Merge remote-tracking branch 'cgal/6.0.x-branch'

.devcontainer/doxygen-cgal/Dockerfile

@@ -0,0 +1,55 @@
+# Use an official Fedora as a parent image for the build stage
+FROM fedora:latest AS sources_deps
+
+# Set environment variables to non-interactive
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Install dependencies
+RUN dnf update -y && dnf install -y \
+    wget \
+    make \
+    gcc \
+    gcc-c++ \
+    patch \
+    cmake \
+    bison \
+    flex \
+    unzip \
+    python3 \
+    && dnf clean all
+
+# Copy the patch file to the build context
+COPY cgal-NO_ADDITIONAL_DETAILS.patch .
+
+FROM sources_deps AS build
+
+# Build and install Doxygen from sources
+ARG DOXYGEN_VERSION=1.9.6
+ARG MAKEFLAGS=-j$(nproc)
+RUN if [ -n "$DEBUG"];then set -x && make --version && ls -lZ /tmp && id; fi \
+    && DOXYGEN_VERSION_UNDERSCORE=$(echo ${DOXYGEN_VERSION} | sed 's/\./_/g') \
+    && wget https://github.com/doxygen/doxygen/archive/refs/tags/Release_${DOXYGEN_VERSION_UNDERSCORE}.zip \
+    && unzip Release_${DOXYGEN_VERSION_UNDERSCORE}.zip \
+    && cd doxygen-Release_${DOXYGEN_VERSION_UNDERSCORE} \
+    && patch -p1 < ../cgal-NO_ADDITIONAL_DETAILS.patch \
+    && mkdir build \
+    && cd build \
+    && cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE=Release .. \
+    && cmake --build . \
+    && cmake --install . \
+    && mkdir -p /usr/local/share/doc/doxygen && cp ../LICENSE /usr/local/share/doc/doxygen/LICENSE.TXT \
+    && cd ../.. \
+    && rm -rf doxygen-Release_${DOXYGEN_VERSION_UNDERSCORE} Release_${DOXYGEN_VERSION_UNDERSCORE}.zip
+
+# Use a smaller base image for the final stage
+FROM fedora:latest
+
+# Install necessary runtime dependencies
+RUN set -x \
+    && dnf update -y && dnf install -y graphviz 'perl(Getopt::Std)' tex-bibtex cmake python3-lxml python3-pyquery \
+    && dnf clean all
+
+# Copy Doxygen from the build stage
+COPY --from=build /usr/local/bin/doxygen /usr/local/bin
+COPY --from=build /usr/local/share/doc/doxygen/LICENSE.TXT /usr/local/share/doc/doxygen/LICENSE.TXT
+RUN doxygen --version

.devcontainer/doxygen-cgal/Makefile

@@ -0,0 +1,23 @@
+SHELL := /bin/bash
+DOXYGEN_VERSIONS := 1.12.0 1.11.0 1.10.0 1.9.8 1.9.7 1.9.6
+
+.PHONY: all build-% push-% build push
+
+all: build
+	@echo "Use `$(MAKE) push` to push the images to the registry."
+
+build-%:
+	@echo "MAKEFLAGS: $(MAKEFLAGS)"
+	@echo "Building Doxygen version $*..."
+	if [ "$$(getenforce || true)" == "Enforcing" ]; then Z=:z; else Z=; fi; \
+	F="$(MAKEFLAGS)"; F=$${F##*fifo:}; F=$${F%% *}; \
+	if [ -p "$$F" ]; then echo "The GNU make FIFO file exists:"; ls -l $$F; VOLUME_ARGS="-v $$F:$$F$$Z"; echo -- $$VOLUME_ARGS; fi; \
+	podman build --build-arg DOXYGEN_VERSION=$* --build-arg "MAKEFLAGS=$(MAKEFLAGS)" $$VOLUME_ARGS -t cgal/doxygen:$* .
+
+push-%: build-%
+	@echo "Pushing cgal/doxygen:$*..."
+	podman push cgal/doxygen:$*
+
+build: $(foreach version,$(DOXYGEN_VERSIONS),build-$(version))
+
+push: $(foreach version,$(DOXYGEN_VERSIONS),push-$(version))

.devcontainer/doxygen-cgal/cgal-NO_ADDITIONAL_DETAILS.patch

@@ -0,0 +1,44 @@
+diff --git a/src/config.xml b/src/config.xml
+index 13910958a6..31f1354e44 100644
+--- a/src/config.xml
++++ b/src/config.xml
+@@ -893,6 +893,18 @@ Go to the <a href="commands.html">next</a> section or return to the
+  \note This will also disable the warnings about undocumented members
+  that are normally produced when \ref cfg_warnings "WARNINGS" is
+  set to \c YES.
++]]>
++      </docs>
++    </option>
++  </group>
++  <group name='Build' docs='Build related configuration options'>
++    <option type='bool' id='NO_ADDITIONAL_DETAILS' defval='0'>
++      <docs>
++<![CDATA[
++ When the \c EXTRACT_ALL tag is set to \c YES and a member or class
++ as no documentation, no detailed section will be produced if
++ the \c NO_ADDITIONAL_DETAILS tag is set to \c YES.
++ This tag has no effect if the \c EXTRACT_ALL tag is set to \c NO.
+ ]]>
+       </docs>
+     </option>
+diff --git a/src/memberdef.cpp b/src/memberdef.cpp
+index 08d9bf24c5..ab04e994c5 100644
+--- a/src/memberdef.cpp
++++ b/src/memberdef.cpp
+@@ -2501,6 +2501,7 @@ bool MemberDefImpl::hasDetailedDescription() const
+   if (!m_hasDetailedDescriptionCached)
+   {
+     bool extractAll            = Config_getBool(EXTRACT_ALL);
++    bool xAllNoDetailedSec = Config_getBool(NO_ADDITIONAL_DETAILS);
+     bool alwaysDetailedSec     = Config_getBool(ALWAYS_DETAILED_SEC);
+     bool repeatBrief           = Config_getBool(REPEAT_BRIEF);
+     bool briefMemberDesc       = Config_getBool(BRIEF_MEMBER_DESC);
+@@ -2512,7 +2513,7 @@ bool MemberDefImpl::hasDetailedDescription() const
+     // the member has detailed documentation because the user added some comments
+     bool docFilter =
+            // extract all is enabled
+-           extractAll ||
++           (extractAll && !xAllNoDetailedSec) ||
+            // has detailed docs
+            !documentation().isEmpty() ||
+            // has inbody docs

.devcontainer/doxygen-cgal/devcontainer.json

@@ -0,0 +1,16 @@
+{
+    "name": "CGAL Doxygen Dev Container, version 1.12.0, with CGAL patch",
+    "image": "docker.io/cgal/doxygen:1.12.0",
+    "features": {
+        "ghcr.io/devcontainers/features/git:1.3.2": {}
+    },
+    "customizations": {
+        "vscode": {
+            "extensions": [
+                "ms-vscode.cmake-tools",
+                "bbenoist.Doxygen",
+                "ms-vscode.cpptools"
+            ]
+        }
+    },
+}

.devcontainer/doxygen-cgal/distrobox.ini

@@ -0,0 +1,29 @@
+[distrobox-doxygen-1.12.0]
+image=cgal/doxygen:1.12.0
+exported_bins="/usr/local/bin/doxygen /usr/bin/perl /usr/bin/cmake /usr/bin/python3"
+exported_bins_path=$HOME/.local/bin-doxygen-1.12.0
+
+[distrobox-doxygen-1.11.0]
+image=cgal/doxygen:1.11.0
+exported_bins="/usr/local/bin/doxygen /usr/bin/perl /usr/bin/cmake /usr/bin/python3"
+exported_bins_path=$HOME/.local/bin-doxygen-1.11.0
+
+[distrobox-doxygen-1.10.0]
+image=cgal/doxygen:1.10.0
+exported_bins="/usr/local/bin/doxygen /usr/bin/perl /usr/bin/cmake /usr/bin/python3"
+exported_bins_path=$HOME/.local/bin-doxygen-1.10.0
+
+[distrobox-doxygen-1.9.8]
+image=cgal/doxygen:1.9.8
+exported_bins="/usr/local/bin/doxygen /usr/bin/perl /usr/bin/cmake /usr/bin/python3"
+exported_bins_path=$HOME/.local/bin-doxygen-1.9.8
+
+[distrobox-doxygen-1.9.7]
+image=cgal/doxygen:1.9.7
+exported_bins="/usr/local/bin/doxygen /usr/bin/perl /usr/bin/cmake /usr/bin/python3"
+exported_bins_path=$HOME/.local/bin-doxygen-1.9.7
+
+[distrobox-doxygen-1.9.6]
+image=cgal/doxygen:1.9.6
+exported_bins="/usr/local/bin/doxygen /usr/bin/perl /usr/bin/cmake /usr/bin/python3"
+exported_bins_path=$HOME/.local/bin-doxygen-1.9.6

BGL/include/CGAL/boost/graph/copy_face_graph.h

@@ -178,6 +178,7 @@ void copy_face_graph_impl(const SourceMesh& sm, TargetMesh& tm,
   }
 
   // detect if there are some non-manifold umbrellas and fix missing halfedge target pointers
+  std::map<sm_vertex_descriptor, std::vector<tm_halfedge_descriptor>> nm_umbrella_map;
   typedef typename std::vector<tm_edge_descriptor>::iterator edge_iterator;
   for (edge_iterator it=new_edges.begin(); it!=new_edges.end(); ++it)
   {
@@ -199,17 +200,38 @@ void copy_face_graph_impl(const SourceMesh& sm, TargetMesh& tm,
             // we recover tm_v using the halfedge associated to the target vertex of
             // the halfedge in sm corresponding to nh_t. This is working because we
             // set the vertex halfedge pointer to the "same" halfedges.
-            tm_vertex_descriptor tm_v =
-              target( get(hs_to_ht, halfedge(target(get(ht_to_hs, nh_t), sm), sm)), tm);
-            for(tm_halfedge_descriptor ht : halfedges_around_target(nh_t, tm))
-              set_target(ht, tm_v, tm);
+
+            sm_vertex_descriptor vs = target(get(ht_to_hs, nh_t), sm);
+            sm_halfedge_descriptor hs = halfedge(vs, sm);
+            if (hs == boost::graph_traits<SourceMesh>::null_halfedge())
+            {  // special case for Face_filtered_graph with a non-manifold input with not all umbrellas selected
+              nm_umbrella_map[vs].push_back(nh_t);
+            }
+            else
+            {
+              tm_vertex_descriptor tm_v = target( get(hs_to_ht, hs), tm);
+              for(tm_halfedge_descriptor ht : halfedges_around_target(nh_t, tm))
+                set_target(ht, tm_v, tm);
+            }
           }
           nh_t = opposite(nh_t, tm);
         }
       }
       break;
     }
   }
+
+  for (const auto& vs_and_hts : nm_umbrella_map)
+  {
+    sm_vertex_descriptor v_sm = vs_and_hts.first;
+    tm_vertex_descriptor v_tm = add_vertex(tm);
+    *v2v++=std::make_pair(v_sm, v_tm);
+    set_halfedge(v_tm, vs_and_hts.second.front(), tm);
+    put(tm_vpm, v_tm, conv(get(sm_vpm, v_sm)));
+
+    for (tm_halfedge_descriptor h_tm : vs_and_hts.second)
+      set_target(h_tm, v_tm, tm);
+  }
 }
 
 } // end of namespace internal

BGL/test/BGL/test_Face_filtered_graph.cpp

@@ -579,6 +579,102 @@ void test_Polyhedron_tetrahedron()
   test_mesh<Polyhedron, FCMap, Poly_Adapter>(poly_adapter);
 }
 
+void non_manifoldness_test1()
+{
+  // works out-of-the-box because Face_filtered_graph handles already non-manifold cycles
+  SM mesh;
+  SM::Vertex_index v0=add_vertex(mesh);
+  SM::Vertex_index v1=add_vertex(mesh);
+  SM::Vertex_index v2=add_vertex(mesh);
+  SM::Vertex_index v3=add_vertex(mesh);
+  SM::Vertex_index v4=add_vertex(mesh);
+  SM::Vertex_index v5=add_vertex(mesh);
+  SM::Vertex_index v6=add_vertex(mesh);
+
+  SM::Face_index f0=mesh.add_face(v0,v1,v2);
+  SM::Face_index f1=mesh.add_face(v0,v3,v4);
+  SM::Face_index f2=mesh.add_face(v0,v5,v6);
+  SM::Halfedge_index h = halfedge(f0,mesh);
+  while(target(h, mesh)!=v0)
+    h=next(h,mesh);
+  set_halfedge(v0, h, mesh);
+
+  std::vector<SM::Face_index> selection = {f1, f2};
+  CGAL::Face_filtered_graph<SM> ffg(mesh, selection);
+
+  SM out;
+  CGAL::copy_face_graph(ffg, out);
+
+  assert(vertices(out).size()==5);
+  assert(faces(out).size()==2);
+}
+
+void non_manifoldness_test2()
+{
+  SM mesh;
+  SM::Vertex_index v0=add_vertex(mesh);
+  SM::Vertex_index v0b=add_vertex(mesh);
+  SM::Vertex_index v0t=add_vertex(mesh);
+
+  SM::Vertex_index v1=add_vertex(mesh);
+  SM::Vertex_index v2=add_vertex(mesh);
+  SM::Vertex_index v3=add_vertex(mesh);
+
+  SM::Vertex_index v4=add_vertex(mesh);
+  SM::Vertex_index v5=add_vertex(mesh);
+  SM::Vertex_index v6=add_vertex(mesh);
+
+  SM::Vertex_index v7=add_vertex(mesh);
+  SM::Vertex_index v8=add_vertex(mesh);
+  SM::Vertex_index v9=add_vertex(mesh);
+
+  SM::Face_index f00=mesh.add_face(v1,v2,v0);
+  SM::Face_index f01=mesh.add_face(v2,v3,v0);
+  SM::Face_index f02=mesh.add_face(v3,v1,v0);
+
+  SM::Face_index f10=mesh.add_face(v4,v5,v0b);
+  SM::Face_index f11=mesh.add_face(v5,v6,v0b);
+  SM::Face_index f12=mesh.add_face(v6,v4,v0b);
+
+  SM::Face_index f20=mesh.add_face(v7,v8,v0t);
+  SM::Face_index f21=mesh.add_face(v8,v9,v0t);
+  SM::Face_index f22=mesh.add_face(v9,v7,v0t);
+
+  assert(f00!=SM::Face_index());
+  assert(f01!=SM::Face_index());
+  assert(f02!=SM::Face_index());
+  assert(f10!=SM::Face_index());
+  assert(f11!=SM::Face_index());
+  assert(f12!=SM::Face_index());
+  assert(f20!=SM::Face_index());
+  assert(f21!=SM::Face_index());
+  assert(f22!=SM::Face_index());
+
+  #define UPDATE_V(fX, vX) \
+  { SM::Halfedge_index h = halfedge(fX,mesh);\
+  while(target(h, mesh)!=vX) h=next(h,mesh);\
+  set_target(h, v0, mesh); }
+
+  UPDATE_V(f10, v0b)
+  UPDATE_V(f11, v0b)
+  UPDATE_V(f12, v0b)
+  UPDATE_V(f20, v0t)
+  UPDATE_V(f21, v0t)
+  UPDATE_V(f22, v0t)
+
+  remove_vertex(v0b, mesh);
+  remove_vertex(v0t, mesh);
+
+  std::vector<SM::Face_index> selection = {f10, f11, f12, f20, f21, f22};
+  CGAL::Face_filtered_graph<SM> ffg(mesh, selection);
+
+  SM out;
+  CGAL::copy_face_graph(ffg, out);
+
+  assert(vertices(out).size()==7);
+  assert(faces(out).size()==6);
+}
+
 int main(int, char**)
 {
   test_graph_range(poly_data());
@@ -590,6 +686,8 @@ int main(int, char**)
 #endif
 
   test_invalid_selections();
+  non_manifoldness_test1();
+  non_manifoldness_test2();
 
   test_SM_tetrahedron();
   test_Polyhedron_tetrahedron();