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-rw-r--r--src/cython/CMakeLists.txt6
-rw-r--r--src/cython/doc/_templates/layout.html4
-rw-r--r--src/cython/doc/alpha_complex_sum.rst2
-rw-r--r--src/cython/doc/alpha_complex_user.rst104
-rw-r--r--src/cython/doc/bottleneck_distance_user.rst7
-rw-r--r--src/cython/doc/cubical_complex_user.rst3
-rw-r--r--src/cython/doc/index.rst19
-rw-r--r--src/cython/doc/installation.rst4
-rw-r--r--src/cython/doc/persistence_graphical_tools_user.rst1
-rw-r--r--src/cython/doc/persistent_cohomology_user.rst3
-rw-r--r--src/cython/doc/rips_complex_user.rst157
-rw-r--r--src/cython/doc/simplex_tree_user.rst1
-rw-r--r--src/cython/doc/tangential_complex_user.rst36
-rw-r--r--src/cython/doc/witness_complex_user.rst6
-rwxr-xr-xsrc/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py45
15 files changed, 192 insertions, 206 deletions
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 51c208aa..96c2acb3 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -1,8 +1,8 @@
cmake_minimum_required(VERSION 2.8)
project(Cython)
-if(CYTHON_PATH)
- message("${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_PATH} - py.test is ${PYTEST_PATH} - Sphinx is ${SPHINX_PATH}")
+if(CYTHON_FOUND)
+ message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_EXECUTABLE} - py.test is ${PYTEST_PATH} - Sphinx is ${SPHINX_PATH}")
set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_RESULT_OF_USE_DECLTYPE', ")
set(GUDHI_CYTHON_EXTRA_COMPILE_ARGS "${GUDHI_CYTHON_EXTRA_COMPILE_ARGS}'-DBOOST_ALL_NO_LIB', ")
@@ -281,4 +281,4 @@ if(CYTHON_PATH)
COMMAND make.bat html doctest)
endif (UNIX)
endif(SPHINX_PATH)
-endif(CYTHON_PATH)
+endif(CYTHON_FOUND)
diff --git a/src/cython/doc/_templates/layout.html b/src/cython/doc/_templates/layout.html
index af0eef64..b11c1236 100644
--- a/src/cython/doc/_templates/layout.html
+++ b/src/cython/doc/_templates/layout.html
@@ -205,8 +205,8 @@
<ul class="dropdown">
<li><a href="http://gudhi.gforge.inria.fr/doc/latest/">C++ documentation</a></li>
<li><a href="http://gudhi.gforge.inria.fr/doc/latest/installation.html">C++ installation manual</a></li>
- <li><a href="http://gudhi.gforge.inria.fr/cython/latest/">Cython documentation</a></li>
- <li><a href="http://gudhi.gforge.inria.fr/cython/latest/installation.html">Cython installation manual</a></li>
+ <li><a href="http://gudhi.gforge.inria.fr/python/latest/">Python documentation</a></li>
+ <li><a href="http://gudhi.gforge.inria.fr/python/latest/installation.html">Python installation manual</a></li>
</ul>
</li>
<li class="divider"></li>
diff --git a/src/cython/doc/alpha_complex_sum.rst b/src/cython/doc/alpha_complex_sum.rst
index 8437e901..a5f6420a 100644
--- a/src/cython/doc/alpha_complex_sum.rst
+++ b/src/cython/doc/alpha_complex_sum.rst
@@ -16,7 +16,7 @@
| | complex. |
| | |
| | This package requires having CGAL version 4.7 or higher (4.8.1 is |
-| | advised for better perfomances). |
+| | 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 2356944d..e8268ef1 100644
--- a/src/cython/doc/alpha_complex_user.rst
+++ b/src/cython/doc/alpha_complex_user.rst
@@ -1,4 +1,3 @@
-=========================
Alpha complex user manual
=========================
Definition
@@ -30,39 +29,40 @@ This example builds the Delaunay triangulation from the given points, and initia
repr(simplex_tree.num_simplices()) + ' simplices - ' + \
repr(simplex_tree.num_vertices()) + ' vertices.'
print(result_str)
+ fmt = '%s -> %.2f'
for filtered_value in simplex_tree.get_filtration():
- print(filtered_value)
+ print(fmt % tuple(filtered_value))
The output is:
.. testoutput::
Alpha complex is of dimension 2 - 25 simplices - 7 vertices.
- ([0], 0.0)
- ([1], 0.0)
- ([2], 0.0)
- ([3], 0.0)
- ([4], 0.0)
- ([5], 0.0)
- ([6], 0.0)
- ([2, 3], 6.25)
- ([4, 5], 7.25)
- ([0, 2], 8.5)
- ([0, 1], 9.25)
- ([1, 3], 10.0)
- ([1, 2], 11.25)
- ([1, 2, 3], 12.5)
- ([0, 1, 2], 12.995867768595042)
- ([5, 6], 13.25)
- ([2, 4], 20.0)
- ([4, 6], 22.736686390532547)
- ([4, 5, 6], 22.736686390532547)
- ([3, 6], 30.25)
- ([2, 6], 36.5)
- ([2, 3, 6], 36.5)
- ([2, 4, 6], 37.24489795918368)
- ([0, 4], 59.710743801652896)
- ([0, 2, 4], 59.710743801652896)
+ [0] -> 0.00
+ [1] -> 0.00
+ [2] -> 0.00
+ [3] -> 0.00
+ [4] -> 0.00
+ [5] -> 0.00
+ [6] -> 0.00
+ [2, 3] -> 6.25
+ [4, 5] -> 7.25
+ [0, 2] -> 8.50
+ [0, 1] -> 9.25
+ [1, 3] -> 10.00
+ [1, 2] -> 11.25
+ [1, 2, 3] -> 12.50
+ [0, 1, 2] -> 13.00
+ [5, 6] -> 13.25
+ [2, 4] -> 20.00
+ [4, 6] -> 22.74
+ [4, 5, 6] -> 22.74
+ [3, 6] -> 30.25
+ [2, 6] -> 36.50
+ [2, 3, 6] -> 36.50
+ [2, 4, 6] -> 37.24
+ [0, 4] -> 59.71
+ [0, 2, 4] -> 59.71
Algorithm
@@ -164,39 +164,39 @@ Then, it is asked to display information about the alpha complex:
repr(simplex_tree.num_simplices()) + ' simplices - ' + \
repr(simplex_tree.num_vertices()) + ' vertices.'
print(result_str)
+ fmt = '%s -> %.2f'
for filtered_value in simplex_tree.get_filtration():
- print(filtered_value)
+ print(fmt % tuple(filtered_value))
the program output is:
.. testoutput::
Alpha complex is of dimension 2 - 23 simplices - 7 vertices.
- ([0], 0.0)
- ([1], 0.0)
- ([2], 0.0)
- ([3], 0.0)
- ([4], 0.0)
- ([5], 0.0)
- ([6], 0.0)
- ([2, 3], 6.25)
- ([4, 5], 7.25)
- ([0, 2], 8.5)
- ([0, 1], 9.25)
- ([1, 3], 10.0)
- ([1, 2], 11.25)
- ([1, 2, 3], 12.5)
- ([0, 1, 2], 12.995867768595042)
- ([5, 6], 13.25)
- ([2, 4], 20.0)
- ([4, 6], 22.736686390532547)
- ([4, 5, 6], 22.736686390532547)
- ([3, 6], 30.25)
- ([2, 6], 36.5)
- ([2, 3, 6], 36.5)
- ([2, 4, 6], 37.24489795918368)
+ [0] -> 0.00
+ [1] -> 0.00
+ [2] -> 0.00
+ [3] -> 0.00
+ [4] -> 0.00
+ [5] -> 0.00
+ [6] -> 0.00
+ [2, 3] -> 6.25
+ [4, 5] -> 7.25
+ [0, 2] -> 8.50
+ [0, 1] -> 9.25
+ [1, 3] -> 10.00
+ [1, 2] -> 11.25
+ [1, 2, 3] -> 12.50
+ [0, 1, 2] -> 13.00
+ [5, 6] -> 13.25
+ [2, 4] -> 20.00
+ [4, 6] -> 22.74
+ [4, 5, 6] -> 22.74
+ [3, 6] -> 30.25
+ [2, 6] -> 36.50
+ [2, 3, 6] -> 36.50
+ [2, 4, 6] -> 37.24
-==============
CGAL citations
==============
diff --git a/src/cython/doc/bottleneck_distance_user.rst b/src/cython/doc/bottleneck_distance_user.rst
index 8c29d069..0066992f 100644
--- a/src/cython/doc/bottleneck_distance_user.rst
+++ b/src/cython/doc/bottleneck_distance_user.rst
@@ -1,4 +1,3 @@
-===============================
Bottleneck distance user manual
===============================
Definition
@@ -23,15 +22,15 @@ This example computes the bottleneck distance from 2 persistence diagrams:
diag1 = [[2.7, 3.7],[9.6, 14.],[34.2, 34.974], [3.,float('Inf')]]
diag2 = [[2.8, 4.45],[9.5, 14.1],[3.2,float('Inf')]]
- message = "Bottleneck distance approximation=" + repr(gudhi.bottleneck_distance(diag1, diag2, 0.1))
+ message = "Bottleneck distance approximation=" + '%.2f' % gudhi.bottleneck_distance(diag1, diag2, 0.1)
print(message)
- message = "Bottleneck distance exact value=" + repr(gudhi.bottleneck_distance(diag1, diag2, 0))
+ message = "Bottleneck distance exact value=" + '%.2f' % gudhi.bottleneck_distance(diag1, diag2, 0)
print(message)
The output is:
.. testoutput::
- Bottleneck distance approximation=0.8081763781405569
+ Bottleneck distance approximation=0.81
Bottleneck distance exact value=0.75
diff --git a/src/cython/doc/cubical_complex_user.rst b/src/cython/doc/cubical_complex_user.rst
index 692acdd9..344b9554 100644
--- a/src/cython/doc/cubical_complex_user.rst
+++ b/src/cython/doc/cubical_complex_user.rst
@@ -1,4 +1,3 @@
-===========================
Cubical complex user manual
===========================
Definition
@@ -154,7 +153,7 @@ Examples.
End user programs are available in cython/example/ folder.
Bibliography
-************
+============
.. bibliography:: bibliography.bib
:filter: docnames
diff --git a/src/cython/doc/index.rst b/src/cython/doc/index.rst
index fca63d65..f6d10567 100644
--- a/src/cython/doc/index.rst
+++ b/src/cython/doc/index.rst
@@ -1,5 +1,5 @@
-GUDHI documentation
-###################
+GUDHI Python module documentation
+#################################
.. image:: img/Gudhi_banner.png
:align: center
@@ -7,9 +7,9 @@ GUDHI documentation
Introduction
************
-The Gudhi library (Geometry Understanding in Higher Dimensions) is a generic
-open source `C++ library <http://gudhi.gforge.inria.fr/doc/latest/>`_, with a
-`Cython interface <http://gudhi.gforge.inria.fr/cython/latest/>`_, for
+The Python interface for the Gudhi library (Geometry Understanding in Higher
+Dimensions) is a generic open source
+`Python module <http://gudhi.gforge.inria.fr/python/latest/>`_, for
Computational Topology and Topological Data Analysis
(`TDA <https://en.wikipedia.org/wiki/Topological_data_analysis>`_).
The GUDHI library intends to help the development of new algorithmic solutions
@@ -20,12 +20,11 @@ data structures.
The current release of the GUDHI library includes:
* Data structures to represent, construct and manipulate simplicial complexes.
-* Algorithms to compute persistent homology and multi-field persistent homology.
-* Simplication of simplicial complexes by edge contraction.
+* Simplification of simplicial complexes by edge contraction.
+* Algorithms to compute persistent homology and bottleneck distance.
-All data-structures are generic and several of their aspects can be
-parameterized via template classes. We refer to :cite:`gudhilibrary_ICMS14`
-for a detailed description of the design of the library.
+We refer to :cite:`gudhilibrary_ICMS14` for a detailed description of the
+design of the library.
Data structures
***************
diff --git a/src/cython/doc/installation.rst b/src/cython/doc/installation.rst
index 373e0717..f98a5039 100644
--- a/src/cython/doc/installation.rst
+++ b/src/cython/doc/installation.rst
@@ -33,7 +33,7 @@ To build the GUDHI cython module, run the following commands in a terminal:
Test suites
===========
-To test your build, `py.test <http://doc.pytest.org>`_ is required. Run the
+To test your build, `py.test <http://doc.pytest.org>`_ is optional. Run the
following command in a terminal:
.. code-block:: bash
@@ -41,7 +41,7 @@ following command in a terminal:
cd /path-to-gudhi/build/cython
# For windows, you have to set PYTHONPATH environment variable
export PYTHONPATH='$PYTHONPATH:/path-to-gudhi/build/cython'
- py.test
+ ctest -R py_test
Documentation
=============
diff --git a/src/cython/doc/persistence_graphical_tools_user.rst b/src/cython/doc/persistence_graphical_tools_user.rst
index f713e971..cae18323 100644
--- a/src/cython/doc/persistence_graphical_tools_user.rst
+++ b/src/cython/doc/persistence_graphical_tools_user.rst
@@ -1,4 +1,3 @@
-=======================================
Persistence graphical tools user manual
=======================================
Definition
diff --git a/src/cython/doc/persistent_cohomology_user.rst b/src/cython/doc/persistent_cohomology_user.rst
index 69be3b86..72f1a7f7 100644
--- a/src/cython/doc/persistent_cohomology_user.rst
+++ b/src/cython/doc/persistent_cohomology_user.rst
@@ -1,4 +1,3 @@
-=================================
Persistent cohomology user manual
=================================
Definition
@@ -108,7 +107,7 @@ We provide several example files: run these examples with -h for details on thei
* :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>`
Bibliography
-************
+============
.. bibliography:: bibliography.bib
:filter: docnames
diff --git a/src/cython/doc/rips_complex_user.rst b/src/cython/doc/rips_complex_user.rst
index c89409a0..f9760976 100644
--- a/src/cython/doc/rips_complex_user.rst
+++ b/src/cython/doc/rips_complex_user.rst
@@ -1,4 +1,3 @@
-=========================
Rips complex user manual
=========================
Definition
@@ -60,8 +59,9 @@ Finally, it is asked to display information about the simplicial complex.
repr(simplex_tree.num_simplices()) + ' simplices - ' + \
repr(simplex_tree.num_vertices()) + ' vertices.'
print(result_str)
+ fmt = '%s -> %.2f'
for filtered_value in simplex_tree.get_filtration():
- print(filtered_value)
+ print(fmt % tuple(filtered_value))
When launching (Rips maximal distance between 2 points is 12.0, is expanded
until dimension 1 - one skeleton graph in other words), the output is:
@@ -69,24 +69,24 @@ until dimension 1 - one skeleton graph in other words), the output is:
.. testoutput::
Rips complex is of dimension 1 - 18 simplices - 7 vertices.
- ([0], 0.0)
- ([1], 0.0)
- ([2], 0.0)
- ([3], 0.0)
- ([4], 0.0)
- ([5], 0.0)
- ([6], 0.0)
- ([2, 3], 5.0)
- ([4, 5], 5.385164807134504)
- ([0, 2], 5.830951894845301)
- ([0, 1], 6.082762530298219)
- ([1, 3], 6.324555320336759)
- ([1, 2], 6.708203932499369)
- ([5, 6], 7.280109889280518)
- ([2, 4], 8.94427190999916)
- ([0, 3], 9.433981132056603)
- ([4, 6], 9.486832980505138)
- ([3, 6], 11.0)
+ [0] -> 0.00
+ [1] -> 0.00
+ [2] -> 0.00
+ [3] -> 0.00
+ [4] -> 0.00
+ [5] -> 0.00
+ [6] -> 0.00
+ [2, 3] -> 5.00
+ [4, 5] -> 5.39
+ [0, 2] -> 5.83
+ [0, 1] -> 6.08
+ [1, 3] -> 6.32
+ [1, 2] -> 6.71
+ [5, 6] -> 7.28
+ [2, 4] -> 8.94
+ [0, 3] -> 9.43
+ [4, 6] -> 9.49
+ [3, 6] -> 11.00
Example from OFF file
^^^^^^^^^^^^^^^^^^^^^
@@ -107,32 +107,33 @@ Finally, it is asked to display information about the Rips complex.
repr(simplex_tree.num_simplices()) + ' simplices - ' + \
repr(simplex_tree.num_vertices()) + ' vertices.'
print(result_str)
+ fmt = '%s -> %.2f'
for filtered_value in simplex_tree.get_filtration():
- print(filtered_value)
+ print(fmt % tuple(filtered_value))
the program output is:
.. testoutput::
Rips complex is of dimension 1 - 18 simplices - 7 vertices.
- ([0], 0.0)
- ([1], 0.0)
- ([2], 0.0)
- ([3], 0.0)
- ([4], 0.0)
- ([5], 0.0)
- ([6], 0.0)
- ([2, 3], 5.0)
- ([4, 5], 5.385164807134504)
- ([0, 2], 5.830951894845301)
- ([0, 1], 6.082762530298219)
- ([1, 3], 6.324555320336759)
- ([1, 2], 6.708203932499369)
- ([5, 6], 7.280109889280518)
- ([2, 4], 8.94427190999916)
- ([0, 3], 9.433981132056603)
- ([4, 6], 9.486832980505138)
- ([3, 6], 11.0)
+ [0] -> 0.00
+ [1] -> 0.00
+ [2] -> 0.00
+ [3] -> 0.00
+ [4] -> 0.00
+ [5] -> 0.00
+ [6] -> 0.00
+ [2, 3] -> 5.00
+ [4, 5] -> 5.39
+ [0, 2] -> 5.83
+ [0, 1] -> 6.08
+ [1, 3] -> 6.32
+ [1, 2] -> 6.71
+ [5, 6] -> 7.28
+ [2, 4] -> 8.94
+ [0, 3] -> 9.43
+ [4, 6] -> 9.49
+ [3, 6] -> 11.00
Distance matrix
---------------
@@ -162,8 +163,9 @@ Finally, it is asked to display information about the simplicial complex.
repr(simplex_tree.num_simplices()) + ' simplices - ' + \
repr(simplex_tree.num_vertices()) + ' vertices.'
print(result_str)
+ fmt = '%s -> %.2f'
for filtered_value in simplex_tree.get_filtration():
- print(filtered_value)
+ print(fmt % tuple(filtered_value))
When launching (Rips maximal distance between 2 points is 12.0, is expanded
until dimension 1 - one skeleton graph in other words), the output is:
@@ -171,24 +173,24 @@ until dimension 1 - one skeleton graph in other words), the output is:
.. testoutput::
Rips complex is of dimension 1 - 18 simplices - 7 vertices.
- ([0], 0.0)
- ([1], 0.0)
- ([2], 0.0)
- ([3], 0.0)
- ([4], 0.0)
- ([5], 0.0)
- ([6], 0.0)
- ([2, 3], 5.0)
- ([4, 5], 5.3851648071)
- ([0, 2], 5.8309518948)
- ([0, 1], 6.0827625303)
- ([1, 3], 6.3245553203)
- ([1, 2], 6.7082039325)
- ([5, 6], 7.2801098893)
- ([2, 4], 8.94427191)
- ([0, 3], 9.4339811321)
- ([4, 6], 9.4868329805)
- ([3, 6], 11.0)
+ [0] -> 0.00
+ [1] -> 0.00
+ [2] -> 0.00
+ [3] -> 0.00
+ [4] -> 0.00
+ [5] -> 0.00
+ [6] -> 0.00
+ [2, 3] -> 5.00
+ [4, 5] -> 5.39
+ [0, 2] -> 5.83
+ [0, 1] -> 6.08
+ [1, 3] -> 6.32
+ [1, 2] -> 6.71
+ [5, 6] -> 7.28
+ [2, 4] -> 8.94
+ [0, 3] -> 9.43
+ [4, 6] -> 9.49
+ [3, 6] -> 11.00
Example from csv file
^^^^^^^^^^^^^^^^^^^^^
@@ -209,29 +211,30 @@ Finally, it is asked to display information about the Rips complex.
repr(simplex_tree.num_simplices()) + ' simplices - ' + \
repr(simplex_tree.num_vertices()) + ' vertices.'
print(result_str)
+ fmt = '%s -> %.2f'
for filtered_value in simplex_tree.get_filtration():
- print(filtered_value)
+ print(fmt % tuple(filtered_value))
the program output is:
.. testoutput::
Rips complex is of dimension 1 - 18 simplices - 7 vertices.
- ([0], 0.0)
- ([1], 0.0)
- ([2], 0.0)
- ([3], 0.0)
- ([4], 0.0)
- ([5], 0.0)
- ([6], 0.0)
- ([2, 3], 5.0)
- ([4, 5], 5.3851648071)
- ([0, 2], 5.8309518948)
- ([0, 1], 6.0827625303)
- ([1, 3], 6.3245553203)
- ([1, 2], 6.7082039325)
- ([5, 6], 7.2801098893)
- ([2, 4], 8.94427191)
- ([0, 3], 9.4339811321)
- ([4, 6], 9.4868329805)
- ([3, 6], 11.0)
+ [0] -> 0.00
+ [1] -> 0.00
+ [2] -> 0.00
+ [3] -> 0.00
+ [4] -> 0.00
+ [5] -> 0.00
+ [6] -> 0.00
+ [2, 3] -> 5.00
+ [4, 5] -> 5.39
+ [0, 2] -> 5.83
+ [0, 1] -> 6.08
+ [1, 3] -> 6.32
+ [1, 2] -> 6.71
+ [5, 6] -> 7.28
+ [2, 4] -> 8.94
+ [0, 3] -> 9.43
+ [4, 6] -> 9.49
+ [3, 6] -> 11.00
diff --git a/src/cython/doc/simplex_tree_user.rst b/src/cython/doc/simplex_tree_user.rst
index b2efca8b..4b1dde19 100644
--- a/src/cython/doc/simplex_tree_user.rst
+++ b/src/cython/doc/simplex_tree_user.rst
@@ -1,4 +1,3 @@
-========================
Simplex tree user manual
========================
Definition
diff --git a/src/cython/doc/tangential_complex_user.rst b/src/cython/doc/tangential_complex_user.rst
index 24f68f85..03f9fea6 100644
--- a/src/cython/doc/tangential_complex_user.rst
+++ b/src/cython/doc/tangential_complex_user.rst
@@ -1,4 +1,3 @@
-==============================
Tangential complex user manual
==============================
.. include:: tangential_complex_sum.rst
@@ -134,7 +133,7 @@ This example builds the Tangential complex of point set read in an OFF file.
repr(st.num_vertices()) + ' vertices.'
print(result_str)
for filtered_value in st.get_filtration():
- print(filtered_value)
+ print(filtered_value[0])
The output is:
@@ -142,21 +141,21 @@ The output is:
Tangential contains 12 simplices - 7 vertices.
Simplex tree is of dimension 1 - 15 simplices - 7 vertices.
- ([0], 0.0)
- ([1], 0.0)
- ([0, 1], 0.0)
- ([2], 0.0)
- ([0, 2], 0.0)
- ([1, 2], 0.0)
- ([3], 0.0)
- ([1, 3], 0.0)
- ([4], 0.0)
- ([2, 4], 0.0)
- ([5], 0.0)
- ([4, 5], 0.0)
- ([6], 0.0)
- ([3, 6], 0.0)
- ([5, 6], 0.0)
+ [0]
+ [1]
+ [0, 1]
+ [2]
+ [0, 2]
+ [1, 2]
+ [3]
+ [1, 3]
+ [4]
+ [2, 4]
+ [5]
+ [4, 5]
+ [6]
+ [3, 6]
+ [5, 6]
Example with perturbation
@@ -187,8 +186,9 @@ The output is:
Tangential contains 4 vertices.
Inconsistencies has been fixed.
+
Bibliography
-************
+============
.. bibliography:: bibliography.bib
:filter: docnames
diff --git a/src/cython/doc/witness_complex_user.rst b/src/cython/doc/witness_complex_user.rst
index 07945361..aa9cbb2c 100644
--- a/src/cython/doc/witness_complex_user.rst
+++ b/src/cython/doc/witness_complex_user.rst
@@ -1,12 +1,8 @@
-===========================
Witness complex user manual
===========================
-Definition
-----------
.. include:: witness_complex_sum.rst
-
Definitions
-----------
@@ -128,7 +124,7 @@ Here is an example of constructing a strong witness complex filtration and compu
* :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py>`
Bibliography
-************
+============
.. bibliography:: bibliography.bib
:filter: docnames
diff --git a/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py b/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
index 664eb5c4..984dbf1b 100755
--- a/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
+++ b/src/cython/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py
@@ -43,29 +43,22 @@ parser.add_argument('--no-diagram', default=False, action='store_true' , help='F
args = parser.parse_args()
-with open(args.file, 'r') as f:
- first_line = f.readline()
- if (first_line == 'OFF\n') or (first_line == 'nOFF\n'):
- print("#####################################################################")
- print("RipsComplex creation from distance matrix read in a csv file")
-
- message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length)
- print(message)
-
- rips_complex = gudhi.RipsComplex(off_file=args.file, max_edge_length=args.max_edge_length)
- simplex_tree = rips_complex.create_simplex_tree(max_dimension=args.max_dimension)
-
- message = "Number of simplices=" + repr(simplex_tree.num_simplices())
- print(message)
-
- diag = simplex_tree.persistence()
-
- print("betti_numbers()=")
- print(simplex_tree.betti_numbers())
-
- if args.no_diagram == False:
- gudhi.plot_persistence_diagram(diag)
- else:
- print(args.file, "is not a valid OFF file")
-
- f.close()
+print("#####################################################################")
+print("RipsComplex creation from distance matrix read in a csv file")
+
+message = "RipsComplex with max_edge_length=" + repr(args.max_edge_length)
+print(message)
+
+rips_complex = gudhi.RipsComplex(csv_file=args.file, max_edge_length=args.max_edge_length)
+simplex_tree = rips_complex.create_simplex_tree(max_dimension=args.max_dimension)
+
+message = "Number of simplices=" + repr(simplex_tree.num_simplices())
+print(message)
+
+diag = simplex_tree.persistence()
+
+print("betti_numbers()=")
+print(simplex_tree.betti_numbers())
+
+if args.no_diagram == False:
+ gudhi.plot_persistence_diagram(diag)
generated by cgit v1.2.3 (git 2.39.1) at 2024-07-29 01:15:30 +0000