yade-dev team mailing list archive

Thread
Date

[Branch ~yade-pkg/yade/git-trunk] Rev 3742: introduce 2nd edition of the documentation and contact for consuting (in homepage)

To: Yade developers <yade-dev@xxxxxxxxxxxxxxxxxxx>
From: noreply@xxxxxxxxxxxxx
Date: Fri, 20 Nov 2015 04:25:30 -0000
Reply-to: noreply@xxxxxxxxxxxxx
Sender: bounces@xxxxxxxxxxxxx

------------------------------------------------------------
revno: 3742
committer: Bruno Chareyre <bruno.chareyre@xxxxxxxxxxx>
timestamp: Fri 2015-11-20 01:42:30 +0100
message:
  introduce 2nd edition of the documentation and contact for consuting (in homepage)
added:
  doc/sphinx/book/
  doc/sphinx/book/confManual.py
  doc/sphinx/book/confReference.py
  doc/sphinx/book/confTheory.py
  doc/sphinx/book/fullBibliography.rst.in
  doc/sphinx/consulting.rst
  doc/sphinx/yadeBookSphinx.py
modified:
  doc/citing_yade.bib
  doc/sphinx/README
  doc/sphinx/templates/index.html
  doc/yade-docref.bib


--
lp:yade
https://code.launchpad.net/~yade-pkg/yade/git-trunk

Your team Yade developers is subscribed to branch lp:yade.
To unsubscribe from this branch go to https://code.launchpad.net/~yade-pkg/yade/git-trunk/+edit-subscription

=== modified file 'doc/citing_yade.bib'
--- doc/citing_yade.bib	2011-06-07 16:56:16 +0000
+++ doc/citing_yade.bib	2015-11-20 00:42:30 +0000
@@ -1,46 +1,42 @@
-@Book{ yade:doc,
-	PUBLISHER = "The {Y}ade Project",
-	TITLE = "{Y}ade {D}ocumentation",
-	YEAR = "2010",
-	AUTHOR = "V. \v{S}milauer and E. Catalano and B. Chareyre and S. Dorofenko and J. Duriez and A. Gladky and J. Kozicki and C. Modenese and L. Scholt{\`e}s and L. Sibille and J. Str{\'a}nsk{\`y} and K. Thoeni",
-	ALTEDITOR = "V{\'a}clav {\v{S}}milauer",
-	EDITION = "1st",
-	NOTE = "http://yade-dem.org/doc/";,
-	ALTNOTE = "\url{http://yade-dem.org/doc/}";
-}
-
-@InCollection{ yade:manual,
-	AUTHOR = "V. \v{S}milauer and A. Gladky and J. Kozicki and C. Modenese and J. Str{\'a}nsk{\`y}",
-	BOOKTITLE = "{Y}ade {D}ocumentation",
-	EDITOR = "V. \v{S}milauer",
-	PUBLISHER = "{The {Y}ade Project}",
-	TITLE = "{Y}ade {U}sing and {P}rogramming",
-	YEAR = "2010",
-	EDITION = "{1st}",
-	NOTE = "http://yade-dem.org/doc/";,
-	ALTNOTE = "\url{http://yade-dem.org/doc/}";
-}
-
-@InCollection{ yade:background,
-	TITLE = "{Y}ade \textsc{Dem} {F}ormulation",
-	AUTHOR = "V. \v{S}milauer and B. Chareyre",
-	BOOKTITLE = "{Y}ade {D}ocumentation",
-	EDITOR = "V. \v{S}milauer",
-	PUBLISHER = "{The {Y}ade Project}",
-	YEAR = "2010",
-	EDITION = "{1st}",
-	NOTE = "http://yade-dem.org/doc/";,
-	ALTNOTE = "\url{http://yade-dem.org/doc/}";
-}
-
-@InCollection{ yade:reference,
-	AUTHOR = "V. \v{S}milauer and E. Catalano and B. Chareyre and S. Dorofenko and J. Duriez and A. Gladky and J. Kozicki and C. Modenese and L. Scholt{\`e}s and L. Sibille and J. Str{\'a}nsk{\`y} and K. Thoeni",
-	BOOKTITLE = "{Y}ade {D}ocumentation",
-	EDITOR = "V. \v{S}milauer",
-	PUBLISHER = "{The {Y}ade Project}",
-	TITLE = "{Y}ade {R}eference {D}ocumentation",
-	YEAR = "2010",
-	EDITION = "{1st}",
-	NOTE = "http://yade-dem.org/doc/";,
-	ALTNOTE = "\url{http://yade-dem.org/doc/}";
-}
\ No newline at end of file
+@book{yade:doc2,
+	altnote = "\\url{http://yade-dem.org/doc/}";,
+	author = "V. \v{S}milauer et al.",
+	doi = "10.5281/zenodo.32409",
+	note = "http://yade-dem.org/doc/";,
+	title = "{{Y}ade {D}ocumentation 2nd ed}",
+	publisher = "{The {Y}ade Project}",
+	year = "2015"
+}
+
+@incollection{yade:manual2,
+	altnote = "\\url{http://yade-dem.org/doc/}";,
+	author = "V. \v{S}milauer et al.",
+	doi = "10.5281/zenodo.34043",
+	booktitle = "{Y}ade {D}ocumentation 2nd ed",
+	note = "http://yade-dem.org/doc/";,
+	publisher = "{The {Y}ade Project}",
+	title = "Using and Programming",
+	year = "2015"
+}
+
+@incollection{yade:background2,
+	altnote = "\\url{http://yade-dem.org/doc/}";,
+	author = "V. \v{S}milauer et al.",
+	doi = "10.5281/zenodo.34044",
+	booktitle = "{Y}ade {D}ocumentation 2nd ed",
+	note = "http://yade-dem.org/doc/";,
+	publisher = "{The {Y}ade Project}",
+	title = "DEM formulation",
+	year = "2015"
+}
+
+@incollection{yade:reference2,
+	altnote = "\\url{http://yade-dem.org/doc/}";,
+	author = "V. \v{S}milauer et al.",
+	doi = "10.5281/zenodo.34045",
+	booktitle = "{Y}ade {D}ocumentation 2nd ed",
+	note = "http://yade-dem.org/doc/";,
+	publisher = "{The {Y}ade Project}",
+	title = "Reference Manual",
+	year = "2015"
+}

=== modified file 'doc/sphinx/README'
--- doc/sphinx/README	2010-07-15 11:29:59 +0000
+++ doc/sphinx/README	2015-11-20 00:42:30 +0000
@@ -25,3 +25,11 @@
 ====
 
 ipython_console_highlighting.py is copied from matplotlib's trunk/matplotlib/lib/matplotlib/sphinxext
+
+
+Generating yade documentation as a book (for the official chapter references)
+=============================================================================
+
+First run yadeSphinx.py as explained above. It will generate modules documentation and other things that we use for generating the book.
+Second run yadeBookSphinx.py (same command as above, adding 'Book' in the script name)
+

=== added directory 'doc/sphinx/book'
=== added file 'doc/sphinx/book/confManual.py'
--- doc/sphinx/book/confManual.py	1970-01-01 00:00:00 +0000
+++ doc/sphinx/book/confManual.py	2015-11-20 00:42:30 +0000
@@ -0,0 +1,745 @@
+# -*- coding: utf-8 -*-
+#
+# Yade documentation build configuration file, created by
+# sphinx-quickstart on Mon Nov 16 21:49:34 2009.
+#
+# 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.
+
+# relevant posts to sphinx ML
+# http://groups.google.com/group/sphinx-dev/browse_thread/thread/b4fbc8d31d230fc4
+# http://groups.google.com/group/sphinx-dev/browse_thread/thread/118598245d5f479b
+
+#####################
+## custom yade roles
+#####################
+##
+## http://docutils.sourceforge.net/docs/howto/rst-roles.html
+
+import sys, os, re
+from docutils import nodes
+from sphinx import addnodes
+from sphinx.roles import XRefRole
+import docutils
+
+#
+# needed for creating hyperlink targets.
+# it should be cleand up and unified for both LaTeX and HTML via
+# the pending_xref node which gets resolved to real link target
+# by sphinx automatically once all docs have been processed.
+#
+# xrefs: http://groups.google.com/group/sphinx-dev/browse_thread/thread/d719d19307654548
+#
+#
+import __builtin__
+if 'latex' in sys.argv: __builtin__.writer='latex'
+elif 'html' in sys.argv: __builtin__.writer='html'
+elif 'epub' in sys.argv: __builtin__.writer='epub'
+else: raise RuntimeError("Must have either 'latex' or 'html' on the command line (hack for reference styles)")
+
+sys.path.append(os.path.abspath('./..'))
+
+def yaderef_role(role,rawtext,text,lineno,inliner,options={},content=[]):
+	"Handle the :yref:`` role, by making hyperlink to yade.wrapper.*. It supports :yref:`Link text<link target>` syntax, like usual hyperlinking roles."
+	id=rawtext.split(':',2)[2][1:-1]
+	txt=id; explicitText=False
+	m=re.match('(.*)\s*<(.*)>\s*',id)
+	if m:
+		explicitText=True
+		txt,id=m.group(1),m.group(2)
+	id=id.replace('::','.')
+	#node=nodes.reference(rawtext,docutils.utils.unescape(txt),refuri='http://beta.arcig.cz/~eudoxos/yade/doxygen/?search=%s'%id,**options)
+	#node=nodes.reference(rawtext,docutils.utils.unescape(txt),refuri='yade.wrapper.html#yade.wrapper.%s'%id,**options)
+	return [mkYrefNode(id,txt,rawtext,role,explicitText,lineno,options)],[]
+
+def yadesrc_role(role,rawtext,lineno,inliner,options={},content=[]):
+	"Handle the :ysrc:`` role, making hyperlink to git repository webpage with that path. Supports :ysrc:`Link text<file/name>` syntax, like usual hyperlinking roles. If target ends with ``/``, it is assumed to be a directory."
+	id=rawtext.split(':',2)[2][1:-1]
+	txt=id
+	m=re.match('(.*)\s*<(.*)>\s*',id)
+	if m:
+		txt,id=m.group(1),m.group(2)
+	return [nodes.reference(rawtext,docutils.utils.unescape(txt),refuri='https://github.com/yade/trunk/blob/master/%s'%id)],[] ### **options should be passed to nodes.reference as well
+
+# map modules to their html (rst) filenames. Used for sub-modules, where e.g. SpherePack is yade._packSphere.SpherePack, but is documented from yade.pack.rst
+moduleMap={
+	'yade._packPredicates':'yade.pack',
+	'yade._packSpheres':'yade.pack',
+	'yade._packObb':'yade.pack'
+}
+
+class YadeXRefRole(XRefRole):
+	#def process_link
+	def process_link(self, env, refnode, has_explicit_title, title, target):
+		print 'TARGET:','yade.wrapper.'+target
+		return '[['+title+']]','yade.wrapper.'+target
+
+def mkYrefNode(target,text,rawtext,role,explicitText,lineno,options={}):
+	"""Create hyperlink to yade target. Targets starting with literal 'yade.' are absolute, but the leading 'yade.' will be stripped from the link text. Absolute tergets are supposed to live in page named yade.[module].html, anchored at #yade.[module2].[rest of target], where [module2] is identical to [module], unless mapped over by moduleMap.
+	
+	Other targets are supposed to live in yade.wrapper (such as c++ classes)."""
+
+	writer=__builtin__.writer # to make sure not shadowed by a local var
+	import string
+	if target.startswith('yade.'):
+		module='.'.join(target.split('.')[0:2])
+		module2=(module if module not in moduleMap.keys() else moduleMap[module])
+		if target==module: target='' # to reference the module itself
+		uri=('%%%s#%s'%(module2,target) if writer=='latex' else '%s.html#%s'%(module2,target))
+		if not explicitText and module!=module2:
+			text=module2+'.'+'.'.join(target.split('.')[2:])
+		text=string.replace(text,'yade.','',1)
+	elif target.startswith('external:'):
+		exttarget=target.split(':',1)[1]
+		if not explicitText: text=exttarget
+		target=exttarget if '.' in exttarget else 'module-'+exttarget
+		uri=(('%%external#%s'%target) if writer=='latex' else 'external.html#%s'%target)
+	else:
+		uri=(('%%yade.wrapper#yade.wrapper.%s'%target) if writer=='latex' else 'yade.wrapper.html#yade.wrapper.%s'%target)
+		#print writer,uri
+	if 0:
+		refnode=addnodes.pending_xref(rawtext,reftype=role,refexplicit=explicitText,reftarget=target)
+		#refnode.line=lineno
+		#refnode+=nodes.literal(rawtext,text,classes=['ref',role])
+		return [refnode],[]
+		#ret.rawtext,reftype=role,
+	else:
+		return nodes.reference(rawtext,docutils.utils.unescape(text),refuri=uri,**options)
+	#return [refnode],[]
+
+def ydefault_role(role,rawtext,text,lineno,inliner,options={},content=[]):
+	"Handle the :ydefault:`something` role. fixSignature handles it now in the member signature itself, this merely expands to nothing."
+	return [],[]
+def yattrtype_role(role,rawtext,text,lineno,inliner,options={},content=[]):
+	"Handle the :yattrtype:`something` role. fixSignature handles it now in the member signature itself, this merely expands to nothing."
+	return [],[]
+# FIXME: should return readable representation of bits of the number (yade.wrapper.AttrFlags enum)
+def yattrflags_role(role,rawtext,text,lineno,inliner,options={},content=[]):
+	"Handle the :yattrflags:`something` role. fixSignature handles it now in the member signature itself."
+	return [],[]
+
+from docutils.parsers.rst import roles
+def yaderef_role_2(type,rawtext,text,lineno,inliner,options={},content=[]): return YadeXRefRole()('yref',rawtext,text,lineno,inliner,options,content)
+roles.register_canonical_role('yref', yaderef_role)
+roles.register_canonical_role('ysrc', yadesrc_role)
+roles.register_canonical_role('ydefault', ydefault_role)
+roles.register_canonical_role('yattrtype', yattrtype_role)
+roles.register_canonical_role('yattrflags', yattrflags_role)
+
+
+## http://sphinx.pocoo.org/config.html#confval-rst_epilog
+rst_epilog = """
+
+.. |yupdate| replace:: *(auto-updated)*
+.. |ycomp| replace:: *(auto-computed)*
+.. |ystatic| replace:: *(static)*
+"""
+
+import collections
+def customExclude(app, what, name, obj, skip, options):
+	if name=='clone':
+		if 'Serializable.clone' in str(obj): return False
+		return True
+	#escape crash on non iterable __doc__ in some qt object
+	if hasattr(obj,'__doc__') and obj.__doc__ and not isinstance(obj.__doc__, collections.Iterable): return True
+	if hasattr(obj,'__doc__') and obj.__doc__ and ('|ydeprecated|' in obj.__doc__ or '|yhidden|' in obj.__doc__): return True
+	#if re.match(r'\b(__init__|__reduce__|__repr__|__str__)\b',name): return True
+	if name.startswith('_'):
+		if name=='__init__':
+			# skip boost classes with parameterless ctor (arg1=implicit self)
+			if obj.__doc__=="\n__init__( (object)arg1) -> None": return True
+			# skip undocumented ctors
+			if not obj.__doc__: return True
+			# skip default ctor for serializable, taking dict of attrs
+			if obj.__doc__=='\n__init__( (object)arg1) -> None\n\nobject __init__(tuple args, dict kwds)': return True
+			#for i,l in enumerate(obj.__doc__.split('\n')): print name,i,l,'##'
+			return False
+		return True
+	return False
+
+def isBoostFunc(what,obj):
+	return what=='function' and obj.__repr__().startswith('<Boost.Python.function object at 0x')
+
+def isBoostMethod(what,obj):
+	"I don't know how to distinguish boost and non-boost methods..."
+	return what=='method' and obj.__repr__().startswith('<unbound method ');
+
+def replaceLaTeX(s):
+	# replace single non-escaped dollars $...$ by :math:`...`
+	# then \$ by single $
+	s=re.sub(r'(?<!\\)\$([^\$]+)(?<!\\)\$',r'\ :math:`\1`\ ',s)
+	return re.sub(r'\\\$',r'$',s)
+
+def fixSrc(app,docname,source):
+	source[0]=replaceLaTeX(source[0])
+
+def fixDocstring(app,what,name,obj,options,lines):
+	# remove empty default roles, which is not properly interpreted by docutils parser
+	for i in range(0,len(lines)):
+		lines[i]=lines[i].replace(':ydefault:``','')
+		lines[i]=lines[i].replace(':yattrtype:``','')
+		lines[i]=lines[i].replace(':yattrflags:``','')
+		#lines[i]=re.sub(':``',':` `',lines[i])
+	# remove signature of boost::python function docstring, which is the first line of the docstring
+	if isBoostFunc(what,obj):
+		l2=boostFuncSignature(name,obj)[1]
+		# we must replace lines one by one (in-place) :-|
+		# knowing that l2 is always shorter than lines (l2 is docstring with the signature stripped off)
+		for i in range(0,len(lines)):
+			lines[i]=l2[i] if i<len(l2) else ''
+	elif isBoostMethod(what,obj):
+		l2=boostFuncSignature(name,obj)[1]
+		for i in range(0,len(lines)):
+			lines[i]=l2[i] if i<len(l2) else ''
+	# LaTeX: replace $...$ by :math:`...`
+	# must be done after calling boostFuncSignature which uses original docstring
+	for i in range(0,len(lines)): lines[i]=replaceLaTeX(lines[i])
+
+
+def boostFuncSignature(name,obj,removeSelf=False):
+	"""Scan docstring of obj, returning tuple of properly formatted boost python signature
+	(first line of the docstring) and the rest of docstring (as list of lines).
+	The rest of docstring is stripped of 4 leading spaces which are automatically
+	added by boost.
+	
+	removeSelf will attempt to remove the first argument from the signature.
+	"""
+	doc=obj.__doc__
+	if doc==None: # not a boost method
+		return None,None
+	nname=name.split('.')[-1]
+	docc=doc.split('\n')
+	if len(docc)<2: return None,docc
+	doc1=docc[1]
+	# functions with weird docstring, likely not documented by boost
+	if not re.match('^'+nname+r'(.*)->.*$',doc1):
+		return None,docc
+	if doc1.endswith(':'): doc1=doc1[:-1]
+	strippedDoc=doc.split('\n')[2:]
+	# check if all lines are padded
+	allLinesHave4LeadingSpaces=True
+	for l in strippedDoc:
+		if l.startswith('    '): continue
+		allLinesHave4LeadingSpaces=False; break
+	# remove the padding if so
+	if allLinesHave4LeadingSpaces: strippedDoc=[l[4:] for l in strippedDoc]
+	for i in range(len(strippedDoc)):
+		# fix signatures inside docstring (one function with multiple signatures)
+		strippedDoc[i],n=re.subn(r'([a-zA-Z_][a-zA-Z0-9_]*\() \(object\)arg1(, |)',r'\1',strippedDoc[i].replace('->','→'))
+	# inspect dosctring after mangling
+	if 'getViscoelasticFromSpheresInteraction' in name and False:
+		print name
+		print strippedDoc
+		print '======================'
+		for l in strippedDoc: print l
+		print '======================'
+	sig=doc1.split('(',1)[1]
+	if removeSelf:
+		# remove up to the first comma; if no comma present, then the method takes no arguments
+		# if [ precedes the comma, add it to the result (ugly!)
+		try:
+			ss=sig.split(',',1)
+			if ss[0].endswith('['): sig='['+ss[1]
+			else: sig=ss[1]
+		except IndexError:
+			# grab the return value
+			try:
+				sig=') -> '+sig.split('->')[-1]
+		#if 'Serializable' in name: print 1000*'#',name
+			except IndexError:
+				sig=')'
+	return '('+sig,strippedDoc
+
+def fixSignature(app, what, name, obj, options, signature, return_annotation):
+	#print what,name,obj,signature#,dir(obj)
+	if what=='attribute':
+		doc=unicode(obj.__doc__)
+		ret=''
+		m=re.match('.*:ydefault:`(.*?)`.*',doc)
+		if m:
+			typ=''
+			#try:
+			#	clss='.'.join(name.split('.')[:-1])
+			#	instance=eval(clss+'()')
+			#	typ='; '+getattr(instance,name.split('.')[-1]).__class__.__name__
+			#	if typ=='; NoneType': typ=''
+			#except TypeError: ##no registered converted
+			#	typ=''
+			dfl=m.group(1)
+			m2=re.match(r'\s*\(\s*\(\s*void\s*\)\s*\"(.*)\"\s*,\s*(.*)\s*\)\s*',dfl)
+			if m2: dfl="%s, %s"%(m2.group(2),m2.group(1))
+			if dfl!='': ret+=' (='+dfl+'%s)'%typ
+			else: ret+=' (=uninitalized%s)'%typ
+		#m=re.match('.*\[(.{,8})\].*',doc)
+		#m=re.match('.*:yunit:`(.?*)`.*',doc)
+		#if m:
+		#	units=m.group(1)
+		#	print '@@@@@@@@@@@@@@@@@@@@@',name,units
+		#	ret+=' ['+units+']'
+		return ret,None
+	elif what=='class':
+		ret=[]
+		if len(obj.__bases__)>0:
+			base=obj.__bases__[0]
+			while base.__module__!='Boost.Python':
+				ret+=[base.__name__]
+				if len(base.__bases__)>0: base=base.__bases__[0]
+				else: break
+		if len(ret):
+			return ' (inherits '+u' → '.join(ret)+')',None
+		else: return None,None
+	elif isBoostFunc(what,obj):
+		sig=boostFuncSignature(name,obj)[0] or ' (wrapped c++ function)'
+		return sig,None
+	elif isBoostMethod(what,obj):
+		sig=boostFuncSignature(name,obj,removeSelf=True)[0]
+		return sig,None
+	#else: print what,name,obj.__repr__()
+	#return None,None
+		
+
+from sphinx import addnodes
+def parse_ystaticattr(env,attr,attrnode):
+	m=re.match(r'([a-zA-Z0-9_]+)\.(.*)\(=(.*)\)',attr)
+	if not m:
+		print 100*'@'+' Static attribute %s not matched'%attr
+		attrnode+=addnodes.desc_name(attr,attr)
+	klass,name,default=m.groups()
+	#attrnode+=addnodes.desc_type('static','static')
+	attrnode+=addnodes.desc_name(name,name)
+	plist=addnodes.desc_parameterlist()
+	if default=='': default='unspecified'
+	plist+=addnodes.desc_parameter('='+default,'='+default)
+	attrnode+=plist
+	attrnode+=addnodes.desc_annotation('  [static]','  [static]')
+	return klass+'.'+name
+
+#############################
+## set tab size
+###################
+## http://groups.google.com/group/sphinx-dev/browse_thread/thread/35b8071ffe9a8feb
+def setup(app):
+	from sphinx.highlighting import lexers
+	from pygments.lexers.compiled import CppLexer
+	lexers['cpp'] = CppLexer(tabsize=3) 
+	lexers['c++'] = CppLexer(tabsize=3) 
+	from pygments.lexers.agile import PythonLexer
+	lexers['python'] = PythonLexer(tabsize=3) 
+
+	app.connect('source-read',fixSrc)
+	
+	app.connect('autodoc-skip-member',customExclude)
+	app.connect('autodoc-process-signature',fixSignature)
+	app.connect('autodoc-process-docstring',fixDocstring)
+	app.add_description_unit('ystaticattr',None,objname='static attribute',indextemplate='pair: %s; static method',parse_node=parse_ystaticattr)
+
+
+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.append(os.path.abspath('.'))
+
+# -- General configuration -----------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+
+#
+# HACK: change ipython console regexp from ipython_console_highlighting.py
+import re
+sys.path.append(os.path.abspath('.'))
+
+import yade.config
+
+if 1:
+	if yade.runtime.ipython_version<12:
+		import ipython_directive as id
+	else:
+		if 12<=yade.runtime.ipython_version<13:
+			import ipython_directive012 as id
+                elif 13<=yade.runtime.ipython_version<200:
+			import ipython_directive013 as id
+                else:
+			import ipython_directive200 as id
+
+	#The next four lines are for compatibility with IPython 0.13.1
+	ipython_rgxin =re.compile(r'(?:In |Yade )\[(\d+)\]:\s?(.*)\s*')
+	ipython_rgxout=re.compile(r'(?:Out| ->  )\[(\d+)\]:\s?(.*)\s*')
+	ipython_promptin ='Yade [%d]:'
+	ipython_promptout=' ->  [%d]: '
+	ipython_cont_spaces='     '
+	#For IPython <=0.12, the following lines are used
+	id.rgxin =re.compile(r'(?:In |Yade )\[(\d+)\]:\s?(.*)\s*')
+	id.rgxout=re.compile(r'(?:Out| ->  )\[(\d+)\]:\s?(.*)\s*')
+	id.rgxcont=re.compile(r'(?:   +)\.\.+:\s?(.*)\s*')
+	id.fmtin  ='Yade [%d]:'
+	id.fmtout =' ->  [%d]: '  # for some reason, out and cont must have the trailing space
+	id.fmtcont='     .\D.: '
+	id.rc_override=dict(prompt_in1="Yade [\#]:",prompt_in2="     .\D.:",prompt_out=r" ->  [\#]: ")
+	if yade.runtime.ipython_version<12:
+		id.reconfig_shell()
+
+	import ipython_console_highlighting as ich
+	ich.IPythonConsoleLexer.input_prompt = re.compile("(Yade \[[0-9]+\]: )")
+	ich.IPythonConsoleLexer.output_prompt = re.compile("(( ->  |Out)|\[[0-9]+\]: )")
+	ich.IPythonConsoleLexer.continue_prompt = re.compile("\s+\.\.\.+:")
+
+
+extensions = [
+		'sphinx.ext.autodoc',
+		'sphinx.ext.autosummary',
+		'sphinx.ext.coverage',
+		'sphinx.ext.pngmath',
+		'sphinx.ext.graphviz',
+		'sphinx.ext.viewcode',
+		'sphinx.ext.inheritance_diagram',
+		'matplotlib.sphinxext.plot_directive',
+		'matplotlib.sphinxext.only_directives',
+		#'matplotlib.sphinxext.mathmpl',
+		'ipython_console_highlighting',
+		'youtube',
+		'sphinx.ext.todo',
+		]
+
+
+if yade.runtime.ipython_version<12:
+	extensions.append('ipython_directive')
+else:
+	if 12<=yade.runtime.ipython_version<13:
+		extensions.append('ipython_directive012')
+        elif 13<=yade.runtime.ipython_version<200:
+		extensions.append('ipython_directive013')
+        else:
+		extensions.append('ipython_directive200')
+
+# the sidebar extension
+if False:
+	if writer=='html':
+		extensions+=['sphinx.ext.sidebar']
+
+	sidebar_all=True
+	sidebar_relling=True
+	#sidebar_abbrev=True
+	sidebar_tocdepth=3
+
+## http://trac.sagemath.org/sage_trac/attachment/ticket/7549/trac_7549-doc_inheritance_underscore.patch
+# GraphViz includes dot, neato, twopi, circo, fdp. 
+graphviz_dot = 'dot' 
+inheritance_graph_attrs = { 'rankdir' : 'BT' } 
+inheritance_node_attrs = { 'height' : 0.5, 'fontsize' : 12, 'shape' : 'oval' } 
+inheritance_edge_attrs = {} 
+
+my_latex_preamble=r'''
+\usepackage{euler} % must be loaded before fontspec for the whole doc (below); this must be kept for pngmath, however
+\usepackage{hyperref}
+\usepackage{amsmath}
+\usepackage{amsbsy}
+%\usepackage{mathabx}
+\usepackage{underscore}
+\usepackage[all]{xy}
+
+% Metadata of the pdf output
+\hypersetup{pdftitle={Using and Programming}}
+\hypersetup{pdfauthor={Vaclav Smilauer; Bruno Chareyre; Jerome Duriez; Alexander Eulitz; Anton Gladky; Ning Guo; Christian Jakob; Janek Kozicki; Francois Kneib; Chiara Modenese; Jan Stransky; Klaus Thoeni}}
+\hypersetup{pdfkeywords={Discrete element method; dem; yade; documentation; manual; python; c++; git}}
+
+% symbols
+\let\mat\boldsymbol % matrix
+\let\vec\boldsymbol % vector
+\let\tens\boldsymbol % tensor
+
+\def\normalized#1{\widehat{#1}}
+\def\locframe#1{\widetilde{#1}}
+
+% timestep
+\def\Dt{\Delta t}
+\def\Dtcr{\Dt_{\rm cr}}
+
+% algorithm complexity
+\def\bigO#1{\ensuremath{\mathcal{O}(#1)}}
+
+% variants for greek symbols
+\let\epsilon\varepsilon
+\let\theta\vartheta
+\let\phi\varphi
+
+% shorthands
+\let\sig\sigma
+\let\eps\epsilon
+
+% variables at different points of time 
+\def\prev#1{#1^-}
+\def\pprev#1{#1^\ominus}
+\def\curr#1{#1^{\circ}}
+\def\nnext#1{#1^\oplus}
+\def\next#1{#1^+}
+
+% shorthands for geometry
+\def\currn{\curr{\vec{n}}}
+\def\currC{\curr{\vec{C}}}
+\def\uT{\vec{u}_T}
+\def\curruT{\curr{\vec{u}}_T}
+\def\prevuT{\prev{\vec{u}}_T}
+\def\currn{\curr{\vec{n}}}
+\def\prevn{\prev{\vec{n}}}
+
+% motion
+\def\pprevvel{\pprev{\dot{\vec{u}}}}
+\def\nnextvel{\nnext{\dot{\vec{u}}}}
+\def\curraccel{\curr{\ddot{\vec{u}}}}
+\def\prevpos{\prev{\vec{u}}}
+\def\currpos{\curr{\vec{u}}}
+\def\nextpos{\next{\vec{u}}}
+\def\curraaccel{\curr{\dot{\vec{\omega}}}}
+\def\pprevangvel{\pprev{\vec{\omega}}}
+\def\nnextangvel{\nnext{\vec{\omega}}}
+\def\loccurr#1{\curr{\locframe{#1}}}
+
+
+\def\numCPU{n_{\rm cpu}}
+\DeclareMathOperator{\Align}{Align}
+\DeclareMathOperator{\sign}{sgn}
+
+
+% sorting algorithms
+\def\isleq#1{\currelem{#1}\ar@/^/[ll]^{\leq}}
+\def\isnleq#1{\currelem{#1}\ar@/^/[ll]^{\not\leq}}
+\def\currelem#1{\fbox{$#1$}}
+\def\sortSep{||}
+\def\sortInv{\hbox{\phantom{||}}}
+\def\sortlines#1{\xymatrix@=3pt{#1}}
+\def\crossBound{||\mkern-18mu<}
+
+'''
+
+pngmath_latex_preamble=r'\usepackage[active]{preview}'+my_latex_preamble
+
+pngmath_use_preview=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'
+
+# The master toctree document.
+master_doc = 'index-toctree-manuals'
+
+# General information about the project.
+project = u'Yade'
+copyright = u'2009, Václav Šmilauer'
+
+# 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 = 'Yade documentation 2nd ed.'
+# The full version, including alpha/beta/rc tags.
+release = 'Yade documentation 2nd ed.'
+
+# 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 documents that shouldn't be included in the build.
+#unused_docs = []
+
+# List of directories, relative to source directory, that shouldn't be searched
+# for source files.
+exclude_trees = ['_build','../_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 = ['yade.']
+
+
+# -- Options for HTML output ---------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  Major themes that come with
+# Sphinx are currently 'default' and 'sphinxdoc'.
+html_theme = 'default'
+
+# 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 = {'stickysidebar':'true','collapsiblesidebar':'true','rightsidebar':'false'}
+
+# 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 = '../fig/yade-logo.png'
+
+# 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 = '../fig/yade-favicon.ico'
+
+# 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-html']
+
+# 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 = {}
+
+html_index='index.html'
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+html_additional_pages = { 'index':'index.html'}
+
+# If false, no module index is generated.
+#html_use_modindex = 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, 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 = ''
+
+# If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = ''
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'Yadedoc'
+
+
+# -- Options for LaTeX output --------------------------------------------------
+
+my_maketitle=r'''
+\begin{titlepage}
+
+\begin{flushright}
+\hrule{}
+
+% Upper part of the page
+\begin{flushright}
+\includegraphics[width=0.15\textwidth]{yade-logo.png}\par
+\end{flushright}
+\vspace{20 mm}
+\text{\sffamily\bfseries\Huge Using and Programming}\\
+\vspace{20 mm}
+%\vspace{70 mm}
+\begin{sffamily}\bfseries\Large
+V\'{a}clav \v{S}milauer, Bruno Chareyre, J\'er\^ome Duriez, Alexander Eulitz, Anton Gladky, Ning Guo, Christian Jakob, Janek Kozicki, Fran\c{c}ois Kneib, Chiara Modenese, Jan Str\'{a}nsk\'{y}, Klaus Thoeni
+\end{sffamily}
+\vspace{20 mm}
+\hrule{}
+\vfill
+\textit{\large Yade Documentation 2nd edition, 2015}\\
+\textit{based on Yade 1.14.0}\\
+\end{flushright}
+
+\end{titlepage}
+
+
+\text{\sffamily\bfseries\large Citing this document:}\\
+\v{S}milauer V. et al. (2015). Using and Programming. In:\textit{Yade Documentation 2nd ed.} doi:10.5281/zenodo.34043. http://yade-dem.org\\
+See also http://yade-dem/doc/citing.html.
+
+'''
+
+
+latex_elements=dict(
+	papersize='a4paper',
+	fontpkg=r'''
+\usepackage{euler}
+\usepackage{fontspec,xunicode,xltxtra}
+%\setmainfont[BoldFont={LMRoman10 Bold}]{CMU Concrete} %% CMU Concrete must be installed by hand as otf
+	''',
+	utf8extra='',
+	fncychap='',
+	preamble=my_latex_preamble,
+	footer='',
+	inputenc='',
+	fontenc='',
+	maketitle=my_maketitle,
+)
+
+# The paper size ('letter' or 'a4').
+#latex_paper_size = 'letter'
+
+# The font size ('10pt', '11pt' or '12pt').
+#latex_font_size = '10pt'
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass [howto/manual]).
+latex_documents = [
+   ('index-toctree-manuals', 'YadeManuals.tex', u'Using and Programming',
+   u'Václav Šmilauer et al.', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+latex_logo = '../fig/yade-logo.png'
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+latex_use_parts = False
+
+# Additional stuff for the LaTeX preamble.
+#latex_preamble = ''
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_use_modindex = True

=== added file 'doc/sphinx/book/confReference.py'
--- doc/sphinx/book/confReference.py	1970-01-01 00:00:00 +0000
+++ doc/sphinx/book/confReference.py	2015-11-20 00:42:30 +0000
@@ -0,0 +1,745 @@
+# -*- coding: utf-8 -*-
+#
+# Yade documentation build configuration file, created by
+# sphinx-quickstart on Mon Nov 16 21:49:34 2009.
+#
+# 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.
+
+# relevant posts to sphinx ML
+# http://groups.google.com/group/sphinx-dev/browse_thread/thread/b4fbc8d31d230fc4
+# http://groups.google.com/group/sphinx-dev/browse_thread/thread/118598245d5f479b
+
+#####################
+## custom yade roles
+#####################
+##
+## http://docutils.sourceforge.net/docs/howto/rst-roles.html
+
+import sys, os, re
+from docutils import nodes
+from sphinx import addnodes
+from sphinx.roles import XRefRole
+import docutils
+
+#
+# needed for creating hyperlink targets.
+# it should be cleand up and unified for both LaTeX and HTML via
+# the pending_xref node which gets resolved to real link target
+# by sphinx automatically once all docs have been processed.
+#
+# xrefs: http://groups.google.com/group/sphinx-dev/browse_thread/thread/d719d19307654548
+#
+#
+import __builtin__
+if 'latex' in sys.argv: __builtin__.writer='latex'
+elif 'html' in sys.argv: __builtin__.writer='html'
+elif 'epub' in sys.argv: __builtin__.writer='epub'
+else: raise RuntimeError("Must have either 'latex' or 'html' on the command line (hack for reference styles)")
+
+sys.path.append(os.path.abspath('./..'))
+
+def yaderef_role(role,rawtext,text,lineno,inliner,options={},content=[]):
+	"Handle the :yref:`` role, by making hyperlink to yade.wrapper.*. It supports :yref:`Link text<link target>` syntax, like usual hyperlinking roles."
+	id=rawtext.split(':',2)[2][1:-1]
+	txt=id; explicitText=False
+	m=re.match('(.*)\s*<(.*)>\s*',id)
+	if m:
+		explicitText=True
+		txt,id=m.group(1),m.group(2)
+	id=id.replace('::','.')
+	#node=nodes.reference(rawtext,docutils.utils.unescape(txt),refuri='http://beta.arcig.cz/~eudoxos/yade/doxygen/?search=%s'%id,**options)
+	#node=nodes.reference(rawtext,docutils.utils.unescape(txt),refuri='yade.wrapper.html#yade.wrapper.%s'%id,**options)
+	return [mkYrefNode(id,txt,rawtext,role,explicitText,lineno,options)],[]
+
+def yadesrc_role(role,rawtext,lineno,inliner,options={},content=[]):
+	"Handle the :ysrc:`` role, making hyperlink to git repository webpage with that path. Supports :ysrc:`Link text<file/name>` syntax, like usual hyperlinking roles. If target ends with ``/``, it is assumed to be a directory."
+	id=rawtext.split(':',2)[2][1:-1]
+	txt=id
+	m=re.match('(.*)\s*<(.*)>\s*',id)
+	if m:
+		txt,id=m.group(1),m.group(2)
+	return [nodes.reference(rawtext,docutils.utils.unescape(txt),refuri='https://github.com/yade/trunk/blob/master/%s'%id)],[] ### **options should be passed to nodes.reference as well
+
+# map modules to their html (rst) filenames. Used for sub-modules, where e.g. SpherePack is yade._packSphere.SpherePack, but is documented from yade.pack.rst
+moduleMap={
+	'yade._packPredicates':'yade.pack',
+	'yade._packSpheres':'yade.pack',
+	'yade._packObb':'yade.pack'
+}
+
+class YadeXRefRole(XRefRole):
+	#def process_link
+	def process_link(self, env, refnode, has_explicit_title, title, target):
+		print 'TARGET:','yade.wrapper.'+target
+		return '[['+title+']]','yade.wrapper.'+target
+
+def mkYrefNode(target,text,rawtext,role,explicitText,lineno,options={}):
+	"""Create hyperlink to yade target. Targets starting with literal 'yade.' are absolute, but the leading 'yade.' will be stripped from the link text. Absolute tergets are supposed to live in page named yade.[module].html, anchored at #yade.[module2].[rest of target], where [module2] is identical to [module], unless mapped over by moduleMap.
+	
+	Other targets are supposed to live in yade.wrapper (such as c++ classes)."""
+
+	writer=__builtin__.writer # to make sure not shadowed by a local var
+	import string
+	if target.startswith('yade.'):
+		module='.'.join(target.split('.')[0:2])
+		module2=(module if module not in moduleMap.keys() else moduleMap[module])
+		if target==module: target='' # to reference the module itself
+		uri=('%%%s#%s'%(module2,target) if writer=='latex' else '%s.html#%s'%(module2,target))
+		if not explicitText and module!=module2:
+			text=module2+'.'+'.'.join(target.split('.')[2:])
+		text=string.replace(text,'yade.','',1)
+	elif target.startswith('external:'):
+		exttarget=target.split(':',1)[1]
+		if not explicitText: text=exttarget
+		target=exttarget if '.' in exttarget else 'module-'+exttarget
+		uri=(('%%external#%s'%target) if writer=='latex' else 'external.html#%s'%target)
+	else:
+		uri=(('%%yade.wrapper#yade.wrapper.%s'%target) if writer=='latex' else 'yade.wrapper.html#yade.wrapper.%s'%target)
+		#print writer,uri
+	if 0:
+		refnode=addnodes.pending_xref(rawtext,reftype=role,refexplicit=explicitText,reftarget=target)
+		#refnode.line=lineno
+		#refnode+=nodes.literal(rawtext,text,classes=['ref',role])
+		return [refnode],[]
+		#ret.rawtext,reftype=role,
+	else:
+		return nodes.reference(rawtext,docutils.utils.unescape(text),refuri=uri,**options)
+	#return [refnode],[]
+
+def ydefault_role(role,rawtext,text,lineno,inliner,options={},content=[]):
+	"Handle the :ydefault:`something` role. fixSignature handles it now in the member signature itself, this merely expands to nothing."
+	return [],[]
+def yattrtype_role(role,rawtext,text,lineno,inliner,options={},content=[]):
+	"Handle the :yattrtype:`something` role. fixSignature handles it now in the member signature itself, this merely expands to nothing."
+	return [],[]
+# FIXME: should return readable representation of bits of the number (yade.wrapper.AttrFlags enum)
+def yattrflags_role(role,rawtext,text,lineno,inliner,options={},content=[]):
+	"Handle the :yattrflags:`something` role. fixSignature handles it now in the member signature itself."
+	return [],[]
+
+from docutils.parsers.rst import roles
+def yaderef_role_2(type,rawtext,text,lineno,inliner,options={},content=[]): return YadeXRefRole()('yref',rawtext,text,lineno,inliner,options,content)
+roles.register_canonical_role('yref', yaderef_role)
+roles.register_canonical_role('ysrc', yadesrc_role)
+roles.register_canonical_role('ydefault', ydefault_role)
+roles.register_canonical_role('yattrtype', yattrtype_role)
+roles.register_canonical_role('yattrflags', yattrflags_role)
+
+
+## http://sphinx.pocoo.org/config.html#confval-rst_epilog
+rst_epilog = """
+
+.. |yupdate| replace:: *(auto-updated)*
+.. |ycomp| replace:: *(auto-computed)*
+.. |ystatic| replace:: *(static)*
+"""
+
+import collections
+def customExclude(app, what, name, obj, skip, options):
+	if name=='clone':
+		if 'Serializable.clone' in str(obj): return False
+		return True
+	#escape crash on non iterable __doc__ in some qt object
+	if hasattr(obj,'__doc__') and obj.__doc__ and not isinstance(obj.__doc__, collections.Iterable): return True
+	if hasattr(obj,'__doc__') and obj.__doc__ and ('|ydeprecated|' in obj.__doc__ or '|yhidden|' in obj.__doc__): return True
+	#if re.match(r'\b(__init__|__reduce__|__repr__|__str__)\b',name): return True
+	if name.startswith('_'):
+		if name=='__init__':
+			# skip boost classes with parameterless ctor (arg1=implicit self)
+			if obj.__doc__=="\n__init__( (object)arg1) -> None": return True
+			# skip undocumented ctors
+			if not obj.__doc__: return True
+			# skip default ctor for serializable, taking dict of attrs
+			if obj.__doc__=='\n__init__( (object)arg1) -> None\n\nobject __init__(tuple args, dict kwds)': return True
+			#for i,l in enumerate(obj.__doc__.split('\n')): print name,i,l,'##'
+			return False
+		return True
+	return False
+
+def isBoostFunc(what,obj):
+	return what=='function' and obj.__repr__().startswith('<Boost.Python.function object at 0x')
+
+def isBoostMethod(what,obj):
+	"I don't know how to distinguish boost and non-boost methods..."
+	return what=='method' and obj.__repr__().startswith('<unbound method ');
+
+def replaceLaTeX(s):
+	# replace single non-escaped dollars $...$ by :math:`...`
+	# then \$ by single $
+	s=re.sub(r'(?<!\\)\$([^\$]+)(?<!\\)\$',r'\ :math:`\1`\ ',s)
+	return re.sub(r'\\\$',r'$',s)
+
+def fixSrc(app,docname,source):
+	source[0]=replaceLaTeX(source[0])
+
+def fixDocstring(app,what,name,obj,options,lines):
+	# remove empty default roles, which is not properly interpreted by docutils parser
+	for i in range(0,len(lines)):
+		lines[i]=lines[i].replace(':ydefault:``','')
+		lines[i]=lines[i].replace(':yattrtype:``','')
+		lines[i]=lines[i].replace(':yattrflags:``','')
+		#lines[i]=re.sub(':``',':` `',lines[i])
+	# remove signature of boost::python function docstring, which is the first line of the docstring
+	if isBoostFunc(what,obj):
+		l2=boostFuncSignature(name,obj)[1]
+		# we must replace lines one by one (in-place) :-|
+		# knowing that l2 is always shorter than lines (l2 is docstring with the signature stripped off)
+		for i in range(0,len(lines)):
+			lines[i]=l2[i] if i<len(l2) else ''
+	elif isBoostMethod(what,obj):
+		l2=boostFuncSignature(name,obj)[1]
+		for i in range(0,len(lines)):
+			lines[i]=l2[i] if i<len(l2) else ''
+	# LaTeX: replace $...$ by :math:`...`
+	# must be done after calling boostFuncSignature which uses original docstring
+	for i in range(0,len(lines)): lines[i]=replaceLaTeX(lines[i])
+
+
+def boostFuncSignature(name,obj,removeSelf=False):
+	"""Scan docstring of obj, returning tuple of properly formatted boost python signature
+	(first line of the docstring) and the rest of docstring (as list of lines).
+	The rest of docstring is stripped of 4 leading spaces which are automatically
+	added by boost.
+	
+	removeSelf will attempt to remove the first argument from the signature.
+	"""
+	doc=obj.__doc__
+	if doc==None: # not a boost method
+		return None,None
+	nname=name.split('.')[-1]
+	docc=doc.split('\n')
+	if len(docc)<2: return None,docc
+	doc1=docc[1]
+	# functions with weird docstring, likely not documented by boost
+	if not re.match('^'+nname+r'(.*)->.*$',doc1):
+		return None,docc
+	if doc1.endswith(':'): doc1=doc1[:-1]
+	strippedDoc=doc.split('\n')[2:]
+	# check if all lines are padded
+	allLinesHave4LeadingSpaces=True
+	for l in strippedDoc:
+		if l.startswith('    '): continue
+		allLinesHave4LeadingSpaces=False; break
+	# remove the padding if so
+	if allLinesHave4LeadingSpaces: strippedDoc=[l[4:] for l in strippedDoc]
+	for i in range(len(strippedDoc)):
+		# fix signatures inside docstring (one function with multiple signatures)
+		strippedDoc[i],n=re.subn(r'([a-zA-Z_][a-zA-Z0-9_]*\() \(object\)arg1(, |)',r'\1',strippedDoc[i].replace('->','→'))
+	# inspect dosctring after mangling
+	if 'getViscoelasticFromSpheresInteraction' in name and False:
+		print name
+		print strippedDoc
+		print '======================'
+		for l in strippedDoc: print l
+		print '======================'
+	sig=doc1.split('(',1)[1]
+	if removeSelf:
+		# remove up to the first comma; if no comma present, then the method takes no arguments
+		# if [ precedes the comma, add it to the result (ugly!)
+		try:
+			ss=sig.split(',',1)
+			if ss[0].endswith('['): sig='['+ss[1]
+			else: sig=ss[1]
+		except IndexError:
+			# grab the return value
+			try:
+				sig=') -> '+sig.split('->')[-1]
+		#if 'Serializable' in name: print 1000*'#',name
+			except IndexError:
+				sig=')'
+	return '('+sig,strippedDoc
+
+def fixSignature(app, what, name, obj, options, signature, return_annotation):
+	#print what,name,obj,signature#,dir(obj)
+	if what=='attribute':
+		doc=unicode(obj.__doc__)
+		ret=''
+		m=re.match('.*:ydefault:`(.*?)`.*',doc)
+		if m:
+			typ=''
+			#try:
+			#	clss='.'.join(name.split('.')[:-1])
+			#	instance=eval(clss+'()')
+			#	typ='; '+getattr(instance,name.split('.')[-1]).__class__.__name__
+			#	if typ=='; NoneType': typ=''
+			#except TypeError: ##no registered converted
+			#	typ=''
+			dfl=m.group(1)
+			m2=re.match(r'\s*\(\s*\(\s*void\s*\)\s*\"(.*)\"\s*,\s*(.*)\s*\)\s*',dfl)
+			if m2: dfl="%s, %s"%(m2.group(2),m2.group(1))
+			if dfl!='': ret+=' (='+dfl+'%s)'%typ
+			else: ret+=' (=uninitalized%s)'%typ
+		#m=re.match('.*\[(.{,8})\].*',doc)
+		#m=re.match('.*:yunit:`(.?*)`.*',doc)
+		#if m:
+		#	units=m.group(1)
+		#	print '@@@@@@@@@@@@@@@@@@@@@',name,units
+		#	ret+=' ['+units+']'
+		return ret,None
+	elif what=='class':
+		ret=[]
+		if len(obj.__bases__)>0:
+			base=obj.__bases__[0]
+			while base.__module__!='Boost.Python':
+				ret+=[base.__name__]
+				if len(base.__bases__)>0: base=base.__bases__[0]
+				else: break
+		if len(ret):
+			return ' (inherits '+u' → '.join(ret)+')',None
+		else: return None,None
+	elif isBoostFunc(what,obj):
+		sig=boostFuncSignature(name,obj)[0] or ' (wrapped c++ function)'
+		return sig,None
+	elif isBoostMethod(what,obj):
+		sig=boostFuncSignature(name,obj,removeSelf=True)[0]
+		return sig,None
+	#else: print what,name,obj.__repr__()
+	#return None,None
+		
+
+from sphinx import addnodes
+def parse_ystaticattr(env,attr,attrnode):
+	m=re.match(r'([a-zA-Z0-9_]+)\.(.*)\(=(.*)\)',attr)
+	if not m:
+		print 100*'@'+' Static attribute %s not matched'%attr
+		attrnode+=addnodes.desc_name(attr,attr)
+	klass,name,default=m.groups()
+	#attrnode+=addnodes.desc_type('static','static')
+	attrnode+=addnodes.desc_name(name,name)
+	plist=addnodes.desc_parameterlist()
+	if default=='': default='unspecified'
+	plist+=addnodes.desc_parameter('='+default,'='+default)
+	attrnode+=plist
+	attrnode+=addnodes.desc_annotation('  [static]','  [static]')
+	return klass+'.'+name
+
+#############################
+## set tab size
+###################
+## http://groups.google.com/group/sphinx-dev/browse_thread/thread/35b8071ffe9a8feb
+def setup(app):
+	from sphinx.highlighting import lexers
+	from pygments.lexers.compiled import CppLexer
+	lexers['cpp'] = CppLexer(tabsize=3) 
+	lexers['c++'] = CppLexer(tabsize=3) 
+	from pygments.lexers.agile import PythonLexer
+	lexers['python'] = PythonLexer(tabsize=3) 
+
+	app.connect('source-read',fixSrc)
+	
+	app.connect('autodoc-skip-member',customExclude)
+	app.connect('autodoc-process-signature',fixSignature)
+	app.connect('autodoc-process-docstring',fixDocstring)
+	app.add_description_unit('ystaticattr',None,objname='static attribute',indextemplate='pair: %s; static method',parse_node=parse_ystaticattr)
+
+
+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.append(os.path.abspath('.'))
+
+# -- General configuration -----------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+
+#
+# HACK: change ipython console regexp from ipython_console_highlighting.py
+import re
+sys.path.append(os.path.abspath('.'))
+
+import yade.config
+
+if 1:
+	if yade.runtime.ipython_version<12:
+		import ipython_directive as id
+	else:
+		if 12<=yade.runtime.ipython_version<13:
+			import ipython_directive012 as id
+                elif 13<=yade.runtime.ipython_version<200:
+			import ipython_directive013 as id
+                else:
+			import ipython_directive200 as id
+
+	#The next four lines are for compatibility with IPython 0.13.1
+	ipython_rgxin =re.compile(r'(?:In |Yade )\[(\d+)\]:\s?(.*)\s*')
+	ipython_rgxout=re.compile(r'(?:Out| ->  )\[(\d+)\]:\s?(.*)\s*')
+	ipython_promptin ='Yade [%d]:'
+	ipython_promptout=' ->  [%d]: '
+	ipython_cont_spaces='     '
+	#For IPython <=0.12, the following lines are used
+	id.rgxin =re.compile(r'(?:In |Yade )\[(\d+)\]:\s?(.*)\s*')
+	id.rgxout=re.compile(r'(?:Out| ->  )\[(\d+)\]:\s?(.*)\s*')
+	id.rgxcont=re.compile(r'(?:   +)\.\.+:\s?(.*)\s*')
+	id.fmtin  ='Yade [%d]:'
+	id.fmtout =' ->  [%d]: '  # for some reason, out and cont must have the trailing space
+	id.fmtcont='     .\D.: '
+	id.rc_override=dict(prompt_in1="Yade [\#]:",prompt_in2="     .\D.:",prompt_out=r" ->  [\#]: ")
+	if yade.runtime.ipython_version<12:
+		id.reconfig_shell()
+
+	import ipython_console_highlighting as ich
+	ich.IPythonConsoleLexer.input_prompt = re.compile("(Yade \[[0-9]+\]: )")
+	ich.IPythonConsoleLexer.output_prompt = re.compile("(( ->  |Out)|\[[0-9]+\]: )")
+	ich.IPythonConsoleLexer.continue_prompt = re.compile("\s+\.\.\.+:")
+
+
+extensions = [
+		'sphinx.ext.autodoc',
+		'sphinx.ext.autosummary',
+		'sphinx.ext.coverage',
+		'sphinx.ext.pngmath',
+		'sphinx.ext.graphviz',
+		'sphinx.ext.viewcode',
+		'sphinx.ext.inheritance_diagram',
+		'matplotlib.sphinxext.plot_directive',
+		'matplotlib.sphinxext.only_directives',
+		#'matplotlib.sphinxext.mathmpl',
+		'ipython_console_highlighting',
+		'youtube',
+		'sphinx.ext.todo',
+		]
+
+
+if yade.runtime.ipython_version<12:
+	extensions.append('ipython_directive')
+else:
+	if 12<=yade.runtime.ipython_version<13:
+		extensions.append('ipython_directive012')
+        elif 13<=yade.runtime.ipython_version<200:
+		extensions.append('ipython_directive013')
+        else:
+		extensions.append('ipython_directive200')
+
+# the sidebar extension
+if False:
+	if writer=='html':
+		extensions+=['sphinx.ext.sidebar']
+
+	sidebar_all=True
+	sidebar_relling=True
+	#sidebar_abbrev=True
+	sidebar_tocdepth=3
+
+## http://trac.sagemath.org/sage_trac/attachment/ticket/7549/trac_7549-doc_inheritance_underscore.patch
+# GraphViz includes dot, neato, twopi, circo, fdp. 
+graphviz_dot = 'dot' 
+inheritance_graph_attrs = { 'rankdir' : 'BT' } 
+inheritance_node_attrs = { 'height' : 0.5, 'fontsize' : 12, 'shape' : 'oval' } 
+inheritance_edge_attrs = {} 
+
+my_latex_preamble=r'''
+\usepackage{euler} % must be loaded before fontspec for the whole doc (below); this must be kept for pngmath, however
+\usepackage{hyperref}
+\usepackage{amsmath}
+\usepackage{amsbsy}
+%\usepackage{mathabx}
+\usepackage{underscore}
+\usepackage[all]{xy}
+
+% Metadata of the pdf output
+\hypersetup{pdftitle={Reference Manual}}
+\hypersetup{pdfauthor={Vaclav Smilauer; Emanuele Catalano; Bruno Chareyre; Sergei Dorofeenko; Jerome Duriez; Nolan Dyck; Burak Er; Jan Elias; Alexander Eulitz; Anton Gladky; Christian Jakob; Francois Kneib; Janek Kozicki; Donia Marzougui; Raphael Maurin; Chiara Modenese; Luc Scholtes; Luc Sibille; Jan Stransky; Thomas Sweijen; Klaus Thoeni; Chao Yuan}}
+\hypersetup{pdfkeywords={Discrete element method; dem; yade; documentation; manual; python; c++; git}}
+
+% symbols
+\let\mat\boldsymbol % matrix
+\let\vec\boldsymbol % vector
+\let\tens\boldsymbol % tensor
+
+\def\normalized#1{\widehat{#1}}
+\def\locframe#1{\widetilde{#1}}
+
+% timestep
+\def\Dt{\Delta t}
+\def\Dtcr{\Dt_{\rm cr}}
+
+% algorithm complexity
+\def\bigO#1{\ensuremath{\mathcal{O}(#1)}}
+
+% variants for greek symbols
+\let\epsilon\varepsilon
+\let\theta\vartheta
+\let\phi\varphi
+
+% shorthands
+\let\sig\sigma
+\let\eps\epsilon
+
+% variables at different points of time 
+\def\prev#1{#1^-}
+\def\pprev#1{#1^\ominus}
+\def\curr#1{#1^{\circ}}
+\def\nnext#1{#1^\oplus}
+\def\next#1{#1^+}
+
+% shorthands for geometry
+\def\currn{\curr{\vec{n}}}
+\def\currC{\curr{\vec{C}}}
+\def\uT{\vec{u}_T}
+\def\curruT{\curr{\vec{u}}_T}
+\def\prevuT{\prev{\vec{u}}_T}
+\def\currn{\curr{\vec{n}}}
+\def\prevn{\prev{\vec{n}}}
+
+% motion
+\def\pprevvel{\pprev{\dot{\vec{u}}}}
+\def\nnextvel{\nnext{\dot{\vec{u}}}}
+\def\curraccel{\curr{\ddot{\vec{u}}}}
+\def\prevpos{\prev{\vec{u}}}
+\def\currpos{\curr{\vec{u}}}
+\def\nextpos{\next{\vec{u}}}
+\def\curraaccel{\curr{\dot{\vec{\omega}}}}
+\def\pprevangvel{\pprev{\vec{\omega}}}
+\def\nnextangvel{\nnext{\vec{\omega}}}
+\def\loccurr#1{\curr{\locframe{#1}}}
+
+
+\def\numCPU{n_{\rm cpu}}
+\DeclareMathOperator{\Align}{Align}
+\DeclareMathOperator{\sign}{sgn}
+
+
+% sorting algorithms
+\def\isleq#1{\currelem{#1}\ar@/^/[ll]^{\leq}}
+\def\isnleq#1{\currelem{#1}\ar@/^/[ll]^{\not\leq}}
+\def\currelem#1{\fbox{$#1$}}
+\def\sortSep{||}
+\def\sortInv{\hbox{\phantom{||}}}
+\def\sortlines#1{\xymatrix@=3pt{#1}}
+\def\crossBound{||\mkern-18mu<}
+
+'''
+
+pngmath_latex_preamble=r'\usepackage[active]{preview}'+my_latex_preamble
+
+pngmath_use_preview=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'
+
+# The master toctree document.
+master_doc = 'index-toctree-reference'
+
+# General information about the project.
+project = u'Yade'
+copyright = u'2009, Václav Šmilauer'
+
+# 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 = 'Yade documentation 2nd ed.'
+# The full version, including alpha/beta/rc tags.
+release = 'Yade documentation 2nd ed.'
+
+# 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 documents that shouldn't be included in the build.
+#unused_docs = []
+
+# List of directories, relative to source directory, that shouldn't be searched
+# for source files.
+exclude_trees = ['_build','../_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 = ['yade.']
+
+
+# -- Options for HTML output ---------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  Major themes that come with
+# Sphinx are currently 'default' and 'sphinxdoc'.
+html_theme = 'default'
+
+# 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 = {'stickysidebar':'true','collapsiblesidebar':'true','rightsidebar':'false'}
+
+# 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 = '../fig/yade-logo.png'
+
+# 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 = '../fig/yade-favicon.ico'
+
+# 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-html']
+
+# 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 = {}
+
+html_index='index.html'
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+html_additional_pages = { 'index':'index.html'}
+
+# If false, no module index is generated.
+#html_use_modindex = 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, 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 = ''
+
+# If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = ''
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'Yadedoc'
+
+
+# -- Options for LaTeX output --------------------------------------------------
+
+my_maketitle=r'''
+\begin{titlepage}
+
+\begin{flushright}
+\hrule{}
+
+% Upper part of the page
+\begin{flushright}
+\includegraphics[width=0.15\textwidth]{yade-logo.png}\par
+\end{flushright}
+\vspace{20 mm}
+\text{\sffamily\bfseries\Huge Reference Manual}\\
+\vspace{20 mm}
+%\vspace{70 mm}
+\begin{sffamily}\bfseries\Large
+V\'{a}clav \v{S}milauer, Emanuele Catalano, Bruno Chareyre, Sergei Dorofeenko, J\'er\^ome Duriez, Nolan Dyck, Jan Eliáš, Burak Er, Alexander Eulitz, Anton Gladky, Christian Jakob, Fran\c{c}ois Kneib, Janek Kozicki, Donia Marzougui, Rapha\"el Maurin, Chiara Modenese, Luc Scholt\`{e}s, Luc Sibille, Jan Str\'{a}nsk\'{y}, Thomas Sweijen, Klaus Thoeni, Chao Yuan
+\end{sffamily}
+\vspace{20 mm}
+\hrule{}
+\vfill
+\textit{\large Yade Documentation 2nd edition, 2015}\\
+\textit{based on Yade 1.14.0}\\
+\end{flushright}
+
+\end{titlepage}
+
+
+\text{\sffamily\bfseries\large Citing this document:}\\
+\v{S}milauer V. et al. (2015). Reference Manual. In:\textit{Yade Documentation 2nd ed.} doi:10.5281/zenodo.34045. http://yade-dem.org\\
+See also http://yade-dem/doc/citing.html.
+
+'''
+
+
+latex_elements=dict(
+	papersize='a4paper',
+	fontpkg=r'''
+\usepackage{euler}
+\usepackage{fontspec,xunicode,xltxtra}
+%\setmainfont[BoldFont={LMRoman10 Bold}]{CMU Concrete} %% CMU Concrete must be installed by hand as otf
+	''',
+	utf8extra='',
+	fncychap='',
+	preamble=my_latex_preamble,
+	footer='',
+	inputenc='',
+	fontenc='',
+	maketitle=my_maketitle,
+)
+
+# The paper size ('letter' or 'a4').
+#latex_paper_size = 'letter'
+
+# The font size ('10pt', '11pt' or '12pt').
+#latex_font_size = '10pt'
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass [howto/manual]).
+latex_documents = [
+   ('index-toctree-reference', 'YadeReference.tex', u'Reference Manual',
+   u'Václav Šmilauer et al.', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+latex_logo = '../fig/yade-logo.png'
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+latex_use_parts = False
+
+# Additional stuff for the LaTeX preamble.
+#latex_preamble = ''
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_use_modindex = True

=== added file 'doc/sphinx/book/confTheory.py'
--- doc/sphinx/book/confTheory.py	1970-01-01 00:00:00 +0000
+++ doc/sphinx/book/confTheory.py	2015-11-20 00:42:30 +0000
@@ -0,0 +1,745 @@
+# -*- coding: utf-8 -*-
+#
+# Yade documentation build configuration file, created by
+# sphinx-quickstart on Mon Nov 16 21:49:34 2009.
+#
+# 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.
+
+# relevant posts to sphinx ML
+# http://groups.google.com/group/sphinx-dev/browse_thread/thread/b4fbc8d31d230fc4
+# http://groups.google.com/group/sphinx-dev/browse_thread/thread/118598245d5f479b
+
+#####################
+## custom yade roles
+#####################
+##
+## http://docutils.sourceforge.net/docs/howto/rst-roles.html
+
+import sys, os, re
+from docutils import nodes
+from sphinx import addnodes
+from sphinx.roles import XRefRole
+import docutils
+
+#
+# needed for creating hyperlink targets.
+# it should be cleand up and unified for both LaTeX and HTML via
+# the pending_xref node which gets resolved to real link target
+# by sphinx automatically once all docs have been processed.
+#
+# xrefs: http://groups.google.com/group/sphinx-dev/browse_thread/thread/d719d19307654548
+#
+#
+import __builtin__
+if 'latex' in sys.argv: __builtin__.writer='latex'
+elif 'html' in sys.argv: __builtin__.writer='html'
+elif 'epub' in sys.argv: __builtin__.writer='epub'
+else: raise RuntimeError("Must have either 'latex' or 'html' on the command line (hack for reference styles)")
+
+sys.path.append(os.path.abspath('./..'))
+
+def yaderef_role(role,rawtext,text,lineno,inliner,options={},content=[]):
+	"Handle the :yref:`` role, by making hyperlink to yade.wrapper.*. It supports :yref:`Link text<link target>` syntax, like usual hyperlinking roles."
+	id=rawtext.split(':',2)[2][1:-1]
+	txt=id; explicitText=False
+	m=re.match('(.*)\s*<(.*)>\s*',id)
+	if m:
+		explicitText=True
+		txt,id=m.group(1),m.group(2)
+	id=id.replace('::','.')
+	#node=nodes.reference(rawtext,docutils.utils.unescape(txt),refuri='http://beta.arcig.cz/~eudoxos/yade/doxygen/?search=%s'%id,**options)
+	#node=nodes.reference(rawtext,docutils.utils.unescape(txt),refuri='yade.wrapper.html#yade.wrapper.%s'%id,**options)
+	return [mkYrefNode(id,txt,rawtext,role,explicitText,lineno,options)],[]
+
+def yadesrc_role(role,rawtext,lineno,inliner,options={},content=[]):
+	"Handle the :ysrc:`` role, making hyperlink to git repository webpage with that path. Supports :ysrc:`Link text<file/name>` syntax, like usual hyperlinking roles. If target ends with ``/``, it is assumed to be a directory."
+	id=rawtext.split(':',2)[2][1:-1]
+	txt=id
+	m=re.match('(.*)\s*<(.*)>\s*',id)
+	if m:
+		txt,id=m.group(1),m.group(2)
+	return [nodes.reference(rawtext,docutils.utils.unescape(txt),refuri='https://github.com/yade/trunk/blob/master/%s'%id)],[] ### **options should be passed to nodes.reference as well
+
+# map modules to their html (rst) filenames. Used for sub-modules, where e.g. SpherePack is yade._packSphere.SpherePack, but is documented from yade.pack.rst
+moduleMap={
+	'yade._packPredicates':'yade.pack',
+	'yade._packSpheres':'yade.pack',
+	'yade._packObb':'yade.pack'
+}
+
+class YadeXRefRole(XRefRole):
+	#def process_link
+	def process_link(self, env, refnode, has_explicit_title, title, target):
+		print 'TARGET:','yade.wrapper.'+target
+		return '[['+title+']]','yade.wrapper.'+target
+
+def mkYrefNode(target,text,rawtext,role,explicitText,lineno,options={}):
+	"""Create hyperlink to yade target. Targets starting with literal 'yade.' are absolute, but the leading 'yade.' will be stripped from the link text. Absolute tergets are supposed to live in page named yade.[module].html, anchored at #yade.[module2].[rest of target], where [module2] is identical to [module], unless mapped over by moduleMap.
+	
+	Other targets are supposed to live in yade.wrapper (such as c++ classes)."""
+
+	writer=__builtin__.writer # to make sure not shadowed by a local var
+	import string
+	if target.startswith('yade.'):
+		module='.'.join(target.split('.')[0:2])
+		module2=(module if module not in moduleMap.keys() else moduleMap[module])
+		if target==module: target='' # to reference the module itself
+		uri=('%%%s#%s'%(module2,target) if writer=='latex' else '%s.html#%s'%(module2,target))
+		if not explicitText and module!=module2:
+			text=module2+'.'+'.'.join(target.split('.')[2:])
+		text=string.replace(text,'yade.','',1)
+	elif target.startswith('external:'):
+		exttarget=target.split(':',1)[1]
+		if not explicitText: text=exttarget
+		target=exttarget if '.' in exttarget else 'module-'+exttarget
+		uri=(('%%external#%s'%target) if writer=='latex' else 'external.html#%s'%target)
+	else:
+		uri=(('%%yade.wrapper#yade.wrapper.%s'%target) if writer=='latex' else 'yade.wrapper.html#yade.wrapper.%s'%target)
+		#print writer,uri
+	if 0:
+		refnode=addnodes.pending_xref(rawtext,reftype=role,refexplicit=explicitText,reftarget=target)
+		#refnode.line=lineno
+		#refnode+=nodes.literal(rawtext,text,classes=['ref',role])
+		return [refnode],[]
+		#ret.rawtext,reftype=role,
+	else:
+		return nodes.reference(rawtext,docutils.utils.unescape(text),refuri=uri,**options)
+	#return [refnode],[]
+
+def ydefault_role(role,rawtext,text,lineno,inliner,options={},content=[]):
+	"Handle the :ydefault:`something` role. fixSignature handles it now in the member signature itself, this merely expands to nothing."
+	return [],[]
+def yattrtype_role(role,rawtext,text,lineno,inliner,options={},content=[]):
+	"Handle the :yattrtype:`something` role. fixSignature handles it now in the member signature itself, this merely expands to nothing."
+	return [],[]
+# FIXME: should return readable representation of bits of the number (yade.wrapper.AttrFlags enum)
+def yattrflags_role(role,rawtext,text,lineno,inliner,options={},content=[]):
+	"Handle the :yattrflags:`something` role. fixSignature handles it now in the member signature itself."
+	return [],[]
+
+from docutils.parsers.rst import roles
+def yaderef_role_2(type,rawtext,text,lineno,inliner,options={},content=[]): return YadeXRefRole()('yref',rawtext,text,lineno,inliner,options,content)
+roles.register_canonical_role('yref', yaderef_role)
+roles.register_canonical_role('ysrc', yadesrc_role)
+roles.register_canonical_role('ydefault', ydefault_role)
+roles.register_canonical_role('yattrtype', yattrtype_role)
+roles.register_canonical_role('yattrflags', yattrflags_role)
+
+
+## http://sphinx.pocoo.org/config.html#confval-rst_epilog
+rst_epilog = """
+
+.. |yupdate| replace:: *(auto-updated)*
+.. |ycomp| replace:: *(auto-computed)*
+.. |ystatic| replace:: *(static)*
+"""
+
+import collections
+def customExclude(app, what, name, obj, skip, options):
+	if name=='clone':
+		if 'Serializable.clone' in str(obj): return False
+		return True
+	#escape crash on non iterable __doc__ in some qt object
+	if hasattr(obj,'__doc__') and obj.__doc__ and not isinstance(obj.__doc__, collections.Iterable): return True
+	if hasattr(obj,'__doc__') and obj.__doc__ and ('|ydeprecated|' in obj.__doc__ or '|yhidden|' in obj.__doc__): return True
+	#if re.match(r'\b(__init__|__reduce__|__repr__|__str__)\b',name): return True
+	if name.startswith('_'):
+		if name=='__init__':
+			# skip boost classes with parameterless ctor (arg1=implicit self)
+			if obj.__doc__=="\n__init__( (object)arg1) -> None": return True
+			# skip undocumented ctors
+			if not obj.__doc__: return True
+			# skip default ctor for serializable, taking dict of attrs
+			if obj.__doc__=='\n__init__( (object)arg1) -> None\n\nobject __init__(tuple args, dict kwds)': return True
+			#for i,l in enumerate(obj.__doc__.split('\n')): print name,i,l,'##'
+			return False
+		return True
+	return False
+
+def isBoostFunc(what,obj):
+	return what=='function' and obj.__repr__().startswith('<Boost.Python.function object at 0x')
+
+def isBoostMethod(what,obj):
+	"I don't know how to distinguish boost and non-boost methods..."
+	return what=='method' and obj.__repr__().startswith('<unbound method ');
+
+def replaceLaTeX(s):
+	# replace single non-escaped dollars $...$ by :math:`...`
+	# then \$ by single $
+	s=re.sub(r'(?<!\\)\$([^\$]+)(?<!\\)\$',r'\ :math:`\1`\ ',s)
+	return re.sub(r'\\\$',r'$',s)
+
+def fixSrc(app,docname,source):
+	source[0]=replaceLaTeX(source[0])
+
+def fixDocstring(app,what,name,obj,options,lines):
+	# remove empty default roles, which is not properly interpreted by docutils parser
+	for i in range(0,len(lines)):
+		lines[i]=lines[i].replace(':ydefault:``','')
+		lines[i]=lines[i].replace(':yattrtype:``','')
+		lines[i]=lines[i].replace(':yattrflags:``','')
+		#lines[i]=re.sub(':``',':` `',lines[i])
+	# remove signature of boost::python function docstring, which is the first line of the docstring
+	if isBoostFunc(what,obj):
+		l2=boostFuncSignature(name,obj)[1]
+		# we must replace lines one by one (in-place) :-|
+		# knowing that l2 is always shorter than lines (l2 is docstring with the signature stripped off)
+		for i in range(0,len(lines)):
+			lines[i]=l2[i] if i<len(l2) else ''
+	elif isBoostMethod(what,obj):
+		l2=boostFuncSignature(name,obj)[1]
+		for i in range(0,len(lines)):
+			lines[i]=l2[i] if i<len(l2) else ''
+	# LaTeX: replace $...$ by :math:`...`
+	# must be done after calling boostFuncSignature which uses original docstring
+	for i in range(0,len(lines)): lines[i]=replaceLaTeX(lines[i])
+
+
+def boostFuncSignature(name,obj,removeSelf=False):
+	"""Scan docstring of obj, returning tuple of properly formatted boost python signature
+	(first line of the docstring) and the rest of docstring (as list of lines).
+	The rest of docstring is stripped of 4 leading spaces which are automatically
+	added by boost.
+	
+	removeSelf will attempt to remove the first argument from the signature.
+	"""
+	doc=obj.__doc__
+	if doc==None: # not a boost method
+		return None,None
+	nname=name.split('.')[-1]
+	docc=doc.split('\n')
+	if len(docc)<2: return None,docc
+	doc1=docc[1]
+	# functions with weird docstring, likely not documented by boost
+	if not re.match('^'+nname+r'(.*)->.*$',doc1):
+		return None,docc
+	if doc1.endswith(':'): doc1=doc1[:-1]
+	strippedDoc=doc.split('\n')[2:]
+	# check if all lines are padded
+	allLinesHave4LeadingSpaces=True
+	for l in strippedDoc:
+		if l.startswith('    '): continue
+		allLinesHave4LeadingSpaces=False; break
+	# remove the padding if so
+	if allLinesHave4LeadingSpaces: strippedDoc=[l[4:] for l in strippedDoc]
+	for i in range(len(strippedDoc)):
+		# fix signatures inside docstring (one function with multiple signatures)
+		strippedDoc[i],n=re.subn(r'([a-zA-Z_][a-zA-Z0-9_]*\() \(object\)arg1(, |)',r'\1',strippedDoc[i].replace('->','→'))
+	# inspect dosctring after mangling
+	if 'getViscoelasticFromSpheresInteraction' in name and False:
+		print name
+		print strippedDoc
+		print '======================'
+		for l in strippedDoc: print l
+		print '======================'
+	sig=doc1.split('(',1)[1]
+	if removeSelf:
+		# remove up to the first comma; if no comma present, then the method takes no arguments
+		# if [ precedes the comma, add it to the result (ugly!)
+		try:
+			ss=sig.split(',',1)
+			if ss[0].endswith('['): sig='['+ss[1]
+			else: sig=ss[1]
+		except IndexError:
+			# grab the return value
+			try:
+				sig=') -> '+sig.split('->')[-1]
+		#if 'Serializable' in name: print 1000*'#',name
+			except IndexError:
+				sig=')'
+	return '('+sig,strippedDoc
+
+def fixSignature(app, what, name, obj, options, signature, return_annotation):
+	#print what,name,obj,signature#,dir(obj)
+	if what=='attribute':
+		doc=unicode(obj.__doc__)
+		ret=''
+		m=re.match('.*:ydefault:`(.*?)`.*',doc)
+		if m:
+			typ=''
+			#try:
+			#	clss='.'.join(name.split('.')[:-1])
+			#	instance=eval(clss+'()')
+			#	typ='; '+getattr(instance,name.split('.')[-1]).__class__.__name__
+			#	if typ=='; NoneType': typ=''
+			#except TypeError: ##no registered converted
+			#	typ=''
+			dfl=m.group(1)
+			m2=re.match(r'\s*\(\s*\(\s*void\s*\)\s*\"(.*)\"\s*,\s*(.*)\s*\)\s*',dfl)
+			if m2: dfl="%s, %s"%(m2.group(2),m2.group(1))
+			if dfl!='': ret+=' (='+dfl+'%s)'%typ
+			else: ret+=' (=uninitalized%s)'%typ
+		#m=re.match('.*\[(.{,8})\].*',doc)
+		#m=re.match('.*:yunit:`(.?*)`.*',doc)
+		#if m:
+		#	units=m.group(1)
+		#	print '@@@@@@@@@@@@@@@@@@@@@',name,units
+		#	ret+=' ['+units+']'
+		return ret,None
+	elif what=='class':
+		ret=[]
+		if len(obj.__bases__)>0:
+			base=obj.__bases__[0]
+			while base.__module__!='Boost.Python':
+				ret+=[base.__name__]
+				if len(base.__bases__)>0: base=base.__bases__[0]
+				else: break
+		if len(ret):
+			return ' (inherits '+u' → '.join(ret)+')',None
+		else: return None,None
+	elif isBoostFunc(what,obj):
+		sig=boostFuncSignature(name,obj)[0] or ' (wrapped c++ function)'
+		return sig,None
+	elif isBoostMethod(what,obj):
+		sig=boostFuncSignature(name,obj,removeSelf=True)[0]
+		return sig,None
+	#else: print what,name,obj.__repr__()
+	#return None,None
+		
+
+from sphinx import addnodes
+def parse_ystaticattr(env,attr,attrnode):
+	m=re.match(r'([a-zA-Z0-9_]+)\.(.*)\(=(.*)\)',attr)
+	if not m:
+		print 100*'@'+' Static attribute %s not matched'%attr
+		attrnode+=addnodes.desc_name(attr,attr)
+	klass,name,default=m.groups()
+	#attrnode+=addnodes.desc_type('static','static')
+	attrnode+=addnodes.desc_name(name,name)
+	plist=addnodes.desc_parameterlist()
+	if default=='': default='unspecified'
+	plist+=addnodes.desc_parameter('='+default,'='+default)
+	attrnode+=plist
+	attrnode+=addnodes.desc_annotation('  [static]','  [static]')
+	return klass+'.'+name
+
+#############################
+## set tab size
+###################
+## http://groups.google.com/group/sphinx-dev/browse_thread/thread/35b8071ffe9a8feb
+def setup(app):
+	from sphinx.highlighting import lexers
+	from pygments.lexers.compiled import CppLexer
+	lexers['cpp'] = CppLexer(tabsize=3) 
+	lexers['c++'] = CppLexer(tabsize=3) 
+	from pygments.lexers.agile import PythonLexer
+	lexers['python'] = PythonLexer(tabsize=3) 
+
+	app.connect('source-read',fixSrc)
+	
+	app.connect('autodoc-skip-member',customExclude)
+	app.connect('autodoc-process-signature',fixSignature)
+	app.connect('autodoc-process-docstring',fixDocstring)
+	app.add_description_unit('ystaticattr',None,objname='static attribute',indextemplate='pair: %s; static method',parse_node=parse_ystaticattr)
+
+
+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.append(os.path.abspath('.'))
+
+# -- General configuration -----------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+
+#
+# HACK: change ipython console regexp from ipython_console_highlighting.py
+import re
+sys.path.append(os.path.abspath('.'))
+
+import yade.config
+
+if 1:
+	if yade.runtime.ipython_version<12:
+		import ipython_directive as id
+	else:
+		if 12<=yade.runtime.ipython_version<13:
+			import ipython_directive012 as id
+                elif 13<=yade.runtime.ipython_version<200:
+			import ipython_directive013 as id
+                else:
+			import ipython_directive200 as id
+
+	#The next four lines are for compatibility with IPython 0.13.1
+	ipython_rgxin =re.compile(r'(?:In |Yade )\[(\d+)\]:\s?(.*)\s*')
+	ipython_rgxout=re.compile(r'(?:Out| ->  )\[(\d+)\]:\s?(.*)\s*')
+	ipython_promptin ='Yade [%d]:'
+	ipython_promptout=' ->  [%d]: '
+	ipython_cont_spaces='     '
+	#For IPython <=0.12, the following lines are used
+	id.rgxin =re.compile(r'(?:In |Yade )\[(\d+)\]:\s?(.*)\s*')
+	id.rgxout=re.compile(r'(?:Out| ->  )\[(\d+)\]:\s?(.*)\s*')
+	id.rgxcont=re.compile(r'(?:   +)\.\.+:\s?(.*)\s*')
+	id.fmtin  ='Yade [%d]:'
+	id.fmtout =' ->  [%d]: '  # for some reason, out and cont must have the trailing space
+	id.fmtcont='     .\D.: '
+	id.rc_override=dict(prompt_in1="Yade [\#]:",prompt_in2="     .\D.:",prompt_out=r" ->  [\#]: ")
+	if yade.runtime.ipython_version<12:
+		id.reconfig_shell()
+
+	import ipython_console_highlighting as ich
+	ich.IPythonConsoleLexer.input_prompt = re.compile("(Yade \[[0-9]+\]: )")
+	ich.IPythonConsoleLexer.output_prompt = re.compile("(( ->  |Out)|\[[0-9]+\]: )")
+	ich.IPythonConsoleLexer.continue_prompt = re.compile("\s+\.\.\.+:")
+
+
+extensions = [
+		'sphinx.ext.autodoc',
+		'sphinx.ext.autosummary',
+		'sphinx.ext.coverage',
+		'sphinx.ext.pngmath',
+		'sphinx.ext.graphviz',
+		'sphinx.ext.viewcode',
+		'sphinx.ext.inheritance_diagram',
+		'matplotlib.sphinxext.plot_directive',
+		'matplotlib.sphinxext.only_directives',
+		#'matplotlib.sphinxext.mathmpl',
+		'ipython_console_highlighting',
+		'youtube',
+		'sphinx.ext.todo',
+		]
+
+
+if yade.runtime.ipython_version<12:
+	extensions.append('ipython_directive')
+else:
+	if 12<=yade.runtime.ipython_version<13:
+		extensions.append('ipython_directive012')
+        elif 13<=yade.runtime.ipython_version<200:
+		extensions.append('ipython_directive013')
+        else:
+		extensions.append('ipython_directive200')
+
+# the sidebar extension
+if False:
+	if writer=='html':
+		extensions+=['sphinx.ext.sidebar']
+
+	sidebar_all=True
+	sidebar_relling=True
+	#sidebar_abbrev=True
+	sidebar_tocdepth=3
+
+## http://trac.sagemath.org/sage_trac/attachment/ticket/7549/trac_7549-doc_inheritance_underscore.patch
+# GraphViz includes dot, neato, twopi, circo, fdp. 
+graphviz_dot = 'dot' 
+inheritance_graph_attrs = { 'rankdir' : 'BT' } 
+inheritance_node_attrs = { 'height' : 0.5, 'fontsize' : 12, 'shape' : 'oval' } 
+inheritance_edge_attrs = {} 
+
+my_latex_preamble=r'''
+\usepackage{euler} % must be loaded before fontspec for the whole doc (below); this must be kept for pngmath, however
+\usepackage{hyperref}
+\usepackage{amsmath}
+\usepackage{amsbsy}
+%\usepackage{mathabx}
+\usepackage{underscore}
+\usepackage[all]{xy}
+
+% Metadata of the pdf output
+\hypersetup{pdftitle={DEM formulation}}
+\hypersetup{pdfauthor={Vaclav Smilauer; Bruno Chareyre}}
+\hypersetup{pdfkeywords={Discrete element method; micromechanics; granular materials; contact law; hydromechanical coupling; yade; documentation}}
+
+% symbols
+\let\mat\boldsymbol % matrix
+\let\vec\boldsymbol % vector
+\let\tens\boldsymbol % tensor
+
+\def\normalized#1{\widehat{#1}}
+\def\locframe#1{\widetilde{#1}}
+
+% timestep
+\def\Dt{\Delta t}
+\def\Dtcr{\Dt_{\rm cr}}
+
+% algorithm complexity
+\def\bigO#1{\ensuremath{\mathcal{O}(#1)}}
+
+% variants for greek symbols
+\let\epsilon\varepsilon
+\let\theta\vartheta
+\let\phi\varphi
+
+% shorthands
+\let\sig\sigma
+\let\eps\epsilon
+
+% variables at different points of time 
+\def\prev#1{#1^-}
+\def\pprev#1{#1^\ominus}
+\def\curr#1{#1^{\circ}}
+\def\nnext#1{#1^\oplus}
+\def\next#1{#1^+}
+
+% shorthands for geometry
+\def\currn{\curr{\vec{n}}}
+\def\currC{\curr{\vec{C}}}
+\def\uT{\vec{u}_T}
+\def\curruT{\curr{\vec{u}}_T}
+\def\prevuT{\prev{\vec{u}}_T}
+\def\currn{\curr{\vec{n}}}
+\def\prevn{\prev{\vec{n}}}
+
+% motion
+\def\pprevvel{\pprev{\dot{\vec{u}}}}
+\def\nnextvel{\nnext{\dot{\vec{u}}}}
+\def\curraccel{\curr{\ddot{\vec{u}}}}
+\def\prevpos{\prev{\vec{u}}}
+\def\currpos{\curr{\vec{u}}}
+\def\nextpos{\next{\vec{u}}}
+\def\curraaccel{\curr{\dot{\vec{\omega}}}}
+\def\pprevangvel{\pprev{\vec{\omega}}}
+\def\nnextangvel{\nnext{\vec{\omega}}}
+\def\loccurr#1{\curr{\locframe{#1}}}
+
+
+\def\numCPU{n_{\rm cpu}}
+\DeclareMathOperator{\Align}{Align}
+\DeclareMathOperator{\sign}{sgn}
+
+
+% sorting algorithms
+\def\isleq#1{\currelem{#1}\ar@/^/[ll]^{\leq}}
+\def\isnleq#1{\currelem{#1}\ar@/^/[ll]^{\not\leq}}
+\def\currelem#1{\fbox{$#1$}}
+\def\sortSep{||}
+\def\sortInv{\hbox{\phantom{||}}}
+\def\sortlines#1{\xymatrix@=3pt{#1}}
+\def\crossBound{||\mkern-18mu<}
+
+'''
+
+pngmath_latex_preamble=r'\usepackage[active]{preview}'+my_latex_preamble
+
+pngmath_use_preview=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'
+
+# The master toctree document.
+master_doc = 'index-toctree-theory'
+
+# General information about the project.
+project = u'Yade'
+copyright = u'2009, Václav Šmilauer'
+
+# 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 = 'Yade documentation 2nd ed.'
+# The full version, including alpha/beta/rc tags.
+release = 'Yade documentation 2nd ed.'
+
+# 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 documents that shouldn't be included in the build.
+#unused_docs = []
+
+# List of directories, relative to source directory, that shouldn't be searched
+# for source files.
+exclude_trees = ['_build','../_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 = ['yade.']
+
+
+# -- Options for HTML output ---------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  Major themes that come with
+# Sphinx are currently 'default' and 'sphinxdoc'.
+html_theme = 'default'
+
+# 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 = {'stickysidebar':'true','collapsiblesidebar':'true','rightsidebar':'false'}
+
+# 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 = '../fig/yade-logo.png'
+
+# 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 = '../fig/yade-favicon.ico'
+
+# 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-html']
+
+# 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 = {}
+
+html_index='index.html'
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+html_additional_pages = { 'index':'index.html'}
+
+# If false, no module index is generated.
+#html_use_modindex = 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, 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 = ''
+
+# If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = ''
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'Yadedoc'
+
+
+# -- Options for LaTeX output --------------------------------------------------
+
+my_maketitle=r'''
+\begin{titlepage}
+
+\begin{flushright}
+\hrule{}
+
+% Upper part of the page
+\begin{flushright}
+\includegraphics[width=0.15\textwidth]{yade-logo.png}\par
+\end{flushright}
+\vspace{20 mm}
+\text{\sffamily\bfseries\Huge DEM Formulation}\\
+\vspace{20 mm}
+%\vspace{70 mm}
+\begin{sffamily}\bfseries\Large
+V\'{a}clav \v{S}milauer, Bruno Chareyre
+\end{sffamily}
+\vspace{20 mm}
+\hrule{}
+\vfill
+\textit{\large Yade Documentation 2nd edition, 2015}\\
+\textit{based on Yade 1.14.0}\\
+\end{flushright}
+
+\end{titlepage}
+
+
+\text{\sffamily\bfseries\large Citing this document:}\\
+\v{S}milauer V. and Chareyre B. (2015). DEM Formulation. In:\textit{Yade Documentation 2nd ed.} doi:10.5281/zenodo.34044. http://yade-dem.org\\
+See also http://yade-dem/doc/citing.html.
+
+'''
+
+
+latex_elements=dict(
+	papersize='a4paper',
+	fontpkg=r'''
+\usepackage{euler}
+\usepackage{fontspec,xunicode,xltxtra}
+%\setmainfont[BoldFont={LMRoman10 Bold}]{CMU Concrete} %% CMU Concrete must be installed by hand as otf
+	''',
+	utf8extra='',
+	fncychap='',
+	preamble=my_latex_preamble,
+	footer='',
+	inputenc='',
+	fontenc='',
+	maketitle=my_maketitle,
+)
+
+# The paper size ('letter' or 'a4').
+#latex_paper_size = 'letter'
+
+# The font size ('10pt', '11pt' or '12pt').
+#latex_font_size = '10pt'
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass [howto/manual]).
+latex_documents = [
+   ('index-toctree-theory', 'YadeTheory.tex', u'DEM Formulation',
+   u'Václav Šmilauer', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+latex_logo = '../fig/yade-logo.png'
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+latex_use_parts = False
+
+# Additional stuff for the LaTeX preamble.
+#latex_preamble = ''
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_use_modindex = True

=== added file 'doc/sphinx/book/fullBibliography.rst.in'
--- doc/sphinx/book/fullBibliography.rst.in	1970-01-01 00:00:00 +0000
+++ doc/sphinx/book/fullBibliography.rst.in	2015-11-20 00:42:30 +0000
@@ -0,0 +1,6 @@
+.. This complete list of references is used for tex build, in which sectionning of the bibliography fails (see )
+
+@bib2rst.bib2rst('../yade-docref.bib')@
+@bib2rst.bib2rst('../yade-articles.bib')@
+@bib2rst.bib2rst('../yade-theses.bib')@
+@bib2rst.bib2rst('../references.bib')@
\ No newline at end of file

=== added file 'doc/sphinx/consulting.rst'
--- doc/sphinx/consulting.rst	1970-01-01 00:00:00 +0000
+++ doc/sphinx/consulting.rst	2015-11-20 00:42:30 +0000
@@ -0,0 +1,10 @@
+.. _consulting:
+
+########################
+Support and consulting
+########################
+
+We can provide technical support and training sessions on DEM modeling for researchers and engineers, as well as consulting services for specific problems.
+Feel free to contact us by email at consult|A|yade-dem.org for any inquiry on such aspects.
+
+Please use this contact for discussing paid support and/or consulting, exclusively. Basic questions on using Yade should follow the `regular way <https://yade-dem.org/wiki/Contact>`_ or will be disregarded. 
\ No newline at end of file

=== modified file 'doc/sphinx/templates/index.html'
--- doc/sphinx/templates/index.html	2015-03-05 20:44:30 +0000
+++ doc/sphinx/templates/index.html	2015-11-20 00:42:30 +0000
@@ -28,23 +28,24 @@
            <span class="linkdescr">latest news about Yade project</span></p>
         <p class="biglink"><a class="biglink" href="https://yade-dem.org/wiki/Authors_and_contributors";>Authors and contributors</a><br/>
            <span class="linkdescr">information about the people working on Yade</span></p>
-        <p class="biglink"><a class="biglink" href="https://yade-dem.org/wiki/Contact";>Contact</a><br/>
-           <span class="linkdescr">contact details, mailing lists</span></p>
-        <p class="biglink"><a class="biglink" href="https://yade-dem.org/wiki/WhoIsDoingWhat";>Who Is Doing What (Wiki)</a><br/>
-           <span class="linkdescr">you may introduce yourself here</span></p>
-        <p class="biglink"><a class="biglink" href="https://yade-dem.org/wiki/Screenshots_and_videos";>Screenshots and videos (Wiki)</a><br/>
-           <span class="linkdescr">Simulation examples (wiki); feel free to add yours.</span></p>
-      </td>
-      <td width="50%">
-
+        <p class="biglink"><a class="biglink" href="https://www.yade-dem.org/doc/publications.html";>Publications</a><br/>
+           <span class="linkdescr">on Yade itself or done with Yade</span></p>
+        <p class="biglink"><a class="biglink" href="https://yade-dem.org/wiki/Contact";>Public Mailing Lists</a><br/>
+           <span class="linkdescr">Discussions between users and developpers</span></p>
         <p class="biglink"><a class="biglink" href="{{ pathto("citing") }}">Acknowledging Yade</a><br/>
            <span class="linkdescr">How to cite Yade in publications</span></p>
-        <p class="biglink"><a class="biglink" href="https://www.yade-dem.org/doc/publications.html";>Publications</a><br/>
-           <span class="linkdescr">on Yade itself or done with Yade</span></p>
+      </td>
+      <td width="50%">
+        <p class="biglink"><a class="biglink" href={{ pathto("consulting") }}>Support and Consulting</a><br/>
+           <span class="linkdescr">Need professional help?</span></p>
         <p class="biglink"><a class="biglink" href="https://answers.launchpad.net/yade";>Questions and answers</a><br/>
-           <span class="linkdescr">Users questions and discussions, hosted at launchpad</span></p>
+           <span class="linkdescr">Users questions, hosted at launchpad</span></p>
         <p class="biglink"><a class="biglink" href="https://yade-dem.org/wiki/";>Wiki pages</a><br/>
            <span class="linkdescr">A less formal place to report results and more, worth a look</span></p>
+        <p class="biglink"><a class="biglink" href="https://yade-dem.org/wiki/WhoIsDoingWhat";>Who Is Doing What (Wiki)</a><br/>
+           <span class="linkdescr">you may introduce yourself here</span></p>
+        <p class="biglink"><a class="biglink" href="https://yade-dem.org/wiki/Screenshots_and_videos";>Screenshots and videos (Wiki)</a><br/>
+           <span class="linkdescr">Simulation examples (wiki); feel free to add yours.</span></p>
       </td>
     </tr>
  </table>
@@ -76,20 +77,18 @@
     </tr>
     <tr>
       <td width="50%">
-        <p class="biglink"><a class="biglink" href="{{ pathto("publications") }}">Publications</a><br/>
-           <span class="linkdescr">on Yade itself or done with Yade</span></p>
         <p class="biglink"><a class="biglink" href="{{ pathto("references") }}">References</a><br/>
            <span class="linkdescr">articles cited in the documentation</span></p>
         <p class="biglink"><a class="biglink" href="{{ pathto("installation") }}">Installation</a><br/>
            <span class="linkdescr">from binaries and sources</span></p>
+       <p class="biglink"><a class="biglink" href="{{ pathto("index-toctree") }}">Full contents</a><br/>
+           <span class="linkdescr">with all the details</span></p>
       </td>
       <td width="50%">
         <p class="biglink"><a class="biglink" href="{{ pathto("genindex") }}">Index</a><br/>
            <span class="linkdescr">all functions, classes, attributes</span></p>
         <p class="biglink"><a class="biglink" href="{{ pathto("search") }}">Search</a><br/>
            <span class="linkdescr">search the documentation</span></p>
-        <p class="biglink"><a class="biglink" href="{{ pathto("index-toctree") }}">Full contents</a><br/>
-           <span class="linkdescr">with all the details</span></p>
       </td>
     </tr>
   </table>

=== added file 'doc/sphinx/yadeBookSphinx.py'
--- doc/sphinx/yadeBookSphinx.py	1970-01-01 00:00:00 +0000
+++ doc/sphinx/yadeBookSphinx.py	2015-11-20 00:42:30 +0000
@@ -0,0 +1,261 @@
+#!/usr/bin/python
+# encoding: utf-8
+#
+# module documentation
+#
+import sys,os,os.path
+
+outDir=sys.argv[2] if len(sys.argv)>2 else 'book/_build/'
+for d in (outDir,outDir+'/latex',outDir+'/html',outDir+'/html/_static'):
+	if not os.path.exists(d):
+		os.mkdir(d)
+		
+#We assume that modules have been documented by a previous run of yadeSphinx
+#def moduleDoc(module,submodules=[]):
+	#f=open('yade.'+module+'.rst','w')
+	#modFmt=""".. automodule:: yade.%s
+	#:members:
+	#:undoc-members:
+	#:inherited-members:
+
+#"""
+	#f.write(""".. _yade.%s:
+
+#yade.%s module
+#==========================================
+
+#"""%(module,module))
+	##f.write(".. module:: yade.%s\n\n"%module+modFmt%module)
+	#f.write(modFmt%module)
+	#for sub in submodules:
+		##f.write(".. submodule:: yade.%s\n\n"%sub+modFmt%sub)
+		#f.write(".. currentmodule:: yade.%s\n\n%s\n\n"%(module,modFmt%sub))
+	#f.close()
+##
+## put all yade modules here, as {module:[submodules]}
+##
+## don't forget to put the module in index.rst as well!
+##
+#mods={'export':[],'post2d':[],'pack':['_packSpheres','_packPredicates','_packObb'],'plot':[],'timing':[],'utils':['_utils'],'polyhedra_utils':['_polyhedra_utils'],'ymport':[],'geom':[],'bodiesHandling':[],'qt':['qt._GLViewer'],'linterpolation':[]}
+##
+## generate documentation, in alphabetical order
+#mm=mods.keys(); mm.sort()
+#for m in mm: moduleDoc(m,mods[m])
+
+#with open('modules.rst','w') as f:
+	#f.write("Yade modules\n=============\n\n.. toctree::\n\t:maxdepth: 2\n\n")
+	#for m in mm: f.write('\tyade.%s.rst\n\n'%m)
+
+
+
+#import sys
+#sys.exit(0)
+
+#
+# wrapper documentation
+#
+
+# classes already documented
+docClasses=set()
+
+def autodocClass(klass):
+	global docClasses
+	docClasses.add(klass)
+	return ".. autoclass:: %s\n\t:members:\n\t:undoc-members:\n\t:inherited-members:\n\n"%(klass) # \t:inherited-members:\n # \n\t:show-inheritance:
+def autodocDerived(klass,doSections=True):
+	global docClasses
+	ret=''
+	if doSections: ret+='%s\n'%klass+'^'*100+'\n\n'
+	#ret+='.. inheritance-diagram:: %s\n\n'%klass
+	ret+=inheritanceDiagram(klass)
+	ret+=autodocClass(klass)
+	childs=list(yade.system.childClasses(klass));
+	childs.sort();
+	for k in childs:
+		if not k in docClasses: ret+=autodocClass(k)
+	return ret
+def inheritanceDiagram(klass):
+	"""Generate simple inheritance graph for given classname *klass* using dot (http://www.graphviz.org) syntax.
+	Classes in the docClasses set (already documented) are framed differently and the inheritance tree stops there.
+	"""
+	global docClasses
+	def mkUrl(c):
+		global writer
+		# useless, doesn't work in LaTeX anyway...
+		return ('#yade.wrapper.%s'%c if writer=='html' else '%%yade.wrapper#yade.wrapper.%s'%c) # HTML/LaTeX
+	def mkNode(c,style='solid',fillcolor=None): return '\t\t"%s" [shape="box",fontsize=8,style="setlinewidth(0.5),%s",%sheight=0.2,URL="yade.wrapper.html#yade.wrapper.%s"];\n'%(c,style,'fillcolor=%s,'%fillcolor if fillcolor else '',c)
+	ret=".. graphviz::\n\n\tdigraph %s {\n\t\trankdir=RL;\n\t\tmargin=.2;\n"%klass+mkNode(klass)
+	childs=yade.system.childClasses(klass)
+	if len(childs)==0: return ''
+	for c in childs:
+		try:
+			base=eval(c).__bases__[0].__name__
+			if base!=klass and base in docClasses:
+				continue # skip classes deriving from classes that are already documented
+			if c not in docClasses: ret+=mkNode(c)
+			else: # classes of which childs are documented elsewhere are marked specially
+				ret+=mkNode(c,style='filled,dashed',fillcolor='grey')
+			ret+='\t\t"%s" -> "%s" [arrowsize=0.5,style="setlinewidth(0.5)"];\n'%(c,base)
+		except NameError:
+			pass
+			#print 'WARN: unable to find class object for',c
+	return ret+'\t}\n\n'
+
+
+def sect(title,text,tops,reverse=False):
+	subsects=[autodocDerived(top,doSections=(len(tops)>1)) for top in tops]
+	if reverse: subsects.reverse()
+	return title+'\n'+100*'-'+'\n\n'+text+'\n\n'+'\n\n'.join(subsects)+'\n'
+
+
+def genWrapperRst():
+	global docClasses
+	docClasses=set() # reset globals
+	wrapper=file('yade.wrapper.rst','w')
+	wrapper.write(""".. _yade.wrapper::
+
+Class reference (yade.wrapper module)
+=======================================
+
+.. toctree::
+  :maxdepth: 2
+
+
+.. currentmodule:: yade.wrapper
+.. autosummary::
+
+"""+
+	sect('Bodies','',['Body','Shape','State','Material','Bound'])+
+	sect('Interactions','',['Interaction','IGeom','IPhys'])+
+	sect('Global engines','',['FieldApplier','Collider','BoundaryController','GlobalEngine'],reverse=True)+
+	sect('Partial engines','',['PartialEngine'])+
+	sect('Bounding volume creation','',['BoundFunctor','BoundDispatcher'])+
+	sect('Interaction Geometry creation','',['IGeomFunctor','IGeomDispatcher'])+
+	sect('Interaction Physics creation','',['IPhysFunctor','IPhysDispatcher'])+
+	sect('Constitutive laws','',['LawFunctor','LawDispatcher'])+
+	sect('Callbacks','',[#'BodyCallback',
+		'IntrCallback'])+
+	sect('Preprocessors','',['FileGenerator'])+
+	sect('Rendering','',['OpenGLRenderer','GlShapeFunctor','GlStateFunctor','GlBoundFunctor','GlIGeomFunctor','GlIPhysFunctor'])+ # ,'GlShapeDispatcher','GlStateDispatcher','GlBoundDispatcher','GlIGeomDispatcher','GlIPhysDispatcher'])+
+	sect('Simulation data','',['Omega','BodyContainer','InteractionContainer','ForceContainer','MaterialContainer','Scene','Cell'])
+	+"""
+Other classes
+---------------
+
+"""
+	+''.join([autodocClass(k) for k in (yade.system.childClasses('Serializable')-docClasses)|set(['Serializable','TimingDeltas','Cell'])])
+	)
+
+	wrapper.close()
+
+def makeBaseClassesClickable(f,writer):
+	out=[]
+	import re,shutil
+	changed=False
+	for l in open(f):
+		if writer=='html':
+			if not '(</big><em>inherits ' in l:
+				out.append(l)
+				continue
+			m=re.match(r'(^.*\(</big><em>inherits )([a-zA-Z0-9_ →]*)(</em><big>\).*$)',l)
+			if not m:
+				out.append(l)
+				continue
+				#raise RuntimeError("Line %s unmatched?"%l)
+			bases=m.group(2)
+			bb=bases.split(' → ')
+			#print bases,'@',bb	
+			bbb=' → '.join(['<a class="reference external" href="yade.wrapper.html#yade.wrapper.%s">%s</a>'%(b,b) for b in bb])
+			out.append(m.group(1)+bbb+m.group(3))
+		elif writer=='latex':
+			if not (r'\pysiglinewithargsret{\strong{class }\code{yade.wrapper.}\bfcode{' in l and r'\emph{inherits' in l):
+				out.append(l)
+				continue
+			#print l
+			m=re.match(r'(^.*}}{\\emph{inherits )([a-zA-Z0-9_\\() -]*)(}}.*$)',l)
+			if not m:
+				#print 'WARN: Line %s unmatched?'%l
+				continue
+			bases=m.group(2)
+			bb=bases.split(r' \(\rightarrow\) ')
+			bbb=r' \(\rightarrow\) '.join([r'\hyperref[yade.wrapper:yade.wrapper.%s]{%s}'%(b.replace(r'\_',r'_'),b) for b in bb])
+			out.append(m.group(1)+bbb+m.group(3)+'\n')
+		changed=True
+	if changed:
+		shutil.move(f,f+'_')
+		ff=open(f,'w')
+		for l in out:
+			ff.write(l)
+		ff.close()
+	
+def processTemplate(f1,f2):
+	"Copy file f1 to f2, evaluating all occurences of @...@ with eval(); they should expand to a string and can contain arbitrary python expressions."
+	import re
+	def doEval(match):
+		import bib2rst
+		return str(eval(match.group(1)))
+	ff2=open(f2,'w')
+	for l in open(f1):
+		ff2.write(re.sub(r'@([^@]*)@',doEval,l))
+
+def genReferences():
+	import sys
+	processTemplate('book/fullBibliography.rst.in','fullPublications.rst')
+
+import sphinx,sys,shutil
+sys.path.append('.') # for bib2rst
+
+genReferences()
+for bib in ('references','yade-articles','yade-theses','yade-conferences','yade-docref'):
+	shutil.copyfile('../%s.bib'%bib,outDir+'/latex/%s.bib'%bib)
+
+global writer
+writer=None
+#writers=['html','latex','epub']
+writers=['latex']
+
+volumes=['Book','Reference','Manual','Theory'] #would work if yade was exiting correctly (it seems)
+for vol in volumes:
+	# no way to use custom file name for conf.py, instead we replace it by the variants
+	shutil.copy('book/conf'+vol+'.py','book/conf.py')
+	for writer in writers:
+		#genWrapperRst()
+		# HACK: must rewrite sys.argv, since reference generator in conf.py determines if we output latex/html by inspecting it
+		sys.argv=['sphinx-build','-a','-c','book','-E','-b','%s'%writer,'-d',outDir+'/doctrees','.',outDir+'/%s'%writer]
+		try:
+			sphinx.main(sys.argv)
+		except SystemExit:
+			pass
+		import glob
+		texDocs=glob.glob(outDir+'latex/*.tex')
+		if writer=='html':
+			makeBaseClassesClickable((outDir+'/html/yade.wrapper.html'),writer)
+		elif writer=='latex':
+			for texdoc in texDocs: makeBaseClassesClickable(texdoc,writer)
+		if (os.path.exists('/usr/share/javascript/jquery/jquery.js')): #Check, whether jquery.js installed in system
+			if os.path.isfile(outDir+'/html/_static/jquery.js'): os.system('rm '+ outDir+'/html/_static/jquery.js')
+			os.system('ln -s /usr/share/javascript/jquery/jquery.js '+ outDir+'/html/_static/jquery.js')
+
+		# HACK!!!!==========================================================================
+		# New sphinx-python versions (hopefully) are producing empty "verbatim"-environments.
+		# That is why xelatex crashes. 
+		# The following "script" removes all empty environments. Needs to be fixed in python-sphinx.
+		if (writer=='latex'):
+			for texdoc in texDocs: 
+				infile = open(texdoc,"r")
+				lines = infile.readlines()
+				infile.close()
+				
+				out=[]
+				for i in range(0,len(lines)):
+					if (i<>len(lines) and
+							lines[i].strip()=="\\begin{Verbatim}[commandchars=\\\\\{\\}]" and
+							lines[i+1].strip()=="\\end{Verbatim}"):
+							lines[i]=''; lines[i+1]=''
+					else:
+						out.append(lines[i])
+				file(texdoc,'w').write('')
+				for i in out:
+					file(texdoc,'a').write(i)
+# HACK!!!!==========================================================================
+sys.exit()

=== modified file 'doc/yade-docref.bib'
--- doc/yade-docref.bib	2011-10-14 11:31:54 +0000
+++ doc/yade-docref.bib	2015-11-20 00:42:30 +0000
@@ -1,50 +1,45 @@
-@Book{ yade:doc,
-	PUBLISHER = "{The {Y}ade Project}",
-	TITLE = "{Y}ade {D}ocumentation",
-	YEAR = "2010",
-	AUTHOR = "V. Šmilauer and E. Catalano and B. Chareyre and S. Dorofeenko and J. Duriez and A. Gladky and J. Kozicki and C. Modenese and L. Scholtès and L. Sibille and J. Stránský and K. Thoeni",
-	ALTEDITOR = "Václav Šmilauer",
-	EDITION = "{1st}",
-	NOTE = "{http://yade-dem.org/doc/}";,
-	ALTNOTE = "\\url{http://yade-dem.org/doc/}";
-}
-
-@incollection{ yade:manual,
-	author={V. Šmilauer and A. Gladky and J. Kozicki and C. Modenese and J. Stránský},
-	booktitle={Yade {D}ocumentation},
-	editor={V. Šmilauer},
-	publisher={The Yade Project},
-	title={Yade, Using and Programming},
-	year={2010},
-	edition={1st},
-	url={https://yade-dem.org/w/images/0/09/YadeManuals.pdf},
-	note={http://yade-dem.org/doc/}
-}
-
-@incollection{ yade:background,
-	title = "{Y}ade DEM Formulation",
-	author = "V. Šmilauer and B. Chareyre",
-	booktitle = "{Y}ade {D}ocumentation",
-	editor = "V. Šmilauer",
-	publisher = "{The {Y}ade Project}",
-	year = "2010",
-	edition = "{1st}",
-	note = "http://yade-dem.org/doc/formulation.html";,
-	altnote = "\\url{http://yade-dem.org/doc/formulation.html}";,
-	url={https://yade-dem.org/w/images/e/e0/YadeFormulation.pdf}
-}
-
-@incollection{ yade:reference,
-	author = "V. Šmilauer and E. Catalano and B. Chareyre and S. Dorofeenko and J. Duriez and A. Gladky and J. Kozicki and C. Modenese and L. Scholtès and L. Sibille and J. Stránský and K. Thoeni",
-	booktitle = "{Y}ade {D}ocumentation",
-	editor = "V. Šmilauer",
-	publisher = "{The {Y}ade Project}",
-	title = "{Y}ade {R}eference {D}ocumentation",
-	year = "2010",
-	edition = "{1st}",
-	note = "http://yade-dem.org/doc/";,
-	altnote = "\\url{http://yade-dem.org/doc/}";,
-	url= {https://yade-dem.org/w/images/9/98/YadeRefDoc.pdf}
+
+@book{yade:doc2,
+	altnote = "\\url{http://yade-dem.org/doc/}";,
+	author = "V. Šmilauer et al.",
+	doi = "10.5281/zenodo.32409",
+	note = "http://yade-dem.org/doc/";,
+	title = "{{Y}ade {D}ocumentation 2nd ed}",
+	publisher = "{The {Y}ade Project}",
+	year = "2015"
+}
+
+@incollection{yade:manual2,
+	altnote = "\\url{http://yade-dem.org/doc/}";,
+	author = "V. Šmilauer et al.",
+	doi = "10.5281/zenodo.34043",
+	booktitle = "{Y}ade {D}ocumentation 2nd ed",
+	note = "http://yade-dem.org/doc/";,
+	publisher = "{The {Y}ade Project}",
+	title = "Using and Programming",
+	year = "2015"
+}
+
+@incollection{yade:background2,
+	altnote = "\\url{http://yade-dem.org/doc/}";,
+	author = "V. Šmilauer et al.",
+	doi = "10.5281/zenodo.34044",
+	booktitle = "{Y}ade {D}ocumentation 2nd ed",
+	note = "http://yade-dem.org/doc/";,
+	publisher = "{The {Y}ade Project}",
+	title = "DEM formulation",
+	year = "2015"
+}
+
+@incollection{yade:reference2,
+	altnote = "\\url{http://yade-dem.org/doc/}";,
+	author = "V. Šmilauer et al.",
+	doi = "10.5281/zenodo.34045",
+	booktitle = "{Y}ade {D}ocumentation 2nd ed",
+	note = "http://yade-dem.org/doc/";,
+	publisher = "{The {Y}ade Project}",
+	title = "Reference Manual",
+	year = "2015"
 }

Follow ups

Re: [Branch ~yade-pkg/yade/git-trunk] Rev 3742: introduce 2nd edition of the documentation and contact for consuting (in homepage)
From: Jerome Duriez, 2015-11-20