Add stacklevel to warnings

discretize/_extensions/tree_ext.pyx

@@ -869,8 +869,8 @@ cdef class _TreeMesh:
         >>> import discretize
         >>> import matplotlib.pyplot as plt
         >>> import matplotlib.patches as patches
-        >>> tree_mesh = discretize.TreeMesh([32, 32, 32])
-        >>> tree_mesh.max_level
+        >>> mesh = discretize.TreeMesh([32, 32, 32])
+        >>> mesh.max_level
         5
 
         Next we define the bottom points of the prism, its heights, and the level we

discretize/base/base_mesh.py

@@ -172,6 +172,7 @@ def save(self, file_name="mesh.json", verbose=False, **kwargs):
                 "The filename keyword argument has been deprecated, please use file_name. "
                 "This will be removed in discretize 1.0.0",
                 FutureWarning,
+                stacklevel=2,
             )
         f = os.path.abspath(file_name)  # make sure we are working with abs path
         with open(f, "w") as outfile:

discretize/base/base_regular_mesh.py

@@ -529,6 +529,7 @@ def axis_u(self):
             "The axis_u property is deprecated, please access as self.orientation[0]. "
             "This will be removed in discretize 1.0.0.",
             FutureWarning,
+            stacklevel=2,
         )
         return self.orientation[0]
 
@@ -539,6 +540,7 @@ def axis_u(self, value):
             "directly set the self.orientation property. This will be removed in "
             "discretize 1.0.0.",
             FutureWarning,
+            stacklevel=2,
         )
         self.orientation[0] = value
 
@@ -554,6 +556,7 @@ def axis_v(self):
             "The axis_v property is deprecated, please access as self.orientation[1]. "
             "This will be removed in discretize 1.0.0.",
             FutureWarning,
+            stacklevel=2,
         )
         return self.orientation[1]
 
@@ -564,6 +567,7 @@ def axis_v(self, value):
             "directly set the self.orientation property. This will be removed in "
             "discretize 1.0.0.",
             FutureWarning,
+            stacklevel=2,
         )
         value = value / np.linalg.norm(value)
         self.orientation[1] = value
@@ -580,6 +584,7 @@ def axis_w(self):
             "The axis_w property is deprecated, please access as self.orientation[2]. "
             "This will be removed in discretize 1.0.0.",
             FutureWarning,
+            stacklevel=2,
         )
         return self.orientation[2]
 
@@ -590,6 +595,7 @@ def axis_w(self, value):
             "directly set the self.orientation property. This will be removed in "
             "discretize 1.0.0.",
             FutureWarning,
+            stacklevel=2,
         )
         value = value / np.linalg.norm(value)
         self.orientation[2] = value
@@ -872,20 +878,23 @@ def reshape(
                 "The xType keyword argument has been deprecated, please use x_type. "
                 "This will be removed in discretize 1.0.0",
                 FutureWarning,
+                stacklevel=2,
             )
             x_type = kwargs["xType"]
         if "outType" in kwargs:
             warnings.warn(
                 "The outType keyword argument has been deprecated, please use out_type. "
                 "This will be removed in discretize 1.0.0",
                 FutureWarning,
+                stacklevel=2,
             )
             out_type = kwargs["outType"]
         if "format" in kwargs:
             warnings.warn(
                 "The format keyword argument has been deprecated, please use return_format. "
                 "This will be removed in discretize 1.0.0",
                 FutureWarning,
+                stacklevel=2,
             )
             return_format = kwargs["format"]
 
@@ -1039,6 +1048,7 @@ def nCx(self):
         warnings.warn(
             "nCx has been deprecated, please access as mesh.shape_cells[0]",
             FutureWarning,
+            stacklevel=2,
         )
         return self.shape_cells[0]
 
@@ -1058,6 +1068,7 @@ def nCy(self):
         warnings.warn(
             "nCy has been deprecated, please access as mesh.shape_cells[1]",
             FutureWarning,
+            stacklevel=2,
         )
         if self.dim < 2:
             return None
@@ -1079,6 +1090,7 @@ def nCz(self):
         warnings.warn(
             "nCz has been deprecated, please access as mesh.shape_cells[2]",
             FutureWarning,
+            stacklevel=2,
         )
         if self.dim < 3:
             return None
@@ -1099,6 +1111,7 @@ def nNx(self):
         warnings.warn(
             "nNx has been deprecated, please access as mesh.shape_nodes[0]",
             FutureWarning,
+            stacklevel=2,
         )
         return self.shape_nodes[0]
 
@@ -1118,6 +1131,7 @@ def nNy(self):
         warnings.warn(
             "nNy has been deprecated, please access as mesh.shape_nodes[1]",
             FutureWarning,
+            stacklevel=2,
         )
         if self.dim < 2:
             return None
@@ -1139,6 +1153,7 @@ def nNz(self):
         warnings.warn(
             "nNz has been deprecated, please access as mesh.shape_nodes[2]",
             FutureWarning,
+            stacklevel=2,
         )
         if self.dim < 3:
             return None

discretize/base/base_tensor_mesh.py

@@ -661,6 +661,7 @@ def is_inside(self, pts, location_type="nodes", **kwargs):
                 "The locType keyword argument has been deprecated, please use location_type. "
                 "This will be removed in discretize 1.0.0",
                 FutureWarning,
+                stacklevel=2,
             )
             location_type = kwargs["locType"]
         pts = as_array_n_by_dim(pts, self.dim)
@@ -783,13 +784,15 @@ def get_interpolation_matrix(  # NOQA D102
                 "The locType keyword argument has been deprecated, please use location_type. "
                 "This will be removed in discretize 1.0.0",
                 FutureWarning,
+                stacklevel=2,
             )
             location_type = kwargs["locType"]
         if "zerosOutside" in kwargs:
             warnings.warn(
                 "The zerosOutside keyword argument has been deprecated, please use zeros_outside. "
                 "This will be removed in discretize 1.0.0",
                 FutureWarning,
+                stacklevel=2,
             )
             zeros_outside = kwargs["zerosOutside"]
         return self._getInterpolationMat(loc, location_type, zeros_outside)
@@ -993,6 +996,7 @@ def innerProductDeriv(v=None):
                         " You should be supplying a vector. "
                         "Use: sdiag(u)*dMdprop",
                         FutureWarning,
+                        stacklevel=2,
                     )
                     return dMdprop
                 return sdiag(v) * dMdprop
@@ -1015,7 +1019,9 @@ def hx(self):
           please use `mesh.h[0]`.
         """
         warnings.warn(
-            "hx has been deprecated, please access as mesh.h[0]", FutureWarning
+            "hx has been deprecated, please access as mesh.h[0]",
+            FutureWarning,
+            stacklevel=2,
         )
         return self.h[0]
 
@@ -1032,7 +1038,9 @@ def hy(self):
           please use `mesh.h[1]`.
         """
         warnings.warn(
-            "hy has been deprecated, please access as mesh.h[1]", FutureWarning
+            "hy has been deprecated, please access as mesh.h[1]",
+            FutureWarning,
+            stacklevel=2,
         )
         return None if self.dim < 2 else self.h[1]
 
@@ -1049,7 +1057,9 @@ def hz(self):
           please use `mesh.h[2]`.
         """
         warnings.warn(
-            "hz has been deprecated, please access as mesh.h[2]", FutureWarning
+            "hz has been deprecated, please access as mesh.h[2]",
+            FutureWarning,
+            stacklevel=2,
         )
         return None if self.dim < 3 else self.h[2]
 

discretize/cylindrical_mesh.py

@@ -1680,13 +1680,15 @@ def get_interpolation_matrix(
                 "The locType keyword argument has been deprecated, please use location_type. "
                 "This will be removed in discretize 1.0.0",
                 FutureWarning,
+                stacklevel=2,
             )
             location_type = kwargs["locType"]
         if "zerosOutside" in kwargs:
             warnings.warn(
                 "The zerosOutside keyword argument has been deprecated, please use zeros_outside. "
                 "This will be removed in discretize 1.0.0",
                 FutureWarning,
+                stacklevel=2,
             )
             zeros_outside = kwargs["zerosOutside"]
 
@@ -1879,6 +1881,7 @@ def cartesian_grid(self, location_type="cell_centers", theta_shift=None, **kwarg
                 "The locType keyword argument has been deprecated, please use location_type. "
                 "This will be removed in discretize 1.0.0",
                 FutureWarning,
+                stacklevel=2,
             )
             location_type = kwargs["locType"]
         try:
@@ -1923,13 +1926,15 @@ def get_interpolation_matrix_cartesian_mesh(
                 "The locType keyword argument has been deprecated, please use location_type. "
                 "This will be removed in discretize 1.0.0",
                 FutureWarning,
+                stacklevel=2,
             )
             location_type = kwargs["locType"]
         if "locTypeTo" in kwargs:
             warnings.warn(
                 "The locTypeTo keyword argument has been deprecated, please use location_type_to. "
                 "This will be removed in discretize 1.0.0",
                 FutureWarning,
+                stacklevel=2,
             )
             location_type_to = kwargs["locTypeTo"]
 

discretize/mixins/mesh_io.py

@@ -421,6 +421,7 @@ def readUBC(TensorMesh, file_name, directory=""):
             "TensorMesh.readUBC has been deprecated and will be removed in"
             "discretize 1.0.0. please use TensorMesh.read_UBC",
             FutureWarning,
+            stacklevel=2,
         )
         return TensorMesh.read_UBC(file_name, directory)
 
@@ -615,6 +616,7 @@ def readUBC(TreeMesh, file_name, directory=""):
             "TensorMesh.readUBC has been deprecated and will be removed in"
             "discretize 1.0.0. please use TensorMesh.read_UBC",
             FutureWarning,
+            stacklevel=2,
         )
         return TreeMesh.read_UBC(file_name, directory)