From bc073e49b54a46306cde328c7fc0b4283e4828d4 Mon Sep 17 00:00:00 2001
From: Rowan Cockett <rowan@3ptscience.com>
Date: Sun, 29 May 2016 18:57:38 -0700
Subject: [PATCH] Updates to docs errors.

---
 SimPEG/EM/FDEM/FieldsFDEM.py  | 20 ++++++++++----------
 SimPEG/Utils/meshutils.py     | 23 ++++++++++++++---------
 docs/_ext/__init__.py         |  1 +
 docs/_ext/environmentSetup.py | 15 +++++++++++++++
 docs/api_Maps.rst             |  6 ++++--
 docs/api_Utils.rst            | 12 +++++++++---
 docs/conf.py                  |  3 +++
 7 files changed, 56 insertions(+), 24 deletions(-)
 create mode 100644 docs/_ext/__init__.py
 create mode 100644 docs/_ext/environmentSetup.py

diff --git a/SimPEG/EM/FDEM/FieldsFDEM.py b/SimPEG/EM/FDEM/FieldsFDEM.py
index 253b9984..c2e4bfa6 100644
--- a/SimPEG/EM/FDEM/FieldsFDEM.py
+++ b/SimPEG/EM/FDEM/FieldsFDEM.py
@@ -165,7 +165,7 @@ class Fields3D_e(Fields):
     Fields object for Problem3D_e.
 
     :param Mesh mesh: mesh
-    :param Survey survey: survey
+    :param SimPEG.EM.FDEM.SurveyFDEM.Survey survey: survey
     """
 
     knownFields = {'eSolution':'E'}
@@ -431,7 +431,7 @@ class Fields3D_b(Fields):
     Fields object for Problem3D_b.
 
     :param Mesh mesh: mesh
-    :param Survey survey: survey
+    :param SimPEG.EM.FDEM.SurveyFDEM.Survey survey: survey
     """
 
     knownFields = {'bSolution':'F'}
@@ -446,8 +446,8 @@ class Fields3D_b(Fields):
                     'h' : ['bSolution','CCV','_h'],
                   }
 
-    def __init__(self,mesh,survey,**kwargs):
-        Fields.__init__(self,mesh,survey,**kwargs)
+    def __init__(self, mesh, survey, **kwargs):
+        Fields.__init__(self, mesh, survey, **kwargs)
 
     def startup(self):
         self.prob = self.survey.prob
@@ -698,7 +698,7 @@ class Fields3D_j(Fields):
     Fields object for Problem3D_j.
 
     :param Mesh mesh: mesh
-    :param Survey survey: survey
+    :param SimPEG.EM.FDEM.SurveyFDEM.Survey survey: survey
     """
 
     knownFields = {'jSolution':'F'}
@@ -713,8 +713,8 @@ class Fields3D_j(Fields):
                     'b' : ['jSolution','CCV','_b'],
                   }
 
-    def __init__(self,mesh,survey,**kwargs):
-        Fields.__init__(self,mesh,survey,**kwargs)
+    def __init__(self, mesh, survey, **kwargs):
+        Fields.__init__(self, mesh, survey, **kwargs)
 
     def startup(self):
         self.prob = self.survey.prob
@@ -993,7 +993,7 @@ class Fields3D_h(Fields):
     Fields object for Problem3D_h.
 
     :param Mesh mesh: mesh
-    :param Survey survey: survey
+    :param SimPEG.EM.FDEM.SurveyFDEM.Survey survey: survey
     """
 
     knownFields = {'hSolution':'E'}
@@ -1008,8 +1008,8 @@ class Fields3D_h(Fields):
                     'b' : ['hSolution','CCV','_b'],
                   }
 
-    def __init__(self,mesh,survey,**kwargs):
-        Fields.__init__(self,mesh,survey,**kwargs)
+    def __init__(self, mesh, survey, **kwargs):
+        Fields.__init__(self, mesh, survey, **kwargs)
 
     def startup(self):
         self.prob = self.survey.prob
diff --git a/SimPEG/Utils/meshutils.py b/SimPEG/Utils/meshutils.py
index eb5d13a1..1415e7b8 100644
--- a/SimPEG/Utils/meshutils.py
+++ b/SimPEG/Utils/meshutils.py
@@ -105,15 +105,20 @@ def closestPoints(mesh, pts, gridLoc='CC'):
 def ExtractCoreMesh(xyzlim, mesh, meshType='tensor'):
     """
         Extracts Core Mesh from Global mesh
-        xyzlim: 2D array [ndim x 2]
-        mesh: SimPEG mesh
-        This function ouputs:
+
+        :param numpy.ndarray xyzlim: 2D array [ndim x 2]
+        :param simpeg.Mesh.BaseMesh mesh: The mesh
+
+        This function ouputs::
+
             - actind: corresponding boolean index from global to core
             - meshcore: core SimPEG mesh
+
         Warning: 1D and 2D has not been tested
+
     """
     from SimPEG import Mesh
-    if mesh.dim ==1:
+    if mesh.dim == 1:
         xyzlim = xyzlim.flatten()
         xmin, xmax = xyzlim[0], xyzlim[1]
 
@@ -125,11 +130,11 @@ def ExtractCoreMesh(xyzlim, mesh, meshType='tensor'):
 
         x0 = [xc[0]-hx[0]*0.5, yc[0]-hy[0]*0.5]
 
-        meshCore = Mesh.TensorMesh([hx, hy] ,x0=x0)
+        meshCore = Mesh.TensorMesh([hx, hy], x0=x0)
 
         actind = (mesh.gridCC[:,0]>xmin) & (mesh.gridCC[:,0]<xmax)
 
-    elif mesh.dim ==2:
+    elif mesh.dim == 2:
         xmin, xmax = xyzlim[0,0], xyzlim[0,1]
         ymin, ymax = xyzlim[1,0], xyzlim[1,1]
 
@@ -144,12 +149,12 @@ def ExtractCoreMesh(xyzlim, mesh, meshType='tensor'):
 
         x0 = [xc[0]-hx[0]*0.5, yc[0]-hy[0]*0.5]
 
-        meshCore = Mesh.TensorMesh([hx, hy] ,x0=x0)
+        meshCore = Mesh.TensorMesh([hx, hy], x0=x0)
 
         actind = (mesh.gridCC[:,0]>xmin) & (mesh.gridCC[:,0]<xmax) \
                & (mesh.gridCC[:,1]>ymin) & (mesh.gridCC[:,1]<ymax) \
 
-    elif mesh.dim==3:
+    elif mesh.dim == 3:
         xmin, xmax = xyzlim[0,0], xyzlim[0,1]
         ymin, ymax = xyzlim[1,0], xyzlim[1,1]
         zmin, zmax = xyzlim[2,0], xyzlim[2,1]
@@ -168,7 +173,7 @@ def ExtractCoreMesh(xyzlim, mesh, meshType='tensor'):
 
         x0 = [xc[0]-hx[0]*0.5, yc[0]-hy[0]*0.5, zc[0]-hz[0]*0.5]
 
-        meshCore = Mesh.TensorMesh([hx, hy, hz] ,x0=x0)
+        meshCore = Mesh.TensorMesh([hx, hy, hz], x0=x0)
 
         actind = (mesh.gridCC[:,0]>xmin) & (mesh.gridCC[:,0]<xmax) \
                & (mesh.gridCC[:,1]>ymin) & (mesh.gridCC[:,1]<ymax) \
diff --git a/docs/_ext/__init__.py b/docs/_ext/__init__.py
new file mode 100644
index 00000000..5dacceb5
--- /dev/null
+++ b/docs/_ext/__init__.py
@@ -0,0 +1 @@
+from environmentSetup import supress_nonlocal_image_warn
diff --git a/docs/_ext/environmentSetup.py b/docs/_ext/environmentSetup.py
new file mode 100644
index 00000000..16296018
--- /dev/null
+++ b/docs/_ext/environmentSetup.py
@@ -0,0 +1,15 @@
+
+def supress_nonlocal_image_warn():
+    import sphinx.environment
+    sphinx.environment.BuildEnvironment.warn_node = _supress_nonlocal_image_warn
+
+def _supress_nonlocal_image_warn(self, msg, node):
+    from docutils.utils import get_source_line
+
+    if not msg.startswith('nonlocal image URI found:'):
+        self._warnfunc(msg, '%s:%s' % get_source_line(node))
+
+
+
+if __name__ == '__main__':
+    checkDependencies()
diff --git a/docs/api_Maps.rst b/docs/api_Maps.rst
index 4b376194..887f42ef 100644
--- a/docs/api_Maps.rst
+++ b/docs/api_Maps.rst
@@ -27,7 +27,8 @@ back to conductivity. This is a relatively trivial example (we are just taking
 the exponential!) but by defining maps we can start to combine and manipulate
 exactly what we think about as our model, \\\(m\\\). In code, this looks like
 
-::
+.. code-block:: python
+    :linenos:
 
     M = Mesh.TensorMesh([100]) # Create a mesh
     expMap = Maps.ExpMap(M)    # Create a mapping
@@ -50,7 +51,8 @@ To do this we will introduce the vertical 1D map (:class:`SimPEG.Maps.SurjectVer
 which does the first part of what we just described. The second part will be
 done by the :class:`SimPEG.Maps.ExpMap` described above.
 
-::
+.. code-block:: python
+    :linenos:
 
     M = Mesh.TensorMesh([7,5])
     v1dMap = Maps.SurjectVertical1D(M)
diff --git a/docs/api_Utils.rst b/docs/api_Utils.rst
index 1bf86516..f051f51a 100644
--- a/docs/api_Utils.rst
+++ b/docs/api_Utils.rst
@@ -21,7 +21,7 @@ Solver Utilities
     :undoc-members:
 
 Curv Utilities
-=============
+==============
 
 .. automodule:: SimPEG.Utils.curvutils
     :members:
@@ -51,7 +51,10 @@ Interpolation Utilities
 Counter Utilities
 =================
 
-::
+
+.. code-block:: python
+    :linenos:
+
     class MyClass(object):
         def __init__(self, url):
             self.counter = Counter()
@@ -69,7 +72,10 @@ Counter Utilities
     for i in range(300): c.MySecondMethod()
     c.counter.summary()
 
-::
+
+
+.. code-block:: text
+    :linenos:
 
     Counters:
       MyClass.MyMethod                        :      100
diff --git a/docs/conf.py b/docs/conf.py
index 45407435..6c03c6ee 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -251,3 +251,6 @@ texinfo_documents = [
 #texinfo_show_urls = 'footnote'
 
 autodoc_member_order = 'bysource'
+
+from _ext import supress_nonlocal_image_warn
+supress_nonlocal_image_warn()