simpeg · jcapriot · Jun 6, 2023 · Jun 6, 2023 · Jun 6, 2023 · Jun 6, 2023
diff --git a/SimPEG/electromagnetics/__init__.py b/SimPEG/electromagnetics/__init__.py
@@ -22,9 +22,9 @@
 .. autosummary::
   :toctree: generated/
 
-  analytics.h[2]AnalyticDipoleT
-  analytics.h[2]AnalyticCentLoopT
-  analytics.h[2]AnalyticDipoleF
+  analytics.hzAnalyticDipoleT
+  analytics.hzAnalyticCentLoopT
+  analytics.hzAnalyticDipoleF
   analytics.getCasingEphiMagDipole
   analytics.getCasingHrMagDipole
   analytics.getCasingHzMagDipole

diff --git a/SimPEG/electromagnetics/analytics/FDEM.py b/SimPEG/electromagnetics/analytics/FDEM.py
@@ -9,25 +9,24 @@ def hzAnalyticDipoleF(r, freq, sigma, secondary=True, mu=mu_0):
     1988, and the example reproduces their Figure 4.2.
 
 
-    .. plot::
-
-        import numpy as np
-        import matplotlib.pyplot as plt
-        from SimPEG import electromagnetics as EM
-        freq = np.logspace(-1, 5, 301)
-        test = EM.analytics.h[2]AnalyticDipoleF(
-                100, freq, 0.01, secondary=False)
-        plt.loglog(freq, test.real, 'C0-', label='Real')
-        plt.loglog(freq, -test.real, 'C0--')
-        plt.loglog(freq, test.imag, 'C1-', label='Imaginary')
-        plt.loglog(freq, -test.imag, 'C1--')
-        plt.title('Response at $r=100$ m')
-        plt.xlim([1e-1, 1e5])
-        plt.ylim([1e-12, 1e-6])
-        plt.xlabel('Frequency (Hz)')
-        plt.ylabel('$H_z$ (A/m)')
-        plt.legend(loc=6)
-        plt.show()
+    Examples
+    --------
+    >>> import matplotlib.pyplot as plt
+    >>> from SimPEG import electromagnetics as em
+    >>> freq = np.logspace(-1, 5, 301)
+    >>> test = em.analytics.hzAnalyticDipoleF(
+    >>>        100, freq, 0.01, secondary=False)
+    >>> plt.loglog(freq, test.real, 'C0-', label='Real')
+    >>> plt.loglog(freq, -test.real, 'C0--')
+    >>> plt.loglog(freq, test.imag, 'C1-', label='Imaginary')
+    >>> plt.loglog(freq, -test.imag, 'C1--')
+    >>> plt.title('Response at $r=100$ m')
+    >>> plt.xlim([1e-1, 1e5])
+    >>> plt.ylim([1e-12, 1e-6])
+    >>> plt.xlabel('Frequency (Hz)')
+    >>> plt.ylabel('$H_z$ (A/m)')
+    >>> plt.legend(loc=6)
+    >>> plt.show()
 
 
     **Reference**

diff --git a/SimPEG/electromagnetics/static/spontaneous_potential/__init__.py b/SimPEG/electromagnetics/static/spontaneous_potential/__init__.py
@@ -21,7 +21,7 @@
 .. autosummary::
   :toctree: generated/
 
-  sources.StreamingPotential
+  sources.StreamingCurrents
 
 Surveys
 =======

diff --git a/SimPEG/fields.py b/SimPEG/fields.py
@@ -6,12 +6,13 @@
 
 class Fields:
     """Fancy Field Storage
-    .. code::python
-        fields = Fields(
-            simulation=simulation, knownFields={"phi": "CC"}
-        )
-        fields[:,'phi'] = phi
-        print(fields[src0,'phi'])
+
+    Examples
+    --------
+    >>> fields = Fields(
+    ...     simulation=simulation, knownFields={"phi": "CC"}
+    ... )
+    >>> fields[:,'phi'] = phi
     """
 
     _dtype = float

diff --git a/SimPEG/potential_fields/gravity/__init__.py b/SimPEG/potential_fields/gravity/__init__.py
@@ -16,7 +16,7 @@
   Simulation3DDifferential
 
 Survey, Sources and Receivers
-============================
+=============================
 
 .. autosummary::
   :toctree: generated/

diff --git a/SimPEG/regularization/__init__.py b/SimPEG/regularization/__init__.py
@@ -164,6 +164,7 @@
 
 .. autosummary::
   :toctree: generated/
+
   CrossReferenceRegularization
 
 Joint Regularizations

diff --git a/SimPEG/regularization/base.py b/SimPEG/regularization/base.py
@@ -403,7 +403,7 @@ class Smallness(BaseRegularization):
     :math:`\mathbf{m_{ref}}` is a reference model,
     :math:`\mathbf{V}` are square root of cell volumes and
     :math:`\mathbf{W}` is a weighting matrix (default Identity). If fixed or
-        free weights are provided, then it is :code:`diag(np.sqrt(weights))`).
+    free weights are provided, then it is :code:`diag(np.sqrt(weights))`).
 
 
     **Optional Inputs**

diff --git a/SimPEG/utils/__init__.py b/SimPEG/utils/__init__.py
@@ -11,15 +11,6 @@
 documentation for many details on items.
 
 
-Coordinates Utility Functions
-=============================
-
-.. autosummary::
-  :toctree: generated/
-
-  rotation_matrix_from_normals
-  rotate_points_from_normals
-
 Counter Utility Functions
 =========================
 
@@ -30,17 +21,6 @@
   count
   timeIt
 
-Curvilinear Utility Functions
-=============================
-
-.. autosummary::
-  :toctree: generated/
-
-  example_curvilinear_grid
-  face_info
-  index_cube
-  volume_tetrahedron
-
 
 IO Utility Functions
 ====================
@@ -71,30 +51,12 @@
 .. autosummary::
   :toctree: generated/
 
-  av
-  av_extrap
   cartesian2spherical
   coterminal
-  ddx
   define_plane_from_points
-  diagEst
   eigenvalue_by_power_iteration
   estimate_diagonal
-  get_subarray
-  kron3
-  ind2sub
-  inverse_2x2_block_diagonal
-  inverse_3x3_block_diagonal
-  inverse_property_tensor
-  make_property_tensor
-  mkvc
-  ndgrid
-  sdiag
-  sdinv
-  speye
   spherical2cartesian
-  spzeros
-  sub2ind
   unique_rows
 
 
@@ -104,9 +66,6 @@
 .. autosummary::
   :toctree: generated/
 
-  closest_points_index
-  extract_core_mesh
-  unpack_widths
   surface2inds
 
 
@@ -157,7 +116,6 @@
 .. autosummary::
   :toctree: generated/
 
-  as_array_n_by_dim
   call_hooks
   check_stoppers
   mem_profile_class
@@ -169,7 +127,6 @@
   deprecate_property
   hook
   print_done
-  printDone
   print_line
   print_stoppers
   print_titles

diff --git a/SimPEG/utils/code_utils.py b/SimPEG/utils/code_utils.py
@@ -1232,21 +1232,31 @@ def validate_active_indices(property_name, index_arr, n_cells):
 #                      DEPRECATIONS
 ###############################################################
 memProfileWrapper = deprecate_function(
-    mem_profile_class, "memProfileWrapper", removal_version="0.18.0"
+    mem_profile_class, "memProfileWrapper", removal_version="0.18.0", future_warn=True
+)
+setKwargs = deprecate_function(
+    set_kwargs, "setKwargs", removal_version="0.18.0", future_warn=True
+)
+printTitles = deprecate_function(
+    print_titles, "printTitles", removal_version="0.18.0", future_warn=True
+)
+printLine = deprecate_function(
+    print_line, "printLine", removal_version="0.18.0", future_warn=True
 )
-setKwargs = deprecate_function(set_kwargs, "setKwargs", removal_version="0.18.0")
-printTitles = deprecate_function(print_titles, "printTitles", removal_version="0.18.0")
-printLine = deprecate_function(print_line, "printLine", removal_version="0.18.0")
 printStoppers = deprecate_function(
-    print_stoppers, "printStoppers", removal_version="0.18.0"
+    print_stoppers, "printStoppers", removal_version="0.18.0", future_warn=True
 )
 checkStoppers = deprecate_function(
-    check_stoppers, "checkStoppers", removal_version="0.18.0"
+    check_stoppers, "checkStoppers", removal_version="0.18.0", future_warn=True
+)
+printDone = deprecate_function(
+    print_done, "printDone", removal_version="0.18.0", future_warn=True
+)
+callHooks = deprecate_function(
+    call_hooks, "callHooks", removal_version="0.18.0", future_warn=True
 )
-printDone = deprecate_function(print_done, "printDone", removal_version="0.18.0")
-callHooks = deprecate_function(call_hooks, "callHooks", removal_version="0.18.0")
 dependentProperty = deprecate_function(
-    dependent_property, "dependentProperty", removal_version="0.18.0"
+    dependent_property, "dependentProperty", removal_version="0.18.0", future_warn=True
 )
 asArray_N_x_Dim = deprecate_function(
     as_array_n_by_dim, "asArray_N_x_Dim", removal_version="0.19.0", future_warn=True

diff --git a/SimPEG/utils/io_utils/io_utils_pf.py b/SimPEG/utils/io_utils/io_utils_pf.py
@@ -387,14 +387,26 @@ def write_gg3d_ubc(filename, data_object):
 
 
 readUBCmagneticsObservations = deprecate_method(
-    read_mag3d_ubc, "readUBCmagneticsObservations", removal_version="0.14.4"
+    read_mag3d_ubc,
+    "readUBCmagneticsObservations",
+    removal_version="0.14.4",
+    future_warn=True,
 )
 writeUBCmagneticsObservations = deprecate_method(
-    write_mag3d_ubc, "writeUBCmagneticsObservations", removal_version="0.14.4"
+    write_mag3d_ubc,
+    "writeUBCmagneticsObservations",
+    removal_version="0.14.4",
+    future_warn=True,
 )
 readUBCgravityObservations = deprecate_method(
-    read_grav3d_ubc, "readUBCgravityObservations", removal_version="0.14.4"
+    read_grav3d_ubc,
+    "readUBCgravityObservations",
+    removal_version="0.14.4",
+    future_warn=True,
 )
 writeUBCgravityObservations = deprecate_method(
-    write_grav3d_ubc, "writeUBCgravityObservations", removal_version="0.14.4"
+    write_grav3d_ubc,
+    "writeUBCgravityObservations",
+    removal_version="0.14.4",
+    future_warn=True,
 )
diff --git a/SimPEG/utils/model_builder.py b/SimPEG/utils/model_builder.py
@@ -517,40 +517,51 @@ def get_indices_polygon(mesh, pts):
 ################################################
 
 
-addBlock = deprecate_function(add_block, "addBlock", removal_version="0.19.0")
+addBlock = deprecate_function(
+    add_block, "addBlock", removal_version="0.19.0", future_warn=True
+)
 
 getIndicesBlock = deprecate_function(
-    get_indices_block, "getIndicesBlock", removal_version="0.19.0"
+    get_indices_block, "getIndicesBlock", removal_version="0.19.0", future_warn=True
 )
 
 defineBlock = deprecate_function(
-    create_block_in_wholespace, "defineBlock", removal_version="0.19.0"
+    create_block_in_wholespace,
+    "defineBlock",
+    removal_version="0.19.0",
+    future_warn=True,
 )
 
 defineEllipse = deprecate_function(
-    create_ellipse_in_wholespace, "defineEllipse", removal_version="0.19.0"
+    create_ellipse_in_wholespace,
+    "defineEllipse",
+    removal_version="0.19.0",
+    future_warn=True,
 )
 
 getIndicesSphere = deprecate_function(
-    get_indices_sphere, "getIndicesSphere", removal_version="0.19.0"
+    get_indices_sphere, "getIndicesSphere", removal_version="0.19.0", future_warn=True
 )
 
 defineTwoLayers = deprecate_function(
-    create_2_layer_model, "defineTwoLayers", removal_version="0.19.0"
+    create_2_layer_model, "defineTwoLayers", removal_version="0.19.0", future_warn=True
 )
 
 layeredModel = deprecate_function(
-    create_layers_model, "layeredModel", removal_version="0.19.0"
+    create_layers_model, "layeredModel", removal_version="0.19.0", future_warn=True
 )
 
 randomModel = deprecate_function(
-    create_random_model, "randomModel", removal_version="0.19.0"
+    create_random_model, "randomModel", removal_version="0.19.0", future_warn=True
 )
 
 polygonInd = deprecate_function(
-    get_indices_polygon, "polygonInd", removal_version="0.19.0"
+    get_indices_polygon, "polygonInd", removal_version="0.19.0", future_warn=True
 )
 
 scalarConductivity = deprecate_function(
-    create_from_function, "scalarConductivity", removal_version="0.19.0"
+    create_from_function,
+    "scalarConductivity",
+    removal_version="0.19.0",
+    future_warn=True,
 )
diff --git a/tutorials/07-fdem/plot_fwd_2_fem_cyl.py b/tutorials/07-fdem/plot_fwd_2_fem_cyl.py
@@ -50,7 +50,7 @@
 #
 # Here we define a x-offset borehole survey that consists of a single vertical line
 # of source-receiver pairs which measred the secondary magnetic flux density
-#  over a range of frequencies.
+# over a range of frequencies.
 #
 
 # Frequencies being predicted (10 Hz to 10000 Hz)