Merged in docs (pull request #11)

Documentation for SimPEG

SimPEG/BaseMesh.py

@@ -3,31 +3,12 @@ from utils import mkvc
 
 
 class BaseMesh(object):
-    """BaseMesh does all the counting you don't want to do.
+    """
+    BaseMesh does all the counting you don't want to do.
+    BaseMesh should be inherited by meshes with a regular structure.
 
-    x0          origin                    ndarray   (dim, )
-    n           number of cells           ndarray   (dim, )
-    dim         dimension of mesh         int       1, 2, or 3
-
-    nCx         num cells in x dir        int
-    nCy         num cells in y dir        int
-    nCz         num cells in z dir        int
-    nC          total number of cells     int
-
-    nNx         num nodes in x dir        int
-    nNy         num nodes in y dir        int
-    nNz         num nodes in z dir        int
-    nN          total number of nodes     int
-
-    nEx         num edges in x dir        ndarray   [nEx_x, nEx_y, nEx_z]
-    nEy         num edges in y dir        ndarray   [nEy_x, nEy_y, nEy_z]
-    nEz         num edges in z dir        ndarray   [nEz_x, nEz_y, nEz_z]
-    nE          total number of edges     ndarray   (dim, )
-
-    nFx         num faces in x dir        ndarray   [nFx_x, nFx_y, nFx_z]
-    nFy         num faces in y dir        ndarray   [nFy_x, nFy_y, nFy_z]
-    nFz         num faces in z dir        ndarray   [nFz_x, nFz_y, nFz_z]
-    nF          total number of faces     ndarray   (dim, )
+    :param numpy.array,list n: number of cells in each direction (dim, )
+    :param numpy.array,list x0: Origin of the mesh (dim, )
 
     """
     def __init__(self, n, x0=None):
@@ -48,7 +29,12 @@ class BaseMesh(object):
         self._dim = len(n)
 
     def x0():
-        doc = "Origin of the mesh"
+        doc = """
+        Origin of the mesh
+
+        :rtype: numpy.array (dim, )
+        :return: x0
+        """
         fget = lambda self: self._x0
         return locals()
     x0 = property(**x0())
@@ -161,25 +147,45 @@ class BaseMesh(object):
             return switchKernal(x)
 
     def n():
-        doc = "Number of Cells in each dimension (array of integers)"
+        doc = """
+        Number of Cells in each dimension (array of integers)
+
+        :rtype: numpy.array
+        :return: n
+        """
         fget = lambda self: self._n
         return locals()
     n = property(**n())
 
     def dim():
-        doc = "The dimension of the mesh (1, 2, or 3)."
+        doc = """
+        The dimension of the mesh (1, 2, or 3).
+
+        :rtype: int
+        :return: dim
+        """
         fget = lambda self: self._dim
         return locals()
     dim = property(**dim())
 
     def nCx():
-        doc = "Number oc cells in the x direction"
+        doc = """
+        Number of cells in the x direction
+
+        :rtype: int
+        :return: nCx
+        """
         fget = lambda self: self.n[0]
         return locals()
     nCx = property(**nCx())
 
     def nCy():
-        doc = "Number of cells in the y direction"
+        doc = """
+        Number of cells in the y direction
+
+        :rtype: int
+        :return: nCy or None if dim < 2
+        """
 
         def fget(self):
             if self.dim > 1:
@@ -190,7 +196,11 @@ class BaseMesh(object):
     nCy = property(**nCy())
 
     def nCz():
-        doc = "Number of cells in the z direction"
+        doc = """Number of cells in the z direction
+
+        :rtype: int
+        :return: nCz or None if dim < 3
+        """
 
         def fget(self):
             if self.dim > 2:
@@ -201,19 +211,34 @@ class BaseMesh(object):
     nCz = property(**nCz())
 
     def nC():
-        doc = "Total number of cells"
+        doc = """
+        Total number of cells in the model.
+
+        :rtype: int
+        :return: nC
+        """
         fget = lambda self: np.prod(self.n)
         return locals()
     nC = property(**nC())
 
     def nNx():
-        doc = "Number of nodes in the x-direction"
+        doc = """
+        Number of nodes in the x-direction
+
+        :rtype: int
+        :return: nNx
+        """
         fget = lambda self: self.nCx + 1
         return locals()
     nNx = property(**nNx())
 
     def nNy():
-        doc = "Number of noes in the y-direction"
+        doc = """
+        Number of noes in the y-direction
+
+        :rtype: int
+        :return: nNy or None if dim < 2
+        """
 
         def fget(self):
             if self.dim > 1:
@@ -224,7 +249,12 @@ class BaseMesh(object):
     nNy = property(**nNy())
 
     def nNz():
-        doc = "Number of nodes in the z-direction"
+        doc = """
+        Number of nodes in the z-direction
+
+        :rtype: int
+        :return: nNz or None if dim < 3
+        """
 
         def fget(self):
             if self.dim > 2:
@@ -235,19 +265,34 @@ class BaseMesh(object):
     nNz = property(**nNz())
 
     def nN():
-        doc = "Total number of nodes"
+        doc = """
+        Total number of nodes
+
+        :rtype: int
+        :return: nN
+        """
         fget = lambda self: np.prod(self.n + 1)
         return locals()
     nN = property(**nN())
 
     def nEx():
-        doc = "Number of x-edges"
+        doc = """
+        Number of x-edges in each direction
+
+        :rtype: numpy.array (dim, )
+        :return: nEx
+        """
         fget = lambda self: np.array([x for x in [self.nCx, self.nNy, self.nNz] if not x is None])
         return locals()
     nEx = property(**nEx())
 
     def nEy():
-        doc = "Number of y-edges"
+        doc = """
+        Number of y-edges in each direction
+
+        :rtype: numpy.array (dim, )
+        :return: nEy or None if dim < 2
+        """
 
         def fget(self):
             if self.dim > 1:
@@ -258,7 +303,12 @@ class BaseMesh(object):
     nEy = property(**nEy())
 
     def nEz():
-        doc = "Number of z-edges"
+        doc = """
+        Number of z-edges in each direction
+
+        :rtype: numpy.array (dim, )
+        :return: nEz or None if dim < 3
+        """
 
         def fget(self):
             if self.dim > 2:
@@ -269,19 +319,34 @@ class BaseMesh(object):
     nEz = property(**nEz())
 
     def nE():
-        doc = "Total number of edges"
+        doc = """
+        Total number of edges in each direction
+
+        :rtype: numpy.array (dim, )
+        :return: [prod(nEx), prod(nEy), prod(nEz)]
+        """
         fget = lambda self: np.array([np.prod(x) for x in [self.nEx, self.nEy, self.nEz] if not x is None])
         return locals()
     nE = property(**nE())
 
     def nFx():
-        doc = "Number of x-faces"
+        doc = """
+        Number of x-faces in each direction
+
+        :rtype: numpy.array (dim, )
+        :return: nFx
+        """
         fget = lambda self: np.array([x for x in [self.nNx, self.nCy, self.nCz] if not x is None])
         return locals()
     nFx = property(**nFx())
 
     def nFy():
-        doc = "Number of y-faces"
+        doc = """
+        Number of y-faces in each direction
+
+        :rtype: numpy.array (dim, )
+        :return: nFy or None if dim < 2
+        """
 
         def fget(self):
             if self.dim > 1:
@@ -292,7 +357,12 @@ class BaseMesh(object):
     nFy = property(**nFy())
 
     def nFz():
-        doc = "Number of z-faces"
+        doc = """
+        Number of z-faces in each direction
+
+        :rtype: numpy.array (dim, )
+        :return: nFz or None if dim < 3
+        """
 
         def fget(self):
             if self.dim > 2:
@@ -303,13 +373,23 @@ class BaseMesh(object):
     nFz = property(**nFz())
 
     def nF():
-        doc = "Total number of faces in each dimension"
+        doc = """
+        Total number of faces in each direction
+
+        :rtype: numpy.array (dim, )
+        :return: [prod(nFx), prod(nFy), prod(nFz)]
+        """
         fget = lambda self: np.array([np.prod(x) for x in [self.nFx, self.nFy, self.nFz] if not x is None])
         return locals()
     nF = property(**nF())
 
     def normals():
-        doc = "Face Normals"
+        doc = """
+        Face Normals
+
+        :rtype: numpy.array (sum(nF), dim)
+        :return: normals
+        """
 
         def fget(self):
             if self.dim == 2:
@@ -325,7 +405,12 @@ class BaseMesh(object):
     normals = property(**normals())
 
     def tangents():
-        doc = "Edge Tangents"
+        doc = """
+        Edge Tangents
+
+        :rtype: numpy.array (sum(nE), dim)
+        :return: normals
+        """
 
         def fget(self):
             if self.dim == 2:

SimPEG/TensorView.py

@@ -13,7 +13,7 @@ class TensorView(object):
     def __init__(self):
         pass
 
-    def plotImage(self, I, imageType='CC', figNum=1,ax=None,direction='z',numbering=True,annotationColor='w'):
+    def plotImage(self, I, imageType='CC', figNum=1,ax=None,direction='z',numbering=True,annotationColor='w',showIt=False):
         """
         Mesh.plotImage(I)
 
@@ -21,15 +21,23 @@ class TensorView(object):
 
         Input:
 
-            I           - scalar field (np.array)
+        :param numpy.array I: scalar field
 
         Optional Input:
 
-            imageType   - type of image ('CC','N','Fx','Fy','Fz','Ex','Ey','Ez')
-            figNum      - number of figure to plot to
-            ax          - axis to plot to
-            direction   - 3D only. slice dimensions
-            numbering   - 3D only. show numbering of slices
+        :param str imageType: type of image ('CC','N','Fx','Fy','Fz','Ex','Ey','Ez')
+        :param int figNum: number of figure to plot to
+        :param matplotlib.axes.Axes ax: axis to plot to
+        :param str direction: slice dimensions, 3D only ('x', 'y', 'z')
+        :param bool numbering: show numbering of slices, 3D only
+        :param str annotationColor: color of annotation, e.g. 'w', 'k', 'b'
+        :param bool showIt: call plt.show()
+
+        .. plot:: examples/mesh/plot_image_2D.py
+           :include-source:
+
+        .. plot:: examples/mesh/plot_image_3D.py
+           :include-source:
         """
         assert type(I) == np.ndarray, "I must be a numpy array"
         assert type(numbering) == bool, "numbering must be a bool"
@@ -154,6 +162,7 @@ class TensorView(object):
                 gyY = np.c_[gy, gy, gy+np.nan].ravel()
                 ax.plot(gxX, gxY, annotationColor+'-', linewidth=2)
                 ax.plot(gyX, gyY, annotationColor+'-', linewidth=2)
+                ax.axis('tight')
 
                 if numbering:
                     pad = np.sum(self.hx)*0.04
@@ -164,11 +173,18 @@ class TensorView(object):
                                 ax.text((ix+1)*self.vectorNx[-1]-pad,(iy)*self.vectorNy[-1]+pad,
                                          '#%i'%iz,color=annotationColor,verticalalignment='bottom',horizontalalignment='right',size='x-large')
 
-        plt.show()
+        if showIt: plt.show()
         return ph
 
-    def plotGrid(self):
-        """Plot the nodal, cell-centered and staggered grids for 1,2 and 3 dimensions."""
+    def plotGrid(self, showIt=False):
+        """Plot the nodal, cell-centered and staggered grids for 1,2 and 3 dimensions.
+
+        .. plot:: examples/mesh/plot_grid_2D.py
+           :include-source:
+
+        .. plot:: examples/mesh/plot_grid_3D.py
+           :include-source:
+        """
         if self.dim == 1:
             fig = plt.figure(1)
             fig.clf()
@@ -182,7 +198,7 @@ class TensorView(object):
             ax.grid(True)
             ax.hold(False)
             ax.set_xlabel('x1')
-            plt.show()
+            if showIt: plt.show()
         elif self.dim == 2:
             fig = plt.figure(2)
             fig.clf()
@@ -201,7 +217,7 @@ class TensorView(object):
             ax.hold(False)
             ax.set_xlabel('x1')
             ax.set_ylabel('x2')
-            plt.show()
+            if showIt: plt.show()
         elif self.dim == 3:
             fig = plt.figure(3)
             fig.clf()
@@ -230,4 +246,4 @@ class TensorView(object):
             ax.set_xlabel('x1')
             ax.set_ylabel('x2')
             ax.set_zlabel('x3')
-            plt.show()
+            if showIt: plt.show()

docs/Makefile

@@ -0,0 +1,153 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = _build
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	-rm -rf $(BUILDDIR)/*
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/SimPEG.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/SimPEG.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/SimPEG"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/SimPEG"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."

docs/api_BaseMesh.rst

@@ -0,0 +1,8 @@
+.. _api_BaseMesh:
+
+Base Mesh
+*********
+
+.. automodule:: SimPEG.BaseMesh
+    :members:
+    :undoc-members:

docs/api_DiffOperators.rst

@@ -0,0 +1,8 @@
+.. _api_DiffOperators:
+
+Differential Operators
+**********************
+
+.. automodule:: SimPEG.DiffOperators
+    :members:
+    :undoc-members:

docs/api_GaussNewton.rst

@@ -0,0 +1,8 @@
+.. _api_GaussNewton:
+
+Gauss Newton
+************
+
+.. automodule:: SimPEG.GaussNewton
+    :members:
+    :undoc-members:

docs/api_InnerProducts.rst

@@ -0,0 +1,8 @@
+.. _api_InnerProducts:
+
+Inner Products
+**************
+
+.. automodule:: SimPEG.InnerProducts
+    :members:
+    :undoc-members:

docs/api_LOMView.rst

@@ -0,0 +1,8 @@
+.. _api_LOMView:
+
+LOM View
+***********
+
+.. automodule:: SimPEG.LOMView
+    :members:
+    :undoc-members:

docs/api_LogicallyOrthogonalMesh.rst

@@ -0,0 +1,8 @@
+.. _api_LogicallyOrthogonalMesh:
+
+Logically Orthogonal Mesh
+*************************
+
+.. automodule:: SimPEG.LogicallyOrthogonalMesh
+    :members:
+    :undoc-members:

docs/api_TensorMesh.rst

@@ -0,0 +1,8 @@
+.. _api_TensorMesh:
+
+Tensor Mesh
+***********
+
+.. automodule:: SimPEG.TensorMesh
+    :members:
+    :undoc-members:

docs/api_TensorView.rst

@@ -0,0 +1,8 @@
+.. _api_TensorView:
+
+Tensor View
+***********
+
+.. automodule:: SimPEG.TensorView
+    :members:
+    :undoc-members:

docs/conf.py

@@ -0,0 +1,244 @@
+# -*- coding: utf-8 -*-
+#
+# SimPEG documentation build configuration file, created by
+# sphinx-quickstart on Fri Aug 30 18:42:44 2013.
+#
+# This file is execfile()d with the current directory set to its containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys, os
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#sys.path.insert(0, os.path.abspath('.'))
+
+sys.path.append('../')
+
+# -- General configuration -----------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = ['sphinx.ext.todo', 'sphinx.ext.mathjax', 'sphinx.ext.viewcode', 'sphinx.ext.autodoc', 'matplotlib.sphinxext.plot_directive']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'SimPEG'
+copyright = u'2013, SimPEG Developers'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = '0.0.1'
+# The full version, including alpha/beta/rc tags.
+release = '0.0.1'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = ['_build']
+
+# The reST default role (used for this markup: `text`) to use for all documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+
+# -- Options for HTML output ---------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+html_theme = 'default'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = None
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'SimPEGdoc'
+
+
+# -- Options for LaTeX output --------------------------------------------------
+
+latex_elements = {
+# The paper size ('letterpaper' or 'a4paper').
+#'papersize': 'letterpaper',
+
+# The font size ('10pt', '11pt' or '12pt').
+#'pointsize': '10pt',
+
+# Additional stuff for the LaTeX preamble.
+#'preamble': '',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass [howto/manual]).
+latex_documents = [
+  ('index', 'SimPEG.tex', u'SimPEG Documentation',
+   u'Rowan Cockett', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# If true, show page references after internal links.
+#latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_domain_indices = True
+
+
+# -- Options for manual page output --------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    ('index', 'simpeg', u'SimPEG Documentation',
+     [u'Rowan Cockett'], 1)
+]
+
+# If true, show URL addresses after external links.
+#man_show_urls = False
+
+
+# -- Options for Texinfo output ------------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+  ('index', 'SimPEG', u'SimPEG Documentation',
+   u'Rowan Cockett', 'SimPEG', 'One line description of project.',
+   'Miscellaneous'),
+]
+
+# Documents to append as an appendix to all manuals.
+#texinfo_appendices = []
+
+# If false, no module index is generated.
+#texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#texinfo_show_urls = 'footnote'

docs/examples/mesh/plot_grid_2D.py

@@ -0,0 +1,11 @@
+import numpy as np
+import matplotlib.pyplot as plt
+from SimPEG import TensorMesh
+
+h1 = np.linspace(.1,.5,3)
+h2 = np.linspace(.1,.5,5)
+mesh = TensorMesh([h1, h2])
+mesh.plotGrid()
+
+plt.show()
+

docs/examples/mesh/plot_grid_3D.py

@@ -0,0 +1,12 @@
+import numpy as np
+import matplotlib.pyplot as plt
+from SimPEG import TensorMesh
+
+h1 = np.linspace(.1,.5,3)
+h2 = np.linspace(.1,.5,5)
+h3 = np.linspace(.1,.5,3)
+mesh = TensorMesh([h1,h2,h3])
+mesh.plotGrid()
+
+plt.show()
+

docs/examples/mesh/plot_image_2D.py

@@ -0,0 +1,11 @@
+import numpy as np
+import matplotlib.pyplot as plt
+from SimPEG import TensorMesh
+
+n = 20
+h = np.ones(n)/n
+M = TensorMesh([h, h])
+I = np.sin(M.gridCC[:,0]*2*np.pi)*np.sin(M.gridCC[:,1]*2*np.pi)
+M.plotImage(I)
+
+plt.show()

docs/examples/mesh/plot_image_3D.py

@@ -0,0 +1,12 @@
+import numpy as np
+import matplotlib.pyplot as plt
+from SimPEG import TensorMesh
+
+n = 20
+h = np.ones(n)/n
+M = TensorMesh([h,h,h])
+
+I = np.sin(M.gridCC[:,0]*2*np.pi)*np.sin(M.gridCC[:,1]*2*np.pi)*np.sin(M.gridCC[:,2]*2*np.pi)
+M.plotImage(I, annotationColor='k')
+
+plt.show()

docs/examples/mesh/plot_nodes.py

@@ -0,0 +1,13 @@
+import numpy as np
+import matplotlib.pyplot as plt
+from SimPEG import TensorMesh
+
+x0 = np.zeros(2)
+h1 = np.linspace(.1,.5,3)
+h2 = np.linspace(.1,.5,5)
+M = TensorMesh([h1,h2],x0)
+M.plotGrid()
+plt.hold()
+plt.plot(M.gridN[:,0], M.gridN[:,1], 'ks', markersize=10)
+plt.show()
+

docs/index.rst

@@ -0,0 +1,55 @@
+.. SimPEG documentation master file, created by
+   sphinx-quickstart on Fri Aug 30 18:42:44 2013.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+SimPEG
+======
+
+SimPEG (Simulation and Parameter Estimation in Geophysics) is a python package for simulation and gradient based parameter estimation in the context of geophysical applications.
+
+The vision is to create a package for finite volume simulation with applications to geophysical imaging and subsurface flow. To enable the understanding of the many different components, this package has the following features:
+
+* modular with respect to the spacial discretization
+* is built with the inverse problem in mind
+* supports different hyperbolic solvers (Euler, Semi-Lagrangian, Lagrangian)
+* supports 2D and 3D problems
+
+
+Meshing & Operators
+===================
+
+.. toctree::
+   :maxdepth: 2
+
+   api_BaseMesh
+   api_TensorMesh
+   api_TensorView
+   api_LogicallyOrthogonalMesh
+   api_LomView
+   api_DiffOperators
+   api_InnerProducts
+
+Inversion
+=========
+
+.. toctree::
+   :maxdepth: 2
+
+   api_GaussNewton
+
+Example Problems
+================
+
+.. toctree::
+   :maxdepth: 2
+
+
+
+Project Index & Search
+======================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+

docs/make.bat

@@ -0,0 +1,190 @@
+@ECHO OFF
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set BUILDDIR=_build
+set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% .
+set I18NSPHINXOPTS=%SPHINXOPTS% .
+if NOT "%PAPER%" == "" (
+	set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
+	set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS%
+)
+
+if "%1" == "" goto help
+
+if "%1" == "help" (
+	:help
+	echo.Please use `make ^<target^>` where ^<target^> is one of
+	echo.  html       to make standalone HTML files
+	echo.  dirhtml    to make HTML files named index.html in directories
+	echo.  singlehtml to make a single large HTML file
+	echo.  pickle     to make pickle files
+	echo.  json       to make JSON files
+	echo.  htmlhelp   to make HTML files and a HTML help project
+	echo.  qthelp     to make HTML files and a qthelp project
+	echo.  devhelp    to make HTML files and a Devhelp project
+	echo.  epub       to make an epub
+	echo.  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter
+	echo.  text       to make text files
+	echo.  man        to make manual pages
+	echo.  texinfo    to make Texinfo files
+	echo.  gettext    to make PO message catalogs
+	echo.  changes    to make an overview over all changed/added/deprecated items
+	echo.  linkcheck  to check all external links for integrity
+	echo.  doctest    to run all doctests embedded in the documentation if enabled
+	goto end
+)
+
+if "%1" == "clean" (
+	for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
+	del /q /s %BUILDDIR%\*
+	goto end
+)
+
+if "%1" == "html" (
+	%SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/html.
+	goto end
+)
+
+if "%1" == "dirhtml" (
+	%SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.
+	goto end
+)
+
+if "%1" == "singlehtml" (
+	%SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml.
+	goto end
+)
+
+if "%1" == "pickle" (
+	%SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can process the pickle files.
+	goto end
+)
+
+if "%1" == "json" (
+	%SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can process the JSON files.
+	goto end
+)
+
+if "%1" == "htmlhelp" (
+	%SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can run HTML Help Workshop with the ^
+.hhp project file in %BUILDDIR%/htmlhelp.
+	goto end
+)
+
+if "%1" == "qthelp" (
+	%SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can run "qcollectiongenerator" with the ^
+.qhcp project file in %BUILDDIR%/qthelp, like this:
+	echo.^> qcollectiongenerator %BUILDDIR%\qthelp\SimPEG.qhcp
+	echo.To view the help file:
+	echo.^> assistant -collectionFile %BUILDDIR%\qthelp\SimPEG.ghc
+	goto end
+)
+
+if "%1" == "devhelp" (
+	%SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished.
+	goto end
+)
+
+if "%1" == "epub" (
+	%SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The epub file is in %BUILDDIR%/epub.
+	goto end
+)
+
+if "%1" == "latex" (
+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.
+	goto end
+)
+
+if "%1" == "text" (
+	%SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The text files are in %BUILDDIR%/text.
+	goto end
+)
+
+if "%1" == "man" (
+	%SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The manual pages are in %BUILDDIR%/man.
+	goto end
+)
+
+if "%1" == "texinfo" (
+	%SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo.
+	goto end
+)
+
+if "%1" == "gettext" (
+	%SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The message catalogs are in %BUILDDIR%/locale.
+	goto end
+)
+
+if "%1" == "changes" (
+	%SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.The overview file is in %BUILDDIR%/changes.
+	goto end
+)
+
+if "%1" == "linkcheck" (
+	%SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Link check complete; look for any errors in the above output ^
+or in %BUILDDIR%/linkcheck/output.txt.
+	goto end
+)
+
+if "%1" == "doctest" (
+	%SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Testing of doctests in the sources finished, look at the ^
+results in %BUILDDIR%/doctest/output.txt.
+	goto end
+)
+
+:end