Merge pull request geodynamics#221 from tjhei/documentation_fixes

Documentation fixes

burnman/eos/equation_of_state.py

@@ -324,8 +324,8 @@ def validate_parameters(self, params):
         and an equation of state is not required to implement it.  This function will
         not return anything, though it may raise warnings or errors.
 
-        Params
-        ------
+        Parameters
+        ----------
         params : dictionary
             Dictionary containing material parameters required by the equation of state.
         """

sphinx/background_userinputs.txt

@@ -101,11 +101,11 @@ an object that provides pressure, density, and seismic velocities (:math:`V_P, V
 
 To compare to seismically constrained profiles, BurnMan provides the 1D seismic velocity model PREM :cite:`dziewonski1981`.
 One can choose to evaluate :math:`V_P, V_\Phi, V_S, \rho, K_S` and/or :math:`G`.
-The user can input their own seismic profile, an example of which is included using AK135 :cite:`Kennett1995`.
+The user can input their own seismic profile, an example of which is included using AK135 :cite:`kennett1995`.
 
 Besides standardized 1D radial profiles, one can also compare to regionalized average profiles for the lower mantle.
 This option accommodates the observation that the lowermost mantle can be clustered into two regions, a 'slow' region, which represents the so-called Large Low Shear Velocity Provinces, and 'fast' region, the continuous surrounding region where slabs might subduct :cite:`Lekic2012`.
-This clustering as well as the averaging of the 1D model occurs over five tomographic S wave velocity  models (SAW24B16: :cite:`megnin2000`; HMSL-S: :cite:`houser2008`; S362ANI: :cite:`Kustowski2008`; GyPSuM: :cite:`Simmons2010`; S40RTS: :cite:`Ritsema2011`).
+This clustering as well as the averaging of the 1D model occurs over five tomographic S wave velocity  models (SAW24B16: :cite:`megnin2000`; HMSL-S: :cite:`houser2008`; S362ANI: :cite:`kustowski2008`; GyPSuM: :cite:`Simmons2010`; S40RTS: :cite:`Ritsema2011`).
 The strongest deviations from PREM occur in the lowermost 1000 km.
 Using the 'fast' and 'slow' S wave velocity profiles is therefore most important when interpreting the lowermost mantle. Suggestion of compositional variation between these regions comes from seismology :cite:`to2005,He2012` as well as geochemistry :cite:`Deschamps2012,jackson2010`.
 Based on thermo-chemical convection models, :cite:`Styles2011` also show that averaging profiles in thermal boundary layers may cause problems for seismic interpretation.

sphinx/conf.py

@@ -288,7 +288,7 @@
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
-  ('index', 'BurnMan.tex', u'BurnMan Documentation',
+  ('index_pdf', 'BurnMan.tex', u'BurnMan Documentation',
    u'Sanne Cottaar, Timo Heister, Robert Myhill, Ian Rose, Cayman Unterborn', 'manual'),
 ]
 
@@ -310,7 +310,7 @@
 #latex_appendices = []
 
 # If false, no module index is generated.
-#latex_domain_indices = True
+latex_domain_indices = False
 
 
 # -- Options for manual page output --------------------------------------------
@@ -319,7 +319,7 @@
 # (source start file, name, description, authors, manual section).
 man_pages = [
     ('index', 'burnman', u'BurnMan Documentation',
-     [u'Sanne Cottaar, Timo Heister, Robert Myhill, Ian rose, Cayman Unterborn'], 1)
+     [u'Sanne Cottaar, Timo Heister, Robert Myhill, Ian Rose, Cayman Unterborn'], 1)
 ]
 
 # If true, show URL addresses after external links.
@@ -333,7 +333,7 @@
 #  dir menu entry, description, category)
 texinfo_documents = [
   ('index', 'BurnMan', u'BurnMan Documentation',
-   u'Sanne Cottaar, Timo Heister, Robert Myhill, Ian rose, Cayman Unterborn', 'BurnMan', 'One line description of project.',
+   u'Sanne Cottaar, Timo Heister, Robert Myhill, Ian Rose, Cayman Unterborn', 'BurnMan', 'One line description of project.',
    'Miscellaneous'),
 ]
 

sphinx/examples.rst

@@ -24,9 +24,6 @@ The tutorial for BurnMan currently consists of three separate units:
 
 .. _ref-example-tut1:
 
-.. #CIDER 2014 BurnMan Tutorial --- step 1
-.. #--------------------------------------
-
 .. automodule:: tutorial.step_1
 
 When run (without putting in a more realistic composition), the program produces the following image:
@@ -36,19 +33,13 @@ When run (without putting in a more realistic composition), the program produces
 Your goal in this tutorial is to improve this awful fit...
 
 
-link to source code: `tutorial/step1.py <../../../tutorial/step_1.py>`_
-
-
-
 
 .. automodule:: tutorial.step_2
 
 Whithout changing any input, the program should produce the following image showing the misfit as a function of perovskite content:
 
 .. image:: figures/tut-step2.png
 
-link to source code: `tutorial/step_2.py <../../../tutorial/step_2.py>`_
-
 
 
 .. automodule:: tutorial.step_3

sphinx/index_pdf.rst

@@ -0,0 +1,24 @@
+.. BurnMan documentation master file, created by
+   sphinx-quickstart on Mon Apr 21 16:47:58 2014.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to BurnMan's documentation!
+===================================
+
+The code documentation including class and function description can be found online at `burnman.org/current-doc <http://burnman.org/current-doc>`_.
+
+.. automodule:: burnman
+
+.. toctree::
+   :maxdepth: 2
+
+   overview
+   background
+   examples
+
+
+
+
+
+

sphinx/zreferences.rst

@@ -1,3 +1,6 @@
+References
+==========
+
 .. rubric:: References
 
 .. bibliography:: ref.bib