diff --git a/Doc/Sphinx/Makefile b/Doc/Sphinx/Makefile
deleted file mode 100644
index 19563d5f487459a0483f3c4e10feb9ce7fca9e52..0000000000000000000000000000000000000000
--- a/Doc/Sphinx/Makefile
+++ /dev/null
@@ -1,153 +0,0 @@
-# Makefile for Sphinx documentation
-#
-
-# You can set these variables from the command line.
-SPHINXOPTS =
-SPHINXBUILD = sphinx-build
-PAPER =
-BUILDDIR = _build
-
-# Internal variables.
-PAPEROPT_a4 = -D latex_paper_size=a4
-PAPEROPT_letter = -D latex_paper_size=letter
-ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
-# the i18n builder cannot share the environment and doctrees with the others
-I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
-
-.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
-
-help:
- @echo "Please use \`make <target>' where <target> is one of"
- @echo " html to make standalone HTML files"
- @echo " dirhtml to make HTML files named index.html in directories"
- @echo " singlehtml to make a single large HTML file"
- @echo " pickle to make pickle files"
- @echo " json to make JSON files"
- @echo " htmlhelp to make HTML files and a HTML help project"
- @echo " qthelp to make HTML files and a qthelp project"
- @echo " devhelp to make HTML files and a Devhelp project"
- @echo " epub to make an epub"
- @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
- @echo " latexpdf to make LaTeX files and run them through pdflatex"
- @echo " text to make text files"
- @echo " man to make manual pages"
- @echo " texinfo to make Texinfo files"
- @echo " info to make Texinfo files and run them through makeinfo"
- @echo " gettext to make PO message catalogs"
- @echo " changes to make an overview of all changed/added/deprecated items"
- @echo " linkcheck to check all external links for integrity"
- @echo " doctest to run all doctests embedded in the documentation (if enabled)"
-
-clean:
- -rm -rf $(BUILDDIR)/*
-
-html:
- $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
- @echo
- @echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
-
-dirhtml:
- $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
- @echo
- @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
-
-singlehtml:
- $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
- @echo
- @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
-
-pickle:
- $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
- @echo
- @echo "Build finished; now you can process the pickle files."
-
-json:
- $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
- @echo
- @echo "Build finished; now you can process the JSON files."
-
-htmlhelp:
- $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
- @echo
- @echo "Build finished; now you can run HTML Help Workshop with the" \
- ".hhp project file in $(BUILDDIR)/htmlhelp."
-
-qthelp:
- $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
- @echo
- @echo "Build finished; now you can run "qcollectiongenerator" with the" \
- ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
- @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/BornAgain.qhcp"
- @echo "To view the help file:"
- @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/BornAgain.qhc"
-
-devhelp:
- $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
- @echo
- @echo "Build finished."
- @echo "To view the help file:"
- @echo "# mkdir -p $$HOME/.local/share/devhelp/BornAgain"
- @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/BornAgain"
- @echo "# devhelp"
-
-epub:
- $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
- @echo
- @echo "Build finished. The epub file is in $(BUILDDIR)/epub."
-
-latex:
- $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
- @echo
- @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
- @echo "Run \`make' in that directory to run these through (pdf)latex" \
- "(use \`make latexpdf' here to do that automatically)."
-
-latexpdf:
- $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
- @echo "Running LaTeX files through pdflatex..."
- $(MAKE) -C $(BUILDDIR)/latex all-pdf
- @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
-
-text:
- $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
- @echo
- @echo "Build finished. The text files are in $(BUILDDIR)/text."
-
-man:
- $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
- @echo
- @echo "Build finished. The manual pages are in $(BUILDDIR)/man."
-
-texinfo:
- $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
- @echo
- @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
- @echo "Run \`make' in that directory to run these through makeinfo" \
- "(use \`make info' here to do that automatically)."
-
-info:
- $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
- @echo "Running Texinfo files through makeinfo..."
- make -C $(BUILDDIR)/texinfo info
- @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
-
-gettext:
- $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
- @echo
- @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
-
-changes:
- $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
- @echo
- @echo "The overview file is in $(BUILDDIR)/changes."
-
-linkcheck:
- $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
- @echo
- @echo "Link check complete; look for any errors in the above output " \
- "or in $(BUILDDIR)/linkcheck/output.txt."
-
-doctest:
- $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
- @echo "Testing of doctests in the sources finished, look at the " \
- "results in $(BUILDDIR)/doctest/output.txt."
diff --git a/Doc/Sphinx/_static/bornagain.css b/Doc/Sphinx/_static/bornagain.css
deleted file mode 100644
index c0344a92047b610ff529e896800cff49318132a5..0000000000000000000000000000000000000000
--- a/Doc/Sphinx/_static/bornagain.css
+++ /dev/null
@@ -1,350 +0,0 @@
-/*
- * sphinxdoc.css_t
- * ~~~~~~~~~~~~~~~
- *
- * Sphinx stylesheet -- sphinxdoc theme. Originally created by
- * Armin Ronacher for Werkzeug.
- *
- * :copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
- */
-
-@import url("basic.css");
-
-/* -- page layout ----------------------------------------------------------- */
-
-body {
- font-family: 'Lucida Grande', 'Lucida Sans Unicode', 'Geneva',
- 'Verdana', sans-serif;
- font-size: 14px;
- letter-spacing: -0.01em;
- line-height: 150%;
- text-align: center;
- background-color: #BFD1D4;
- color: black;
- padding: 0;
- border: 1px solid #aaa;
-
- margin: 0px 80px 0px 80px;
- min-width: 740px;
-}
-
-div.document {
- background-color: white;
- text-align: left;
- background-image: url(contents.png);
- background-repeat: repeat-x;
-}
-
-div.bodywrapper {
- margin: 0 240px 0 0;
- border-right: 1px solid #ccc;
-}
-
-div.body {
- margin: 0;
- padding: 0.5em 20px 20px 20px;
-}
-
-div.related {
- font-size: 1em;
-}
-
-div.related ul {
- background-image: url(navigation.png);
- height: 2em;
- border-top: 1px solid #ddd;
- border-bottom: 1px solid #ddd;
-}
-
-div.related ul li {
- margin: 0;
- padding: 0;
- height: 2em;
- float: left;
-}
-
-div.related ul li.right {
- float: right;
- margin-right: 5px;
-}
-
-div.related ul li a {
- margin: 0;
- padding: 0 5px 0 5px;
- line-height: 1.75em;
- color: #EE9816;
-}
-
-div.related ul li a:hover {
- color: #3CA8E7;
-}
-
-div.sphinxsidebarwrapper {
- padding: 0;
-}
-
-div.sphinxsidebar {
- margin: 0;
- padding: 0.5em 15px 15px 0;
- width: 210px;
- float: right;
- font-size: 1em;
- text-align: left;
-}
-
-div.sphinxsidebar h3, div.sphinxsidebar h4 {
- margin: 1em 0 0.5em 0;
- font-size: 1em;
- padding: 0.1em 0 0.1em 0.5em;
- color: white;
- border: 1px solid #86989B;
- background-color: #AFC1C4;
-}
-
-div.sphinxsidebar h3 a {
- color: white;
-}
-
-div.sphinxsidebar ul {
- padding-left: 1.5em;
- margin-top: 7px;
- padding: 0;
- line-height: 130%;
-}
-
-div.sphinxsidebar ul ul {
- margin-left: 20px;
-}
-
-div.footer {
- background-color: #E3EFF1;
- color: #86989B;
- padding: 3px 8px 3px 0;
- clear: both;
- font-size: 0.8em;
- text-align: right;
-}
-
-div.footer a {
- color: #86989B;
- text-decoration: underline;
-}
-
-/* -- body styles ----------------------------------------------------------- */
-
-p {
- margin: 0.8em 0 0.5em 0;
-}
-
-a {
- color: #CA7900;
- text-decoration: none;
-}
-
-a:hover {
- color: #2491CF;
-}
-
-div.body a {
- text-decoration: underline;
-}
-
-h1 {
- margin: 0;
- padding: 0.7em 0 0.3em 0;
- font-size: 1.5em;
- color: #11557C;
-}
-
-h2 {
- margin: 1.3em 0 0.2em 0;
- font-size: 1.35em;
- padding: 0;
-}
-
-h3 {
- margin: 1em 0 -0.3em 0;
- font-size: 1.2em;
-}
-
-div.body h1 a, div.body h2 a, div.body h3 a, div.body h4 a, div.body h5 a, div.body h6 a {
- color: black!important;
-}
-
-h1 a.anchor, h2 a.anchor, h3 a.anchor, h4 a.anchor, h5 a.anchor, h6 a.anchor {
- display: none;
- margin: 0 0 0 0.3em;
- padding: 0 0.2em 0 0.2em;
- color: #aaa!important;
-}
-
-h1:hover a.anchor, h2:hover a.anchor, h3:hover a.anchor, h4:hover a.anchor,
-h5:hover a.anchor, h6:hover a.anchor {
- display: inline;
-}
-
-h1 a.anchor:hover, h2 a.anchor:hover, h3 a.anchor:hover, h4 a.anchor:hover,
-h5 a.anchor:hover, h6 a.anchor:hover {
- color: #777;
- background-color: #eee;
-}
-
-a.headerlink {
- color: #c60f0f!important;
- font-size: 1em;
- margin-left: 6px;
- padding: 0 4px 0 4px;
- text-decoration: none!important;
-}
-
-a.headerlink:hover {
- background-color: #ccc;
- color: white!important;
-}
-
-cite, code, tt {
- font-family: 'Consolas', 'Deja Vu Sans Mono',
- 'Bitstream Vera Sans Mono', monospace;
- font-size: 0.95em;
- letter-spacing: 0.01em;
-}
-
-tt {
- background-color: #f2f2f2;
- border-bottom: 1px solid #ddd;
- color: #333;
-}
-
-tt.descname, tt.descclassname, tt.xref {
- border: 0;
-}
-
-hr {
- border: 1px solid #abc;
- margin: 2em;
-}
-
-a tt {
- border: 0;
- color: #CA7900;
-}
-
-a tt:hover {
- color: #2491CF;
-}
-
-pre {
- font-family: 'Consolas', 'Deja Vu Sans Mono',
- 'Bitstream Vera Sans Mono', monospace;
- font-size: 0.95em;
- letter-spacing: 0.015em;
- line-height: 120%;
- padding: 0.5em;
- border: 1px solid #ccc;
- background-color: #f8f8f8;
-}
-
-pre a {
- color: inherit;
- text-decoration: underline;
-}
-
-td.linenos pre {
- padding: 0.5em 0;
-}
-
-div.quotebar {
- background-color: #f8f8f8;
- max-width: 250px;
- float: right;
- padding: 2px 7px;
- border: 1px solid #ccc;
-}
-
-div.topic {
- background-color: #f8f8f8;
-}
-
-table {
- border-collapse: collapse;
- margin: 0 -0.5em 0 -0.5em;
-}
-
-table td, table th {
- padding: 0.2em 0.5em 0.2em 0.5em;
-}
-
-div.admonition, div.warning {
- font-size: 0.9em;
- margin: 1em 0 1em 0;
- border: 1px solid #86989B;
- background-color: #f7f7f7;
- padding: 0;
-}
-
-div.admonition p, div.warning p {
- margin: 0.5em 1em 0.5em 1em;
- padding: 0;
-}
-
-div.admonition pre, div.warning pre {
- margin: 0.4em 1em 0.4em 1em;
-}
-
-div.admonition p.admonition-title,
-div.warning p.admonition-title {
- margin: 0;
- padding: 0.1em 0 0.1em 0.5em;
- color: white;
- border-bottom: 1px solid #86989B;
- font-weight: bold;
- background-color: #AFC1C4;
-}
-
-div.warning {
- border: 1px solid #940000;
-}
-
-div.warning p.admonition-title {
- background-color: #CF0000;
- border-bottom-color: #940000;
-}
-
-div.admonition ul, div.admonition ol,
-div.warning ul, div.warning ol {
- margin: 0.1em 0.5em 0.5em 3em;
- padding: 0;
-}
-
-div.versioninfo {
- margin: 1em 0 0 0;
- border: 1px solid #ccc;
- background-color: #DDEAF0;
- padding: 8px;
- line-height: 1.3em;
- font-size: 0.9em;
-}
-
-.viewcode-back {
- font-family: 'Lucida Grande', 'Lucida Sans Unicode', 'Geneva',
- 'Verdana', sans-serif;
-}
-
-div.viewcode-block:target {
- background-color: #f4debf;
- border-top: 1px solid #ac9;
- border-bottom: 1px solid #ac9;
-}
-
-div.leftside {
- width: 550px;
- float: left;
- margin-top: 25px;
-}
-
-div.rightside {
- margin-left: 550px;
- margin-bottom: 25px;
-}
diff --git a/Doc/Sphinx/_static/bornagainapp_32.png b/Doc/Sphinx/_static/bornagainapp_32.png
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deleted file mode 100644
index 1bc185fc10ecd4f55fc973af72a100725b3805af..0000000000000000000000000000000000000000
--- a/Doc/Sphinx/_templates/layout.html
+++ /dev/null
@@ -1,21 +0,0 @@
-{% extends "!layout.html" %}
-
-{% block rootrellink %}
- <li><a href="{{ pathto('index') }}">Home</a>| </li>
- <li><a href="{{ pathto('documentation/documentation') }}">Documentation</a>| </li>
-
-{% endblock %}
-
-
-{% block relbar1 %}
-
-<div style="background-color: white; text-align: left; padding: 10px 10px 15px 15px">
-<a href="{{ pathto('index') }}"><img src="{{
-pathto("_static/logo.png", 1) }}" border="0" alt="sampledoc"/></a>
-</div>
-{{ super() }}
-{% endblock %}
-
-{# put the sidebar before the body #}
-{% block sidebar1 %}{{ sidebar() }}{% endblock %}
-{% block sidebar2 %}{% endblock %}
diff --git a/Doc/Sphinx/conf.py b/Doc/Sphinx/conf.py
deleted file mode 100644
index cbd95ff529c9891a9673c23992a98f575d84ed62..0000000000000000000000000000000000000000
--- a/Doc/Sphinx/conf.py
+++ /dev/null
@@ -1,243 +0,0 @@
-# -*- coding: utf-8 -*-
-#
-# BornAgain documentation build configuration file, created by
-# sphinx-quickstart on Mon Nov 3 09:40:56 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.
-
-import sys, os
-
-# 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('.'))
-
-# -- General configuration -----------------------------------------------------
-
-# If your documentation needs a minimal Sphinx version, state it here.
-#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.
-extensions = []
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
-
-# The suffix of source filenames.
-source_suffix = '.rst'
-
-# The encoding of source files.
-#source_encoding = 'utf-8-sig'
-
-# The master toctree document.
-master_doc = 'index'
-
-# General information about the project.
-project = u'BornAgain'
-copyright = u'2014, Scientific Computing Group at MLZ'
-
-# 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 = '0.9.9'
-# The full version, including alpha/beta/rc tags.
-release = '0.9.9'
-
-# 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
-
-# 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 = []
-
-
-# -- 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'
-html_theme = 'sphinxdoc'
-html_style = 'bornagain.css'
-
-# 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']
-
-# 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 = 'BornAgaindoc'
-
-# -- 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': '',
-}
-
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title, author, documentclass [howto/manual]).
-latex_documents = [
- ('index', 'BornAgain.tex', u'BornAgain Documentation',
- u'Scientific Computing Group at MLZ', '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 = [
- ('index', 'bornagain', u'BornAgain Documentation',
- [u'Scientific Computing Group at MLZ'], 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 = [
- ('index', 'BornAgain', u'BornAgain Documentation',
- u'Scientific Computing Group at MLZ', 'BornAgain', 'One line description of project.',
- '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'
diff --git a/Doc/Sphinx/documentation/documentation.rst b/Doc/Sphinx/documentation/documentation.rst
deleted file mode 100644
index 88a192e54d7073c8b07a1a815a227c679d8ea5d2..0000000000000000000000000000000000000000
--- a/Doc/Sphinx/documentation/documentation.rst
+++ /dev/null
@@ -1,24 +0,0 @@
-
-Documentation
-#############################
-
-
-.. toctree::
- :maxdepth: 2
-
- introduction/introduction.rst
- getting_started/getting_started.rst
- installation/installation.rst
- working_with_bornagain/working_with_bornagain.rst
- python_api/python_api.rst
-
-
-.. toctree::
- :maxdepth: 1
-
- troubleshooting/troubleshooting.rst
-
-.. toctree::
- :maxdepth: 1
-
- faq/faq.rst
diff --git a/Doc/Sphinx/documentation/faq/faq.rst b/Doc/Sphinx/documentation/faq/faq.rst
deleted file mode 100644
index 0f07e563a3a3997b7937f7f41506e68039333b3c..0000000000000000000000000000000000000000
--- a/Doc/Sphinx/documentation/faq/faq.rst
+++ /dev/null
@@ -1,28 +0,0 @@
-
-Frequently Asked Questions
-################################
-
-
-.. contents::
- :depth: 1
- :local:
- :backlinks: none
-
-
-How to request the new feature?
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-Create feature request using `BornAgain Bug and Issue Tracker <http://apps.jcns.fz-juelich.de/redmine/projects/bornagain/issues>`_
-
-
-How to use the bug and issue tracker?
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Users of the software who encounter problems during the installation
-of the framework or during the run of a simulation can use the web-based issue tracking system
-at `link <http://apps.jcns.fz-juelich.de/redmine/projects/bornagain/issues>`_
-to report a bug. The same system can be used to request new features.
-This system is open for all users in read mode, while
-submitting bug reports and feature requests are possible only after a simple registration
-procedure.
-
-
diff --git a/Doc/Sphinx/documentation/getting_started/getting_started.rst b/Doc/Sphinx/documentation/getting_started/getting_started.rst
deleted file mode 100644
index d32c42c9a0f3897c342930763eacdffd5951f9b8..0000000000000000000000000000000000000000
--- a/Doc/Sphinx/documentation/getting_started/getting_started.rst
+++ /dev/null
@@ -1,40 +0,0 @@
-
-Getting Started
-##############################
-
-BornAgain is supported under Windows, Mac OS X and Linux operating systems.
-For Windows and MacOS we provide binary installer packages, for Unix flavor we support build and installation from source.
-
-
-Download
-^^^^^^^^^^^^^^^^^^^^^^^^
-
-You can select and download appropriate package from `server <http://apps.jcns.fz-juelich.de/src/BornAgain>`_ or use one of direct links below.
-
-* Windows 7,8 binary installer `package <http://apps.jcns.fz-juelich.de/src/BornAgain/BornAgain-0.9.8-win32.exe>`_
-* MacOS 10.8 (Mountaign Lion) binary installer `package <http://apps.jcns.fz-juelich.de/src/BornAgain/BornAgain-0.9.8-win32.exe>`_
-* MacOS 10.9 (Maverick), 10.10 (Yousemite) binary installer `package <http://apps.jcns.fz-juelich.de/src/BornAgain/BornAgain-0.9.8-win32.exe>`_
-* Source `tarball <http://apps.jcns.fz-juelich.de/src/BornAgain/BornAgain-0.9.8-win32.exe>`_
-
-Alternatively one can obtain BornAgain source from our public Git repository.
-
-.. code-block:: bash
-
- $ git clone git://apps.jcns.fz-juelich.de/BornAgain.git
-
-Install
-^^^^^^^^^^^^^^^^^^^^^^^^
-
-There are installation instructions for following environments:
-
-* :ref:`installation_windows`
-* :ref:`installation_macos`
-* :ref:`installation_unix`
-
-First steps
-^^^^^^^^^^^^^^^^^^^^^^^^
-
-See :ref:`working_with_bornagain_label`
-
-
-
diff --git a/Doc/Sphinx/documentation/installation/installation.rst b/Doc/Sphinx/documentation/installation/installation.rst
deleted file mode 100644
index adc61d4caa2e7c2868caa5f53489ed61d96ecba9..0000000000000000000000000000000000000000
--- a/Doc/Sphinx/documentation/installation/installation.rst
+++ /dev/null
@@ -1,15 +0,0 @@
-
-Installation instructions
-================================
-
-BornAgain is supported under Windows, Mac OS X and Linux operating systems.
-For Windows and MacOS we provide binary installer packages, for Unix flavor (MacOS included) we support build and installation from source.
-
-There are installation instructions for the following environments:
-
-.. toctree::
- :maxdepth: 2
-
- installation_windows.rst
- installation_macos.rst
- installation_unix.rst
diff --git a/Doc/Sphinx/documentation/installation/installation_macos.rst b/Doc/Sphinx/documentation/installation/installation_macos.rst
deleted file mode 100644
index 147a19901e37f381a034d5ac9296e6d0786a8edd..0000000000000000000000000000000000000000
--- a/Doc/Sphinx/documentation/installation/installation_macos.rst
+++ /dev/null
@@ -1,5 +0,0 @@
-.. _installation_macos:
-
-Installation on MacOS
-----------------------------------------------------
-
diff --git a/Doc/Sphinx/documentation/installation/installation_unix.rst b/Doc/Sphinx/documentation/installation/installation_unix.rst
deleted file mode 100644
index e890f07e8b4f352a0a079277e11aff35de539899..0000000000000000000000000000000000000000
--- a/Doc/Sphinx/documentation/installation/installation_unix.rst
+++ /dev/null
@@ -1,24 +0,0 @@
-.. _installation_unix:
-
-Installation on Unix
-----------------------------------------------------
-
-This section describes how to build and install BornAgain libraries
-from source on Unix Platforms (MacOS included).
-
-.. toctree::
- :maxdepth: 3
-
- installation_unix_short.rst
- installation_unix_detailed.rst
-
-
-This advanced section explains in details how to build BornAgain's Graphical User Interface
-
-.. toctree::
- :maxdepth: 3
-
- installation_unix_gui.rst
-
-
-
\ No newline at end of file
diff --git a/Doc/Sphinx/documentation/installation/installation_unix_detailed.rst b/Doc/Sphinx/documentation/installation/installation_unix_detailed.rst
deleted file mode 100644
index a4b4c3bff6dff5cf6a5f916618b1d44b6779c475..0000000000000000000000000000000000000000
--- a/Doc/Sphinx/documentation/installation/installation_unix_detailed.rst
+++ /dev/null
@@ -1,241 +0,0 @@
-.. _detailed_installation_instruction_label:
-
-Detailed installation instruction
---------------------------------------
-
-This section describes in details how to build and install BornAgain core libraries
-from source on Unix Platforms (MacOS included).
-
-BornAgain uses ``CMake`` to configure a build system for compiling and installing the framework.
-There are following major steps to get BornAgain running
-
-.. contents::
- :depth: 1
- :local:
- :backlinks: none
-
-Install the third party software
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-To successfully build BornAgain a number of prerequisite packages must be installed.
-
-**Required**
-
- * compilers: clang versions >= 3.1 or GCC versions >= 4.1.2
- * cmake >= 2.8
- * boost library >=1.48
- * GNU scientific library >= 1.15
- * fftw3 library >= 3.3.1
- * python-2.7, python-devel, python-numpy-devel, python-matplotlib
-
-**Optional**
- * ROOT5 framework >= 5.34 (for additional fitting algorithms in BornAgain)
-
-All required packages can be easily installed on most Linux distributions using the system's package
-manager.
-
-Below we give a few examples for several selected operation systems. Please note,
-that other distributions (Fedora, Mint, etc) may have different commands for invoking the package manager and slightly different names of packages (like ``boost`` instead of ``libboost`` etc).
-Besides that, the installation should be very similar.
-
-
-
-
-Ubuntu, Debian
-""""""""""""""""""""
-
-Installing required packages
-
-.. code-block:: bash
-
- sudo apt-get install git cmake libgsl0-dev libboost-all-dev libfftw3-dev python-dev python-numpy python-matplotlib
-
-Installing optional packages
-
-.. code-block:: bash
-
- sudo apt-get install root-system
-
-OpenSuse
-""""""""""""""""""""
-
-Installing required packages
-
-.. code-block:: bash
-
- sudo zypper install git-core cmake gsl-devel boost-devel fftw3-devel python-devel python-numpy-devel python-matplotlib python-matplotlib-tk
-
-Installing optional packages. Adding ''scientific'' repository (for OpenSuse 13.1, for other versions use corresponding repository)
-
-.. code-block:: bash
-
- sudo zypper ar http://download.opensuse.org/repositories/science/openSUSE_13.1 science
-
-and then installing packages
-
-.. code-block:: bash
-
- sudo zypper install root-system
-
-
-
-Mac OS X
-""""""""""""""""""""
-
-To simplify the installation of third party open-source software on a Mac OS X system we recommend the use of
-`MacPorts <http://www.macports.org/install.php>`_ package manager. The easiest way to install ``MacPorts`` is by downloading the
-`dmg <http://www.macports.org/install.php>`_ and running the system's installer.
-After installation new command ``port`` will be available in terminal window of your Mac.
-
-Installing required packages
-
-.. code-block:: bash
-
- sudo port -v selfupdate
- sudo port install git-core cmake fftw-3 gsl py27-matplotlib py27-numpy py27-scipy
- sudo port install boost -no_single-no_static+python27
- sudo port select --set python python27
-
-Installing optional packages
-
-.. code-block:: bash
-
- sudo port install root +fftw3+python27
-
-.. important::
- By default ``MacPorts`` will be installed to separate ``/opt/local`` directory.
- This path has to be specified explicitely during ``CMake`` configuration using ``-DCMAKE_PREFIX_PATH=/opt/local``, see :ref:`below <important_cmake_prefix>`.
-
-Get the source
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-
-Download BornAgain source tarball from `link <http://apps.jcns.fz-juelich.de/src/BornAgain>`_ and unpack it
-
-.. code-block:: bash
-
- cd <some_directory>
- tar xfz BornAgain-0.9.9.tar.gz
-
-
-Alternatively, instead of downloading the tarball you can get access to the source code by cloning our public Git repository
-
-.. code-block:: bash
-
- cd <some_directory>
- git clone git://apps.jcns.fz-juelich.de/BornAgain.git
-
-.. note::
- Our Git repository holds two main branches called ``master`` and ``develop``. We consider ``master`` branch to be the main branch where the source code of HEAD always reflect latest stable release. Cloning the repository
-
- - gives you source code snapshot corresponding to the latest stable release,
- - automatically sets up your local master branch to track our remote master branch, so you will be able to fetch changes from remote branch at any time using ``git pull`` command.
-
- Master branch is updating approximately once per month. The second branch, ``develop`` branch, is a snapshot of the current development. This is where any automatic nightly builds are built from. The develop branch is
- always expected to work, so to get the most recent features one can switch source tree to it by
-
- .. code-block:: bash
-
- cd BornAgain
- git checkout develop
- git pull
-
-
-Build and install the framework
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-BornAgain should be build using `CMake <http://www.cmake.org>`_ cross platform build system. Having third-party libraries installed and BornAgain
-source code acquired as was explained in previous sections, type build commands
-
-
-.. code-block:: bash
-
- mkdir <build_dir>
- cd <build_dir>
- cmake -DCMAKE_INSTALL_PREFIX=<install_dir> <source_dir>
- make -j4
- make check
- make install
-
-.. _important_cmake_prefix:
-
- .. important::
-
- * Especially for MacOS users who has installed third party libraries using ``MacPorts`` package manager.
-
- In the case of a complex system setup, with libraries of different versions
- scattered across multiple places (``/opt/local``, ``/usr/local`` etc.),
- you may want to help ``CMake`` in finding the correct library paths
- by running it with additional parameter
-
- .. code-block:: bash
-
- cmake -DCMAKE_PREFIX_PATH=/opt/local -DCMAKE_INSTALL_PREFIX=<install_dir> <source_dir>
-
-
-Here ``<source_dir>`` is the name of directory, where BornAgain source code has been copied, ``<install_dir>`` is the directory, where user wants the package
-to be installed, and ``<build_dir>`` is the directory where building will occur.
-
-.. note::
-
- Having dedicated directory ``<build_dir>`` for build process is recommended by ``CMake``.
- That allows several builds with different compilers/options from the same source and keeps source directory clean from build remnants.
-
-
-Compilation process invoked by the command ``make`` lasts about 10 min for an average laptop of 2012 edition. On multi-core machines the compilation can be
-decreased by invoking command make with the parameter ``make -j[N]``, where N is the number of cores.
-
-Running functional tests is an optional but recommended step. Command ``make check``
-will compile several additional tests and run them one by one. Every tests contains
-simulation of typical GISAS geometry and comparison of simulation results with reference files on numerical level. Having 100% tests passed ensures that your local installation
-is correct.
-
-.. code-block:: bash
-
- make check
- ...
- 100% tests passed, 0 tests failed out of 61
- Total Test time (real) = 31.14 sec
- [100%] Build target check
-
-The last command ``make install`` copies compiled libraries and some usage examples
-into installation directory.
-
-After installation is completed, the location of BornAgain libraries needs to be included into
-``LD_LIBRARY_PATH`` and ``PYTHONPATH`` environment variables.
-This can be done by running BornAgain setup script in the terminal session
-
-.. code-block:: bash
-
- source <install_dir>/bin/thisbornagain.sh
-
-Conveniently, given call can be placed in your ``.bashrc`` file.
-
-
-Running the first simulation
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-In your installation directory you will find:
-
-+----------------------------------------------------+----------------------------------------------------------------------+
-| <install_dir>/share/BornAgain/Examples | directory with examples |
-+----------------------------------------------------+----------------------------------------------------------------------+
-| <install_dir>/lib | libraries to import into python or link with your C++ program |
-+----------------------------------------------------+----------------------------------------------------------------------+
-| <install_dir>/include | C++ headers to dive into the development |
-+----------------------------------------------------+----------------------------------------------------------------------+
-
-Run your first example and enjoy the first BornAgain simulation plot.
-
-.. code-block:: bash
-
- python <install_dir>/share/BornAgain/Examples/python/simulation/ex001_CylindersAndPrisms/CylindersAndPrisms.py
-
-
-.. seealso::
-
- :ref:`working_from_python_label`
-
- :ref:`building_gui_label`
-
- :ref:`troubleshooting_label`
diff --git a/Doc/Sphinx/documentation/installation/installation_unix_gui.rst b/Doc/Sphinx/documentation/installation/installation_unix_gui.rst
deleted file mode 100644
index b9c20414044bd8b3cc65091d9a2b22453a8d36f7..0000000000000000000000000000000000000000
--- a/Doc/Sphinx/documentation/installation/installation_unix_gui.rst
+++ /dev/null
@@ -1,151 +0,0 @@
-.. _building_gui_label:
-
-Building Graphical User Interface
----------------------------------------
-
-This section describes how to build and install BornAgain graphical user interface on Unix platforms (MacOS included).
-
-Please follow first the :ref:`detailed_installation_instruction_label`
-to learn how to build and install BornAgain core libraries. When completed, proceed with the following additional steps:
-
-
-.. contents::
- :depth: 1
- :local:
- :backlinks: none
-
-
-
-Install Qt5 libraries
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-BornAgain GUI depends on `Qt5 <http://qt-project.org/qt5>`_ libraries.
-Most of Linux distributions, as well as MacOS, do not have it by default and you have to install it either via system package manager or using Qt binary installer
-downloaded from the developers site.
-
-Below we provide recipe we use, to install latest Qt5 libraries on our Linux and MacOS operation systems
-
-
-MacOS systems
-"""""""""""""""
-
-1. Download *Qt Online installer for Mac* from developers `site <http://qt-project.org/doc/qt-5/linux.html>`_
-
-2. Run installer, then follow the instructions:
-
- By default Qt will be installed in the directory ``/Users/yourname/Qt``
-
-3. After the installation insert following environment variables into ``.profile`` file of your home directory::
-
- export QTDIR=/Users/yourname/Qt/5.3/clang_64
- export PATH=$QTDIR/bin:$PATH
- export DYLD_LIBRARY_PATH=$QTDIR/lib:$DYLD_LIBRARY_PATH
-
-..
-
- You have to adjust ``QTDIR`` variable for the Qt version number and ``yourname`` to point to the right Qt directory.
-
-
-
-
-Linux systems
-"""""""""""""""
-
-1. Download *Qt online installer for Linux 64-bit* from developers `site <http://qt-project.org/doc/qt-5/linux.html>`_
-
-2. Run installer from the command line, then follow the instructions::
-
- ./qt-opensource-linux-x64-1.6.0-4-online.run
-
-..
-
- By default Qt will be installed in the directory ``/home/yourname/Qt``
-
-3. Specify following variables in your ``.bashrc`` file::
-
- export QTDIR=/home/yourname/Qt/5.3/gcc_64
- export PATH=$QTDIR/bin:$PATH
- export LD_LIBRARY_PATH=$QTDIR/lib:$LD_LIBRARY_PATH
-
-..
-
- You have to adjust ``QTDIR`` variable for the Qt version number and ``yourname`` to point to the right Qt directory.
-
-
-.. note::
-
- Open new terminal and validate that ``qmake --version`` command gives you the right Qt version you have just installed::
-
- Linux> Using Qt version 5.3.1 in /home/yourname/Qt/5.3/gcc_64/lib
-
- MacOS> Using Qt version 5.3.1 in /Users/yourname/Qt/5.3/clang_64/lib
-
-
-
-
-Buld and install BornAgain GUI
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-We assume that you have already BornAgain libraries compiled and installed as explained in :ref:`detailed_installation_instruction_label`
-and that
-
-+------------------------+-----------------------------------------------------+
-| <source_dir> | is your BornAgain source directory |
-+------------------------+-----------------------------------------------------+
-| <build_dir> | the directory were BornAgain core was build |
-+------------------------+-----------------------------------------------------+
-| <install_dir> | the directory where BornAgain core was installed |
-+------------------------+-----------------------------------------------------+
-
-Change the directory to ``<build_dir>``
-
-.. code-block:: bash
-
- cd <build_dir>
-
-type following cmake configuration command
-
-**MacOS system (with third party librarties in /opt/local)**
-
-.. code-block:: bash
-
- cmake -DBORNAGAIN_GUI=ON -DCMAKE_PREFIX_PATH=/opt/local -DCMAKE_INSTALL_PREFIX=<install_dir> <source_dir>
-
-**Linux systems**
-
-.. code-block:: bash
-
- cmake -DBORNAGAIN_GUI=ON -DCMAKE_INSTALL_PREFIX=<install_dir> <source_dir>
-
-
-Finally, compile and install the graphical users interface
-
-.. code-block:: bash
-
- make -j4
- make install
-
-
-Run BornAgain GUI
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-After installation is complete the new ``BornAgain`` executable will appear in ``<install_dir>/bin`` directory.
-Make sure that BornAgain core libraries are in your PATH by running
-
-.. code-block:: bash
-
- source <install_dir>/bin/thisbornagain.sh
-
-and launch GUI
-
-
-.. code-block:: bash
-
- <install_dir>/bin/BornAgain
-
-
-.. seealso::
-
- :ref:`using_gui_label`
-
- :ref:`troubleshooting_label`
diff --git a/Doc/Sphinx/documentation/installation/installation_unix_short.rst b/Doc/Sphinx/documentation/installation/installation_unix_short.rst
deleted file mode 100644
index f2aaa8743a08010e0dde9ed3ef9e003b0ae27127..0000000000000000000000000000000000000000
--- a/Doc/Sphinx/documentation/installation/installation_unix_short.rst
+++ /dev/null
@@ -1,55 +0,0 @@
-Installation instruction (short version)
------------------------
-
-This page shortly explains how to build and install BornAgain framework from source on Unix platforms.
-
-Install the third party software
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-* cmake (>= 2.8)
-* boost library (>= 1.48)
-* GNU scientific library (>= 1.15)
-* fftw3 library (>= 3.3.1)
-* python-2.7, python-devel, python-numpy-devel
-
-
-
-Get the source
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Download BornAgain source tarball from `link <http://apps.jcns.fz-juelich.de/src/BornAgain>`_
-or use following git repository
-
-.. code-block:: bash
-
- $ git clone git://apps.jcns.fz-juelich.de/BornAgain.git
-
-
-Build and install the framework
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-**Without Graphical User Interface**
-
-.. code-block:: bash
-
- $ mkdir <build_dir>; cd <build_dir>;
- $ cmake -DCMAKE_INSTALL_PREFIX=<install_dir> <source_dir>
- $ make -j4
- $ make check
- $ make install
-
-**With Graphical User Interface**
-
-* Install additionally Qt5 libraries
-* Use additional key ``-DBORNAGAIN_GUI=ON`` during CMake configuration
-
-.. code-block:: bash
-
- $ cmake -DBORNAGAIN_GUI=ON -DCMAKE_INSTALL_PREFIX=<install_dir> <source_dir>
-
-.. seealso::
-
- :ref:`detailed_installation_instruction_label`
-
-
-
\ No newline at end of file
diff --git a/Doc/Sphinx/documentation/installation/installation_windows.rst b/Doc/Sphinx/documentation/installation/installation_windows.rst
deleted file mode 100644
index 1c053081bfa38cbf57bb8e20a9d93768d4f6dbe7..0000000000000000000000000000000000000000
--- a/Doc/Sphinx/documentation/installation/installation_windows.rst
+++ /dev/null
@@ -1,80 +0,0 @@
-.. _installation_windows:
-
-
-Installation on Windows
-----------------------------------------------------
-
-For the moment, we provide 32-bit installer package which can be installed into either a 32-bit or a 64-bit Windows 7,8 systems.
-
-To install and run BornAgain for the first time proceed with the following steps:
-
-.. contents::
- :depth: 1
- :local:
- :backlinks: none
-
-
-Install the third party software
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-The current version of BornAgain requires ``python-2.7, matplotlib, numpy``
-to be installed on the system. These set of packages is known as `SciPy stack <http://www.scipy.org>`_ and for most users
-the easiest way to install it, is to download one of free Python distributions, which includes all the key packages.
-
-The list of possible options is given on SciPy installation `site <http://www.scipy.org/install.html>`_.
-
-We have tested `Anaconda Python Distribution <https://store.continuum.io/cshop/anaconda>`_ and suggest to use it if you do not have any other preferences.
-
-* Download and install Anaconda *Windows 32-bit — Python 2.7 — Graphical Installer* from `link <http://continuum.io/downloads>`_ before proceeding to
- the installation of BornAgain.
-
-
-
-
-Use BornAgain installer
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-BornAgain installation package for Windows 7,8 can be downloaded from `link <http://apps.jcns.fz-juelich.de/src/BornAgain>`_.
-After downloading the installer, double click ``.exe`` file and follow the instructions on the screen.
-
-
-Run the first simulation
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Run Graphical User Interface
-""""""""""""""""""""""""""""
-
-Use BornAgain icon |BornAgainIcon| located on the desktop to start GUI.
-
-.. |BornAgainIcon| image:: ../../_static/bornagainapp_32.png
- :align: top
-
-.. seealso::
-
- :ref:`using_gui_label`
-
-
-Run Python example
-""""""""""""""""""""""""""""
-
-Run an example located in BornAgain installation directory by double-clicking on python file:
-
-.. code-block:: bash
-
- python C:/BornAgain-<Version>/Examples/python/simulation/ex001_CylindersAndPrisms/CylindersAndPrisms.py
-
-You have to see immediately a scattering image appeared on the screen.
-
-.. hint::
- This step will work only if Python file extensions ``*.py`` are associated by the system with Python interpreter.
- If it is not the case, Windows will ask to choose what program to use to open the file. Depending from your Python installation
- it might be, for example,
- ``C:\Anaconda\python.exe`` or ``C:\Users\yourname\Anaconda\python.exe``.
-
-
-.. seealso::
-
- :ref:`working_from_python_label`
-
-
-
-
diff --git a/Doc/Sphinx/documentation/introduction/introduction.rst b/Doc/Sphinx/documentation/introduction/introduction.rst
deleted file mode 100644
index 202f5771877de62d95e6a4b2f7be70498dc895cd..0000000000000000000000000000000000000000
--- a/Doc/Sphinx/documentation/introduction/introduction.rst
+++ /dev/null
@@ -1,2 +0,0 @@
-Introduction
-##############################
diff --git a/Doc/Sphinx/documentation/python_api/python_api.rst b/Doc/Sphinx/documentation/python_api/python_api.rst
deleted file mode 100644
index a3c446fa844b9797d8ae02ed9015bcdcbc507cc5..0000000000000000000000000000000000000000
--- a/Doc/Sphinx/documentation/python_api/python_api.rst
+++ /dev/null
@@ -1,3 +0,0 @@
-Python API
-#####################
-
diff --git a/Doc/Sphinx/documentation/troubleshooting/troubleshooting.rst b/Doc/Sphinx/documentation/troubleshooting/troubleshooting.rst
deleted file mode 100644
index c7fa6802edfe3411cfc450aecd5f96d9459b66b5..0000000000000000000000000000000000000000
--- a/Doc/Sphinx/documentation/troubleshooting/troubleshooting.rst
+++ /dev/null
@@ -1,26 +0,0 @@
-.. _troubleshooting_label:
-
-Troubleshooting
-==========================
-
-
-BornAgain was successfully tested on a variety of Windows, MacOS and Unix platforms.
-Nevertheless, problems can still occur.
-
-We welcome feedback and bug reports related to the
-installation and use of BornAgain framework via
-
-* bornagain.project@gmail.com
-
-* `BornAgain Bug and Issue Tracker <http://apps.jcns.fz-juelich.de/redmine/projects/bornagain/issues>`_
-
-
-Please send us e-mail or fill in bug report providing all relevant information which will help us to quickly spot the problem.
-
-
-Please refer to the following sections which might help to identify the source of the problem
-
-.. toctree::
- :maxdepth: 1
-
- troubleshooting_installation_unix.rst
diff --git a/Doc/Sphinx/documentation/troubleshooting/troubleshooting_installation_unix.rst b/Doc/Sphinx/documentation/troubleshooting/troubleshooting_installation_unix.rst
deleted file mode 100644
index 575394d9351818d1760dcf7a1c14e3191b97761a..0000000000000000000000000000000000000000
--- a/Doc/Sphinx/documentation/troubleshooting/troubleshooting_installation_unix.rst
+++ /dev/null
@@ -1,45 +0,0 @@
-
-
-Installation problems on Unix platforms
-------------------------------------------
-
-.. contents::
- :depth: 1
- :local:
- :backlinks: none
-
-
-
-CMake configuration fails
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-CMake might fail with the error message::
-
- Configuring incomplete, errors occurred!
-
-or similar if some of the third party libraries are not installed on the system, or cmake is not able to find them.
-Please send us the log file ``my_cmake.log`` generated by running the following command in the empty ``<build_dir>``
-
-.. code-block:: bash
-
- cmake -DCMAKE_INSTALL_PREFIX=<install_dir> <source_dir> >& my_cmake.log
-
-
-
-
-
-Compilation fails
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-In the case of a complex system setup, with libraries of different versions
-scattered across multiple places ``cmake`` might make an error in identifying correct paths to the libraries or include directories.
-This might lead at some point to the compilation failure.
-This might happen, for example, during compilation of BornAgain graphical user interface if the system has both Qt4 and Qt5 libraries installed.
-Please send us the build log generated by running following make command
-
-.. code-block:: bash
-
- make VERBOSE=1 >& my_build.log
-
-
-
diff --git a/Doc/Sphinx/documentation/working_with_bornagain/functionality_overview.rst b/Doc/Sphinx/documentation/working_with_bornagain/functionality_overview.rst
deleted file mode 100644
index eecd53df33241ee88f32a39c508cb3088279c20b..0000000000000000000000000000000000000000
--- a/Doc/Sphinx/documentation/working_with_bornagain/functionality_overview.rst
+++ /dev/null
@@ -1,113 +0,0 @@
-
-Functionality overview
-=============================
-BornAgain enables the simulation and fitting of the scattering from different geometries of samples. Below is a list of the building blocks and their features, which are available in BornAgain.
-
-Layers
-----------------------------------------------------
-
-* Support multilayers without any restrictions on the number of layers
-* Interface roughness correlation
-* Magnetic materials
-
-.. figure:: ../../_static/fct_layer.png
- :width: 200px
- :align: center
- :figclass: align-center
-
- *Multilayered structure with roughness*
-
-
-
-Particles
-----------------------------------------------------
-
-* Choice between different shapes of nanoparticles (form factors)
-* Particles with inner structures
-* Assemblies of particles
-* Size distribution of the particles (polydispersity)
-
-.. figure:: ../../_static/fct_diff_ff.png
- :align: center
-
- *Selection of shapes available in BornAgain:*
-
- *elementary shapes, combination of particles, core-shell particles, and polydisperse distribution.*
-
-
-
-
-Positions of particles
-----------------------------------------------------
-* Decoupled implementations between vertical and planar positions
-* Vertical distributions:
-
-
-.. figure:: ../../_static/fct_buried_emb_part.png
- :width: 200px
- :align: center
- :figclass: align-center
-
- *Deposited or embedded layers of particles*
-
-
-
-
-* Planar distributions:
-
- * Disordered systems
- * Short-range order distribution (paracrystals)
- * 2D lattices
-
-
-.. figure:: ../../_static/fct_disorder_lattice.png
- :width: 400px
- :align: center
- :figclass: align-center
-
- *Examples of planar distribution of particles: disordered and lattice*
-
-
-
-
-* Fine tuning by rotating and / or translating the particles
-
-
-
-Input beam
-----------------------------------------------------
-* Polarized or unpolarized neutrons
-* X-ray
-* Divergence of the input beam (wavelength, incident angles...)
- following different distributions
-* Possible normalization of the input intensity
-
-
-.. figure:: ../../_static/fct_beamdiv.png
- :width: 250px
- :align: center
- :figclass: align-center
-
- *Input beam with wavelength divergence*
-
-
-Detector
-----------------------------------------------------
-* Off specular scattering
-* 2D intensity matrix, function of the output angles
-
-
-
-Use of BornAgain
-----------------------------------------------------
-* Simulation of GISAXS and GISANS from the generated sample
-* Fitting to reference data (experimental or numerical)
-* Interactions via
-
- * Python scripting
-
- see :ref:`working_from_python_label`
-
- * Graphical User Interface
-
- see :ref:`using_gui_label`
diff --git a/Doc/Sphinx/documentation/working_with_bornagain/usage_examples.rst b/Doc/Sphinx/documentation/working_with_bornagain/usage_examples.rst
deleted file mode 100644
index 2dc6ac0b5417e21d200c852bb1c0b695a80ec641..0000000000000000000000000000000000000000
--- a/Doc/Sphinx/documentation/working_with_bornagain/usage_examples.rst
+++ /dev/null
@@ -1,3 +0,0 @@
-
-Examples of BornAgain usage
-=============================
diff --git a/Doc/Sphinx/documentation/working_with_bornagain/using_gui.rst b/Doc/Sphinx/documentation/working_with_bornagain/using_gui.rst
deleted file mode 100644
index eda5e4c21ec35d161482f2690e91eea4031ef1e9..0000000000000000000000000000000000000000
--- a/Doc/Sphinx/documentation/working_with_bornagain/using_gui.rst
+++ /dev/null
@@ -1,36 +0,0 @@
-.. _using_gui_label:
-
-Using Graphical User Interface
-=================================
-
-
-The current beta version of BornAgain GUI allows the user
-to create multi-layered samples, populate them with particles, run
-scattering simulations and save the results in a publication quality form.
-
-The following video presents how to use BornAgain graphical user interface
-
-.. raw:: html
-
- <object width="480" height="385"><param name="movie"
- value="http://www.youtube.com/v/SBqYZ3KdAUc&hl=en_US&fs=1&rel=0"></param><param
- name="allowFullScreen" value="true"></param><param
- name="allowscriptaccess" value="always"></param><embed
- src="http://www.youtube.com/v/SBqYZ3KdAUc&hl=en_US&fs=1&rel=0"
- type="application/x-shockwave-flash" allowscriptaccess="always"
- allowfullscreen="true" width="480"
- height="385"></embed></object>
-
-
-See also
-
-.. toctree::
- :maxdepth: 2
-
- using_gui_quickstart.rst
- using_gui_overview.rst
- using_gui_details.rst
-
-
-
-
\ No newline at end of file
diff --git a/Doc/Sphinx/documentation/working_with_bornagain/using_gui_details.rst b/Doc/Sphinx/documentation/working_with_bornagain/using_gui_details.rst
deleted file mode 100644
index 3a47fed5f4d6da63036548f33c3317a8aab267cb..0000000000000000000000000000000000000000
--- a/Doc/Sphinx/documentation/working_with_bornagain/using_gui_details.rst
+++ /dev/null
@@ -1,5 +0,0 @@
-.. _using_gui_details_label:
-
-Using GUI in more details
-===================================
-
diff --git a/Doc/Sphinx/documentation/working_with_bornagain/using_gui_overview.rst b/Doc/Sphinx/documentation/working_with_bornagain/using_gui_overview.rst
deleted file mode 100644
index 622999176e4f726345cde59151b9836a261135ae..0000000000000000000000000000000000000000
--- a/Doc/Sphinx/documentation/working_with_bornagain/using_gui_overview.rst
+++ /dev/null
@@ -1,219 +0,0 @@
-.. _using_gui_overview_label:
-
-
-BornAGain GUI Overview
-============================
-
-The basic features of interface are explained below.
-
-Welcome view
--------------------
-
-
-When you start BornAgain GUI, you will be presented with the Welcome View, where you can
-
-* Create new projects
-* Open recent projects
-
-
-.. image:: ../../_static/gui_welcomeview_l800.png
- :align: center
- :target: ../../_static/gui_welcomeview_l.png
-
-
-You can use the view selector located on the left vertical panel (1) to change to one of the following views :
-
-* |InstrumentIcon| The :ref:`instrument_view_label` is used to change the settings of the scattering instrument
-* |SampleIcon| The :ref:`sample_view_label` is used to construct the samples
-* |SimulationIcon| The :ref:`simulation_view_label` is used to run the simulation
-* |JobsIcon| The :ref:`jobs_view_label` represents the results of the simulation
-
-.. |InstrumentIcon| image:: ../../_static/icon_instrument.png
- :align: bottom
-
-.. |SampleIcon| image:: ../../_static/icon_sample.png
- :align: bottom
-
-.. |SimulationIcon| image:: ../../_static/icon_simulation.png
- :align: bottom
-
-.. |JobsIcon| image:: ../../_static/icon_jobs.png
- :align: bottom
-
-
-
-
-.. _instrument_view_label:
-
-Instrument View
--------------------
-
-The Instrument View is used to create new scattering instruments and adjust their settings. The view consists in the instrument selector located on the left (1)
-and the instrument settings window located on the right (2).
-
-.. image:: ../../_static/gui_instrumentview_l800.png
- :align: center
- :target: ../../_static/gui_instrumentview_l.png
-
-On the instrument settings window (2) you can modify the settings of the currently selected instrument:
-
-* The name of the instrument
-* The beam parameters
-* The detector parameters
-
-
-
-
-.. _sample_view_label:
-
-Sample View
--------------------
-
-The Sample View allows you to design the sample via a drag-and-drop interface. It consists in a 4 main parts
-
-* The item toolbox (1) contains a variety of items to build the sample
-* The sample canvas (2) is used to assemble the sample
-* The sample tree view (3) represents the hierarchy of the objects composing the sample
-* The property editor (4) can be used to edit the parameters of the currently selected item
-
-
-.. image:: ../../_static/gui_sampleview_l800.png
- :align: center
- :target: ../../_static/gui_sampleview_l.png
-
-The sample constructed in this figure comprises a substrate on which are deposited, in equal proportion, cylinders and prisms. The interference between scattered waves is provided
-via two-dimensional paracrystal interference function.
-
-The sample is constructed by dragging items from the item toolbox (1), dropping them on the sample canvas (2), connecting the items of the appropriate types together and adjusting their properties,
-if necessary, using the property editor (4).
-
-In given figure, the property editor shows the parameters of currently selected cylindrical particles (radius and height of cylinders, their material, particles depth and abundance).
-
-.. note::
-
- The sample shown on this plot was constructed using the following steps:
-
- * The multilayer item was taken from the item toolbox and placed on the sample canvas
- * Two layer items were taken from the item toolbox and placed on top of the multilayer
-
- * The materials of the top and buttom layers were changed from the default one using the property editor
-
- * ParticleLayout item was taken from item toolbox, placed on sample canvas and connected with the top layer
-
- * Cylinders and prisms were dropped on the sample canvas and connected with the ParticleLayout
-
- * The materials of particles were changed from the default one using the property editor
-
- * The interference function representing a 2D paracrystal was placed on the sample canvas and connected with the ParticleLayout item
-
-.. note::
- * The sample canvas can have any number of multilayers. If this is the case, during the configuration of the simulation user will have to choose which multilayer to simulate.
- * The multilayer is considered as valid for the simulation, if it contains at least one layer
-
-
-
-
-.. User can have as many objects on sample canvas as he likes. But only multi-layers (with at least one layer inside) will be available for consequent simulation.
-
-
-
-.. _simulation_view_label:
-
-Simulation View
--------------------
-
-The Simulation View contains three important elements
-
-* The data selection box for selecting the instrument and the sample to simulate (1)
-* Simulation Parameters box for changing main simulation parameters (2)
-* The Run Simulation button (3)
-
-.. image:: ../../_static/gui_simulationview_l800.png
- :align: center
- :target: ../../_static/gui_simulationview_l.png
-
-The names of the defined instruments and samples are displayed in Data Selection box (1). From where the user can select a combination to run the simulation.
-
-Clicking on the Run Simulation button (3) immideately starts the simulation. When completed, the current view is automatically switched to the Jobs View showing the simulation results.
-This behaviour can be modified by changing Run Policy in (2).
-
-
-.. _jobs_view_label:
-
-Jobs View
--------------------
-
-The Jobs View displays results of the simulation. It has two different presentations called
-
-.. contents::
- :depth: 1
- :local:
- :backlinks: none
-
-Job View Activity is shown by default.
-
-Job View Activity
-""""""""""""""""""""""""""""
-
-The layout of the Job View Activity consists of three elements
-
-* The jobs selector widget (1) for selecting the specific job to be displayed
-* The job properties widget (2) contains basic information about the currently selected job
-* The intensity data widget (3) shows the intensity data of the currently selected job
-
-The toolbar (4) contains set of control elements for job selector and intensity data widgets. The right corner of toolbar is occupied by the Jobs Activity selector.
-
-.. image:: ../../_static/gui_jobview_l800.png
- :align: center
- :target: ../../_static/gui_jobview_l.png
-
-The two completed jobs can be seen in the job selector widget (1), with job2 currently selected and dislayed.
-
-.. note::
-
- The intensity image in widget (3) offers several ways of interaction:
-
- * Using the mouse wheel to zoom in and out
- * Dragging the color palette on the right of the image to change the min, max range of z-axis
- * The toolbar (4) on top of intensity data widget gives access to more options via Plot Properties and Projections buttons
-
-.. image:: ../../_static/gui_jobview_proj_l800.png
- :align: center
- :target: ../../_static/gui_jobview_proj_l.png
-
-The image represents the results of job2 with the Projections (1) and Plot Properties (2) widgets switched On. The type of colorbar gradient is changed from the default Polar to Spectrum.
-
-Real Time Activity
-""""""""""""""""""""""""""""
-
-The second layout of Job View is called the Real Time Activity. It can be switched on by selecting the appropriate item in the box located in the right corner of tool bar (1).
-
-.. image:: ../../_static/gui_jobview_realtime_l800.png
- :align: center
- :target: ../../_static/gui_jobview_realtime_l.png
-
-The layout of Job View consist of Intensity Data widget on the left (2), and additional parameter tree located on the right (3).
-
-
-The parameter tree represents all parameters which have been used during the construction of scattering instrument and the sample.
-Each displayed parameter value can be adjusted using the slider.
-The simulation will run in the background and the Intensity Data widget will be constantly updated
-reflecting the influence of this given parameter on the simulation results.
-
-.. note::
-
- Real Time View works smoothly only for simple geometries, when the simulation requires fractions of a second to run.
- For more complex geometries, demanding lots of CPU, the user will see a progress bar and any movements of the slider will not have any influence on the Intensity Data widget.
- In this case the user may try to speed up the simulation by decreasing the number of detector channels in the Instrument View and submitting new job by running the simulation from Simulation View.
-
-.. important::
-
- The jobs in Jobs View are completely isolated from the rest of the program. Any adjustments of sample parameters in Sample View or
- instrument parameters in Instrument View
- won't have any influence on jobs already completed or still running in Jobs View. Similarly, any parameter adjustments made in the parameter tree (3)
- will not be propagated back into Sample or Instrument Views.
-
-
-
-
-
\ No newline at end of file
diff --git a/Doc/Sphinx/documentation/working_with_bornagain/using_gui_quickstart.rst b/Doc/Sphinx/documentation/working_with_bornagain/using_gui_quickstart.rst
deleted file mode 100644
index 13d45c77b578ab44aeed7eb5b556c25e217fefdd..0000000000000000000000000000000000000000
--- a/Doc/Sphinx/documentation/working_with_bornagain/using_gui_quickstart.rst
+++ /dev/null
@@ -1,64 +0,0 @@
-.. _using_gui_quickstart_label:
-
-
-Quick Start
-===================================
-
-This tutorial demonstrates how to run the simulation and get simulated intensity data image in a few mouse clicks.
-
-
-**1. Run BornAgain Graphical User Interface**
-
-Use BornAgain icon |BornAgainIcon| located on the desktop (Windows) or look for it on Launchpad (MacOS) to start GUI.
-
-.. |BornAgainIcon| image:: ../../_static/bornagainapp_32.png
- :align: top
-
-
-For Linux users run an executable located in BornAgain installation directory from command line
-
-.. code-block:: bash
-
- $ <install_dir>/bin/BornAgain
-
-
-**2. Switch to the Sample View**
-
-.. image:: ../../_static/gui_quickstart1_700.png
- :align: center
- :target: ../../_static/gui_quickstart1.png
-
-When you start BornAgain GUI, you will be presented with the Welcome View as shown on the plot.
-Switch to the Sample View by clicking on the pictogram marked on the left panel.
-
-
-**3. Construct the sample**
-
-.. image:: ../../_static/gui_quickstart2_700.png
- :align: center
- :target: ../../_static/gui_quickstart2.png
-
-
-Drag predefined standard sample with the name Example#1 from item toolbox and drop it on the canvas.
-
-.. image:: ../../_static/gui_quickstart2b_700.png
- :align: center
- :target: ../../_static/gui_quickstart2b.png
-
-You will get the sample representing the multilayer with two types of particles on top of substrate
-
-**4. Run the simulation**
-
-
-.. image:: ../../_static/gui_quickstart3_700.png
- :align: center
- :target: ../../_static/gui_quickstart3.png
-
-Switch to the Simulation View and press Run Simulation button.
-
-
-.. image:: ../../_static/gui_quickstart3b_700.png
- :align: center
- :target: ../../_static/gui_quickstart3b.png
-
-When simulation is completed, the current view will be automatically switched to the Jobs View showing the intensity data results.
diff --git a/Doc/Sphinx/documentation/working_with_bornagain/working_from_python.rst b/Doc/Sphinx/documentation/working_with_bornagain/working_from_python.rst
deleted file mode 100644
index c2bf2d0553977214c89ec18299764cb1abf19e2b..0000000000000000000000000000000000000000
--- a/Doc/Sphinx/documentation/working_with_bornagain/working_from_python.rst
+++ /dev/null
@@ -1,6 +0,0 @@
-.. _working_from_python_label:
-
-
-Working with Python scripting
-==============================
-
diff --git a/Doc/Sphinx/documentation/working_with_bornagain/working_with_bornagain.rst b/Doc/Sphinx/documentation/working_with_bornagain/working_with_bornagain.rst
deleted file mode 100644
index a49000bd1b2021758d5c58865d7893c3568faf3b..0000000000000000000000000000000000000000
--- a/Doc/Sphinx/documentation/working_with_bornagain/working_with_bornagain.rst
+++ /dev/null
@@ -1,16 +0,0 @@
-.. _working_with_bornagain_label:
-
-
-Working with BornAgain
-####################################
-
-
-.. toctree::
- :maxdepth: 2
-
-
- functionality_overview.rst
- using_gui.rst
- working_from_python.rst
- usage_examples.rst
-
\ No newline at end of file
diff --git a/Doc/Sphinx/index.rst b/Doc/Sphinx/index.rst
deleted file mode 100644
index a12122f484064c8a731f863dcfcc5c79b9b03aa5..0000000000000000000000000000000000000000
--- a/Doc/Sphinx/index.rst
+++ /dev/null
@@ -1,24 +0,0 @@
-.. BornAgain documentation master file, created by
- sphinx-quickstart on Mon Nov 3 09:40:56 2014.
- You can adapt this file completely to your liking, but it should at least
- contain the root `toctree` directive.
-
-Welcome to BornAgain's documentation!
-=====================================
-
-Contents:
-
-.. toctree::
- :maxdepth: 2
-
- documentation/documentation.rst
-
-
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
-