Merge branch 'develop' into ticket638-numpy_1_7_1_test_failures_with_…

…physicalField_py

INSTALLATION.txt

@@ -432,7 +432,7 @@ your home directory).  You will then need to append
 :file:`{dir}/lib/python` to your :envvar:`PYTHONPATH` environment
 variable.  See the `Alternate Installation`_ section of the
 :term:`Python` document "`Installing Python Modules`_"
-[InstallingPythonModules]_ for more information, such as circumstances
+:cite:`InstallingPythonModules` for more information, such as circumstances
 in which you should use :option:`--prefix` instead of
 :option:`--home`.
 

README.txt

@@ -25,12 +25,12 @@ Overview
 The :term:`FiPy` framework includes terms for transient diffusion,
 convection and standard sources, enabling the solution of arbitrary
 combinations of coupled elliptic, hyperbolic and parabolic PDEs. Currently
-implemented models include phase field [BoettingerReview:2002]_
-[ChenReview:2002]_ [McFaddenReview:2002]_ treatments of polycrystalline,
+implemented models include phase field :cite:`BoettingerReview:2002`
+:cite:`ChenReview:2002` :cite:`McFaddenReview:2002` treatments of polycrystalline,
 dendritic, and electrochemical phase transformations, as well as drug
-eluting stents [Saylor:2011p2794]_, reactive wetting [PhysRevE.82.051601]_,
-photovoltaics [Hangarter:2011p2795]_ and a level set treatment of the
-electrodeposition process [NIST:damascene:2001]_.
+eluting stents :cite:`Saylor:2011p2794`, reactive wetting :cite:`PhysRevE.82.051601`,
+photovoltaics :cite:`Hangarter:2011p2795` and a level set treatment of the
+electrodeposition process :cite:`NIST:damascene:2001`.
 
 .. only:: latex
 
@@ -254,11 +254,8 @@ or a
 .. _NIST:                 http://www.nist.gov/
 .. _compressed archive:   http://www.ctcms.nist.gov/fipy/download/FiPy-1.1.tar.gz
 .. _tracking system:      http://matforge.org/fipy/report
-.. _mailing list:         http://www.ctcms.nist.gov/fipy/mail.html
+.. _mailing list:         http://www.ctcms.nist.gov/fipy/documentation/MAIL.html
 .. _Sourceforge:          http://www.sourceforge.net/projects/fipy
 .. _Materials Digital Library Pathway: http://matdl.org
 .. _MatForge:             http://matforge.org/
 
-.. bibmissing:: /documentation/refs.bib
-    :sort:
-

documentation/EFFICIENCY.txt

@@ -18,7 +18,7 @@ problem can be executed by running::
 
 from the base :term:`FiPy` directory. The in-house code was written by Ryo
 Kobayashi and is used to generate the results presented in
-[WarrenPolycrystal]_.
+:cite:`WarrenPolycrystal`.
 
 The raw CPU execution times for 10 time steps are presented in the
 following table. The run times are in seconds and the memory usage is

documentation/GIT.txt

@@ -81,7 +81,7 @@ Any other branches will not generally be of interest to most users.
 
 For those who are interested in learning more about Git, a wide variety of 
 online sources are available, starting with the `official Git website`_. 
-The `Pro Git book`_ [ProGit]_ is particularly instructive.
+The `Pro Git book`_ :cite:`ProGit` is particularly instructive.
 
 .. _official Git website: http://git-scm.com/
 

documentation/USAGE.txt

@@ -34,8 +34,8 @@ examples.
 
 In order to customize the examples, or to develop your own scripts, some
 knowledge of Python syntax is required.  We recommend you familiarize
-yourself with the excellent `Python tutorial`_ [PythonTutorial]_ 
-or with `Dive Into Python`_ [DiveIntoPython]_.
+yourself with the excellent `Python tutorial`_ :cite:`PythonTutorial` 
+or with `Dive Into Python`_ :cite:`DiveIntoPython`.
 
 .. _Python tutorial: http://docs.python.org/tut/tut.html
 .. _Dive Into Python: http://diveintopython.org
@@ -655,6 +655,8 @@ command in the base directory::
    you will need at least version 1.1.2 of `Sphinx
    <http://sphinx.pocoo.org/latest>`_, plus all of its prerequisites.
 
+   You will also need to `pip install sphinxcontrib-bibtex`.
+
 .. _download the latest manual:  http://matforge.org/fipy/wiki/FiPyManual
 
 

documentation/_templates/index.html

@@ -37,15 +37,15 @@ <h1>FiPy: A Finite Volume PDE Solver Using Python</h1>
   combinations of coupled elliptic, hyperbolic and parabolic PDEs.
   Currently implemented models include phase field <a class="reference
   external"
-  href="documentation/manual/refs.bib_cited.html#boettingerreview-2002">[BoettingerReview:2002]</a>
+  href="documentation/references.html#boettingerreview-2002">[BoettingerReview:2002]</a>
   <a class="reference external"
-  href="documentation/manual/refs.bib_cited.html#chenreview-2002">[ChenReview:2002]</a>
+  href="documentation/references.html#chenreview-2002">[ChenReview:2002]</a>
   <a class="reference external"
-  href="documentation/manual/refs.bib_cited.html#mcfaddenreview-2002">[McFaddenReview:2002]</a>
+  href="documentation/references.html#mcfaddenreview-2002">[McFaddenReview:2002]</a>
   treatments of polycrystalline, dendritic, and electrochemical phase
   transformations as well as a level set treatment of the electrodeposition
   process <a class="reference external"
-  href="documentation/manual/refs.bib_cited.html#nist-damascene-2001">[NIST:damascene:2001]</a>.</p>
+  href="documentation/references.html#nist-damascene-2001">[NIST:damascene:2001]</a>.</p>
   <div class="admonition attention">
   <p class="first admonition-title">If you use FiPy in your research, please cite:
   <a href="_static/fipy.bib">(bibtex)</a>
@@ -133,6 +133,8 @@ <h2>Indices and tables</h2>
           <span class="linkdescr">search this documentation</span></p>
        <p class="biglink"><a class="biglink" href="{{ pathto("documentation/contents") }}">Complete Table of Contents</a><br/>
           <span class="linkdescr">lists all sections and subsections</span></p>
+       <p class="biglink"><a class="biglink" href="{{  pathto("documentation/references") }}">References</a><br/>
+          <span class="linkdescr">lists of source materials</span></p>
      </td></tr>
    </table>
  {% endblock %}

documentation/_themes/nist/layout.html

@@ -7,6 +7,7 @@
 <script type="text/javascript" src="http://www.nist.gov/js/spry/SpryDOMUtils.js"></script>
 <script type="text/javascript" src="http://www.nist.gov/js/spry/SpryMenuBar.js"></script>
 <script type="text/javascript" src="http://www.nist.gov/js/spry/menu_bar.js"></script>
+<script language="JavaScript" id="_fed_an_js_tag" src="/js/federated-analytics.all.min.js?agency=NIST&subagency=ctcms&pua=UA-37115410-17&yt=true"></script>
 {{ super() }}
 {% endblock %}
 {% set reldelim1 = ' &gt;' %}

documentation/conf.py

@@ -32,9 +32,9 @@
               'sphinx.ext.ifconfig',
               'sphinx.ext.autosummary',
               'numpydoc',
-              'bibstuff.sphinxext.bibref',
               'sphinxcontrib.traclinks',
-              'redirecting_html']
+              'redirecting_html',
+              'sphinxcontrib.bibtex']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

documentation/contents.txt

@@ -18,6 +18,7 @@ FiPy Contents
    VKML
    ../DISCLAIMER
    manual
+   references
 
 .. toctree::
    :hidden:

documentation/manual.txt

@@ -7,4 +7,4 @@ FiPy Manual
    introduction
    ../examples/README
    API
-
+   references-latex

documentation/numerical/discret.txt

@@ -174,7 +174,7 @@ where the value of :math:`d_{AP}` is the distance between neighboring cell
 centers.  This estimate relies on the orthogonality of the mesh, and
 becomes increasingly inaccurate as the non-orthogonality increases.
 Correction terms have been derived to improve this error but are not
-currently included in :term:`FiPy` [croftphd]_.
+currently included in :term:`FiPy` :cite:`croftphd`.
 
 This term is represented in :term:`FiPy` as
 

documentation/numerical/equation.txt

@@ -58,10 +58,10 @@ For example, the diffusion term can represent conventional Fickean
 diffusion [*i.e.*, :math:`\nabla\cdot(\Gamma\nabla\phi)`] when the
 exponent :math:`n = 1` or a Cahn-Hilliard term [*i.e.*, :math:`\nabla
 \cdot (\Gamma_1 \nabla [ \nabla \cdot \Gamma_2 \nabla \phi ) ] )`
-[CahnHilliardI]_ [CahnHilliardII]_ [CahnHilliardIII]_] when :math:`n = 2`,
+:cite:`CahnHilliardI` :cite:`CahnHilliardII` :cite:`CahnHilliardIII`] when :math:`n = 2`,
 or a phase field crystal term [*i.e.*, :math:`\nabla \cdot (\Gamma_1 \nabla
 [ \nabla \cdot \Gamma_2 \nabla \{ \nabla \cdot \Gamma_3 \nabla \phi ) \} )
-] )` [Elder:2011p2811]_] when :math:`n = 3`, although spectral methods are probably a
+] )` :cite:`Elder:2011p2811`] when :math:`n = 3`, although spectral methods are probably a
 better approach. Higher order terms (:math:`n > 3`) are also possible, but
 the matrix condition number becomes quite poor.
 

documentation/numerical/index.txt

@@ -8,8 +8,8 @@ This chapter describes the numerical methods used to solve equations
 in the :term:`FiPy` programming environment. :term:`FiPy` uses the finite volume
 method (FVM) to solve coupled sets of partial differential equations
 (PDEs). For a good introduction to the FVM see Nick Croft's PhD
-thesis [croftphd]_, Patankar [patankar]_ or Versteeg and
-Malalasekera [versteegMalalasekera]_.
+thesis :cite:`croftphd`, Patankar :cite:`patankar` or Versteeg and
+Malalasekera :cite:`versteegMalalasekera`.
 
 Essentially, the FVM consists of dividing the solution domain into
 discrete finite volumes over which the state variables are
@@ -23,7 +23,7 @@ The FVM can be thought of as a subset of the Finite Element Method
 (FEM), just as the Finite Difference Method (FDM) is a subset of the FVM. A
 system of equations fully equivalent to the FVM can be obtained with
 the FEM using as weighting functions the characteristic functions of
-FV cells, i.e., functions equal to unity [Mattiussi:1997]_. Analogously,
+FV cells, i.e., functions equal to unity :cite:`Mattiussi:1997`. Analogously,
 the discretization of equations with the FVM reduces to the FDM on
 Cartesian grids.
 

documentation/references-latex.txt

@@ -0,0 +1,3 @@
+.. bibliography:: /documentation/refs.bib
+   :style: unsrt
+   :all:

documentation/references.txt

@@ -0,0 +1,7 @@
+==========
+References
+==========
+
+.. bibliography:: /documentation/refs.bib
+   :style: unsrt
+   :all:

documentation/refs.bib

@@ -72,10 +72,8 @@ @article{McFaddenReview:2002
 }
 
 @book{NumericalRecipes,
-   author =    {William H. Press and Saul A. Teukolsky and 
-   William T. Vetterling and Brian P. Flannery},
-   title =     {Numerical Recipes in {C}: the Art of Scientific 
-   Computing},
+   author =    {William H. Press and Saul A. Teukolsky and William T. Vetterling and Brian P. Flannery},
+   title =     {Numerical Recipes in {C}: the Art of Scientific Computing},
    edition = {2nd},
    publisher = {Cambridge University Press},
    year =      1999,
@@ -84,7 +82,7 @@ @book{NumericalRecipes
 @article{NIST:damascene:2001,
    author =  {D. Josell and D. Wheeler and W. H. Huber and T. P. Moffat},
    title =   {Superconformal Electrodeposition in Submicron Features},
-   journal = prl,
+   journal = {Physical Review Letters},
    volume =  87,
    number =  1,
    year =    2001,
@@ -130,7 +128,7 @@ @article{Wheeler:1992
    author = {A. A. Wheeler and W. J. Boettinger and G. B. {McF}adden},
    title = {Phase-field model for isothermal phase transitions in binary 
             alloys},
-   journal = pra,
+   journal = {Physical Review A},
    volume =  45,
    number =  10,
    year =    1992,
@@ -140,7 +138,7 @@ @article{Wheeler:1992
 @article{CahnHilliardI,
 	author = {John W. Cahn and John E. Hilliard},
 	title = {Free energy of a nonuniform system. {I}. {I}nterfacial free energy},
-	journal = jcp,
+	journal = {Journal of Chemical Physics},
 	year = {1958},
 	volume = {28},
 	number = {2},
@@ -150,7 +148,7 @@ @article{CahnHilliardI
 @article{CahnHilliardII,
 	author = {John W. Cahn},
 	title = {Free energy of a nonuniform system. {II}. {T}hermodynamic basis},
-	journal = jcp,
+	journal = {Journal of Chemical Physics},
 	year = {1959},
 	volume = {30},
 	number = {5},
@@ -160,7 +158,7 @@ @article{CahnHilliardII
 @article{CahnHilliardIII,
 	author = {John W. Cahn and John E. Hilliard},
 	title = {Free energy of a nonuniform system. {III}. {N}ucleation in a two-component incompressible fluid},
-	journal = jcp,
+	journal = {Journal of Chemical Physics},
 	year = {1959},
 	volume = {31},
 	number = {3},
@@ -195,8 +193,8 @@ @article{WarrenPolycrystal
 @article{ElPhFI,
    author =  {J. E. Guyer and W. J. Boettinger and J. A. Warren and G. B.
               McFadden},
-   title =   {Phase field modeling of electrochemistry I: Equilibrium},
-   journal = pre,
+   title =   {Phase field modeling of electrochemistry {I}: {E}quilibrium},
+   journal = {Physical Review E},
    volume =  69,
    year =    2004,
    pages =   {021603},
@@ -208,8 +206,8 @@ @article{ElPhFI
 @article{ElPhFII,
    author =  {J. E. Guyer and W. J. Boettinger and J. A. Warren and G. B.
               McFadden},
-   title =   {Phase field modeling of electrochemistry II: Kinetics},
-   journal = pre,
+   title =   {Phase field modeling of electrochemistry {II}: {K}inetics},
+   journal = {Physical Review E},
    volume =  69,
    year =    2004,
    pages =   {021604},
@@ -218,11 +216,6 @@ @article{ElPhFII
    doi =     {10.1103/PhysRevE.69.021604},
 }
 
-@misc{Python,
-   note = {The Python Programming Language},
-   url = {http://www.python.org/}
-}
-
 @manual{InstallingPythonModules,
    title = {Installing Python Modules},
    author = {Greg Ward},
@@ -289,7 +282,7 @@ @book{ferziger
 @Article{PhysRevE.82.051601,
   title = {Modeling the early stages of reactive wetting},
   author = {Wheeler, Daniel  and Warren, James A. and Boettinger, William J.},
-  journal = {Phys. Rev. E},
+  journal = {Physical Review E},
   volume = {82},
   number = {5},
   pages = {051601},
@@ -314,7 +307,7 @@ @Article{Hangarter:2011p2795
 
 @Article{Saylor:2011p2794,
 author = {David M Saylor and Jonathan E Guyer and Daniel Wheeler and James A Warren}, 
-journal = {Acta Biomater},
+journal = {Acta Biomaterialia},
 title = {Predicting microstructure development during casting of drug-eluting coatings},
 number = {2},
 pages = {604--613},
@@ -326,7 +319,7 @@ @Article{Saylor:2011p2794
 
 @Article{Elder:2011p2811,
 author = {K. R Elder and K Thornton and J. J Hoyt}, 
-journal = {Philos Mag},
+journal = {Philosophical Magagazine},
 title = {The Kirkendall effect in the phase field crystal model},
 number = {1},
 pages = {151--164},