Merge tag 'tags/gudhi-release-3.2.0' into dfsg/latest

3 files changed, 42 insertions, 38 deletions

diff --git a/src/Alpha_complex/utilities/CMakeLists.txt b/src/Alpha_complex/utilities/CMakeLists.txt
index 57b92942..2ffbdde0 100644
--- a/src/Alpha_complex/utilities/CMakeLists.txt
+++ b/src/Alpha_complex/utilities/CMakeLists.txt
@@ -2,7 +2,7 @@ project(Alpha_complex_utilities)
 
 if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
   add_executable (alpha_complex_persistence alpha_complex_persistence.cpp)
-  target_link_libraries(alpha_complex_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+  target_link_libraries(alpha_complex_persistence ${CGAL_LIBRARY} Boost::program_options)
 
   if (TBB_FOUND)
     target_link_libraries(alpha_complex_persistence ${TBB_LIBRARIES})
@@ -16,14 +16,20 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
   if (DIFF_PATH)
     add_test(Alpha_complex_utilities_diff_exact_alpha_complex ${DIFF_PATH}
              "exact.pers" "safe.pers")
+    set_tests_properties(Alpha_complex_utilities_diff_exact_alpha_complex PROPERTIES DEPENDS
+             "Alpha_complex_utilities_exact_alpha_complex_persistence;Alpha_complex_utilities_safe_alpha_complex_persistence")
+             
     add_test(Alpha_complex_utilities_diff_fast_alpha_complex ${DIFF_PATH}
              "fast.pers" "safe.pers")
+    set_tests_properties(Alpha_complex_utilities_diff_fast_alpha_complex PROPERTIES DEPENDS
+             "Alpha_complex_utilities_fast_alpha_complex_persistence;Alpha_complex_utilities_safe_alpha_complex_persistence")
+
   endif()
   
   install(TARGETS alpha_complex_persistence DESTINATION bin)
 
   add_executable(alpha_complex_3d_persistence alpha_complex_3d_persistence.cpp)
-  target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY} ${Boost_PROGRAM_OPTIONS_LIBRARY})
+  target_link_libraries(alpha_complex_3d_persistence ${CGAL_LIBRARY} Boost::program_options)
   if (TBB_FOUND)
     target_link_libraries(alpha_complex_3d_persistence ${TBB_LIBRARIES})
   endif(TBB_FOUND)
@@ -36,15 +42,19 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
           "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off"
           "-p" "2" "-m" "0.45" "-o" "exact_3d.pers" "-e")
 
-  add_test(NAME Alpha_complex_utilities_safe_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence>
+  add_test(NAME Alpha_complex_utilities_fast_alpha_complex_3d COMMAND $<TARGET_FILE:alpha_complex_3d_persistence>
           "${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off"
           "-p" "2" "-m" "0.45" "-o" "fast_3d.pers" "-f")
 
   if (DIFF_PATH)
     add_test(Alpha_complex_utilities_diff_exact_alpha_complex_3d ${DIFF_PATH}
             "exact_3d.pers" "safe_3d.pers")
+    set_tests_properties(Alpha_complex_utilities_diff_exact_alpha_complex_3d PROPERTIES DEPENDS
+            "Alpha_complex_utilities_exact_alpha_complex_3d;Alpha_complex_utilities_alpha_complex_3d")
     add_test(Alpha_complex_utilities_diff_fast_alpha_complex_3d ${DIFF_PATH}
             "fast_3d.pers" "safe_3d.pers")
+    set_tests_properties(Alpha_complex_utilities_diff_fast_alpha_complex_3d PROPERTIES DEPENDS
+            "Alpha_complex_utilities_fast_alpha_complex_3d;Alpha_complex_utilities_alpha_complex_3d")
   endif()
 
   add_test(NAME Alpha_complex_utilities_periodic_alpha_complex_3d_persistence COMMAND $<TARGET_FILE:alpha_complex_3d_persistence>
diff --git a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp
index 929fc2e8..91899040 100644
--- a/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp
+++ b/src/Alpha_complex/utilities/alpha_complex_3d_persistence.cpp
@@ -222,10 +222,7 @@ int main(int argc, char **argv) {
       break;
   }
 
-  // Sort the simplices in the order of the filtration
-  simplex_tree.initialize_filtration();
-
-  std::cout << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl;
+  std::clog << "Simplex_tree dim: " << simplex_tree.dimension() << std::endl;
   // Compute the persistence diagram of the complex
   Persistent_cohomology pcoh(simplex_tree, true);
   // initializes the coefficient field for homology
@@ -237,7 +234,7 @@ int main(int argc, char **argv) {
   if (output_file_diag.empty()) {
     pcoh.output_diagram();
   } else {
-    std::cout << "Result in file: " << output_file_diag << std::endl;
+    std::clog << "Result in file: " << output_file_diag << std::endl;
     std::ofstream out(output_file_diag);
     pcoh.output_diagram(out);
     out.close();
@@ -266,7 +263,7 @@ void program_options(int argc, char *argv[], std::string &off_file_points, bool
       "cuboid-file,c", po::value<std::string>(&cuboid_file),
       "Name of file describing the periodic domain. Format is:\n  min_hx min_hy min_hz\n  max_hx max_hy max_hz")(
       "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")(
+      "Name of file in which the persistence diagram is written. Default print in std::clog")(
       "max-alpha-square-value,r",
       po::value<Filtration_value>(&alpha_square_max_value)
           ->default_value(std::numeric_limits<Filtration_value>::infinity()),
@@ -288,18 +285,18 @@ void program_options(int argc, char *argv[], std::string &off_file_points, bool
   po::notify(vm);
 
   if (vm.count("help") || !vm.count("input-file") || !vm.count("weight-file")) {
-    std::cout << std::endl;
-    std::cout << "Compute the persistent homology with coefficient field Z/pZ \n";
-    std::cout << "of a 3D Alpha complex defined on a set of input points.\n";
-    std::cout << "3D Alpha complex can be safe (by default) exact or fast, weighted and/or periodic\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.\n\n";
+    std::clog << std::endl;
+    std::clog << "Compute the persistent homology with coefficient field Z/pZ \n";
+    std::clog << "of a 3D Alpha complex defined on a set of input points.\n";
+    std::clog << "3D Alpha complex can be safe (by default) exact or fast, weighted and/or periodic\n\n";
+    std::clog << "The output diagram contains one bar per line, written with the convention: \n";
+    std::clog << "   p   dim b d \n";
+    std::clog << "where dim is the dimension of the homological feature,\n";
+    std::clog << "b and d are respectively the birth and death of the feature and \n";
+    std::clog << "p is the characteristic of the field Z/pZ used for homology coefficients.\n\n";
 
-    std::cout << "Usage: " << argv[0] << " [options] input-file weight-file\n\n";
-    std::cout << visible << std::endl;
+    std::clog << "Usage: " << argv[0] << " [options] input-file weight-file\n\n";
+    std::clog << visible << std::endl;
     exit(-1);
   }
 }
diff --git a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp
index 486347cc..7c898dfd 100644
--- a/src/Alpha_complex/utilities/alpha_complex_persistence.cpp
+++ b/src/Alpha_complex/utilities/alpha_complex_persistence.cpp
@@ -72,13 +72,10 @@ int main(int argc, char **argv) {
   // ----------------------------------------------------------------------------
   // Display information about the alpha complex
   // ----------------------------------------------------------------------------
-  std::cout << "Simplicial complex is of dimension " << simplex.dimension() << " - " << simplex.num_simplices()
+  std::clog << "Simplicial complex is of dimension " << simplex.dimension() << " - " << simplex.num_simplices()
             << " simplices - " << simplex.num_vertices() << " vertices." << std::endl;
 
-  // Sort the simplices in the order of the filtration
-  simplex.initialize_filtration();
-
-  std::cout << "Simplex_tree dim: " << simplex.dimension() << std::endl;
+  std::clog << "Simplex_tree dim: " << simplex.dimension() << std::endl;
   // Compute the persistence diagram of the complex
   Gudhi::persistent_cohomology::Persistent_cohomology<Simplex_tree, Gudhi::persistent_cohomology::Field_Zp> pcoh(
       simplex);
@@ -91,7 +88,7 @@ int main(int argc, char **argv) {
   if (output_file_diag.empty()) {
     pcoh.output_diagram();
   } else {
-    std::cout << "Result in file: " << output_file_diag << std::endl;
+    std::clog << "Result in file: " << output_file_diag << std::endl;
     std::ofstream out(output_file_diag);
     pcoh.output_diagram(out);
     out.close();
@@ -114,7 +111,7 @@ void program_options(int argc, char *argv[], std::string &off_file_points, bool
       "fast,f", po::bool_switch(&fast),
       "To activate fast version of Alpha complex (default is false, not available if exact is set)")(
       "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")(
+      "Name of file in which the persistence diagram is written. Default print in std::clog")(
       "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.")(
@@ -135,17 +132,17 @@ void program_options(int argc, char *argv[], std::string &off_file_points, bool
   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::clog << std::endl;
+    std::clog << "Compute the persistent homology with coefficient field Z/pZ \n";
+    std::clog << "of an Alpha complex defined on a set of input points.\n \n";
+    std::clog << "The output diagram contains one bar per line, written with the convention: \n";
+    std::clog << "   p   dim b d \n";
+    std::clog << "where dim is the dimension of the homological feature,\n";
+    std::clog << "b and d are respectively the birth and death of the feature and \n";
+    std::clog << "p is the characteristic of the field Z/pZ used for homology coefficients." << std::endl << std::endl;
+
+    std::clog << "Usage: " << argv[0] << " [options] input-file" << std::endl << std::endl;
+    std::clog << visible << std::endl;
     exit(-1);
   }
 }