Merge pull request #81 from carterbox/revise-docs

DOC: Revise documentation

Author: carterbox

docs/source/conf.py

@@ -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
@@ -79,55 +80,17 @@
 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
 
@@ -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
@@ -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 = {
@@ -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)

docs/source/examples.rst

@@ -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:

src/xdesign/phantom/custom.py

@@ -9,7 +9,6 @@
 __all__ = [
     'Soil',
     'WetCircles',
-    'SiemensStar',
     'Foam',
     'Softwood',
 ]