update the doc and api doc to 1.0b4

Author: XiaohaoYang

doc/manual/source/_static/.empty

@@ -1,130 +1,134 @@
-pyobjcryst Package
+pyobjcryst package
 ==================
 
-:mod:`pyobjcryst` Package
--------------------------
-
-.. automodule:: pyobjcryst.__init__
-    :members:
-    :undoc-members:
-    :show-inheritance:
+Submodules
+----------
 
-:mod:`atom` Module
-------------------
+pyobjcryst.atom module
+----------------------
 
 .. automodule:: pyobjcryst.atom
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`crystal` Module
----------------------
+pyobjcryst.crystal module
+-------------------------
 
 .. automodule:: pyobjcryst.crystal
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`general` Module
----------------------
+pyobjcryst.general module
+-------------------------
 
 .. automodule:: pyobjcryst.general
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`io` Module
-----------------
+pyobjcryst.io module
+--------------------
 
 .. automodule:: pyobjcryst.io
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`molecule` Module
-----------------------
+pyobjcryst.molecule module
+--------------------------
 
 .. automodule:: pyobjcryst.molecule
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`polyhedron` Module
-------------------------
+pyobjcryst.polyhedron module
+----------------------------
 
 .. automodule:: pyobjcryst.polyhedron
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`refinableobj` Module
---------------------------
+pyobjcryst.refinableobj module
+------------------------------
 
 .. automodule:: pyobjcryst.refinableobj
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`scatterer` Module
------------------------
+pyobjcryst.scatterer module
+---------------------------
 
 .. automodule:: pyobjcryst.scatterer
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`scatteringpower` Module
------------------------------
+pyobjcryst.scatteringpower module
+---------------------------------
 
 .. automodule:: pyobjcryst.scatteringpower
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`scatteringpowersphere` Module
------------------------------------
+pyobjcryst.scatteringpowersphere module
+---------------------------------------
 
 .. automodule:: pyobjcryst.scatteringpowersphere
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`spacegroup` Module
-------------------------
+pyobjcryst.spacegroup module
+----------------------------
 
 .. automodule:: pyobjcryst.spacegroup
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`unitcell` Module
-----------------------
+pyobjcryst.unitcell module
+--------------------------
 
 .. automodule:: pyobjcryst.unitcell
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`utils` Module
--------------------
+pyobjcryst.utils module
+-----------------------
 
 .. automodule:: pyobjcryst.utils
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`version` Module
----------------------
+pyobjcryst.version module
+-------------------------
 
 .. automodule:: pyobjcryst.version
     :members:
     :undoc-members:
     :show-inheritance:
 
-:mod:`zscatterer` Module
-------------------------
+pyobjcryst.zscatterer module
+----------------------------
 
 .. automodule:: pyobjcryst.zscatterer
     :members:
     :undoc-members:
     :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: pyobjcryst
+    :members:
+    :undoc-members:
+    :show-inheritance:

doc/manual/source/api/pyobjcryst.rst

@@ -10,12 +10,12 @@
 # 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.append(os.path.abspath('.'))
-#sys.path.insert(0, os.path.abspath('../../..'))
+# sys.path.insert(0, os.path.abspath('../../..'))
 
 # -- General configuration -----------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
+# needs_sphinx = '1.0'
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
@@ -28,7 +28,7 @@
 source_suffix = '.rst'
 
 # The encoding of source files.
-#source_encoding = 'utf-8-sig'
+# source_encoding = 'utf-8-sig'
 
 # The master toctree document.
 master_doc = 'index'
@@ -43,23 +43,24 @@
 sys.path.insert(0, os.path.abspath('../../..'))
 from setup import versiondata
 fullversion = versiondata.get('DEFAULT', 'version')
+# sys.path.remove(os.path.abspath('../../..'))
 # The short X.Y version.
 version = '.'.join(fullversion.split('.')[:2])
 # The full version, including alpha/beta/rc tags.
 release = fullversion
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
-#language = None
+# language = None
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
-#today = ''
+# today = ''
 today_seconds = versiondata.getint('DEFAULT', 'timestamp')
 today = time.strftime('%B %d, %Y', time.localtime(today_seconds))
 year = today.split()[-1]
 # Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
+# today_fmt = '%B %d, %Y'
 # substitute YEAR in the copyright string
 copyright = copyright.replace('%Y', year)
 
@@ -68,27 +69,27 @@
 exclude_patterns = []
 
 # The reST default role (used for this markup: `text`) to use for all documents.
-#default_role = None
+# default_role = None
 
 # If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
+# 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
+# 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 = False
 
 # 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 = []
+# modindex_common_prefix = []
 
 # Display all warnings for missing links.
-#nitpicky = True
+# nitpicky = True
 
 # -- Options for HTML output ---------------------------------------------------
 
@@ -99,27 +100,27 @@
 # 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 = {}
+# html_theme_options = {}
 html_theme_options = {'collapsiblesidebar' : 'true'}
 
 # Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
+# html_theme_path = []
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-#html_title = None
+# html_title = None
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
-#html_short_title = None
+# 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_logo = None
 
 # 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
+# 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,
@@ -128,44 +129,44 @@
 
 # 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'
+# 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
+# html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
+# html_sidebars = {}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
-#html_additional_pages = {}
+# html_additional_pages = {}
 
 # If false, no module index is generated.
-#html_domain_indices = True
+# html_domain_indices = True
 
 # If false, no index is generated.
-#html_use_index = True
+# html_use_index = True
 
 # If true, the index is split into individual pages for each letter.
 html_split_index = True
 
 # If true, links to the reST sources are added to the pages.
-#html_show_sourcelink = True
+# html_show_sourcelink = True
 
 # If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
-#html_show_sphinx = True
+# html_show_sphinx = True
 
 # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
-#html_show_copyright = 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 = ''
+# html_use_opensearch = ''
 
 # This is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = None
+# html_file_suffix = None
 
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'pyobjcrystdoc'
@@ -175,13 +176,13 @@
 
 latex_elements = {
 # The paper size ('letterpaper' or 'a4paper').
-#'papersize': 'letterpaper',
+# 'papersize': 'letterpaper',
 
 # The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
+# 'pointsize': '10pt',
 
 # Additional stuff for the LaTeX preamble.
-#'preamble': '',
+# 'preamble': '',
 }
 
 # Grouping the document tree into LaTeX files. List of tuples
@@ -190,20 +191,20 @@
 
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
-#latex_logo = None
+# latex_logo = None
 
 # For "manual" documents, if this is true, then toplevel headings are parts,
 # not chapters.
-#latex_use_parts = False
+# latex_use_parts = False
 
 # If true, show page references after internal links.
-#latex_show_pagerefs = False
+# latex_show_pagerefs = False
 
 # If true, show URL addresses after external links.
-#latex_show_urls = False
+# latex_show_urls = False
 
 # Documents to append as an appendix to all manuals.
-#latex_appendices = []
+# latex_appendices = []
 
 # If false, no module index is generated.
-#latex_domain_indices = True
+# latex_domain_indices = True