formatting

cellpack/autopack/Analysis.py

@@ -755,10 +755,7 @@ def add_ingredient_positions_to_plot(
                 )
                 # plot the sphere
                 if ingr.use_rbsphere:
-                    (
-                        ext_recipe,
-                        pts,
-                    ) = ingr.getInterpolatedSphere(
+                    (ext_recipe, pts,) = ingr.getInterpolatedSphere(
                         seed_ingredient_positions[-i - 1],
                         seed_ingredient_positions[-i],
                     )
@@ -860,9 +857,9 @@ def update_pairwise_distances(
                 ingr.name,
                 ingr2.name,
             ):
-                pairwise_distance_dict[seed_index][f"{ingr.name}_{ingr2.name}"] = (
-                    self.env.calc_pairwise_distances(ingr.name, ingr2.name).tolist()
-                )
+                pairwise_distance_dict[seed_index][
+                    f"{ingr.name}_{ingr2.name}"
+                ] = self.env.calc_pairwise_distances(ingr.name, ingr2.name).tolist()
 
         return pairwise_distance_dict
 

cellpack/autopack/DBRecipeHandler.py

@@ -201,13 +201,13 @@ def resolve_local_regions(self, local_data, recipe_data, db):
                 if not DataDoc.is_key(key_or_dict):
                     obj_item = local_data["regions"][region_name][index]["object"]
                     if DataDoc.is_key(obj_item):
-                        local_data["regions"][region_name][index]["object"] = (
-                            prep_recipe_data["objects"][obj_item]
-                        )
+                        local_data["regions"][region_name][index][
+                            "object"
+                        ] = prep_recipe_data["objects"][obj_item]
                     else:
-                        local_data["regions"][region_name][index]["object"] = (
-                            prep_recipe_data["objects"][obj_item["name"]]
-                        )
+                        local_data["regions"][region_name][index][
+                            "object"
+                        ] = prep_recipe_data["objects"][obj_item["name"]]
                     # replace reference in obj with actual data
                     obj_data = local_data["regions"][region_name][index]["object"]
                     self.resolve_object_data(obj_data, prep_recipe_data)
@@ -362,9 +362,9 @@ def convert_representation(doc, db):
                 and doc_value["packing"] is not None
             ):
                 position_value = doc_value["packing"]["positions"]
-                convert_doc["representations"]["packing"]["positions"] = (
-                    ObjectDoc.convert_positions_in_representation(position_value)
-                )
+                convert_doc["representations"]["packing"][
+                    "positions"
+                ] = ObjectDoc.convert_positions_in_representation(position_value)
         return convert_doc
 
     @staticmethod

cellpack/autopack/Environment.py

@@ -628,10 +628,10 @@ def resolve_gradient_data_objects(self, gradient_data):
         """
         # TODO: check if other modes need to be resolved
         if gradient_data["mode"] == "surface":
-            gradient_data["mode_settings"]["object"] = (
-                self.get_compartment_object_by_name(
-                    gradient_data["mode_settings"]["object"]
-                )
+            gradient_data["mode_settings"][
+                "object"
+            ] = self.get_compartment_object_by_name(
+                gradient_data["mode_settings"]["object"]
             )
         return gradient_data
 
@@ -2567,9 +2567,9 @@ def store_asJson(self, resultfilename=None, indent=True):
         if r:
             self.result_json["exteriorRecipe"] = OrderedDict()
             for ingr in r.ingredients:
-                self.result_json["exteriorRecipe"][ingr.composition_name] = (
-                    self.dropOneIngrJson(ingr, self.result_json["exteriorRecipe"])
-                )
+                self.result_json["exteriorRecipe"][
+                    ingr.composition_name
+                ] = self.dropOneIngrJson(ingr, self.result_json["exteriorRecipe"])
 
         # compartment ingr
         for orga in self.compartments:

cellpack/autopack/GeometryTools.py

@@ -165,7 +165,12 @@ def region_2_integrand(self, theta, rho, d):
 
     def region_2(self, rho, d):
         # require scipy
-        i4 = d**3 / 6.0 * (rho**2 / d**2 - 1) * (pi / 4 - self.region_1_2_theta(rho, d))
+        i4 = (
+            d**3
+            / 6.0
+            * (rho**2 / d**2 - 1)
+            * (pi / 4 - self.region_1_2_theta(rho, d))
+        )
         i3 = (
             d**2
             * rho

cellpack/autopack/Graphics.py

@@ -1523,9 +1523,9 @@ def displayCompartmentsIngredients(self):
                         elif self.vi.host == "dejavu":
                             self.orgaToMasterGeom[ingr] = ingr.mesh
                         elif self.vi.host == "softimage":
-                            self.orgaToMasterGeom[ingr] = (
-                                ingr.mesh
-                            )  # self.getMasterInstance(polygon)
+                            self.orgaToMasterGeom[
+                                ingr
+                            ] = ingr.mesh  # self.getMasterInstance(polygon)
                             # polygon already an instance from a different object\
 
                     j += 1

cellpack/autopack/ingredient/single_cube.py

@@ -366,7 +366,9 @@ def cube_surface_distance(
                     current_distance = numpy.sqrt(dist_x**2 + dist_y**2)
                 else:
                     # vertex is the closest
-                    current_distance = numpy.sqrt(dist_x**2 + dist_y**2 + dist_z**2)
+                    current_distance = numpy.sqrt(
+                        dist_x**2 + dist_y**2 + dist_z**2
+                    )
         return current_distance
 
     def get_signed_distance(

cellpack/autopack/ingredient/single_sphere.py

@@ -188,10 +188,7 @@ def collision_jitter(
                 distance_to_packing_location - radius_of_ing_being_packed
             )
 
-            (
-                insidePoints,
-                newDistPoints,
-            ) = self.get_new_distances_and_inside_points(
+            (insidePoints, newDistPoints,) = self.get_new_distances_and_inside_points(
                 env,
                 jtrans,
                 rotMat,

cellpack/autopack/loaders/recipe_loader.py

@@ -254,9 +254,9 @@ def _load_json(self):
                         ):
                             node = {"include": compartment["from"]}
                             sub_recipe = self._request_sub_recipe(inode=node)
-                            recipe_data["compartments"][compartment["from"]] = (
-                                sub_recipe["compartments"]
-                            )
+                            recipe_data["compartments"][
+                                compartment["from"]
+                            ] = sub_recipe["compartments"]
                         continue
                     compartment_dict = recipe_data["compartments"][cname]
                     rep = None

cellpack/autopack/writers/__init__.py

@@ -292,10 +292,10 @@ def save_Mixed_asJson(
                         "include": ing_filename,
                     }
                 else:
-                    env.jsondic["cytoplasme"]["ingredients"][ingr.composition_name] = (
-                        io_ingr.ingrJsonNode(
-                            ingr, result=result, kwds=kwds, transpose=transpose
-                        )
+                    env.jsondic["cytoplasme"]["ingredients"][
+                        ingr.composition_name
+                    ] = io_ingr.ingrJsonNode(
+                        ingr, result=result, kwds=kwds, transpose=transpose
                     )  # {"name":ingr.composition_name}
                     env.jsondic["cytoplasme"]["ingredients"][ingr.composition_name][
                         "name"