mpcd/collide.py

@@ -198,7 +198,9 @@ class AndersenThermostat(CollisionMethod):
 
     .. code-block:: python
 
-        andersen_thermostat = hoomd.mpcd.collide.AndersenThermostat(period=1, kT=1.0)
+        andersen_thermostat = hoomd.mpcd.collide.AndersenThermostat(
+            period=1, kT=1.0
+        )
         simulation.operations.integrator.collision_method = andersen_thermostat
 
     Collision including embedded particles.
@@ -315,7 +317,9 @@ class StochasticRotationDynamics(CollisionMethod):
 
     .. code-block:: python
 
-        srd = hoomd.mpcd.collide.StochasticRotationDynamics(period=1, angle=130, kT=1.0)
+        srd = hoomd.mpcd.collide.StochasticRotationDynamics(
+            period=1, angle=130, kT=1.0
+        )
         simulation.operations.integrator.collision_method = srd
 
     Collision including embedded particles.

hoomd/mpcd/force.py

@@ -193,7 +193,9 @@ class SineForce(BodyForce):
     .. code-block:: python
 
         Ly = simulation.state.box.Ly
-        force = hoomd.mpcd.force.SineForce(amplitude=1.0, wavenumber=2 * numpy.pi / Ly)
+        force = hoomd.mpcd.force.SineForce(
+            amplitude=1.0, wavenumber=2 * numpy.pi / Ly
+        )
         stream = hoomd.mpcd.stream.Bulk(period=1, mpcd_particle_force=force)
         simulation.operations.integrator.streaming_method = stream
 

hoomd/mpcd/geometry.py

@@ -322,15 +322,19 @@ class ParallelPlates(Geometry):
 
     .. code-block:: python
 
-        plates = hoomd.mpcd.geometry.ParallelPlates(separation=6.0, no_slip=False)
+        plates = hoomd.mpcd.geometry.ParallelPlates(
+            separation=6.0, no_slip=False
+        )
         stream = hoomd.mpcd.stream.BounceBack(period=1, geometry=plates)
         simulation.operations.integrator.streaming_method = stream
 
     Moving parallel plates.
 
     .. code-block:: python
 
-        plates = hoomd.mpcd.geometry.ParallelPlates(separation=6.0, speed=1.0, no_slip=True)
+        plates = hoomd.mpcd.geometry.ParallelPlates(
+            separation=6.0, speed=1.0, no_slip=True
+        )
         stream = hoomd.mpcd.stream.BounceBack(period=1, geometry=plates)
         simulation.operations.integrator.streaming_method = stream
 

hoomd/mpcd/integrate.py

@@ -89,7 +89,9 @@ class Integrator(_MDIntegrator):
     .. code-block:: python
 
         stream = hoomd.mpcd.stream.Bulk(period=1)
-        collide = hoomd.mpcd.collide.StochasticRotationDynamics(period=1, angle=130)
+        collide = hoomd.mpcd.collide.StochasticRotationDynamics(
+            period=1, angle=130
+        )
         integrator = hoomd.mpcd.Integrator(
             dt=0.1,
             streaming_method=stream,
@@ -111,7 +113,9 @@ class Integrator(_MDIntegrator):
             angle=130,
             embedded_particles=hoomd.filter.All(),
         )
-        solute_method = hoomd.md.methods.ConstantVolume(filter=collide.embedded_particles)
+        solute_method = hoomd.md.methods.ConstantVolume(
+            filter=collide.embedded_particles
+        )
 
         integrator = hoomd.mpcd.Integrator(
             dt=dt_md,
@@ -130,7 +134,9 @@ class Integrator(_MDIntegrator):
 
         plates = hoomd.mpcd.geometry.ParallelPlates(separation=6.0)
         stream = hoomd.mpcd.stream.BounceBack(period=1, geometry=plates)
-        collide = hoomd.mpcd.collide.StochasticRotationDynamics(period=1, angle=130, kT=1.0)
+        collide = hoomd.mpcd.collide.StochasticRotationDynamics(
+            period=1, angle=130, kT=1.0
+        )
         filler = hoomd.mpcd.fill.GeometryFiller(
             type="A", density=5.0, kT=1.0, geometry=plates
         )

hoomd/mpcd/methods.py

@@ -66,7 +66,9 @@ class BounceBack(Method):
     .. code-block:: python
 
         plates = hoomd.mpcd.geometry.ParallelPlates(separation=6.0)
-        nve = hoomd.mpcd.methods.BounceBack(filter=hoomd.filter.All(), geometry=plates)
+        nve = hoomd.mpcd.methods.BounceBack(
+            filter=hoomd.filter.All(), geometry=plates
+        )
         simulation.operations.integrator.methods.append(nve)
 
     {inherited}

hoomd/mpcd/stream.py

@@ -237,7 +237,9 @@ class BounceBack(StreamingMethod):
 
         stream = hoomd.mpcd.stream.BounceBack(
             period=1,
-            geometry=hoomd.mpcd.geometry.ParallelPlates(separation=6.0, no_slip=True),
+            geometry=hoomd.mpcd.geometry.ParallelPlates(
+                separation=6.0, no_slip=True
+            ),
             mpcd_particle_force=hoomd.mpcd.force.ConstantForce((1, 0, 0)),
         )
         simulation.operations.integrator.streaming_method = stream

hoomd/state.py

@@ -806,7 +806,9 @@ def thermalize_particle_momenta(self, filter, kT):
 
         .. code-block:: python
 
-            simulation.state.thermalize_particle_momenta(filter=hoomd.filter.All(), kT=1.5)
+            simulation.state.thermalize_particle_momenta(
+                filter=hoomd.filter.All(), kT=1.5
+            )
         """
         self._simulation._warn_if_seed_unset()
         group = self._get_group(filter)

hoomd/update/remove_drift.py

@@ -49,7 +49,9 @@ class RemoveDrift(Updater):
 
     .. code-block:: python
 
-        remove_drift = hoomd.update.RemoveDrift(reference_positions=[(0, 0, 0), (1, 0, 0)])
+        remove_drift = hoomd.update.RemoveDrift(
+            reference_positions=[(0, 0, 0), (1, 0, 0)]
+        )
         simulation.operations.updaters.append(remove_drift)
 
     {inherited}

hoomd/variant/scalar.py

@@ -151,7 +151,9 @@ class Ramp(_hoomd.VariantRamp, Variant):
 
     .. code-block:: python
 
-            variant = hoomd.variant.Ramp(A=1.0, B=2.0, t_start=10_000, t_ramp=100_000)
+            variant = hoomd.variant.Ramp(
+                A=1.0, B=2.0, t_start=10_000, t_ramp=100_000
+            )
 
     {inherited}
 
@@ -258,7 +260,9 @@ class Power(_hoomd.VariantPower, Variant):
 
     .. code-block:: python
 
-        variant = hoomd.variant.Power(A=2, B=8, power=1 / 10, t_start=10, t_ramp=20)
+        variant = hoomd.variant.Power(
+            A=2, B=8, power=1 / 10, t_start=10, t_ramp=20
+        )
 
     {inherited}
 

ruff.toml

@@ -46,4 +46,5 @@ convention = "google"
 [format]
 indent-style = "space"
 line-ending = "auto"
+docstring-code-line-length = 72
 docstring-code-format = true