Merge remote-tracking branch 'cgal/master' into SDG-Fix_doc-GF

Author: MaelRL

.github/install.sh

@@ -3,7 +3,7 @@ sudo add-apt-repository ppa:mikhailnov/pulseeffects -y
 sudo apt-get update
 sudo apt-get install -y  libmpfr-dev \
  libeigen3-dev qtbase5-dev libqt5sql5-sqlite libqt5opengl5-dev qtscript5-dev \
- libqt5svg5-dev qttools5-dev qttools5-dev-tools libboost1.72-dev
+ libqt5svg5-dev qttools5-dev qttools5-dev-tools libboost1.72-dev zsh
 #update cmake to 3.18.4
 sudo apt purge --auto-remove cmake
 cd /tmp

.github/workflows/checks.yml

@@ -0,0 +1,30 @@
+name: CMake Test Merge Branch
+
+on: [push, pull_request]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    
+    steps:
+    - uses: actions/[email protected]
+    - name: install dependencies
+      run: |
+        .github/install.sh
+        set -x
+        sudo apt-get update && sudo apt-get install -y graphviz ssh bibtex2html
+        sudo pip install lxml 
+        sudo pip install 'pyquery==1.4.1' # it seems to be the last py2 compatible version
+        wget --no-verbose -O doxygen_exe https://cgal.geometryfactory.com/~mgimeno/doxygen/build_1_8_13/bin/doxygen
+        sudo mv doxygen_exe /usr/bin/doxygen
+        sudo chmod +x /usr/bin/doxygen
+        git config --global user.email "[email protected]"
+        git config --global user.name "Maxime Gimeno"
+        
+    - name: Run checks
+      run: |
+        zsh Scripts/developer_scripts/test_merge_of_branch HEAD
+        #test dependencies
+        bash Scripts/developer_scripts/cgal_check_dependencies.sh --check_headers /usr/bin/doxygen
+

.github/workflows/demo.yml

@@ -1,6 +1,6 @@
 name: Test Polyhedron Demo
 
-on: [pull_request]
+on: [push, pull_request]
 
 jobs:
   batch_1:

.travis.yml

@@ -23,36 +23,35 @@ env:
     - PACKAGE='Homogeneous_kernel Hyperbolic_triangulation_2 Inscribed_areas '
     - PACKAGE='Installation Interpolation Intersections_2 '
     - PACKAGE='Intersections_3 Interval_skip_list Interval_support '
-    - PACKAGE='Inventor Jet_fitting_3 Kernel_23 '
-    - PACKAGE='Kernel_d LEDA Linear_cell_complex '
-    - PACKAGE='MacOSX Maintenance Matrix_search '
-    - PACKAGE='Mesh_2 Mesh_3 Mesher_level '
-    - PACKAGE='Minkowski_sum_2 Minkowski_sum_3 Modifier '
-    - PACKAGE='Modular_arithmetic Nef_2 Nef_3 '
-    - PACKAGE='Nef_S2 NewKernel_d Number_types '
-    - PACKAGE='OpenNL Optimal_bounding_box Optimal_transportation_reconstruction_2 '
-    - PACKAGE='Optimisation_basic Partition_2 Periodic_2_triangulation_2 '
-    - PACKAGE='Periodic_3_mesh_3 Periodic_3_triangulation_3 Periodic_4_hyperbolic_triangulation_2 '
-    - PACKAGE='Point_set_2 Point_set_3 Point_set_processing_3 '
-    - PACKAGE='Poisson_surface_reconstruction_3 Polygon Polygon_mesh_processing '
-    - PACKAGE='Polygonal_surface_reconstruction Polyhedron Polyhedron_IO '
-    - PACKAGE='Polyline_simplification_2 Polynomial Polytope_distance_d '
-    - PACKAGE='Principal_component_analysis Principal_component_analysis_LGPL Profiling_tools '
-    - PACKAGE='Property_map QP_solver Random_numbers '
-    - PACKAGE='Ridges_3 STL_Extension Scale_space_reconstruction_3 '
-    - PACKAGE='Scripts SearchStructures Segment_Delaunay_graph_2 '
-    - PACKAGE='Segment_Delaunay_graph_Linf_2 Set_movable_separability_2 Shape_detection '
-    - PACKAGE='Skin_surface_3 Snap_rounding_2 Solver_interface '
-    - PACKAGE='Spatial_searching Spatial_sorting Straight_skeleton_2 '
-    - PACKAGE='Stream_lines_2 Stream_support Subdivision_method_3 '
-    - PACKAGE='Surface_mesh Surface_mesh_approximation Surface_mesh_deformation '
-    - PACKAGE='Surface_mesh_parameterization Surface_mesh_segmentation Surface_mesh_shortest_path '
-    - PACKAGE='Surface_mesh_simplification Surface_mesh_skeletonization Surface_mesh_topology '
-    - PACKAGE='Surface_mesher Surface_sweep_2 TDS_2 '
-    - PACKAGE='TDS_3 Testsuite Tetrahedral_remeshing '
-    - PACKAGE='Three Triangulation Triangulation_2 '
-    - PACKAGE='Triangulation_3 Union_find Visibility_2 '
-    - PACKAGE='Voronoi_diagram_2 wininst '
+    - PACKAGE='Jet_fitting_3 Kernel_23 Kernel_d '
+    - PACKAGE='LEDA Linear_cell_complex MacOSX '
+    - PACKAGE='Maintenance Matrix_search Mesh_2 '
+    - PACKAGE='Mesh_3 Mesher_level Minkowski_sum_2 '
+    - PACKAGE='Minkowski_sum_3 Modifier Modular_arithmetic '
+    - PACKAGE='Nef_2 Nef_3 Nef_S2 '
+    - PACKAGE='NewKernel_d Number_types OpenNL '
+    - PACKAGE='Optimal_bounding_box Optimal_transportation_reconstruction_2 Optimisation_basic '
+    - PACKAGE='Partition_2 Periodic_2_triangulation_2 Periodic_3_mesh_3 '
+    - PACKAGE='Periodic_3_triangulation_3 Periodic_4_hyperbolic_triangulation_2 Point_set_2 '
+    - PACKAGE='Point_set_3 Point_set_processing_3 Poisson_surface_reconstruction_3 '
+    - PACKAGE='Polygon Polygon_mesh_processing Polygonal_surface_reconstruction '
+    - PACKAGE='Polyhedron Polyline_simplification_2 Polynomial '
+    - PACKAGE='Polytope_distance_d Principal_component_analysis Principal_component_analysis_LGPL '
+    - PACKAGE='Profiling_tools Property_map QP_solver '
+    - PACKAGE='Random_numbers Ridges_3 STL_Extension '
+    - PACKAGE='Scale_space_reconstruction_3 Scripts SearchStructures '
+    - PACKAGE='Segment_Delaunay_graph_2 Segment_Delaunay_graph_Linf_2 Set_movable_separability_2 '
+    - PACKAGE='Shape_detection Skin_surface_3 Snap_rounding_2 '
+    - PACKAGE='Solver_interface Spatial_searching Spatial_sorting '
+    - PACKAGE='Straight_skeleton_2 Stream_lines_2 Stream_support '
+    - PACKAGE='Subdivision_method_3 Surface_mesh Surface_mesh_approximation '
+    - PACKAGE='Surface_mesh_deformation Surface_mesh_parameterization Surface_mesh_segmentation '
+    - PACKAGE='Surface_mesh_shortest_path Surface_mesh_simplification Surface_mesh_skeletonization '
+    - PACKAGE='Surface_mesh_topology Surface_mesher Surface_sweep_2 '
+    - PACKAGE='TDS_2 TDS_3 Testsuite '
+    - PACKAGE='Tetrahedral_remeshing Three Triangulation '
+    - PACKAGE='Triangulation_2 Triangulation_3 Union_find '
+    - PACKAGE='Visibility_2 Voronoi_diagram_2 wininst '
 compiler: clang
 install:
   - echo "$PWD"

.travis/packages.txt

@@ -49,7 +49,6 @@ Intersections_2
 Intersections_3
 Interval_skip_list
 Interval_support
-Inventor
 Jet_fitting_3
 Kernel_23
 Kernel_d
@@ -87,7 +86,6 @@ Polygon
 Polygon_mesh_processing
 Polygonal_surface_reconstruction
 Polyhedron
-Polyhedron_IO
 Polyline_simplification_2
 Polynomial
 Polytope_distance_d

AABB_tree/doc/AABB_tree/PackageDescription.txt

@@ -35,7 +35,7 @@
 \cgalCRPSection{Primitives}
 - `CGAL::AABB_triangle_primitive<GeomTraits, Iterator, CacheDatum>`
 - `CGAL::AABB_segment_primitive<GeomTraits, Iterator, CacheDatum>`
-- `CGAL::AABB_primitive<Id,ObjectPropertyMap,PointPropertyMapPolyhedron,ExternalPropertyMaps,CacheDatum>`
+- `CGAL::AABB_primitive<Id,ObjectPropertyMap,PointPropertyMap,ExternalPropertyMaps,CacheDatum>`
 - `CGAL::AABB_halfedge_graph_segment_primitive<HalfedgeGraph,Vpm,OneHalfedgeGraphPerTree,CacheDatum>`
 - `CGAL::AABB_face_graph_triangle_primitive<FaceGraph,Vpm,OneFaceGraphPerTree,CacheDatum>`
 */

AABB_tree/examples/AABB_tree/AABB_cached_bbox_example.cpp

@@ -1,14 +1,15 @@
-#include <iostream>
-#include <fstream>
-
 #include <CGAL/Exact_predicates_inexact_constructions_kernel.h>
+
 #include <CGAL/AABB_tree.h>
 #include <CGAL/AABB_traits.h>
 #include <CGAL/Polyhedron_3.h>
 #include <CGAL/Surface_mesh.h>
 #include <CGAL/AABB_face_graph_triangle_primitive.h>
 #include <CGAL/Timer.h>
 
+#include <iostream>
+#include <fstream>
+
 typedef CGAL::Exact_predicates_inexact_constructions_kernel K;
 typedef K::FT FT;
 typedef K::Point_3 Point_3;
@@ -26,8 +27,12 @@ void triangle_mesh(const char* fname)
   typedef CGAL::AABB_tree<Traits> Tree;
 
   TriangleMesh tmesh;
-  std::ifstream in(fname);
-  in >> tmesh;
+  if(!CGAL::read_polygon_mesh(fname, tmesh) || CGAL::is_triangle_mesh(tmesh))
+  {
+    std::cerr << "Invalid input." << std::endl;
+    return;
+  }
+
   Timer t;
   t.start();
   Tree tree(faces(tmesh).first, faces(tmesh).second, tmesh);
@@ -36,7 +41,6 @@ void triangle_mesh(const char* fname)
   std::cout << "Closest point to ORIGIN:" << tree.closest_point(CGAL::ORIGIN) << std::endl;
 }
 
-
 Bbox_3 bbox(boost::graph_traits<Surface_mesh>::face_descriptor fd,
             const Surface_mesh& p)
 {
@@ -47,7 +51,6 @@ Bbox_3 bbox(boost::graph_traits<Surface_mesh>::face_descriptor fd,
   return res;
 }
 
-
 void surface_mesh_cache_bbox(const char* fname)
 {
   typedef boost::graph_traits<Surface_mesh>::face_descriptor face_descriptor;
@@ -64,9 +67,9 @@ void surface_mesh_cache_bbox(const char* fname)
   t.start();
   Bbox_pmap bb = tmesh.add_property_map<face_descriptor,Bbox_3>("f:bbox",Bbox_3()).first;
 
-  for(face_descriptor fd : faces(tmesh)){
+  for(face_descriptor fd : faces(tmesh))
     put(bb, fd, bbox(fd,tmesh));
-  }
+
   Traits traits(bb);
   Tree tree(traits);
   tree.insert(faces(tmesh).first, faces(tmesh).second, tmesh);
@@ -77,7 +80,6 @@ void surface_mesh_cache_bbox(const char* fname)
    std::cout << "Closest point to ORIGIN:" << tree.closest_point(CGAL::ORIGIN) << std::endl;
 }
 
-
 int main(int argc, char* argv[])
 {
   std::cout << "Polyhedron_3" << std::endl;

AABB_tree/examples/AABB_tree/AABB_ray_shooting_example.cpp

@@ -1,14 +1,15 @@
-#include <iostream>
-#include <fstream>
-
 #include <CGAL/Simple_cartesian.h>
+#include <CGAL/Surface_mesh.h>
+
 #include <CGAL/AABB_tree.h>
 #include <CGAL/AABB_traits.h>
-#include <CGAL/Surface_mesh.h>
 #include <CGAL/AABB_face_graph_triangle_primitive.h>
 #include <CGAL/Polygon_mesh_processing/compute_normal.h>
 #include <CGAL/Polygon_mesh_processing/orientation.h>
 
+#include <iostream>
+#include <fstream>
+
 typedef CGAL::Simple_cartesian<double> K;
 typedef K::FT FT;
 typedef K::Point_3 Point;
@@ -24,8 +25,8 @@ typedef CGAL::AABB_traits<K, Primitive> Traits;
 typedef CGAL::AABB_tree<Traits> Tree;
 typedef boost::optional<Tree::Intersection_and_primitive_id<Ray>::Type> Ray_intersection;
 
-
-struct Skip {
+struct Skip
+{
   face_descriptor fd;
 
   Skip(const face_descriptor fd)
@@ -44,14 +45,20 @@ struct Skip {
 int main(int argc, char* argv[])
 {
   const char* filename = (argc > 1) ? argv[1] : "data/tetrahedron.off";
-  std::ifstream input(filename);
+
   Mesh mesh;
-  input >> mesh;
+  if(!CGAL::read_polygon_mesh(filename, mesh))
+  {
+    std::cerr << "Invalid input." << std::endl;
+    return 1;
+  }
+
   Tree tree(faces(mesh).first, faces(mesh).second, mesh);
 
   double d = CGAL::Polygon_mesh_processing::is_outward_oriented(mesh)?-1:1;
 
-  for(face_descriptor fd : faces(mesh)){
+  for(face_descriptor fd : faces(mesh))
+  {
     halfedge_descriptor hd = halfedge(fd,mesh);
     Point p = CGAL::centroid(mesh.point(source(hd,mesh)),
                              mesh.point(target(hd,mesh)),
@@ -61,13 +68,16 @@ int main(int argc, char* argv[])
     Ray ray(p,d * v);
     Skip skip(fd);
     Ray_intersection intersection = tree.first_intersection(ray, skip);
-    if(intersection){
+    if(intersection)
+    {
       if(boost::get<Point>(&(intersection->first))){
         const Point* p =  boost::get<Point>(&(intersection->first) );
         std::cout <<  *p << std::endl;
       }
     }
   }
+
   std::cerr << "done" << std::endl;
+
   return 0;
 }

AABB_tree/include/CGAL/AABB_face_graph_triangle_primitive.h

@@ -98,7 +98,7 @@ class AABB_face_graph_triangle_primitive
   }
 
 public:
-  #ifdef DOXYGEN_RUNNING
+#ifdef DOXYGEN_RUNNING
   /// \name Types
   /// @{
   /*!
@@ -122,37 +122,45 @@ class AABB_face_graph_triangle_primitive
   If `OneFaceGraphPerTree` is CGAL::Tag_true, constructs a `Shared_data` object from a reference to the polyhedon `graph`.
   */
   static unspecified_type construct_shared_data( FaceGraph& graph );
-  #else
+#else
   typedef typename Base::Id Id;
-  #endif
+#endif
   typedef typename boost::graph_traits<FaceGraph>::face_descriptor face_descriptor;
 
   // constructors
+
+#ifdef DOXYGEN_RUNNING
   /*!
+    constructs a primitive.
+
     \tparam Iterator an input iterator with `Id` as value type.
+
+    If `VertexPointPMap` is the default of the class, an additional constructor
+    is available with `vppm` set to `get(vertex_point, graph)`.
+  */
+  template <class Iterator>
+  AABB_face_graph_triangle_primitive(Iterator it, const FaceGraph& graph, VertexPointPMap vppm);
+
+  /*!
     constructs a primitive.
     If `VertexPointPMap` is the default of the class, an additional constructor
     is available with `vppm` set to `get(vertex_point, graph)`.
   */
+  AABB_face_graph_triangle_primitive(face_descriptor fd, const FaceGraph& graph, VertexPointPMap vppm);
+#else
   template <class Iterator>
   AABB_face_graph_triangle_primitive(Iterator it, const FaceGraph& graph, VertexPointPMap_ vppm)
     : Base( Id_(make_id(*it, graph, OneFaceGraphPerTree())),
             Triangle_property_map(const_cast<FaceGraph*>(&graph),vppm),
             Point_property_map(const_cast<FaceGraph*>(&graph),vppm) )
   {}
 
-  /*!
-    constructs a primitive.
-    If `VertexPointPMap` is the default of the class, an additional constructor
-    is available with `vppm` set to `get(vertex_point, graph)`.
-  */
   AABB_face_graph_triangle_primitive(face_descriptor fd, const FaceGraph& graph, VertexPointPMap_ vppm)
     : Base( Id_(make_id(fd, graph, OneFaceGraphPerTree())),
             Triangle_property_map(const_cast<FaceGraph*>(&graph),vppm),
             Point_property_map(const_cast<FaceGraph*>(&graph),vppm) )
   {}
 
-#ifndef DOXYGEN_RUNNING
   template <class Iterator>
   AABB_face_graph_triangle_primitive(Iterator it, const FaceGraph& graph)
     : Base( Id_(make_id(*it, graph, OneFaceGraphPerTree())),