Merge branch 'fix/docs_and_cleanup' of github.com:Loop3D/LoopStructural into fix/docs_and_cleanup

Author: lachlangrose

LoopStructural/datatypes/_bounding_box.py

@@ -326,9 +326,7 @@ def get_value(self, name):
         if iy == -1:
             return self.origin[ix]
 
-        return self.bb[
-            ix,
-        ]
+        return self.bb[ix,]
 
     def __getitem__(self, name):
         if isinstance(name, str):

LoopStructural/interpolators/_finite_difference_interpolator.py

@@ -272,7 +272,12 @@ def add_gradient_constraints(self, w=1.0):
             idc[inside, :] = gi[node_idx[inside, :]]
             inside = np.logical_and(~np.any(idc == -1, axis=1), inside)
 
-            (vertices, T, elements, inside_,) = self.support.get_element_gradient_for_location(
+            (
+                vertices,
+                T,
+                elements,
+                inside_,
+            ) = self.support.get_element_gradient_for_location(
                 points[inside, : self.support.dimension]
             )
             # normalise constraint vector and scale element matrix by this
@@ -335,7 +340,12 @@ def add_norm_constraints(self, w=1.0):
             # calculate unit vector for node gradients
             # this means we are only constraining direction of grad not the
             # magnitude
-            (vertices, T, elements, inside_,) = self.support.get_element_gradient_for_location(
+            (
+                vertices,
+                T,
+                elements,
+                inside_,
+            ) = self.support.get_element_gradient_for_location(
                 points[inside, : self.support.dimension]
             )
             # T*=np.product(self.support.step_vector)
@@ -422,7 +432,12 @@ def add_gradient_orthogonal_constraints(
             vectors[norm > 0, :] /= norm[norm > 0, None]
 
             # normalise element vector to unit vector for dot product
-            (vertices, T, elements, inside_,) = self.support.get_element_gradient_for_location(
+            (
+                vertices,
+                T,
+                elements,
+                inside_,
+            ) = self.support.get_element_gradient_for_location(
                 points[inside, : self.support.dimension]
             )
             T[norm > 0, :, :] /= norm[norm > 0, None, None]

LoopStructural/interpolators/supports/_3d_base_structured.py

@@ -162,9 +162,9 @@ def origin(self, origin):
         length = self.maximum - origin
         length /= self.step_vector
         self._nsteps = np.ceil(length).astype(np.int64)
-        self._nsteps[
-            self._nsteps == 0
-        ] = 3  # need to have a minimum of 3 elements to apply the finite difference mask
+        self._nsteps[self._nsteps == 0] = (
+            3  # need to have a minimum of 3 elements to apply the finite difference mask
+        )
         if np.any(~(self._nsteps > 0)):
             logger.error(
                 f"Cannot resize the interpolation support. The proposed number of steps is {self._nsteps}, these must be all > 0"

LoopStructural/interpolators/supports/_3d_structured_tetra.py

@@ -166,9 +166,9 @@ def _init_face_table(self):
         shared_face_index[:] = -1
         shared_face_index[row.reshape(-1, 3)[:, 0], :] = col.reshape(-1, 3)
 
-        self.shared_elements[
-            np.arange(self.shared_element_relationships.shape[0]), :
-        ] = shared_face_index
+        self.shared_elements[np.arange(self.shared_element_relationships.shape[0]), :] = (
+            shared_face_index
+        )
         # resize
         self.shared_elements = self.shared_elements[: len(self.shared_element_relationships), :]
 

LoopStructural/interpolators/supports/_3d_unstructured_tetra.py

@@ -173,9 +173,9 @@ def _init_face_table(self):
         shared_face_index[:] = -1
         shared_face_index[row.reshape(-1, 3)[:, 0], :] = col.reshape(-1, 3)
 
-        self.shared_elements[
-            np.arange(self.shared_element_relationships.shape[0]), :
-        ] = shared_face_index
+        self.shared_elements[np.arange(self.shared_element_relationships.shape[0]), :] = (
+            shared_face_index
+        )
         # resize
         self.shared_elements = self.shared_elements[: len(self.shared_element_relationships), :]
         # flag = np.zeros(self.elements.shape[0])

LoopStructural/interpolators/supports/_face_table.py

@@ -63,8 +63,8 @@ def _init_face_table(grid):
     shared_face_index = np.zeros((shared_faces.shape[0], grid.dimension), dtype=int)
     shared_face_index[:] = -1
     shared_face_index[row.reshape(-1, grid.dimension)[:, 0], :] = col.reshape(-1, grid.dimension)
-    grid._shared_elements[
-        np.arange(grid.shared_element_relationships.shape[0]), :
-    ] = shared_face_index
+    grid._shared_elements[np.arange(grid.shared_element_relationships.shape[0]), :] = (
+        shared_face_index
+    )
     # resize
     grid._shared_elements = grid.shared_elements[: len(grid.shared_element_relationships), :]

LoopStructural/modelling/core/geological_model.py

@@ -598,12 +598,10 @@ def data(self, data: pd.DataFrame):
                 * self._data.loc[mask, "polarity"].to_numpy()[:, None]
             )
             self._data.drop(["strike", "dip"], axis=1, inplace=True)
-        self._data[
-            ['X', 'Y', 'Z', 'val', 'nx', 'ny', 'nz', 'gx', 'gy', 'gz', 'tx', 'ty', 'tz']
-        ] = self._data[
-            ['X', 'Y', 'Z', 'val', 'nx', 'ny', 'nz', 'gx', 'gy', 'gz', 'tx', 'ty', 'tz']
-        ].astype(
-            float
+        self._data[['X', 'Y', 'Z', 'val', 'nx', 'ny', 'nz', 'gx', 'gy', 'gz', 'tx', 'ty', 'tz']] = (
+            self._data[
+                ['X', 'Y', 'Z', 'val', 'nx', 'ny', 'nz', 'gx', 'gy', 'gz', 'tx', 'ty', 'tz']
+            ].astype(float)
         )
 
     def set_model_data(self, data):

LoopStructural/modelling/input/process_data.py

@@ -299,9 +299,9 @@ def fault_properties(self, fault_properties):
             pts = self.fault_locations.loc[
                 self.fault_locations["feature_name"] == fname, ["X", "Y", "Z"]
             ]
-            fault_properties.loc[
-                fname, ["centreEasting", "centreNorthing", "centreAltitude"]
-            ] = np.nanmean(pts, axis=0)
+            fault_properties.loc[fname, ["centreEasting", "centreNorthing", "centreAltitude"]] = (
+                np.nanmean(pts, axis=0)
+            )
         if (
             "avgNormalEasting" not in fault_properties.columns
             or "avgNormalNorthing" not in fault_properties.columns
@@ -449,9 +449,9 @@ def _stratigraphic_value(self):
         for _name, sg in self.stratigraphic_order:
             value = 0.0  # reset for each supergroup
             if sg[0] not in self.thicknesses or self.thicknesses[sg[0]] <= 0:
-                self.thicknesses[
-                    sg[0]
-                ] = np.inf  # make the top unit infinite as it should extend to the top of the model
+                self.thicknesses[sg[0]] = (
+                    np.inf
+                )  # make the top unit infinite as it should extend to the top of the model
             for g in reversed(
                 sg[:-1]
             ):  # don't add the last unit as we never see the base of this unit.