[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

cmeutils/visualize.py

@@ -17,17 +17,17 @@ def __init__(
         metal=0,
         view_axis=(1, 0, 0),
         height=10,
-        device=fresnel.Device()
+        device=fresnel.Device(),
     ):
         self.scene = fresnel.Scene()
         self.gsd_file = gsd_file
         with gsd.hoomd.open(gsd_file) as traj:
             self._n_frames = len(traj)
         self._unwrap_positions = False
         self._snapshot = None
-        self._frame = 0 
+        self._frame = 0
         self.frame = frame
-        self._height = height 
+        self._height = height
         self._color_dict = color_dict
         self._diameter_scale = diameter_scale
         self._device = device
@@ -46,9 +46,7 @@ def frame(self):
     @frame.setter
     def frame(self, frame):
         if frame > self._n_frames - 1:
-            raise ValueError(
-                    f"The GSD file only has {self._n_frames} frames."
-            )
+            raise ValueError(f"The GSD file only has {self._n_frames} frames.")
         self._frame = frame
         with gsd.hoomd.open(self.gsd_file) as f:
             self._snapshot = f[frame]
@@ -73,15 +71,15 @@ def color_dict(self):
     def color_dict(self, value):
         if not isinstance(value, dict):
             raise ValueError(
-                    "Pass in a dicitonary with "
-                    "keys of particle type, values of color"
+                "Pass in a dicitonary with "
+                "keys of particle type, values of color"
             )
         self._color_dict = value
 
     def set_type_color(self, particle_type, color):
         if not particle_type in set(self.particle_types):
             raise ValueError(
-                    f"Particle type of {particle_type} is not in the Snapshot"
+                f"Particle type of {particle_type} is not in the Snapshot"
             )
         self._color_dict[particle_type] = color
 
@@ -95,7 +93,7 @@ def unwrap_positions(self, value):
             raise ValueError(
                 "Set to True or False where "
                 "True uses unwrapped particle positions"
-        )
+            )
         self._unwrap_positions = value
 
     @property
@@ -144,7 +142,7 @@ def view_axis(self):
 
     @view_axis.setter
     def view_axis(self, value):
-        #TODO Assert is 1,3  array
+        # TODO Assert is 1,3  array
         self._view_axis = np.asarray(value)
 
     @property
@@ -169,37 +167,35 @@ def camera_position(self):
 
     @property
     def look_at(self):
-        return self.snapshot.configuration.box[:3] * -self.view_axis 
+        return self.snapshot.configuration.box[:3] * -self.view_axis
 
     @property
     def positions(self):
         if self.unwrap_positions:
-           pos = self.snapshot.particles.position
-           imgs = self.snapshot.particles.image
-           box_lengths = self.snapshot.configuration.box[:3]
-           return pos + (imgs * box_lengths)
+            pos = self.snapshot.particles.position
+            imgs = self.snapshot.particles.image
+            box_lengths = self.snapshot.configuration.box[:3]
+            return pos + (imgs * box_lengths)
         else:
             return self.snapshot.particles.position
 
     @property
     def radius(self):
-        return self.snapshot.particles.diameter * self.diameter_scale 
-    
+        return self.snapshot.particles.diameter * self.diameter_scale
+
     @property
     def particle_types(self):
         return np.array(
-                [
-                    self.snapshot.particles.types[i] for
-                    i in self.snapshot.particles.typeid
-                ]
+            [
+                self.snapshot.particles.types[i]
+                for i in self.snapshot.particles.typeid
+            ]
         )
 
     @property
     def colors(self):
         if self.color_dict:
-            return np.array(
-                    [self.color_dict[i] for i in self.particle_types]
-            )
+            return np.array([self.color_dict[i] for i in self.particle_types])
         else:
             return np.array([0.5, 0.25, 0.5])
 
@@ -215,43 +211,44 @@ def geometry(self):
 
     def material(self):
         material = fresnel.material.Material(
-                primitive_color_mix=1,
-                solid=self.solid,
-                roughness=self.roughness,
-                specular=self.specular,
-                spec_trans=self.specular_trans,
-                metal=self.metal
+            primitive_color_mix=1,
+            solid=self.solid,
+            roughness=self.roughness,
+            specular=self.specular,
+            spec_trans=self.specular_trans,
+            metal=self.metal,
         )
         return material
 
     def camera(self):
-        camera=fresnel.camera.Orthographic(
-                position=self.camera_position,
-                look_at=self.look_at,
-                up=self.up,
-                height=self.height
+        camera = fresnel.camera.Orthographic(
+            position=self.camera_position,
+            look_at=self.look_at,
+            up=self.up,
+            height=self.height,
         )
         return camera
 
-
     def view(self, width=300, height=300):
         self.scene.camera = self.camera()
         self.scene.geometry = [self.geometry()]
         return fresnel.preview(scene=self.scene, w=width, h=height)
-    
+
     def path_trace(self, width=300, height=300, samples=64, light_samples=1):
         self.scene.camera = self.camera()
         self.scene.geometry = [self.geometry()]
         return fresnel.pathtrace(
-                scene=self.scene,
-                w=width,
-                h=height,
-                samples=samples,
-                light_samples=light_samples
+            scene=self.scene,
+            w=width,
+            h=height,
+            samples=samples,
+            light_samples=light_samples,
         )
 
     def trace(self, width=300, height=300, n_samples=1):
         self.scene.camera = self.camera()
         self.scene.geometry = [self.geometry()]
-        tracer = fresnel.tracer.Preview(device=self.scene.device, w=width, h=height)
+        tracer = fresnel.tracer.Preview(
+            device=self.scene.device, w=width, h=height
+        )
         return tracer.render(self.scene)