Merge last trunk modifications

Fix doxygen warnings


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2888 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: b80b28a10495b6f2519b53885b1bf31be85ed7ac

9 files changed, 46 insertions, 43 deletions

diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index ec8589f0..afca9d60 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -185,6 +185,19 @@ if(CYTHON_FOUND)
 
     add_gudhi_py_test(test_tangential_complex)
 
+    # Witness complex AND Subsampling
+    add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
+             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+
+    add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
+             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+
     # Subsampling
     add_gudhi_py_test(test_subsampling)
 
@@ -218,18 +231,6 @@ if(CYTHON_FOUND)
 
   if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
     # Euclidean witness
-    add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
-             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
-
-    add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
-             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
-
     add_gudhi_py_test(test_euclidean_witness_complex)
 
   endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.6.0)
diff --git a/src/cython/cython/simplex_tree.pyx b/src/cython/cython/simplex_tree.pyx
index 45487158..32b91028 100644
--- a/src/cython/cython/simplex_tree.pyx
+++ b/src/cython/cython/simplex_tree.pyx
@@ -312,7 +312,7 @@ cdef class SimplexTree:
         """This function returns the persistence of the simplicial complex.
 
         :param homology_coeff_field: The homology coefficient field. Must be a
-            prime number
+            prime number. Default value is 11.
         :type homology_coeff_field: int.
         :param min_persistence: The minimum persistence value to take into
             account (strictly greater than min_persistence). Default value is
diff --git a/src/cython/doc/citation.rst b/src/cython/doc/citation.rst
index 6cdfb7cc..f4fdf83b 100644
--- a/src/cython/doc/citation.rst
+++ b/src/cython/doc/citation.rst
@@ -12,4 +12,4 @@ Manual, as well as for publications directly related to the GUDHI library.
 GUDHI bibtex
 ************
 
-.. literalinclude:: how_to_cite_gudhi.bib
+.. literalinclude:: ../../biblio/how_to_cite_gudhi.bib
diff --git a/src/cython/doc/cubical_complex_user.rst b/src/cython/doc/cubical_complex_user.rst
index 36fa3ba9..2bfac62a 100644
--- a/src/cython/doc/cubical_complex_user.rst
+++ b/src/cython/doc/cubical_complex_user.rst
@@ -59,7 +59,7 @@ directions, allows to determine, dimension, neighborhood, boundary and coboundar
 :math:`C \in \mathcal{K}`.
 
 .. figure::
-    img/Cubical_complex_representation.png
+    ../../doc/Bitmap_cubical_complex/Cubical_complex_representation.png
     :alt: Cubical complex.
     :figclass: align-center
 
@@ -87,7 +87,7 @@ in the example below). Next, in lexicographical order, the filtration of top dim
 20 4 7 6 5 in the example below).
 
 .. figure::
-    img/exampleBitmap.png
+    ../../doc/Bitmap_cubical_complex/exampleBitmap.png
     :alt: Example of a input data.
     :figclass: align-center
 
@@ -95,9 +95,9 @@ in the example below). Next, in lexicographical order, the filtration of top dim
 
 The input file for the following complex is:
 
-.. literalinclude:: cubicalcomplexdoc.txt
+.. literalinclude:: ../../data/bitmap/cubicalcomplexdoc.txt
 
-.. centered:: data/bitmap/cubicalcomplexdoc.txt
+.. centered:: ../../data/bitmap/cubicalcomplexdoc.txt
 
 .. testcode::
 
@@ -128,9 +128,9 @@ complex with periodic boundary conditions. One can also use Perseus style input
 conditions in a given direction, then number of top dimensional cells in this direction have to be multiplied by -1.
 For instance:
 
-.. literalinclude:: periodiccubicalcomplexdoc.txt
+.. literalinclude:: ../../data/bitmap/periodiccubicalcomplexdoc.txt
 
-.. centered:: data/bitmap/periodiccubicalcomplexdoc.txt
+.. centered:: ../../data/bitmap/periodiccubicalcomplexdoc.txt
 
 Indicate that we have imposed periodic boundary conditions in the direction x, but not in the direction y.
 
diff --git a/src/cython/doc/installation.rst b/src/cython/doc/installation.rst
index f98a5039..c182f176 100644
--- a/src/cython/doc/installation.rst
+++ b/src/cython/doc/installation.rst
@@ -68,31 +68,32 @@ The :doc:`Alpha complex </alpha_complex_user>`,
 C++ library which provides easy access to efficient and reliable geometric
 algorithms.
 
-Having CGAL version 4.6.0 or higher installed is recommended. The procedure to
-install this library according to your operating system is detailed
+Having CGAL,  the Computational Geometry Algorithms Library, version 4.7.0 or
+higher installed is recommended. The procedure to install this library
+according to your operating system is detailed
 `here <http://doc.cgal.org/latest/Manual/installation.html>`_.
 
-The following examples require the Computational Geometry Algorithms Library:
-
-.. only:: builder_html
-
-    * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>`
-    * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>`
-
-The following example requires CGAL version ≥ 4.7.0:
+The following examples requires CGAL version ≥ 4.7.0:
 
 .. only:: builder_html
 
     * :download:`alpha_complex_diagram_persistence_from_off_file_example.py <../example/alpha_complex_diagram_persistence_from_off_file_example.py>`
     * :download:`alpha_complex_from_points_example.py <../example/alpha_complex_from_points_example.py>`
 
-The following example requires CGAL version ≥ 4.8.0:
+The following examples requires CGAL version ≥ 4.8.0:
 
 .. only:: builder_html
 
     * :download:`bottleneck_basic_example.py <../example/bottleneck_basic_example.py>`
     * :download:`tangential_complex_plain_homology_from_off_file_example.py <../example/tangential_complex_plain_homology_from_off_file_example.py>`
 
+The following examples requires CGAL version ≥ 4.8.1:
+
+.. only:: builder_html
+
+    * :download:`euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py>`
+    * :download:`euclidean_witness_complex_diagram_persistence_from_off_file_example.py <../example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py>`
+
 Eigen3
 ======
 
diff --git a/src/cython/example/simplex_tree_example.py b/src/cython/example/simplex_tree_example.py
index 831d9da8..51a60e73 100755
--- a/src/cython/example/simplex_tree_example.py
+++ b/src/cython/example/simplex_tree_example.py
@@ -48,8 +48,6 @@ if st.insert([0, 1, 2], filtration=4.0):
 else:
     print("Not inserted...")
 
-# FIXME: Remove this line
-st.set_dimension(3)
 print("dimension=", st.dimension())
 
 st.initialize_filtration()
diff --git a/src/cython/include/Tangential_complex_interface.h b/src/cython/include/Tangential_complex_interface.h
index 5e9dc0e4..ecf014b3 100644
--- a/src/cython/include/Tangential_complex_interface.h
+++ b/src/cython/include/Tangential_complex_interface.h
@@ -106,8 +106,6 @@ class Tangential_complex_interface {
 
   void create_simplex_tree(Simplex_tree<>* simplex_tree) {
     int max_dim = tangential_complex_->create_complex<Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_full_featured>>(*simplex_tree);
-    // FIXME
-    simplex_tree->set_dimension(max_dim);
     simplex_tree->initialize_filtration();
   }
 
diff --git a/src/cython/test/test_cubical_complex.py b/src/cython/test/test_cubical_complex.py
index 9a365823..0e81554d 100755
--- a/src/cython/test/test_cubical_complex.py
+++ b/src/cython/test/test_cubical_complex.py
@@ -62,17 +62,17 @@ def test_dimension_or_perseus_file_constructor():
     assert cub.__is_defined() == False
     assert cub.__is_persistence_defined() == False
 
-def test_dimension_constructor():
+def test_dimension_simple_constructor():
     cub = CubicalComplex(dimensions=[3, 3],
                          top_dimensional_cells = [1,2,3,4,5,6,7,8,9])
     assert cub.__is_defined() == True
     assert cub.__is_persistence_defined() == False
-    assert cub.persistence() == [(1, (0.0, 100.0)), (0, (0.0, float('inf')))]
+    assert cub.persistence() == [(0, (1.0, float('inf')))]
     assert cub.__is_persistence_defined() == True
-    assert cub.betti_numbers() == [1, 0]
-    assert cub.persistent_betti_numbers(0, 1000) == [0, 0]
+    assert cub.betti_numbers() == [1, 0, 0]
+    assert cub.persistent_betti_numbers(0, 1000) == [0, 0, 0]
 
-def test_dimension_constructor():
+def test_dimension_file_constructor():
     # Create test file
     test_file = open('CubicalOneSphere.txt', 'w')
     test_file.write('2\n3\n3\n0\n0\n0\n0\n100\n0\n0\n0\n0\n')
diff --git a/src/cython/test/test_simplex_tree.py b/src/cython/test/test_simplex_tree.py
index 4d452d7d..801d52b7 100755
--- a/src/cython/test/test_simplex_tree.py
+++ b/src/cython/test/test_simplex_tree.py
@@ -34,9 +34,13 @@ def test_insertion():
 
     # insert test
     assert st.insert([0, 1]) == True
+
+    assert st.dimension() == 1
+
     assert st.insert([0, 1, 2], filtration=4.0) == True
-    # FIXME: Remove this line
-    st.set_dimension(2)
+
+    assert st.dimension() == 2
+
     assert st.num_simplices() == 7
     assert st.num_vertices() == 3
 
@@ -86,8 +90,9 @@ def test_insertion():
     assert st.find([2]) == True
 
     st.initialize_filtration()
-    assert st.persistence() == [(1, (4.0, float('inf'))), (0, (0.0, float('inf')))]
+    assert st.persistence(persistence_dim_max = True) == [(1, (4.0, float('inf'))), (0, (0.0, float('inf')))]
     assert st.__is_persistence_defined() == True
+
     assert st.betti_numbers() == [1, 1]
     assert st.persistent_betti_numbers(-0.1, 10000.0) == [0, 0]
     assert st.persistent_betti_numbers(0.0, 10000.0) == [1, 0]