Ingredient docstrings and hint types

cellpack/autopack/Analysis.py

@@ -36,7 +36,7 @@
 class Analysis:
     def __init__(
         self,
-        env: Environment,
+        env: Optional[Environment] = None,
         packing_results_path: Optional[Union[Path, str]] = None,
         output_path: Optional[Union[Path, str]] = None,
     ) -> None:
@@ -52,9 +52,7 @@ def __init__(
         output_path
             Path to the output folder for analysis results. If None, uses env.out_folder.
         """
-        self.env = None
-        if env:
-            self.env = env
+        self.env = env
         self.center = [0, 0, 0]
         self.plotly = PlotlyAnalysis()
 

cellpack/autopack/DBRecipeHandler.py

@@ -247,9 +247,9 @@ def replace_region_references(uploader, composition_data):
                     continue
                 for index, item in enumerate(composition_data["regions"][region_name]):
                     if isinstance(item, str):
-                        composition_data["regions"][region_name][index] = (
-                            uploader.comp_to_path_map.get(item)
-                        )
+                        composition_data["regions"][region_name][
+                            index
+                        ] = uploader.comp_to_path_map.get(item)
                     elif isinstance(item, dict):
                         # process nested regions recursively
                         CompositionDoc.replace_region_references(uploader, item)
@@ -299,9 +299,9 @@ 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

@@ -2001,7 +2001,7 @@ def getPointToDrop(
         nbFreePoints: int,
         distance: List[float],
         spacing: float,
-        compId: int,
+        comp_ids: np.ndarray[int],
         vRangeStart: float,
         vThreshStart: float,
     ) -> Tuple[bool, Union[int, float]]:
@@ -2022,8 +2022,8 @@ def getPointToDrop(
             Distance array
         spacing
             Grid spacing
-        compId
-            Compartment ID
+        comp_ids
+            Compartment IDs
         vRangeStart
             Range start value
         vThreshStart
@@ -2039,7 +2039,7 @@ def getPointToDrop(
             free_points,
             nbFreePoints,
             spacing,
-            compId,
+            comp_ids,
             self.freePtsUpdateThreshold,
         )
 
@@ -3530,7 +3530,9 @@ def getRotTransRB(self, node: Any) -> None:
         """
         return None
 
-    def runBullet(self, ingr: Ingredient, simulationTimes: int, runTimeDisplay: bool) -> None:
+    def runBullet(
+        self, ingr: Ingredient, simulationTimes: int, runTimeDisplay: bool
+    ) -> None:
         """
         Run bullet physics simulation for an ingredient.
 

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