Doc with sphinx

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@1369 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: ad4fe8083b2659af5f34c71fa02decf63403bce4

11 files changed, 893 insertions, 83 deletions

diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 27f6b99d..3989d5a1 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -74,6 +74,7 @@ if(PYTHON_PATH AND CYTHON_PATH)
   
   add_custom_target(cythonize_gudhi ALL DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so")
 
+  # Unitary tests are available through py.test
   find_program( PYTEST_PATH py.test )
   if(PYTEST_PATH)
     add_test(
@@ -83,4 +84,25 @@ if(PYTHON_PATH AND CYTHON_PATH)
     set_tests_properties(gudhi_cython_py_test PROPERTIES ENVIRONMENT "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}")
   endif(PYTEST_PATH)
 
+  # Documentation generation is available through sphinx
+  find_program( SPHINX_PATH sphinx-build )
+  if(SPHINX_PATH)
+    file(COPY doc DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+    # Developper version
+    file(GLOB GUDHI_DEV_DOC_IMAGES "${CMAKE_SOURCE_DIR}/src/*/doc/*.png")
+    file(COPY ${GUDHI_DEV_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/source/img")
+    # User version
+    file(GLOB GUDHI_USER_DOC_IMAGES "${CMAKE_SOURCE_DIR}/doc/*/*.png")
+    file(COPY ${GUDHI_USER_DOC_IMAGES} DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/doc/source/img")
+    if (UNIX)
+      add_custom_target(html 
+          WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc
+          COMMAND make html)
+    else (UNIX)
+      add_custom_target(html 
+          WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/doc
+          COMMAND make.bat html)
+    endif (UNIX)
+  endif(SPHINX_PATH)
+
 endif(PYTHON_PATH AND CYTHON_PATH)
diff --git a/src/cython/doc/Makefile b/src/cython/doc/Makefile
new file mode 100644
index 00000000..e500e250
--- /dev/null
+++ b/src/cython/doc/Makefile
@@ -0,0 +1,177 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = build
+
+# User-friendly check for sphinx-build
+ifeq ($(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) source
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  xml        to make Docutils-native XML files"
+	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	rm -rf $(BUILDDIR)/*
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/GUDHI.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/GUDHI.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/GUDHI"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/GUDHI"
+	@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/make.bat b/src/cython/doc/make.bat
new file mode 100644
index 00000000..cc6418d0
--- /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% source

+set I18NSPHINXOPTS=%SPHINXOPTS% source

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

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

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

+)

+

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

+

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

+	:help

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

+	echo.  html       to make standalone HTML files

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

+	echo.  singlehtml to make a single large HTML file

+	echo.  pickle     to make pickle files

+	echo.  json       to make JSON files

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

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

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

+	echo.  epub       to make an epub

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

+	echo.  text       to make text files

+	echo.  man        to make manual pages

+	echo.  texinfo    to make Texinfo files

+	echo.  gettext    to make PO message catalogs

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

+	echo.  xml        to make Docutils-native XML files

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

+	echo.  linkcheck  to check all external links for integrity

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

+	goto end

+)

+

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

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

+	del /q /s %BUILDDIR%\*

+	goto end

+)

+

+

+%SPHINXBUILD% 2> nul

+if errorlevel 9009 (

+	echo.

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

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

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

+	echo.may add the Sphinx directory to PATH.

+	echo.

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

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

+	exit /b 1

+)

+

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

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

+	if errorlevel 1 exit /b 1

+	echo.

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

+	goto end

+)

+

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

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

+	if errorlevel 1 exit /b 1

+	echo.

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

+	goto end

+)

+

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

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

+	if errorlevel 1 exit /b 1

+	echo.

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

+	goto end

+)

+

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

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

+	if errorlevel 1 exit /b 1

+	echo.

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

+	goto end

+)

+

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

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

+	if errorlevel 1 exit /b 1

+	echo.

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

+	goto end

+)

+

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

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

+	if errorlevel 1 exit /b 1

+	echo.

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

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

+	goto end

+)

+

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

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

+	if errorlevel 1 exit /b 1

+	echo.

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

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

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

+	echo.To view the help file:

+	echo.^> assistant -collectionFile %BUILDDIR%\qthelp\GUDHI.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/source/conf.py b/src/cython/doc/source/conf.py
new file mode 100755
index 00000000..094020f7
--- /dev/null
+++ b/src/cython/doc/source/conf.py
@@ -0,0 +1,269 @@
+# -*- 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',
+]
+
+# 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 = []
+
+# 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/source/index.rst b/src/cython/doc/source/index.rst
new file mode 100644
index 00000000..7dfea239
--- /dev/null
+++ b/src/cython/doc/source/index.rst
@@ -0,0 +1,64 @@
+.. 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.
+
+.. toctree::
+   :maxdepth: 2
+
+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). 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 [14] for a detailed
+description of the design of the library.
+
+Data structures
+***************
+
+Alpha complex
+=============
+
+.. image:: img/alpha_complex_representation.png
+   :align: center
+
+Alpha_complex is a simplicial complex constructed from the finite 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).
+
+* :ref:`alphacomplex`
+
+
+.. automodule:: gudhi
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
diff --git a/src/cython/src/cython/alpha_complex.pyx b/src/cython/src/cython/alpha_complex.pyx
index 39e930f4..f36de661 100644
--- a/src/cython/src/cython/alpha_complex.pyx
+++ b/src/cython/src/cython/alpha_complex.pyx
@@ -193,7 +193,7 @@ cdef class AlphaComplex:
         value (default value is '0.0').
 
         :param simplex: The N-simplex to insert, represented by a list of
-        vertex.
+            vertex.
         :type simplex: list of int.
         :param filtration: The filtration value of the simplex.
         :type filtration: float.
@@ -210,7 +210,7 @@ cdef class AlphaComplex:
         values.
 
         :returns:  list of tuples(simplex, filtration) -- the tree sorted by
-        increasing filtration values.
+            increasing filtration values.
         """
         cdef vector[pair[vector[int], double]] coface_tree \
             = self.thisptr.get_filtered_tree()
@@ -229,7 +229,7 @@ cdef class AlphaComplex:
         :param dimension: The skeleton dimension value.
         :type dimension: int.
         :returns:  list of tuples(simplex, filtration) -- the skeleton tree
-        of a maximum dimension.
+            of a maximum dimension.
         """
         cdef vector[pair[vector[int], double]] coface_tree \
             = self.thisptr.get_skeleton_tree(<int>dimension)
@@ -247,7 +247,7 @@ cdef class AlphaComplex:
         :param simplex: The N-simplex, represented by a list of vertex.
         :type simplex: list of int.
         :returns:  list of tuples(simplex, filtration) -- the star tree of a
-        simplex.
+            simplex.
         """
         cdef vector[int] complex
         for i in simplex:
@@ -269,10 +269,10 @@ cdef class AlphaComplex:
         :param simplex: The N-simplex, represented by a list of vertex.
         :type simplex: list of int.
         :param codimension: The codimension. If codimension = 0, all cofaces
-        are returned (equivalent of get_star_tree function)
+            are returned (equivalent of get_star_tree function)
         :type codimension: int.
-        :returns:  list of tuples(simplex, filtration) -- the coface tree of a
-        simplex.
+        :returns: list of tuples(simplex, filtration) -- the coface tree of a
+            simplex.
         """
         cdef vector[int] complex
         for i in simplex:
@@ -310,14 +310,15 @@ cdef class AlphaComplex:
         """This function returns the persistence of the simplicial complex.
 
         :param homology_coeff_field: The homology coefficient field. Must be a
-        prime number
+            prime number
         :type homology_coeff_field: int.
         :param min_persistence: The minimum persistence value to take into
-        account (strictly greater than min_persistence). Default value is 0.0.
-        Sets min_persistence to -1.0 to see all values.
+            account (strictly greater than min_persistence). Default value is
+            0.0.
+            Sets min_persistence to -1.0 to see all values.
         :type min_persistence: float.
-        :returns: list of tuples(dimension, tuple(birth, death)) -- the star tree of a
-        simplex.
+        :returns: list of tuples(dimension, tuple(birth, death)) -- the
+            persistence of the simplicial complex.
         """
         if self.pcohptr != NULL:
             del self.pcohptr
@@ -333,6 +334,9 @@ cdef class AlphaComplex:
         """This function returns the Betti numbers of the simplicial complex.
 
         :returns: list of int -- The Betti numbers ([B0, B1, ..., Bn]).
+
+        :note: betti_numbers function requires persistence function to be
+            launched first.
         """
         cdef vector[int] bn_result
         if self.pcohptr != NULL:
@@ -347,14 +351,17 @@ cdef class AlphaComplex:
         simplicial complex.
 
         :param from_value: The persistence birth limit to be added in the
-        numbers (persistent birth <= from_value).
+            numbers (persistent birth <= from_value).
         :type from_value: float.
         :param to_value: The persistence death limit to be added in the
-        numbers (persistent death > to_value).
+            numbers (persistent death > to_value).
         :type to_value: float.
 
         :returns: list of int -- The persistent Betti numbers ([B0, B1, ...,
-        Bn]).
+            Bn]).
+
+        :note: persistent_betti_numbers function requires persistence
+            function to be launched first.
         """
         cdef vector[int] pbn_result
         if self.pcohptr != NULL:
diff --git a/src/cython/src/cython/cubical_complex.pyx b/src/cython/src/cython/cubical_complex.pyx
index 402d264c..52137520 100644
--- a/src/cython/src/cython/cubical_complex.pyx
+++ b/src/cython/src/cython/cubical_complex.pyx
@@ -98,14 +98,15 @@ cdef class CubicalComplex:
         """This function returns the persistence of the simplicial complex.
 
         :param homology_coeff_field: The homology coefficient field. Must be a
-        prime number
+            prime number
         :type homology_coeff_field: int.
         :param min_persistence: The minimum persistence value to take into
-        account (strictly greater than min_persistence). Default value is 0.0.
-        Sets min_persistence to -1.0 to see all values.
+            account (strictly greater than min_persistence). Default value is
+            0.0.
+            Sets min_persistence to -1.0 to see all values.
         :type min_persistence: float.
-        :returns: list of tuples(dimension, tuple(birth, death)) -- the star tree of a
-        simplex.
+        :returns: list of pairs(dimension, pair(birth, death)) -- the
+            persistence of the simplicial complex.
         """
         if self.pcohptr != NULL:
             del self.pcohptr
@@ -121,8 +122,8 @@ cdef class CubicalComplex:
 
         :returns: list of int -- The Betti numbers ([B0, B1, ..., Bn]).
 
-        :warning: betti_numbers function requires persistence function to be
-        launched first.
+        :note: betti_numbers function requires persistence function to be
+            launched first.
         """
         cdef vector[int] bn_result
         if self.pcohptr != NULL:
@@ -134,17 +135,17 @@ cdef class CubicalComplex:
         simplicial complex.
 
         :param from_value: The persistence birth limit to be added in the
-        numbers (persistent birth <= from_value).
+            numbers (persistent birth <= from_value).
         :type from_value: float.
         :param to_value: The persistence death limit to be added in the
-        numbers (persistent death > to_value).
+            numbers (persistent death > to_value).
         :type to_value: float.
 
         :returns: list of int -- The persistent Betti numbers ([B0, B1, ...,
-        Bn]).
+            Bn]).
 
-        :warning: betti_numbers function requires persistence function to be
-        launched first.
+        :note: persistent_betti_numbers function requires persistence
+            function to be launched first.
         """
         cdef vector[int] pbn_result
         if self.pcohptr != NULL:
diff --git a/src/cython/src/cython/mini_simplex_tree.pyx b/src/cython/src/cython/mini_simplex_tree.pyx
index 813316af..c045c727 100644
--- a/src/cython/src/cython/mini_simplex_tree.pyx
+++ b/src/cython/src/cython/mini_simplex_tree.pyx
@@ -179,7 +179,7 @@ cdef class MiniSimplexTree:
         value (default value is '0.0').
 
         :param simplex: The N-simplex to insert, represented by a list of
-        vertex.
+            vertex.
         :type simplex: list of int.
         :param filtration: The filtration value of the simplex.
         :type filtration: float.
@@ -196,7 +196,7 @@ cdef class MiniSimplexTree:
         values.
 
         :returns:  list of tuples(simplex, filtration) -- the tree sorted by
-        increasing filtration values.
+            increasing filtration values.
         """
         cdef vector[pair[vector[int], double]] coface_tree \
             = self.thisptr.get_filtered_tree()
@@ -215,7 +215,7 @@ cdef class MiniSimplexTree:
         :param dimension: The skeleton dimension value.
         :type dimension: int.
         :returns:  list of tuples(simplex, filtration) -- the skeleton tree
-        of a maximum dimension.
+            of a maximum dimension.
         """
         cdef vector[pair[vector[int], double]] coface_tree \
             = self.thisptr.get_skeleton_tree(<int>dimension)
@@ -233,7 +233,7 @@ cdef class MiniSimplexTree:
         :param simplex: The N-simplex, represented by a list of vertex.
         :type simplex: list of int.
         :returns:  list of tuples(simplex, filtration) -- the star tree of a
-        simplex.
+            simplex.
         """
         cdef vector[int] complex
         for i in simplex:
@@ -255,10 +255,10 @@ cdef class MiniSimplexTree:
         :param simplex: The N-simplex, represented by a list of vertex.
         :type simplex: list of int.
         :param codimension: The codimension. If codimension = 0, all cofaces
-        are returned (equivalent of get_star_tree function)
+            are returned (equivalent of get_star_tree function)
         :type codimension: int.
         :returns:  list of tuples(simplex, filtration) -- the coface tree of a
-        simplex.
+            simplex.
         """
         cdef vector[int] complex
         for i in simplex:
@@ -286,14 +286,15 @@ cdef class MiniSimplexTree:
         """This function returns the persistence of the simplicial complex.
 
         :param homology_coeff_field: The homology coefficient field. Must be a
-        prime number
+            prime number
         :type homology_coeff_field: int.
         :param min_persistence: The minimum persistence value to take into
-        account (strictly greater than min_persistence). Default value is 0.0.
-        Sets min_persistence to -1.0 to see all values.
+            account (strictly greater than min_persistence). Default value is
+            0.0.
+            Sets min_persistence to -1.0 to see all values.
         :type min_persistence: float.
-        :returns: list of tuples(dimension, tuple(birth, death)) -- the star tree of a
-        simplex.
+        :returns: list of pairs(dimension, pair(birth, death)) -- the
+            persistence of the simplicial complex.
         """
         if self.pcohptr != NULL:
             del self.pcohptr
@@ -307,6 +308,9 @@ cdef class MiniSimplexTree:
         """This function returns the Betti numbers of the simplicial complex.
 
         :returns: list of int -- The Betti numbers ([B0, B1, ..., Bn]).
+
+        :note: betti_numbers function requires persistence function to be
+            launched first.
         """
         cdef vector[int] bn_result
         if self.pcohptr != NULL:
@@ -321,14 +325,17 @@ cdef class MiniSimplexTree:
         simplicial complex.
 
         :param from_value: The persistence birth limit to be added in the
-        numbers (persistent birth <= from_value).
+            numbers (persistent birth <= from_value).
         :type from_value: float.
         :param to_value: The persistence death limit to be added in the
-        numbers (persistent death > to_value).
+            numbers (persistent death > to_value).
         :type to_value: float.
 
         :returns: list of int -- The persistent Betti numbers ([B0, B1, ...,
-        Bn]).
+            Bn]).
+
+        :note: persistent_betti_numbers function requires persistence
+            function to be launched first.
         """
         cdef vector[int] pbn_result
         if self.pcohptr != NULL:
diff --git a/src/cython/src/cython/rips_complex.pyx b/src/cython/src/cython/rips_complex.pyx
index 4d713304..7e07f36b 100644
--- a/src/cython/src/cython/rips_complex.pyx
+++ b/src/cython/src/cython/rips_complex.pyx
@@ -195,7 +195,7 @@ cdef class RipsComplex:
         value (default value is '0.0').
 
         :param simplex: The N-simplex to insert, represented by a list of
-        vertex.
+            vertex.
         :type simplex: list of int.
         :param filtration: The filtration value of the simplex.
         :type filtration: float.
@@ -212,7 +212,7 @@ cdef class RipsComplex:
         values.
 
         :returns:  list of tuples(simplex, filtration) -- the tree sorted by
-        increasing filtration values.
+            increasing filtration values.
         """
         cdef vector[pair[vector[int], double]] coface_tree \
             = self.thisptr.get_filtered_tree()
@@ -231,7 +231,7 @@ cdef class RipsComplex:
         :param dimension: The skeleton dimension value.
         :type dimension: int.
         :returns:  list of tuples(simplex, filtration) -- the skeleton tree
-        of a maximum dimension.
+            of a maximum dimension.
         """
         cdef vector[pair[vector[int], double]] coface_tree \
             = self.thisptr.get_skeleton_tree(<int>dimension)
@@ -249,7 +249,7 @@ cdef class RipsComplex:
         :param simplex: The N-simplex, represented by a list of vertex.
         :type simplex: list of int.
         :returns:  list of tuples(simplex, filtration) -- the star tree of a
-        simplex.
+            simplex.
         """
         cdef vector[int] complex
         for i in simplex:
@@ -271,10 +271,10 @@ cdef class RipsComplex:
         :param simplex: The N-simplex, represented by a list of vertex.
         :type simplex: list of int.
         :param codimension: The codimension. If codimension = 0, all cofaces
-        are returned (equivalent of get_star_tree function)
+            are returned (equivalent of get_star_tree function)
         :type codimension: int.
         :returns:  list of tuples(simplex, filtration) -- the coface tree of a
-        simplex.
+            simplex.
         """
         cdef vector[int] complex
         for i in simplex:
@@ -302,14 +302,15 @@ cdef class RipsComplex:
         """This function returns the persistence of the simplicial complex.
 
         :param homology_coeff_field: The homology coefficient field. Must be a
-        prime number
+            prime number
         :type homology_coeff_field: int.
         :param min_persistence: The minimum persistence value to take into
-        account (strictly greater than min_persistence). Default value is 0.0.
-        Sets min_persistence to -1.0 to see all values.
+            account (strictly greater than min_persistence). Default value is
+            0.0.
+            Sets min_persistence to -1.0 to see all values.
         :type min_persistence: float.
-        :returns: list of tuples(dimension, tuple(birth, death)) -- the star tree of a
-        simplex.
+        :note: list of pairs(dimension, pair(birth, death)) -- the
+            persistence of the simplicial complex.
         """
         if self.pcohptr != NULL:
             del self.pcohptr
@@ -323,6 +324,9 @@ cdef class RipsComplex:
         """This function returns the Betti numbers of the simplicial complex.
 
         :returns: list of int -- The Betti numbers ([B0, B1, ..., Bn]).
+
+        :note: betti_numbers function requires persistence function to be
+            launched first.
         """
         cdef vector[int] bn_result
         if self.pcohptr != NULL:
@@ -337,14 +341,17 @@ cdef class RipsComplex:
         simplicial complex.
 
         :param from_value: The persistence birth limit to be added in the
-        numbers (persistent birth <= from_value).
+            numbers (persistent birth <= from_value).
         :type from_value: float.
         :param to_value: The persistence death limit to be added in the
-        numbers (persistent death > to_value).
+            numbers (persistent death > to_value).
         :type to_value: float.
 
         :returns: list of int -- The persistent Betti numbers ([B0, B1, ...,
-        Bn]).
+            Bn]).
+
+        :note: persistent_betti_numbers function requires persistence
+            function to be launched first.
         """
         cdef vector[int] pbn_result
         if self.pcohptr != NULL:
diff --git a/src/cython/src/cython/simplex_tree.pyx b/src/cython/src/cython/simplex_tree.pyx
index c0c783b4..772ea73d 100644
--- a/src/cython/src/cython/simplex_tree.pyx
+++ b/src/cython/src/cython/simplex_tree.pyx
@@ -179,7 +179,7 @@ cdef class SimplexTree:
         value (default value is '0.0').
 
         :param simplex: The N-simplex to insert, represented by a list of
-        vertex.
+            vertex.
         :type simplex: list of int.
         :param filtration: The filtration value of the simplex.
         :type filtration: float.
@@ -196,7 +196,7 @@ cdef class SimplexTree:
         values.
 
         :returns:  list of tuples(simplex, filtration) -- the tree sorted by
-        increasing filtration values.
+            increasing filtration values.
         """
         cdef vector[pair[vector[int], double]] coface_tree \
             = self.thisptr.get_filtered_tree()
@@ -215,7 +215,7 @@ cdef class SimplexTree:
         :param dimension: The skeleton dimension value.
         :type dimension: int.
         :returns:  list of tuples(simplex, filtration) -- the skeleton tree
-        of a maximum dimension.
+            of a maximum dimension.
         """
         cdef vector[pair[vector[int], double]] coface_tree \
             = self.thisptr.get_skeleton_tree(<int>dimension)
@@ -233,7 +233,7 @@ cdef class SimplexTree:
         :param simplex: The N-simplex, represented by a list of vertex.
         :type simplex: list of int.
         :returns:  list of tuples(simplex, filtration) -- the star tree of a
-        simplex.
+            simplex.
         """
         cdef vector[int] complex
         for i in simplex:
@@ -255,10 +255,10 @@ cdef class SimplexTree:
         :param simplex: The N-simplex, represented by a list of vertex.
         :type simplex: list of int.
         :param codimension: The codimension. If codimension = 0, all cofaces
-        are returned (equivalent of get_star_tree function)
+            are returned (equivalent of get_star_tree function)
         :type codimension: int.
         :returns:  list of tuples(simplex, filtration) -- the coface tree of a
-        simplex.
+            simplex.
         """
         cdef vector[int] complex
         for i in simplex:
@@ -286,14 +286,15 @@ cdef class SimplexTree:
         """This function returns the persistence of the simplicial complex.
 
         :param homology_coeff_field: The homology coefficient field. Must be a
-        prime number
+            prime number
         :type homology_coeff_field: int.
         :param min_persistence: The minimum persistence value to take into
-        account (strictly greater than min_persistence). Default value is 0.0.
-        Sets min_persistence to -1.0 to see all values.
+            account (strictly greater than min_persistence). Default value is
+            0.0.
+            Sets min_persistence to -1.0 to see all values.
         :type min_persistence: float.
-        :returns: list of tuples(dimension, tuple(birth, death)) -- the star tree of a
-        simplex.
+        :note: list of pairs(dimension, pair(birth, death)) -- the
+            persistence of the simplicial complex.
         """
         if self.pcohptr != NULL:
             del self.pcohptr
@@ -307,6 +308,9 @@ cdef class SimplexTree:
         """This function returns the Betti numbers of the simplicial complex.
 
         :returns: list of int -- The Betti numbers ([B0, B1, ..., Bn]).
+
+        :note: betti_numbers function requires persistence function to be
+            launched first.
         """
         cdef vector[int] bn_result
         if self.pcohptr != NULL:
@@ -321,14 +325,17 @@ cdef class SimplexTree:
         simplicial complex.
 
         :param from_value: The persistence birth limit to be added in the
-        numbers (persistent birth <= from_value).
+            numbers (persistent birth <= from_value).
         :type from_value: float.
         :param to_value: The persistence death limit to be added in the
-        numbers (persistent death > to_value).
+            numbers (persistent death > to_value).
         :type to_value: float.
 
         :returns: list of int -- The persistent Betti numbers ([B0, B1, ...,
-        Bn]).
+            Bn]).
+
+        :note: persistent_betti_numbers function requires persistence
+            function to be launched first.
         """
         cdef vector[int] pbn_result
         if self.pcohptr != NULL:
diff --git a/src/cython/src/cython/witness_complex.pyx b/src/cython/src/cython/witness_complex.pyx
index 0f08bdcb..bdbdc393 100644
--- a/src/cython/src/cython/witness_complex.pyx
+++ b/src/cython/src/cython/witness_complex.pyx
@@ -168,7 +168,7 @@ cdef class WitnessComplex:
         value (default value is '0.0').
 
         :param simplex: The N-simplex to insert, represented by a list of
-        vertex.
+            vertex.
         :type simplex: list of int.
         :param filtration: The filtration value of the simplex.
         :type filtration: float.
@@ -185,7 +185,7 @@ cdef class WitnessComplex:
         values.
 
         :returns:  list of tuples(simplex, filtration) -- the tree sorted by
-        increasing filtration values.
+            increasing filtration values.
         """
         cdef vector[pair[vector[int], double]] coface_tree \
             = self.thisptr.get_filtered_tree()
@@ -204,7 +204,7 @@ cdef class WitnessComplex:
         :param dimension: The skeleton dimension value.
         :type dimension: int.
         :returns:  list of tuples(simplex, filtration) -- the skeleton tree
-        of a maximum dimension.
+            of a maximum dimension.
         """
         cdef vector[pair[vector[int], double]] coface_tree \
             = self.thisptr.get_skeleton_tree(<int>dimension)
@@ -222,7 +222,7 @@ cdef class WitnessComplex:
         :param simplex: The N-simplex, represented by a list of vertex.
         :type simplex: list of int.
         :returns:  list of tuples(simplex, filtration) -- the star tree of a
-        simplex.
+            simplex.
         """
         cdef vector[int] complex
         for i in simplex:
@@ -244,10 +244,10 @@ cdef class WitnessComplex:
         :param simplex: The N-simplex, represented by a list of vertex.
         :type simplex: list of int.
         :param codimension: The codimension. If codimension = 0, all cofaces
-        are returned (equivalent of get_star_tree function)
+            are returned (equivalent of get_star_tree function)
         :type codimension: int.
         :returns:  list of tuples(simplex, filtration) -- the coface tree of a
-        simplex.
+            simplex.
         """
         cdef vector[int] complex
         for i in simplex:
@@ -275,14 +275,15 @@ cdef class WitnessComplex:
         """This function returns the persistence of the simplicial complex.
 
         :param homology_coeff_field: The homology coefficient field. Must be a
-        prime number
+            prime number
         :type homology_coeff_field: int.
         :param min_persistence: The minimum persistence value to take into
-        account (strictly greater than min_persistence). Default value is 0.0.
-        Sets min_persistence to -1.0 to see all values.
+            account (strictly greater than min_persistence). Default value is
+            0.0.
+            Sets min_persistence to -1.0 to see all values.
         :type min_persistence: float.
-        :returns: list of tuples(dimension, tuple(birth, death)) -- the star tree of a
-        simplex.
+        :note: list of pairs(dimension, pair(birth, death)) -- the
+            persistence of the simplicial complex.
         """
         return self.thisptr.get_persistence(homology_coeff_field, min_persistence)
 
@@ -290,6 +291,9 @@ cdef class WitnessComplex:
         """This function returns the Betti numbers of the simplicial complex.
 
         :returns: list of int -- The Betti numbers ([B0, B1, ..., Bn]).
+
+        :note: betti_numbers function requires persistence function to be
+            launched first.
         """
         return self.thisptr.get_betti_numbers()
 
@@ -298,13 +302,16 @@ cdef class WitnessComplex:
         simplicial complex.
 
         :param from_value: The persistence birth limit to be added in the
-        numbers (persistent birth <= from_value).
+            numbers (persistent birth <= from_value).
         :type from_value: float.
         :param to_value: The persistence death limit to be added in the
-        numbers (persistent death > to_value).
+            numbers (persistent death > to_value).
         :type to_value: float.
 
         :returns: list of int -- The persistent Betti numbers ([B0, B1, ...,
-        Bn]).
+            Bn]).
+
+        :note: persistent_betti_numbers function requires persistence
+            function to be launched first.
         """
         return self.thisptr.get_persistent_betti_numbers(from_value, to_value)