Doc update

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2051 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 718698efa6fdb133b51923c449d97cd2365f75ae

6 files changed, 196 insertions, 15 deletions

diff --git a/src/cython/doc/_templates/layout.html b/src/cython/doc/_templates/layout.html
new file mode 100644
index 00000000..809df09e
--- /dev/null
+++ b/src/cython/doc/_templates/layout.html
@@ -0,0 +1,42 @@
+{#
+    This file is part of the Gudhi Library. The Gudhi library
+    (Geometric Understanding in Higher Dimensions) is a generic C++
+    library for computational topology.
+
+    Author(s):       Vincent Rouvreau
+
+    Copyright (C) 2016 INRIA
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#}
+
+{% extends "!layout.html" %}
+
+{#
+    Redefine empties relbar1 and relbar2 to have no relbar
+#}
+{% block relbar1 %}{% endblock %}
+{% block relbar2 %}{% endblock %}
+
+{#
+    Add specific links in the sidebar
+#}
+{% block sidebartoc %}
+<h2><a href="index.html">GUDHI</a></h2>
+<h2><a href="installation.html">GUDHI installation</a></h2>
+<h2><a href="citation.html">Acknowledging the GUDHI library</a></h2>
+<h2><a href="genindex.html">Index</a></h2>
+<h2><a href="examples.html">Examples</a></h2>
+    {{ super() }}
+{% endblock %}
diff --git a/src/cython/doc/citation.rst b/src/cython/doc/citation.rst
new file mode 100644
index 00000000..6cdfb7cc
--- /dev/null
+++ b/src/cython/doc/citation.rst
@@ -0,0 +1,15 @@
+Acknowledging the GUDHI library
+###############################
+
+We kindly ask users to cite the GUDHI library as appropriately as possible in
+their papers, and to mention the use of the GUDHI library on the web pages of
+their projects using GUDHI and provide us with links to these web pages. Feel
+free to contact us in case you have any question or remark on this topic.
+
+We provide GUDHI bibtex entries for the modules of the User and Reference
+Manual, as well as for publications directly related to the GUDHI library.
+
+GUDHI bibtex
+************
+
+.. literalinclude:: how_to_cite_gudhi.bib
diff --git a/src/cython/doc/conf.py b/src/cython/doc/conf.py
index 680377b3..04e65e67 100755
--- a/src/cython/doc/conf.py
+++ b/src/cython/doc/conf.py
@@ -60,16 +60,16 @@ master_doc = 'index'
 
 # General information about the project.
 project = u'GUDHI'
-copyright = u'2016, Vincent Rouvreau'
+copyright = u'2016, GUDHI Editorial Board'
 
 # 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 = '1.4.beta'
+version = '2.0'
 # The full version, including alpha/beta/rc tags.
-release = '1.4.beta'
+release = '2.0.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -133,12 +133,12 @@ html_theme = 'bizstyle'
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-#html_logo = None
+#html_logo =
 
 # 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
+#html_favicon =
 
 # 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,
@@ -163,7 +163,7 @@ html_static_path = ['_static']
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
-#html_additional_pages = {}
+#html_additional_pages = {'installation': 'installation.html'}
 
 # If false, no module index is generated.
 #html_domain_indices = True
diff --git a/src/cython/doc/examples.rst b/src/cython/doc/examples.rst
new file mode 100644
index 00000000..32b173c3
--- /dev/null
+++ b/src/cython/doc/examples.rst
@@ -0,0 +1,4 @@
+Examples
+########
+
+
diff --git a/src/cython/doc/index.rst b/src/cython/doc/index.rst
index 236ef3a4..26580880 100644
--- a/src/cython/doc/index.rst
+++ b/src/cython/doc/index.rst
@@ -1,10 +1,5 @@
-.. 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
-#####################
+GUDHI documentation
+###################
 
 .. image:: img/Gudhi_banner.png
    :align: center
@@ -13,8 +8,10 @@ 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>`_).
+open source `C++ library <http://gudhi.gforge.inria.fr/doc/latest/>`_, with a
+`cython interface <http://gudhi.gforge.inria.fr/cython/latest/>`_, 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
diff --git a/src/cython/doc/installation.rst b/src/cython/doc/installation.rst
new file mode 100644
index 00000000..4359c744
--- /dev/null
+++ b/src/cython/doc/installation.rst
@@ -0,0 +1,123 @@
+Installation
+############
+
+Compiling
+*********
+
+The library uses c++11 and requires `Boost <http://www.boost.org/>`_ with version
+1.48.0 or more recent. It is a multi-platform library and compiles on Linux,
+Mac OSX and Visual Studio 2015.
+It also requires cmake to generate makefiles, and cython to compile the
+library.
+
+Demos and examples
+==================
+
+To build the demos and examples, run the following commands in a terminal:
+
+.. code-block:: bash
+
+    cd /path-to-gudhi/
+    mkdir build
+    cd build/
+    cmake ..
+    make cython
+
+A list of examples is available here.
+
+Test suites
+===========
+
+To test your build, `py.test <http://doc.pytest.org>`_ is required. Run the
+following command in a terminal:
+
+.. code-block:: bash
+
+    cd /path-to-gudhi/build/src/cython
+    # For windows, you have to set PYTHONPATH environment variable
+    export PYTHONPATH='$PYTHONPATH:/path-to-gudhi/build/src/cython'
+    py.test
+
+Documentation
+=============
+
+To build the documentation, `sphinx-doc <http://http://www.sphinx-doc.org>`_ is
+required. Run the following commands in a terminal:
+
+.. code-block:: bash
+
+    make sphynx
+
+Optional third-party library
+****************************
+
+CGAL
+====
+
+The :doc:`Alpha complex </alpha_complex_user>` data structure and
+:doc:`Tangential complex </tangential_complex_user>` data structures,
+:doc:`Bottleneck distance </bottleneck_distance_user>`requires CGAL, which is a
+C++ library which provides easy access to efficient and reliable geometric
+algorithms.
+
+Having CGAL version 4.7.0 or higher installed is recommended. The procedure to
+install this library according to your operating system is detailed
+`here <http://doc.cgal.org/latest/Manual/installation.html>`_.
+
+The following examples require the Computational Geometry Algorithms Library:
+
+* alpha_complex_diagram_persistence_from_off_file_example.py
+* alpha_complex_from_points_example.py
+
+The following example requires CGAL version ≥ 4.8.0:
+
+* bottleneck_basic_example.py
+* tangential_complex_plain_homology_from_off_file_example.py
+
+Eigen3
+======
+
+The :doc:`Alpha complex </alpha_complex_user>` and
+:doc:`Tangential complex </tangential_complex_user>` data structures and few
+examples requires `Eigen3 <http://eigen.tuxfamily.org/>`_, a C++ template
+library for linear algebra: matrices, vectors, numerical solvers, and related
+algorithms.
+
+The following examples require the `Eigen3 <http://eigen.tuxfamily.org/>`_:
+
+* alpha_complex_diagram_persistence_from_off_file_example.py
+* alpha_complex_from_points_example.py
+* tangential_complex_plain_homology_from_off_file_example.py
+
+Matplotlib
+==========
+
+The :doc:`persistence graphical tools </persistence_graphical_tools_user>`
+module requires `Matplotlib <http://matplotlib.org>`_, a Python 2D plotting
+library which produces publication quality figures in a variety of hardcopy
+formats and interactive environments across platforms.
+
+The following examples require the `Matplotlib <http://matplotlib.org>`_:
+
+* alpha_complex_diagram_persistence_from_off_file_example.py
+* gudhi_graphical_tools_example.py
+* periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py
+* rips_complex_diagram_persistence_with_pandas_interface_example.py
+* rips_persistence_diagram.py
+* tangential_complex_plain_homology_from_off_file_example.py
+
+Numpy
+=====
+
+The :doc:`persistence graphical tools </persistence_graphical_tools_user>`
+module requires `NumPy <http://numpy.org>`_, a fundamental package for
+scientific computing with Python.
+
+The following examples require the `NumPy <http://numpy.org>`_:
+
+* alpha_complex_diagram_persistence_from_off_file_example.py
+* gudhi_graphical_tools_example.py
+* periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py
+* rips_complex_diagram_persistence_with_pandas_interface_example.py
+* rips_persistence_diagram.py
+* tangential_complex_plain_homology_from_off_file_example.py