Merge branch 'master' into toplex_map

4 files changed, 22 insertions, 28 deletions

diff --git a/src/common/doc/examples.h b/src/common/doc/examples.h
index 40f202c7..c19b3444 100644
--- a/src/common/doc/examples.h
+++ b/src/common/doc/examples.h
@@ -53,10 +53,7 @@
  * @example Spatial_searching/example_spatial_searching.cpp
  * @example Alpha_complex/alpha_complex_3d_persistence.cpp
  * @example Alpha_complex/alpha_complex_persistence.cpp
- * @example Alpha_complex/weighted_periodic_alpha_complex_3d_persistence.cpp
- * @example Alpha_complex/weighted_alpha_complex_3d_persistence.cpp
- * @example Alpha_complex/periodic_alpha_complex_3d_persistence.cpp
- * @example Alpha_complex/exact_alpha_complex_3d_persistence.cpp
+ * @example Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp
  * @example Bottleneck_distance/bottleneck_distance.cpp
  * @example Witness_complex/weak_witness_persistence.cpp
  * @example Witness_complex/strong_witness_persistence.cpp
diff --git a/src/common/doc/file_formats.h b/src/common/doc/file_formats.h
index 523153b8..23214e25 100644
--- a/src/common/doc/file_formats.h
+++ b/src/common/doc/file_formats.h
@@ -72,7 +72,7 @@ namespace Gudhi {
 
  \section FileFormatsPerseus Perseus
 
- This file format is the format used by the Perseus software
+ This file format is a format inspired from the Perseus software
  (http://www.sas.upenn.edu/~vnanda/perseus/) by Vidit Nanda.
  The first line contains a number d begin the dimension of the
  bitmap (2 in the example below). Next d lines are the numbers of top dimensional cubes in each dimensions (3 and 3
@@ -118,6 +118,10 @@ namespace Gudhi {
  Indicate that we have imposed periodic boundary conditions in the direction x, but not in the direction y.
 
  Other sample files can be found in the `data/bitmap` folder.
+ 
+ \note Unlike in Perseus format the filtration on the maximal cubes can be any double precision number.
+ Consequently one cannot mark the cubes that are not present with `-1`'s. To do that please set their filtration value
+ to \f$+\infty\f$ (aka. `inf` in the file).
 
 */
 }  // namespace Gudhi
diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h
index df7eed37..8fb8b330 100644
--- a/src/common/doc/installation.h
+++ b/src/common/doc/installation.h
@@ -5,7 +5,7 @@
  * Examples of GUDHI headers inclusion can be found in \ref utilities.
  * 
  * \section compiling Compiling
- * The library uses c++11 and requires <a target="_blank" href="http://www.boost.org/">Boost</a>  &ge; 1.48.0
+ * The library uses c++11 and requires <a target="_blank" href="http://www.boost.org/">Boost</a>  &ge; 1.56.0
  * and <a target="_blank" href="https://www.cmake.org/">CMake</a> &ge; 3.1.
  * It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2015.
  * 
@@ -72,12 +72,6 @@ make doxygen
  * 
  * The following examples/utilities require the <a target="_blank" href="http://www.cgal.org/">Computational Geometry Algorithms
  * Library</a> (CGAL \cite cgal:eb-15b) and will not be built if CGAL is not installed:
- * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html">
- * Alpha_complex/alpha_complex_3d_persistence.cpp</a>
- * \li <a href="_alpha_complex_2exact_alpha_complex_3d_persistence_8cpp-example.html">
- * Alpha_complex/exact_alpha_complex_3d_persistence.cpp</a>
- * \li <a href="_alpha_complex_2weighted_alpha_complex_3d_persistence_8cpp-example.html">
- * Alpha_complex/weighted_alpha_complex_3d_persistence.cpp</a>
  * \li <a href="_simplex_tree_2example_alpha_shapes_3_simplex_tree_from_off_file_8cpp-example.html">
  * Simplex_tree/example_alpha_shapes_3_simplex_tree_from_off_file.cpp</a>
  * 
@@ -100,8 +94,6 @@ make doxygen
  * Alpha_complex/Alpha_complex_from_points.cpp</a>
  * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html">
  * Alpha_complex/alpha_complex_persistence.cpp</a>
- * \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html">
- * Alpha_complex/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>
  * 
@@ -135,6 +127,12 @@ make doxygen
  * \li <a href="_tangential_complex_2example_with_perturb_8cpp-example.html">
  * Tangential_complex/example_with_perturb.cpp</a>
  *
+ * The following example requires CGAL version &ge; 4.11.0:
+ * \li <a href="_alpha_complex_2_weighted_alpha_complex_3d_from_points_8cpp-example.html">
+ * Alpha_complex/Weighted_alpha_complex_3d_from_points.cpp</a>
+ * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html">
+ * Alpha_complex/alpha_complex_3d_persistence.cpp</a>
+ *
  * \subsection eigen3 Eigen3
  * The \ref alpha_complex data structure and few examples requires
  * <a target="_blank" href="http://eigen.tuxfamily.org/">Eigen3</a> is a C++ template library for linear algebra:
@@ -148,8 +146,10 @@ make doxygen
  * Alpha_complex/Alpha_complex_from_points.cpp</a>
  * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html">
  * Alpha_complex/alpha_complex_persistence.cpp</a>
- * \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html">
- * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_alpha_complex_2alpha_complex_3d_persistence_8cpp-example.html">
+ * Alpha_complex/alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_alpha_complex_2_weighted_alpha_complex_3d_from_points_8cpp-example.html">
+ * Alpha_complex/Weighted_alpha_complex_3d_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_2custom_persistence_sort_8cpp-example.html">
@@ -195,12 +195,6 @@ make doxygen
  * Alpha_complex/alpha_complex_3d_persistence.cpp</a>
  * \li <a href="_alpha_complex_2alpha_complex_persistence_8cpp-example.html">
  * Alpha_complex/alpha_complex_persistence.cpp</a>
- * \li <a href="_alpha_complex_2exact_alpha_complex_3d_persistence_8cpp-example.html">
- * Alpha_complex/exact_alpha_complex_3d_persistence.cpp</a>
- * \li <a href="_alpha_complex_2periodic_alpha_complex_3d_persistence_8cpp-example.html">
- * Alpha_complex/periodic_alpha_complex_3d_persistence.cpp</a>
- * \li <a href="_alpha_complex_2weighted_alpha_complex_3d_persistence_8cpp-example.html">
- * Alpha_complex/weighted_alpha_complex_3d_persistence.cpp</a>
  * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_8cpp-example.html">
  * Bitmap_cubical_complex/cubical_complex_persistence.cpp</a>
  * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_periodic_boundary_conditions_8cpp-example.html">
@@ -239,10 +233,6 @@ make doxygen
  * Persistent_cohomology/rips_multifield_persistence.cpp</a>
  * \li <a href="_persistent_cohomology_2rips_persistence_step_by_step_8cpp-example.html">
  * Persistent_cohomology/rips_persistence_step_by_step.cpp</a>
- * \li <a href="_persistent_cohomology_2exact_alpha_complex_3d_persistence_8cpp-example.html">
- * Persistent_cohomology/exact_alpha_complex_3d_persistence.cpp</a>
- * \li <a href="_persistent_cohomology_2weighted_alpha_complex_3d_persistence_8cpp-example.html">
- * Persistent_cohomology/weighted_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="_rips_complex_2example_one_skeleton_rips_from_points_8cpp-example.html">
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index 5ccb648f..afe9b68c 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -29,7 +29,9 @@
       <b>Author:</b> Vincent Rouvreau<br>
       <b>Introduced in:</b> GUDHI 1.3.0<br>
       <b>Copyright:</b> GPL v3<br>
-      <b>Requires:</b> \ref cgal &ge; 4.7.0 and \ref eigen3
+      <b>Requires:</b> \ref eigen3 and<br>
+      \ref cgal &ge; 4.7.0 for Alpha_complex<br>
+      \ref cgal &ge; 4.11.0 for Alpha_complex_3d
     </td>
     <td width="75%">
     Alpha_complex is a simplicial complex constructed from the finite cells of a Delaunay Triangulation.<br>
@@ -38,7 +40,8 @@
     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.<br>
-    <b>User manual:</b> \ref alpha_complex - <b>Reference manual:</b> Gudhi::alpha_complex::Alpha_complex
+    <b>User manual:</b> \ref alpha_complex - <b>Reference manual:</b> Gudhi::alpha_complex::Alpha_complex and
+    Gudhi::alpha_complex::Alpha_complex_3d
     </td>
  </tr>
 </table>