Merge from trunk

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/add_utils_in_gudhi_v2@2732 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 7872aa224ee471c05e9213b81192d304254e608a

2 files changed, 77 insertions, 2 deletions

diff --git a/src/common/doc/file_formats.h b/src/common/doc/file_formats.h
new file mode 100644
index 00000000..d715aa4d
--- /dev/null
+++ b/src/common/doc/file_formats.h
@@ -0,0 +1,59 @@
+/*    This file is part of the Gudhi Library. The Gudhi library
+*    (Geometric Understanding in Higher Dimensions) is a generic C++
+*    library for computational topology.
+*
+*    Author(s):       Clément Jamin
+*
+*    Copyright (C) 2017  INRIA
+*
+*    This program is free software: you can redistribute it and/or modify
+*    it under the terms of the GNU General Public License as published by
+*    the Free Software Foundation, either version 3 of the License, or
+*    (at your option) any later version.
+*
+*    This program is distributed in the hope that it will be useful,
+*    but WITHOUT ANY WARRANTY; without even the implied warranty of
+*    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+*    GNU General Public License for more details.
+*
+*    You should have received a copy of the GNU General Public License
+*    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
+
+#ifndef DOC_COMMON_FILE_FORMAT_H_
+#define DOC_COMMON_FILE_FORMAT_H_
+
+namespace Gudhi {
+
+/*! \page fileformats File formats
+
+ \tableofcontents
+
+ \section FileFormatsPers Persistence Diagram
+
+ Such a file, whose extension is usually `.pers`, contains a list of persistence intervals.<br>
+ Lines starting with `#` are ignored (comments).<br>
+ Other lines might contain 2, 3 or 4 values (the number of values on each line must be the same for all lines):
+ \verbatim
+   [[field] dimension] birth death
+ \endverbatim
+
+ Here is a simple sample file:
+ \verbatim
+   # Persistence diagram example
+   2 2.7 3.7
+   2 9.6 14.
+   # Some comments
+   3 34.2 34.974
+   4 3. inf
+ \endverbatim
+
+ Other sample files can be found in the `data/persistence_diagram` folder.
+
+ Such files can be generated with `Gudhi::persistent_cohomology::Persistent_cohomology::output_diagram()` and read with
+ `Gudhi::read_persistence_intervals_and_dimension()`, `Gudhi::read_persistence_intervals_grouped_by_dimension()` or
+ `Gudhi::read_persistence_intervals_in_dimension()`.
+*/
+}  // namespace Gudhi
+
+#endif  // DOC_COMMON_FILE_FORMAT_H_
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index 6ff3f94d..cee0c28b 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -160,7 +160,7 @@
       <b>Author:</b> Fran&ccedil;ois Godi<br>
       <b>Introduced in:</b> GUDHI 2.0.0<br>
       <b>Copyright:</b> GPL v3<br>
-      <b>Requires:</b> \ref cgal &ge; 4.8.1 and \ref eigen3
+      <b>Requires:</b> \ref cgal &ge; 4.8.1
     </td>
     <td width="75%">
     Bottleneck distance measures the similarity between two persistence diagrams. 
@@ -329,13 +329,29 @@ make doxygen
  * Alpha_complex/Alpha_complex_from_off.cpp</a>
  * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html">
  * Alpha_complex/Alpha_complex_from_points.cpp</a>
+ * \li <a href="_bottleneck_distance_2alpha_rips_persistence_bottleneck_distance_8cpp-example.html">
+ * Bottleneck_distance/alpha_rips_persistence_bottleneck_distance.cpp.cpp</a>
  * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
  * Persistent_cohomology/alpha_complex_persistence.cpp</a>
  * \li <a href="_persistent_cohomology_2periodic_alpha_complex_3d_persistence_8cpp-example.html">
  * Persistent_cohomology/periodic_alpha_complex_3d_persistence.cpp</a>
  * \li <a href="_persistent_cohomology_2custom_persistence_sort_8cpp-example.html">
  * Persistent_cohomology/custom_persistence_sort.cpp</a>
- * 
+ * \li <a href="_spatial_searching_2example_spatial_searching_8cpp-example.html">
+ * Spatial_searching/example_spatial_searching.cpp</a>
+ * \li <a href="_subsampling_2example_choose_n_farthest_points_8cpp-example.html">
+ * Subsampling/example_choose_n_farthest_points.cpp</a>
+ * \li <a href="_subsampling_2example_custom_kernel_8cpp-example.html">
+ * Subsampling/example_custom_kernel.cpp</a>
+ * \li <a href="_subsampling_2example_pick_n_random_points_8cpp-example.html">
+ * Subsampling/example_pick_n_random_points.cpp</a>
+ * \li <a href="_subsampling_2example_sparsify_point_set_8cpp-example.html">
+ * Subsampling/example_sparsify_point_set.cpp</a>
+ * \li <a href="_tangential_complex_2example_basic_8cpp-example.html">
+ * Tangential_complex/example_basic.cpp</a>
+ * \li <a href="_tangential_complex_2example_with_perturb_8cpp-example.html">
+ * Tangential_complex/example_with_perturb.cpp</a>
+ *
  * \subsection tbb Threading Building Blocks
  * <a target="_blank" href="https://www.threadingbuildingblocks.org/">Intel&reg; TBB</a> lets you easily write parallel
  * C++ programs that take full advantage of multicore performance, that are portable and composable, and that have