From e64a8b5cfd08759b2e43804539db05f44c2615ad Mon Sep 17 00:00:00 2001
From: vrouvrea
Date: Wed, 6 Jun 2018 09:16:00 +0000
Subject: Fix sphinx warning and issues due to new version of sphinx Modify the
doc for persistence diagram
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/python_2.1.0_fix_vincent@3543 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: 3efbc052bce9a11a6b4a758f8229e91eece2a7f4
---
src/cython/doc/_templates/layout.html | 13 +++---
src/cython/doc/alpha_complex_ref.rst | 4 ++
src/cython/doc/alpha_complex_sum.inc | 22 +++++++++
src/cython/doc/alpha_complex_sum.rst | 22 ---------
src/cython/doc/alpha_complex_user.rst | 12 +++--
src/cython/doc/bottleneck_distance_sum.inc | 15 ++++++
src/cython/doc/bottleneck_distance_sum.rst | 15 ------
src/cython/doc/bottleneck_distance_user.rst | 6 ++-
src/cython/doc/citation.rst | 4 ++
src/cython/doc/conf.py | 3 +-
src/cython/doc/cubical_complex_ref.rst | 4 ++
src/cython/doc/cubical_complex_sum.inc | 15 ++++++
src/cython/doc/cubical_complex_sum.rst | 15 ------
src/cython/doc/cubical_complex_user.rst | 5 ++
.../doc/euclidean_strong_witness_complex_ref.rst | 4 ++
src/cython/doc/euclidean_witness_complex_ref.rst | 4 ++
src/cython/doc/examples.rst | 4 ++
src/cython/doc/fileformats.rst | 4 ++
src/cython/doc/index.rst | 18 ++++----
src/cython/doc/installation.rst | 4 ++
src/cython/doc/periodic_cubical_complex_ref.rst | 4 ++
src/cython/doc/persistence_graphical_tools_ref.rst | 4 ++
src/cython/doc/persistence_graphical_tools_sum.inc | 12 +++++
src/cython/doc/persistence_graphical_tools_sum.rst | 12 -----
.../doc/persistence_graphical_tools_user.rst | 53 ++++++++++++----------
src/cython/doc/persistent_cohomology_sum.inc | 27 +++++++++++
src/cython/doc/persistent_cohomology_sum.rst | 27 -----------
src/cython/doc/persistent_cohomology_user.rst | 4 ++
src/cython/doc/pyplots/barcode_persistence.py | 7 ---
src/cython/doc/pyplots/diagram_persistence.py | 9 ----
src/cython/doc/reader_utils_ref.rst | 4 ++
src/cython/doc/rips_complex_ref.rst | 4 ++
src/cython/doc/rips_complex_sum.inc | 17 +++++++
src/cython/doc/rips_complex_sum.rst | 17 -------
src/cython/doc/rips_complex_user.rst | 6 ++-
src/cython/doc/simplex_tree_ref.rst | 4 ++
src/cython/doc/simplex_tree_sum.inc | 14 ++++++
src/cython/doc/simplex_tree_sum.rst | 14 ------
src/cython/doc/simplex_tree_user.rst | 6 ++-
src/cython/doc/strong_witness_complex_ref.rst | 4 ++
src/cython/doc/tangential_complex_ref.rst | 4 ++
src/cython/doc/tangential_complex_sum.inc | 15 ++++++
src/cython/doc/tangential_complex_sum.rst | 15 ------
src/cython/doc/tangential_complex_user.rst | 6 ++-
src/cython/doc/todos.rst | 4 ++
src/cython/doc/witness_complex_ref.rst | 4 ++
src/cython/doc/witness_complex_sum.inc | 19 ++++++++
src/cython/doc/witness_complex_sum.rst | 19 --------
src/cython/doc/witness_complex_user.rst | 6 ++-
src/cython/setup.py.in | 2 -
50 files changed, 311 insertions(+), 225 deletions(-)
create mode 100644 src/cython/doc/alpha_complex_sum.inc
delete mode 100644 src/cython/doc/alpha_complex_sum.rst
create mode 100644 src/cython/doc/bottleneck_distance_sum.inc
delete mode 100644 src/cython/doc/bottleneck_distance_sum.rst
create mode 100644 src/cython/doc/cubical_complex_sum.inc
delete mode 100644 src/cython/doc/cubical_complex_sum.rst
create mode 100644 src/cython/doc/persistence_graphical_tools_sum.inc
delete mode 100644 src/cython/doc/persistence_graphical_tools_sum.rst
create mode 100644 src/cython/doc/persistent_cohomology_sum.inc
delete mode 100644 src/cython/doc/persistent_cohomology_sum.rst
delete mode 100755 src/cython/doc/pyplots/barcode_persistence.py
delete mode 100755 src/cython/doc/pyplots/diagram_persistence.py
create mode 100644 src/cython/doc/rips_complex_sum.inc
delete mode 100644 src/cython/doc/rips_complex_sum.rst
create mode 100644 src/cython/doc/simplex_tree_sum.inc
delete mode 100644 src/cython/doc/simplex_tree_sum.rst
create mode 100644 src/cython/doc/tangential_complex_sum.inc
delete mode 100644 src/cython/doc/tangential_complex_sum.rst
create mode 100644 src/cython/doc/witness_complex_sum.inc
delete mode 100644 src/cython/doc/witness_complex_sum.rst
(limited to 'src')
diff --git a/src/cython/doc/_templates/layout.html b/src/cython/doc/_templates/layout.html
index c9356116..797afb27 100644
--- a/src/cython/doc/_templates/layout.html
+++ b/src/cython/doc/_templates/layout.html
@@ -56,6 +56,12 @@
{%- endif %}
{%- endblock %}
+
+
+
+
+
+
{%- if sidebars != None %}
{#- new style sidebar: explicitly include/exclude templates #}
{%- for sidebartemplate in sidebars %}
@@ -64,13 +70,6 @@
{%- else %}
{#- old style sidebars: using blocks -- should be deprecated #}
{%- block sidebartoc %}
-
-
-
-
-
-
-
{%- include "localtoc.html" %}
{%- endblock %}
{%- block sidebarrel %}
diff --git a/src/cython/doc/alpha_complex_ref.rst b/src/cython/doc/alpha_complex_ref.rst
index 6a122b09..7da79543 100644
--- a/src/cython/doc/alpha_complex_ref.rst
+++ b/src/cython/doc/alpha_complex_ref.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
==============================
Alpha complex reference manual
==============================
diff --git a/src/cython/doc/alpha_complex_sum.inc b/src/cython/doc/alpha_complex_sum.inc
new file mode 100644
index 00000000..1680a712
--- /dev/null
+++ b/src/cython/doc/alpha_complex_sum.inc
@@ -0,0 +1,22 @@
+================================================================= =================================== ===================================
+:Author: Vincent Rouvreau :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3
+:Requires: CGAL :math:`\geq` 4.7.0 Eigen3
+================================================================= =================================== ===================================
+
++----------------------------------------------------------------+------------------------------------------------------------------------+
+| .. figure:: | Alpha_complex is a simplicial complex constructed from the finite |
+| ../../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 |
+| Alpha complex representation | 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 performance). |
++----------------------------------------------------------------+------------------------------------------------------------------------+
+| :doc:`alpha_complex_user` | :doc:`alpha_complex_ref` |
++----------------------------------------------------------------+------------------------------------------------------------------------+
diff --git a/src/cython/doc/alpha_complex_sum.rst b/src/cython/doc/alpha_complex_sum.rst
deleted file mode 100644
index 1680a712..00000000
--- a/src/cython/doc/alpha_complex_sum.rst
+++ /dev/null
@@ -1,22 +0,0 @@
-================================================================= =================================== ===================================
-:Author: Vincent Rouvreau :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3
-:Requires: CGAL :math:`\geq` 4.7.0 Eigen3
-================================================================= =================================== ===================================
-
-+----------------------------------------------------------------+------------------------------------------------------------------------+
-| .. figure:: | Alpha_complex is a simplicial complex constructed from the finite |
-| ../../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 |
-| Alpha complex representation | 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 performance). |
-+----------------------------------------------------------------+------------------------------------------------------------------------+
-| :doc:`alpha_complex_user` | :doc:`alpha_complex_ref` |
-+----------------------------------------------------------------+------------------------------------------------------------------------+
diff --git a/src/cython/doc/alpha_complex_user.rst b/src/cython/doc/alpha_complex_user.rst
index db7edd6f..d1e9c7cd 100644
--- a/src/cython/doc/alpha_complex_user.rst
+++ b/src/cython/doc/alpha_complex_user.rst
@@ -1,11 +1,15 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
Alpha complex user manual
=========================
Definition
----------
-.. include:: alpha_complex_sum.rst
+.. include:: alpha_complex_sum.inc
-Alpha_complex is constructing a :doc:`Simplex_tree ` using
+Alpha_complex is constructing a :doc:`Simplex_tree ` using
`Delaunay Triangulation `_
:cite:`cgal:hdj-t-15b` from `CGAL `_ (the Computational Geometry Algorithms Library
:cite:`cgal:eb-15b`).
@@ -99,9 +103,9 @@ Filtration value computation algorithm
**end for**
**end for**
**end for**
-
+
make_filtration_non_decreasing()
-
+
prune_above_filtration()
Dimension 2
diff --git a/src/cython/doc/bottleneck_distance_sum.inc b/src/cython/doc/bottleneck_distance_sum.inc
new file mode 100644
index 00000000..030fad9e
--- /dev/null
+++ b/src/cython/doc/bottleneck_distance_sum.inc
@@ -0,0 +1,15 @@
+================================================================= =================================== ===================================
+:Author: François Godi :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3
+:Requires: CGAL :math:`\geq` 4.8.0
+================================================================= =================================== ===================================
+
++-----------------------------------------------------------------+----------------------------------------------------------------------+
+| .. figure:: | Bottleneck distance measures the similarity between two persistence |
+| ../../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. |
+| the longest edge | |
++-----------------------------------------------------------------+----------------------------------------------------------------------+
+| :doc:`bottleneck_distance_user` | |
++-----------------------------------------------------------------+----------------------------------------------------------------------+
diff --git a/src/cython/doc/bottleneck_distance_sum.rst b/src/cython/doc/bottleneck_distance_sum.rst
deleted file mode 100644
index 030fad9e..00000000
--- a/src/cython/doc/bottleneck_distance_sum.rst
+++ /dev/null
@@ -1,15 +0,0 @@
-================================================================= =================================== ===================================
-:Author: François Godi :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3
-:Requires: CGAL :math:`\geq` 4.8.0
-================================================================= =================================== ===================================
-
-+-----------------------------------------------------------------+----------------------------------------------------------------------+
-| .. figure:: | Bottleneck distance measures the similarity between two persistence |
-| ../../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. |
-| the longest edge | |
-+-----------------------------------------------------------------+----------------------------------------------------------------------+
-| :doc:`bottleneck_distance_user` | |
-+-----------------------------------------------------------------+----------------------------------------------------------------------+
diff --git a/src/cython/doc/bottleneck_distance_user.rst b/src/cython/doc/bottleneck_distance_user.rst
index 7692dce2..605db022 100644
--- a/src/cython/doc/bottleneck_distance_user.rst
+++ b/src/cython/doc/bottleneck_distance_user.rst
@@ -1,9 +1,13 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
Bottleneck distance user manual
===============================
Definition
----------
-.. include:: bottleneck_distance_sum.rst
+.. include:: bottleneck_distance_sum.inc
Function
--------
diff --git a/src/cython/doc/citation.rst b/src/cython/doc/citation.rst
index f4fdf83b..117eb9dd 100644
--- a/src/cython/doc/citation.rst
+++ b/src/cython/doc/citation.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
Acknowledging the GUDHI library
###############################
diff --git a/src/cython/doc/conf.py b/src/cython/doc/conf.py
index a13c9751..4a54d4fd 100755
--- a/src/cython/doc/conf.py
+++ b/src/cython/doc/conf.py
@@ -85,7 +85,7 @@ version = gudhi.__version__
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
-exclude_patterns = ['_build']
+exclude_patterns = ['_build', '*.inc']
# The reST default role (used for this markup: `text`) to use for all
# documents.
@@ -125,6 +125,7 @@ html_theme_options = {
"sidebarbgcolor": "#A1ADCD",
"sidebartextcolor": "black",
"sidebarlinkcolor": "#334D5C",
+ "body_max_width": "1200px",
}
# Add any paths that contain custom themes here, relative to this directory.
diff --git a/src/cython/doc/cubical_complex_ref.rst b/src/cython/doc/cubical_complex_ref.rst
index 84aa4223..1fe9d5fb 100644
--- a/src/cython/doc/cubical_complex_ref.rst
+++ b/src/cython/doc/cubical_complex_ref.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
Cubical complex reference manual
################################
diff --git a/src/cython/doc/cubical_complex_sum.inc b/src/cython/doc/cubical_complex_sum.inc
new file mode 100644
index 00000000..280ad0e0
--- /dev/null
+++ b/src/cython/doc/cubical_complex_sum.inc
@@ -0,0 +1,15 @@
+================================================================= =================================== ===================================
+: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 |
+| ../../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_sum.rst b/src/cython/doc/cubical_complex_sum.rst
deleted file mode 100644
index 280ad0e0..00000000
--- a/src/cython/doc/cubical_complex_sum.rst
+++ /dev/null
@@ -1,15 +0,0 @@
-================================================================= =================================== ===================================
-: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 |
-| ../../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 dd82ad93..320bd79b 100644
--- a/src/cython/doc/cubical_complex_user.rst
+++ b/src/cython/doc/cubical_complex_user.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
Cubical complex user manual
===========================
Definition
@@ -144,6 +148,7 @@ the program output is:
.. testoutput::
Periodic cubical complex is of dimension 2 - 42 simplices.
+
Examples.
---------
diff --git a/src/cython/doc/euclidean_strong_witness_complex_ref.rst b/src/cython/doc/euclidean_strong_witness_complex_ref.rst
index bebf0f9a..1a602cd5 100644
--- a/src/cython/doc/euclidean_strong_witness_complex_ref.rst
+++ b/src/cython/doc/euclidean_strong_witness_complex_ref.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
=================================================
Euclidean strong witness complex reference manual
=================================================
diff --git a/src/cython/doc/euclidean_witness_complex_ref.rst b/src/cython/doc/euclidean_witness_complex_ref.rst
index 29b8806f..28daf965 100644
--- a/src/cython/doc/euclidean_witness_complex_ref.rst
+++ b/src/cython/doc/euclidean_witness_complex_ref.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
==========================================
Euclidean witness complex reference manual
==========================================
diff --git a/src/cython/doc/examples.rst b/src/cython/doc/examples.rst
index 1e596e18..d42f5a92 100644
--- a/src/cython/doc/examples.rst
+++ b/src/cython/doc/examples.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
Examples
########
diff --git a/src/cython/doc/fileformats.rst b/src/cython/doc/fileformats.rst
index 4f0b6f6d..ff20f26e 100644
--- a/src/cython/doc/fileformats.rst
+++ b/src/cython/doc/fileformats.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
File formats
############
diff --git a/src/cython/doc/index.rst b/src/cython/doc/index.rst
index 3945d72a..4e444fb0 100644
--- a/src/cython/doc/index.rst
+++ b/src/cython/doc/index.rst
@@ -34,32 +34,32 @@ Data structures
Alpha complex
=============
-.. include:: alpha_complex_sum.rst
+.. include:: alpha_complex_sum.inc
Cubical complex
===============
-.. include:: cubical_complex_sum.rst
+.. include:: cubical_complex_sum.inc
Rips complex
============
-.. include:: rips_complex_sum.rst
+.. include:: rips_complex_sum.inc
Simplex tree
============
-.. include:: simplex_tree_sum.rst
+.. include:: simplex_tree_sum.inc
Tangential complex
==================
-.. include:: tangential_complex_sum.rst
+.. include:: tangential_complex_sum.inc
Witness complex
===============
-.. include:: witness_complex_sum.rst
+.. include:: witness_complex_sum.inc
Toolbox
@@ -68,17 +68,17 @@ Toolbox
Bottleneck distance
===================
-.. include:: bottleneck_distance_sum.rst
+.. include:: bottleneck_distance_sum.inc
Persistence cohomology
======================
-.. include:: persistent_cohomology_sum.rst
+.. include:: persistent_cohomology_sum.inc
Persistence graphical tools
===========================
-.. include:: persistence_graphical_tools_sum.rst
+.. include:: persistence_graphical_tools_sum.inc
Bibliography
************
diff --git a/src/cython/doc/installation.rst b/src/cython/doc/installation.rst
index b0bc5f38..43ff85c5 100644
--- a/src/cython/doc/installation.rst
+++ b/src/cython/doc/installation.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
Installation
############
diff --git a/src/cython/doc/periodic_cubical_complex_ref.rst b/src/cython/doc/periodic_cubical_complex_ref.rst
index c6190a1b..4b831647 100644
--- a/src/cython/doc/periodic_cubical_complex_ref.rst
+++ b/src/cython/doc/periodic_cubical_complex_ref.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
Periodic cubical complex reference manual
#########################################
diff --git a/src/cython/doc/persistence_graphical_tools_ref.rst b/src/cython/doc/persistence_graphical_tools_ref.rst
index a69c8ba2..a2c6bcef 100644
--- a/src/cython/doc/persistence_graphical_tools_ref.rst
+++ b/src/cython/doc/persistence_graphical_tools_ref.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
============================================
Persistence graphical tools reference manual
============================================
diff --git a/src/cython/doc/persistence_graphical_tools_sum.inc b/src/cython/doc/persistence_graphical_tools_sum.inc
new file mode 100644
index 00000000..d602daa7
--- /dev/null
+++ b/src/cython/doc/persistence_graphical_tools_sum.inc
@@ -0,0 +1,12 @@
+================================================================= =================================== ===================================
+:Author: Vincent Rouvreau :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3
+:Requires: Matplotlib Numpy
+================================================================= =================================== ===================================
+
++-----------------------------------------------------------------+-----------------------------------------------------------------------+
+| .. figure:: | These graphical tools comes on top of persistence results and allows |
+| img/graphical_tools_representation.png | the user to build easily barcode and persistence diagram. |
+| | |
++-----------------------------------------------------------------+-----------------------------------------------------------------------+
+| :doc:`persistence_graphical_tools_user` | :doc:`persistence_graphical_tools_ref` |
++-----------------------------------------------------------------+-----------------------------------------------------------------------+
diff --git a/src/cython/doc/persistence_graphical_tools_sum.rst b/src/cython/doc/persistence_graphical_tools_sum.rst
deleted file mode 100644
index d602daa7..00000000
--- a/src/cython/doc/persistence_graphical_tools_sum.rst
+++ /dev/null
@@ -1,12 +0,0 @@
-================================================================= =================================== ===================================
-:Author: Vincent Rouvreau :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3
-:Requires: Matplotlib Numpy
-================================================================= =================================== ===================================
-
-+-----------------------------------------------------------------+-----------------------------------------------------------------------+
-| .. figure:: | These graphical tools comes on top of persistence results and allows |
-| img/graphical_tools_representation.png | the user to build easily barcode and persistence diagram. |
-| | |
-+-----------------------------------------------------------------+-----------------------------------------------------------------------+
-| :doc:`persistence_graphical_tools_user` | :doc:`persistence_graphical_tools_ref` |
-+-----------------------------------------------------------------+-----------------------------------------------------------------------+
diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst
index 46f871c7..292915eb 100644
--- a/src/cython/doc/persistence_graphical_tools_user.rst
+++ b/src/cython/doc/persistence_graphical_tools_user.rst
@@ -1,8 +1,12 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
Persistence graphical tools user manual
=======================================
Definition
----------
-.. include:: persistence_graphical_tools_sum.rst
+.. include:: persistence_graphical_tools_sum.inc
Show persistence as a barcode
@@ -10,22 +14,13 @@ Show persistence as a barcode
This function can display the persistence result as a barcode:
-.. testcode::
-
- import gudhi
-
- periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \
- '/data/bitmap/3d_torus.txt')
- diag = periodic_cc.persistence()
- plt = gudhi.plot_persistence_barcode(diag)
- plt.show()
-
.. plot::
+ :include-source:
import gudhi
- periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \
- '/data/bitmap/3d_torus.txt')
+ perseus_file = gudhi.__root_source_dir__ + '/data/bitmap/3d_torus.txt'
+ periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=perseus_file)
diag = periodic_cc.persistence()
print("diag = ", diag)
plt = gudhi.plot_persistence_barcode(diag)
@@ -36,24 +31,32 @@ Show persistence as a diagram
This function can display the persistence result as a diagram:
-.. testcode::
+.. plot::
+ :include-source:
import gudhi
-
- point_cloud = gudhi.read_off(off_file=gudhi.__root_source_dir__ + '/data/points/tore3D_1307.off')
- rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.3)
- simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
- diag = simplex_tree.persistence()
- plt = gudhi.plot_persistence_diagram(diag)
+
+ # rips_on_tore3D_1307.pers obtained from write_persistence_diagram method
+ persistence_file=gudhi.__root_source_dir__ + \
+ '/data/persistence_diagram/rips_on_tore3D_1307.pers'
+ plt = gudhi.plot_persistence_diagram(persistence_file=persistence_file,
+ legend=True)
plt.show()
+If you want more information on a specific dimension, for instance:
+
.. plot::
+ :include-source:
import gudhi
- point_cloud = gudhi.read_off(off_file=gudhi.__root_source_dir__ + '/data/points/tore3D_1307.off')
- rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.3)
- simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
- diag = simplex_tree.persistence()
- plt = gudhi.plot_persistence_diagram(diag)
+ persistence_file=gudhi.__root_source_dir__ + \
+ '/data/persistence_diagram/rips_on_tore3D_1307.pers'
+ diag = \
+ gudhi.read_persistence_intervals_grouped_by_dimension(persistence_file=\
+ persistence_file)
+ dim = 1
+ # Display all points with some transparency
+ plt = gudhi.plot_persistence_diagram([(dim,interval) for interval in diag[dim]],
+ max_plots=0, alpha=0.1)
plt.show()
diff --git a/src/cython/doc/persistent_cohomology_sum.inc b/src/cython/doc/persistent_cohomology_sum.inc
new file mode 100644
index 00000000..a26df1dc
--- /dev/null
+++ b/src/cython/doc/persistent_cohomology_sum.inc
@@ -0,0 +1,27 @@
+================================================================= =================================== ===================================
+:Author: Clément Maria :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3
+================================================================= =================================== ===================================
+
++-----------------------------------------------------------------+-----------------------------------------------------------------------+
+| .. figure:: | The theory of homology consists in attaching to a topological space |
+| ../../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 |
+| Torus | theory is essentially composed of three elements: topological spaces, |
+| | their homology groups and an evolution scheme. |
+| | |
+| | Computation of persistent cohomology using the algorithm of |
+| | :cite:`DBLP:journals/dcg/SilvaMV11` and |
+| | :cite:`DBLP:journals/corr/abs-1208-5018` and the Compressed |
+| | Annotation Matrix implementation of |
+| | :cite:`DBLP:conf/esa/BoissonnatDM13`. |
+| | |
++-----------------------------------------------------------------+-----------------------------------------------------------------------+
+| :doc:`persistent_cohomology_user` | Please refer to each data structure that contains persistence |
+| | feature for reference: |
+| | |
+| | * :doc:`simplex_tree_ref` |
+| | * :doc:`cubical_complex_ref` |
+| | * :doc:`periodic_cubical_complex_ref` |
++-----------------------------------------------------------------+-----------------------------------------------------------------------+
diff --git a/src/cython/doc/persistent_cohomology_sum.rst b/src/cython/doc/persistent_cohomology_sum.rst
deleted file mode 100644
index a26df1dc..00000000
--- a/src/cython/doc/persistent_cohomology_sum.rst
+++ /dev/null
@@ -1,27 +0,0 @@
-================================================================= =================================== ===================================
-:Author: Clément Maria :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3
-================================================================= =================================== ===================================
-
-+-----------------------------------------------------------------+-----------------------------------------------------------------------+
-| .. figure:: | The theory of homology consists in attaching to a topological space |
-| ../../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 |
-| Torus | theory is essentially composed of three elements: topological spaces, |
-| | their homology groups and an evolution scheme. |
-| | |
-| | Computation of persistent cohomology using the algorithm of |
-| | :cite:`DBLP:journals/dcg/SilvaMV11` and |
-| | :cite:`DBLP:journals/corr/abs-1208-5018` and the Compressed |
-| | Annotation Matrix implementation of |
-| | :cite:`DBLP:conf/esa/BoissonnatDM13`. |
-| | |
-+-----------------------------------------------------------------+-----------------------------------------------------------------------+
-| :doc:`persistent_cohomology_user` | Please refer to each data structure that contains persistence |
-| | feature for reference: |
-| | |
-| | * :doc:`simplex_tree_ref` |
-| | * :doc:`cubical_complex_ref` |
-| | * :doc:`periodic_cubical_complex_ref` |
-+-----------------------------------------------------------------+-----------------------------------------------------------------------+
diff --git a/src/cython/doc/persistent_cohomology_user.rst b/src/cython/doc/persistent_cohomology_user.rst
index bf90c163..ce7fc685 100644
--- a/src/cython/doc/persistent_cohomology_user.rst
+++ b/src/cython/doc/persistent_cohomology_user.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
Persistent cohomology user manual
=================================
Definition
diff --git a/src/cython/doc/pyplots/barcode_persistence.py b/src/cython/doc/pyplots/barcode_persistence.py
deleted file mode 100755
index de33d506..00000000
--- a/src/cython/doc/pyplots/barcode_persistence.py
+++ /dev/null
@@ -1,7 +0,0 @@
-import gudhi
-
-periodic_cc = gudhi.PeriodicCubicalComplex(perseus_file=gudhi.__root_source_dir__ + \
- '/data/bitmap/3d_torus.txt')
-diag = periodic_cc.persistence()
-plt = gudhi.plot_persistence_barcode(diag)
-plt.show()
diff --git a/src/cython/doc/pyplots/diagram_persistence.py b/src/cython/doc/pyplots/diagram_persistence.py
deleted file mode 100755
index 3bab0ca1..00000000
--- a/src/cython/doc/pyplots/diagram_persistence.py
+++ /dev/null
@@ -1,9 +0,0 @@
-import gudhi
-
-point_cloud = gudhi.read_off(off_file=gudhi.__root_source_dir__ + \
- '/data/points/tore3D_1307.off')
-rips_complex = gudhi.RipsComplex(points=point_cloud, max_edge_length=0.3)
-simplex_tree = rips_complex.create_simplex_tree(max_dimension=3)
-diag = simplex_tree.persistence()
-plt = gudhi.plot_persistence_diagram(diag)
-plt.show()
diff --git a/src/cython/doc/reader_utils_ref.rst b/src/cython/doc/reader_utils_ref.rst
index 9c1ea6fc..f3ecebad 100644
--- a/src/cython/doc/reader_utils_ref.rst
+++ b/src/cython/doc/reader_utils_ref.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
=============================
Reader utils reference manual
=============================
diff --git a/src/cython/doc/rips_complex_ref.rst b/src/cython/doc/rips_complex_ref.rst
index b17dc4e0..22b5616c 100644
--- a/src/cython/doc/rips_complex_ref.rst
+++ b/src/cython/doc/rips_complex_ref.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
=============================
Rips complex reference manual
=============================
diff --git a/src/cython/doc/rips_complex_sum.inc b/src/cython/doc/rips_complex_sum.inc
new file mode 100644
index 00000000..5616bfa9
--- /dev/null
+++ b/src/cython/doc/rips_complex_sum.inc
@@ -0,0 +1,17 @@
+================================================================= =================================== ===================================
+:Author: Clément Maria, Pawel Dlotko, Vincent Rouvreau :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3
+================================================================= =================================== ===================================
+
++----------------------------------------------------------------+------------------------------------------------------------------------+
+| .. figure:: | Rips complex is a simplicial complex constructed from a one skeleton |
+| ../../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 |
+| | value. |
+| | |
+| | This complex can be built from a point cloud and a distance function, |
+| | or from a distance matrix. |
++----------------------------------------------------------------+------------------------------------------------------------------------+
+| :doc:`rips_complex_user` | :doc:`rips_complex_ref` |
++----------------------------------------------------------------+------------------------------------------------------------------------+
diff --git a/src/cython/doc/rips_complex_sum.rst b/src/cython/doc/rips_complex_sum.rst
deleted file mode 100644
index 5616bfa9..00000000
--- a/src/cython/doc/rips_complex_sum.rst
+++ /dev/null
@@ -1,17 +0,0 @@
-================================================================= =================================== ===================================
-:Author: Clément Maria, Pawel Dlotko, Vincent Rouvreau :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3
-================================================================= =================================== ===================================
-
-+----------------------------------------------------------------+------------------------------------------------------------------------+
-| .. figure:: | Rips complex is a simplicial complex constructed from a one skeleton |
-| ../../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 |
-| | value. |
-| | |
-| | This complex can be built from a point cloud and a distance function, |
-| | or from a distance matrix. |
-+----------------------------------------------------------------+------------------------------------------------------------------------+
-| :doc:`rips_complex_user` | :doc:`rips_complex_ref` |
-+----------------------------------------------------------------+------------------------------------------------------------------------+
diff --git a/src/cython/doc/rips_complex_user.rst b/src/cython/doc/rips_complex_user.rst
index 7738aef0..a8c06cf9 100644
--- a/src/cython/doc/rips_complex_user.rst
+++ b/src/cython/doc/rips_complex_user.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
Rips complex user manual
=========================
Definition
@@ -243,7 +247,7 @@ the program output is:
[3, 6] -> 11.00
Correlation matrix
----------------
+------------------
Example from a correlation matrix
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
diff --git a/src/cython/doc/simplex_tree_ref.rst b/src/cython/doc/simplex_tree_ref.rst
index 6d196843..9eb8c199 100644
--- a/src/cython/doc/simplex_tree_ref.rst
+++ b/src/cython/doc/simplex_tree_ref.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
=============================
Simplex tree reference manual
=============================
diff --git a/src/cython/doc/simplex_tree_sum.inc b/src/cython/doc/simplex_tree_sum.inc
new file mode 100644
index 00000000..fb0e54c1
--- /dev/null
+++ b/src/cython/doc/simplex_tree_sum.inc
@@ -0,0 +1,14 @@
+================================================================= =================================== ===================================
+:Author: Clément Maria :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3
+================================================================= =================================== ===================================
+
++----------------------------------------------------------------+------------------------------------------------------------------------+
+| .. figure:: | The simplex tree is an efficient and flexible data structure for |
+| ../../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` |
+| Simplex tree representation | |
++----------------------------------------------------------------+------------------------------------------------------------------------+
+| :doc:`simplex_tree_user` | :doc:`simplex_tree_ref` |
++----------------------------------------------------------------+------------------------------------------------------------------------+
diff --git a/src/cython/doc/simplex_tree_sum.rst b/src/cython/doc/simplex_tree_sum.rst
deleted file mode 100644
index fb0e54c1..00000000
--- a/src/cython/doc/simplex_tree_sum.rst
+++ /dev/null
@@ -1,14 +0,0 @@
-================================================================= =================================== ===================================
-:Author: Clément Maria :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3
-================================================================= =================================== ===================================
-
-+----------------------------------------------------------------+------------------------------------------------------------------------+
-| .. figure:: | The simplex tree is an efficient and flexible data structure for |
-| ../../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` |
-| Simplex tree representation | |
-+----------------------------------------------------------------+------------------------------------------------------------------------+
-| :doc:`simplex_tree_user` | :doc:`simplex_tree_ref` |
-+----------------------------------------------------------------+------------------------------------------------------------------------+
diff --git a/src/cython/doc/simplex_tree_user.rst b/src/cython/doc/simplex_tree_user.rst
index 4b1dde19..aebeb29f 100644
--- a/src/cython/doc/simplex_tree_user.rst
+++ b/src/cython/doc/simplex_tree_user.rst
@@ -1,9 +1,13 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
Simplex tree user manual
========================
Definition
----------
-.. include:: simplex_tree_sum.rst
+.. include:: simplex_tree_sum.inc
A simplicial complex :math:`\mathbf{K}` on a set of vertices :math:`V = \{1, \cdots ,|V|\}` is a collection of
simplices :math:`\{\sigma\}`, :math:`\sigma \subseteq V` such that
diff --git a/src/cython/doc/strong_witness_complex_ref.rst b/src/cython/doc/strong_witness_complex_ref.rst
index 4ed4fe46..d624d711 100644
--- a/src/cython/doc/strong_witness_complex_ref.rst
+++ b/src/cython/doc/strong_witness_complex_ref.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
=======================================
Strong witness complex reference manual
=======================================
diff --git a/src/cython/doc/tangential_complex_ref.rst b/src/cython/doc/tangential_complex_ref.rst
index 35589475..cdfda082 100644
--- a/src/cython/doc/tangential_complex_ref.rst
+++ b/src/cython/doc/tangential_complex_ref.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
===================================
Tangential complex reference manual
===================================
diff --git a/src/cython/doc/tangential_complex_sum.inc b/src/cython/doc/tangential_complex_sum.inc
new file mode 100644
index 00000000..72b4d7ba
--- /dev/null
+++ b/src/cython/doc/tangential_complex_sum.inc
@@ -0,0 +1,15 @@
+================================================================= =================================== ===================================
+:Author: Clément Jamin :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3
+:Requires: CGAL :math:`\geq` 4.8.0 Eigen3
+================================================================= =================================== ===================================
+
++----------------------------------------------------------------+------------------------------------------------------------------------+
+| .. figure:: | A Tangential Delaunay complex is a simplicial complex designed to |
+| ../../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 |
+| | dimension :math:`k`. |
++----------------------------------------------------------------+------------------------------------------------------------------------+
+| :doc:`tangential_complex_user` | :doc:`tangential_complex_ref` |
++----------------------------------------------------------------+------------------------------------------------------------------------+
diff --git a/src/cython/doc/tangential_complex_sum.rst b/src/cython/doc/tangential_complex_sum.rst
deleted file mode 100644
index 72b4d7ba..00000000
--- a/src/cython/doc/tangential_complex_sum.rst
+++ /dev/null
@@ -1,15 +0,0 @@
-================================================================= =================================== ===================================
-:Author: Clément Jamin :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3
-:Requires: CGAL :math:`\geq` 4.8.0 Eigen3
-================================================================= =================================== ===================================
-
-+----------------------------------------------------------------+------------------------------------------------------------------------+
-| .. figure:: | A Tangential Delaunay complex is a simplicial complex designed to |
-| ../../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 |
-| | 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 fafb3193..5ce69e86 100644
--- a/src/cython/doc/tangential_complex_user.rst
+++ b/src/cython/doc/tangential_complex_user.rst
@@ -1,6 +1,10 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
Tangential complex user manual
==============================
-.. include:: tangential_complex_sum.rst
+.. include:: tangential_complex_sum.inc
Definition
----------
diff --git a/src/cython/doc/todos.rst b/src/cython/doc/todos.rst
index 78972a4c..ca274ced 100644
--- a/src/cython/doc/todos.rst
+++ b/src/cython/doc/todos.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
==========
To be done
==========
diff --git a/src/cython/doc/witness_complex_ref.rst b/src/cython/doc/witness_complex_ref.rst
index c78760cb..9987d3fd 100644
--- a/src/cython/doc/witness_complex_ref.rst
+++ b/src/cython/doc/witness_complex_ref.rst
@@ -1,3 +1,7 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
================================
Witness complex reference manual
================================
diff --git a/src/cython/doc/witness_complex_sum.inc b/src/cython/doc/witness_complex_sum.inc
new file mode 100644
index 00000000..a8a126a0
--- /dev/null
+++ b/src/cython/doc/witness_complex_sum.inc
@@ -0,0 +1,19 @@
+================================================================= =================================== ===================================
+:Author: Siargey Kachanovich :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3
+:Euclidean version requires: CGAL :math:`\geq` 4.6.0 Eigen3
+================================================================= =================================== ===================================
+
++-------------------------------------------------------------------+----------------------------------------------------------------------+
+| .. 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_sum.rst b/src/cython/doc/witness_complex_sum.rst
deleted file mode 100644
index a8a126a0..00000000
--- a/src/cython/doc/witness_complex_sum.rst
+++ /dev/null
@@ -1,19 +0,0 @@
-================================================================= =================================== ===================================
-:Author: Siargey Kachanovich :Introduced in: GUDHI 2.0.0 :Copyright: GPL v3
-:Euclidean version requires: CGAL :math:`\geq` 4.6.0 Eigen3
-================================================================= =================================== ===================================
-
-+-------------------------------------------------------------------+----------------------------------------------------------------------+
-| .. 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 99be5185..40e94134 100644
--- a/src/cython/doc/witness_complex_user.rst
+++ b/src/cython/doc/witness_complex_user.rst
@@ -1,7 +1,11 @@
+:orphan:
+
+.. To get rid of WARNING: document isn't included in any toctree
+
Witness complex user manual
===========================
-.. include:: witness_complex_sum.rst
+.. include:: witness_complex_sum.inc
Definitions
-----------
diff --git a/src/cython/setup.py.in b/src/cython/setup.py.in
index a798717d..ee381a1b 100644
--- a/src/cython/setup.py.in
+++ b/src/cython/setup.py.in
@@ -46,8 +46,6 @@ setup(
version='@GUDHI_VERSION@',
url='http://gudhi.gforge.inria.fr/',
ext_modules = cythonize(gudhi),
-
- #install_requires = required,
install_requires = [
"matplotlib",
"numpy",
--
cgit v1.2.3