Move cython/src/* in cython/

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@1436 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 8f971ef16ef6df597d5d3667db0eecbca94233b2

21 files changed, 1459 insertions, 0 deletions

diff --git a/src/cython/doc/Makefile b/src/cython/doc/Makefile
new file mode 100644
index 00000000..fc353a37
--- /dev/null
+++ b/src/cython/doc/Makefile
@@ -0,0 +1,177 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = _build
+
+# User-friendly check for sphinx-build
+ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
+$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
+endif
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  xml        to make Docutils-native XML files"
+	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	rm -rf $(BUILDDIR)/*
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/pouet.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/pouet.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/pouet"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/pouet"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+latexpdfja:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through platex and dvipdfmx..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+xml:
+	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+	@echo
+	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+pseudoxml:
+	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+	@echo
+	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
diff --git a/src/cython/doc/alpha_complex_ref.rst b/src/cython/doc/alpha_complex_ref.rst
new file mode 100644
index 00000000..6a122b09
--- /dev/null
+++ b/src/cython/doc/alpha_complex_ref.rst
@@ -0,0 +1,10 @@
+==============================
+Alpha complex reference manual
+==============================
+
+.. autoclass:: gudhi.AlphaComplex
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+   .. automethod:: gudhi.AlphaComplex.__init__
diff --git a/src/cython/doc/alpha_complex_sum.rst b/src/cython/doc/alpha_complex_sum.rst
new file mode 100644
index 00000000..b608050e
--- /dev/null
+++ b/src/cython/doc/alpha_complex_sum.rst
@@ -0,0 +1,21 @@
+=====================================  =====================================  =====================================
+:Author: Vincent Rouvreau              :Introduced in: GUDHI PYTHON 1.4.0     :Copyright: GPL v3
+=====================================  =====================================  =====================================
+
++-------------------------------------------+----------------------------------------------------------------------+
+| .. image::                                | Alpha_complex is a simplicial complex constructed from the finite    |
+|      img/alpha_complex_representation.png | cells of a Delaunay Triangulation.                                   |
+|                                           |                                                                      |
+|                                           | The filtration value of each simplex is computed as the square of the|
+|                                           | circumradius of the simplex if the circumsphere is empty (the simplex|
+|                                           | is then said to be Gabriel), and as the minimum of the filtration    |
+|                                           | values of the codimension 1 cofaces that make it not Gabriel         |
+|                                           | otherwise. All simplices that have a filtration value strictly       |
+|                                           | greater than a given alpha squared value are not inserted into the   |
+|                                           | complex.                                                             |
+|                                           |                                                                      |
+|                                           | This package requires having CGAL version 4.7 or higher (4.8.1 is    |
+|                                           | advised for better perfomances).                                     |
++-------------------------------------------+----------------------------------------------------------------------+
+| :doc:`alpha_complex_user`                 | :doc:`alpha_complex_ref`                                             |
++-------------------------------------------+----------------------------------------------------------------------+
diff --git a/src/cython/doc/alpha_complex_user.rst b/src/cython/doc/alpha_complex_user.rst
new file mode 100644
index 00000000..b6b6e550
--- /dev/null
+++ b/src/cython/doc/alpha_complex_user.rst
@@ -0,0 +1,192 @@
+=========================
+Alpha complex user manual
+=========================
+Definition
+----------
+
+.. include:: alpha_complex_sum.rst
+
+Alpha_complex is constructing a :doc:`Simplex_tree <simplex_tree_sum>` using
+`Delaunay Triangulation  <http://doc.cgal.org/latest/Triangulation/index.html#Chapter_Triangulations>`_ 
+:cite:`cgal:hdj-t-15b` from `CGAL <http://www.cgal.org/>`_ (the Computational Geometry Algorithms Library
+:cite:`cgal:eb-15b`).
+
+Remarks
+^^^^^^^
+When Alpha_complex is constructed with an infinite value of :math:`\alpha`, the complex is a Delaunay complex.
+
+Example from points
+-------------------
+
+This example builds the Delaunay triangulation from the given points, and initializes the alpha complex with it:
+
+.. testcode::
+
+   import gudhi
+   alpha_complex = gudhi.AlphaComplex(points=[[1, 1], [7, 0], [4, 6], [9, 6], [0, 14], [2, 19], [9, 17]],
+                                      max_alpha_square=60.0)
+   result_str = 'Alpha complex is of dimension ' + repr(alpha_complex.dimension()) + ' - ' + \
+       repr(alpha_complex.num_simplices()) + ' simplices - ' + \
+       repr(alpha_complex.num_vertices()) + ' vertices.'
+   print(result_str)
+   for fitered_value in alpha_complex.get_filtered_tree():
+       print(fitered_value)
+
+The output is:
+
+.. testoutput::
+
+   Alpha complex is of dimension 2 - 25 simplices - 7 vertices.
+   ([0], 0.0)
+   ([1], 0.0)
+   ([2], 0.0)
+   ([3], 0.0)
+   ([4], 0.0)
+   ([5], 0.0)
+   ([6], 0.0)
+   ([2, 3], 6.25)
+   ([4, 5], 7.25)
+   ([0, 2], 8.5)
+   ([0, 1], 9.25)
+   ([1, 3], 10.0)
+   ([1, 2], 11.25)
+   ([1, 2, 3], 12.5)
+   ([0, 1, 2], 12.995867768595042)
+   ([5, 6], 13.25)
+   ([2, 4], 20.0)
+   ([4, 6], 22.736686390532547)
+   ([4, 5, 6], 22.736686390532547)
+   ([3, 6], 30.25)
+   ([2, 6], 36.5)
+   ([2, 3, 6], 36.5)
+   ([2, 4, 6], 37.24489795918368)
+   ([0, 4], 59.710743801652896)
+   ([0, 2, 4], 59.710743801652896)
+
+
+Algorithm
+---------
+
+Data structure
+^^^^^^^^^^^^^^
+
+In order to build the alpha complex, first, a Simplex tree is built from the cells of a Delaunay Triangulation.
+(The filtration value is set to NaN, which stands for unknown value):
+
+.. image::
+    img/alpha_complex_doc.png
+    :align: center
+    :alt: Simplex tree structure construction example
+
+Filtration value computation algorithm
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+  **for** i : dimension :math:`\rightarrow` 0 **do**
+    **for all** :math:`\sigma` of dimension i
+      **if** filtration(:math:`\sigma`) is NaN **then**
+        filtration(:math:`\sigma`) = :math:`\alpha^2(\sigma)`
+      **end if**
+  
+      *//propagate alpha filtration value*
+  
+      **for all** :math:`\tau` face of :math:`\sigma`
+        **if** filtration(:math:`\tau`) is not NaN **then**
+          filtration(:math:`\tau`) = filtration(:math:`\sigma`)
+        **end if**
+      **end for**
+    **end for**
+  **end for**
+  
+  make_filtration_non_decreasing()
+  
+  prune_above_filtration()
+
+Dimension 2
+^^^^^^^^^^^
+
+From the example above, it means the algorithm looks into each triangle ([0,1,2], [0,2,4], [1,2,3], ...),
+computes the filtration value of the triangle, and then propagates the filtration value as described
+here:
+
+.. image::
+    img/alpha_complex_doc_420.png
+    :align: center
+    :alt: Filtration value propagation example
+
+Dimension 1
+^^^^^^^^^^^
+
+Then, the algorithm looks into each edge ([0,1], [0,2], [1,2], ...),
+computes the filtration value of the edge (in this case, propagation will have no effect).
+
+Dimension 0
+^^^^^^^^^^^
+
+Finally, the algorithm looks into each vertex ([0], [1], [2], [3], [4], [5] and [6]) and
+sets the filtration value (0 in case of a vertex - propagation will have no effect).
+
+Non decreasing filtration values
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+As the squared radii computed by CGAL are an approximation, it might happen that these alpha squared values do not
+quite define a proper filtration (i.e. non-decreasing with respect to inclusion).
+We fix that up by calling `Simplex_tree::make_filtration_non_decreasing()` (cf.
+`C++ version <http://gudhi.gforge.inria.fr/doc/latest/index.html>`_).
+
+Prune above given filtration value
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The simplex tree is pruned from the given maximum alpha squared value (cf. `Simplex_tree::prune_above_filtration()`
+int he `C++ version <http://gudhi.gforge.inria.fr/doc/latest/index.html>`_).
+In the following example, the value is given by the user as argument of the program.
+
+
+Example from OFF file
+^^^^^^^^^^^^^^^^^^^^^
+
+This example builds the Delaunay triangulation from the points given by an OFF file, and initializes the alpha complex
+with it.
+
+
+Then, it is asked to display information about the alpha complex:
+
+.. testcode::
+
+   import gudhi
+   alpha_complex = gudhi.AlphaComplex(off_file='alphacomplexdoc.off',
+                                      max_alpha_square=59.0)
+   result_str = 'Alpha complex is of dimension ' + repr(alpha_complex.dimension()) + ' - ' + \
+       repr(alpha_complex.num_simplices()) + ' simplices - ' + \
+       repr(alpha_complex.num_vertices()) + ' vertices.'
+   print(result_str)
+   for fitered_value in alpha_complex.get_filtered_tree():
+       print(fitered_value)
+
+the program output is:
+
+.. testoutput::
+
+   Alpha complex is of dimension 2 - 23 simplices - 7 vertices.
+   ([0], 0.0)
+   ([1], 0.0)
+   ([2], 0.0)
+   ([3], 0.0)
+   ([4], 0.0)
+   ([5], 0.0)
+   ([6], 0.0)
+   ([2, 3], 6.25)
+   ([4, 5], 7.25)
+   ([0, 2], 8.5)
+   ([0, 1], 9.25)
+   ([1, 3], 10.0)
+   ([1, 2], 11.25)
+   ([1, 2, 3], 12.5)
+   ([0, 1, 2], 12.995867768595042)
+   ([5, 6], 13.25)
+   ([2, 4], 20.0)
+   ([4, 6], 22.736686390532547)
+   ([4, 5, 6], 22.736686390532547)
+   ([3, 6], 30.25)
+   ([2, 6], 36.5)
+   ([2, 3, 6], 36.5)
+   ([2, 4, 6], 37.24489795918368)
diff --git a/src/cython/doc/biblio.rst b/src/cython/doc/biblio.rst
new file mode 100644
index 00000000..b8e733ed
--- /dev/null
+++ b/src/cython/doc/biblio.rst
@@ -0,0 +1,7 @@
+============
+Bibliography
+============
+
+.. bibliography:: bibliography.bib
+   :filter: docnames
+   :style: unsrt
diff --git a/src/cython/doc/cgal_citation.rst b/src/cython/doc/cgal_citation.rst
new file mode 100644
index 00000000..bbc4ef9e
--- /dev/null
+++ b/src/cython/doc/cgal_citation.rst
@@ -0,0 +1,8 @@
+==============
+CGAL citations
+==============
+
+..
+    bibliography:: how_to_cite_cgal.bib
+        :filter: docnames
+        :style: unsrt
diff --git a/src/cython/doc/conf.py b/src/cython/doc/conf.py
new file mode 100755
index 00000000..bc138025
--- /dev/null
+++ b/src/cython/doc/conf.py
@@ -0,0 +1,271 @@
+# -*- coding: utf-8 -*-
+#
+# GUDHI documentation build configuration file, created by
+# sphinx-quickstart on Thu Jun 30 09:55:51 2016.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys
+import os
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#sys.path.insert(0, os.path.abspath('.'))
+
+# Path to Gudhi.so from source path
+sys.path.insert(0, os.path.abspath('../..'))
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.doctest',
+    'sphinx.ext.todo',
+    'sphinx.ext.coverage',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.ifconfig',
+    'sphinx.ext.viewcode',
+    'sphinxcontrib.bibtex',
+]
+
+todo_include_todos = True
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'GUDHI'
+copyright = u'2016, Vincent Rouvreau'
+
+# 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 = '1.3.1'
+# The full version, including alpha/beta/rc tags.
+release = '1.3.1'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = ['_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 = []
+
+# If true, keep warnings as "system message" paragraphs in the built documents.
+#keep_warnings = False
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+html_theme = '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 = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = None
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# Add any extra paths that contain custom files (such as robots.txt or
+# .htaccess) here, relative to this directory. These files are copied
+# directly to the root of the documentation.
+#html_extra_path = []
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'GUDHIdoc'
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+# The paper size ('letterpaper' or 'a4paper').
+#'papersize': 'letterpaper',
+
+# The font size ('10pt', '11pt' or '12pt').
+#'pointsize': '10pt',
+
+# Additional stuff for the LaTeX preamble.
+#'preamble': '',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+  ('index', 'GUDHI.tex', u'GUDHI Documentation',
+   u'Vincent Rouvreau', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# If true, show page references after internal links.
+#latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_domain_indices = True
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    ('index', 'gudhi', u'GUDHI Documentation',
+     [u'Vincent Rouvreau'], 1)
+]
+
+# If true, show URL addresses after external links.
+#man_show_urls = False
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+  ('index', 'GUDHI', u'GUDHI Documentation',
+   u'Vincent Rouvreau', 'GUDHI', 'One line description of project.',
+   'Miscellaneous'),
+]
+
+# Documents to append as an appendix to all manuals.
+#texinfo_appendices = []
+
+# If false, no module index is generated.
+#texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#texinfo_show_urls = 'footnote'
+
+# If true, do not generate a @detailmenu in the "Top" node's menu.
+#texinfo_no_detailmenu = False
diff --git a/src/cython/doc/cubical_complex_ref.rst b/src/cython/doc/cubical_complex_ref.rst
new file mode 100644
index 00000000..84aa4223
--- /dev/null
+++ b/src/cython/doc/cubical_complex_ref.rst
@@ -0,0 +1,9 @@
+Cubical complex reference manual
+################################
+
+.. autoclass:: gudhi.CubicalComplex
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+   .. automethod:: gudhi.CubicalComplex.__init__
diff --git a/src/cython/doc/cubical_complex_sum.rst b/src/cython/doc/cubical_complex_sum.rst
new file mode 100644
index 00000000..4008a1fd
--- /dev/null
+++ b/src/cython/doc/cubical_complex_sum.rst
@@ -0,0 +1,12 @@
+=====================================  =====================================  =====================================
+:Author: Pawel Dlotko                  :Introduced in: GUDHI PYTHON 1.4.0     :Copyright: GPL v3
+=====================================  =====================================  =====================================
+
++---------------------------------------------+----------------------------------------------------------------------+
+| .. image::                                  | The cubical complex is an example of a structured complex useful in  |
+|      img/Cubical_complex_representation.png | computational mathematics (specially rigorous numerics) and image    |
+|                                             | analysis.                                                            |
++---------------------------------------------+----------------------------------------------------------------------+
+| :doc:`cubical_complex_user`                 | * :doc:`cubical_complex_ref`                                         |
+|                                             | * :doc:`periodic_cubical_complex_ref`                                |
++---------------------------------------------+----------------------------------------------------------------------+
diff --git a/src/cython/doc/cubical_complex_user.rst b/src/cython/doc/cubical_complex_user.rst
new file mode 100644
index 00000000..2cd85c0a
--- /dev/null
+++ b/src/cython/doc/cubical_complex_user.rst
@@ -0,0 +1,150 @@
+===========================
+Cubical complex user manual
+===========================
+Definition
+----------
+
+=====================================  =====================================  =====================================
+:Author: Pawel Dlotko                  :Introduced in: GUDHI PYTHON 1.4.0     :Copyright: GPL v3
+=====================================  =====================================  =====================================
+
++---------------------------------------------+----------------------------------------------------------------------+
+| :doc:`cubical_complex_user`                 | * :doc:`cubical_complex_ref`                                         |
+|                                             | * :doc:`periodic_cubical_complex_ref`                                |
++---------------------------------------------+----------------------------------------------------------------------+
+
+The cubical complex is an example of a structured complex useful in computational mathematics (specially rigorous
+numerics) and image analysis.
+
+An *elementary interval* is an interval of a form :math:`[n,n+1]`, or :math:`[n,n]`, for :math:`n \in \mathcal{Z}`.
+The first one is called *non-degenerate*, while the second one is a *degenerate* interval. A
+*boundary of a elementary interval* is a chain  :math:`\partial [n,n+1] = [n+1,n+1]-[n,n]` in case of
+non-degenerated elementary interval and :math:`\partial [n,n] = 0` in case of degenerate elementary interval. An
+*elementary cube* :math:`C` is a product of elementary intervals, :math:`C=I_1 \times \ldots \times I_n`.
+*Embedding dimension* of a cube is n, the number of elementary intervals (degenerate or not) in the product.
+A *dimension of a cube* :math:`C=I_1 \times ... \times I_n` is the number of non degenerate elementary
+intervals in the product. A *boundary of a cube* :math:`C=I_1 \times \ldots \times I_n` is a chain obtained
+in the following way:
+
+.. math::
+
+    \partial C = (\partial I_1 \times \ldots \times I_n) + (I_1 \times \partial I_2 \times \ldots \times I_n) +
+    \ldots + (I_1 \times I_2 \times \ldots \times \partial I_n).
+
+A *cubical complex* :math:`\mathcal{K}` is a collection of cubes closed under operation of taking boundary
+(i.e. boundary of every cube from the collection is in the collection). A cube :math:`C` in cubical complex
+:math:`\mathcal{K}` is *maximal* if it is not in a boundary of any other cube in :math:`\mathcal{K}`. A
+*support* of a cube :math:`C` is the set in :math:`\mathbb{R}^n` occupied by :math:`C` (:math:`n` is the embedding
+dimension of :math:`C`).
+
+Cubes may be equipped with a filtration values in which case we have filtered cubical complex. All the cubical
+complexes considered in this implementation are filtered cubical complexes (although, the range of a filtration may
+be a set of two elements).
+
+For further details and theory of cubical complexes, please consult :cite:`kaczynski2004computational` as well as the
+following paper :cite:`peikert2012topological`.
+
+Data structure.
+---------------
+
+The implementation of Cubical complex provides a representation of complexes that occupy a rectangular region in
+:math:`\mathbb{R}^n`. This extra assumption allows for a memory efficient way of storing cubical complexes in a form
+of so called bitmaps. Let
+:math:`R = [b_1,e_1] \times \ldots \times [b_n,e_n]`, for :math:`b_1,...b_n,e_1,...,e_n \in \mathbb{Z}`,
+:math:`b_i \leq d_i` be the considered rectangular region and let :math:`\mathcal{K}` be a filtered
+cubical complex having the rectangle :math:`R` as its support. Note that the structure of the coordinate system gives
+a way a lexicographical ordering of cells of :math:`\mathcal{K}`. This ordering is a base of the presented
+bitmap-based implementation. In this implementation, the whole cubical complex is stored as a vector of the values
+of filtration. This, together with dimension of :math:`\mathcal{K}` and the sizes of :math:`\mathcal{K}` in all
+directions, allows to determine, dimension, neighborhood, boundary and coboundary of every cube
+:math:`C \in \mathcal{K}`.
+
+.. image::
+    img/Cubical_complex_representation.png
+    :align: center
+    :alt: Cubical complex.
+
+Note that the cubical complex in the figure above is, in a natural way, a product of one dimensional cubical
+complexes in :math:`\mathbb{R}`. The number of all cubes in each direction is equal :math:`2n+1`, where :math:`n` is
+the number of maximal cubes in the considered direction. Let us consider a cube at the position :math:`k` in the
+bitmap.
+Knowing the sizes of the bitmap, by a series of modulo operation, we can determine which elementary intervals are
+present in the product that gives the cube :math:`C`. In a similar way, we can compute boundary and the coboundary of
+each cube. Further details can be found in the literature.
+
+Input Format.
+-------------
+
+In the current implantation, filtration is given at the maximal cubes, and it is then extended by the lower star
+filtration to all cubes. There are a number of constructors that can be used to construct cubical complex by users
+who want to use the code directly. They can be found in the :doc:`cubical_complex_ref`.
+Currently one input from a text file is used. It uses a format used already in
+`Perseus software <http://www.sas.upenn.edu/~vnanda/perseus/>`_ by Vidit Nanda.
+Below we are providing a description of the format. The first line contains a number d begin the dimension of the
+bitmap (2 in the example below). Next d lines are the numbers of top dimensional cubes in each dimensions (3 and 3
+in the example below). Next, in lexicographical order, the filtration of top dimensional cubes is given (1 4 6 8
+20 4 7 6 5 in the example below).
+
+.. image::
+    img/exampleBitmap.png
+    :align: center
+    :alt: Example of a input data.
+
+The input file for the following complex is:
+
+.. literalinclude:: cubicalcomplexdoc.txt
+
+.. centered:: cubicalcomplexdoc.txt
+
+.. testcode::
+
+    import gudhi
+    cubical_complex = gudhi.CubicalComplex(perseus_file='cubicalcomplexdoc.txt')
+    result_str = 'Cubical complex is of dimension ' + repr(cubical_complex.dimension()) + ' - ' + \
+        repr(cubical_complex.num_simplices()) + ' simplices.'
+    print(result_str)
+
+the program output is:
+
+.. testoutput::
+    
+    Cubical complex is of dimension 2 - 49 simplices.
+
+Periodic boundary conditions.
+-----------------------------
+
+Often one would like to impose periodic boundary conditions to the cubical complex (cf.
+:doc:`periodic_cubical_complex_ref`).
+Let :math:`I_1\times ... \times I_n` be a box that is decomposed with a cubical complex :math:`\mathcal{K}`.
+Imposing periodic boundary conditions in the direction i, means that the left and the right side of a complex
+:math:`\mathcal{K}` are considered the same. In particular, if for a bitmap :math:`\mathcal{K}` periodic boundary
+conditions are imposed in all directions, then complex :math:`\mathcal{K}` became n-dimensional torus. One can use
+various constructors from the file Bitmap_cubical_complex_periodic_boundary_conditions_base.h to construct cubical
+complex with periodic boundary conditions. One can also use Perseus style input files. To indicate periodic boundary
+conditions in a given direction, then number of top dimensional cells in this direction have to be multiplied by -1.
+For instance:
+
+.. literalinclude:: periodiccubicalcomplexdoc.txt
+
+.. centered:: periodiccubicalcomplexdoc.txt
+
+Indicate that we have imposed periodic boundary conditions in the direction x, but not in the direction y.
+
+.. testcode::
+
+    import gudhi
+    periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file='periodiccubicalcomplexdoc.txt')
+    result_str = 'Periodic cubical complex is of dimension ' + repr(periodic_cc.dimension()) + ' - ' + \
+        repr(periodic_cc.num_simplices()) + ' simplices.'
+    print(result_str)
+
+the program output is:
+
+.. testoutput::
+    
+    Periodic cubical complex is of dimension 2 - 42 simplices.
+
+Examples.
+---------
+
+End user programs are available in cython/example/ folder.
diff --git a/src/cython/doc/index.rst b/src/cython/doc/index.rst
new file mode 100644
index 00000000..5245d69d
--- /dev/null
+++ b/src/cython/doc/index.rst
@@ -0,0 +1,63 @@
+.. GUDHI documentation master file, created by
+   sphinx-quickstart on Thu Jun 30 09:55:51 2016.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+GUDHI's documentation
+#####################
+
+.. image:: img/Gudhi_banner.png
+   :align: center
+
+Introduction
+************
+
+The Gudhi library (Geometry Understanding in Higher Dimensions) is a generic
+open source C++ library for Computational Topology and Topological Data
+Analysis (`TDA <https://en.wikipedia.org/wiki/Topological_data_analysis>`_).
+The GUDHI library intends to help the development of new algorithmic solutions
+in TDA and their transfer to applications. It provides robust, efficient,
+flexible and easy to use implementations of state-of-the-art algorithms and
+data structures.
+
+The current release of the GUDHI library includes:
+
+* Data structures to represent, construct and manipulate simplicial complexes.
+* Algorithms to compute persistent homology and multi-field persistent homology.
+* Simplication of simplicial complexes by edge contraction.
+
+All data-structures are generic and several of their aspects can be
+parameterized via template classes. We refer to :cite:`gudhilibrary_ICMS14`
+for a detailed description of the design of the library.
+
+Data structures
+***************
+
+Alpha complex
+=============
+
+.. include:: alpha_complex_sum.rst
+
+Cubical complex
+===============
+
+.. include:: cubical_complex_sum.rst
+
+Simplex tree
+============
+
+.. include:: simplex_tree_sum.rst
+
+Witness complex
+===============
+
+.. include:: witness_complex_sum.rst
+
+
+Toolbox
+*******
+
+Persistence cohomology
+======================
+
+.. include:: persistent_cohomology_sum.rst
diff --git a/src/cython/doc/make.bat b/src/cython/doc/make.bat
new file mode 100644
index 00000000..656c0105
--- /dev/null
+++ b/src/cython/doc/make.bat
@@ -0,0 +1,242 @@
+@ECHO OFF

+

+REM Command file for Sphinx documentation

+

+if "%SPHINXBUILD%" == "" (

+	set SPHINXBUILD=sphinx-build

+)

+set BUILDDIR=_build

+set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% .

+set I18NSPHINXOPTS=%SPHINXOPTS% .

+if NOT "%PAPER%" == "" (

+	set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%

+	set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS%

+)

+

+if "%1" == "" goto help

+

+if "%1" == "help" (

+	:help

+	echo.Please use `make ^<target^>` where ^<target^> is one of

+	echo.  html       to make standalone HTML files

+	echo.  dirhtml    to make HTML files named index.html in directories

+	echo.  singlehtml to make a single large HTML file

+	echo.  pickle     to make pickle files

+	echo.  json       to make JSON files

+	echo.  htmlhelp   to make HTML files and a HTML help project

+	echo.  qthelp     to make HTML files and a qthelp project

+	echo.  devhelp    to make HTML files and a Devhelp project

+	echo.  epub       to make an epub

+	echo.  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter

+	echo.  text       to make text files

+	echo.  man        to make manual pages

+	echo.  texinfo    to make Texinfo files

+	echo.  gettext    to make PO message catalogs

+	echo.  changes    to make an overview over all changed/added/deprecated items

+	echo.  xml        to make Docutils-native XML files

+	echo.  pseudoxml  to make pseudoxml-XML files for display purposes

+	echo.  linkcheck  to check all external links for integrity

+	echo.  doctest    to run all doctests embedded in the documentation if enabled

+	goto end

+)

+

+if "%1" == "clean" (

+	for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i

+	del /q /s %BUILDDIR%\*

+	goto end

+)

+

+

+%SPHINXBUILD% 2> nul

+if errorlevel 9009 (

+	echo.

+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx

+	echo.installed, then set the SPHINXBUILD environment variable to point

+	echo.to the full path of the 'sphinx-build' executable. Alternatively you

+	echo.may add the Sphinx directory to PATH.

+	echo.

+	echo.If you don't have Sphinx installed, grab it from

+	echo.http://sphinx-doc.org/

+	exit /b 1

+)

+

+if "%1" == "html" (

+	%SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished. The HTML pages are in %BUILDDIR%/html.

+	goto end

+)

+

+if "%1" == "dirhtml" (

+	%SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.

+	goto end

+)

+

+if "%1" == "singlehtml" (

+	%SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml.

+	goto end

+)

+

+if "%1" == "pickle" (

+	%SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished; now you can process the pickle files.

+	goto end

+)

+

+if "%1" == "json" (

+	%SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished; now you can process the JSON files.

+	goto end

+)

+

+if "%1" == "htmlhelp" (

+	%SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished; now you can run HTML Help Workshop with the ^

+.hhp project file in %BUILDDIR%/htmlhelp.

+	goto end

+)

+

+if "%1" == "qthelp" (

+	%SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished; now you can run "qcollectiongenerator" with the ^

+.qhcp project file in %BUILDDIR%/qthelp, like this:

+	echo.^> qcollectiongenerator %BUILDDIR%\qthelp\pouet.qhcp

+	echo.To view the help file:

+	echo.^> assistant -collectionFile %BUILDDIR%\qthelp\pouet.ghc

+	goto end

+)

+

+if "%1" == "devhelp" (

+	%SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished.

+	goto end

+)

+

+if "%1" == "epub" (

+	%SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished. The epub file is in %BUILDDIR%/epub.

+	goto end

+)

+

+if "%1" == "latex" (

+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.

+	goto end

+)

+

+if "%1" == "latexpdf" (

+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex

+	cd %BUILDDIR%/latex

+	make all-pdf

+	cd %BUILDDIR%/..

+	echo.

+	echo.Build finished; the PDF files are in %BUILDDIR%/latex.

+	goto end

+)

+

+if "%1" == "latexpdfja" (

+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex

+	cd %BUILDDIR%/latex

+	make all-pdf-ja

+	cd %BUILDDIR%/..

+	echo.

+	echo.Build finished; the PDF files are in %BUILDDIR%/latex.

+	goto end

+)

+

+if "%1" == "text" (

+	%SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished. The text files are in %BUILDDIR%/text.

+	goto end

+)

+

+if "%1" == "man" (

+	%SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished. The manual pages are in %BUILDDIR%/man.

+	goto end

+)

+

+if "%1" == "texinfo" (

+	%SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo.

+	goto end

+)

+

+if "%1" == "gettext" (

+	%SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished. The message catalogs are in %BUILDDIR%/locale.

+	goto end

+)

+

+if "%1" == "changes" (

+	%SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.The overview file is in %BUILDDIR%/changes.

+	goto end

+)

+

+if "%1" == "linkcheck" (

+	%SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Link check complete; look for any errors in the above output ^

+or in %BUILDDIR%/linkcheck/output.txt.

+	goto end

+)

+

+if "%1" == "doctest" (

+	%SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Testing of doctests in the sources finished, look at the ^

+results in %BUILDDIR%/doctest/output.txt.

+	goto end

+)

+

+if "%1" == "xml" (

+	%SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished. The XML files are in %BUILDDIR%/xml.

+	goto end

+)

+

+if "%1" == "pseudoxml" (

+	%SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml

+	if errorlevel 1 exit /b 1

+	echo.

+	echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml.

+	goto end

+)

+

+:end

diff --git a/src/cython/doc/periodic_cubical_complex_ref.rst b/src/cython/doc/periodic_cubical_complex_ref.rst
new file mode 100644
index 00000000..c6190a1b
--- /dev/null
+++ b/src/cython/doc/periodic_cubical_complex_ref.rst
@@ -0,0 +1,9 @@
+Periodic cubical complex reference manual
+#########################################
+
+.. autoclass:: gudhi.PeriodicCubicalComplex
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+   .. automethod:: gudhi.PeriodicCubicalComplex.__init__
diff --git a/src/cython/doc/persistent_cohomology_sum.rst b/src/cython/doc/persistent_cohomology_sum.rst
new file mode 100644
index 00000000..081399a5
--- /dev/null
+++ b/src/cython/doc/persistent_cohomology_sum.rst
@@ -0,0 +1,28 @@
+=====================================  =====================================  =====================================
+:Author: Clément Maria                 :Introduced in: GUDHI PYTHON 1.4.0     :Copyright: GPL v3
+=====================================  =====================================  =====================================
+
++---------------------------------------------+----------------------------------------------------------------------+
+| .. image::                                  | The theory of homology consists in attaching to a topological space  |
+|      img/3DTorus_poch.png                   | a sequence of (homology) groups, capturing global topological        |
+|                                             | features like connected components, holes, cavities, etc. Persistent |
+|                                             | homology studies the evolution -- birth, life and death -- of these  |
+|                                             | features when the topological space is changing. Consequently, the   |
+|                                             | theory is essentially composed of three elements: topological spaces,|
+|                                             | their homology groups and an evolution scheme.                       |
+|                                             |                                                                      |
+|                                             | Computation of persistent cohomology using the algorithm of          |
+|                                             | :cite:`DBLP:journals/dcg/SilvaMV11` and                              |
+|                                             | :cite:`DBLP:journals/corr/abs-1208-5018` and the Compressed          |
+|                                             | Annotation Matrix implementation of                                  |
+|                                             | :cite:`DBLP:conf/esa/BoissonnatDM13`.                                |
+|                                             |                                                                      |
++---------------------------------------------+----------------------------------------------------------------------+
+|  :doc:`persistent_cohomology_user`          | Please refer to each data structure that contains persistence        |
+|                                             | feature for reference:                                               |
+|                                             |                                                                      |
+|                                             | * :doc:`alpha_complex_ref`                                           |
+|                                             | * :doc:`cubical_complex_ref`                                         |
+|                                             | * :doc:`simplex_tree_ref`                                            |
+|                                             | * :doc:`witness_complex_ref`                                         |
++---------------------------------------------+----------------------------------------------------------------------+
diff --git a/src/cython/doc/persistent_cohomology_user.rst b/src/cython/doc/persistent_cohomology_user.rst
new file mode 100644
index 00000000..33b19ce2
--- /dev/null
+++ b/src/cython/doc/persistent_cohomology_user.rst
@@ -0,0 +1,104 @@
+=================================
+Persistent cohomology user manual
+=================================
+Definition
+----------
+=====================================  =====================================  =====================================
+:Author: Clément Maria                 :Introduced in: GUDHI PYTHON 1.4.0     :Copyright: GPL v3
+=====================================  =====================================  =====================================
+
++---------------------------------------------+----------------------------------------------------------------------+
+|  :doc:`persistent_cohomology_user`          | Please refer to each data structure that contains persistence        |
+|                                             | feature for reference:                                               |
+|                                             |                                                                      |
+|                                             | * :doc:`alpha_complex_ref`                                           |
+|                                             | * :doc:`cubical_complex_ref`                                         |
+|                                             | * :doc:`simplex_tree_ref`                                            |
+|                                             | * :doc:`witness_complex_ref`                                         |
++---------------------------------------------+----------------------------------------------------------------------+
+
+
+Computation of persistent cohomology using the algorithm of :cite:`DBLP:journals/dcg/SilvaMV11` and
+:cite:`DBLP:journals/corr/abs-1208-5018` and the Compressed Annotation Matrix implementation of
+:cite:`DBLP:conf/esa/BoissonnatDM13`.
+     
+The theory of homology consists in attaching to a topological space a sequence of (homology) groups, capturing global
+topological features like connected components, holes, cavities, etc. Persistent homology studies the evolution --
+birth, life and death -- of these features when the topological space is changing. Consequently, the theory is
+essentially composed of three elements:
+
+* topological spaces
+* their homology groups
+* an evolution scheme.
+
+Topological Spaces
+------------------
+
+Topological spaces are represented by simplicial complexes.
+Let :math:`V = \{1, \cdots ,|V|\}` be a set of *vertices*.
+A *simplex* :math:`\sigma` is a subset of vertices :math:`\sigma \subseteq V`.
+A *simplicial complex* :math:`\mathbf{K}` on :math:`V` is a collection of simplices :math:`\{\sigma\}`,
+:math:`\sigma \subseteq V`, such that :math:`\tau \subseteq \sigma \in \mathbf{K} \Rightarrow \tau \in \mathbf{K}`.
+The dimension :math:`n=|\sigma|-1` of :math:`\sigma` is its number of elements minus 1.
+A *filtration* of a simplicial complex is a function :math:`f:\mathbf{K} \rightarrow \mathbb{R}` satisfying
+:math:`f(\tau)\leq f(\sigma)` whenever :math:`\tau \subseteq \sigma`.
+
+Homology
+--------
+
+For a ring :math:`\mathcal{R}`, the group of *n-chains*, denoted :math:`\mathbf{C}_n(\mathbf{K},\mathcal{R})`, of
+:math:`\mathbf{K}` is the group of formal sums of n-simplices with :math:`\mathcal{R}` coefficients. The
+*boundary operator* is a linear operator
+:math:`\partial_n: \mathbf{C}_n(\mathbf{K},\mathcal{R}) \rightarrow \mathbf{C}_{n-1}(\mathbf{K},\mathcal{R})`
+such that :math:`\partial_n \sigma = \partial_n [v_0, \cdots , v_n] = \sum_{i=0}^n (-1)^{i}[v_0,\cdots ,\widehat{v_i}, \cdots,v_n]`,
+where :math:`\widehat{v_i}` means :math:`v_i` is omitted from the list. The chain groups form a sequence:
+
+.. math::
+
+    \cdots \ \ \mathbf{C}_n(\mathbf{K},\mathcal{R}) \xrightarrow{\ \partial_n\ }
+    \mathbf{C}_{n-1}(\mathbf{K},\mathcal{R}) \xrightarrow{\partial_{n-1}} \cdots \xrightarrow{\ \partial_2 \ }
+    \mathbf{C}_1(\mathbf{K},\mathcal{R}) \xrightarrow{\ \partial_1 \ }  \mathbf{C}_0(\mathbf{K},\mathcal{R})
+
+of finitely many groups :math:`\mathbf{C}_n(\mathbf{K},\mathcal{R})` and homomorphisms :math:`\partial_n`, indexed by
+the dimension :math:`n \geq 0`. The boundary operators satisfy the property :math:`\partial_n \circ \partial_{n+1}=0`
+for every :math:`n > 0` and we define the homology groups:
+
+.. math::
+
+    \mathbf{H}_n(\mathbf{K},\mathcal{R}) = \ker \partial_n / \mathrm{im} \  \partial_{n+1}
+
+We refer to :cite:`Munkres-elementsalgtop1984` for an introduction to homology
+theory and to :cite:`DBLP:books/daglib/0025666` for an introduction to persistent homology.
+
+Indexing Scheme
+---------------
+
+"Changing" a simplicial complex consists in applying a simplicial map. An *indexing scheme* is a directed graph
+together with a traversal order, such that two consecutive nodes in the graph are connected by an arrow (either forward
+or backward).
+The nodes represent simplicial complexes and the directed edges simplicial maps.
+
+From the computational point of view, there are two types of indexing schemes of interest in persistent homology:
+    
+* linear ones
+  :math:`\bullet \longrightarrow \bullet \longrightarrow \cdots \longrightarrow \bullet \longrightarrow \bullet`
+  in persistent homology :cite:`DBLP:journals/dcg/ZomorodianC05`,
+* zigzag ones
+  :math:`\bullet \longrightarrow \bullet \longleftarrow \cdots \longrightarrow \bullet \longleftarrow \bullet`
+  in zigzag persistent homology :cite:`DBLP:journals/focm/CarlssonS10`.
+  
+These indexing schemes have a natural left-to-right traversal order, and we describe them with ranges and iterators.
+In the current release of the Gudhi library, only the linear case is implemented.
+
+In the following, we consider the case where the indexing scheme is induced by a filtration.
+
+Ordering the simplices by increasing filtration values (breaking ties so as a simplex appears after its subsimplices of
+same filtration value) provides an indexing scheme.
+
+Examples
+--------
+
+We provide several example files: run these examples with -h for details on their use.
+
+.. todo::
+    examples for persistence
diff --git a/src/cython/doc/simplex_tree_ref.rst b/src/cython/doc/simplex_tree_ref.rst
new file mode 100644
index 00000000..6d196843
--- /dev/null
+++ b/src/cython/doc/simplex_tree_ref.rst
@@ -0,0 +1,10 @@
+=============================
+Simplex tree reference manual
+=============================
+
+.. autoclass:: gudhi.SimplexTree
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+   .. automethod:: gudhi.SimplexTree.__init__
diff --git a/src/cython/doc/simplex_tree_sum.rst b/src/cython/doc/simplex_tree_sum.rst
new file mode 100644
index 00000000..ffdb2cf4
--- /dev/null
+++ b/src/cython/doc/simplex_tree_sum.rst
@@ -0,0 +1,13 @@
+=====================================  =====================================  =====================================
+:Author: Clément Maria                 :Introduced in: GUDHI PYTHON 1.4.0     :Copyright: GPL v3
+=====================================  =====================================  =====================================
+
++-------------------------------------------+----------------------------------------------------------------------+
+| .. image::                                | The simplex tree is an efficient and flexible data structure for     |
+|      img/Simplex_tree_representation.png  | representing general (filtered) simplicial complexes.                |
+|                                           |                                                                      |
+|                                           | The data structure is described in                                   |
+|                                           | :cite:`boissonnatmariasimplextreealgorithmica`                       |
++-------------------------------------------+----------------------------------------------------------------------+
+| :doc:`simplex_tree_user`                  | :doc:`simplex_tree_ref`                                              |
++-------------------------------------------+----------------------------------------------------------------------+
diff --git a/src/cython/doc/simplex_tree_user.rst b/src/cython/doc/simplex_tree_user.rst
new file mode 100644
index 00000000..3a00f1ac
--- /dev/null
+++ b/src/cython/doc/simplex_tree_user.rst
@@ -0,0 +1,67 @@
+========================
+Simplex tree user manual
+========================
+Definition
+----------
+
+.. include:: simplex_tree_sum.rst
+
+A simplicial complex :math:`\mathbf{K}` on a set of vertices :math:`V = \{1, \cdots ,|V|\}` is a collection of
+simplices :math:`\{\sigma\}`, :math:`\sigma \subseteq V` such that
+:math:`\tau \subseteq \sigma \in \mathbf{K} \rightarrow \tau \in \mathbf{K}`. The dimension :math:`n=|\sigma|-1` of
+:math:`\sigma` is its number of elements minus `1`.
+
+A filtration of a simplicial complex is a function :math:`f:\mathbf{K} \rightarrow \mathbb{R}` satisfying
+:math:`f(\tau)\leq f(\sigma)` whenever :math:`\tau \subseteq \sigma`. Ordering the simplices by increasing filtration
+values (breaking ties so as a simplex appears after its subsimplices of same filtration value) provides an indexing
+scheme.
+
+
+Implementation
+--------------
+
+There are two implementation of complexes. The first on is the Simplex_tree data structure.
+The simplex tree is an efficient and flexible data structure for representing general (filtered) simplicial complexes.
+The data structure is described in :cite`boissonnatmariasimplextreealgorithmica`.
+
+The second one is the Hasse_complex. The Hasse complex is a data structure representing explicitly all co-dimension 1
+incidence relations in a complex. It is consequently faster when accessing the boundary of a simplex, but is less
+compact and harder to construct from scratch.
+
+Example
+-------
+
+.. testcode::
+
+   import gudhi
+   st = gudhi.SimplexTree()
+   if st.insert([0, 1]):
+       print("[0, 1] inserted")
+   if st.insert([0, 1, 2], filtration=4.0):
+       print("[0, 1, 2] inserted")
+   if st.find([0, 1]):
+       print("[0, 1] found")
+   print("num_vertices=", st.num_vertices())
+   print("num_simplices=", st.num_simplices())
+   print("skeleton_tree(2) =")
+   for sk_value in st.get_skeleton_tree(2):
+       print(sk_value)
+
+
+The output is:
+
+.. testoutput::
+
+   [0, 1] inserted
+   [0, 1, 2] inserted
+   [0, 1] found
+   ('num_vertices=', 3)
+   ('num_simplices=', 7)
+   skeleton_tree(2) =
+   ([0, 1, 2], 4.0)
+   ([0, 1], 0.0)
+   ([0, 2], 4.0)
+   ([0], 0.0)
+   ([1, 2], 4.0)
+   ([1], 0.0)
+   ([2], 4.0)
diff --git a/src/cython/doc/witness_complex_ref.rst b/src/cython/doc/witness_complex_ref.rst
new file mode 100644
index 00000000..c78760cb
--- /dev/null
+++ b/src/cython/doc/witness_complex_ref.rst
@@ -0,0 +1,10 @@
+================================
+Witness complex reference manual
+================================
+
+.. autoclass:: gudhi.WitnessComplex
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+   .. automethod:: gudhi.WitnessComplex.__init__
diff --git a/src/cython/doc/witness_complex_sum.rst b/src/cython/doc/witness_complex_sum.rst
new file mode 100644
index 00000000..0d65d420
--- /dev/null
+++ b/src/cython/doc/witness_complex_sum.rst
@@ -0,0 +1,25 @@
+=====================================  =====================================  =====================================
+:Author: Siargey Kachanovich           :Introduced in: GUDHI PYTHON 1.4.0     :Copyright: GPL v3
+=====================================  =====================================  =====================================
+
++---------------------------------------------+----------------------------------------------------------------------+
+| .. image::                                  | Witness complex :math:`Wit(W,L)` is a simplicial complex defined on  |
+|      img/Witness_complex_representation.png | two sets of points in :math:`\mathbb{R}^D`:Wit(W,L)` is a simplicial |
+|                                             | complex defined on two sets of points in :math:`\mathbb{R}^D`:       |
+|                                             |                                                                      |
+|                                             | * :math:`W` set of **witnesses** and                                 |
+|                                             | * :math:`L \subseteq W` set of **landmarks**.                        |
+|                                             |                                                                      |
+|                                             | The simplices are based on landmarks and a simplex belongs to the    |
+|                                             | witness complex if and only if it is witnessed, that is:             |
+|                                             |                                                                      |
+|                                             | :math:`\sigma \subset L` is witnessed if there exists a point        |
+|                                             | :math:`w \in W` such that w is closer to the vertices of             |
+|                                             | :math:`\sigma` than other points in :math:`L` and all of its faces   |
+|                                             | are witnessed as well.                                               |
+|                                             |                                                                      |
+|                                             | The data structure is described in                                   |
+|                                             | :cite:`boissonnatmariasimplextreealgorithmica`.                      |
++---------------------------------------------+----------------------------------------------------------------------+
+| :doc:`witness_complex_user`                 | :doc:`witness_complex_ref`                                           |
++---------------------------------------------+----------------------------------------------------------------------+
diff --git a/src/cython/doc/witness_complex_user.rst b/src/cython/doc/witness_complex_user.rst
new file mode 100644
index 00000000..604c7357
--- /dev/null
+++ b/src/cython/doc/witness_complex_user.rst
@@ -0,0 +1,31 @@
+===========================
+Witness complex user manual
+===========================
+Definition
+----------
+
+.. include:: witness_complex_sum.rst
+
+Implementation
+--------------
+
+The principal class of this module is Gudhi::Witness_complex.
+
+In both cases, the constructor for this class takes a {witness}x{closest_landmarks} table, where each row represents a
+witness and consists of landmarks sorted by distance to this witness.
+
+.. todo::
+    This table can be constructed by two additional classes Landmark_choice_by_furthest_point and
+    Landmark_choice_by_random_point also included in the module.
+
+.. figure::
+    img/bench_Cy8.png
+    :align: center
+    
+    Running time as function on number of landmarks.
+
+.. figure::
+    img/bench_sphere.png
+    :align: center
+    
+    Running time as function on number of witnesses for |L|=300.