Fix doc for user_version

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2650 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 18aebd67968fd48ccfcfcfbff75c614496f4424e

15 files changed, 52 insertions, 48 deletions

diff --git a/src/cython/doc/alpha_complex_sum.rst b/src/cython/doc/alpha_complex_sum.rst
index a5f6420a..1680a712 100644
--- a/src/cython/doc/alpha_complex_sum.rst
+++ b/src/cython/doc/alpha_complex_sum.rst
@@ -5,7 +5,7 @@
 
 +----------------------------------------------------------------+------------------------------------------------------------------------+
 | .. figure::                                                    | Alpha_complex is a simplicial complex constructed from the finite      |
-|      img/alpha_complex_representation.png                      | cells of a Delaunay Triangulation.                                     |
+|      ../../doc/Alpha_complex/alpha_complex_representation.png  | cells of a Delaunay Triangulation.                                     |
 |      :alt: Alpha complex representation                        |                                                                        |
 |      :figclass: align-center                                   | The filtration value of each simplex is computed as the square of the  |
 |                                                                | circumradius of the simplex if the circumsphere is empty (the simplex  |
diff --git a/src/cython/doc/alpha_complex_user.rst b/src/cython/doc/alpha_complex_user.rst
index e541e6d3..c3a13bef 100644
--- a/src/cython/doc/alpha_complex_user.rst
+++ b/src/cython/doc/alpha_complex_user.rst
@@ -75,7 +75,7 @@ In order to build the alpha complex, first, a Simplex tree is built from the cel
 (The filtration value is set to NaN, which stands for unknown value):
 
 .. figure::
-    img/alpha_complex_doc.png
+    ../../doc/Alpha_complex/alpha_complex_doc.png
     :figclass: align-center
     :alt: Simplex tree structure construction example
 
@@ -112,7 +112,7 @@ computes the filtration value of the triangle, and then propagates the filtratio
 here:
 
 .. figure::
-    img/alpha_complex_doc_420.png
+    ../../doc/Alpha_complex/alpha_complex_doc_420.png
     :figclass: align-center
     :alt: Filtration value propagation example
 
@@ -201,6 +201,6 @@ the program output is:
 CGAL citations
 ==============
 
-.. bibliography:: how_to_cite_cgal.bib
+.. bibliography:: ../../biblio/how_to_cite_cgal.bib
    :filter: docnames
    :style: unsrt
diff --git a/src/cython/doc/bottleneck_distance_sum.rst b/src/cython/doc/bottleneck_distance_sum.rst
index 5c475d0d..030fad9e 100644
--- a/src/cython/doc/bottleneck_distance_sum.rst
+++ b/src/cython/doc/bottleneck_distance_sum.rst
@@ -5,7 +5,7 @@
 
 +-----------------------------------------------------------------+----------------------------------------------------------------------+
 | .. figure::                                                     | Bottleneck distance measures the similarity between two persistence  |
-|      img/perturb_pd.png                                         | diagrams. It's the shortest distance b for which there exists a      |
+|      ../../doc/Bottleneck_distance/perturb_pd.png               | diagrams. It's the shortest distance b for which there exists a      |
 |      :figclass: align-center                                    | perfect matching between the points of the two diagrams (+ all the   |
 |                                                                 | diagonal points) such that any couple of matched points are at       |
 |      Bottleneck distance is the length of                       | distance at most b.                                                  |
diff --git a/src/cython/doc/cubical_complex_sum.rst b/src/cython/doc/cubical_complex_sum.rst
index 3ddf6375..280ad0e0 100644
--- a/src/cython/doc/cubical_complex_sum.rst
+++ b/src/cython/doc/cubical_complex_sum.rst
@@ -2,14 +2,14 @@
 :Author: Pawel Dlotko                                              :Introduced in: GUDHI 2.0.0          :Copyright: GPL v3
 =================================================================  ===================================  ===================================
 
-+-----------------------------------------------------------------+----------------------------------------------------------------------+
-| .. figure::                                                     | The cubical complex is an example of a structured complex useful in  |
-|      img/Cubical_complex_representation.png                     | computational mathematics (specially rigorous numerics) and image    |
-|      :alt: Cubical complex representation                       | analysis.                                                            |
-|      :figclass: align-center                                    |                                                                      |
-|                                                                 |                                                                      |
-|      Cubical complex representation                             |                                                                      |
-+-----------------------------------------------------------------+----------------------------------------------------------------------+
-| :doc:`cubical_complex_user`                                     | * :doc:`cubical_complex_ref`                                         |
-|                                                                 | * :doc:`periodic_cubical_complex_ref`                                |
-+-----------------------------------------------------------------+----------------------------------------------------------------------+
++--------------------------------------------------------------------------+----------------------------------------------------------------------+
+| .. figure::                                                              | The cubical complex is an example of a structured complex useful in  |
+|      ../../doc/Bitmap_cubical_complex/Cubical_complex_representation.png | computational mathematics (specially rigorous numerics) and image    |
+|      :alt: Cubical complex representation                                | analysis.                                                            |
+|      :figclass: align-center                                             |                                                                      |
+|                                                                          |                                                                      |
+|      Cubical complex representation                                      |                                                                      |
++--------------------------------------------------------------------------+----------------------------------------------------------------------+
+| :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
index 8c9a3ed6..36fa3ba9 100644
--- a/src/cython/doc/cubical_complex_user.rst
+++ b/src/cython/doc/cubical_complex_user.rst
@@ -157,6 +157,6 @@ End user programs are available in cython/example/ folder.
 Bibliography
 ============
 
-.. bibliography:: bibliography.bib
+.. bibliography:: ../../bibliography.bib
    :filter: docnames
    :style: unsrt
diff --git a/src/cython/doc/index.rst b/src/cython/doc/index.rst
index f6d10567..3945d72a 100644
--- a/src/cython/doc/index.rst
+++ b/src/cython/doc/index.rst
@@ -1,8 +1,10 @@
 GUDHI Python module documentation
 #################################
 
-.. image:: img/Gudhi_banner.png
-   :align: center
+.. figure::
+     ../../doc/common/Gudhi_banner.png
+     :alt: Gudhi banner
+     :figclass: align-center
 
 Introduction
 ************
@@ -81,6 +83,6 @@ Persistence graphical tools
 Bibliography
 ************
 
-.. bibliography:: bibliography.bib
+.. bibliography:: ../../biblio/bibliography.bib
    :filter: docnames
    :style: unsrt
diff --git a/src/cython/doc/persistent_cohomology_sum.rst b/src/cython/doc/persistent_cohomology_sum.rst
index d1f79cb4..a26df1dc 100644
--- a/src/cython/doc/persistent_cohomology_sum.rst
+++ b/src/cython/doc/persistent_cohomology_sum.rst
@@ -4,7 +4,7 @@
 
 +-----------------------------------------------------------------+-----------------------------------------------------------------------+
 | .. figure::                                                     | The theory of homology consists in attaching to a topological space   |
-|      img/3DTorus_poch.png                                       | a sequence of (homology) groups, capturing global topological         |
+|      ../../doc/Persistent_cohomology/3DTorus_poch.png           | a sequence of (homology) groups, capturing global topological         |
 |      :figclass: align-center                                    | features like connected components, holes, cavities, etc. Persistent  |
 |                                                                 | homology studies the evolution -- birth, life and death -- of these   |
 |      Rips Persistent Cohomology on a 3D                         | features when the topological space is changing. Consequently, the    |
diff --git a/src/cython/doc/persistent_cohomology_user.rst b/src/cython/doc/persistent_cohomology_user.rst
index 72f1a7f7..bf90c163 100644
--- a/src/cython/doc/persistent_cohomology_user.rst
+++ b/src/cython/doc/persistent_cohomology_user.rst
@@ -109,6 +109,6 @@ We provide several example files: run these examples with -h for details on thei
 Bibliography
 ============
 
-.. bibliography:: bibliography.bib
+.. bibliography:: ../../biblio/bibliography.bib
    :filter: docnames
    :style: unsrt
diff --git a/src/cython/doc/rips_complex_sum.rst b/src/cython/doc/rips_complex_sum.rst
index 2b65fc19..5616bfa9 100644
--- a/src/cython/doc/rips_complex_sum.rst
+++ b/src/cython/doc/rips_complex_sum.rst
@@ -4,7 +4,7 @@
 
 +----------------------------------------------------------------+------------------------------------------------------------------------+
 | .. figure::                                                    | Rips complex is a simplicial complex constructed from a one skeleton   |
-|      img/rips_complex_representation.png                       | graph.                                                                 |
+|      ../../doc/Rips_complex/rips_complex_representation.png    | graph.                                                                 |
 |      :figclass: align-center                                   |                                                                        |
 |                                                                | The filtration value of each edge is computed from a user-given        |
 |      Rips complex representation                               | distance function and is inserted until a user-given threshold         |
diff --git a/src/cython/doc/rips_complex_user.rst b/src/cython/doc/rips_complex_user.rst
index 6b48422b..96ba9944 100644
--- a/src/cython/doc/rips_complex_user.rst
+++ b/src/cython/doc/rips_complex_user.rst
@@ -26,7 +26,7 @@ structure, and then expands the simplicial complex when required.
 Vertex name correspond to the index of the point in the given range (aka. the point cloud).
 
 .. figure::
-    img/rips_complex_representation.png
+    ../../doc/Rips_complex/rips_complex_representation.png
     :align: center
 
     Rips-complex one skeleton graph representation
diff --git a/src/cython/doc/simplex_tree_sum.rst b/src/cython/doc/simplex_tree_sum.rst
index 3174fb62..fb0e54c1 100644
--- a/src/cython/doc/simplex_tree_sum.rst
+++ b/src/cython/doc/simplex_tree_sum.rst
@@ -4,7 +4,7 @@
 
 +----------------------------------------------------------------+------------------------------------------------------------------------+
 | .. figure::                                                    | The simplex tree is an efficient and flexible data structure for       |
-|      img/Simplex_tree_representation.png                       | representing general (filtered) simplicial complexes.                  |
+|      ../../doc/Simplex_tree/Simplex_tree_representation.png    | representing general (filtered) simplicial complexes.                  |
 |      :alt: Simplex tree representation                         |                                                                        |
 |      :figclass: align-center                                   | The data structure is described in                                     |
 |                                                                | :cite:`boissonnatmariasimplextreealgorithmica`                         |
diff --git a/src/cython/doc/tangential_complex_sum.rst b/src/cython/doc/tangential_complex_sum.rst
index 2b05bc10..72b4d7ba 100644
--- a/src/cython/doc/tangential_complex_sum.rst
+++ b/src/cython/doc/tangential_complex_sum.rst
@@ -5,10 +5,10 @@
 
 +----------------------------------------------------------------+------------------------------------------------------------------------+
 | .. figure::                                                    | A Tangential Delaunay complex is a simplicial complex designed to      |
-|      img/tc_examples.png                                       | reconstruct a :math:`k`-dimensional manifold embedded in :math:`d`-    |
+|      ../../doc/Tangential_complex/tc_examples.png              | reconstruct a :math:`k`-dimensional manifold embedded in :math:`d`-    |
 |      :figclass: align-center                                   | dimensional Euclidean space. The input is a point sample coming from   |
 |                                                                | an unknown manifold. The running time depends only linearly on the     |
-|      **Tangential complex representation**                     | extrinsic dimension :math:`d` and exponentially on the intrinsic       |
+|      Tangential complex representation                         | extrinsic dimension :math:`d` and exponentially on the intrinsic       |
 |                                                                | dimension :math:`k`.                                                   |
 +----------------------------------------------------------------+------------------------------------------------------------------------+
 | :doc:`tangential_complex_user`                                 | :doc:`tangential_complex_ref`                                          |
diff --git a/src/cython/doc/tangential_complex_user.rst b/src/cython/doc/tangential_complex_user.rst
index d670cfdb..efa6d7ce 100644
--- a/src/cython/doc/tangential_complex_user.rst
+++ b/src/cython/doc/tangential_complex_user.rst
@@ -22,7 +22,7 @@ Let us start with the description of the Tangential complex of a simple
 example, with :math:`k = 1` and :math:`d = 2`. The input data is 4 points
 :math:`P` located on a curve embedded in 2D.
 
-.. figure:: img/tc_example_01.png
+.. figure:: ../../doc/Tangential_complex/tc_example_01.png
     :alt: The input
     :figclass: align-center
 
@@ -31,7 +31,7 @@ example, with :math:`k = 1` and :math:`d = 2`. The input data is 4 points
 For each point :math:`p`, estimate its tangent subspace :math:`T_p` (e.g.
 using PCA). 
 
-.. figure:: img/tc_example_02.png
+.. figure:: ../../doc/Tangential_complex/tc_example_02.png
     :alt: The estimated normals
     :figclass: align-center
 
@@ -42,7 +42,7 @@ Let us add the Voronoi diagram of the points in orange. For each point
 :math:`p`, construct its star in the Delaunay triangulation of :math:`P`
 restricted to :math:`T_p`.
 
-.. figure:: img/tc_example_03.png
+.. figure:: ../../doc/Tangential_complex/tc_example_03.png
     :alt: The Voronoi diagram
     :figclass: align-center
 
@@ -62,7 +62,7 @@ simplex is not in the star of all its vertices.
 
 Let us take the same example.
 
-.. figure:: img/tc_example_07_before.png
+.. figure:: ../../doc/Tangential_complex/tc_example_07_before.png
     :alt: Before
     :figclass: align-center
 
@@ -70,7 +70,7 @@ Let us take the same example.
 
 Let us slightly move the tangent subspace :math:`T_q`
 
-.. figure:: img/tc_example_07_after.png
+.. figure:: ../../doc/Tangential_complex/tc_example_07_after.png
     :alt: After
     :figclass: align-center
 
@@ -79,7 +79,7 @@ Let us slightly move the tangent subspace :math:`T_q`
 Now, the star of :math:`Q` contains :math:`QP`, but the star of :math:`P` does
 not contain :math:`QP`. We have an inconsistency.
 
-.. figure:: img/tc_example_08.png
+.. figure:: ../../doc/Tangential_complex/tc_example_08.png
     :alt: After
     :figclass: align-center
 
@@ -191,6 +191,6 @@ The output is:
 Bibliography
 ============
 
-.. bibliography:: bibliography.bib
+.. bibliography:: ../../biblio/bibliography.bib
    :filter: docnames
    :style: unsrt
diff --git a/src/cython/doc/witness_complex_sum.rst b/src/cython/doc/witness_complex_sum.rst
index b65522ba..a8a126a0 100644
--- a/src/cython/doc/witness_complex_sum.rst
+++ b/src/cython/doc/witness_complex_sum.rst
@@ -3,15 +3,17 @@
 :Euclidean version requires: CGAL :math:`\geq` 4.6.0               Eigen3
 =================================================================  ===================================  ===================================
 
-+-----------------------------------------------------------------+----------------------------------------------------------------------+
-| .. 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`.                          |
-|                                                                 |                                                                      |
-|                                                                 | The data structure is described in                                   |
-|                                                                 | :cite:`boissonnatmariasimplextreealgorithmica`.                      |
-+-----------------------------------------------------------------+----------------------------------------------------------------------+
-| :doc:`witness_complex_user`                                     | * :doc:`witness_complex_ref`                                         |
-|                                                                 | * :doc:`strong_witness_complex_ref`                                  |
-|                                                                 | * :doc:`euclidean_witness_complex_ref`                               |
-|                                                                 | * :doc:`euclidean_strong_witness_complex_ref`                        |
-+-----------------------------------------------------------------+----------------------------------------------------------------------+
++-------------------------------------------------------------------+----------------------------------------------------------------------+
+| .. figure::                                                       | Witness complex :math:`Wit(W,L)` is a simplicial complex defined on  |
+|      ../../doc/Witness_complex/Witness_complex_representation.png | two sets of points in :math:`\mathbb{R}^D`.                          |
+|      :alt: Witness complex representation                         |                                                                      |
+|      :figclass: align-center                                      | The data structure is described in                                   |
+|                                                                   | :cite:`boissonnatmariasimplextreealgorithmica`.                      |
+|                                                                   |                                                                      |
+|      Witness complex representation                               |                                                                      |
++-------------------------------------------------------------------+----------------------------------------------------------------------+
+| :doc:`witness_complex_user`                                       | * :doc:`witness_complex_ref`                                         |
+|                                                                   | * :doc:`strong_witness_complex_ref`                                  |
+|                                                                   | * :doc:`euclidean_witness_complex_ref`                               |
+|                                                                   | * :doc:`euclidean_strong_witness_complex_ref`                        |
++-------------------------------------------------------------------+----------------------------------------------------------------------+
diff --git a/src/cython/doc/witness_complex_user.rst b/src/cython/doc/witness_complex_user.rst
index aa9cbb2c..29413269 100644
--- a/src/cython/doc/witness_complex_user.rst
+++ b/src/cython/doc/witness_complex_user.rst
@@ -33,7 +33,7 @@ Both definitions can be relaxed by a real value :math:`\alpha`:
 which leads to definitions of **weak relaxed witness complex** (or just relaxed witness complex for short) and
 **strong relaxed witness complex** respectively.
 
-.. figure:: img/swit.svg
+.. figure:: ../../doc/Witness_complex/swit.svg
     :alt: Strongly witnessed simplex
     :figclass: align-center
 
@@ -126,6 +126,6 @@ Here is an example of constructing a strong witness complex filtration and compu
 Bibliography
 ============
 
-.. bibliography:: bibliography.bib
+.. bibliography:: ../../biblio/bibliography.bib
    :filter: docnames
    :style: unsrt