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update docs to python 3
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bobmyhill committed Aug 1, 2021
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192 changes: 58 additions & 134 deletions sphinx/conf.py
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# -*- coding: utf-8 -*-
# Configuration file for the Sphinx documentation builder.
#
# BurnMan documentation build configuration file, created by
# sphinx-quickstart on Mon Apr 21 16:47:58 2014.
#
# 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.
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html

import sys
import os
# -- Path setup --------------------------------------------------------------

# 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.
#
import os
import sys
sys.path.insert(0, os.path.abspath('..'))

import burnman
import burnman.version

# 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('.'))
# -- Project information -----------------------------------------------------

project = 'BurnMan'
copyright = '2021, Sanne Cottaar, Timo Heister, Robert Myhill, Ian Rose, Cayman Unterborn'
author = 'Sanne Cottaar, Timo Heister, Robert Myhill, Ian Rose, Cayman Unterborn'

# The full version, including alpha/beta/rc tags
version = burnman.version.short_version
release = burnman.__version__

# -- General configuration -----------------------------------------------

# If your documentation needs a minimal Sphinx version, state it here.
# needs_sphinx = '1.0'
# -- General configuration ---------------------------------------------------

# Add any Sphinx extension module names here, as strings. They can be extensions
# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
# 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.autodoc', 'sphinx.ext.autosummary', 'sphinx.ext.mathjax',
'numpydoc', 'sphinx.ext.intersphinx', 'sphinx.ext.ifconfig', 'sphinx.ext.inheritance_diagram',
'sphinx.ext.viewcode', 'sphinxcontrib.bibtex']
'sphinx.ext.viewcode', 'sphinxcontrib.bibtex'
]
bibtex_bibfiles = ['ref.bib']

numpydoc_show_class_members = False

autodoc_default_flags = [
'members', 'undoc-members', 'show-inheritance', 'inherited-members']
'members', 'undoc-members', 'show-inheritance', 'inherited-members'
]

autodoc_member_order = 'bysource'



# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']

Expand All @@ -52,42 +62,10 @@
# The master toctree document.
master_doc = 'index'

# General information about the project.
project = u'BurnMan'
copyright = u'2014, Sanne Cottaar, Timo Heister, Robert Myhill, Ian Rose, Cayman Unterborn'

# 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 = burnman.version.short_version
# The full version, including alpha/beta/rc tags.
release = burnman.__version__

# 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
# This pattern also affects html_static_path and html_extra_path.
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']

# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
Expand All @@ -99,87 +77,21 @@
# A list of ignored prefixes for module index sorting.
# modindex_common_prefix = []


# -- Options for HTML output ---------------------------------------------
# -- 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
#
html_theme = 'alabaster'

# 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
# Output file base name for HTML help builder.
htmlhelp_basename = 'BurnMandoc'

# 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 = 'BurnMandoc'


# -- Options for LaTeX output --------------------------------------------

preamble1 = '''
Expand All @@ -191,7 +103,12 @@
\newcommand{\burnman}{\texttt{\bf BurnMan}}
\renewcommand{\maketitle}{
'''

latex_maketitle = r'''
\begin{titlepage}
{
\definecolor{dark_grey}{gray}{0.3}
\definecolor{aspect_blue}{rgb}{0.9,0.35,0.3}
Expand Down Expand Up @@ -277,16 +194,22 @@
\pagebreak
}
'''
\end{titlepage}
'''

language='en'

latex_logo='burnjack-small.png'

latex_elements = {
'sphinxsetup': '',
'passoptionstopackages': r'\PassOptionsToPackage{table}{xcolor}',
# The paper size ('letterpaper' or 'a4paper').
'papersize': 'letterpaper',
'babel': '\usepackage[english]{babel}',
# The font size ('10pt', '11pt' or '12pt').
'pointsize': '11pt',
'classoptions': ',openany',
'preamble': preamble
'preamble': preamble,
'maketitle': latex_maketitle
}

# Grouping the document tree into LaTeX files. List of tuples
Expand All @@ -296,6 +219,7 @@
u'Sanne Cottaar, Timo Heister, Robert Myhill, Ian Rose, Cayman Unterborn', 'manual'),
]


# The name of an image file (relative to this directory) to place at the top of
# the title page.
# latex_logo = None
Expand Down
68 changes: 34 additions & 34 deletions sphinx/index.rst
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
.. BurnMan documentation master file, created by
sphinx-quickstart on Mon Apr 21 16:47:58 2014.
sphinx-quickstart on Sun Aug 1 20:20:43 2021.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Expand All @@ -8,64 +8,64 @@ BurnMan: a thermodynamic and geophysics toolkit for the Earth and planetary scie


.. image:: burnjack-bar.png

BurnMan is a Python library for computing the thermodynamic and thermoelastic properties
of geological materials from simple mineral endmembers to complex multilayered planetary interiors.

BurnMan is released under the GNU GPL v2 or newer. It relies heavily on numpy, scipy, and matplotlib.

- Homepage: http://burnman.org
- Documentation: http://burnman.readthedocs.io
- Source code: https://github.com/geodynamics/burnman
- Homepage: http://burnman.org
- Documentation: http://burnman.readthedocs.io
- Source code: https://github.com/geodynamics/burnman

If you haven't yet installed BurnMan, you can go straight to :ref:`ref-installation` for detailed
instructions. After that, you might want to try out our :ref:`ref-example-tutorial` or the other
:ref:`ref-examples`. Finally, and most importantly, have fun!


Citing BurnMan
--------------

If you use BurnMan in your work, we ask that you cite the following publications:

- Cottaar, S., Heister, T., Myhill, R., Rose, I., and Unterborn, C. (2017):
BurnMan v0.10.0 [Software]. Computational Infrastructure for Geodynamics. Zenodo.
`(link) <https://doi.org/10.5281/zenodo.546210>`_
- Cottaar, S., Heister, T., Myhill, R., Rose, I., and Unterborn, C. (2017):
BurnMan v0.10.0 [Software]. Computational Infrastructure for Geodynamics. Zenodo.
`(link) <https://doi.org/10.5281/zenodo.546210>`_

- Cottaar S., Heister, T., Rose, I., and Unterborn, C., 2014, BurnMan: A
lower mantle mineral physics toolkit, Geochemistry, Geophysics, and
Geosystems, 15(4), 1164-1179 `(link) <https://doi.org/10.1002/2013GC005122>`_
- Cottaar S., Heister, T., Rose, I., and Unterborn, C., 2014, BurnMan: A
lower mantle mineral physics toolkit, Geochemistry, Geophysics, and
Geosystems, 15(4), 1164-1179 `(link) <https://doi.org/10.1002/2013GC005122>`_

Contributing to BurnMan
Contributing to BurnMan
-----------------------

We welcome the submission of scripts used to create published results. If you
We welcome the submission of scripts used to create published results. If you
have any scripts that you would like to contribute, please contact us at info@burnman.org
or make a pull request at `https://github.com/geodynamics/burnman <https://github.com/geodynamics/burnman>`_

Acknowledgement and Support
---------------------------

- This project was initiated at, and follow-up research support was received
through, Cooperative Institute of Deep Earth Research, CIDER (NSF FESD
grant 1135452) -- see `www.deep-earth.org <http://www.deep-earth.org>`_
- This project was initiated at, and follow-up research support was received
through, Cooperative Institute of Deep Earth Research, CIDER (NSF FESD
grant 1135452) -- see `www.deep-earth.org <http://www.deep-earth.org>`_

- We thank all the members of the CIDER Mg/Si team for their input:
Valentina Magni, Yu Huang, JiaChao Liu, Marc Hirschmann, and Barbara
Romanowicz. We also thank Lars Stixrude for providing benchmarking calculations
and Zack Geballe, Motohiko Murakami, Bill McDonough, Quentin Williams,
Wendy Panero, and Wolfgang Bangerth for helpful discussions.

- We thank CIG (`www.geodynamics.org <http://www.geodynamics.org>`_) for support
and accepting our donation of BurnMan as an official project.

- We thank all the members of the CIDER Mg/Si team for their input:
Valentina Magni, Yu Huang, JiaChao Liu, Marc Hirschmann, and Barbara
Romanowicz. We also thank Lars Stixrude for providing benchmarking calculations
and Zack Geballe, Motohiko Murakami, Bill McDonough, Quentin Williams,
Wendy Panero, and Wolfgang Bangerth for helpful discussions.

- We thank CIG (`www.geodynamics.org <http://www.geodynamics.org>`_) for support
and accepting our donation of BurnMan as an official project.


.. toctree::
:maxdepth: 4
introduction
background
tutorial
examples
api
zreferences
:maxdepth: 4

introduction
background
tutorial
examples
api
zreferences
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