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

41 files changed, 155 insertions, 69 deletions

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 @@
             </a></p>
           {%- endif %}
           {%- endblock %}
+            <h2><a href="index.html">GUDHI</a></h2>
+            <h2><a href="fileformats.html">File formats</a></h2>
+            <h2><a href="installation.html">GUDHI installation</a></h2>
+            <h2><a href="citation.html">Acknowledging the GUDHI library</a></h2>
+            <h2><a href="genindex.html">Index</a></h2>
+            <h2><a href="examples.html">Examples</a></h2>
           {%- 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 %}
-<h2><a href="index.html">GUDHI</a></h2>
-<h2><a href="fileformats.html">File formats</a></h2>
-<h2><a href="installation.html">GUDHI installation</a></h2>
-<h2><a href="citation.html">Acknowledging the GUDHI library</a></h2>
-<h2><a href="genindex.html">Index</a></h2>
-<h2><a href="examples.html">Examples</a></h2>
-
             {%- 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.rst b/src/cython/doc/alpha_complex_sum.inc
index 1680a712..1680a712 100644
--- a/src/cython/doc/alpha_complex_sum.rst
+++ b/src/cython/doc/alpha_complex_sum.inc
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 <simplex_tree_sum>` using
+Alpha_complex is constructing a :doc:`Simplex_tree <simplex_tree_ref>` using
 `Delaunay Triangulation  <http://doc.cgal.org/latest/Triangulation/index.html#Chapter_Triangulations>`_ 
 :cite:`cgal:hdj-t-15b` from `CGAL <http://www.cgal.org/>`_ (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.rst b/src/cython/doc/bottleneck_distance_sum.inc
index 030fad9e..030fad9e 100644
--- a/src/cython/doc/bottleneck_distance_sum.rst
+++ b/src/cython/doc/bottleneck_distance_sum.inc
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.rst b/src/cython/doc/cubical_complex_sum.inc
index 280ad0e0..280ad0e0 100644
--- a/src/cython/doc/cubical_complex_sum.rst
+++ b/src/cython/doc/cubical_complex_sum.inc
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.rst b/src/cython/doc/persistence_graphical_tools_sum.inc
index d602daa7..d602daa7 100644
--- a/src/cython/doc/persistence_graphical_tools_sum.rst
+++ b/src/cython/doc/persistence_graphical_tools_sum.inc
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.rst b/src/cython/doc/persistent_cohomology_sum.inc
index a26df1dc..a26df1dc 100644
--- a/src/cython/doc/persistent_cohomology_sum.rst
+++ b/src/cython/doc/persistent_cohomology_sum.inc
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.rst b/src/cython/doc/rips_complex_sum.inc
index 5616bfa9..5616bfa9 100644
--- a/src/cython/doc/rips_complex_sum.rst
+++ b/src/cython/doc/rips_complex_sum.inc
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.rst b/src/cython/doc/simplex_tree_sum.inc
index fb0e54c1..fb0e54c1 100644
--- a/src/cython/doc/simplex_tree_sum.rst
+++ b/src/cython/doc/simplex_tree_sum.inc
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.rst b/src/cython/doc/tangential_complex_sum.inc
index 72b4d7ba..72b4d7ba 100644
--- a/src/cython/doc/tangential_complex_sum.rst
+++ b/src/cython/doc/tangential_complex_sum.inc
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.rst b/src/cython/doc/witness_complex_sum.inc
index a8a126a0..a8a126a0 100644
--- a/src/cython/doc/witness_complex_sum.rst
+++ b/src/cython/doc/witness_complex_sum.inc
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",