added API documentation and source docstrings

Some API tidies for consistency etc.

GetDist.py

@@ -168,7 +168,7 @@ def filterParList(namestring, num=None):
     if thin_factor != 0:
         thin_ix = mc.thin_indices(thin_factor)
         filename = rootdirname + '_thin.txt'
-        mc.WriteThinData(filename, thin_ix, thin_cool)
+        mc.writeThinData(filename, thin_ix, thin_cool)
 
     print(mc.getNumSampleSummaryText().strip())
     if mc.likeStats: print(mc.likeStats.likeSummary().strip())
@@ -186,7 +186,7 @@ def filterParList(namestring, num=None):
     mc.plot_data_dir = plot_data_dir
 
     # Do 1D bins
-    mc.setDensitiesandMarge1D(writeDataToFile=not no_plots and plot_data_dir, meanlikes=plot_meanlikes)
+    mc._setDensitiesandMarge1D(writeDataToFile=not no_plots and plot_data_dir, meanlikes=plot_meanlikes)
 
     if not no_plots:
         # Output files for 1D plots
@@ -245,7 +245,7 @@ def filterParList(namestring, num=None):
         done2D = {}
 
         filename = rootdirname + '.' + plot_ext
-        mc.WriteScriptPlots1D(filename, plotparams)
+        mc.writeScriptPlots1D(filename, plotparams)
         if make_plots: runScript(filename)
 
         # Do 2D bins
@@ -260,15 +260,15 @@ def filterParList(namestring, num=None):
         if cust2DPlots or plot_2D_param:
             print('...producing 2D plots')
             filename = rootdirname + '_2D.' + plot_ext
-            done2D = mc.WriteScriptPlots2D(filename, plot_2D_param, cust2DPlots,
+            done2D = mc.writeScriptPlots2D(filename, plot_2D_param, cust2DPlots,
                                            writeDataToFile=plot_data_dir, shade_meanlikes=shade_meanlikes)
             if make_plots: runScript(filename)
 
         if triangle_plot:
             # Add the off-diagonal 2D plots
             print('...producing triangle plot')
             filename = rootdirname + '_tri.' + plot_ext
-            mc.WriteScriptPlotsTri(filename, triangle_params)
+            mc.writeScriptPlotsTri(filename, triangle_params)
             for i, p2 in enumerate(triangle_params):
                 for p1 in triangle_params[i + 1:]:
                     if not done2D.get((p1, p2)) and plot_data_dir:
@@ -279,7 +279,7 @@ def filterParList(namestring, num=None):
         if num_3D_plots:
             print('...producing ', num_3D_plots, '2D colored scatter plots')
             filename = rootdirname + '_3D.' + plot_ext
-            mc.WriteScriptPlots3D(filename, plot_3D)
+            mc.writeScriptPlots3D(filename, plot_3D)
             if make_plots: runScript(filename)
 
     if not plots_only:

docs/source/chains.rst

@@ -0,0 +1,7 @@
+getdist.chains
+==================================
+
+
+.. automodule:: getdist.chains
+   :members:
+

docs/source/conf.py

@@ -0,0 +1,290 @@
+# -*- coding: utf-8 -*-
+#
+# MyProj documentation build configuration file, created by
+# sphinx-quickstart on Thu Jun 18 20:57:49 2015.
+#
+# 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.
+
+import sys
+import os
+import shlex
+
+# autoclass_content = 'both'
+
+# 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('exts'))
+sys.path.insert(0, os.path.abspath('../../getdist/'))
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+needs_sphinx = '1.3'
+
+# 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.intersphinx', 'sphinx.ext.viewcode', 'sphinx.ext.autosummary', 'plot_directive'
+]
+
+intersphinx_mapping = {'python': ('http://docs.python.org/2', None),
+                       'numpy': ('http://docs.scipy.org/doc/numpy/', None),
+                       'scipy': ('http://docs.scipy.org/doc/scipy/reference/', None),
+                       'matplotlib': ('http://matplotlib.sourceforge.net/', None)}
+
+plot_formats = [('png', 80)]
+plot_html_show_formats = False
+plot_html_show_source_link = False
+
+autosummary_generate = True
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'GetDist API'
+copyright = u'2015, Antony Lewis'
+author = u'Antony Lewis'
+
+import getdist
+version = getdist.__version__
+release = getdist.__version__
+
+# 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 = []
+
+# 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
+
+# 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 = False
+
+
+# -- 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 = 'sphinx_rtd_theme'
+
+# 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
+
+# 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
+
+# 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'
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'GetDistDoc'
+
+# -- 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, 'GetDist.tex', u'GetDist Documentation',
+   author, 'manual'),
+]
+
+# 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
+
+# If true, show URL addresses after external links.
+# latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+# latex_appendices = []
+
+# 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, 'GetDist', u'GetDist 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, 'GetDist', u'GetDist Documentation',
+   author, 'GetDist', 'Sample analysis and plotting.',
+   'Miscellaneous'),
+]
+
+# Documents to append as an appendix to all manuals.
+# texinfo_appendices = []
+
+# If false, no module index is generated.
+# texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+# texinfo_show_urls = 'footnote'
+
+# If true, do not generate a @detailmenu in the "Top" node's menu.
+# texinfo_no_detailmenu = False

docs/source/covmat.rst

@@ -0,0 +1,12 @@
+getdist.covmat
+==================================
+
+
+
+.. automodule:: getdist.covmat
+   :members:
+
+
+
+
+

docs/source/densities.rst

@@ -0,0 +1,12 @@
+getdist.densities
+==================================
+
+
+
+.. automodule:: getdist.densities
+   :members:
+
+
+
+
+