Merge of alpha complex feature from trunk

Add Eigen3 in installation
Add alpha complex in introduction
All examples directory moved to example (was example/common, example/Alpha_complex)


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Doxygen_for_GUDHI_1.3.0@1110 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 0b88a4f2b102e2189f4b916b8358ffb2458a72f0

62 files changed, 4832 insertions, 165 deletions

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 94336e19..6ad3a58f 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -3,7 +3,7 @@ project(GUDHIdev)
 
 include(CMakeGUDHIVersion.txt)
 # Generate GUDHI official version file
-configure_file(GUDHIVersion.cmake.in "${PROJECT_BINARY_DIR}/GUDHIVersion.cmake" @ONLY)
+configure_file(GUDHIVersion.cmake.in "${CMAKE_SOURCE_DIR}/GUDHIVersion.cmake" @ONLY)
 
 find_package(Boost REQUIRED COMPONENTS system filesystem unit_test_framework chrono timer program_options thread REQUIRED)
 
@@ -78,7 +78,10 @@ else()
   if (GPROF_PATH)
     message("gprof found in ${GPROF_PATH}")
   endif()
-
+FIND_PROGRAM( DIFF_PATH diff )
+if (DIFF_PATH)
+  message("diff found in ${DIFF_PATH}")
+endif()
 
   # BOOST ISSUE result_of vs C++11
   add_definitions(-DBOOST_RESULT_OF_USE_DECLTYPE)
@@ -91,7 +94,14 @@ else()
   message(STATUS "boost include dirs:" ${Boost_INCLUDE_DIRS})
   message(STATUS "boost library dirs:" ${Boost_LIBRARY_DIRS})
 
+  if (DEBUG_TRACES)
+    # For programs to be more verbose
+    message(STATUS "DEBUG_TRACES are activated")
+    add_definitions(-DDEBUG_TRACES)
+  endif()
+
   include_directories(src/common/include/)
+  include_directories(src/Alpha_complex/include/)
   include_directories(src/Bitmap_cubical_complex/include/)
   include_directories(src/Bottleneck/include/)
   include_directories(src/Contraction/include/)
@@ -101,6 +111,8 @@ else()
   include_directories(src/Skeleton_blocker/include/)
   include_directories(src/Witness_complex/include/)
 
+  add_subdirectory(src/common/example)
+  add_subdirectory(src/common/test)
   add_subdirectory(src/Simplex_tree/test)
   add_subdirectory(src/Simplex_tree/example)
   add_subdirectory(src/Persistent_cohomology/test)
@@ -112,6 +124,8 @@ else()
   add_subdirectory(src/Witness_complex/example)
   add_subdirectory(src/Bitmap_cubical_complex/test)
   add_subdirectory(src/Bitmap_cubical_complex/example)
+  add_subdirectory(src/Alpha_complex/example)
+  add_subdirectory(src/Alpha_complex/test)
 
   # data points generator
   add_subdirectory(data/points/generator)
@@ -121,3 +135,5 @@ else()
   add_subdirectory(src/GudhUI)
 
 endif()  
+
+
diff --git a/biblio/how_to_cite_cgal.bib b/biblio/how_to_cite_cgal.bib
new file mode 100644
index 00000000..7336ee81
--- /dev/null
+++ b/biblio/how_to_cite_cgal.bib
@@ -0,0 +1,947 @@
+@book{ cgal:eb-15b
+, title        = "{CGAL} User and Reference Manual"
+, author      = "{The CGAL Project}"
+, publisher     = "{CGAL Editorial Board}"
+, edition     = "{4.7}"
+, year         = 2015
+, url =    "http://doc.cgal.org/4.7/Manual/packages.html"
+}
+@incollection{cgal:h-af-15b
+, author =  "Michael Hemmer"
+, title =   "Algebraic Foundations"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgAlgebraicFoundationsSummary"
+, year =        2015
+}
+
+@incollection{cgal:hhkps-nt-15b
+, author =  "Michael Hemmer and Susan Hert and Sylvain Pion and Stefan Schirra"
+, title =   "Number Types"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgNumberTypesSummary"
+, year =        2015
+}
+
+@incollection{cgal:h-ma-15b
+, author =  "Michael Hemmer and Sylvain Pion"
+, title =   "Modular Arithmetic"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgModularArithmeticSummary"
+, year =        2015
+}
+
+@incollection{cgal:h-p-15b
+, author =  "Michael Hemmer"
+, title =   "Polynomial"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgPolynomialSummary"
+, year =        2015
+}
+
+@incollection{cgal:bht-ak-15b
+, author =  "Eric Berberich and Michael Hemmer and Michael Kerber and Sylvain Lazard and Luis Pe{\~n}aranda and Monique Teillaud"
+, title =   "Algebraic Kernel"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgAlgebraicKerneldSummary"
+, year =        2015
+}
+
+@incollection{cgal:h-msms-15b
+, author =  "Michael Hoffmann"
+, title =   "Monotone and Sorted Matrix Search"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgMatrixSearchSummary"
+, year =        2015
+}
+
+@incollection{cgal:fgsw-lqps-15b
+, author =  "Kaspar Fischer and Bernd G{\"a}rtner and Sven Sch{\"o}nherr and Frans Wessendorp"
+, title =   "Linear and Quadratic Programming Solver"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgQPSolverSummary"
+, year =        2015
+}
+
+@incollection{cgal:bfghhkps-lgk23-15b
+, author =  "Herv{\'e} Br{\"o}nnimann and Andreas Fabri and Geert-Jan Giezeman and Susan Hert and Michael Hoffmann and Lutz Kettner and Sylvain Pion and Stefan Schirra"
+, title =   "{2D} and {3D} Linear Geometry Kernel"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgKernel23Summary"
+, year =        2015
+}
+
+@incollection{cgal:s-gkd-15b
+, author =  "Michael Seel"
+, title =   "{dD} Geometry Kernel"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgKernelDSummary"
+, year =        2015
+}
+
+@incollection{cgal:cpt-cgk2-15b
+, author =  "Pedro Machado Manh{\~a}es de Castro and Sylvain Pion and Monique Teillaud"
+, title =   "{2D} Circular Geometry Kernel"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgCircularKernel2Summary"
+, year =        2015
+}
+
+@incollection{cgal:cclt-sgk3-15b
+, author =  "Pedro Machado Manh{\~a}es de Castro and Fr{\'e}d{\'e}ric Cazals and S{\'e}bastien Loriot and Monique Teillaud"
+, title =   "{3D} Spherical Geometry Kernel"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSphericalKernel3Summary"
+, year =        2015
+}
+
+@incollection{cgal:hs-chep2-15b
+, author =  "Susan Hert and Stefan Schirra"
+, title =   "{2D} Convex Hulls and Extreme Points"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgConvexHull2Summary"
+, year =        2015
+}
+
+@incollection{cgal:hs-ch3-15b
+, author =  "Susan Hert and Stefan Schirra"
+, title =   "{3D} Convex Hulls"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgConvexHull3Summary"
+, year =        2015
+}
+
+@incollection{cgal:hs-chdt3-15b
+, author =  "Susan Hert and Michael Seel"
+, title =   "{dD} Convex Hulls and Delaunay Triangulations"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgConvexHullDSummary"
+, year =        2015
+}
+
+@incollection{cgal:gw-p2-15b
+, author =  "Geert-Jan Giezeman and Wieger Wesselink"
+, title =   "{2D} Polygons"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgPolygon2Summary"
+, year =        2015
+}
+
+@incollection{cgal:fwzh-rbso2-15b
+, author =  "Efi Fogel and Ophir Setter and Ron Wein and Guy Zucker and Baruch Zukerman and Dan Halperin"
+, title =   "{2D} Regularized Boolean Set-Operations"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgBooleanSetOperations2Summary"
+, year =        2015
+}
+
+@incollection{cgal:s-bonp2-15b
+, author =  "Michael Seel"
+, title =   "{2D} Boolean Operations on Nef Polygons"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgNef2Summary"
+, year =        2015
+}
+
+@incollection{cgal:hk-bonpes2-15b
+, author =  "Peter Hachenberger and Lutz Kettner"
+, title =   "{2D} Boolean Operations on Nef Polygons Embedded on the Sphere"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgNefS2Summary"
+, year =        2015
+}
+
+@incollection{cgal:h-pp2-15b
+, author =  "Susan Hert"
+, title =   "{2D} Polygon Partitioning"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgPolygonPartitioning2Summary"
+, year =        2015
+}
+
+@incollection{cgal:c-sspo2-15b
+, author =  "Fernando Cacciola"
+, title =   "{2D} Straight Skeleton and Polygon Offsetting"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgStraightSkeleton2Summary"
+, year =        2015
+}
+
+@incollection{cgal:w-rms2-15b
+, author =  "Ron Wein and Alon Baram and Eyal Flato and Efi Fogel and Michael Hemmer and Sebastian Morr"
+, title =   "{2D} Minkowski Sums"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgMinkowskiSum2Summary"
+, year =        2015
+}
+
+@incollection{cgal:f-ps2-15b
+, author =  "Andreas Fabri"
+, title =   "{2D} Polyline Simplification"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgPolylineSimplification2Summary"
+, year =        2015
+}
+
+@incollection{hhb-visibility-2-15b
+, author =  "Michael Hemmer and Kan Huang and Francisc Bungiu and Ning Xu"
+, title =   "{2D} Visibility Computation"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgVisibility_2Summary"
+, year =        2015
+}
+
+@incollection{cgal:k-ps-15b
+, author =  "Lutz Kettner"
+, title =   "{3D} Polyhedral Surface"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgPolyhedronSummary"
+, year =        2015
+}
+
+@incollection{cgal:k-hds-15b
+, author =  "Lutz Kettner"
+, title =   "Halfedge Data Structures"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgHDSSummary"
+, year =        2015
+}
+
+@incollection{cgal:bsmf-sm-15b
+, author =  "Mario Botsch and Daniel Sieger and Philipp Moeller and Andreas Fabri"
+, title =   "Surface Mesh"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSurfaceMeshSummary"
+, year =        2015
+}
+
+@incollection{cgal:d-cm-15b
+, author =  "Guillaume Damiand"
+, title =   "Combinatorial Maps"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgCombinatorialMapsSummary"
+, year =        2015
+}
+
+@incollection{cgal:d-lcc-12-15b
+, author =  "Guillaume Damiand"
+, title =   "Linear Cell Complex"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgLinearCellComplexSummary"
+, year =        2015
+}
+
+@incollection{cgal:hk-bonp3-15b
+, author =  "Peter Hachenberger and Lutz Kettner"
+, title =   "{3D} Boolean Operations on Nef Polyhedra"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgNef3Summary"
+, year =        2015
+}
+
+@incollection{cgal:h-emspe-15b
+, author =  "Peter Hachenberger"
+, title =   "Convex Decomposition of Polyhedra"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgConvexDecomposition3Summary"
+, year =        2015
+}
+
+@incollection{cgal:h-msp3-15b
+, author =  "Peter Hachenberger"
+, title =   "{3D} Minkowski Sum of Polyhedra"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgMinkowskiSum3Summary"
+, year =        2015
+}
+
+@incollection{cgal:wfzh-a2-15b
+, author =  "Ron Wein and Eric Berberich and Efi Fogel and Dan Halperin and Michael Hemmer and Oren Salzman and Baruch Zukerman"
+, title =   "{2D} Arrangements"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgArrangement2Summary"
+, year =        2015
+}
+
+@incollection{cgal:wfz-ic2-15b
+, author =  "Baruch Zukerman and Ron Wein and Efi Fogel"
+, title =   "{2D} Intersection of Curves"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgIntersectionOfCurves2Summary"
+, year =        2015
+}
+
+@incollection{cgal:p-sr2-15b
+, author =  "Eli Packer"
+, title =   "{2D} Snap Rounding"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSnapRounding2Summary"
+, year =        2015
+}
+
+@incollection{cgal:w-e2-15b
+, author =  "Ron Wein"
+, title =   "{2D} Envelopes"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgEnvelope2Summary"
+, year =        2015
+}
+
+@incollection{cgal:mwz-e3-15b
+, author =  "Dan Halperin and Michal Meyerovitch and Ron Wein and Baruch Zukerman"
+, title =   "{3D} Envelopes"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgEnvelope3Summary"
+, year =        2015
+}
+
+@incollection{cgal:y-t2-15b
+, author =  "Mariette Yvinec"
+, title =   "{2D} Triangulation"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgTriangulation2Summary"
+, year =        2015
+}
+
+@incollection{cgal:py-tds2-15b
+, author =  "Sylvain Pion and Mariette Yvinec"
+, title =   "{2D} Triangulation Data Structure"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgTDS2Summary"
+, year =        2015
+}
+
+@incollection{cgal:k-pt2-13-15b
+, author =  "Nico Kruithof"
+, title =   "{2D} Periodic Triangulations"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgPeriodic2Triangulation2Summary"
+, year =        2015
+}
+
+@incollection{cgal:pt-t3-15b
+, author =  "Cl{\'e}ment Jamin and Sylvain Pion and Monique Teillaud"
+, title =   "{3D} Triangulations"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgTriangulation3Summary"
+, year =        2015
+}
+
+@incollection{cgal:pt-tds3-15b
+, author =  "Cl{\'e}ment Jamin and Sylvain Pion and Monique Teillaud"
+, title =   "{3D} Triangulation Data Structure"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgTDS3Summary"
+, year =        2015
+}
+
+@incollection{cgal:ct-pt3-15b
+, author =  "Manuel Caroli and Monique Teillaud"
+, title =   "{3D} Periodic Triangulations"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgPeriodic3Triangulation3Summary"
+, year =        2015
+}
+
+@incollection{cgal:hdj-t-15b
+, author =  "Samuel Hornus and Olivier Devillers and Cl{\'e}ment Jamin"
+, title =   "{dD} Triangulations"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgTriangulationsSummary"
+, year =        2015
+}
+
+@incollection{cgal:d-as2-15b
+, author =  "Tran Kai Frank Da"
+, title =   "{2D} Alpha Shapes"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgAlphaShape2Summary"
+, year =        2015
+}
+
+@incollection{cgal:dy-as3-15b
+, author =  "Tran Kai Frank Da and S{\'e}bastien Loriot and Mariette Yvinec"
+, title =   "{3D} Alpha Shapes"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgAlphaShapes3Summary"
+, year =        2015
+}
+
+@incollection{cgal:k-sdg2-15b
+, author =  "Menelaos Karavelas"
+, title =   "{2D} Segment Delaunay Graphs"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSegmentDelaunayGraph2Summary"
+, year =        2015
+}
+
+@incollection{cgal:cdp-sdglinf2-15b
+, author =  "Panagiotis Cheilaris and Sandeep Kumar Dey and Evanthia Papadopoulou"
+, title =   "L Infinity Segment Delaunay Graphs"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSDGLinfSummary"
+, year =        2015
+}
+
+@incollection{cgal:ky-ag2-15b
+, author =  "Menelaos Karavelas and Mariette Yvinec"
+, title =   "{2D} Apollonius Graphs (Delaunay Graphs of Disks)"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgApolloniusGraph2Summary"
+, year =        2015
+}
+
+@incollection{cgal:k-vda2-15b
+, author =  "Menelaos Karavelas"
+, title =   "{2D} Voronoi Diagram Adaptor"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgVoronoiDiagramAdaptor2Summary"
+, year =        2015
+}
+
+@incollection{cgal:r-ctm2-15b
+, author =  "Laurent Rineau"
+, title =   "{2D} Conforming Triangulations and Meshes"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgMesh2Summary"
+, year =        2015
+}
+
+@incollection{cgal:ry-smg-15b
+, author =  "Laurent Rineau and Mariette Yvinec"
+, title =   "{3D} Surface Mesh Generation"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSurfaceMesher3Summary"
+, year =        2015
+}
+
+@incollection{cgal:asg-srps-15b
+, author =  "Pierre Alliez and Laurent Saboret and Ga{\"e}l Guennebaud"
+, title =   "Surface Reconstruction from Point Sets"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSurfaceReconstructionFromPointSetsSummary"
+, year =        2015
+}
+
+@incollection{cgal:ssr3-15b
+, author =  "Thijs van Lankveld"
+, title =   "Scale-Space Surface Reconstruction"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgScaleSpaceReconstruction3Summary"
+, year =        2015
+}
+
+@incollection{cgal:dc-afsr-15b
+, author =  "Tran Kai Frank Da and David Cohen-Steiner"
+, title =   "Advancing Front Surface Reconstruction"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgAdvancingFrontSurfaceReconstructionSummary"
+, year =        2015
+}
+
+@incollection{cgal:k-ssm3-15b
+, author =  "Nico Kruithof"
+, title =   "{3D} Skin Surface Meshing"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSkinSurface3Summary"
+, year =        2015
+}
+
+@incollection{cgal:rty-m3-15b
+, author =  "Pierre Alliez and Cl{\'e}ment Jamin and Laurent Rineau and St{\'e}phane Tayeb and Jane Tournois and Mariette Yvinec"
+, title =   "{3D} Mesh Generation"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgMesh_3Summary"
+, year =        2015
+}
+
+@incollection{cgal:lty-pmp-15b
+, author =  "S{\'e}bastien Loriot and Jane Tournois and Ilker O. Yaz"
+, title =   "Polygon Mesh Processing"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgPolygonMeshProcessingSummary"
+, year =        2015
+}
+
+@incollection{cgal:s-ssm2-15b
+, author =  "Le-Jeng Andy Shiue"
+, title =   "{3D} Surface Subdivision Methods"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSurfaceSubdivisionMethods3Summary"
+, year =        2015
+}
+
+@incollection{cgal:y-smsimpl-15b
+, author =  "Ilker O. Yaz and S{\'e}bastien Loriot"
+, title =   "Triangulated Surface Mesh Segmentation"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSurfaceSegmentationSummary"
+, year =        2015
+}
+
+@incollection{cgal:c-tsms-12-15b
+, author =  "Fernando Cacciola"
+, title =   "Triangulated Surface Mesh Simplification"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSurfaceMeshSimplificationSummary"
+, year =        2015
+}
+
+@incollection{cgal:lsxy-tsmd-15b
+, author =  "S{\'e}bastien Loriot and Olga Sorkine-Hornung and Yin Xu and Ilker O. Yaz"
+, title =   "Triangulated Surface Mesh Deformation"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSurfaceModelingSummary"
+, year =        2015
+}
+
+@incollection{cgal:sal-pptsm2-15b
+, author =  "Laurent Saboret and Pierre Alliez and Bruno L{\'e}vy"
+, title =   "Planar Parameterization of Triangulated Surface Meshes"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSurfaceParameterizationSummary"
+, year =        2015
+}
+
+@incollection{cgal:klcdv-tsmsp-15b
+, author =  "Stephen Kiazyk and S{\'e}bastien Loriot and {\'E}ric Colin de Verdi{\`e}re"
+, title =   "Triangulated Surface Mesh Shortest Paths"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSurfaceMeshShortestPathSummary"
+, year =        2015
+}
+
+@incollection{cgal:glt-tsms-15b
+, author =  "Xiang Gao and S{\'e}bastien Loriot and Andrea Tagliasacchi"
+, title =   "Triangulated Surface Mesh Skeletonization"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgMeanCurvatureSkeleton3Summary"
+, year =        2015
+}
+
+@incollection{cgal:cp-arutsm-15b
+, author =  "Marc Pouget and Fr{\'e}d{\'e}ric Cazals"
+, title =   "Approximation of Ridges and Umbilics on Triangulated Surface Meshes"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgRidges_3Summary"
+, year =        2015
+}
+
+@incollection{cgal:pc-eldp-15b
+, author =  "Marc Pouget  and Fr{\'e}d{\'e}ric Cazals"
+, title =   "Estimation of Local Differential Properties of Point-Sampled Surfaces"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgJet_fitting_3Summary"
+, year =        2015
+}
+
+@incollection{cgal:ass-psp-15b
+, author =  "Pierre Alliez and Cl{\'e}ment Jamin and Quentin M{\'e}rigot and Jocelyn Meyron and Laurent Saboret and Nader Salman and Shihao Wu"
+, title =   "Point Set Processing"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgPointSetProcessingSummary"
+, year =        2015
+}
+
+@incollection{cgal:ovja-pssd-15b
+, author =  "Sven Oesau and Yannick Verdie and Cl{\'e}ment Jamin and Pierre Alliez"
+, title =   "Point Set Shape Detection"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgPointSetShapeDetection3Summary"
+, year =        2015
+}
+
+@incollection{cgal:m-ps-15b
+, author =  "Abdelkrim Mebarki"
+, title =   "{2D} Placement of Streamlines"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgPlacementOfStreamlines2Summary"
+, year =        2015
+}
+
+@incollection{cgal:b-ss2-15b
+, author =  "Matthias B{\"a}sken"
+, title =   "{2D} Range and Neighbor Search"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgPointSet2Summary"
+, year =        2015
+}
+
+@incollection{cgal:f-isl-15b
+, author =  "Andreas Fabri"
+, title =   "Interval Skip List"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgIntervalSkipListSummary"
+, year =        2015
+}
+
+@incollection{cgal:tf-ssd-15b
+, author =  "Hans Tangelder and Andreas Fabri"
+, title =   "{dD} Spatial Searching"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSpatialSearchingDSummary"
+, year =        2015
+}
+
+@incollection{cgal:n-rstd-15b
+, author =  "Gabriele Neyer"
+, title =   "{dD} Range and Segment Trees"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgRangeSegmentTreesDSummary"
+, year =        2015
+}
+
+@incollection{cgal:kmz-isiobd-15b
+, author =  "Lutz Kettner and Andreas Meyer and Afra Zomorodian"
+, title =   "Intersecting Sequences of {dD} Iso-oriented Boxes"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgBoxIntersectionDSummary"
+, year =        2015
+}
+
+@incollection{cgal:atw-aabb-15b
+, author =  "Pierre Alliez and St{\'e}phane Tayeb and Camille Wormser"
+, title =   "{3D} Fast Intersection and Distance Computation"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgAABB_treeSummary"
+, year =        2015
+}
+
+@incollection{cgal:dd-ss-15b
+, author =  "Christophe Delage and Olivier Devillers"
+, title =   "Spatial Sorting"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgSpatialSortingSummary"
+, year =        2015
+}
+
+@incollection{cgal:fghhs-bv-15b
+, author =  "Kaspar Fischer and Bernd G{\"a}rtner and Thomas Herrmann and Michael Hoffmann and Sven Sch{\"o}nherr"
+, title =   "Bounding Volumes"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgBoundingVolumesSummary"
+, year =        2015
+}
+
+@incollection{cgal:hp-ia-15b
+, author =  "Michael Hoffmann and Eli Packer"
+, title =   "Inscribed Areas"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgInscribedAreasSummary"
+, year =        2015
+}
+
+@incollection{cgal:fghhs-od-15b
+, author =  "Kaspar Fischer and Bernd G{\"a}rtner and Thomas Herrmann and Michael Hoffmann and Sven Sch{\"o}nherr"
+, title =   "Optimal Distances"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgOptimalDistancesSummary"
+, year =        2015
+}
+
+@incollection{cgal:ap-pcad-15b
+, author =  "Pierre Alliez and Sylvain Pion and Ankit Gupta"
+, title =   "Principal Component Analysis"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgPrincipalComponentAnalysisDSummary"
+, year =        2015
+}
+
+@incollection{cgal:f-i-15b
+, author =  "Julia Fl{\"o}totto"
+, title =   "{2D} and Surface Function Interpolation"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgInterpolation2Summary"
+, year =        2015
+}
+
+@incollection{cgal:abha-gbc-15b
+, author =  "Dmitry Anisimov and David Bommes and Kai Hormann and Pierre Alliez"
+, title =   "{2D} Generalized Barycentric Coordinates"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgBarycentric_coordinates_2Summary"
+, year =        2015
+}
+
+@incollection{cgal:r-kds-15b
+, author =  "Daniel Russel"
+, title =   "Kinetic Data Structures"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgKdsSummary"
+, year =        2015
+}
+
+@incollection{cgal:r-kdsf-15b
+, author =  "Daniel Russel"
+, title =   "Kinetic Framework"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgKdsFrameworkSummary"
+, year =        2015
+}
+
+@incollection{cgal:hkpw-se-15b
+, author =  "Michael Hoffmann and Lutz Kettner and Sylvain Pion and Ron Wein"
+, title =   "STL Extensions for {CGAL}"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgStlExtensionSummary"
+, year =        2015
+}
+
+@incollection{cgal:cfw-cbgl-15b
+, author =  "Andreas Fabri and Fernando Cacciola and Philipp Moeller and Ron Wein"
+, title =   "{CGAL} and the {Boost} Graph Library"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgBGLSummary"
+, year =        2015
+}
+
+@incollection{cgal:fs-cbpm-15b
+, author =  "Andreas Fabri and Laurent Saboret"
+, title =   "{CGAL} and {Boost} Property Maps"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgProperty_mapSummary"
+, year =        2015
+}
+
+@incollection{cgal:dksy-hc-15b
+, author =  "Olivier Devillers and Lutz Kettner and Sylvain Pion and Michael Seel and Mariette Yvinec"
+, title =   "Handles and Circulators"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgHandlesAndCirculatorsSummary"
+, year =        2015
+}
+
+@incollection{cgal:dhhk-gog-15b
+, author =  "Pedro M. M. de Castro and Olivier Devillers and Susan Hert and Michael Hoffmann and Lutz Kettner and Sven Sch{\"o}nherr and Alexandru Tifrea"
+, title =   "Geometric Object Generators"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgGeneratorsSummary"
+, year =        2015
+}
+
+@incollection{cgal:kps-pthum-15b
+, author =  "Lutz Kettner and Sylvain Pion and Michael Seel"
+, title =   "Profiling tools, Hash Map, Union-find, Modifiers"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgProfilingToolsSummary"
+, year =        2015
+}
+
+@incollection{cgal:fgk-ios-12-15b
+, author =  "Andreas Fabri and Geert-Jan Giezeman and Lutz Kettner"
+, title =   "IO Streams"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgIOstreamsSummary"
+, year =        2015
+}
+
+@incollection{cgal:fp-gv-15b
+, author =  "Andreas Fabri and Sylvain Pion"
+, title =   "Geomview"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgGeomviewSummary"
+, year =        2015
+}
+
+@incollection{cgal:fr-cqgvf-15b
+, author =  "Andreas Fabri and Laurent Rineau"
+, title =   "{CGAL} and the {Qt} Graphics View Framework"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgGraphicsViewSummary"
+, year =        2015
+}
+
+@incollection{cgal:lp-gi-15b
+, author =  "Olivier Devillers and S{\'e}bastien Loriot and Sylvain Pion"
+, title =   "{CGAL} Ipelets"
+, publisher =  "{CGAL Editorial Board}"
+, edition =     "{4.7}"
+, booktitle =   "{CGAL} User and Reference Manual"
+, url = "http://doc.cgal.org/4.7/Manual/packages.html#PkgCGALIpeletsSummary"
+, year =        2015
+}
diff --git a/biblio/how_to_cite_gudhi.bib b/biblio/how_to_cite_gudhi.bib
index 851dd5d9..c899d9fc 100644
--- a/biblio/how_to_cite_gudhi.bib
+++ b/biblio/how_to_cite_gudhi.bib
@@ -42,3 +42,12 @@
 , year =        2015
 }
 
+@incollection{gudhi:Alpha complex
+, author =  "Vincent Rouvreau"
+, title =   "Alpha complex"
+, publisher =  "{GUDHI Editorial Board}"
+, booktitle =   "{GUDHI} User and Reference Manual"
+, url = "http://gudhi.gforge.inria.fr/doc/latest/group__alpha__complex.html"
+, year =        2015
+}
+
diff --git a/data/points/alphacomplexdoc.off b/data/points/alphacomplexdoc.off
new file mode 100755
index 00000000..bb790193
--- /dev/null
+++ b/data/points/alphacomplexdoc.off
@@ -0,0 +1,10 @@
+nOFF
+2 7 0 0
+1.0 1.0
+7.0 0.0
+4.0 6.0
+9.0 6.0
+0.0 14.0
+2.0 19.0
+9.0 17.0
+
diff --git a/scripts/generate_version.sh b/scripts/generate_version.sh
index 323396dc..6f66a638 100755
--- a/scripts/generate_version.sh
+++ b/scripts/generate_version.sh
@@ -44,8 +44,6 @@ echo $VERSION_DIR
 mkdir "$VERSION_DIR"
 
 # TOP LEVEL FILE COPY
-cp $VERSION_FILE $VERSION_DIR
-cp $ROOT_DIR/CMakeGUDHIVersion.txt $VERSION_DIR
 cp $ROOT_DIR/README $VERSION_DIR
 cp $ROOT_DIR/Conventions.txt $VERSION_DIR
 cp $ROOT_DIR/COPYING $VERSION_DIR
@@ -55,11 +53,11 @@ cp $ROOT_DIR/src/Doxyfile $VERSION_DIR
 cp -R $ROOT_DIR/biblio $VERSION_DIR
 cp $ROOT_DIR/src/GUDHIConfigVersion.cmake.in $VERSION_DIR
 cp $ROOT_DIR/src/GUDHIConfig.cmake.in $VERSION_DIR
+cp $ROOT_DIR/CMakeGUDHIVersion.txt $VERSION_DIR
 cp $ROOT_DIR/GUDHIVersion.cmake.in $VERSION_DIR
 
 # PACKAGE LEVEL COPY
 PACKAGE_INC_DIR="/include"
-#PACKAGE_SRC_DIR="/source"
 PACKAGE_EX_DIR="/example"
 PACKAGE_CONCEPT_DIR="/concept"
 PACKAGE_DOC_DIR="/doc"
diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h
new file mode 100644
index 00000000..226bb257
--- /dev/null
+++ b/src/Alpha_complex/doc/Intro_alpha_complex.h
@@ -0,0 +1,168 @@
+/*    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):       Vincent Rouvreau
+ *
+ *    Copyright (C) 2015  INRIA Saclay (France)
+ *
+ *    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_ALPHA_COMPLEX_INTRO_ALPHA_COMPLEX_H_
+#define DOC_ALPHA_COMPLEX_INTRO_ALPHA_COMPLEX_H_
+
+// needs namespace for Doxygen to link on classes
+namespace Gudhi {
+// needs namespace for Doxygen to link on classes
+namespace alphacomplex {
+
+/**  \defgroup alpha_complex Alpha complex
+ * 
+ * \author    Vincent Rouvreau
+ * 
+ * @{
+ * 
+ * \section definition Definition
+ * 
+ * Alpha_complex is a <a target="_blank" href="https://en.wikipedia.org/wiki/Simplicial_complex">simplicial complex</a>
+ * constructed from the finite cells of a Delaunay Triangulation.
+ * 
+ * The filtration value of each simplex is computed as the square of the circumradius of the simplex if the circumsphere is empty (the simplex is then said to be Gabriel), and as the minimum of the filtration
+ * 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.
+ * 
+ * \image html "alpha_complex_representation.png" "Alpha-complex representation"
+ * 
+ * Alpha_complex is constructing a `Simplex_tree` using <a target="_blank"
+ * href="http://doc.cgal.org/latest/Triangulation/index.html#Chapter_Triangulations">Delaunay Triangulation</a>
+ * \cite cgal:hdj-t-15b from <a target="_blank" href="http://www.cgal.org/">CGAL</a> (the Computational Geometry
+ * Algorithms Library \cite cgal:eb-15b).
+ * 
+ * The complex is a template class requiring an Epick_d <a target="_blank"
+ * href="http://doc.cgal.org/latest/Kernel_d/index.html#Chapter_dD_Geometry_Kernel">dD Geometry Kernel</a>
+ * \cite cgal:s-gkd-15b from CGAL as template parameter.
+ * 
+ * \remark When Alpha_complex is constructed with an infinite value of alpha, the complex is a Delaunay complex.
+ * 
+ * \section pointsexample Example from points
+ * 
+ * This example builds the Delaunay triangulation from the given points in a 2D static kernel, and initializes the
+ * alpha complex with it.
+ * 
+ * Then, it is asked to display information about the alpha complex.
+ * 
+ * \include Alpha_complex/Alpha_complex_from_points.cpp
+ * 
+ * When launching:
+ * 
+ * \code $> ./alphapoints
+ * \endcode
+ *
+ * the program output is:
+ * 
+ * \include Alpha_complex/alphaoffreader_for_doc_60.txt
+ * 
+ * \section algorithm Algorithm
+ * 
+ * \subsection datastructure Data structure
+ * 
+ * In order to build the alpha complex, first, a Simplex tree is built from the cells of a Delaunay Triangulation.
+ * (The filtration value is set to NaN, which stands for unknown value):
+ * \image html "alpha_complex_doc.png" "Simplex tree structure construction example"
+ *
+ * \subsection filtrationcomputation Filtration value computation algorithm
+ * 
+ * \f{algorithm}{ 
+ * \caption{Filtration value computation algorithm}\label{alpha}
+ * \begin{algorithmic}
+ * \For{i : dimension $\rightarrow$ 0}
+ *   \ForAll{$\sigma$ of dimension i}
+ *     \If {filtration($\sigma$) is NaN}
+ *       \State filtration($\sigma$) = $\alpha^2(\sigma)$
+ *     \EndIf
+ *     \ForAll{$\tau$ face of $\sigma$} \Comment{propagate alpha filtration value}
+ *       \If {filtration($\tau$) is not NaN} 
+ *         \State filtration($\tau$) = min (filtration($\tau$), filtration($\sigma$))
+ *       \Else
+ *         \If {$\tau$ is not Gabriel for $\sigma$} 
+ *           \State filtration($\tau$) = filtration($\sigma$)
+ *         \EndIf
+ *       \EndIf
+ *     \EndFor
+ *   \EndFor
+ * \EndFor
+ * \State make\_filtration\_non\_decreasing()
+ * \State prune\_above\_filtration()
+ * \end{algorithmic}
+ * \f}
+ * 
+ * \subsubsection dimension2 Dimension 2
+ * 
+ * From the example above, it means the algorithm looks into each triangle ([0,1,2], [0,2,4], [1,2,3], ...),
+ * computes the filtration value of the triangle, and then propagates the filtration value as described
+ * here :
+ * \image html "alpha_complex_doc_420.png" "Filtration value propagation example"
+ * 
+ * \subsubsection dimension1 Dimension 1
+ * 
+ * Then, the algorithm looks into each edge ([0,1], [0,2], [1,2], ...),
+ * computes the filtration value of the edge (in this case, propagation will have no effect).
+ * 
+ * \subsubsection dimension0 Dimension 0
+ * 
+ * Finally, the algorithm looks into each vertex ([0], [1], [2], [3], [4], [5] and [6]) and
+ * sets the filtration value (0 in case of a vertex - propagation will have no effect).
+ * 
+ * \subsubsection nondecreasing Non decreasing filtration values
+ * 
+ * As the squared radii computed by CGAL are an approximation, it might happen that these alpha squared values do not quite define a proper filtration (i.e. non-decreasing with respect to inclusion).
+ * We fix that up by calling `Simplex_tree::make_filtration_non_decreasing()`.
+ * 
+ * \subsubsection pruneabove Prune above given filtration value
+ * 
+ * The simplex tree is pruned from the given maximum alpha squared value (cf. `Simplex_tree::prune_above_filtration()`).
+ * In the following example, the value is given by the user as argument of the program.
+ * 
+ * 
+ * \section offexample Example from OFF file
+ * 
+ * This example builds the Delaunay triangulation in a dynamic kernel, and initializes the alpha complex with it.
+ * 
+ * 
+ * Then, it is asked to display information about the alpha complex.
+ * 
+ * \include Alpha_complex/Alpha_complex_from_off.cpp
+ * 
+ * When launching:
+ * 
+ * \code $> ./alphaoffreader ../../data/points/alphacomplexdoc.off 32.0
+ * \endcode
+ *
+ * the program output is:
+ * 
+ * \include Alpha_complex/alphaoffreader_for_doc_32.txt
+ * 
+ * \copyright GNU General Public License v3.                         
+ * \verbatim  Contact: gudhi-users@lists.gforge.inria.fr \endverbatim
+ */
+/** @} */  // end defgroup alpha_complex
+
+}  // namespace alphacomplex
+
+}  // namespace Gudhi
+
+#endif  // DOC_ALPHA_COMPLEX_INTRO_ALPHA_COMPLEX_H_
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diff --git a/src/Alpha_complex/doc/alpha_complex_representation.png b/src/Alpha_complex/doc/alpha_complex_representation.png
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index 00000000..7b81cd69
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diff --git a/src/Alpha_complex/example/Alpha_complex_from_off.cpp b/src/Alpha_complex/example/Alpha_complex_from_off.cpp
new file mode 100644
index 00000000..963ef5ca
--- /dev/null
+++ b/src/Alpha_complex/example/Alpha_complex_from_off.cpp
@@ -0,0 +1,56 @@
+#include <gudhi/Alpha_complex.h>
+#include <CGAL/Epick_d.h>
+
+#include <iostream>
+#include <string>
+
+void usage(int nbArgs, char * const progName) {
+  std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n";
+  std::cerr << "Usage: " << progName << " filename.off alpha_square_max_value [ouput_file.txt]\n";
+  std::cerr << "       i.e.: " << progName << " ../../data/points/alphacomplexdoc.off 60.0\n";
+  exit(-1);  // ----- >>
+}
+
+int main(int argc, char **argv) {
+  if ((argc != 3) && (argc != 4)) usage(argc, (argv[0] - 1));
+
+  std::string off_file_name(argv[1]);
+  double alpha_square_max_value = atof(argv[2]);
+
+  // ----------------------------------------------------------------------------
+  // Init of an alpha complex from an OFF file
+  // ----------------------------------------------------------------------------
+  typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel;
+  Gudhi::alphacomplex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_name, alpha_square_max_value);
+
+  std::streambuf* streambufffer;
+  std::ofstream ouput_file_stream;
+
+  if (argc == 4) {
+    ouput_file_stream.open(std::string(argv[3]));
+    streambufffer = ouput_file_stream.rdbuf();
+  } else {
+    streambufffer = std::cout.rdbuf();
+  }
+
+  std::ostream output_stream(streambufffer);
+
+  // ----------------------------------------------------------------------------
+  // Display information about the alpha complex
+  // ----------------------------------------------------------------------------
+  output_stream << "Alpha complex is of dimension " << alpha_complex_from_file.dimension() <<
+      " - " << alpha_complex_from_file.num_simplices() << " simplices - " <<
+      alpha_complex_from_file.num_vertices() << " vertices." << std::endl;
+
+  output_stream << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl;
+  for (auto f_simplex : alpha_complex_from_file.filtration_simplex_range()) {
+    output_stream << "   ( ";
+    for (auto vertex : alpha_complex_from_file.simplex_vertex_range(f_simplex)) {
+      output_stream << vertex << " ";
+    }
+    output_stream << ") -> " << "[" << alpha_complex_from_file.filtration(f_simplex) << "] ";
+    output_stream << std::endl;
+  }
+  ouput_file_stream.close();
+  return 0;
+}
diff --git a/src/Alpha_complex/example/Alpha_complex_from_points.cpp b/src/Alpha_complex/example/Alpha_complex_from_points.cpp
new file mode 100644
index 00000000..cd17af1e
--- /dev/null
+++ b/src/Alpha_complex/example/Alpha_complex_from_points.cpp
@@ -0,0 +1,62 @@
+#include <CGAL/Epick_d.h>
+#include <gudhi/Alpha_complex.h>
+
+#include <iostream>
+#include <string>
+#include <vector>
+#include <limits>  // for numeric limits
+
+typedef CGAL::Epick_d< CGAL::Dimension_tag<2> > Kernel;
+typedef Kernel::Point_d Point;
+typedef std::vector<Point> Vector_of_points;
+
+void usage(int nbArgs, char * const progName) {
+  std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n";
+  std::cerr << "Usage: " << progName << " [alpha_square_max_value]\n";
+  std::cerr << "       i.e.: " << progName << " 60.0\n";
+  exit(-1);  // ----- >>
+}
+
+int main(int argc, char **argv) {
+  if ((argc != 1) && (argc != 2)) usage(argc, (argv[0] - 1));
+
+  // Delaunay complex if alpha_square_max_value is not given by the user.
+  double alpha_square_max_value = std::numeric_limits<double>::infinity();
+  if (argc == 2)
+    alpha_square_max_value = atof(argv[1]);
+
+  // ----------------------------------------------------------------------------
+  // Init of a list of points
+  // ----------------------------------------------------------------------------
+  Vector_of_points points;
+  points.push_back(Point(1.0, 1.0));
+  points.push_back(Point(7.0, 0.0));
+  points.push_back(Point(4.0, 6.0));
+  points.push_back(Point(9.0, 6.0));
+  points.push_back(Point(0.0, 14.0));
+  points.push_back(Point(2.0, 19.0));
+  points.push_back(Point(9.0, 17.0));
+
+  // ----------------------------------------------------------------------------
+  // Init of an alpha complex from the list of points
+  // ----------------------------------------------------------------------------
+  Gudhi::alphacomplex::Alpha_complex<Kernel> alpha_complex_from_points(points, alpha_square_max_value);
+
+  // ----------------------------------------------------------------------------
+  // Display information about the alpha complex
+  // ----------------------------------------------------------------------------
+  std::cout << "Alpha complex is of dimension " << alpha_complex_from_points.dimension() <<
+      " - " << alpha_complex_from_points.num_simplices() << " simplices - " <<
+      alpha_complex_from_points.num_vertices() << " vertices." << std::endl;
+
+  std::cout << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl;
+  for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) {
+    std::cout << "   ( ";
+    for (auto vertex : alpha_complex_from_points.simplex_vertex_range(f_simplex)) {
+      std::cout << vertex << " ";
+    }
+    std::cout << ") -> " << "[" << alpha_complex_from_points.filtration(f_simplex) << "] ";
+    std::cout << std::endl;
+  }
+  return 0;
+}
diff --git a/src/Alpha_complex/example/CMakeLists.txt b/src/Alpha_complex/example/CMakeLists.txt
new file mode 100644
index 00000000..f1346867
--- /dev/null
+++ b/src/Alpha_complex/example/CMakeLists.txt
@@ -0,0 +1,43 @@
+cmake_minimum_required(VERSION 2.6)
+project(GUDHIAlphaShapesExample)
+
+# need CGAL 4.7
+# cmake -DCGAL_DIR=~/workspace/CGAL-4.7-Ic-41 ../../..
+if(CGAL_FOUND)
+  if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+    message(STATUS "CGAL version: ${CGAL_VERSION}.")
+
+    find_package(Eigen3 3.1.0)
+    if (EIGEN3_FOUND)
+      message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
+      include( ${EIGEN3_USE_FILE} )
+
+      add_executable ( alphapoints Alpha_complex_from_points.cpp )
+      target_link_libraries(alphapoints  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+      add_executable ( alphaoffreader Alpha_complex_from_off.cpp )
+      target_link_libraries(alphaoffreader  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+      if (TBB_FOUND)
+        target_link_libraries(alphapoints ${TBB_RELEASE_LIBRARY})
+        target_link_libraries(alphaoffreader ${TBB_RELEASE_LIBRARY})
+      endif()
+
+      add_test(alphapoints ${CMAKE_CURRENT_BINARY_DIR}/alphapoints)
+      # Do not forget to copy test files in current binary dir
+      file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+      add_test(alphaoffreader_doc_60 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader alphacomplexdoc.off 60.0 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt)
+      add_test(alphaoffreader_doc_32 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader alphacomplexdoc.off 32.0 ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt)
+      if (DIFF_PATH)
+        # Do not forget to copy test results files in current binary dir
+        file(COPY "alphaoffreader_for_doc_32.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+        file(COPY "alphaoffreader_for_doc_60.txt" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+
+        add_test(alphaoffreader_doc_60_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_60.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_60.txt)
+        add_test(alphaoffreader_doc_32_diff_files ${DIFF_PATH} ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt)
+      endif()
+    else()
+      message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.")
+    endif()
+  else()
+    message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.")
+  endif ()
+endif()
diff --git a/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt b/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt
new file mode 100644
index 00000000..13183e86
--- /dev/null
+++ b/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt
@@ -0,0 +1,22 @@
+Alpha complex is of dimension 2 - 20 simplices - 7 vertices.
+Iterator on alpha complex simplices in the filtration order, with [filtration value]:
+   ( 0 ) -> [0] 
+   ( 1 ) -> [0] 
+   ( 2 ) -> [0] 
+   ( 3 ) -> [0] 
+   ( 4 ) -> [0] 
+   ( 5 ) -> [0] 
+   ( 6 ) -> [0] 
+   ( 3 2 ) -> [6.25] 
+   ( 5 4 ) -> [7.25] 
+   ( 2 0 ) -> [8.5] 
+   ( 1 0 ) -> [9.25] 
+   ( 3 1 ) -> [10] 
+   ( 2 1 ) -> [11.25] 
+   ( 3 2 1 ) -> [12.5] 
+   ( 2 1 0 ) -> [12.9959] 
+   ( 6 5 ) -> [13.25] 
+   ( 4 2 ) -> [20] 
+   ( 6 4 ) -> [22.7367] 
+   ( 6 5 4 ) -> [22.7367] 
+   ( 6 3 ) -> [30.25] 
diff --git a/src/Alpha_complex/example/alphaoffreader_for_doc_60.txt b/src/Alpha_complex/example/alphaoffreader_for_doc_60.txt
new file mode 100644
index 00000000..71f29a00
--- /dev/null
+++ b/src/Alpha_complex/example/alphaoffreader_for_doc_60.txt
@@ -0,0 +1,27 @@
+Alpha complex is of dimension 2 - 25 simplices - 7 vertices.
+Iterator on alpha complex simplices in the filtration order, with [filtration value]:
+   ( 0 ) -> [0] 
+   ( 1 ) -> [0] 
+   ( 2 ) -> [0] 
+   ( 3 ) -> [0] 
+   ( 4 ) -> [0] 
+   ( 5 ) -> [0] 
+   ( 6 ) -> [0] 
+   ( 3 2 ) -> [6.25] 
+   ( 5 4 ) -> [7.25] 
+   ( 2 0 ) -> [8.5] 
+   ( 1 0 ) -> [9.25] 
+   ( 3 1 ) -> [10] 
+   ( 2 1 ) -> [11.25] 
+   ( 3 2 1 ) -> [12.5] 
+   ( 2 1 0 ) -> [12.9959] 
+   ( 6 5 ) -> [13.25] 
+   ( 4 2 ) -> [20] 
+   ( 6 4 ) -> [22.7367] 
+   ( 6 5 4 ) -> [22.7367] 
+   ( 6 3 ) -> [30.25] 
+   ( 6 2 ) -> [36.5] 
+   ( 6 3 2 ) -> [36.5] 
+   ( 6 4 2 ) -> [37.2449] 
+   ( 4 0 ) -> [59.7107] 
+   ( 4 2 0 ) -> [59.7107] 
diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h
new file mode 100644
index 00000000..ca2b68ca
--- /dev/null
+++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h
@@ -0,0 +1,415 @@
+/*    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):       Vincent Rouvreau
+ *
+ *    Copyright (C) 2015  INRIA Saclay (France)
+ *
+ *    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 ALPHA_COMPLEX_H_
+#define ALPHA_COMPLEX_H_
+
+// to construct a simplex_tree from Delaunay_triangulation
+#include <gudhi/graph_simplicial_complex.h>
+#include <gudhi/Simplex_tree.h>
+#include <gudhi/Debug_utils.h>
+// to construct Alpha_complex from a OFF file of points
+#include <gudhi/Points_off_io.h>
+
+#include <stdlib.h>
+#include <math.h>  // isnan, fmax
+
+#include <CGAL/Delaunay_triangulation.h>
+#include <CGAL/Epick_d.h>
+#include <CGAL/Spatial_sort_traits_adapter_d.h>
+
+#include <iostream>
+#include <vector>
+#include <string>
+#include <limits>  // NaN
+#include <map>
+#include <utility>  // std::pair
+#include <stdexcept>
+#include <numeric>  // for std::iota
+
+namespace Gudhi {
+
+namespace alphacomplex {
+
+/**
+ * \class Alpha_complex Alpha_complex.h gudhi/Alpha_complex.h
+ * \brief Alpha complex data structure.
+ * 
+ * \ingroup alpha_complex
+ * 
+ * \details
+ * The data structure can be constructed from a CGAL Delaunay triangulation (for more informations on CGAL Delaunay 
+ * triangulation, please refer to the corresponding chapter in page http://doc.cgal.org/latest/Triangulation/) or from
+ * an OFF file (cf. Points_off_reader).
+ * 
+ * Please refer to \ref alpha_complex for examples.
+ *
+ * The complex is a template class requiring an Epick_d <a target="_blank"
+ * href="http://doc.cgal.org/latest/Kernel_d/index.html#Chapter_dD_Geometry_Kernel">dD Geometry Kernel</a>
+ * \cite cgal:s-gkd-15b from CGAL as template, default value is <a target="_blank"
+ * href="http://doc.cgal.org/latest/Kernel_d/classCGAL_1_1Epick__d.html">CGAL::Epick_d</a>
+ * < <a target="_blank" href="http://doc.cgal.org/latest/Kernel_23/classCGAL_1_1Dynamic__dimension__tag.html">
+ * CGAL::Dynamic_dimension_tag </a> >
+ * 
+ * \remark When Alpha_complex is constructed with an infinite value of alpha, the complex is a Delaunay complex.
+ * 
+ */
+template<class Kernel = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>>
+class Alpha_complex : public Simplex_tree<> {
+ public:
+  // Add an int in TDS to save point index in the structure
+  typedef CGAL::Triangulation_data_structure<CGAL::Dynamic_dimension_tag,
+                              CGAL::Triangulation_vertex<Kernel, std::ptrdiff_t>,
+                              CGAL::Triangulation_full_cell<Kernel> > TDS;
+  /** \brief A Delaunay triangulation of a set of points in \f$ \mathbb{R}^D\f$.*/
+  typedef CGAL::Delaunay_triangulation<Kernel, TDS> Delaunay_triangulation;
+
+  /** \brief A point in Euclidean space.*/
+  typedef typename Kernel::Point_d Point_d;
+  /** \brief Geometric traits class that provides the geometric types and predicates needed by Delaunay
+   * triangulations.*/
+  typedef Kernel Geom_traits;
+
+ private:
+  // From Simplex_tree
+  // Type required to insert into a simplex_tree (with or without subfaces).
+  typedef std::vector<Vertex_handle> Vector_vertex;
+
+  // Simplex_result is the type returned from simplex_tree insert function.
+  typedef typename std::pair<Simplex_handle, bool> Simplex_result;
+
+  typedef typename Kernel::Compute_squared_radius_d Squared_Radius;
+  typedef typename Kernel::Side_of_bounded_sphere_d Is_Gabriel;
+  typedef typename Kernel::Point_dimension_d        Point_Dimension;
+
+  // Type required to compute squared radius, or side of bounded sphere on a vector of points.
+  typedef typename std::vector<Point_d> Vector_of_CGAL_points;
+
+  // Vertex_iterator type from CGAL.
+  typedef typename Delaunay_triangulation::Vertex_iterator CGAL_vertex_iterator;
+
+  // size_type type from CGAL.
+  typedef typename Delaunay_triangulation::size_type size_type;
+
+  // Map type to switch from simplex tree vertex handle to CGAL vertex iterator.
+  typedef typename std::map< Vertex_handle, CGAL_vertex_iterator > Vector_vertex_iterator;
+
+ private:
+  /** \brief Vertex iterator vector to switch from simplex tree vertex handle to CGAL vertex iterator.
+   * Vertex handles are inserted sequentially, starting at 0.*/
+  Vector_vertex_iterator vertex_handle_to_iterator_;
+  /** \brief Pointer on the CGAL Delaunay triangulation.*/
+  Delaunay_triangulation* triangulation_;
+  /** \brief Kernel for triangulation_ functions access.*/
+  Kernel kernel_;
+
+ public:
+  /** \brief Alpha_complex constructor from an OFF file name.
+   * Uses the Delaunay_triangulation_off_reader to construct the Delaunay triangulation required to initialize 
+   * the Alpha_complex.
+   * 
+   * Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous.
+   *
+   * @param[in] off_file_name OFF file [path and] name.
+   * @param[in] max_alpha_square maximum for alpha square value. Default value is +\f$\infty\f$.
+   */
+  Alpha_complex(const std::string& off_file_name,
+                Filtration_value max_alpha_square = std::numeric_limits<Filtration_value>::infinity())
+      : triangulation_(nullptr) {
+    Gudhi::Points_off_reader<Point_d> off_reader(off_file_name);
+    if (!off_reader.is_valid()) {
+      std::cerr << "Alpha_complex - Unable to read file " << off_file_name << "\n";
+      exit(-1);  // ----- >>
+    }
+
+    init_from_range(off_reader.get_point_cloud(), max_alpha_square);
+  }
+
+  /** \brief Alpha_complex constructor from a list of points.
+   *
+   * Duplicate points are inserted once in the Alpha_complex. This is the reason why the vertices may be not contiguous.
+   * 
+   * @param[in] points Range of points to triangulate. Points must be in Kernel::Point_d
+   * @param[in] max_alpha_square maximum for alpha square value. Default value is +\f$\infty\f$.
+   * 
+   * The type InputPointRange must be a range for which std::begin and
+   * std::end return input iterators on a Kernel::Point_d.
+   * 
+   * @post Compare num_simplices with InputPointRange points number (not the same in case of duplicate points). 
+   */
+  template<typename InputPointRange >
+  Alpha_complex(const InputPointRange& points,
+                Filtration_value max_alpha_square = std::numeric_limits<Filtration_value>::infinity())
+      : triangulation_(nullptr) {
+    init_from_range(points, max_alpha_square);
+  }
+
+  /** \brief Alpha_complex destructor.
+   *
+   * @warning Deletes the Delaunay triangulation.
+   */
+  ~Alpha_complex() {
+    delete triangulation_;
+  }
+
+  // Forbid copy/move constructor/assignment operator
+  Alpha_complex(const Alpha_complex& other) = delete;
+  Alpha_complex& operator= (const Alpha_complex& other) = delete;
+  Alpha_complex (Alpha_complex&& other) = delete;
+  Alpha_complex& operator= (Alpha_complex&& other) = delete;
+
+  /** \brief get_point returns the point corresponding to the vertex given as parameter.
+   *
+   * @param[in] vertex Vertex handle of the point to retrieve.
+   * @return The point found.
+   * @exception std::out_of_range In case vertex is not found (cf. std::vector::at).
+   */
+  Point_d get_point(Vertex_handle vertex) const {
+    return vertex_handle_to_iterator_.at(vertex)->point();
+  }
+
+ private:
+  template<typename InputPointRange >
+  void init_from_range(const InputPointRange& points, Filtration_value max_alpha_square) {
+    auto first = std::begin(points);
+    auto last = std::end(points);
+    if (first != last) {
+      // point_dimension function initialization
+      Point_Dimension point_dimension = kernel_.point_dimension_d_object();
+
+      // Delaunay triangulation is point dimension.
+      triangulation_ = new Delaunay_triangulation(point_dimension(*first));
+
+      std::vector<Point_d> points(first, last);
+
+      // Creates a vector {0, 1, ..., N-1}
+      std::vector<std::ptrdiff_t> indices(boost::counting_iterator<std::ptrdiff_t>(0),
+                                          boost::counting_iterator<std::ptrdiff_t>(points.size()));
+
+      // Sort indices considering CGAL spatial sort
+      typedef CGAL::Spatial_sort_traits_adapter_d<Kernel, Point_d*> Search_traits_d;
+      spatial_sort(indices.begin(), indices.end(), Search_traits_d(&(points[0])));
+
+      typename Delaunay_triangulation::Full_cell_handle hint;
+      for (auto index : indices) {
+        typename Delaunay_triangulation::Vertex_handle pos = triangulation_->insert(points[index], hint);
+        // Save index value as data to retrieve it after insertion
+        pos->data() = index;
+        hint = pos->full_cell();
+      }
+      init(max_alpha_square);
+    }
+  }
+
+  /** \brief Initialize the Alpha_complex from the Delaunay triangulation.
+   *
+   * @param[in] max_alpha_square maximum for alpha square value.
+   * 
+   * @warning Delaunay triangulation must be already constructed with at least one vertex and dimension must be more 
+   * than 0.
+   * 
+   * Initialization can be launched once.
+   */
+  void init(Filtration_value max_alpha_square) {
+    if (triangulation_ == nullptr) {
+      std::cerr << "Alpha_complex init - Cannot init from a NULL triangulation\n";
+      return;  // ----- >>
+    }
+    if (triangulation_->number_of_vertices() < 1) {
+      std::cerr << "Alpha_complex init - Cannot init from a triangulation without vertices\n";
+      return;  // ----- >>
+    }
+    if (triangulation_->maximal_dimension() < 1) {
+      std::cerr << "Alpha_complex init - Cannot init from a zero-dimension triangulation\n";
+      return;  // ----- >>
+    }
+    if (num_vertices() > 0) {
+      std::cerr << "Alpha_complex init - Cannot init twice\n";
+      return;  // ----- >>
+    }
+
+    set_dimension(triangulation_->maximal_dimension());
+
+    // --------------------------------------------------------------------------------------------
+    // double map to retrieve simplex tree vertex handles from CGAL vertex iterator and vice versa
+    // Loop on triangulation vertices list
+    for (CGAL_vertex_iterator vit = triangulation_->vertices_begin(); vit != triangulation_->vertices_end(); ++vit) {
+      if (!triangulation_->is_infinite(*vit)) {
+#ifdef DEBUG_TRACES
+        std::cout << "Vertex insertion - " << vit->data() << " -> " << vit->point() << std::endl;
+#endif  // DEBUG_TRACES
+        vertex_handle_to_iterator_.emplace(vit->data(), vit);
+      }
+    }
+    // --------------------------------------------------------------------------------------------
+
+    // --------------------------------------------------------------------------------------------
+    // Simplex_tree construction from loop on triangulation finite full cells list
+    for (auto cit = triangulation_->finite_full_cells_begin(); cit != triangulation_->finite_full_cells_end(); ++cit) {
+      Vector_vertex vertexVector;
+#ifdef DEBUG_TRACES
+      std::cout << "Simplex_tree insertion ";
+#endif  // DEBUG_TRACES
+      for (auto vit = cit->vertices_begin(); vit != cit->vertices_end(); ++vit) {
+        if (*vit != nullptr) {
+#ifdef DEBUG_TRACES
+          std::cout << " " << (*vit)->data();
+#endif  // DEBUG_TRACES
+          // Vector of vertex construction for simplex_tree structure
+          vertexVector.push_back((*vit)->data());
+        }
+      }
+#ifdef DEBUG_TRACES
+      std::cout << std::endl;
+#endif  // DEBUG_TRACES
+      // Insert each simplex and its subfaces in the simplex tree - filtration is NaN
+      insert_simplex_and_subfaces(vertexVector, std::numeric_limits<double>::quiet_NaN());
+    }
+    // --------------------------------------------------------------------------------------------
+
+    // --------------------------------------------------------------------------------------------
+    // ### For i : d -> 0
+    for (int decr_dim = dimension(); decr_dim >= 0; decr_dim--) {
+      // ### Foreach Sigma of dim i
+      for (auto f_simplex : skeleton_simplex_range(decr_dim)) {
+        int f_simplex_dim = dimension(f_simplex);
+        if (decr_dim == f_simplex_dim) {
+          Vector_of_CGAL_points pointVector;
+#ifdef DEBUG_TRACES
+          std::cout << "Sigma of dim " << decr_dim << " is";
+#endif  // DEBUG_TRACES
+          for (auto vertex : simplex_vertex_range(f_simplex)) {
+            pointVector.push_back(get_point(vertex));
+#ifdef DEBUG_TRACES
+            std::cout << " " << vertex;
+#endif  // DEBUG_TRACES
+          }
+#ifdef DEBUG_TRACES
+          std::cout << std::endl;
+#endif  // DEBUG_TRACES
+          // ### If filt(Sigma) is NaN : filt(Sigma) = alpha(Sigma)
+          if (isnan(filtration(f_simplex))) {
+            Filtration_value alpha_complex_filtration = 0.0;
+            // No need to compute squared_radius on a single point - alpha is 0.0
+            if (f_simplex_dim > 0) {
+              // squared_radius function initialization
+              Squared_Radius squared_radius = kernel_.compute_squared_radius_d_object();
+
+              alpha_complex_filtration = squared_radius(pointVector.begin(), pointVector.end());
+            }
+            assign_filtration(f_simplex, alpha_complex_filtration);
+#ifdef DEBUG_TRACES
+            std::cout << "filt(Sigma) is NaN : filt(Sigma) =" << filtration(f_simplex) << std::endl;
+#endif  // DEBUG_TRACES
+          }
+          propagate_alpha_filtration(f_simplex, decr_dim);
+        }
+      }
+    }
+    // --------------------------------------------------------------------------------------------
+
+    // --------------------------------------------------------------------------------------------
+    // As Alpha value is an approximation, we have to make filtration non decreasing while increasing the dimension
+    bool modified_filt = make_filtration_non_decreasing();
+    // Remove all simplices that have a filtration value greater than max_alpha_square
+    // Remark: prune_above_filtration does not require initialize_filtration to be done before.
+    modified_filt |= prune_above_filtration(max_alpha_square);
+    if (modified_filt) {
+      initialize_filtration();
+    }
+    // --------------------------------------------------------------------------------------------
+  }
+
+  template<typename Simplex_handle>
+  void propagate_alpha_filtration(Simplex_handle f_simplex, int decr_dim) {
+    // ### Foreach Tau face of Sigma
+    for (auto f_boundary : boundary_simplex_range(f_simplex)) {
+#ifdef DEBUG_TRACES
+      std::cout << " | --------------------------------------------------\n";
+      std::cout << " | Tau ";
+      for (auto vertex : simplex_vertex_range(f_boundary)) {
+        std::cout << vertex << " ";
+      }
+      std::cout << "is a face of Sigma\n";
+      std::cout << " | isnan(filtration(Tau)=" << isnan(filtration(f_boundary)) << std::endl;
+#endif  // DEBUG_TRACES
+      // ### If filt(Tau) is not NaN
+      if (!isnan(filtration(f_boundary))) {
+        // ### filt(Tau) = fmin(filt(Tau), filt(Sigma))
+        Filtration_value alpha_complex_filtration = fmin(filtration(f_boundary), filtration(f_simplex));
+        assign_filtration(f_boundary, alpha_complex_filtration);
+#ifdef DEBUG_TRACES
+        std::cout << " | filt(Tau) = fmin(filt(Tau), filt(Sigma)) = " << filtration(f_boundary) << std::endl;
+#endif  // DEBUG_TRACES
+        // ### Else
+      } else {
+        // No need to compute is_gabriel for dimension <= 2
+        // i.e. : Sigma = (3,1) => Tau = 1
+        if (decr_dim > 1) {
+          // insert the Tau points in a vector for is_gabriel function
+          Vector_of_CGAL_points pointVector;
+#ifdef DEBUG_TRACES
+          Vertex_handle vertexForGabriel = Vertex_handle();
+#endif  // DEBUG_TRACES
+          for (auto vertex : simplex_vertex_range(f_boundary)) {
+            pointVector.push_back(get_point(vertex));
+          }
+          // Retrieve the Sigma point that is not part of Tau - parameter for is_gabriel function
+          Point_d point_for_gabriel;
+          for (auto vertex : simplex_vertex_range(f_simplex)) {
+            point_for_gabriel = get_point(vertex);
+            if (std::find(pointVector.begin(), pointVector.end(), point_for_gabriel) == pointVector.end()) {
+#ifdef DEBUG_TRACES
+              // vertex is not found in Tau
+              vertexForGabriel = vertex;
+#endif  // DEBUG_TRACES
+              // No need to continue loop
+              break;
+            }
+          }
+          // is_gabriel function initialization
+          Is_Gabriel is_gabriel = kernel_.side_of_bounded_sphere_d_object();
+          bool is_gab = is_gabriel(pointVector.begin(), pointVector.end(), point_for_gabriel)
+              != CGAL::ON_BOUNDED_SIDE;
+#ifdef DEBUG_TRACES
+          std::cout << " | Tau is_gabriel(Sigma)=" << is_gab << " - vertexForGabriel=" << vertexForGabriel << std::endl;
+#endif  // DEBUG_TRACES
+          // ### If Tau is not Gabriel of Sigma
+          if (false == is_gab) {
+            // ### filt(Tau) = filt(Sigma)
+            Filtration_value alpha_complex_filtration = filtration(f_simplex);
+            assign_filtration(f_boundary, alpha_complex_filtration);
+#ifdef DEBUG_TRACES
+            std::cout << " | filt(Tau) = filt(Sigma) = " << filtration(f_boundary) << std::endl;
+#endif  // DEBUG_TRACES
+          }
+        }
+      }
+    }
+  }
+};
+
+}  // namespace alphacomplex
+
+}  // namespace Gudhi
+
+#endif  // ALPHA_COMPLEX_H_
diff --git a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp
new file mode 100644
index 00000000..80b39924
--- /dev/null
+++ b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp
@@ -0,0 +1,243 @@
+/*    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):       Vincent Rouvreau
+ *
+ *    Copyright (C) 2015  INRIA Saclay (France)
+ *
+ *    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/>.
+ */
+
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "alpha_complex"
+#include <boost/test/unit_test.hpp>
+
+#include <CGAL/Delaunay_triangulation.h>
+#include <CGAL/Epick_d.h>
+
+#include <cmath>  // float comparison
+#include <limits>
+#include <string>
+#include <vector>
+
+#include <gudhi/Alpha_complex.h>
+
+// Use dynamic_dimension_tag for the user to be able to set dimension
+typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel_d;
+// The triangulation uses the default instantiation of the TriangulationDataStructure template parameter
+
+BOOST_AUTO_TEST_CASE(ALPHA_DOC_OFF_file) {
+  // ----------------------------------------------------------------------------
+  //
+  // Init of an alpha-complex from a OFF file
+  //
+  // ----------------------------------------------------------------------------
+  std::string off_file_name("alphacomplexdoc.off");
+  double max_alpha_square_value = 60.0;
+  std::cout << "========== OFF FILE NAME = " << off_file_name << " - alpha²=" <<
+      max_alpha_square_value << "==========" << std::endl;
+
+  Gudhi::alphacomplex::Alpha_complex<Kernel_d> alpha_complex_from_file(off_file_name, max_alpha_square_value);
+
+  const int DIMENSION = 2;
+  std::cout << "alpha_complex_from_file.dimension()=" << alpha_complex_from_file.dimension() << std::endl;
+  BOOST_CHECK(alpha_complex_from_file.dimension() == DIMENSION);
+
+  const int NUMBER_OF_VERTICES = 7;
+  std::cout << "alpha_complex_from_file.num_vertices()=" << alpha_complex_from_file.num_vertices() << std::endl;
+  BOOST_CHECK(alpha_complex_from_file.num_vertices() == NUMBER_OF_VERTICES);
+
+  const int NUMBER_OF_SIMPLICES = 25;
+  std::cout << "alpha_complex_from_file.num_simplices()=" << alpha_complex_from_file.num_simplices() << std::endl;
+  BOOST_CHECK(alpha_complex_from_file.num_simplices() == NUMBER_OF_SIMPLICES);
+
+}
+
+BOOST_AUTO_TEST_CASE(ALPHA_DOC_OFF_file_filtered) {
+  // ----------------------------------------------------------------------------
+  //
+  // Init of an alpha-complex from a OFF file
+  //
+  // ----------------------------------------------------------------------------
+  std::string off_file_name("alphacomplexdoc.off");
+  double max_alpha_square_value = 59.0;
+  std::cout << "========== OFF FILE NAME = " << off_file_name << " - alpha²=" <<
+      max_alpha_square_value << "==========" << std::endl;
+
+  // Use of the default dynamic kernel
+  Gudhi::alphacomplex::Alpha_complex<> alpha_complex_from_file(off_file_name, max_alpha_square_value);
+
+  const int DIMENSION = 2;
+  std::cout << "alpha_complex_from_file.dimension()=" << alpha_complex_from_file.dimension() << std::endl;
+  BOOST_CHECK(alpha_complex_from_file.dimension() == DIMENSION);
+
+  const int NUMBER_OF_VERTICES = 7;
+  std::cout << "alpha_complex_from_file.num_vertices()=" << alpha_complex_from_file.num_vertices() << std::endl;
+  BOOST_CHECK(alpha_complex_from_file.num_vertices() == NUMBER_OF_VERTICES);
+
+  const int NUMBER_OF_SIMPLICES = 23;
+  std::cout << "alpha_complex_from_file.num_simplices()=" << alpha_complex_from_file.num_simplices() << std::endl;
+  BOOST_CHECK(alpha_complex_from_file.num_simplices() == NUMBER_OF_SIMPLICES);
+}
+
+bool are_almost_the_same(float a, float b) {
+  return std::fabs(a - b) < std::numeric_limits<float>::epsilon();
+}
+
+// Use dynamic_dimension_tag for the user to be able to set dimension
+typedef CGAL::Epick_d< CGAL::Dimension_tag<4> > Kernel_s;
+typedef Kernel_s::Point_d Point;
+typedef std::vector<Point> Vector_of_points;
+
+
+bool is_point_in_list(Vector_of_points points_list, Point point) {
+  for (auto& point_in_list : points_list) {
+    if (point_in_list == point) {
+      return true;  // point found
+    }
+  }
+  return false;  // point not found
+}
+
+BOOST_AUTO_TEST_CASE(Alpha_complex_from_points) {
+  // ----------------------------------------------------------------------------
+  // Init of a list of points
+  // ----------------------------------------------------------------------------
+  Vector_of_points points;
+  std::vector<double> coords = { 0.0, 0.0, 0.0, 1.0 };
+  points.push_back(Point(coords.begin(), coords.end()));
+  coords = { 0.0, 0.0, 1.0, 0.0 };
+  points.push_back(Point(coords.begin(), coords.end()));
+  coords = { 0.0, 1.0, 0.0, 0.0 };
+  points.push_back(Point(coords.begin(), coords.end()));
+  coords = { 1.0, 0.0, 0.0, 0.0 };
+  points.push_back(Point(coords.begin(), coords.end()));
+
+  // ----------------------------------------------------------------------------
+  // Init of an alpha complex from the list of points
+  // ----------------------------------------------------------------------------
+  Gudhi::alphacomplex::Alpha_complex<Kernel_s> alpha_complex_from_points(points);
+
+  std::cout << "========== Alpha_complex_from_points ==========" << std::endl;
+
+  // Another way to check num_simplices
+  std::cout << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl;
+  int num_simplices = 0;
+  for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) {
+    num_simplices++;
+    std::cout << "   ( ";
+    for (auto vertex : alpha_complex_from_points.simplex_vertex_range(f_simplex)) {
+      std::cout << vertex << " ";
+    }
+    std::cout << ") -> " << "[" << alpha_complex_from_points.filtration(f_simplex) << "] ";
+    std::cout << std::endl;
+  }
+  BOOST_CHECK(num_simplices == 15);
+  std::cout << "alpha_complex_from_points.num_simplices()=" << alpha_complex_from_points.num_simplices() << std::endl;
+  BOOST_CHECK(alpha_complex_from_points.num_simplices() == 15);
+
+  std::cout << "alpha_complex_from_points.dimension()=" << alpha_complex_from_points.dimension() << std::endl;
+  BOOST_CHECK(alpha_complex_from_points.dimension() == 4);
+  std::cout << "alpha_complex_from_points.num_vertices()=" << alpha_complex_from_points.num_vertices() << std::endl;
+  BOOST_CHECK(alpha_complex_from_points.num_vertices() == 4);
+
+  for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) {
+    switch (alpha_complex_from_points.dimension(f_simplex)) {
+      case 0:
+        BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 0.0));
+        break;
+      case 1:
+        BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 1.0/2.0));
+        break;
+      case 2:
+        BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 2.0/3.0));
+        break;
+      case 3:
+        BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 3.0/4.0));
+        break;
+      default:
+        BOOST_CHECK(false);  // Shall not happen
+        break;
+    }
+  }
+
+  Point p0 = alpha_complex_from_points.get_point(0);
+  std::cout << "alpha_complex_from_points.get_point(0)=" << p0 << std::endl;
+  BOOST_CHECK(4 == p0.dimension());
+  BOOST_CHECK(is_point_in_list(points, p0));
+
+  Point p1 = alpha_complex_from_points.get_point(1);
+  std::cout << "alpha_complex_from_points.get_point(1)=" << p1 << std::endl;
+  BOOST_CHECK(4 == p1.dimension());
+  BOOST_CHECK(is_point_in_list(points, p1));
+
+  Point p2 = alpha_complex_from_points.get_point(2);
+  std::cout << "alpha_complex_from_points.get_point(2)=" << p2 << std::endl;
+  BOOST_CHECK(4 == p2.dimension());
+  BOOST_CHECK(is_point_in_list(points, p2));
+
+  Point p3 = alpha_complex_from_points.get_point(3);
+  std::cout << "alpha_complex_from_points.get_point(3)=" << p3 << std::endl;
+  BOOST_CHECK(4 == p3.dimension());
+  BOOST_CHECK(is_point_in_list(points, p3));
+
+  // Test to the limit
+  BOOST_CHECK_THROW (alpha_complex_from_points.get_point(4), std::out_of_range);
+  BOOST_CHECK_THROW (alpha_complex_from_points.get_point(-1), std::out_of_range);
+  BOOST_CHECK_THROW (alpha_complex_from_points.get_point(1234), std::out_of_range);
+  
+  // Test after prune_above_filtration
+  bool modified = alpha_complex_from_points.prune_above_filtration(0.6);
+  if (modified) {
+    alpha_complex_from_points.initialize_filtration();
+  }
+  BOOST_CHECK(modified);
+  
+  // Another way to check num_simplices
+  std::cout << "Iterator on alpha complex simplices in the filtration order, with [filtration value]:" << std::endl;
+  num_simplices = 0;
+  for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) {
+    num_simplices++;
+    std::cout << "   ( ";
+    for (auto vertex : alpha_complex_from_points.simplex_vertex_range(f_simplex)) {
+      std::cout << vertex << " ";
+    }
+    std::cout << ") -> " << "[" << alpha_complex_from_points.filtration(f_simplex) << "] ";
+    std::cout << std::endl;
+  }
+  BOOST_CHECK(num_simplices == 10);
+  std::cout << "alpha_complex_from_points.num_simplices()=" << alpha_complex_from_points.num_simplices() << std::endl;
+  BOOST_CHECK(alpha_complex_from_points.num_simplices() == 10);
+
+  std::cout << "alpha_complex_from_points.dimension()=" << alpha_complex_from_points.dimension() << std::endl;
+  BOOST_CHECK(alpha_complex_from_points.dimension() == 4);
+  std::cout << "alpha_complex_from_points.num_vertices()=" << alpha_complex_from_points.num_vertices() << std::endl;
+  BOOST_CHECK(alpha_complex_from_points.num_vertices() == 4);
+
+  for (auto f_simplex : alpha_complex_from_points.filtration_simplex_range()) {
+    switch (alpha_complex_from_points.dimension(f_simplex)) {
+      case 0:
+        BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 0.0));
+        break;
+      case 1:
+        BOOST_CHECK(are_almost_the_same(alpha_complex_from_points.filtration(f_simplex), 1.0/2.0));
+        break;
+      default:
+        BOOST_CHECK(false);  // Shall not happen
+        break;
+    }
+  }
+
+}
diff --git a/src/Alpha_complex/test/CMakeLists.txt b/src/Alpha_complex/test/CMakeLists.txt
new file mode 100644
index 00000000..e24588d7
--- /dev/null
+++ b/src/Alpha_complex/test/CMakeLists.txt
@@ -0,0 +1,45 @@
+cmake_minimum_required(VERSION 2.6)
+project(GUDHIAlphaComplexTest)
+
+if (GCOVR_PATH)
+  # for gcovr to make coverage reports - Corbera Jenkins plugin
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
+endif()
+if (GPROF_PATH)
+  # for gprof to make coverage reports - Jenkins
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
+endif()
+
+# need CGAL 4.7
+# cmake -DCGAL_DIR=~/workspace/CGAL-4.7-Ic-41 ../../..
+if(CGAL_FOUND)
+  if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+    message(STATUS "CGAL version: ${CGAL_VERSION}.")
+
+    find_package(Eigen3 3.1.0)
+    if (EIGEN3_FOUND)
+      message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
+      include( ${EIGEN3_USE_FILE} )
+      include_directories (BEFORE "../../include")
+
+      add_executable ( AlphaComplexUT Alpha_complex_unit_test.cpp )
+      target_link_libraries(AlphaComplexUT  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+      if (TBB_FOUND)
+        target_link_libraries(AlphaComplexUT ${TBB_RELEASE_LIBRARY})
+      endif()
+
+      # Do not forget to copy test files in current binary dir
+      file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+
+      add_test(AlphaComplexUT ${CMAKE_CURRENT_BINARY_DIR}/AlphaComplexUT
+      # XML format for Jenkins xUnit plugin 
+      --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/AlphaComplexUT.xml --log_level=test_suite --report_level=no)
+
+    else()
+      message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha complex feature.")
+    endif()
+  else()
+    message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha complex feature. Version 4.6.0 is required.")
+  endif ()
+endif()
+
diff --git a/src/Alpha_complex/test/README b/src/Alpha_complex/test/README
new file mode 100644
index 00000000..45b87d91
--- /dev/null
+++ b/src/Alpha_complex/test/README
@@ -0,0 +1,12 @@
+To compile:
+***********
+
+cmake .
+make
+
+To launch with details:
+***********************
+
+./AlphaComplexUnitTest --report_level=detailed --log_level=all 
+
+   ==> echo $? returns 0 in case of success (non-zero otherwise)
diff --git a/src/Bitmap_cubical_complex/test/CMakeLists.txt b/src/Bitmap_cubical_complex/test/CMakeLists.txt
index 96a41c62..0e5340c7 100644
--- a/src/Bitmap_cubical_complex/test/CMakeLists.txt
+++ b/src/Bitmap_cubical_complex/test/CMakeLists.txt
@@ -4,14 +4,10 @@ project(GUDHIBitmapCCUT)
 if (GCOVR_PATH)
   # for gcovr to make coverage reports - Corbera Jenkins plugin
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage")	
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage")
 endif()
 if (GPROF_PATH)
   # for gprof to make coverage reports - Jenkins
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg")
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg")
 endif()
 
 add_executable ( BitmapCCUT Bitmap_test.cpp )
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 60315338..1700ddaa 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -2,6 +2,8 @@ cmake_minimum_required(VERSION 2.6)
 project(GUDHI)
 
 include("CMakeGUDHIVersion.txt")
+# Generate GUDHI official version file
+configure_file(GUDHIVersion.cmake.in "${CMAKE_SOURCE_DIR}/GUDHIVersion.cmake" @ONLY)
 
 enable_testing()
 
@@ -71,16 +73,24 @@ else()
   INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
   LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})
 
+  if (DEBUG_TRACES)
+    message(STATUS "DEBUG_TRACES are activated")
+    # For programs to be more verbose
+    add_definitions(-DDEBUG_TRACES)
+  endif()
+
   #---------------------------------------------------------------------------------------
   # Gudhi compilation part
   include_directories(include)
 
-  #add_subdirectory(example/Simplex_tree)                   
-  #add_subdirectory(example/Persistent_cohomology)                   
-  #add_subdirectory(example/Skeleton_blocker)                   
-  #add_subdirectory(example/Contraction)                   
+  add_subdirectory(example/common)
+  add_subdirectory(example/Simplex_tree)                   
+  add_subdirectory(example/Persistent_cohomology)                   
+  add_subdirectory(example/Skeleton_blocker)                   
+  add_subdirectory(example/Contraction)                   
   add_subdirectory(example/Bitmap_cubical_complex)
   add_subdirectory(example/Witness_complex)
+  add_subdirectory(example/Alpha_complex)
 
   # data points generator
   add_subdirectory(data/points/generator)
@@ -96,8 +106,9 @@ else()
   # (this registers the build-tree with a global CMake-registry)
   export(PACKAGE GUDHI)
 
+  message("++ make install will install ${PROJECT_NAME} in the following directory : ${CMAKE_INSTALL_PREFIX}")
   # Create the GUDHIConfig.cmake and GUDHIConfigVersion files
-  set(CONF_INCLUDE_DIRS "${PROJECT_SOURCE_DIR}/include")
+  set(CONF_INCLUDE_DIRS "${CMAKE_INSTALL_PREFIX}/include")
   configure_file(GUDHIConfig.cmake.in "${PROJECT_BINARY_DIR}/GUDHIConfig.cmake" @ONLY)
   configure_file(GUDHIConfigVersion.cmake.in "${PROJECT_BINARY_DIR}/GUDHIConfigVersion.cmake" @ONLY)
 
diff --git a/src/Contraction/include/gudhi/Contraction/policies/Link_condition_valid_contraction.h b/src/Contraction/include/gudhi/Contraction/policies/Link_condition_valid_contraction.h
index 919df243..250bba27 100644
--- a/src/Contraction/include/gudhi/Contraction/policies/Link_condition_valid_contraction.h
+++ b/src/Contraction/include/gudhi/Contraction/policies/Link_condition_valid_contraction.h
@@ -23,8 +23,8 @@
 #ifndef CONTRACTION_POLICIES_LINK_CONDITION_VALID_CONTRACTION_H_
 #define CONTRACTION_POLICIES_LINK_CONDITION_VALID_CONTRACTION_H_
 
-#include <gudhi/Utils.h>
 #include <gudhi/Contraction/policies/Valid_contraction_policy.h>
+#include <gudhi/Debug_utils.h>
 
 
 namespace Gudhi {
diff --git a/src/Contraction/include/gudhi/Edge_contraction.h b/src/Contraction/include/gudhi/Edge_contraction.h
index 1fe563d6..1b2cdee9 100644
--- a/src/Contraction/include/gudhi/Edge_contraction.h
+++ b/src/Contraction/include/gudhi/Edge_contraction.h
@@ -30,7 +30,7 @@
 #include <gudhi/Contraction/policies/Valid_contraction_policy.h>
 #include <gudhi/Contraction/policies/Dummy_valid_contraction.h>
 #include <gudhi/Contraction/policies/Link_condition_valid_contraction.h>
-#include <gudhi/Utils.h>
+#include <gudhi/Debug_utils.h>
 
 namespace Gudhi {
 
diff --git a/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h b/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h
index d6350a2c..f650473a 100644
--- a/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h
+++ b/src/Contraction/include/gudhi/Skeleton_blocker_contractor.h
@@ -37,7 +37,7 @@
 #include <gudhi/Contraction/policies/Contraction_visitor.h>
 
 #include <gudhi/Skeleton_blocker/Skeleton_blocker_complex_visitor.h>
-#include <gudhi/Utils.h>
+#include <gudhi/Debug_utils.h>
 
 
 #include <boost/scoped_array.hpp>
diff --git a/src/Doxyfile b/src/Doxyfile
index abafdf16..6ddfb55d 100644
--- a/src/Doxyfile
+++ b/src/Doxyfile
@@ -673,6 +673,7 @@ LAYOUT_FILE            =
 # also \cite for info how to create references.
 
 CITE_BIB_FILES         = biblio/bibliography.bib \
+                        biblio/how_to_cite_cgal.bib \
                         biblio/how_to_cite_gudhi.bib
 
 #---------------------------------------------------------------------------
@@ -836,6 +837,7 @@ EXAMPLE_RECURSIVE      = NO
 # \image command).
 
 IMAGE_PATH             = doc/Skeleton_blocker/ \
+	doc/Alpha_complex/ \
 	doc/common/ \
 	doc/Contraction/ \
 	doc/Simplex_tree/ \
@@ -1602,7 +1604,7 @@ PAPER_TYPE             = a4
 # If left blank no extra packages will be included.
 # This tag requires that the tag GENERATE_LATEX is set to YES.
 
-EXTRA_PACKAGES         = amsfonts amsmath amssymb
+EXTRA_PACKAGES         = amsfonts amsmath amssymb algorithm algpseudocode
 
 # The LATEX_HEADER tag can be used to specify a personal LaTeX header for the
 # generated LaTeX document. The header should contain everything until the first
diff --git a/src/GudhUI/CMakeLists.txt b/src/GudhUI/CMakeLists.txt
index fd7397ea..a7e64319 100644
--- a/src/GudhUI/CMakeLists.txt
+++ b/src/GudhUI/CMakeLists.txt
@@ -61,6 +61,8 @@ if (TBB_FOUND)
   target_link_libraries( GudhUI ${TBB_RELEASE_LIBRARY})
 endif()
 
+###############################################################################
+
 else()
   message(STATUS "NOTICE: GudhUI requires CGAL, the QGLViewer, OpenGL and Qt4, and will not be compiled.")
 endif()
diff --git a/src/GudhUI/model/Model.h b/src/GudhUI/model/Model.h
index 07a67a0c..1c39c0d7 100644
--- a/src/GudhUI/model/Model.h
+++ b/src/GudhUI/model/Model.h
@@ -71,7 +71,7 @@ class CGAL_geometric_flag_complex_wrapper {
 
   void maximal_face(std::vector<int> vertices) {
     if (!load_only_points_) {
-      std::cout << "size:" << vertices.size() << std::endl;
+      // std::cout << "size:" << vertices.size() << std::endl;
       for (int i = 0; i < vertices.size(); ++i)
         for (int j = i + 1; j < vertices.size(); ++j)
           complex_.add_edge(Vertex_handle(vertices[i]), Vertex_handle(vertices[j]));
diff --git a/src/GudhUI/utils/Bar_code_persistence.h b/src/GudhUI/utils/Bar_code_persistence.h
new file mode 100644
index 00000000..b527d684
--- /dev/null
+++ b/src/GudhUI/utils/Bar_code_persistence.h
@@ -0,0 +1,90 @@
+#include <math.h>  // isfinite
+
+#include <QtGui/QApplication>
+
+#include <QGraphicsView>
+#include <QGraphicsScene>
+#include <QPointF>
+#include <QVector>
+#include <QGraphicsTextItem>
+
+#include <iostream>
+#include <vector>
+#include <limits>  // NaN, infinity
+#include <utility>  // for pair
+#include <string>
+
+#ifndef UTILS_BAR_CODE_PERSISTENCE_H_
+#define UTILS_BAR_CODE_PERSISTENCE_H_
+
+class Bar_code_persistence {
+ private:
+  typedef std::vector<std::pair<double, double>> Persistence;
+  Persistence persistence_vector;
+  double min_birth;
+  double max_death;
+
+ public:
+  Bar_code_persistence()
+      : min_birth(std::numeric_limits<double>::quiet_NaN()),
+      max_death(std::numeric_limits<double>::quiet_NaN()) { }
+
+  void insert(double birth, double death) {
+    persistence_vector.push_back(std::make_pair(birth, death));
+    if (std::isfinite(birth)) {
+      if ((birth < min_birth) || (std::isnan(min_birth)))
+        min_birth = birth;
+      if ((birth > max_death) || (std::isnan(max_death)))
+        max_death = birth;
+    }
+    if (std::isfinite(death))
+      if ((death > max_death) || (std::isnan(max_death)))
+        max_death = death;
+  }
+
+  void show(const std::string& window_title) {
+    // Create a view, put a scene in it
+    QGraphicsView * view = new QGraphicsView();
+    QGraphicsScene * scene = new QGraphicsScene();
+    view->setScene(scene);
+    double ratio = 600.0 / (max_death - min_birth);
+    // std::cout << "min_birth=" << min_birth << " - max_death=" << max_death << " - ratio=" << ratio << std::endl;
+
+    double height = 0.0, birth = 0.0, death = 0.0;
+    int pers_num = 1;
+    for (auto& persistence : persistence_vector) {
+      height = 5.0 * pers_num;
+      // std::cout << "[" << pers_num << "] birth=" << persistence.first << " - death=" << persistence.second << std::endl;
+      if (std::isfinite(persistence.first))
+        birth = ((persistence.first - min_birth) * ratio) + 50.0;
+      else
+        birth = 0.0;
+
+      if (std::isfinite(persistence.second))
+        death = ((persistence.second - min_birth) * ratio) + 50.0;
+      else
+        death = 700.0;
+
+      scene->addLine(birth, height, death, height, QPen(Qt::blue, 2));
+      pers_num++;
+    }
+    height += 10.0;
+    // scale line
+    scene->addLine(0, height, 700.0, height, QPen(Qt::black, 1));
+    int modulo = 0;
+    for (double scale = 50.0; scale < 700.0; scale += 50.0) {
+      modulo++;
+      // scale small dash
+      scene->addLine(scale, height - 3.0, scale, height + 3.0, QPen(Qt::black, 1));
+      // scale text
+      QString scale_value = QString::number(((scale - 50.0) / ratio) + min_birth);
+      QGraphicsTextItem* dimText = scene->addText(scale_value, QFont("Helvetica", 8));
+      dimText->setPos(scale - (3.0 * scale_value.size()), height + 9.0 * (modulo % 2));
+    }
+    view->setWindowTitle(window_title.c_str());
+    // Show the view
+    view->show();
+  }
+};
+
+#endif  // UTILS_BAR_CODE_PERSISTENCE_H_
diff --git a/src/GudhUI/utils/Persistence_compute.h b/src/GudhUI/utils/Persistence_compute.h
index 0b9961d3..97165490 100644
--- a/src/GudhUI/utils/Persistence_compute.h
+++ b/src/GudhUI/utils/Persistence_compute.h
@@ -46,10 +46,6 @@ struct Persistence_params {
  * Show persistence into output stream
  */
 template<typename SkBlComplex> class Persistence_compute {
- private:
-  SkBlComplex& complex_;
-  std::ostream& stream_;
-
  public:
   typedef typename SkBlComplex::Vertex_handle Vertex_handle;
   typedef typename SkBlComplex::Edge_handle Edge_handle;
@@ -61,9 +57,7 @@ template<typename SkBlComplex> class Persistence_compute {
    * double threshold
    * int p for coefficient Z_p
    */
-  Persistence_compute(SkBlComplex& complex, std::ostream& stream, const Persistence_params& params) :
-      // double threshold = 0.5,unsigned dim_max = 8):
-      complex_(complex), stream_(stream) {
+  Persistence_compute(SkBlComplex& complex, std::ostream& stream, const Persistence_params& params) {
     // for now everything is copied, todo boost adapt iterators to points of SkBlComplex instead of copying to an
     // initial vector
     typedef std::vector<double> Point_t;
@@ -87,10 +81,10 @@ template<typename SkBlComplex> class Persistence_compute {
     pcoh.init_coefficients(params.p);
     // put params.min_pers
     pcoh.compute_persistent_cohomology(params.min_pers);
-    stream_ << "persistence: \n";
-    stream_ << "p dimension birth death: \n";
+    stream << "persistence: \n";
+    stream << "p dimension birth death: \n";
 
-    pcoh.output_diagram(stream_);
+    pcoh.output_diagram(stream);
   }
 };
 
diff --git a/src/GudhUI/view/FirstCoordProjector.h b/src/GudhUI/view/FirstCoordProjector.h
index 529d2d42..a4027b7f 100644
--- a/src/GudhUI/view/FirstCoordProjector.h
+++ b/src/GudhUI/view/FirstCoordProjector.h
@@ -32,8 +32,10 @@ class FirstCoordProjector3D : public Projector3D {
   typedef Projector3D::Point_3 Point_3;
 
   Point_3 operator()(const Point& p) const {
-    assert(p.dimension() >= 3);
+    if (p.dimension() >= 3)
     return Point_3(p.x(), p.y(), p.z());
+    else if  (p.dimension() >= 2)
+    return Point_3(p.x(), p.y(), 0.0);
   }
 };
 
diff --git a/src/Persistent_cohomology/concept/FilteredComplex.h b/src/Persistent_cohomology/concept/FilteredComplex.h
index e47babe4..c19698df 100644
--- a/src/Persistent_cohomology/concept/FilteredComplex.h
+++ b/src/Persistent_cohomology/concept/FilteredComplex.h
@@ -139,6 +139,6 @@ Filtration_simplex_range filtration_simplex_range();
 * @todo use an enum? Just a bool?
 */
 //int is_before_in_filtration(Simplex_handle s, Simplex_handle t);
-/*************************************************/     
+/*************************************************/
 
 };
diff --git a/src/Persistent_cohomology/example/CMakeLists.txt b/src/Persistent_cohomology/example/CMakeLists.txt
index 9702a5f9..2f94ed15 100644
--- a/src/Persistent_cohomology/example/CMakeLists.txt
+++ b/src/Persistent_cohomology/example/CMakeLists.txt
@@ -7,37 +7,31 @@ add_definitions( -DBOOST_ALL_DYN_LINK )
 
 add_executable(plain_homology plain_homology.cpp)
 target_link_libraries(plain_homology ${Boost_SYSTEM_LIBRARY})
-if (TBB_FOUND)
-  target_link_libraries(plain_homology ${TBB_RELEASE_LIBRARY})
-endif()
-add_test(plain_homology ${CMAKE_CURRENT_BINARY_DIR}/plain_homology)
 
 add_executable(persistence_from_simple_simplex_tree persistence_from_simple_simplex_tree.cpp)
 target_link_libraries(persistence_from_simple_simplex_tree ${Boost_SYSTEM_LIBRARY})
-if (TBB_FOUND)
-  target_link_libraries(persistence_from_simple_simplex_tree ${TBB_RELEASE_LIBRARY})
-endif()
-add_test(persistence_from_simple_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_simple_simplex_tree 1 0)
 
 add_executable(rips_persistence rips_persistence.cpp)
 target_link_libraries(rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
-if (TBB_FOUND)
-  target_link_libraries(rips_persistence ${TBB_RELEASE_LIBRARY})
-endif()
-add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.2 -d 3 -p 3 -m 100)
-   
+
 add_executable(parallel_rips_persistence parallel_rips_persistence.cpp)
 target_link_libraries(parallel_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
-if (TBB_FOUND)
-  target_link_libraries(parallel_rips_persistence ${TBB_RELEASE_LIBRARY})
-endif()
-add_test(parallel_rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/parallel_rips_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.txt -r 0.3 -d 3 -p 3 -m 100)
-   
+
 add_executable(persistence_from_file persistence_from_file.cpp)
 target_link_libraries(persistence_from_file ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+
 if (TBB_FOUND)
+  target_link_libraries(plain_homology ${TBB_RELEASE_LIBRARY})
+  target_link_libraries(persistence_from_simple_simplex_tree ${TBB_RELEASE_LIBRARY})
+  target_link_libraries(rips_persistence ${TBB_RELEASE_LIBRARY})
+  target_link_libraries(parallel_rips_persistence ${TBB_RELEASE_LIBRARY})
   target_link_libraries(persistence_from_file ${TBB_RELEASE_LIBRARY})
 endif()
+
+add_test(plain_homology ${CMAKE_CURRENT_BINARY_DIR}/plain_homology)
+add_test(persistence_from_simple_simplex_tree ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_simple_simplex_tree 1 0)
+add_test(rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/rips_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.2 -d 3 -p 3 -m 100)
+add_test(parallel_rips_persistence_3 ${CMAKE_CURRENT_BINARY_DIR}/parallel_rips_persistence ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.txt -r 0.3 -d 3 -p 3 -m 100)
 add_test(persistence_from_file_3_2_0 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 2 -m 0)
 add_test(persistence_from_file_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/persistence_from_file ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 3 -m 100)
    
@@ -47,29 +41,45 @@ if(GMPXX_FOUND AND GMP_FOUND)
 
    add_executable(rips_multifield_persistence rips_multifield_persistence.cpp )
    target_link_libraries(rips_multifield_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
-   if (TBB_FOUND)
-     target_link_libraries(rips_multifield_persistence ${TBB_RELEASE_LIBRARY})
-   endif()
-   add_test(rips_multifield_persistence_2_71 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.2 -d 3 -p 2 -q 71 -m 100)
-
    add_executable ( performance_rips_persistence performance_rips_persistence.cpp )
    target_link_libraries(performance_rips_persistence ${Boost_SYSTEM_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES})
    if (TBB_FOUND)
+     target_link_libraries(rips_multifield_persistence ${TBB_RELEASE_LIBRARY})
      target_link_libraries(performance_rips_persistence ${TBB_RELEASE_LIBRARY})
    endif()
 
-   if(CGAL_FOUND)
-     if (CMAKE_BUILD_TYPE MATCHES Debug)
-       # For programs to be more verbose
-       add_definitions(-DDEBUG_TRACES)
-     endif()
-     add_executable(alpha_shapes_persistence alpha_shapes_persistence.cpp)
-     target_link_libraries(alpha_shapes_persistence ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY})
-     if (TBB_FOUND)
-       target_link_libraries(alpha_shapes_persistence ${TBB_RELEASE_LIBRARY})
-     endif()
-     add_test(alpha_shapes_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 2 0.5)
-     #add_test(alpha_shapes_persistence_3_3_100 ${CMAKE_CURRENT_BINARY_DIR}/alpha_shapes_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000.st -p 3 -m 100)
-   endif()
+   add_test(rips_multifield_persistence_2_71 ${CMAKE_CURRENT_BINARY_DIR}/rips_multifield_persistence ${CMAKE_SOURCE_DIR}/data/points/Kl.txt -r 0.2 -d 3 -p 2 -q 71 -m 100)
+
+  if(CGAL_FOUND)
+    add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp)
+    target_link_libraries(alpha_complex_3d_persistence ${Boost_SYSTEM_LIBRARY} ${GMPXX_LIBRARIES} ${GMP_LIBRARIES} ${CGAL_LIBRARY})
+    if (TBB_FOUND)
+      target_link_libraries(alpha_complex_3d_persistence ${TBB_RELEASE_LIBRARY})
+    endif()
+    add_test(alpha_complex_3d_persistence_2_0_5 ${CMAKE_CURRENT_BINARY_DIR}/alpha_complex_3d_persistence ${CMAKE_SOURCE_DIR}/data/points/bunny_5000 2 0.5)
+
+    if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+      message(STATUS "CGAL version: ${CGAL_VERSION}.")
+
+      find_package(Eigen3 3.1.0)
+      if (EIGEN3_FOUND)
+        message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
+        include( ${EIGEN3_USE_FILE} )
+      
+        add_executable (alpha_complex_persistence alpha_complex_persistence.cpp)
+        target_link_libraries(alpha_complex_persistence  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+        if (TBB_FOUND)
+          target_link_libraries(alpha_complex_persistence ${TBB_RELEASE_LIBRARY})
+        endif()
+
+      else()
+        message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.")
+      endif()
+    else()
+      message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.")
+    endif ()
+  else()
+    # message(WARNING "CGAL not found.")
+  endif()
    
 endif()
diff --git a/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
index 92c0b065..01497c7c 100644
--- a/src/Persistent_cohomology/example/alpha_shapes_persistence.cpp
+++ b/src/Persistent_cohomology/example/alpha_complex_3d_persistence.cpp
@@ -39,9 +39,6 @@
 #include <list>
 #include <vector>
 
-using namespace Gudhi;
-using namespace Gudhi::persistent_cohomology;
-
 // Alpha_shape_3 templates type definitions
 typedef CGAL::Exact_predicates_inexact_constructions_kernel Kernel;
 typedef CGAL::Alpha_shape_vertex_base_3<Kernel> Vb;
@@ -66,11 +63,12 @@ typedef Alpha_shape_3::Edge Edge_3;
 typedef std::list<Alpha_shape_3::Vertex_handle> Vertex_list;
 
 // gudhi type definition
-typedef Simplex_tree<Simplex_tree_options_fast_persistence> ST;
+typedef Gudhi::Simplex_tree<Gudhi::Simplex_tree_options_fast_persistence> ST;
 typedef ST::Vertex_handle Simplex_tree_vertex;
 typedef std::map<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex > Alpha_shape_simplex_tree_map;
 typedef std::pair<Alpha_shape_3::Vertex_handle, Simplex_tree_vertex> Alpha_shape_simplex_tree_pair;
 typedef std::vector< Simplex_tree_vertex > Simplex_tree_vector_vertex;
+typedef Gudhi::persistent_cohomology::Persistent_cohomology< ST, Gudhi::persistent_cohomology::Field_Zp > PCOH;
 
 Vertex_list from(const Cell_handle& ch) {
   Vertex_list the_list;
@@ -125,26 +123,21 @@ void usage(char * const progName) {
 }
 
 int main(int argc, char * const argv[]) {
-  int coeff_field_characteristic = 0;
-  int returnedScanValue = sscanf(argv[2], "%d", &coeff_field_characteristic);
-  if ((returnedScanValue == EOF) || (coeff_field_characteristic <= 0)) {
-    std::cerr << "Error: " << argv[2] << " is not correct\n";
+  // program args management
+  if (argc != 4) {
+    std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
     usage(argv[0]);
   }
 
+  int coeff_field_characteristic = atoi(argv[2]);
+
   Filtration_value min_persistence = 0.0;
-  returnedScanValue = sscanf(argv[3], "%lf", &min_persistence);
+  int returnedScanValue = sscanf(argv[3], "%lf", &min_persistence);
   if ((returnedScanValue == EOF) || (min_persistence < -1.0)) {
     std::cerr << "Error: " << argv[3] << " is not correct\n";
     usage(argv[0]);
   }
 
-  // program args management
-  if (argc != 4) {
-    std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n";
-    usage(argv[0]);
-  }
-
   // Read points from file
   std::string filegraph = argv[1];
   std::list<Point_3> lp;
@@ -240,7 +233,7 @@ int main(int argc, char * const argv[]) {
       }
     }
     // Construction of the simplex_tree
-    Filtration_value filtr = std::sqrt(*the_alpha_value_iterator);
+    Filtration_value filtr = /*std::sqrt*/(*the_alpha_value_iterator);
 #ifdef DEBUG_TRACES
     std::cout << "filtration = " << filtr << std::endl;
 #endif  // DEBUG_TRACES
@@ -282,7 +275,7 @@ int main(int argc, char * const argv[]) {
 
   std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl;
   // Compute the persistence diagram of the complex
-  Persistent_cohomology< ST, Field_Zp > pcoh(simplex_tree);
+  PCOH pcoh(simplex_tree);
   // initializes the coefficient field for homology
   pcoh.init_coefficients(coeff_field_characteristic);
 
diff --git a/src/Persistent_cohomology/example/alpha_complex_persistence.cpp b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
new file mode 100644
index 00000000..8f9f077c
--- /dev/null
+++ b/src/Persistent_cohomology/example/alpha_complex_persistence.cpp
@@ -0,0 +1,117 @@
+#include <boost/program_options.hpp>
+
+#include <CGAL/Epick_d.h>
+
+#include <gudhi/Alpha_complex.h>
+#include <gudhi/Persistent_cohomology.h>
+
+#include <iostream>
+#include <string>
+#include <limits>  // for numeric_limits
+
+void program_options(int argc, char * argv[]
+                     , std::string & off_file_points
+                     , std::string & output_file_diag
+                     , Filtration_value & alpha_square_max_value
+                     , int & coeff_field_characteristic
+                     , Filtration_value & min_persistence);
+
+int main(int argc, char **argv) {
+  std::string off_file_points;
+  std::string output_file_diag;
+  Filtration_value alpha_square_max_value;
+  int coeff_field_characteristic;
+  Filtration_value min_persistence;
+
+  program_options(argc, argv, off_file_points, output_file_diag, alpha_square_max_value,
+                  coeff_field_characteristic, min_persistence);
+
+  // ----------------------------------------------------------------------------
+  // Init of an alpha complex from an OFF file
+  // ----------------------------------------------------------------------------
+  typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel;
+  Gudhi::alphacomplex::Alpha_complex<Kernel> alpha_complex_from_file(off_file_points, alpha_square_max_value);
+
+  // ----------------------------------------------------------------------------
+  // Display information about the alpha complex
+  // ----------------------------------------------------------------------------
+  std::cout << "Alpha complex is of dimension " << alpha_complex_from_file.dimension() <<
+      " - " << alpha_complex_from_file.num_simplices() << " simplices - " <<
+      alpha_complex_from_file.num_vertices() << " vertices." << std::endl;
+
+  // Sort the simplices in the order of the filtration
+  alpha_complex_from_file.initialize_filtration();
+
+  std::cout << "Simplex_tree dim: " << alpha_complex_from_file.dimension() << std::endl;
+  // Compute the persistence diagram of the complex
+  Gudhi::persistent_cohomology::Persistent_cohomology< Gudhi::alphacomplex::Alpha_complex<Kernel>,
+      Gudhi::persistent_cohomology::Field_Zp > pcoh(alpha_complex_from_file);
+  // initializes the coefficient field for homology
+  pcoh.init_coefficients(coeff_field_characteristic);
+
+  pcoh.compute_persistent_cohomology(min_persistence);
+
+  // Output the diagram in filediag
+  if (output_file_diag.empty()) {
+    pcoh.output_diagram();
+  } else {
+    std::cout << "Result in file: " << output_file_diag << std::endl;
+    std::ofstream out(output_file_diag);
+    pcoh.output_diagram(out);
+    out.close();
+  }
+
+  return 0;
+}
+
+void program_options(int argc, char * argv[]
+                     , std::string & off_file_points
+                     , std::string & output_file_diag
+                     , Filtration_value & alpha_square_max_value
+                     , int & coeff_field_characteristic
+                     , Filtration_value & min_persistence) {
+  namespace po = boost::program_options;
+  po::options_description hidden("Hidden options");
+  hidden.add_options()
+      ("input-file", po::value<std::string>(&off_file_points),
+       "Name of file containing a point set. Format is one point per line:   X1 ... Xd ");
+
+  po::options_description visible("Allowed options", 100);
+  visible.add_options()
+      ("help,h", "produce help message")
+      ("output-file,o", po::value<std::string>(&output_file_diag)->default_value(std::string()),
+       "Name of file in which the persistence diagram is written. Default print in std::cout")
+      ("max-alpha-square-value,r",
+      po::value<Filtration_value>(&alpha_square_max_value)->default_value(std::numeric_limits<Filtration_value>::infinity()),
+       "Maximal alpha square value for the Alpha complex construction.")
+      ("field-charac,p", po::value<int>(&coeff_field_characteristic)->default_value(11),
+       "Characteristic p of the coefficient field Z/pZ for computing homology.")
+      ("min-persistence,m", po::value<Filtration_value>(&min_persistence),
+       "Minimal lifetime of homology feature to be recorded. Default is 0. Enter a negative value to see zero length intervals");
+
+  po::positional_options_description pos;
+  pos.add("input-file", 1);
+
+  po::options_description all;
+  all.add(visible).add(hidden);
+
+  po::variables_map vm;
+  po::store(po::command_line_parser(argc, argv).
+            options(all).positional(pos).run(), vm);
+  po::notify(vm);
+
+  if (vm.count("help") || !vm.count("input-file")) {
+    std::cout << std::endl;
+    std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
+    std::cout << "of an Alpha complex defined on a set of input points.\n \n";
+    std::cout << "The output diagram contains one bar per line, written with the convention: \n";
+    std::cout << "   p   dim b d \n";
+    std::cout << "where dim is the dimension of the homological feature,\n";
+    std::cout << "b and d are respectively the birth and death of the feature and \n";
+    std::cout << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
+
+    std::cout << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
+    std::cout << visible << std::endl;
+    std::abort();
+  }
+}
diff --git a/src/Persistent_cohomology/example/rips_persistence.cpp b/src/Persistent_cohomology/example/rips_persistence.cpp
index 2d926a0d..cab49395 100644
--- a/src/Persistent_cohomology/example/rips_persistence.cpp
+++ b/src/Persistent_cohomology/example/rips_persistence.cpp
@@ -30,6 +30,7 @@
 
 #include <string>
 #include <vector>
+#include <limits>  // infinity
 
 using namespace Gudhi;
 using namespace Gudhi::persistent_cohomology;
@@ -115,7 +116,7 @@ void program_options(int argc, char * argv[]
       ("help,h", "produce help message")
       ("output-file,o", po::value<std::string>(&filediag)->default_value(std::string()),
        "Name of file in which the persistence diagram is written. Default print in std::cout")
-      ("max-edge-length,r", po::value<Filtration_value>(&threshold)->default_value(0),
+      ("max-edge-length,r", po::value<Filtration_value>(&threshold)->default_value(std::numeric_limits<Filtration_value>::infinity()),
        "Maximal length of an edge for the Rips complex construction.")
       ("cpx-dimension,d", po::value<int>(&dim_max)->default_value(1),
        "Maximal dimension of the Rips complex we want to compute.")
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree.h b/src/Simplex_tree/include/gudhi/Simplex_tree.h
index dea475ac..b6dc8e13 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree.h
@@ -30,23 +30,26 @@
 
 #include <gudhi/reader_utils.h>
 #include <gudhi/graph_simplicial_complex.h>
+#include <gudhi/Debug_utils.h>
 
 #include <boost/container/flat_map.hpp>
 #include <boost/iterator/transform_iterator.hpp>
 #include <boost/graph/adjacency_list.hpp>
+#include <boost/range/adaptor/reversed.hpp>
 
 #ifdef GUDHI_USE_TBB
 #include <tbb/parallel_sort.h>
 #endif
 
-#include <algorithm>
 #include <utility>
 #include <vector>
 #include <functional>  // for greater<>
+#include <stdexcept>
+#include <limits>  // Inf
 #include <initializer_list>
+#include <algorithm>  // for std::max
 
 namespace Gudhi {
-
 /** \defgroup simplex_tree Filtered Complexes
  * \author    Cl&eacute;ment Maria
  *
@@ -137,7 +140,8 @@ class Simplex_tree {
     void assign_key(Simplex_key) { }
     Simplex_key key() const { assert(false); return -1; }
   };
-  typedef typename std::conditional<Options::store_key, Key_simplex_base_real, Key_simplex_base_dummy>::type Key_simplex_base;
+  typedef typename std::conditional<Options::store_key, Key_simplex_base_real, Key_simplex_base_dummy>::type
+      Key_simplex_base;
 
   struct Filtration_simplex_base_real {
     Filtration_simplex_base_real() : filt_(0) {}
@@ -303,7 +307,8 @@ class Simplex_tree {
    * of the simplex.
    *
    * @param[in] sh Simplex for which the boundary is computed. */
-  Boundary_simplex_range boundary_simplex_range(Simplex_handle sh) {
+  template<class SimplexHandle>
+  Boundary_simplex_range boundary_simplex_range(SimplexHandle sh) {
     return Boundary_simplex_range(Boundary_simplex_iterator(this, sh),
                                   Boundary_simplex_iterator(this));
   }
@@ -444,6 +449,15 @@ class Simplex_tree {
     }
   }
 
+  /** \brief Sets the filtration value of a simplex.
+   * \exception std::invalid_argument In debug mode, if sh is a null_simplex.
+   */
+  void assign_filtration(Simplex_handle sh, Filtration_value fv) {
+    GUDHI_CHECK(sh != null_simplex(),
+                std::invalid_argument("Simplex_tree::assign_filtration - cannot assign filtration on null_simplex"));
+    sh->second.assign_filtration(fv);
+  }
+
   /** \brief Returns an upper bound of the filtration values of the simplices. */
   Filtration_value filtration() const {
     return threshold_;
@@ -513,9 +527,10 @@ class Simplex_tree {
     return dimension_;
   }
 
-  /** \brief Returns true iff the node in the simplex tree pointed by
+  /** \brief Returns true if the node in the simplex tree pointed by
    * sh has children.*/
-  bool has_children(Simplex_handle sh) const {
+  template<class SimplexHandle>
+  bool has_children(SimplexHandle sh) const {
     return (sh->second.children()->parent() == sh->first);
   }
 
@@ -581,7 +596,19 @@ class Simplex_tree {
 
  private:
   /** \brief Inserts a simplex represented by a vector of vertex.
-   \warning the vector must be sorted by increasing vertex handle order */
+   * @param[in]  simplex    vector of Vertex_handles, representing the vertices of the new simplex. The vector must be
+   * sorted by increasing vertex handle order.
+   * @param[in]  filtration the filtration value assigned to the new simplex.
+   * @return If the new simplex is inserted successfully (i.e. it was not in the
+   * simplicial complex yet) the bool is set to true and the Simplex_handle is the handle assigned
+   * to the new simplex.
+   * If the insertion fails (the simplex is already there), the bool is set to false. If the insertion
+   * fails and the simplex already in the complex has a filtration value strictly bigger than 'filtration',
+   * we assign this simplex with the new value 'filtration', and set the Simplex_handle field of the
+   * output pair to the Simplex_handle of the simplex. Otherwise, we set the Simplex_handle part to
+   * null_simplex.
+   * 
+  */
   std::pair<Simplex_handle, bool> insert_vertex_vector(const std::vector<Vertex_handle>& simplex,
                                                      Filtration_value filtration) {
     Siblings * curr_sib = &root_;
@@ -614,7 +641,7 @@ class Simplex_tree {
    *
    * @param[in]  simplex    range of Vertex_handles, representing the vertices of the new simplex
    * @param[in]  filtration the filtration value assigned to the new simplex.
-   * The return type is a pair. If the new simplex is inserted successfully (i.e. it was not in the
+   * @return If the new simplex is inserted successfully (i.e. it was not in the
    * simplicial complex yet) the bool is set to true and the Simplex_handle is the handle assigned
    * to the new simplex.
    * If the insertion fails (the simplex is already there), the bool is set to false. If the insertion
@@ -653,7 +680,7 @@ class Simplex_tree {
    *
    * @param[in]  Nsimplex   range of Vertex_handles, representing the vertices of the new N-simplex
    * @param[in]  filtration the filtration value assigned to the new N-simplex.
-   * The return type is a pair. If the new simplex is inserted successfully (i.e. it was not in the
+   * @return If the new simplex is inserted successfully (i.e. it was not in the
    * simplicial complex yet) the bool is set to true and the Simplex_handle is the handle assigned
    * to the new simplex.
    * If the insertion fails (the simplex is already there), the bool is set to false. If the insertion
@@ -662,7 +689,7 @@ class Simplex_tree {
    * output pair to the Simplex_handle of the simplex. Otherwise, we set the Simplex_handle part to
    * null_simplex.
    */
-  template<class InputVertexRange=std::initializer_list<Vertex_handle>>
+  template<class InputVertexRange = std::initializer_list<Vertex_handle>>
   std::pair<Simplex_handle, bool> insert_simplex_and_subfaces(const InputVertexRange& Nsimplex,
                                    Filtration_value filtration = 0) {
     auto first = std::begin(Nsimplex);
@@ -716,7 +743,7 @@ class Simplex_tree {
     } else if (the_simplex.size() == 1) {
       // When reaching the end of recursivity, vector of simplices shall be empty and filled on back recursive
       if ((to_be_inserted.size() != 0) || (to_be_propagated.size() != 0)) {
-        std::cerr << "Simplex_tree::rec_insert_simplex_and_subfaces - Error vector not empty" << std::endl;
+        std::cerr << "Simplex_tree::rec_insert_simplex_and_subfaces - Error vector not empty\n";
         exit(-1);
       }
       std::vector<Vertex_handle> first_simplex(1, the_simplex.back());
@@ -725,7 +752,7 @@ class Simplex_tree {
 
       insert_result = insert_vertex_vector(first_simplex, filtration);
     } else {
-        std::cerr << "Simplex_tree::rec_insert_simplex_and_subfaces - Recursivity error" << std::endl;
+        std::cerr << "Simplex_tree::rec_insert_simplex_and_subfaces - Recursivity error\n";
         exit(-1);
     }
     return insert_result;
@@ -738,7 +765,6 @@ class Simplex_tree {
     sh->second.assign_key(key);
   }
 
- public:
   /** Returns the two Simplex_handle corresponding to the endpoints of
    * and edge. sh must point to a 1-dimensional simplex. This is an
    * optimized version of the boundary computation. */
@@ -748,7 +774,8 @@ class Simplex_tree {
   }
 
   /** Returns the Siblings containing a simplex.*/
-  Siblings * self_siblings(Simplex_handle sh) {
+  template<class SimplexHandle>
+  Siblings* self_siblings(SimplexHandle sh) {
     if (sh->second.children()->parent() == sh->first)
       return sh->second.children()->oncles();
     else
@@ -928,7 +955,7 @@ class Simplex_tree {
     bool operator()(const Simplex_handle sh1, const Simplex_handle sh2) const {
       // Not using st_->filtration(sh1) because it uselessly tests for null_simplex.
       if (sh1->second.filtration() != sh2->second.filtration()) {
-	return sh1->second.filtration() < sh2->second.filtration();
+        return sh1->second.filtration() < sh2->second.filtration();
       }
       // is sh1 a proper subface of sh2
       return st_->reverse_lexicographic_order(sh1, sh2);
@@ -1105,6 +1132,120 @@ class Simplex_tree {
     }
   }
 
+ public:
+  /** \brief Browse the simplex tree to ensure the filtration is not decreasing.
+   * The simplex tree is browsed starting from the root until the leaf, and the filtration values are set with their
+   * parent value (increased), in case the values are decreasing.
+   * @return The filtration modification information.
+   * \post Some simplex tree functions require the filtration to be valid. `make_filtration_non_decreasing()`
+   * function is not launching `initialize_filtration()` but returns the filtration modification information. If the
+   * complex has changed , please call `initialize_filtration()` to recompute it.
+   */
+  bool make_filtration_non_decreasing() {
+    bool modified = false;
+    // Loop must be from the end to the beginning, as higher dimension simplex are always on the left part of the tree
+    for (auto& simplex : boost::adaptors::reverse(root_.members())) {
+      if (has_children(&simplex)) {
+        modified |= rec_make_filtration_non_decreasing(simplex.second.children());
+      }
+    }
+    return modified;
+  }
+
+ private:
+  /** \brief Recursively Browse the simplex tree to ensure the filtration is not decreasing.
+   * @param[in] sib Siblings to be parsed.
+   * @return The filtration modification information in order to trigger initialize_filtration.
+   */
+  bool rec_make_filtration_non_decreasing(Siblings * sib) {
+    bool modified = false;
+
+    // Loop must be from the end to the beginning, as higher dimension simplex are always on the left part of the tree
+    for (auto& simplex : boost::adaptors::reverse(sib->members())) {
+      // Find the maximum filtration value in the border
+      Boundary_simplex_range boundary = boundary_simplex_range(&simplex);
+      Boundary_simplex_iterator max_border = std::max_element(std::begin(boundary), std::end(boundary),
+                                                              [](Simplex_handle sh1, Simplex_handle sh2) {
+                                                                return filtration(sh1) < filtration(sh2);
+                                                              });
+
+      Filtration_value max_filt_border_value = filtration(*max_border);
+      if (simplex.second.filtration() < max_filt_border_value) {
+        // Store the filtration modification information
+        modified = true;
+        simplex.second.assign_filtration(max_filt_border_value);
+      }
+      if (has_children(&simplex)) {
+        modified |= rec_make_filtration_non_decreasing(simplex.second.children());
+      }
+    }
+    // Make the modified information to be traced by upper call
+    return modified;
+  }
+
+ public:
+  /** \brief Prune above filtration value given as parameter.
+   * @param[in] filtration Maximum threshold value.
+   * @return The filtration modification information.
+   * \post Some simplex tree functions require the filtration to be valid. `prune_above_filtration()`
+   * function is not launching `initialize_filtration()` but returns the filtration modification information. If the
+   * complex has changed , please call `initialize_filtration()` to recompute it.
+   */
+  bool prune_above_filtration(Filtration_value filtration) {
+    return rec_prune_above_filtration(root(), filtration);
+  }
+
+ private:
+  bool rec_prune_above_filtration(Siblings* sib, Filtration_value filt) {
+    auto&& list = sib->members();
+    auto last = std::remove_if(list.begin(), list.end(), [=](Dit_value_t& simplex) {
+        if (simplex.second.filtration() <= filt) return false;
+        if (has_children(&simplex)) rec_delete(simplex.second.children());
+        return true;
+      });
+
+    bool modified = (last != list.end());
+    if (last == list.begin() && sib != root()) {
+      // Removing the whole siblings, parent becomes a leaf.
+      sib->oncles()->members()[sib->parent()].assign_children(sib->oncles());
+      delete sib;
+      return true;
+    } else {
+      // Keeping some elements of siblings. Remove the others, and recurse in the remaining ones.
+      list.erase(last, list.end());
+      for (auto&& simplex : list)
+        if (has_children(&simplex))
+          modified |= rec_prune_above_filtration(simplex.second.children(), filt);
+    }
+    return modified;
+  }
+
+ public:
+  /** \brief Remove a maximal simplex.
+   * @param[in] sh Simplex handle on the maximal simplex to remove.
+   * \pre Please check the simplex has no coface before removing it.
+   * \exception std::invalid_argument In debug mode, if sh has children.
+   * \post Be aware that removing is shifting data in a flat_map (initialize_filtration to be done).
+   */
+  void remove_maximal_simplex(Simplex_handle sh) {
+    // Guarantee the simplex has no children
+    GUDHI_CHECK(!has_children(sh),
+                std::invalid_argument("Simplex_tree::remove_maximal_simplex - argument has children"));
+
+    // Simplex is a leaf, it means the child is the Siblings owning the leaf
+    Siblings* child = sh->second.children();
+
+    if ((child->size() > 1) || (child == root())) {
+      // Not alone, just remove it from members
+      // Special case when child is the root of the simplex tree, just remove it from members
+      child->erase(sh);
+    } else {
+      // Sibling is emptied : must be deleted, and its parent must point on his own Sibling
+      child->oncles()->members().at(child->parent()).assign_children(child->oncles());
+      delete child;
+    }
+  }
+
  private:
   Vertex_handle null_vertex_;
   /** \brief Upper bound on the filtration values of the simplices.*/
@@ -1119,7 +1260,6 @@ class Simplex_tree {
 };
 
 // Print a Simplex_tree in os.
-
 template<typename...T>
 std::ostream& operator<<(std::ostream & os, Simplex_tree<T...> & st) {
   for (auto sh : st.filtration_simplex_range()) {
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h
index 936b7a1f..7e0a454d 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_iterators.h
@@ -104,7 +104,8 @@ class Simplex_tree_boundary_simplex_iterator : public boost::iterator_facade<
         st_(st)  {
   }
 
-  Simplex_tree_boundary_simplex_iterator(SimplexTree * st, Simplex_handle sh)
+  template<class SimplexHandle>
+  Simplex_tree_boundary_simplex_iterator(SimplexTree * st, SimplexHandle sh)
       : last_(sh->first),
         sib_(nullptr),
         st_(st) {
diff --git a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h
index 072afc8d..1eca7f6f 100644
--- a/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h
+++ b/src/Simplex_tree/include/gudhi/Simplex_tree/Simplex_tree_siblings.h
@@ -116,6 +116,10 @@ class Simplex_tree_siblings {
     return members_.size();
   }
 
+  void erase(const Dictionary_it iterator) {
+    members_.erase(iterator);
+  }
+
   Simplex_tree_siblings * oncles_;
   Vertex_handle parent_;
   Dictionary members_;
diff --git a/src/Simplex_tree/test/simplex_tree_unit_test.cpp b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
index 874c3363..b1bb23b1 100644
--- a/src/Simplex_tree/test/simplex_tree_unit_test.cpp
+++ b/src/Simplex_tree/test/simplex_tree_unit_test.cpp
@@ -795,3 +795,355 @@ BOOST_AUTO_TEST_CASE(non_contiguous) {
   test_simplex_is_vertex(st, *++i, 3);
   BOOST_CHECK(++i == std::end(b));
 }
+
+BOOST_AUTO_TEST_CASE(make_filtration_non_decreasing) {
+  std::cout << "********************************************************************" << std::endl;
+  std::cout << "MAKE FILTRATION NON DECREASING" << std::endl;
+  typedef Simplex_tree<> typeST;
+  typeST st;
+
+  st.insert_simplex_and_subfaces({2, 1, 0}, 2.0);
+  st.insert_simplex_and_subfaces({3, 0}, 2.0);
+  st.insert_simplex_and_subfaces({3, 4, 5}, 2.0);
+  
+  // Inserted simplex:
+  //    1
+  //    o
+  //   /X\
+  //  o---o---o---o
+  //  2   0   3\X/4
+  //            o
+  //            5
+
+  std::cout << "Check default insertion ensures the filtration values are non decreasing" << std::endl;
+  BOOST_CHECK(!st.make_filtration_non_decreasing());
+
+  // Because of non decreasing property of simplex tree, { 0 } , { 1 } and { 0, 1 } are going to be set from value 2.0
+  // to 1.0
+  st.insert_simplex_and_subfaces({0, 1, 6, 7}, 1.0);
+  
+  // Inserted simplex:
+  //    1   6
+  //    o---o
+  //   /X\7/
+  //  o---o---o---o
+  //  2   0   3\X/4
+  //            o
+  //            5
+  
+  std::cout << "Check default second insertion ensures the filtration values are non decreasing" << std::endl;
+  BOOST_CHECK(!st.make_filtration_non_decreasing());
+  
+  // Copy original simplex tree
+  typeST st_copy = st;
+
+  // Modify specific values for st to become like st_copy thanks to make_filtration_non_decreasing
+  st.assign_filtration(st.find({0,1,6,7}), 0.8);
+  st.assign_filtration(st.find({0,1,6}), 0.9);
+  st.assign_filtration(st.find({0,6}), 0.6);
+  st.assign_filtration(st.find({3,4,5}), 1.2);
+  st.assign_filtration(st.find({3,4}), 1.1);
+  st.assign_filtration(st.find({4,5}), 1.99);
+  
+  std::cout << "Check the simplex_tree is rolled back in case of decreasing filtration values" << std::endl;
+  BOOST_CHECK(st.make_filtration_non_decreasing());
+  BOOST_CHECK(st == st_copy);
+
+  // Other simplex tree
+  typeST st_other;
+  st_other.insert_simplex_and_subfaces({2, 1, 0}, 3.0);  // This one is different from st
+  st_other.insert_simplex_and_subfaces({3, 0}, 2.0);
+  st_other.insert_simplex_and_subfaces({3, 4, 5}, 2.0);
+  st_other.insert_simplex_and_subfaces({0, 1, 6, 7}, 1.0);
+
+  // Modify specific values for st to become like st_other thanks to make_filtration_non_decreasing
+  st.assign_filtration(st.find({2}), 3.0);
+  // By modifying just the simplex {2}
+  // {0,1,2}, {1,2} and {0,2} will be modified
+  
+  std::cout << "Check the simplex_tree is repaired in case of decreasing filtration values" << std::endl;
+  BOOST_CHECK(st.make_filtration_non_decreasing());
+  BOOST_CHECK(st == st_other);
+
+  // Modify specific values for st still to be non-decreasing
+  st.assign_filtration(st.find({0,1,2}), 10.0);
+  st.assign_filtration(st.find({0,2}), 9.0);
+  st.assign_filtration(st.find({0,1,6,7}), 50.0);
+  st.assign_filtration(st.find({0,1,6}), 49.0);
+  st.assign_filtration(st.find({0,1,7}), 48.0);
+  // Other copy simplex tree
+  typeST st_other_copy = st;
+  
+  std::cout << "Check the simplex_tree is not modified in case of non-decreasing filtration values" << std::endl;
+  BOOST_CHECK(!st.make_filtration_non_decreasing());
+  BOOST_CHECK(st == st_other_copy);
+  
+}
+
+struct MyOptions : Simplex_tree_options_full_featured {
+  // Not doing persistence, so we don't need those
+  static const bool store_key = false;
+  static const bool store_filtration = false;
+  // I have few vertices
+  typedef short Vertex_handle;
+};
+
+BOOST_AUTO_TEST_CASE(remove_maximal_simplex) {
+  std::cout << "********************************************************************" << std::endl;
+  std::cout << "REMOVE MAXIMAL SIMPLEX" << std::endl;
+
+
+  typedef Simplex_tree<MyOptions> miniST;
+  miniST st;
+
+  // FIXME
+  st.set_dimension(3);
+
+  st.insert_simplex_and_subfaces({0, 1, 6, 7});
+  st.insert_simplex_and_subfaces({3, 4, 5});
+
+  // Constructs a copy at this state for further test purpose
+  miniST st_pruned = st;
+
+  st.insert_simplex_and_subfaces({3, 0});
+  st.insert_simplex_and_subfaces({2, 1, 0});
+
+  // Constructs a copy at this state for further test purpose
+  miniST st_complete = st;
+  // st_complete and st:
+  //    1   6
+  //    o---o
+  //   /X\7/
+  //  o---o---o---o
+  //  2   0   3\X/4
+  //            o
+  //            5
+  // st_pruned:
+  //    1   6
+  //    o---o
+  //     \7/
+  //      o   o---o
+  //      0   3\X/4
+  //            o
+  //            5
+
+#ifdef GUDHI_DEBUG
+  std::cout << "Check exception throw in debug mode" << std::endl;
+  // throw excpt because sh has children
+  BOOST_CHECK_THROW (st.remove_maximal_simplex(st.find({0, 1, 6})), std::invalid_argument);
+  BOOST_CHECK_THROW (st.remove_maximal_simplex(st.find({3})), std::invalid_argument);
+  BOOST_CHECK(st == st_complete);
+#endif
+  
+  st.remove_maximal_simplex(st.find({0, 2}));
+  st.remove_maximal_simplex(st.find({0, 1, 2}));
+  st.remove_maximal_simplex(st.find({1, 2}));
+  st.remove_maximal_simplex(st.find({2}));
+  st.remove_maximal_simplex(st.find({0, 3}));
+  
+  BOOST_CHECK(st == st_pruned);
+  // Remove all, but as the simplex tree is not storing filtration, there is no modification
+  st.prune_above_filtration(0.0);
+  BOOST_CHECK(st == st_pruned);
+  
+  miniST st_wo_seven;
+  // FIXME
+  st_wo_seven.set_dimension(3);
+
+  st_wo_seven.insert_simplex_and_subfaces({0, 1, 6});
+  st_wo_seven.insert_simplex_and_subfaces({3, 4, 5});
+  // st_wo_seven:
+  //    1   6
+  //    o---o
+  //     \X/
+  //      o   o---o
+  //      0   3\X/4
+  //            o
+  //            5
+
+  // Remove all 7 to test the both remove_maximal_simplex cases (when _members is empty or not)
+  st.remove_maximal_simplex(st.find({0, 1, 6, 7}));
+  st.remove_maximal_simplex(st.find({0, 1, 7}));
+  st.remove_maximal_simplex(st.find({0, 6, 7}));
+  st.remove_maximal_simplex(st.find({0, 7}));
+  st.remove_maximal_simplex(st.find({1, 6, 7}));
+  st.remove_maximal_simplex(st.find({1, 7}));
+  st.remove_maximal_simplex(st.find({6, 7}));
+  st.remove_maximal_simplex(st.find({7}));
+  
+  BOOST_CHECK(st == st_wo_seven);
+}
+
+BOOST_AUTO_TEST_CASE(prune_above_filtration) {
+  std::cout << "********************************************************************" << std::endl;
+  std::cout << "PRUNE ABOVE FILTRATION" << std::endl;
+  typedef Simplex_tree<> typeST;
+  typeST st;
+
+  // FIXME
+  st.set_dimension(3);
+
+  st.insert_simplex_and_subfaces({0, 1, 6, 7}, 1.0);
+  st.insert_simplex_and_subfaces({3, 4, 5}, 2.0);
+
+  // Constructs a copy at this state for further test purpose
+  typeST st_pruned = st;
+  st_pruned.initialize_filtration();  // reset
+
+  st.insert_simplex_and_subfaces({3, 0}, 3.0);
+  st.insert_simplex_and_subfaces({2, 1, 0}, 4.0);
+
+  // Constructs a copy at this state for further test purpose
+  typeST st_complete = st;
+  // st_complete and st:
+  //    1   6
+  //    o---o
+  //   /X\7/
+  //  o---o---o---o
+  //  2   0   3\X/4
+  //            o
+  //            5
+  // st_pruned:
+  //    1   6
+  //    o---o
+  //     \7/
+  //      o   o---o
+  //      0   3\X/4
+  //            o
+  //            5
+
+  bool simplex_is_changed = false;
+  // Check the no action cases
+  // greater than initial filtration value
+  simplex_is_changed = st.prune_above_filtration(10.0);
+  if (simplex_is_changed)
+    st.initialize_filtration();
+  BOOST_CHECK(st == st_complete);
+  BOOST_CHECK(!simplex_is_changed);
+  // equal to initial filtration value
+  simplex_is_changed = st.prune_above_filtration(6.0);
+  if (simplex_is_changed)
+    st.initialize_filtration();
+  BOOST_CHECK(st == st_complete);
+  BOOST_CHECK(!simplex_is_changed);
+  // lower than initial filtration value, but still greater than the maximum filtration value
+  simplex_is_changed = st.prune_above_filtration(5.0);
+  if (simplex_is_changed)
+    st.initialize_filtration();
+  BOOST_CHECK(st == st_complete);
+  BOOST_CHECK(!simplex_is_changed);
+
+  // Display the Simplex_tree
+  std::cout << "The complex contains " << st.num_simplices() << " simplices";
+  std::cout << " - dimension " << st.dimension() << std::endl;
+  std::cout << "Iterator on Simplices in the filtration, with [filtration value]:" << std::endl;
+  for (auto f_simplex : st.filtration_simplex_range()) {
+    std::cout << "   " << "[" << st.filtration(f_simplex) << "] ";
+    for (auto vertex : st.simplex_vertex_range(f_simplex)) {
+      std::cout << (int) vertex << " ";
+    }
+    std::cout << std::endl;
+  }
+
+  // Check the pruned cases
+  simplex_is_changed = st.prune_above_filtration(2.5);
+  if (simplex_is_changed)
+    st.initialize_filtration();
+  BOOST_CHECK(st == st_pruned);
+  BOOST_CHECK(simplex_is_changed);
+
+  // Display the Simplex_tree
+  std::cout << "The complex pruned at 2.5 contains " << st.num_simplices() << " simplices";
+  std::cout << " - dimension " << st.dimension() << std::endl;
+
+  simplex_is_changed = st.prune_above_filtration(2.0);
+  if (simplex_is_changed)
+    st.initialize_filtration();
+  
+  std::cout << "The complex pruned at 2.0 contains " << st.num_simplices() << " simplices";
+  std::cout << " - dimension " << st.dimension() << std::endl;
+
+  BOOST_CHECK(st == st_pruned);
+  BOOST_CHECK(!simplex_is_changed);
+
+  typeST st_empty;
+  // FIXME
+  st_empty.set_dimension(3);
+  simplex_is_changed = st.prune_above_filtration(0.0);
+  if (simplex_is_changed)
+    st.initialize_filtration();
+
+  // Display the Simplex_tree
+  std::cout << "The complex pruned at 0.0 contains " << st.num_simplices() << " simplices";
+  std::cout << " - dimension " << st.dimension() << std::endl;
+
+  BOOST_CHECK(st == st_empty);
+  BOOST_CHECK(simplex_is_changed);
+
+  // Test case to the limit
+  simplex_is_changed = st.prune_above_filtration(-1.0);
+  if (simplex_is_changed)
+    st.initialize_filtration();
+  BOOST_CHECK(st == st_empty);
+  BOOST_CHECK(!simplex_is_changed);
+}
+
+BOOST_AUTO_TEST_CASE(mini_prune_above_filtration) {
+  std::cout << "********************************************************************" << std::endl;
+  std::cout << "MINI PRUNE ABOVE FILTRATION" << std::endl;
+  typedef Simplex_tree<MyOptions> typeST;
+  typeST st;
+
+  // FIXME
+  st.set_dimension(3);
+
+  st.insert_simplex_and_subfaces({0, 1, 6, 7});
+  st.insert_simplex_and_subfaces({3, 4, 5});
+  st.insert_simplex_and_subfaces({3, 0});
+  st.insert_simplex_and_subfaces({2, 1, 0});
+
+  // st:
+  //    1   6
+  //    o---o
+  //   /X\7/
+  //  o---o---o---o
+  //  2   0   3\X/4
+  //            o
+  //            5
+
+  st.initialize_filtration();
+  
+  // Display the Simplex_tree
+  std::cout << "The complex contains " << st.num_simplices() << " simplices" << std::endl;
+  BOOST_CHECK(st.num_simplices() == 27);
+
+  // Test case to the limit - With these options, there is no filtration, which means filtration is 0
+  bool simplex_is_changed = st.prune_above_filtration(1.0);
+  if (simplex_is_changed)
+    st.initialize_filtration();
+  // Display the Simplex_tree
+  std::cout << "The complex pruned at 1.0 contains " << st.num_simplices() << " simplices" << std::endl;
+  BOOST_CHECK(!simplex_is_changed);
+  BOOST_CHECK(st.num_simplices() == 27);
+
+  simplex_is_changed = st.prune_above_filtration(0.0);
+  if (simplex_is_changed)
+    st.initialize_filtration();
+  // Display the Simplex_tree
+  std::cout << "The complex pruned at 0.0 contains " << st.num_simplices() << " simplices" << std::endl;
+  BOOST_CHECK(!simplex_is_changed);
+  BOOST_CHECK(st.num_simplices() == 27);
+
+  // Test case to the limit
+  simplex_is_changed = st.prune_above_filtration(-1.0);
+  if (simplex_is_changed)
+    st.initialize_filtration();
+  // Display the Simplex_tree
+  std::cout << "The complex pruned at -1.0 contains " << st.num_simplices() << " simplices" << std::endl;
+  BOOST_CHECK(simplex_is_changed);
+  BOOST_CHECK(st.num_simplices() == 0);
+
+  // Display the Simplex_tree
+  std::cout << "The complex contains " << st.num_simplices() << " simplices" << std::endl;
+
+}
\ No newline at end of file
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
index 74c6a71d..8584cd16 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker.h
@@ -31,7 +31,7 @@
 #include <gudhi/Skeleton_blocker/Skeleton_blocker_simple_traits.h>
 #include <gudhi/Skeleton_blocker/Skeleton_blocker_simple_geometric_traits.h>
 
-#include <gudhi/Utils.h>  // xxx
+#include <gudhi/Debug_utils.h>
 
 namespace Gudhi {
 
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h
index 50a83345..0dd5dd54 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h
@@ -25,7 +25,7 @@
 
 #include <gudhi/Skeleton_blocker_complex.h>
 #include <gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h>
-#include <gudhi/Utils.h>
+#include <gudhi/Debug_utils.h>
 
 #include <map>
 #include <vector>
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h
index ce565166..b8d99201 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h
@@ -25,7 +25,7 @@
 #include <gudhi/Skeleton_blocker_link_complex.h>
 #include <gudhi/Skeleton_blocker/Skeleton_blocker_link_superior.h>
 #include <gudhi/Skeleton_blocker/internal/Trie.h>
-#include <gudhi/Utils.h>
+#include <gudhi/Debug_utils.h>
 
 #include <boost/iterator/iterator_facade.hpp>
 
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h
index 5b774f25..fd85f0c2 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h
@@ -31,7 +31,7 @@
 #include <gudhi/Skeleton_blocker/Skeleton_blocker_complex_visitor.h>
 #include <gudhi/Skeleton_blocker/internal/Top_faces.h>
 #include <gudhi/Skeleton_blocker/internal/Trie.h>
-#include <gudhi/Utils.h>
+#include <gudhi/Debug_utils.h>
 
 #include <boost/graph/adjacency_list.hpp>
 #include <boost/graph/connected_components.hpp>
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h
index 5c898152..040f7950 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h
@@ -22,9 +22,9 @@
 #ifndef SKELETON_BLOCKER_GEOMETRIC_COMPLEX_H_
 #define SKELETON_BLOCKER_GEOMETRIC_COMPLEX_H_
 
-#include <gudhi/Utils.h>
 #include <gudhi/Skeleton_blocker_complex.h>
 #include <gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h>
+#include <gudhi/Debug_utils.h>
 
 namespace Gudhi {
 
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_link_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_link_complex.h
index 85a6b0b5..e3c16d88 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_link_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_link_complex.h
@@ -22,8 +22,8 @@
 #ifndef SKELETON_BLOCKER_LINK_COMPLEX_H_
 #define SKELETON_BLOCKER_LINK_COMPLEX_H_
 
-#include <gudhi/Utils.h>
 #include <gudhi/Skeleton_blocker_complex.h>
+#include <gudhi/Debug_utils.h>
 
 namespace Gudhi {
 
diff --git a/src/Skeleton_blocker/test/TestSkeletonBlockerComplex.cpp b/src/Skeleton_blocker/test/TestSkeletonBlockerComplex.cpp
index 71b1833b..2a3f0501 100644
--- a/src/Skeleton_blocker/test/TestSkeletonBlockerComplex.cpp
+++ b/src/Skeleton_blocker/test/TestSkeletonBlockerComplex.cpp
@@ -24,7 +24,7 @@
 #include <string>
 #include <fstream>
 #include <sstream>
-#include "gudhi/Utils.h"
+#include "gudhi/Debug_utils.h"
 #include "gudhi/Test.h"
 #include "gudhi/Skeleton_blocker.h"
 //#include "gudhi/Skeleton_blocker_link_complex.h"
diff --git a/src/Witness_complex/test/CMakeLists.txt b/src/Witness_complex/test/CMakeLists.txt
index 9422c152..37bef2d0 100644
--- a/src/Witness_complex/test/CMakeLists.txt
+++ b/src/Witness_complex/test/CMakeLists.txt
@@ -4,14 +4,10 @@ project(GUDHIWitnessComplexUT)
 if (GCOVR_PATH)
   # for gcovr to make coverage reports - Corbera Jenkins plugin
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage")	
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage")
 endif()
 if (GPROF_PATH)
   # for gprof to make coverage reports - Jenkins
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-  set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg")
-  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg")
 endif()
 
 add_executable ( simple_witness_complexUT simple_witness_complex.cpp )
diff --git a/src/common/doc/main_page.h b/src/common/doc/main_page.h
index 1e0dbcda..063e0a11 100644
--- a/src/common/doc/main_page.h
+++ b/src/common/doc/main_page.h
@@ -20,6 +20,26 @@
  * We refer to \cite gudhilibrary_ICMS14 for a detailed description of the design of the library.
  *
  \section DataStructures Data structures
+ \subsection AlphaComplexDataStructure Alpha complex
+ \image html "alpha_complex_representation.png" "Alpha complex representation"
+<table border="0">
+  <tr>
+    <td width="25%">
+      <b>Author:</b> Vincent Rouvreau<br>
+      <b>Introduced in:</b> GUDHI 1.3.0<br>
+      <b>Copyright:</b> GPL v3<br>
+    </td>
+    <td width="75%">
+    Alpha_complex is a simplicial complex constructed from the finite cells of a Delaunay Triangulation.<br>
+    The filtration value of each simplex is computed as the square of the circumradius of the simplex if the
+    circumsphere is empty (the simplex is then said to be Gabriel), and as the minimum of the filtration
+    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::alphacomplex::Alpha_complex
+    </td>
+ </tr>
+</table>
  \subsection CubicalComplexDataStructure Cubical complex
  \image html "Cubical_complex_representation.png" "Cubical complex representation"
 <table border="0">
@@ -166,16 +186,43 @@
  * your operating system is detailed here http://doc.cgal.org/latest/Manual/installation.html
  * 
  * The following examples require the <a target="_blank" href="http://www.cgal.org/">Computational Geometry Algorithms
- * Library</a> (CGAL) and will not be built if CGAL is not installed:
- * \li <a href="_persistent_cohomology_2alpha_shapes_persistence_8cpp-example.html">
- * Persistent_cohomology/alpha_shapes_persistence.cpp</a>
+ * Library</a> (CGAL \cite cgal:eb-15b) and will not be built if CGAL is not installed:
+ * \li <a href="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html">
+ * Persistent_cohomology/alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
+ * Persistent_cohomology/alpha_complex_persistence.cpp</a>
  * \li <a href="_simplex_tree_2simplex_tree_from_alpha_shapes_3_8cpp-example.html">
  * Simplex_tree/simplex_tree_from_alpha_shapes_3.cpp</a>
+ * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html">
+ *  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>
  * 
  * The following example requires CGAL version &ge; 4.6:
  * \li <a href="_witness_complex_2witness_complex_sphere_8cpp-example.html">
  * Witness_complex/witness_complex_sphere.cpp</a>
  * 
+ * The following example requires CGAL version &ge; 4.7:
+ * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html">
+ * 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="common_2_c_g_a_l_points_off_reader_8cpp-example.html">
+ * common/CGAL_points_off_reader.cpp</a>
+ * 
+ * \subsection eigen3 Eigen3:
+ * <a target="_blank" href="http://eigen.tuxfamily.org/">Eigen3</a> is a C++ template library for linear algebra:
+ * matrices, vectors, numerical solvers, and related algorithms.
+ * 
+ * The following example requires the <a target="_blank" href="http://eigen.tuxfamily.org/">Eigen3</a> and will not be
+ * built if Eigen3 is not installed:
+ * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html">
+ * Alpha_complex/Alpha_complex_from_off.cpp</a> (requires also Eigen3)
+ * \li <a href="_alpha_complex_2_alpha_complex_from_points_8cpp-example.html">
+ * Alpha_complex/Alpha_complex_from_points.cpp</a> (requires also Eigen3)
+ * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
+ * Persistent_cohomology/alpha_complex_persistence.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
@@ -184,14 +231,20 @@
  * Having Intel&reg; TBB installed is recommended to parallelize and accelerate some GUDHI computations.
  * 
  * The following examples are using Intel&reg; TBB if installed:
+ * \li <a href="_alpha_complex_2_alpha_complex_from_off_8cpp-example.html">
+ * 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="_bitmap_cubical_complex_2_bitmap_cubical_complex_8cpp-example.html">
  * Bitmap_cubical_complex/Bitmap_cubical_complex.cpp</a>
  * \li <a href="_bitmap_cubical_complex_2_bitmap_cubical_complex_periodic_boundary_conditions_8cpp-example.html">
  * Bitmap_cubical_complex/Bitmap_cubical_complex_periodic_boundary_conditions.cpp</a>
  * \li <a href="_bitmap_cubical_complex_2_random_bitmap_cubical_complex_8cpp-example.html">
  * Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp</a>
- * \li <a href="_persistent_cohomology_2alpha_shapes_persistence_8cpp-example.html">
- * Persistent_cohomology/alpha_shapes_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2alpha_complex_3d_persistence_8cpp-example.html">
+ * Persistent_cohomology/alpha_complex_3d_persistence.cpp</a>
+ * \li <a href="_persistent_cohomology_2alpha_complex_persistence_8cpp-example.html">
+ * Persistent_cohomology/alpha_complex_persistence.cpp</a>
  * \li <a href="_simplex_tree_2simple_simplex_tree_8cpp-example.html">
  * Simplex_tree/simple_simplex_tree.cpp</a>
  * \li <a href="_simplex_tree_2simplex_tree_from_alpha_shapes_3_8cpp-example.html">
@@ -249,12 +302,16 @@ make \endverbatim
 
 // List of Gudhi examples - Doxygen needs at least a file tag to analyse comments
 /*! @file Examples
+ * @example Alpha_complex/Alpha_complex_from_off.cpp
+ * @example Alpha_complex/Alpha_complex_from_points.cpp
  * @example Bitmap_cubical_complex/Bitmap_cubical_complex.cpp
  * @example Bitmap_cubical_complex/Bitmap_cubical_complex_periodic_boundary_conditions.cpp
  * @example Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp
+ * @example common/CGAL_points_off_reader.cpp
  * @example Contraction/Garland_heckbert.cpp
  * @example Contraction/Rips_contraction.cpp
- * @example Persistent_cohomology/alpha_shapes_persistence.cpp
+ * @example Persistent_cohomology/alpha_complex_3d_persistence.cpp
+ * @example Persistent_cohomology/alpha_complex_persistence.cpp
  * @example Persistent_cohomology/parallel_rips_persistence.cpp
  * @example Persistent_cohomology/performance_rips_persistence.cpp
  * @example Persistent_cohomology/persistence_from_file.cpp
diff --git a/src/common/example/CGAL_points_off_reader.cpp b/src/common/example/CGAL_points_off_reader.cpp
new file mode 100644
index 00000000..45e9f1e6
--- /dev/null
+++ b/src/common/example/CGAL_points_off_reader.cpp
@@ -0,0 +1,44 @@
+#include <gudhi/Points_off_io.h>
+
+// For CGAL points type in dimension d
+// cf. http://doc.cgal.org/latest/Kernel_d/classCGAL_1_1Point__d.html
+#include <CGAL/Epick_d.h>
+
+#include <iostream>
+#include <string>
+#include <vector>
+
+typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel;
+typedef typename Kernel::Point_d Point_d;
+
+void usage(int argc, char * const progName) {
+  std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl;
+  std::cerr << "Usage: " << progName << " inputFile.off" << std::endl;
+  exit(-1);
+}
+
+int main(int argc, char **argv) {
+  if (argc != 2) usage(argc, (argv[0] - 1));
+
+  std::string offInputFile(argv[1]);
+  // Read the OFF file (input file name given as parameter) and triangulate points
+  Gudhi::Points_off_reader<Point_d> off_reader(offInputFile);
+  // Check the read operation was correct
+  if (!off_reader.is_valid()) {
+    std::cerr << "Unable to read file " << offInputFile << std::endl;
+    exit(-1);
+  }
+
+  // Retrieve the triangulation
+  std::vector<Point_d> point_cloud = off_reader.get_point_cloud();
+
+  int n = 0;
+  for (auto point : point_cloud) {
+    std::cout << "Point[" << n << "] = ";
+    for (int i = 0; i < point.dimension(); i++)
+      std::cout << point[i] << " ";
+    std::cout << "\n";
+    ++n;
+  }
+  return 0;
+}
diff --git a/src/common/example/CMakeLists.txt b/src/common/example/CMakeLists.txt
new file mode 100644
index 00000000..5aeaa8c6
--- /dev/null
+++ b/src/common/example/CMakeLists.txt
@@ -0,0 +1,22 @@
+cmake_minimum_required(VERSION 2.6)
+project(GUDHIDelaunayTriangulationOffFileReadWrite)
+
+# need CGAL 4.7
+if(CGAL_FOUND)
+  if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+    find_package(Eigen3 3.1.0)
+    if (EIGEN3_FOUND)
+      message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
+      include( ${EIGEN3_USE_FILE} )
+      
+      add_executable ( cgaloffreader CGAL_points_off_reader.cpp )
+      target_link_libraries(cgaloffreader  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
+      add_test(cgaloffreader ${CMAKE_CURRENT_BINARY_DIR}/cgaloffreader ${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off)
+
+    else()
+      message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.")
+    endif()
+  else()
+    message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.")
+  endif ()
+endif()
diff --git a/src/common/example/cgaloffreader_result.txt b/src/common/example/cgaloffreader_result.txt
new file mode 100644
index 00000000..1deb8dbd
--- /dev/null
+++ b/src/common/example/cgaloffreader_result.txt
@@ -0,0 +1,7 @@
+Point[0] = 1 1 
+Point[1] = 7 0 
+Point[2] = 4 6 
+Point[3] = 9 6 
+Point[4] = 0 14 
+Point[5] = 2 19 
+Point[6] = 9 17 
diff --git a/src/common/include/gudhi/Utils.h b/src/common/include/gudhi/Debug_utils.h
index 43916f11..7573a9db 100644
--- a/src/common/include/gudhi/Utils.h
+++ b/src/common/include/gudhi/Debug_utils.h
@@ -19,28 +19,37 @@
  *    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 UTILS_H_
-#define UTILS_H_
+#ifndef DEBUG_UTILS_H_
+#define DEBUG_UTILS_H_
 
+#include <iostream>
+
+#ifndef NDEBUG
+  // GUDHI_DEBUG is the Gudhi official flag for debug mode.
+  #define GUDHI_DEBUG
+#endif
+
+// GUDHI_CHECK throw an exception if expression is false in debug mode, but does nothing in release mode
+// Could assert in release mode, but cmake sets NDEBUG (for "NO DEBUG") in this mode, means assert does nothing.
+#ifdef GUDHI_DEBUG
+  #define GUDHI_CHECK(expression, excpt) if ((expression) == 0) throw excpt
+#else
+  #define GUDHI_CHECK(expression, excpt) (void) 0
+#endif
 
 #define PRINT(a) std::cerr << #a << ": " << (a) << " (DISP)" << std::endl
 
 // #define DBG_VERBOSE
 #ifdef DBG_VERBOSE
-#define DBG(a) std::cerr << "DBG: " << (a) << std::endl
-#define DBGMSG(a, b) std::cerr << "DBG: " << a << b << std::endl
-#define DBGVALUE(a) std::cerr << "DBG: " <<  #a << ": " << a << std::endl
-#define DBGCONT(a) std::cerr << "DBG: container " << #a << " -> "; for (auto x : a) std::cerr << x << ","; std::cerr <<
-std::endl
+  #define DBG(a) std::cout << "DBG: " << (a) << std::endl
+  #define DBGMSG(a, b) std::cout << "DBG: " << a << b << std::endl
+  #define DBGVALUE(a) std::cout << "DBG: " <<  #a << ": " << a << std::endl
+  #define DBGCONT(a) std::cout << "DBG: container " << #a << " -> "; for (auto x : a) std::cout << x << ","; std::cout << std::endl
 #else
-// #define DBG(a) a
-// #define DBGMSG(a,b) b
-// #define DBGVALUE(a) a
-// #define DBGCONT(a) a
-#define DBG(a)
-#define DBGMSG(a, b)
-#define DBGVALUE(a)
-#define DBGCONT(a)
+  #define DBG(a) (void) 0
+  #define DBGMSG(a, b) (void) 0
+  #define DBGVALUE(a) (void) 0
+  #define DBGCONT(a) (void) 0
 #endif
 
-#endif  // UTILS_H_
+#endif  // DEBUG_UTILS_H_
diff --git a/src/common/include/gudhi/Off_reader.h b/src/common/include/gudhi/Off_reader.h
index 81b9e634..4fcd2af2 100644
--- a/src/common/include/gudhi/Off_reader.h
+++ b/src/common/include/gudhi/Off_reader.h
@@ -31,40 +31,35 @@
 #include <iterator>
 #include <string>
 #include <vector>
+#include <fstream>
 
 namespace Gudhi {
 
-/**
- * Read an off file and calls a visitor methods while reading it.
- * An off file must have its first/snd line in this format :
- * OFF
- * num_vert num_faces num_edges
- *
- * A noff file must have its first/snd line in this format :
- * nOFF
- * dim num_vert num_faces num_edges
- *
- * The number of edges num_edges is optional and can be left to zero.
+/** \brief OFF file reader top class visitor. 
+ * 
+ * OFF file must be conform to format described here : 
+ * http://www.geomview.org/docs/html/OFF.html
  */
 class Off_reader {
  public:
   Off_reader(std::ifstream& stream) : stream_(stream) { }
-  // Off_reader(const std::string& name):stream_(name){
-  //   if(!stream_.is_open())
-  //   std::cerr <<"could not open file \n";
-  // }
 
   ~Off_reader() {
     stream_.close();
   }
 
-  /**
-   * read an off file and calls the following methods :
-   * void init(int dim,int num_vertices,int num_faces,int num_edges); //num_edges may not be set
-   * void point(const std::vector<double>& point);
-   * void maximal_face(const std::list<int>& face);
-   * void done();
-   * of the visitor when reading a point or a maximal face.
+  /** \brief
+   * Read an OFF file and calls the following methods :
+   * 
+   * <CODE>void init(int dim,int num_vertices,int num_faces,int num_edges);  // from file header - num_edges may not be set
+   * 
+   * void point(const std::vector<double>& point);  // for each point read
+   * 
+   * void maximal_face(const std::list<int>& face);  // for each face read
+   * 
+   * void done();  // upon file read is finished</CODE>
+   * 
+   * of the visitor when reading a point or a maximal face. Edges are not taken into account.
    */
   template<typename OffVisitor>
   bool read(OffVisitor& off_visitor) {
@@ -118,7 +113,7 @@ class Off_reader {
 
     if (!goto_next_uncomment_line(line)) return false;
     std::istringstream iss(line);
-    if (is_off_file) {
+    if ((is_off_file) && (!is_noff_file)) {
       off_info_.dim = 3;
       if (!(iss >> off_info_.num_vertices >> off_info_.num_faces >> off_info_.num_edges)) {
         std::cerr << "incorrect number of vertices/faces/edges\n";
@@ -126,8 +121,8 @@ class Off_reader {
       }
     } else {
       if (!(iss >> off_info_.dim >> off_info_.num_vertices >> off_info_.num_faces >> off_info_.num_edges)) {
-        std::cerr << "incorrect number of vertices/faces/edges\n";
-        return false;
+      std::cerr << "incorrect number of vertices/faces/edges\n";
+      return false;
       }
     }
     off_visitor.init(off_info_.dim, off_info_.num_vertices, off_info_.num_faces, off_info_.num_edges);
@@ -138,7 +133,7 @@ class Off_reader {
   bool goto_next_uncomment_line(std::string& uncomment_line) {
     uncomment_line.clear();
     do
-      std::getline(stream_, uncomment_line); while (uncomment_line[0] == '%');  // || uncomment_line.empty());
+      std::getline(stream_, uncomment_line); while (uncomment_line[0] == '%');
     return (uncomment_line.size() > 0 && uncomment_line[0] != '%');
   }
 
@@ -166,7 +161,7 @@ class Off_reader {
       iss >> num_face_vertices;
       std::vector<int> face;
       face.assign(std::istream_iterator<int>(iss), std::istream_iterator<int>());
-      if (face.size() != off_info_.dim) return false;
+      // if (face.size() != (off_info_.dim + 1)) return false;
       visitor.maximal_face(face);
     }
     return true;
diff --git a/src/common/include/gudhi/Points_off_io.h b/src/common/include/gudhi/Points_off_io.h
new file mode 100644
index 00000000..77f36be2
--- /dev/null
+++ b/src/common/include/gudhi/Points_off_io.h
@@ -0,0 +1,177 @@
+/*    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):       Vincent Rouvreau
+ *
+ *    Copyright (C) 2015  INRIA Saclay (France)
+ *
+ *    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 POINTS_OFF_IO_H_
+#define POINTS_OFF_IO_H_
+
+#include <gudhi/Off_reader.h>
+
+#include <string>
+#include <vector>
+#include <fstream>
+#include <map>
+
+namespace Gudhi {
+
+/** 
+ * \brief OFF file visitor implementation according to Off_reader in order to read points from an OFF file.
+ */
+template<typename Point_d>
+class Points_off_visitor_reader {
+ private:
+  std::vector<Point_d> point_cloud;
+
+ public:
+  /** \brief Off_reader visitor init implementation. 
+   * 
+   * The init parameters are set from OFF file header.
+   * Dimension value is required in order to construct Alpha complex.
+   *
+   * @param[in] dim space dimension of vertices.
+   * @param[in] num_vertices number of vertices in the OFF file (not used).
+   * @param[in] num_faces number of faces in the OFF file (not used).
+   * @param[in] num_edges number of edges in the OFF file (not used).
+   */
+  void init(int dim, int num_vertices, int num_faces, int num_edges) {
+#ifdef DEBUG_TRACES
+    std::cout << "Points_off_visitor_reader::init - dim=" << dim << " - num_vertices=" <<
+        num_vertices << " - num_faces=" << num_faces << " - num_edges=" << num_edges << std::endl;
+#endif  // DEBUG_TRACES
+    if (num_faces > 0) {
+      std::cerr << "Points_off_visitor_reader::init faces are not taken into account from OFF file for Points.\n";
+    }
+    if (num_edges > 0) {
+      std::cerr << "Points_off_visitor_reader::init edges are not taken into account from OFF file for Points.\n";
+    }
+  }
+
+  /** \brief Off_reader visitor point implementation. 
+   * 
+   * The point function is called on each vertex line from OFF file.
+   * This function inserts the vertex in the Alpha complex.
+   *
+   * @param[in] point vector of vertex coordinates.
+   */
+  void point(const std::vector<double>& point) {
+#ifdef DEBUG_TRACES
+    std::cout << "Points_off_visitor_reader::point ";
+    for (auto coordinate : point) {
+      std::cout << coordinate << " | ";
+    }
+    std::cout << std::endl;
+#endif  // DEBUG_TRACES
+    // Fill the point cloud
+    point_cloud.push_back(Point_d(point.size(), point.begin(), point.end()));
+  }
+
+  // Off_reader visitor maximal_face implementation - Only points are read
+  void maximal_face(const std::vector<int>& face) { }
+
+  // Off_reader visitor done implementation - Only points are read
+  void done() { }
+
+  /** \brief Point cloud getter.
+   *
+   * @return point_cloud.
+   */
+  const std::vector<Point_d>& get_point_cloud() const {
+    return point_cloud;
+  }
+};
+
+/** 
+ * \brief OFF file reader implementation in order to read points from an OFF file.
+ * 
+ * This class is using the Points_off_visitor_reader to visit the OFF file according to Off_reader.
+ * 
+ * Point_d must have a constructor with the following form:
+ * 
+ * \code template<class InputIterator > Point_d::Point_d(int d, InputIterator first, InputIterator last) \endcode
+ * 
+ * where d is the point dimension. 		
+ * 
+ * \section Example
+ *
+ * This example loads points from an OFF file and builds a vector of CGAL points in dimension d.
+ * Then, it is asked to display the points.
+ * 
+ * \include common/CGAL_points_off_reader.cpp
+ * 
+ * When launching:
+ * 
+ * \code $> ./cgaloffreader ../../data/points/alphacomplexdoc.off
+ * \endcode
+ *
+ * the program output is:
+ * 
+ * \include common/cgaloffreader_result.txt
+ */
+template<typename Point_d>
+class Points_off_reader {
+ public:
+  /** \brief Reads the OFF file and constructs the Alpha complex from the points
+   * that are in the OFF file.
+   *
+   * @param[in] name_file OFF file to read.
+   * 
+   * \post Check with is_valid() function to see if read operation was successful.
+   */
+  Points_off_reader(const std::string& name_file)
+  : valid_(false) {
+    std::ifstream stream(name_file);
+    if (stream.is_open()) {
+      Off_reader off_reader(stream);
+      Points_off_visitor_reader<Point_d> off_visitor;
+      valid_ = off_reader.read(off_visitor);
+      if (valid_) {
+        point_cloud = off_visitor.get_point_cloud();
+      }
+    } else {
+      std::cerr << "Points_off_reader::Points_off_reader could not open file " << name_file << "\n";
+    }
+  }
+
+  /** \brief Returns if the OFF file read operation was successful or not.
+   *
+   * @return OFF file read status.
+   */
+  bool is_valid() const {
+    return valid_;
+  }
+
+   /** \brief Point cloud getter.
+   *
+   * @return point_cloud.
+   */
+  const std::vector<Point_d>& get_point_cloud() const {
+    return point_cloud;
+  }
+
+ private:
+  /** \brief point_cloud.*/
+  std::vector<Point_d> point_cloud;
+  /** \brief OFF file read status.*/
+  bool valid_;
+};
+
+}  // namespace Gudhi
+
+#endif  // POINTS_OFF_IO_H_
diff --git a/src/common/include/gudhi/distance_functions.h b/src/common/include/gudhi/distance_functions.h
index e5c79ded..cd518581 100644
--- a/src/common/include/gudhi/distance_functions.h
+++ b/src/common/include/gudhi/distance_functions.h
@@ -23,6 +23,8 @@
 #ifndef DISTANCE_FUNCTIONS_H_
 #define DISTANCE_FUNCTIONS_H_
 
+#include <cmath>  // for std::sqrt
+
 /* Compute the Euclidean distance between two Points given
  * by a range of coordinates. The points are assumed to have 
  * the same dimension. */
@@ -35,7 +37,7 @@ double euclidean_distance(Point &p1, Point &p2) {
     double tmp = *it1 - *it2;
     dist += tmp*tmp;
   }
-  return sqrt(dist);
+  return std::sqrt(dist);
 }
 
 #endif  // DISTANCE_FUNCTIONS_H_
diff --git a/src/common/include/gudhi/reader_utils.h b/src/common/include/gudhi/reader_utils.h
index e05714c7..899f9df6 100644
--- a/src/common/include/gudhi/reader_utils.h
+++ b/src/common/include/gudhi/reader_utils.h
@@ -58,7 +58,9 @@ inline void read_points(std::string file_name, std::vector< std::vector< double
     while (iss >> x) {
       point.push_back(x);
     }
-    points.push_back(point);
+    // Check for empty lines
+    if (!point.empty())
+      points.push_back(point);
   }
   in_file.close();
 }
@@ -159,7 +161,7 @@ bool read_simplex(std::istream & in_, std::vector< Vertex_handle > & simplex, Fi
     simplex.push_back(v);
   }
   in_ >> fil;
-  in_.ignore((std::numeric_limits<std::streamsize>::max)(), '\n'); // ignore until the carriage return
+  in_.ignore((std::numeric_limits<std::streamsize>::max)(), '\n');  // ignore until the carriage return
   return true;
 }
 
diff --git a/src/common/test/CMakeLists.txt b/src/common/test/CMakeLists.txt
new file mode 100644
index 00000000..789546ae
--- /dev/null
+++ b/src/common/test/CMakeLists.txt
@@ -0,0 +1,39 @@
+cmake_minimum_required(VERSION 2.6)
+project(GUDHIDelaunayTriangulationOffFileReadWriteUT)
+
+if (GCOVR_PATH)
+  # for gcovr to make coverage reports - Corbera Jenkins plugin
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
+endif()
+if (GPROF_PATH)
+  # for gprof to make coverage reports - Jenkins
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
+endif()
+
+# need CGAL 4.7
+if(CGAL_FOUND)
+  if (NOT CGAL_VERSION VERSION_LESS 4.7.0)
+    find_package(Eigen3 3.1.0)
+    if (EIGEN3_FOUND)
+      message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
+      include( ${EIGEN3_USE_FILE} )
+      
+      add_executable ( poffreader_UT points_off_reader_unit_test.cpp )
+      target_link_libraries(poffreader_UT ${Boost_SYSTEM_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
+
+      # Do not forget to copy test files in current binary dir
+      file(COPY "${CMAKE_SOURCE_DIR}/data/points/alphacomplexdoc.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/)
+
+      # Unitary tests
+      add_test(poffreader_UT ${CMAKE_CURRENT_BINARY_DIR}/poffreader_UT
+      # XML format for Jenkins xUnit plugin 
+      --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/poffreader_UT.xml --log_level=test_suite --report_level=no)
+
+    else()
+      message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.")
+    endif()
+  else()
+    message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.")
+  endif ()
+endif()
+
diff --git a/src/common/test/README b/src/common/test/README
new file mode 100644
index 00000000..f2a7eb5a
--- /dev/null
+++ b/src/common/test/README
@@ -0,0 +1,14 @@
+To compile:
+***********
+
+cmake .
+make
+
+To launch with details:
+***********************
+
+./dtoffrw_UT --report_level=detailed --log_level=all 
+
+   ==> echo $? returns 0 in case of success (non-zero otherwise)
+
+
diff --git a/src/common/test/dtoffrw_alphashapedoc_result.off b/src/common/test/dtoffrw_alphashapedoc_result.off
new file mode 100644
index 00000000..1deb8dbd
--- /dev/null
+++ b/src/common/test/dtoffrw_alphashapedoc_result.off
@@ -0,0 +1,7 @@
+Point[0] = 1 1 
+Point[1] = 7 0 
+Point[2] = 4 6 
+Point[3] = 9 6 
+Point[4] = 0 14 
+Point[5] = 2 19 
+Point[6] = 9 17 
diff --git a/src/common/test/points_off_reader_unit_test.cpp b/src/common/test/points_off_reader_unit_test.cpp
new file mode 100644
index 00000000..73e19cbc
--- /dev/null
+++ b/src/common/test/points_off_reader_unit_test.cpp
@@ -0,0 +1,78 @@
+/*    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):       Vincent Rouvreau
+ *
+ *    Copyright (C) 2015  INRIA Saclay (France)
+ *
+ *    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/>.
+ */
+
+#include <gudhi/Points_off_io.h>
+
+// For CGAL points type in dimension d
+// cf. http://doc.cgal.org/latest/Kernel_d/classCGAL_1_1Point__d.html
+#include <CGAL/Epick_d.h>
+
+#include <iostream>
+#include <string>
+#include <vector>
+
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "points_off_read_write"
+#include <boost/test/unit_test.hpp>
+
+typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel;
+typedef typename Kernel::Point_d Point_d;
+
+BOOST_AUTO_TEST_CASE( points_doc_test )
+{
+  // Read the OFF file (input file name given as parameter) and triangulates points
+  Gudhi::Points_off_reader<Point_d> off_reader("alphacomplexdoc.off");
+  // Check the read operation was correct
+  BOOST_CHECK(off_reader.is_valid());
+  
+  // Retrieve the triangulation
+  std::vector<Point_d> point_cloud = off_reader.get_point_cloud();
+  BOOST_CHECK(point_cloud.size() == 7);
+
+  std::vector<Point_d> expected_points;
+  std::vector<double> point = {1.0, 1.0};
+  expected_points.push_back(Point_d(2, point.begin(), point.end()));
+  point = {7.0, 0.0};
+  expected_points.push_back(Point_d(2, point.begin(), point.end()));
+  point = {4.0, 6.0};
+  expected_points.push_back(Point_d(2, point.begin(), point.end()));
+  point = {9.0, 6.0};
+  expected_points.push_back(Point_d(2, point.begin(), point.end()));
+  point = {0.0, 14.0};
+  expected_points.push_back(Point_d(2, point.begin(), point.end()));
+  point = {2.0, 19.0};
+  expected_points.push_back(Point_d(2, point.begin(), point.end()));
+  point = {9.0, 17.0};
+  expected_points.push_back(Point_d(2, point.begin(), point.end()));
+
+  BOOST_CHECK(point_cloud == expected_points);
+}
+
+BOOST_AUTO_TEST_CASE( Delaunay_triangulation_unexisting_file_read_test )
+{
+  Gudhi::Points_off_reader<Point_d> off_reader("some_impossible_weird_file_name.off");
+  // Check the read operation was correct
+  BOOST_CHECK(!off_reader.is_valid());
+  
+  std::vector<Point_d> point_cloud = off_reader.get_point_cloud();
+  BOOST_CHECK(point_cloud.size() == 0);
+}