Merge branch 'aevol_6' into 'aevol_6'

Make aevol 6 run on macOS

See merge request aevol/aevol!2

.gitignore

@@ -11,6 +11,7 @@ config.log
 config.status
 configure
 .deps/
+build/*
 src/aevol_create
 src/aevol_modify
 src/aevol_propagate
@@ -18,6 +19,8 @@ src/aevol_run
 src/libaevol/SFMT-src-1.4/jump/.dirstamp
 *.a
 src/post_treatments/aevol_misc_ancstats
+src/post_treatments/aevol_misc_ancestor_robustness
+src/post_treatments/aevol_misc_ancestor_stats
 src/post_treatments/aevol_misc_compute_pop_stats
 src/post_treatments/aevol_misc_create_eps
 src/post_treatments/aevol_misc_extract
@@ -28,6 +31,7 @@ src/post_treatments/aevol_misc_robustness
 src/post_treatments/aevol_misc_mutagenesis
 src/post_treatments/aevol_misc_template
 src/post_treatments/aevol_misc_view_generation
+src/post_treatments/aevol_misc_view
 *.o
 
 

CMakeLists.txt

@@ -60,7 +60,8 @@ if(APPLE)
     if(CMAKE_CXX_COMPILER_ID STREQUAL "Clang" OR          
        CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")       
       set(OpenMP_CXX "${CMAKE_CXX_COMPILER}")      
-      set(OpenMP_CXX_FLAGS "-Xpreprocessor -fopenmp -Wno-unused-command-line-argument")       
+	  set(OpenMP_CXX_FLAGS "-Xpreprocessor -fopenmp -Wno-unused-command-line-argument -I /usr/local/opt/libomp/include")
+	  message("\nFLAGS: ${OpenMP_CXX_FLAGS}")
       set(OpenMP_CXX_LIB_NAMES "libomp" "libgomp" "libiomp5")                  
       set(OpenMP_libomp_LIBRARY ${OpenMP_CXX_LIB_NAMES})                       
       set(OpenMP_libgomp_LIBRARY ${OpenMP_CXX_LIB_NAMES})                      

src/libaevol/Fuzzy.cpp

@@ -470,18 +470,34 @@ void Fuzzy::reset() {
   // assert(invariant());
 }
 
+/// Reset the fuzzy set to its original state, two points at
+/// (X_MIN, 0.0) and (X_MAX, 0.0).
 void Fuzzy::clear() {
-  points_.clear();
+  points_ = {Point(X_MIN, 0.0), Point(X_MAX, 0.0)};
 }
 
 void Fuzzy::add_point(ProteinConcentration x, ProteinConcentration y)
 {
+  // points_ must always contain at least two elements, at X_MIN and X_MAX.
+  assert(points_.size() >= 2);
+  assert(points_.begin()->x == X_MIN);
+  assert(points_.rbegin()->x == X_MAX);
+
+  // We don't want to add a new point if there's already a point at the same x.
+  // To find out if there is such a point, we find the first point with
+  // larger x and then look at its predecessor.
   list<Point>::iterator p =
 #ifndef __OPENMP_GPU
       find_if(points_.begin(), points_.end(), [x](Point& q){return q.x > x;});
 #else
       algorithm_cuda::find_if_point_5(points_.begin(), points_.end(), x);
 #endif
+
+  // Since there is always a point at x = X_MAX, we always find such a point,
+  // and since there is always a point at x = X_MIN (which does not
+  // match the condition), that point always has a predecessor.
+  // p should therefore never be points_.begin().
+  assert(p != points_.begin());
   if (prev(p)->x == x) {
     prev(p)->y += y;
   } else {

src/libaevol/SFMT-src-1.4/CMakeLists.txt

@@ -51,4 +51,3 @@ target_compile_definitions(sfmt
 # ============================================================================
 # Use C++11
 # ============================================================================
-target_compile_options(sfmt PRIVATE "-std=c++14")