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Merge pull request #81 from carterbox/revise-docs
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DOC: Revise documentation
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@carterbox
carterbox committed Jan 14, 2022
2 parents bf130c7 + 8e41e80 commit aec3112
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212 changes: 30 additions & 182 deletions docs/source/conf.py
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Expand Up @@ -34,15 +34,16 @@
'sphinx.ext.autosummary',
'sphinx.ext.doctest',
'sphinx.ext.intersphinx',
'sphinx.ext.todo',
'sphinx.ext.coverage',
'sphinx.ext.mathjax',
'sphinx.ext.ifconfig',
'sphinx.ext.viewcode',
'sphinx.ext.napoleon',
'sphinx.ext.viewcode',
'sphinx.ext.todo',
'sphinxcontrib.bibtex',
'nbsphinx',
'IPython.sphinxext.ipython_console_highlighting',
]

bibtex_bibfiles = [
'bibtex/refs.bib',
'bibtex/cite.bib',
]

# Napoleon settings
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copyright = u'2016, UChicago Argonne, LLC'
author = u'Doga Gursoy'

# 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.
# The full version, including alpha/beta/rc tags.
# release = '0.3'

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
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', '**.ipynb_checkpoints']

# 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
show_authors = True

# 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 = []

# If true, keep warnings as "system message" paragraphs in the built documents.
#keep_warnings = False

# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = True

Expand All @@ -154,16 +117,6 @@
"display_version": True,
}

# 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
Expand All @@ -173,149 +126,44 @@
# 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']

# Add any extra paths that contain custom files (such as robots.txt or
# .htaccess) here, relative to this directory. These files are copied
# directly to the root of the documentation.
#html_extra_path = []

# 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

# Language to be used for generating the HTML full-text search index.
# Sphinx supports the following languages:
# 'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'
# 'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr'
#html_search_language = 'en'

# A dictionary with options for the search language support, empty by default.
# Now only 'ja' uses this config value
#html_search_options = {'type': 'default'}

# The name of a javascript file (relative to the configuration directory) that
# implements a search results scorer. If empty, the default will be used.
#html_search_scorer = 'scorer.js'
html_search_language = 'en'

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

# -- 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': '',

# Latex figure (float) alignment
#'figure_align': 'htbp',
}

# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
# author, documentclass [howto, manual, or own class]).
latex_documents = [
(master_doc, 'xdesign.tex', u'XDesign Documentation', copyright, 'manual'),
nbsphinx_execute_arguments = [
"--InlineBackend.figure_formats={'svg', 'pdf'}",
"--InlineBackend.rc={'figure.dpi': 96}",
]

# 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
# This is processed by Jinja2 and inserted before each notebook
nbsphinx_prolog = r"""
{% set docname = env.doc2path(env.docname, base='docs/source') %}
# If true, show URL addresses after external links.
#latex_show_urls = False
.. only:: html
# Documents to append as an appendix to all manuals.
#latex_appendices = []
.. role:: raw-html(raw)
:format: html
# 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 = [(master_doc, 'xdesign', u'XDesign Documentation', [author], 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 = [
(
master_doc, 'xdesign', u'XDesign Documentation', author, copyright,
'Benchmarking tools for tomography.', 'Miscellaneous'
),
]
.. nbinfo::
# Documents to append as an appendix to all manuals.
#texinfo_appendices = []
This page was generated from `{{ docname }}`__.
Interactive online version:
:raw-html:`<a href="https://mybinder.org/v2/gh/tomography/xdesign/{{ env.config.release }}?filepath={{ docname }}"><img alt="Binder badge" src="https://mybinder.org/badge_logo.svg" style="vertical-align:text-bottom"></a>`
# If false, no module index is generated.
# texinfo_domain_indices = True
__ https://github.com/tomography/xdesign/blob/
{{ env.config.release }}/{{ docname }}
# How to display URL addresses: 'footnote', 'no', or 'inline'.
# texinfo_show_urls = 'footnote'
.. raw:: latex
# If true, do not generate a @detailmenu in the "Top" node's menu.
# texinfo_no_detailmenu = False
\nbsphinxstartnotebook{\scriptsize\noindent\strut
\textcolor{gray}{The following section was generated from
\sphinxcode{\sphinxupquote{\strut {{ docname | escape_latex }}}} \dotfill}}
"""

# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {
Expand All @@ -342,13 +190,13 @@ def __getattr__(cls, name):
'matplotlib.patheffects',
'matplotlib.axis',
'matplotlib.collections',
'matplotlib.colors',
'cached_property',
'scipy',
'scipy.stats',
'scipy.ndimage',
'scipy.spatial',
'cycler',
'phasepack',
]

sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
8 changes: 0 additions & 8 deletions docs/source/examples.rst
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Expand Up @@ -16,11 +16,3 @@ To `run <http://jupyter.readthedocs.org/en/latest/running.html>`_ these examples
demos/Parameterized
demos/NoReferenceMetrics
demos/FullReferenceMetrics
demos/WetCircles



.. automodule:: xdesign
:members:
:undoc-members:
:show-inheritance:
1 change: 0 additions & 1 deletion src/xdesign/phantom/custom.py
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Expand Up @@ -9,7 +9,6 @@
__all__ = [
'Soil',
'WetCircles',
'SiemensStar',
'Foam',
'Softwood',
]
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