Last sphinx modifications

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@1380 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 7c7315dcf3fb211451948b67ceba499b6b7e98ca

9 files changed, 125 insertions, 35 deletions

diff --git a/src/cython/doc/source/alpha_complex_ref.rst b/src/cython/doc/source/alpha_complex_ref.rst
new file mode 100644
index 00000000..ab81eee0
--- /dev/null
+++ b/src/cython/doc/source/alpha_complex_ref.rst
@@ -0,0 +1,9 @@
+Alpha complex reference manual
+##############################
+
+.. autoclass:: gudhi.AlphaComplex
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+   .. automethod:: gudhi.AlphaComplex.__init__
diff --git a/src/cython/doc/source/alpha_complex_user.rst b/src/cython/doc/source/alpha_complex_user.rst
new file mode 100644
index 00000000..3b445d13
--- /dev/null
+++ b/src/cython/doc/source/alpha_complex_user.rst
@@ -0,0 +1,8 @@
+Alpha complex user manual
+#########################
+
+blablabla
+
+.. image:: img/alpha_complex_representation.png
+   :align: center
+
diff --git a/src/cython/doc/source/cubical_complex_ref.rst b/src/cython/doc/source/cubical_complex_ref.rst
new file mode 100644
index 00000000..84aa4223
--- /dev/null
+++ b/src/cython/doc/source/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/source/cubical_complex_user.rst b/src/cython/doc/source/cubical_complex_user.rst
new file mode 100644
index 00000000..7ade4b86
--- /dev/null
+++ b/src/cython/doc/source/cubical_complex_user.rst
@@ -0,0 +1,8 @@
+Cubical complex user manual
+###########################
+
+blablabla
+
+.. image:: img/Cubical_complex_representation.png
+   :align: center
+
diff --git a/src/cython/doc/source/index.rst b/src/cython/doc/source/index.rst
index 7dfea239..d08b465c 100644
--- a/src/cython/doc/source/index.rst
+++ b/src/cython/doc/source/index.rst
@@ -38,27 +38,68 @@ 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).
+=====================================  =====================================  =====================================
+: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`                                             |
++-------------------------------------------+----------------------------------------------------------------------+
+
+Cubical complex
+===============
+
+=====================================  =====================================  =====================================
+: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`                                           |
++---------------------------------------------+----------------------------------------------------------------------+
+
+Simplex tree
+============
+
+=====================================  =====================================  =====================================
+:Author: Clément Maria                 :Introduced in: GUDHI PYTHON 1.4.0     :Copyright: GPL v3
+=====================================  =====================================  =====================================
+
+Witness complex
+===============
+
+=====================================  =====================================  =====================================
+:Author: Siargey Kachanovich           :Introduced in: GUDHI PYTHON 1.4.0     :Copyright: GPL v3
+=====================================  =====================================  =====================================
+
+
+Toolbox
+*******
+
+Persistence cohomology
+======================
+
+=====================================  =====================================  =====================================
+:Author: Clément Maria                 :Introduced in: GUDHI PYTHON 1.4.0     :Copyright: GPL v3
+=====================================  =====================================  =====================================
 
-* :ref:`alphacomplex`
 
 
-.. automodule:: gudhi
-   :members:
-   :undoc-members:
-   :show-inheritance:
 
diff --git a/src/cython/src/cpp/Alpha_complex_interface.h b/src/cython/src/cpp/Alpha_complex_interface.h
index c745543a..ee5ab823 100644
--- a/src/cython/src/cpp/Alpha_complex_interface.h
+++ b/src/cython/src/cpp/Alpha_complex_interface.h
@@ -32,7 +32,7 @@
 
 namespace Gudhi {
 
-namespace alphacomplex {
+namespace alpha_complex {
 
 class Alpha_complex_interface : public Alpha_complex< CGAL::Epick_d< CGAL::Dynamic_dimension_tag > > {
   using Alpha_complex = Alpha_complex< CGAL::Epick_d< CGAL::Dynamic_dimension_tag > > ;
@@ -129,7 +129,7 @@ class Alpha_complex_interface : public Alpha_complex< CGAL::Epick_d< CGAL::Dynam
 
 };
 
-}  // namespace alphacomplex
+}  // namespace alpha_complex
 
 } // namespace Gudhi
 
diff --git a/src/cython/src/cpp/Cubical_complex_interface.h b/src/cython/src/cpp/Cubical_complex_interface.h
index f054fbbd..5d17ff6b 100644
--- a/src/cython/src/cpp/Cubical_complex_interface.h
+++ b/src/cython/src/cpp/Cubical_complex_interface.h
@@ -33,7 +33,7 @@
 
 namespace Gudhi {
 
-namespace Cubical_complex {
+namespace cubical_complex {
 
 template<typename CubicalComplexOptions = Bitmap_cubical_complex_base<double>>
 class Cubical_complex_interface : public Bitmap_cubical_complex<CubicalComplexOptions> {
@@ -50,7 +50,7 @@ class Cubical_complex_interface : public Bitmap_cubical_complex<CubicalComplexOp
 
 };
 
-}  // namespace Cubical_complex
+}  // namespace cubical_complex
 
 }  // namespace Gudhi
 
diff --git a/src/cython/src/cython/alpha_complex.pyx b/src/cython/src/cython/alpha_complex.pyx
index f36de661..33fc06ef 100644
--- a/src/cython/src/cython/alpha_complex.pyx
+++ b/src/cython/src/cython/alpha_complex.pyx
@@ -81,13 +81,18 @@ cdef class AlphaComplex:
 
     cdef Alpha_complex_persistence_interface * pcohptr
 
-    def __cinit__(self, points=[], max_alpha_square=float('inf')):
+    # Fake constructor that does nothing but documenting the constructor
+    def __init__(self, points=[], max_alpha_square=float('inf')):
         """AlphaComplex constructor.
 
-        Args:
-           points (list): A list of points in d-Dimension.
-           max_alpha_square (float): Maximum Alpha square value.
+        :param points: A list of points in d-Dimension.
+        :type points: list of list of double
+        :param max_alpha_square: Maximum Alpha square value.
+        :type max_alpha_square: double
         """
+
+    # The real cython constructor
+    def __cinit__(self, points=[], max_alpha_square=float('inf')):
         self.thisptr = new Alpha_complex_interface(points,
                                                    max_alpha_square)
 
@@ -119,7 +124,7 @@ cdef class AlphaComplex:
         given N-simplex.
 
         :param simplex: The N-simplex, represented by a list of vertex.
-        :type simplex: list of int.
+        :type simplex: list of int
         :returns:  float -- the simplicial complex filtration value.
         """
         return self.thisptr.simplex_filtration(simplex)
diff --git a/src/cython/src/cython/cubical_complex.pyx b/src/cython/src/cython/cubical_complex.pyx
index 52137520..fe286dc6 100644
--- a/src/cython/src/cython/cubical_complex.pyx
+++ b/src/cython/src/cython/cubical_complex.pyx
@@ -53,16 +53,26 @@ cdef class CubicalComplex:
 
     cdef Cubical_complex_persistence_interface * pcohptr
 
-    def __cinit__(self, dimensions=None, top_dimensional_cells=None,
+    # Fake constructor that does nothing but documenting the constructor
+    def __init__(self, dimensions=None, top_dimensional_cells=None,
                   perseus_file=''):
         """CubicalComplex constructor from dimensions and
         top_dimensional_cells or from a perseus file style name.
 
-        Args:
-           dimensions (list): A list of number of top dimensional cells.
-           top_dimensional_cells (list): A list of top dimensional cells.
-           perseus_file (string): A perseus file style name.
-         """
+        :param dimensions: A list of number of top dimensional cells.
+        :type dimensions: list of int
+        :param top_dimensional_cells: A list of top dimensional cells.
+        :type top_dimensional_cells: list of double
+
+        Or
+
+        :param perseus_file: A perseus file style name.
+        :type perseus_file: string
+        """
+
+    # The real cython constructor
+    def __cinit__(self, dimensions=None, top_dimensional_cells=None,
+                  perseus_file=''):
         if ((dimensions is not None) or (top_dimensional_cells is not None) and
              (perseus_file is not '')):
             print("CubicalComplex can be constructed from dimensions and "