From 2d81338bd743ca240d018ad194421fb7d325bb61 Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Sun, 27 Dec 2015 05:12:56 -0500 Subject: [PATCH 1/4] fix references --- sphinx/background_userinputs.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/sphinx/background_userinputs.txt b/sphinx/background_userinputs.txt index 88320cc8a..eb37c389c 100644 --- a/sphinx/background_userinputs.txt +++ b/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. From 5917ca1df060dc2183e5ab0c8053bc7b80adbbf6 Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Sun, 27 Dec 2015 05:19:23 -0500 Subject: [PATCH 2/4] shorten pdf - remove code documentation from pdf - remove 2 out of 3 indices at the end --- sphinx/conf.py | 8 ++++---- sphinx/index_pdf.rst | 24 ++++++++++++++++++++++++ 2 files changed, 28 insertions(+), 4 deletions(-) create mode 100644 sphinx/index_pdf.rst diff --git a/sphinx/conf.py b/sphinx/conf.py index 32878d0e7..0d2a36443 100644 --- a/sphinx/conf.py +++ b/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'), ] diff --git a/sphinx/index_pdf.rst b/sphinx/index_pdf.rst new file mode 100644 index 000000000..27fc5ce86 --- /dev/null +++ b/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 ``_. + +.. automodule:: burnman + +.. toctree:: + :maxdepth: 2 + + overview + background + examples + + + + + + From d36f682bf2f57f1dc698be5dbafc0c7b5170a716 Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Sun, 27 Dec 2015 05:19:39 -0500 Subject: [PATCH 3/4] random cleanup --- burnman/eos/equation_of_state.py | 4 ++-- sphinx/examples.rst | 9 --------- sphinx/zreferences.rst | 3 +++ 3 files changed, 5 insertions(+), 11 deletions(-) diff --git a/burnman/eos/equation_of_state.py b/burnman/eos/equation_of_state.py index 9718a42dd..bdf6983b6 100644 --- a/burnman/eos/equation_of_state.py +++ b/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. """ diff --git a/sphinx/examples.rst b/sphinx/examples.rst index 8d9b93b67..300aeed40 100644 --- a/sphinx/examples.rst +++ b/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: @@ -36,10 +33,6 @@ 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 @@ -47,8 +40,6 @@ Whithout changing any input, the program should produce the following image show .. image:: figures/tut-step2.png -link to source code: `tutorial/step_2.py <../../../tutorial/step_2.py>`_ - .. automodule:: tutorial.step_3 diff --git a/sphinx/zreferences.rst b/sphinx/zreferences.rst index c98f0cf9d..0aaa137b5 100644 --- a/sphinx/zreferences.rst +++ b/sphinx/zreferences.rst @@ -1,3 +1,6 @@ +References +========== + .. rubric:: References .. bibliography:: ref.bib From ef651647f6cee67f137ec3e6c3772f4290028608 Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Sun, 27 Dec 2015 05:54:06 -0500 Subject: [PATCH 4/4] update link text --- sphinx/index_pdf.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/sphinx/index_pdf.rst b/sphinx/index_pdf.rst index 27fc5ce86..db062579f 100644 --- a/sphinx/index_pdf.rst +++ b/sphinx/index_pdf.rst @@ -6,7 +6,7 @@ Welcome to BurnMan's documentation! =================================== -The code documentation including class and function description can be found online at ``_. +The code documentation including class and function description can be found online at `burnman.org/current-doc `_. .. automodule:: burnman