Fix doc for C++ and Python.

Fix some warnings on Nerve GIC sphinx doc generation


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cubical_complex_small_fix@4101 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 57eacb8c4108be212e61796c65e3b45bb9c13644

6 files changed, 36 insertions, 13 deletions

diff --git a/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h b/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h
index e1e5885e..5fa02a5e 100644
--- a/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h
+++ b/src/Bitmap_cubical_complex/doc/Gudhi_Cubical_Complex_doc.h
@@ -87,15 +87,16 @@ namespace cubical_complex {
  *
  * \section inputformat Input Format
  *
- * In the current implantation, filtration is given at the maximal cubes, and it is then extended by the lower star
+ * In the current implementation, filtration is given at the maximal cubes, and it is then extended by the lower star
  * filtration to all cubes. There are a number of constructors that can be used to construct cubical complex by users
  * who want to use the code directly. They can be found in the \a Bitmap_cubical_complex class.
  * Currently one input from a text file is used. It uses a format inspired from the Perseus software
- * (http://www.sas.upenn.edu/~vnanda/perseus/) by Vidit Nanda. Note however an important difference: while Perseus
- * assume the filtration of all maximal cubes to be non-negative, over here we do not enforce this and we allow any
- * filtration values.
- * As a consequence one cannot use -1's to indicate missing cubes. If you have missing cubes in your complex, please
- * set their filtration to +Inf. The file format is described in details in here: \ref FileFormatsPerseus.
+ * (http://www.sas.upenn.edu/~vnanda/perseus/) by Vidit Nanda.
+ * \note While Perseus assume the filtration of all maximal cubes to be non-negative, over here we do not enforce this
+ * and we allow any filtration values. As a consequence one cannot use `-1`'s to indicate missing cubes. If you have
+ * missing cubes in your complex, please set their filtration to \f$+\infty\f$ (aka. `inf` in the file).
+ *
+ * The file format is described in details in \ref FileFormatsPerseus file format section.
  *
  * \section PeriodicBoundaryConditions Periodic boundary conditions
  * Often one would like to impose periodic boundary conditions to the cubical complex. Let \f$ I_1\times ... \times
diff --git a/src/common/doc/file_formats.h b/src/common/doc/file_formats.h
index d38d90e0..23214e25 100644
--- a/src/common/doc/file_formats.h
+++ b/src/common/doc/file_formats.h
@@ -72,7 +72,7 @@ namespace Gudhi {
 
  \section FileFormatsPerseus Perseus
 
- This file format is the format used by the Perseus software
+ This file format is a format inspired from the Perseus software
  (http://www.sas.upenn.edu/~vnanda/perseus/) by Vidit Nanda.
  The first line contains a number d begin the dimension of the
  bitmap (2 in the example below). Next d lines are the numbers of top dimensional cubes in each dimensions (3 and 3
@@ -119,9 +119,9 @@ namespace Gudhi {
 
  Other sample files can be found in the `data/bitmap` folder.
  
- Please note that unlike in Perseus format the filtration on the maximal cubes can be any double precision number.
- Consequently one cannot mark the cubes that are not present with -1's. To do that please set their filtration value to
- +Inf.
+ \note Unlike in Perseus format the filtration on the maximal cubes can be any double precision number.
+ Consequently one cannot mark the cubes that are not present with `-1`'s. To do that please set their filtration value
+ to \f$+\infty\f$ (aka. `inf` in the file).
 
 */
 }  // namespace Gudhi
diff --git a/src/cython/doc/cubical_complex_user.rst b/src/cython/doc/cubical_complex_user.rst
index 320bd79b..19120360 100644
--- a/src/cython/doc/cubical_complex_user.rst
+++ b/src/cython/doc/cubical_complex_user.rst
@@ -83,9 +83,15 @@ Input Format.
 In the current implantation, filtration is given at the maximal cubes, and it is then extended by the lower star
 filtration to all cubes. There are a number of constructors that can be used to construct cubical complex by users
 who want to use the code directly. They can be found in the :doc:`cubical_complex_ref`.
-Currently one input from a text file is used. It uses a format used already in
+Currently one input from a text file is used. It uses a format inspired from the Perseus software
 `Perseus software <http://www.sas.upenn.edu/~vnanda/perseus/>`_ by Vidit Nanda.
-The file format is described here: :doc:`Perseus <fileformats>`.
+
+.. note::
+    While Perseus assume the filtration of all maximal cubes to be non-negative, over here we do not enforce this and
+    we allow any filtration values. As a consequence one cannot use ``-1``'s to indicate missing cubes. If you have
+    missing cubes in your complex, please set their filtration to :math:`+\infty` (aka. ``inf`` in the file).
+
+The file format is described in details in :ref:`Perseus file format` file format section.
 
 .. testcode::
 
diff --git a/src/cython/doc/fileformats.rst b/src/cython/doc/fileformats.rst
index ff20f26e..e205cc8b 100644
--- a/src/cython/doc/fileformats.rst
+++ b/src/cython/doc/fileformats.rst
@@ -51,10 +51,12 @@ Here is a simple sample file in the 3D case::
     1. 1. 1.
 
 
+.. _Perseus file format:
+
 Perseus
 *******
 
-This file format is the format used by the
+This file format is a format inspired from the
 `Perseus software <http://www.sas.upenn.edu/~vnanda/perseus/>`_ by Vidit Nanda.
 The first line contains a number d begin the dimension of the bitmap (2 in the
 example below). Next d lines are the numbers of top dimensional cubes in each
@@ -88,3 +90,9 @@ Indicate that we have imposed periodic boundary conditions in the direction x,
 but not in the direction y.
 
 Other sample files can be found in the `data/bitmap` folder.
+
+.. note::
+    Unlike in Perseus format the filtration on the maximal cubes can be any
+    double precision number. Consequently one cannot mark the cubes that are
+    not present with ``-1``'s. To do that please set their filtration value to
+    :math:`+\infty` (aka. ``inf`` in the file).
\ No newline at end of file
diff --git a/src/cython/doc/nerve_gic_complex_ref.rst b/src/cython/doc/nerve_gic_complex_ref.rst
index e24e01fc..abde2e8c 100644
--- a/src/cython/doc/nerve_gic_complex_ref.rst
+++ b/src/cython/doc/nerve_gic_complex_ref.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
 ================================
 Cover complexes reference manual
 ================================
diff --git a/src/cython/doc/nerve_gic_complex_user.rst b/src/cython/doc/nerve_gic_complex_user.rst
index d774827e..44f30e1a 100644
--- a/src/cython/doc/nerve_gic_complex_user.rst
+++ b/src/cython/doc/nerve_gic_complex_user.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
 Cover complexes user manual
 ===========================
 Definition