diff --git a/docs/Makefile b/docs/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..b27f5bfe4ba935861e7c2193daaa20bae660b4b8
--- /dev/null
+++ b/docs/Makefile
@@ -0,0 +1,177 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = build
+
+# User-friendly check for sphinx-build
+ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
+$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
+endif
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+
+.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 "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
+	@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 "  xml        to make Docutils-native XML files"
+	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
+	@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/pyNEMO.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/pyNEMO.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/pyNEMO"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/pyNEMO"
+	@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."
+
+latexpdfja:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through platex and dvipdfmx..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
+	@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."
+
+xml:
+	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+	@echo
+	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+pseudoxml:
+	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+	@echo
+	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
diff --git a/docs/make.bat b/docs/make.bat
new file mode 100644
index 0000000000000000000000000000000000000000..b778f9ff800963f5337a7f1e402592e13fd8aef1
--- /dev/null
+++ b/docs/make.bat
@@ -0,0 +1,242 @@
+@ECHO OFF
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set BUILDDIR=build
+set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% source
+set I18NSPHINXOPTS=%SPHINXOPTS% source
+if NOT "%PAPER%" == "" (
+	set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
+	set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS%
+)
+
+if "%1" == "" goto help
+
+if "%1" == "help" (
+	: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.  text       to make text files
+	echo.  man        to make manual pages
+	echo.  texinfo    to make Texinfo files
+	echo.  gettext    to make PO message catalogs
+	echo.  changes    to make an overview over all changed/added/deprecated items
+	echo.  xml        to make Docutils-native XML files
+	echo.  pseudoxml  to make pseudoxml-XML files for display purposes
+	echo.  linkcheck  to check all external links for integrity
+	echo.  doctest    to run all doctests embedded in the documentation if enabled
+	goto end
+)
+
+if "%1" == "clean" (
+	for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
+	del /q /s %BUILDDIR%\*
+	goto end
+)
+
+
+%SPHINXBUILD% 2> nul
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "html" (
+	%SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/html.
+	goto end
+)
+
+if "%1" == "dirhtml" (
+	%SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.
+	goto end
+)
+
+if "%1" == "singlehtml" (
+	%SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml.
+	goto end
+)
+
+if "%1" == "pickle" (
+	%SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can process the pickle files.
+	goto end
+)
+
+if "%1" == "json" (
+	%SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can process the JSON files.
+	goto end
+)
+
+if "%1" == "htmlhelp" (
+	%SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can run HTML Help Workshop with the ^
+.hhp project file in %BUILDDIR%/htmlhelp.
+	goto end
+)
+
+if "%1" == "qthelp" (
+	%SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can run "qcollectiongenerator" with the ^
+.qhcp project file in %BUILDDIR%/qthelp, like this:
+	echo.^> qcollectiongenerator %BUILDDIR%\qthelp\pyNEMO.qhcp
+	echo.To view the help file:
+	echo.^> assistant -collectionFile %BUILDDIR%\qthelp\pyNEMO.ghc
+	goto end
+)
+
+if "%1" == "devhelp" (
+	%SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished.
+	goto end
+)
+
+if "%1" == "epub" (
+	%SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The epub file is in %BUILDDIR%/epub.
+	goto end
+)
+
+if "%1" == "latex" (
+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.
+	goto end
+)
+
+if "%1" == "latexpdf" (
+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+	cd %BUILDDIR%/latex
+	make all-pdf
+	cd %BUILDDIR%/..
+	echo.
+	echo.Build finished; the PDF files are in %BUILDDIR%/latex.
+	goto end
+)
+
+if "%1" == "latexpdfja" (
+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+	cd %BUILDDIR%/latex
+	make all-pdf-ja
+	cd %BUILDDIR%/..
+	echo.
+	echo.Build finished; the PDF files are in %BUILDDIR%/latex.
+	goto end
+)
+
+if "%1" == "text" (
+	%SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The text files are in %BUILDDIR%/text.
+	goto end
+)
+
+if "%1" == "man" (
+	%SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The manual pages are in %BUILDDIR%/man.
+	goto end
+)
+
+if "%1" == "texinfo" (
+	%SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo.
+	goto end
+)
+
+if "%1" == "gettext" (
+	%SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The message catalogs are in %BUILDDIR%/locale.
+	goto end
+)
+
+if "%1" == "changes" (
+	%SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.The overview file is in %BUILDDIR%/changes.
+	goto end
+)
+
+if "%1" == "linkcheck" (
+	%SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Link check complete; look for any errors in the above output ^
+or in %BUILDDIR%/linkcheck/output.txt.
+	goto end
+)
+
+if "%1" == "doctest" (
+	%SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Testing of doctests in the sources finished, look at the ^
+results in %BUILDDIR%/doctest/output.txt.
+	goto end
+)
+
+if "%1" == "xml" (
+	%SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The XML files are in %BUILDDIR%/xml.
+	goto end
+)
+
+if "%1" == "pseudoxml" (
+	%SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml.
+	goto end
+)
+
+:end
diff --git a/docs/source/_static/add-variable.jpg b/docs/source/_static/add-variable.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..8efe0d74446cbc83724171d8fc3eeae6fc23fe48
Binary files /dev/null and b/docs/source/_static/add-variable.jpg differ
diff --git a/docs/source/_static/eg2.png b/docs/source/_static/eg2.png
new file mode 100644
index 0000000000000000000000000000000000000000..3db4576156149f1157f1d56ded5aed005c0c2ad3
Binary files /dev/null and b/docs/source/_static/eg2.png differ
diff --git a/docs/source/_static/generator-gui.jpg b/docs/source/_static/generator-gui.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..9d77bbabedf5e58445d64424799aa75139840607
Binary files /dev/null and b/docs/source/_static/generator-gui.jpg differ
diff --git a/docs/source/conf.py b/docs/source/conf.py
new file mode 100644
index 0000000000000000000000000000000000000000..0138b9555b599057eecabe06837d476261612639
--- /dev/null
+++ b/docs/source/conf.py
@@ -0,0 +1,274 @@
+# -*- coding: utf-8 -*-
+#
+# pyNEMO documentation build configuration file, created by
+# sphinx-quickstart on Thu Jun 25 15:08:06 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
+
+# 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 = [
+    'sphinx.ext.autodoc', 'sphinx.ext.napoleon', 'sphinx.ext.todo'
+]
+
+# Napoleon settings
+napoleon_google_docstring = True
+napoleon_numpy_docstring = True
+napoleon_include_init_with_doc = False
+napoleon_include_private_with_doc = False
+napoleon_include_special_with_doc = False
+napoleon_use_admonition_for_examples = False
+napoleon_use_admonition_for_notes = False
+napoleon_use_admonition_for_references = False
+napoleon_use_ivar = False
+napoleon_use_param = True
+napoleon_use_rtype = True
+napoleon_use_keyword = True
+
+# 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'pyNEMO'
+copyright = u'2015, James Harle, Srikanth Nagella, Shirley Crompton'
+
+# 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 = '0.1'
+# The full version, including alpha/beta/rc tags.
+release = '0.1'
+
+# 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 = []
+
+# 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
+
+
+# -- 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
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'pyNEMOdoc'
+
+
+# -- 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, or own class]).
+latex_documents = [
+  ('index', 'pyNEMO.tex', u'pyNEMO Documentation',
+   u'James Harle, Srikanth Nagella, Shirley Crompton', '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', 'pynemo', u'pyNEMO Documentation',
+     [u'James Harle, Srikanth Nagella, Shirley Crompton'], 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', 'pyNEMO', u'pyNEMO Documentation',
+   u'James Harle, Srikanth Nagella, Shirley Crompton', 'pyNEMO', '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'
+
+# If true, do not generate a @detailmenu in the "Top" node's menu.
+#texinfo_no_detailmenu = False
diff --git a/docs/source/examples.rst b/docs/source/examples.rst
new file mode 100644
index 0000000000000000000000000000000000000000..dfe9c5c384c029af489ba59eeba045f0e622ffb4
--- /dev/null
+++ b/docs/source/examples.rst
@@ -0,0 +1,354 @@
+Examples
+========
+Here we provide two worked examples using pyNEMO. The first is a setup of the Northwest European Shelf using
+a remote dataset. The second is an end-to-end setup of a small regional model in the tropics.
+
+Example 1: Northwest European Shelf
+===================================
+
+
+.. figure:: _static/eg1.png 
+   :align:   center
+
+   Northwest European Shelf Bathymetry
+   
+
+This example has been tested on the ARCHER HPC facillity *(22 Feb 2017)*.
+
+First, create a working directory into which the code can
+run. All the data required for this example are held on a
+THREDDS server so no addtional data are required.
+
+.. note:: make sure cray-netcdf-hdf5parallel cray-hdf5-parallel are loaded.
+          This example has been consructed under PrgEnv-intel. e.g.
+
+::
+
+   module swap PrgEnv-cray PrgEnv-intel
+   module load cray-netcdf-hdf5parallel
+   module load cray-hdf5-parallel
+
+.. note:: Be careful to avoid symbolic links in NEMO control files.
+
+::
+
+   cd $WDIR
+   mkdir OUTPUT
+
+Now we're ready to generate the boundary conditions using pyNEMO. 
+If this is not installed follow the `installation guide` or a quick
+setup could be as follows:
+
+:: 
+
+   cd ~
+   module load anaconda
+   conda create --name pynemo_env scipy=0.16.0 numpy matplotlib=1.5.1 basemap netcdf4 libgfortran=1.0.0
+   source activate pynemo_env
+   conda install -c conda-forge seawater=3.3.4
+   conda install -c https://conda.anaconda.org/srikanthnagella thredds_crawler
+   conda install -c https://conda.anaconda.org/srikanthnagella pyjnius
+   export LD_LIBRARY_PATH=/opt/java/jdk1.7.0_45/jre/lib/amd64/server:$LD_LIBRARY_PATH
+   svn checkout https://ccpforge.cse.rl.ac.uk/svn/pynemo
+   cd pynemo/trunk/Python
+   python setup.py build
+   export PYTHONPATH=~/.conda/envs/pynemo/lib/python2.7/site-packages/:$PYTHONPATH
+   python setup.py install --prefix ~/.conda/envs/pynemo
+   cp data/namelist.bdy $WDIR
+   cd $WDIR
+
+Next we need to modify the namelist.bdy file to point it to the correct
+data sources. First we need to create an ncml file to gather input data 
+and map variable names. First we update *sn_src_dir*, *sn_dst_dir* and
+*cn_mask_file* to reflect the working path (e.g. sn_src_dir = '$WDIR/test.ncml', 
+sn_dst_dir = '$WDIR/OUTPUT' and cn_mask_file = '$WDIR/mask.nc'). 
+Explicitly write out $WDIR. Next we need to generate test.ncml.
+
+.. note:: pynemo may have to be run on either espp1 or espp2 (e.g. ssh -Y espp1) 
+          as the JVM doesn't have sufficient memory on the login nodes.
+
+::
+
+   ssh -Y espp1
+   module load anaconda
+   source activate pynemo_env
+   cd $WDIR 
+   pynemo_ncml_generator   
+
+For each of the tracer and dynamics variables enter the following URL as
+the source directory:
+
+http://esurgeod.noc.soton.ac.uk:8080/thredds/dodsC/PyNEMO/data
+
+Add a regular expression for each (Temperature, Salinity and Sea Surface 
+Height each use: .\*T\\.nc$ and the velocities use .\*V\\.nc$ and .\*V\\.nc$)
+After each entry click the Add button. Finally fill in the output file 
+including directory path (this should match *sn_src_dir*). Once this is complete
+click on the generate button and an ncml file should be written to $WDIR.
+
+Then using pynemo we define the area we want to model and generate some 
+boundary conditions:
+
+.. note:: I've had to add the conda env path to the $PYTHONPATH as python does
+          seem to be able to pick up pyjnius!?
+
+::
+
+   export LD_LIBRARY_PATH=/opt/java/jdk1.7.0_45/jre/lib/amd64/server:$LD_LIBRARY_PATH
+   export PYTHONPATH=~/.conda/envs/pynemo_env/lib/python2.7/site-packages:$PYTHONPATH
+   pynemo -g -s namelist.bdy
+ 
+Once the area of interest is selected and the close button is clicked,
+open boundary data should be generated in $WDIR/OUTPUT.
+
+
+Example 2: Lighthouse Reef
+==========================
+
+.. figure:: _static/eg2.png 
+   :align:   center
+
+   Regional Mask / SSH after 1 day / SST after 1 day
+   
+
+This example has been tested on the ARCHER HPC facillity.
+
+First, create a working directory into which the NEMO 
+source code can be checked out. Create an inputs directory
+to unpack the forcing tar ball.
+
+.. note:: make sure cray-netcdf-hdf5parallel cray-hdf5-parallel are loaded.
+          This example has been consructed under PrgEnv-intel.
+
+::
+
+   cd $WDIR
+   mkdir INPUTS
+   cd INPUTS
+   wget ftp.nerc-liv.ac.uk:/pub/general/jdha/inputs.tar.gz
+   tar xvfz inputs.tar.gz
+   rm inputs.tar.gz
+   cd ../
+   svn co http://forge.ipsl.jussieu.fr/nemo/svn/branches/2014/dev_r4621_NOC4_BDY_VERT_INTERP@5709
+   svn co http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/branchs/xios-1.0@629
+   cd xios-1.0
+   cp $WDIR/INPUTS/arch-XC30_ARCHER.* ./arch
+   ./make_xios --full --prod --arch XC30_ARCHER --netcdf_lib netcdf4_par
+
+Next we setup our experiment directory and drop an updated 
+dtatsd.F90 into MY_SRC to allow the vertical interpolation 
+of initial conditions on to the new verictal coordinates. 
+We also apply several patches for bugs in the code. 
+
+.. note:: when executing ./makenemo for the first time only choose OPA_SRC.
+          For some reason even though LIM_2 is not chosen key_lim2 is
+          in the cpp keys. This means the first call to ./makenemo will fail.
+          Just vi LH_REEF/cpp_LH_REEF.fcm and remove key_lim2 and re-issue
+          the make command.
+
+::
+
+   export CDIR=$WDIR/dev_r4621_NOC4_BDY_VERT_INTERP/NEMOGCM/CONFIG
+   export TDIR=$WDIR/dev_r4621_NOC4_BDY_VERT_INTERP/NEMOGCM/TOOLS
+   cd $CDIR/../NEMO/OPA_SRC/SBC
+   patch -b < $WDIR/INPUTS/fldread.patch
+   cd ../DOM 
+   patch -b < $WDIR/INPUTS/dommsk.patch
+   cd ../BDY
+   patch -b < $WDIR/INPUTS/bdyini.patch
+   cd $CDIR
+   rm $CDIR/../NEMO/OPA_SRC/TRD/trdmod.F90
+   cp $WDIR/INPUTS/arch-* ../ARCH
+   ./makenemo -n LH_REEF -m XC_ARCHER_INTEL -j 10
+   cp $WDIR/INPUTS/cpp_LH_REEF.fcm ./LH_REEF
+   cp $WDIR/INPUTS/dtatsd.F90 LH_REEF/MY_SRC/ 
+
+To generate bathymetry, initial conditions and grid information
+we first need to compile some of the NEMO TOOLS (after a small
+bugfix - and to allow direct passing of arguments). For some 
+reason GRIDGEN doesn't like INTEL:
+
+::
+
+   cd $WDIR/dev_r4621_NOC4_BDY_VERT_INTERP/NEMOGCM/TOOLS/WEIGHTS/src
+   patch -b < $WDIR/INPUTS/scripinterp_mod.patch
+   patch -b < $WDIR/INPUTS/scripinterp.patch
+   patch -b < $WDIR/INPUTS/scrip.patch
+   patch -b < $WDIR/INPUTS/scripshape.patch
+   patch -b < $WDIR/INPUTS/scripgrid.patch
+   cd ../../
+   ./maketools -n WEIGHTS -m XC_ARCHER_INTEL
+   ./maketools -n REBUILD_NEMO -m XC_ARCHER_INTEL
+   module unload cray-netcdf-hdf5parallel cray-hdf5-parallel
+   module swap PrgEnv-intel PrgEnv-cray
+   module load cray-netcdf cray-hdf5
+   ./maketools -n GRIDGEN -m XC_ARCHER
+   module swap PrgEnv-cray PrgEnv-intel
+   export TDIR=$WDIR/dev_r4621_NOC4_BDY_VERT_INTERP/NEMOGCM/TOOLS
+
+.. note:: my standard ARCHER ENV is intel with parallel netcdf you may need to edit accordingly
+
+Back in $WDIR/INPUTS, create a new coordinates file from the
+existing global 1/12 mesh and refine to 1/84 degree resolution: 
+
+::
+ 
+   cd $TDIR/GRIDGEN
+   cp $WDIR/INPUTS/namelist_R12 ./
+   ln -s namelist_R12 namelist.input
+   ./create_coordinates.exe 
+   cp 1_coordinates_ORCA_R12.nc $WDIR/INPUTS/coordinates.nc
+
+To create the bathymetry we use the gebco dataset. On ARCHER I
+had to use a non-default nco module for netcdf operations to work.
+I also had to cut down the gebco data as the SCRIP routines failed
+for some unknown reason.
+
+::
+
+   cd $WDIR/INPUTS
+   module load nco/4.5.0
+   ncap2 -s 'where(topo > 0) topo=0' gebco_1_cutdown.nc tmp.nc
+   ncflint --fix_rec_crd -w -1.0,0.0 tmp.nc tmp.nc gebco_in.nc
+   rm tmp.nc
+   module unload nco cray-netcdf cray-hdf5
+   module load cray-netcdf-hdf5parallel cray-hdf5-parallel
+   $TDIR/WEIGHTS/scripgrid.exe namelist_reshape_bilin_gebco
+   $TDIR/WEIGHTS/scrip.exe namelist_reshape_bilin_gebco
+   $TDIR/WEIGHTS/scripinterp.exe namelist_reshape_bilin_gebco
+    
+We perform a similar operation to create the initial conditions:
+
+.. note:: I've put a sosie pre-step in here to flood fill the land. 
+          I tried using sosie for 3D intepolation, but not convinced.
+
+::
+
+   cd ~
+   mkdir local 
+   svn co svn://svn.code.sf.net/p/sosie/code/trunk sosie
+   cd sosie
+   cp $WDIR/INPUTS/make.macro ./
+   make
+   make install
+   export PATH=~/local/bin:$PATH   
+   cd $WDIR/INPUTS
+   sosie.x -f initcd_votemper.namelist
+   sosie.x -f initcd_vosaline.namelist
+   $TDIR/WEIGHTS/scripgrid.exe namelist_reshape_bilin_initcd_votemper
+   $TDIR/WEIGHTS/scrip.exe namelist_reshape_bilin_initcd_votemper
+   $TDIR/WEIGHTS/scripinterp.exe namelist_reshape_bilin_initcd_votemper
+   $TDIR/WEIGHTS/scripinterp.exe namelist_reshape_bilin_initcd_vosaline
+
+Finally we setup weights files for the atmospheric forcing:
+
+::
+
+   $TDIR/WEIGHTS/scripgrid.exe namelist_reshape_bilin_atmos
+   $TDIR/WEIGHTS/scrip.exe namelist_reshape_bilin_atmos
+   $TDIR/WEIGHTS/scripshape.exe namelist_reshape_bilin_atmos
+   $TDIR/WEIGHTS/scrip.exe namelist_reshape_bicubic_atmos
+   $TDIR/WEIGHTS/scripshape.exe namelist_reshape_bicubic_atmos
+
+
+Next step is to create the mesh and mask files that will be used 
+in the generation of the open boundary conditions:
+
+::
+
+   cd $CDIR
+   cp $WDIR/INPUTS/cpp_LH_REEF.fcm LH_REEF/
+   ln -s $WDIR/INPUTS/bathy_meter.nc $CDIR/LH_REEF/EXP00/bathy_meter.nc 
+   ln -s $WDIR/INPUTS/coordinates.nc $CDIR/LH_REEF/EXP00/coordinates.nc 
+   cp $WDIR/INPUTS/runscript $CDIR/LH_REEF/EXP00
+   cp $WDIR/INPUTS/namelist_cfg $CDIR/LH_REEF/EXP00/namelist_cfg
+   cp $WDIR/INPUTS/namelist_ref $CDIR/LH_REEF/EXP00/namelist_ref
+   ./makenemo clean
+   ./makenemo -n LH_REEF -m XC_ARCHER_INTEL -j 10
+   cd LH_REEF/EXP00
+   ln -s $WDIR/xios-1.0/bin/xios_server.exe xios_server.exe
+   qsub -q short runscript
+
+
+If that works, we then need to rebuild the mesh and mask files in 
+to single files for the next step:
+
+::
+
+   $TDIR/REBUILD_NEMO/rebuild_nemo -t 24 mesh_zgr 96
+   $TDIR/REBUILD_NEMO/rebuild_nemo -t 24 mesh_hgr 96
+   $TDIR/REBUILD_NEMO/rebuild_nemo -t 24 mask 96
+   mv mesh_zgr.nc mesh_hgr.nc mask.nc $WDIR/INPUTS
+   rm mesh_* mask_* LH_REEF_0000*
+   cd $WDIR/INPUTS
+
+Now we're ready to generate the boundary conditions using pyNEMO. 
+If this is not installed follow the `installation guide` or a quick
+setup could be as follows:
+
+:: 
+
+   cd ~
+   module load anaconda
+   conda create --name pynemo_env scipy=0.16.0 numpy matplotlib=1.5.1 basemap netcdf4 libgfortran=1.0.0
+   source activate pynemo_env
+   conda install -c conda-forge seawater=3.3.4
+   conda install -c https://conda.anaconda.org/srikanthnagella thredds_crawler
+   conda install -c https://conda.anaconda.org/srikanthnagella pyjnius
+   export LD_LIBRARY_PATH=/opt/java/jdk1.7.0_45/jre/lib/amd64/server:$LD_LIBRARY_PATH
+   svn checkout https://ccpforge.cse.rl.ac.uk/svn/pynemo
+   cd pynemo/trunk/Python
+   python setup.py build
+   export PYTHONPATH=~/.conda/envs/pynemo/lib/python2.7/site-packages/:$PYTHONPATH
+   python setup.py install --prefix ~/.conda/envs/pynemo
+   cd $WDIR/INPUTS
+
+Start up pynemo and generate boundary conditions. First we need to
+create a few ncml files to gather input data and map variable names.
+Then using pynemo we define the area we want to model:
+
+.. note:: pynemo may have to be run on either espp1 or espp2 (e.g. ssh -Y espp1) 
+          as the JVM doesn't have sufficient memory on the login nodes.
+
+::
+
+   ssh -Y espp1
+   module load anaconda
+   source activate pynemo_env
+   cd $WDIR/INPUTS 
+   pynemo_ncml_generator   
+
+.. note:: The ncml files already exist in the INPUTS directory. There is no need
+          generate them. It's a little tricky at the momment as the ncml generator
+          doesn't have all the functionality required for this example. Next step
+          is to fire up pynemo. You can change the mask or accept the default by just
+          hitting the close button (that really should say 'build' or 'go' or such like).
+          Also I've had to add the conda env path to the $PYTHONPATH as python does
+          seem to be able to pick up pyjnius!?
+
+::
+
+   export LD_LIBRARY_PATH=/opt/java/jdk1.7.0_45/jre/lib/amd64/server:$LD_LIBRARY_PATH
+   export PYTHONPATH=~/.conda/envs/pynemo_env/lib/python2.7/site-packages:$PYTHONPATH
+   pynemo -g -s namelist.bdy
+
+Let's have a go at running the model after exiting espp1 (after a few variable
+renamings, due to inconsistencies to be ironed out):
+
+::
+ 
+   exit
+   cd $WDIR/INPUTS
+   module unload cray-netcdf-hdf5parallel cray-hdf5-parallel
+   module load nco/4.5.0
+   ncrename -v deptht,gdept LH_REEF_bdyT_y1980m01.nc
+   ncrename -v depthu,gdepu LH_REEF_bdyU_y1980m01.nc
+   ncrename -v depthv,gdepv LH_REEF_bdyV_y1980m01.nc
+   module unload nco
+   module load cray-netcdf-hdf5parallel cray-hdf5-parallel
+   cd $CDIR/LH_REEF/EXP00
+   ln -s $WDIR/INPUTS/coordinates.bdy.nc $CDIR/LH_REEF/EXP00/coordinates.bdy.nc 
+   sed -e 's/nn_msh      =    3/nn_msh      =    0/' namelist_cfg > tmp
+   sed -e 's/nn_itend    =      1/nn_itend    =       1440 /' tmp > namelist_cfg
+   cp $WDIR/INPUTS/*.xml ./
+   qsub -q short runscript
diff --git a/docs/source/index.rst b/docs/source/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..0d69c13f88c214cb74653bf0cb192bcf394cd96e
--- /dev/null
+++ b/docs/source/index.rst
@@ -0,0 +1,24 @@
+NRCT User Guide
+=================
+
+Contents:
+
+.. toctree::
+   :maxdepth: 3
+   
+   intro
+   installation
+   usage
+   ncml_generator_usage
+   examples
+   troubleshooting
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
diff --git a/docs/source/installation.rst b/docs/source/installation.rst
new file mode 100644
index 0000000000000000000000000000000000000000..0f7a7435419d31648c430e95c57d5e3d6c9059f5
--- /dev/null
+++ b/docs/source/installation.rst
@@ -0,0 +1,52 @@
+Installation
+============
+This page provides a guide to installing pyNEMO. 
+
+Dependencies
+^^^^^^^^^^^^
+
+1. Python 2.7 (Not tested with 3.x)
+2. scipy
+3. netCDF4-python
+4. numpy
+5. matplotlib
+6. basemap
+7. thredds_crawler
+8. seawater
+9. pyjnius (optional)
+
+Anaconda
+^^^^^^^^
+
+Using conda: pyNEMO supports Win64, OSX and Linux. for other operating systems please build from source.
+
+.. note:: It is recommended to create a seperate virtual environment for pyNEMO. 
+          Please follow the instructions on doing this at http://www.continuum.io/blog/conda
+
+::
+
+   conda install -c https://conda.anaconda.org/srikanthnagella pynemo
+
+This will install pynemo and its dependencies. This build is generally outdated as development and
+bug fixes to the source are a regular occurrence. It may be better to install from source until a beta
+release is available.
+
+From Source
+^^^^^^^^^^^
+
+Installing pyNEMO using other flavours of software or from source. Install all the dependencies and 
+download the source code from svn and install. 
+
+::
+
+   svn checkout http://ccpforge.cse.rl.ac.uk/svn/pynemo/trunk/Python/
+   python setup.py install
+   
+.. note:: If building from source in the Anaconda environment all dependencies can
+          be installed using conda apart from thredds_crawler and pyjnius which can
+          be installed using the following Anaconda channel:
+
+::
+
+   conda install -c https://conda.anaconda.org/srikanthnagella thredds_crawler
+   conda install -c https://conda.anaconda.org/srikanthnagella pyjnius
diff --git a/docs/source/intro.rst b/docs/source/intro.rst
new file mode 100644
index 0000000000000000000000000000000000000000..463a8df2bc2fc96eb4afb33ba20b3f176263b350
--- /dev/null
+++ b/docs/source/intro.rst
@@ -0,0 +1,21 @@
+Introduction 
+============
+
+
+The NRCT is a tool to set up the lateral boundary conditions for a regional `NEMO <http://www.nemo-ocean.eu>`_
+model configuration.  The tool is written in Python, largely within the
+`Anaconda <https://store.continuum.io/cshop/anaconda/>`_ environment to aid
+wider distribution and to facilitate development.  In their current form these
+tools are by no means generic and polished, but it is hoped will form a foundation
+from which something more formal can be developed. The following sections provide a quick-start guide with
+worked examples to help the user get up and running with the tool.
+
+The tool essentially uses geographical and depth information from the source
+data (e.g. a global ocean simulation) and destination simulation (i.e. the
+proposed regional NEMO model configuration) to determine which source points are required
+for data extraction. This is done using a kdtree approximate nearest neighbour
+algorithm. The idea behind this targetted method is that it provides a generic
+method of interpolation for any flavour of ocean model in order to set up a
+regional NEMO model configuration.  At present (alpha release) the tools do not
+contain many options, but those that exist are accessed either through a NEMO style
+namelist or a convient GUI. 
diff --git a/docs/source/ncml_generator_usage.rst b/docs/source/ncml_generator_usage.rst
new file mode 100644
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@@ -0,0 +1,96 @@
+pyNEMO NcML Generator Usage
+===========================
+
+This GUI tool facilitates the creation of a virtual dataset for input into pyNEMO.  The virtual dataset is defined using NetCDF Markup Language (`NcML <http://www.unidata.ucar.edu/software/thredds/current/netcdf-java/ncml/Tutorial.html>`_ ).
+
+Using NcML, it is possible to:
+
+1.  modify metadata
+2.  modify and restructure variables
+3.  combine or aggregate data from multiple datasets.  The datasets may reside in the local file system or in a remote OPeNDAP (http://www.opendap.org/) server.
+
+
+Generator GUI
+^^^^^^^^^^^^^
+
+.. _NcML_gui:
+.. figure::  _static/generator-gui.jpg
+   :align:   center
+
+   Overview of the NcML Generator GUI.
+
+
+Users need to follow three distinct steps when using the GUI to generate the virtual dataset:
+
+1.  Define a target output NcML file
+2.  Define the individal variable
+3.  Generate the NcML file
+
+Define a Target Output File
+---------------------------
+
+User should provide the path and name of the target NcML file.  The convention is to use *.ncml* as the file suffix.  The target file can be specified manually using the input text box or visually using the *Select file* button.  Clicking the button will bring up a file dialogue. 
+
+
+Define the Individual Data Variable
+-----------------------------------
+
+The nemo data variables are grouped into the following types :
+
+1.  Tracer (temperature, salinity)
+2.  Dynamics (zonal velocity, meridian velocity, sea surface height)
+3.  Ice (ice thickness, leads fraction, snow thickness)
+4.  Ecosystem (reserved for future use)
+5.  Grid (reserved for future use)
+
+Users can access the required variable by selecting the tab widget and the variable from the *Variable* dropdown list.
+
+.. _NcML_gui_completed:
+.. figure::  _static/add-variable.jpg
+   :align:   center
+
+   Example definition of the *Ice thickness variable*.
+
+For each variable, users must provide information for:
+
+*  Source directory - the location of the folder containing the input datasets.  User can provide an absolute path to a local file folder or an OPeNDAP endpoint, e.g. http://esurgeod.noc.soton.ac.uk:8080/thredds/dodsC/PyNEMO/data/ 
+*  Existing variable name - name used in the source datasets
+
+Users may further filter the source datasets using:
+
+* Include subdirs - check the box to include contents in the sub directories under the specified *Source directory*
+* Regular expression - provides a search pattern for filtering the files. See the **Regex** section below for more information.
+
+After completing the variable form, users should click the *Add* button to store the input value.  Alternatively, users can use the *Reset* button to reset the input to the previously saved values. If there are no existing values, the variable tab will be reset to the default state.
+
+Generate the NcML file
+----------------------
+
+After adding all the variables, users can generate the NcML file by clicking the *Generate* button.  If the operation is successful, a pop-up confirmation dialogue will appear.  The generated NcML file can then be used in the bdy file to set up the NEMO simulation.
+
+
+Regular Expression (Regex)
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+Regular expression is a special text string for describing a search pattern to match against some text.  You may compare using regex to filter what files to include in your datasets against using wildcard (*) to specify a file search pattern in your computer.  
+
+A detailed description of how to define regular expression for filtering datasets in NcML is available at http://www.unidata.ucar.edu/software/thredds/current/netcdf-java/ncml/AnnotatedSchema4.html#regexp.  
+
+The following table provides some typical examples of regex:
+
++---------------+------------------------+---------------------------+
+|  Regex        |  Matching File Path    |        Description        |
++===============+========================+===========================+
+| .*V\\.nc$     | c:/dir/dir/dir/abcV.nc | The file path ends in     |
++---------------+------------------------+---------------------------+
+|               | d:/muV.nc              | V.nc                      |
++---------------+------------------------+---------------------------+
+| .*\\.nc$      | c:/dir/dir/dir/\*.nc   | The file suffix is  nc    |
++---------------+------------------------+---------------------------+
+|               | d:/\*.nc               |                           |
++---------------+------------------------+---------------------------+
+|.*/2015.*\\.nc$| c:/dir/2015_01_16.nc   | The file path contains    |
++---------------+------------------------+---------------------------+
+|               | d:/2015*.nc            | 2015 and the file suffix  |
++---------------+------------------------+---------------------------+
+|               | e:/a/b/c/20151106T.nc  | is   nc                   |
++---------------+------------------------+---------------------------+
diff --git a/docs/source/troubleshooting.rst b/docs/source/troubleshooting.rst
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+Troubleshooting
+===============
+
+1. pyNEMO crashing in MacOSX (Yosemite)?
+
+*  Downgrade the scipy package to 0.15
+
+2. How to make pyNEMO to work behind firewall/proxy?
+
+*  Set the environment variable http_proxy. eg. in Linux export http_proxy=<proxy-server>:<proxy-port>
+
+3. Getting this error 'Warning: Please make sure pyjnius is installed and jvm.dll/libjvm.so/libjvm.dylib is in the path' ?
+
+*  This error is displayed when the application cannot find the java installation on the local machine. please install a java 7.x runtime from http://www.oracle.com/technetwork/java/javase/downloads/jre7-downloads-1880261.html and append the path to the library in the system path. eg. on windows SET PATH="C:\\Program Files (x86)\\Java\\jre1.7\\bin\\client"  on Linux in shell export LD_LIBRARY_PATH=/opt/java/jdk1.7.0_45/jre/lib/amd64/server:$LD_LIBRARY_PATH  in osx export DYLD_LIBRARY_PATH=/System/Library/Java/JavaVirtualMachines/jdk1.7.0_09.jdk/Contents/Home/jre/lib/server:$DYLD_LIBRARY_PATH
diff --git a/docs/source/usage.rst b/docs/source/usage.rst
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+Usage
+=====
+There are two tools available in pyNEMO. They are described in detail below. 
+
+pynemo
+------
+
+This command line tool reads a BDY file, extracts boundary data and prepares
+the data for a NEMO simulation. The bdy file is a plain text file containing 
+key value pairs. Please look at the sample `namelist.bdy 
+<http://ccpforge.cse.rl.ac.uk/gf/project/pynemo/scmsvn/?action=browse&path=%2Ftrunk%2FPython%2Fdata%2Fnamelist.bdy&view=markup>`_ 
+file, which shares common syntax with the NEMO simulation namelist input file. 
+
+.. note:: Directory paths in bdy file can be relative or absolute. 
+          The application picks the relative path from the current working 
+          directory.
+
+Syntax for pynemo command is
+
+::
+
+   > pynemo [-g] -s <bdy file>
+
+For help
+
+::
+
+   > pynemo -h 
+   > usage: pynemo [-g] -s <namelist.bdy>
+   >        -g (optional) will open settings editor before extracting the data
+   >        -s <bdy filename> file to use
+
+Example comamnd
+
+::
+
+   > pynemo -g -s namelist.bdy
+
+
+pynemo_settings_editor
+----------------------
+
+This tool will open a window where you can edit the mask and change the values of bdy parameters.
+
+Syntax for pynemo_settings_editor command is
+
+::
+
+   > pynemo_settings_editor [-s <bdy filename>]
+   
+.. note:: If no file name is specified then a file dialog box will open to select a file.
+
+For help
+
+::
+
+   > pynemo_settings_editor -h
+   > usage: pynemo_settings_editor -s <namelist.bdy>
+   
+Example:
+
+::
+   
+   pynemo_settings_editor -s namelist.bdy