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)
   {
@@ -199,10 +200,19 @@ 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);
+            sm_vertex_descriptor vs = target(get(ht_to_hs, nh_t), sm);
-            for(tm_halfedge_descriptor ht : halfedges_around_target(nh_t, tm))
+            sm_halfedge_descriptor hs = halfedge(vs, sm);
-              set_target(ht, tm_v, tm);
+            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);
         }
@@ -210,6 +220,18 @@ void copy_face_graph_impl(const SourceMesh& sm, TargetMesh& 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();

Documentation/doc/CMakeLists.txt

@@ -24,6 +24,8 @@ else()
   set(CGAL_ROOT "${CMAKE_SOURCE_DIR}")
 endif()
 
+cmake_minimum_required(VERSION 3.18..3.29) # for list(SORT ... COMPARE NATURAL)
+
 find_package(Doxygen REQUIRED)
 find_package(Python3 REQUIRED COMPONENTS Interpreter)
 
@@ -32,7 +34,7 @@ if (NOT Python3_EXECUTABLE)
   return()
 endif()
 
-message(STATUS  ${Python3_EXECUTABLE})
+message(VERBOSE "Using Python version ${Python3_VERSION}: ${Python3_EXECUTABLE}")
 
 if(NOT DOXYGEN_FOUND)
   message(WARNING "Cannot build the documentation without Doxygen!")
@@ -275,7 +277,7 @@ set(CGAL_DOC_DXY_DIR "${CMAKE_BINARY_DIR}/doc_dxy")
 file(MAKE_DIRECTORY "${CGAL_DOC_DXY_DIR}")
 
 #Setting the resource directory depending on the version of doxygen
-set(CGAL_DOC_RESOURCE_DIR_DEFAULT "${CMAKE_CURRENT_LIST_DIR}/resources/1.10.0")
+set(CGAL_DOC_RESOURCE_PREFIX_DIR "${CMAKE_CURRENT_LIST_DIR}/resources")
 
 #  first look if resources for the specific doxygen version is available, fallback
 #  on the default otherwise
@@ -283,12 +285,46 @@ set(CGAL_DOC_RESOURCE_DIR_DEFAULT "${CMAKE_CURRENT_LIST_DIR}/resources/1.10.0")
 #select only the version number (not the commit hash)
 string(REPLACE " " ";" DOXYGEN_VERSION ${DOXYGEN_VERSION})
 list(GET DOXYGEN_VERSION 0 DOXYGEN_VERSION)
+message(VERBOSE "Doxygen version ${DOXYGEN_VERSION}: ${DOXYGEN_EXECUTABLE}")
 
-if(EXISTS "${CMAKE_CURRENT_LIST_DIR}/resources/${DOXYGEN_VERSION}")
+# The Doxygen version is search in that sorted list (to find the index for which the version is less or equal)
-  set(CGAL_DOC_RESOURCE_DIR
+set(CGAL_DOXYGEN_RESOURCES_VERSIONS 1.8.13 1.9.6 1.10.0)
-      "${CMAKE_CURRENT_LIST_DIR}/resources/${DOXYGEN_VERSION}")
+list(SORT CGAL_DOXYGEN_RESOURCES_VERSIONS COMPARE NATURAL)
+
+# The GLOB is here to check that the list in CGAL_DOXYGEN_RESOURCES_VERSIONS is correct.
+# CGAL_DOXYGEN_RESOURCES_DIRS is also used below.
+file(GLOB CGAL_DOXYGEN_RESOURCES_DIRS
+    RELATIVE "${CGAL_DOC_RESOURCE_PREFIX_DIR}"
+    "${CGAL_DOC_RESOURCE_PREFIX_DIR}/*")
+list(SORT CGAL_DOXYGEN_RESOURCES_DIRS COMPARE NATURAL)
+
+if(NOT CGAL_DOXYGEN_RESOURCES_DIRS STREQUAL CGAL_DOXYGEN_RESOURCES_VERSIONS)
+  message(FATAL "The directories in ${CGAL_DOC_RESOURCE_PREFIX_DIR} do not match the
+expected versions: [${CGAL_DOXYGEN_RESOURCES_VERSIONS}] vs [${CGAL_DOXYGEN_RESOURCES_DIRS}]")
+endif()
+
+function(CGAL_insert_in_sorted_list list_name value)
+  set(list ${${list_name}})
+  if(NOT value IN_LIST list)
+    list(APPEND list "${value}")
+    list(SORT list COMPARE NATURAL)
+  endif()
+  set(${list_name} ${list} PARENT_SCOPE)
+endfunction()
+
+if(DOXYGEN_VERSION IN_LIST CGAL_DOXYGEN_RESOURCES_VERSIONS)
+  list(FIND CGAL_DOXYGEN_RESOURCES_VERSIONS "${DOXYGEN_VERSION}" DOXYGEN_VERSION_INDEX)
 else()
-  set(CGAL_DOC_RESOURCE_DIR "${CGAL_DOC_RESOURCE_DIR_DEFAULT}")
+  CGAL_insert_in_sorted_list(CGAL_DOXYGEN_RESOURCES_VERSIONS ${DOXYGEN_VERSION})
+  list(FIND CGAL_DOXYGEN_RESOURCES_VERSIONS ${DOXYGEN_VERSION} DOXYGEN_VERSION_INDEX)
+  math(EXPR DOXYGEN_VERSION_INDEX "${DOXYGEN_VERSION_INDEX} - 1")
+endif()
+list(GET CGAL_DOXYGEN_RESOURCES_DIRS "${DOXYGEN_VERSION_INDEX}" CGAL_DOC_RESOURCE_DIR)
+set(CGAL_DOC_RESOURCE_DIR "${CGAL_DOC_RESOURCE_PREFIX_DIR}/${CGAL_DOC_RESOURCE_DIR}")
+if(NOT EXISTS "${CGAL_DOC_RESOURCE_DIR}")
+  message(FATAL_ERROR "Doxygen resources for version ${DOXYGEN_VERSION} not found")
+else()
+  message(VERBOSE "Using Doxygen resources from ${CGAL_DOC_RESOURCE_DIR}")
 endif()
 
 set(CGAL_DOC_BIBLIO_DIR "${CMAKE_CURRENT_LIST_DIR}/biblio")

Documentation/doc/Documentation/Developer_manual/cmakelist_script.txt

@@ -35,6 +35,6 @@ These options should suffice to create a `CMakeLists.txt` script
 for most directories containing programs. However, in some special
 cases, it might still be required to create the script manually, for
 instance, if some source files/executables need a different linking than
-other source files. The Section \subpage devman_create_and_use_a_cmakelist provides more details.
+other source files. The Section \ref devman_create_and_use_a_cmakelist provides more details.
 
 */

Documentation/doc/Documentation/Developer_manual/developer_manual.txt

@@ -23,4 +23,5 @@ The developer manual is primarily aimed at \cgal developers, but may also be int
 - \subpage devman_info
 - \subpage devman_create_cgal_CMakeLists
 - \subpage deprecated
+- \subpage Doxygen_for_CGAL
 */

Documentation/doc/Documentation/Doxyfile.in

@@ -19,6 +19,7 @@ FILTER_PATTERNS     = *.txt=${CMAKE_BINARY_DIR}/pkglist_filter
 
 HTML_EXTRA_FILES += ${CGAL_DOC_RESOURCE_DIR}/hacks.js \
                     ${CGAL_DOC_RESOURCE_DIR}/menu_version.js \
+                    ${CGAL_DOC_RESOURCE_DIR}/cgal_stylesheet.css \
                     ${CMAKE_BINARY_DIR}/how_to_cite_cgal.bib \
                     ${CMAKE_BINARY_DIR}/how_to_cite.html \
                     ${CGAL_PACKAGE_DOC_DIR}/fig/g-196x196-doc.png

Documentation/doc/Documentation/Doxygen_for_CGAL.md

@@ -1,4 +1,4 @@
-# Doxygen for CGAL #
+\page Doxygen_for_CGAL Doxygen for CGAL
 
 This is the documentation of doxygen hacks that are applied to make
 the output of Doxygen more suitable to CGAL. It explains the general
@@ -14,17 +14,17 @@ hacks that create what you see.
 ### Package Overview ###
 
 The package overview is build by having a special command that is
-filtered by the python script pkglist_filter.py.
+filtered by the python script `pkglist_filter.py`.
 
-A command has to be of the form \package_listing{PKG_NAME}, where
+A command has to be of the form `\package_listing{PKG_NAME}`, where
-PKG_NAME cannot contain a closing }.
+`PKG_NAME` cannot contain a closing `}`.
 
 The command is replaced by the text between the two delimiters
-PkgDescBegin and PkgDescEnd in the file ../PKG_NAME/doc/PKG_NAME/PackageDescription.txt
+`cgalPkgDescriptionBegin` and `cgalPkgDescriptionEnd` in the file `../PKG_NAME/doc/PKG_NAME/PackageDescription.txt`
 
-If PKG_NAME is of the form A/B the selected file is
+If `PKG_NAME` is of the form `A/B` the selected file is
-../A/doc/B/PackageDescription.txt. This is to support packages like
+`../A/doc/B/PackageDescription.txt`. This is to support packages like
-TDS_2, which don't reside in their own packages in the SCM.
+`TDS_2`, which don't reside in their own packages in the SCM.
 
 ### Footnotes ###
 
@@ -50,13 +50,13 @@ LaTex.
 This hack fiddles with the internal structures and functions of the
 treeview to remove the unnecessary intermediate top-level module part.
 
-It assigns the first element of the module array (found in module.js)
+It assigns the first element of the module array (found in `module.js`)
 to the Reference Manual entry. This makes the tree view link go to
 that group directly instead of the intermediate link. It also removes
 one level of nesting.
 
 Unfortunately this changes the overall tree structure. To adjust for
-that we hijack the gotoNode function of navtree.js and *augment* it
+that we hijack the `gotoNode` function of `navtree.js` and *augment* it
 with an additional check for the specific tree level we borked and
 redirect it.
 

Documentation/doc/resources/1.10.0/BaseDoxyfile.in

@@ -486,24 +486,6 @@ HTML_HEADER            = ${CGAL_DOC_HEADER_PACKAGE}
 
 HTML_FOOTER            = ${CGAL_DOC_RESOURCE_DIR}/footer.html
 
-# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
-# cascading style sheets that are included after the standard style sheets
-# created by doxygen. Using this option one can overrule certain style aspects.
-# This is preferred over using HTML_STYLESHEET since it does not replace the
-# standard style sheet and is therefore more robust against future updates.
-# Doxygen will copy the style sheet files to the output directory.
-# Note: The order of the extra style sheet files is of importance (e.g. the last
-# style sheet in the list overrules the setting of the previous ones in the
-# list).
-# Note: Since the styling of scrollbars can currently not be overruled in
-# Webkit/Chromium, the styling will be left out of the default doxygen.css if
-# one or more extra stylesheets have been specified. So if scrollbar
-# customization is desired it has to be added explicitly. For an example see the
-# documentation.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_EXTRA_STYLESHEET  = ${CGAL_DOC_RESOURCE_DIR}/cgal_stylesheet.css
-
 # Doxygen stores a couple of settings persistently in the browser (via e.g.
 # cookies). By default these settings apply to all HTML pages generated by
 # doxygen across all projects. The HTML_PROJECT_COOKIE tag can be used to store

Documentation/doc/resources/1.10.0/header.html

@@ -26,6 +26,7 @@ $search
 $mathjax
 $darkmode
 <link href="$relpath^$stylesheet" rel="stylesheet" type="text/css" />
+<link href="$relpath$../Manual/cgal_stylesheet.css" rel="stylesheet" type="text/css" />
 $extrastylesheet
 </head>
 <body>

Documentation/doc/resources/1.10.0/header_package.html

@@ -43,6 +43,7 @@
 <script type="text/javascript" src="../Manual/search/search.js"></script>
 <!-- Manually done below. -->
 <link href="$relpath^../Manual/$stylesheet" rel="stylesheet" type="text/css" />
+<link href="$relpath$../Manual/cgal_stylesheet.css" rel="stylesheet" type="text/css" />
 $mathjax
 $darkmode
 <script src="$relpath^topics.js" type="text/javascript"></script>

Documentation/doc/resources/1.8.13/BaseDoxyfile.in

@@ -477,24 +477,6 @@ HTML_HEADER            = ${CGAL_DOC_HEADER_PACKAGE}
 
 HTML_FOOTER            = ${CGAL_DOC_RESOURCE_DIR}/footer.html
 
-# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
-# cascading style sheets that are included after the standard style sheets
-# created by doxygen. Using this option one can overrule certain style aspects.
-# This is preferred over using HTML_STYLESHEET since it does not replace the
-# standard style sheet and is therefore more robust against future updates.
-# Doxygen will copy the style sheet files to the output directory.
-# Note: The order of the extra style sheet files is of importance (e.g. the last
-# style sheet in the list overrules the setting of the previous ones in the
-# list).
-# Note: Since the styling of scrollbars can currently not be overruled in
-# Webkit/Chromium, the styling will be left out of the default doxygen.css if
-# one or more extra stylesheets have been specified. So if scrollbar
-# customization is desired it has to be added explicitly. For an example see the
-# documentation.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_EXTRA_STYLESHEET  = ${CGAL_DOC_RESOURCE_DIR}/cgal_stylesheet.css
-
 # If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
 # page will contain the date and time when the page was generated. Setting this
 # to YES can help to show when doxygen was last run and thus if the

Documentation/doc/resources/1.8.13/header.html

@@ -17,7 +17,6 @@ $treeview
 $search
 $mathjax
 <link href="$relpath^$stylesheet" rel="stylesheet" type="text/css" />
-<!-- This should probably be an extrastylesheet instead of hardcoded. -->
 <link href="$relpath$../Manual/cgal_stylesheet.css" rel="stylesheet" type="text/css" />
 $extrastylesheet
 </head>

Documentation/doc/resources/1.8.13/header_package.html

@@ -33,7 +33,6 @@
 <script type="text/javascript" src="../Manual/search/search.js"></script>
 <!-- Manually done below. -->
 <link href="$relpath^../Manual/$stylesheet" rel="stylesheet" type="text/css" />
-<!-- This should probably be an extrastylesheet instead of hardcoded. -->
 <link href="$relpath$../Manual/cgal_stylesheet.css" rel="stylesheet" type="text/css" />
 <script type="text/x-mathjax-config">
 MathJax.Hub.Config({

Documentation/doc/resources/1.9.6/BaseDoxyfile.in

@@ -486,24 +486,6 @@ HTML_HEADER            = ${CGAL_DOC_HEADER_PACKAGE}
 
 HTML_FOOTER            = ${CGAL_DOC_RESOURCE_DIR}/footer.html
 
-# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined
-# cascading style sheets that are included after the standard style sheets
-# created by doxygen. Using this option one can overrule certain style aspects.
-# This is preferred over using HTML_STYLESHEET since it does not replace the
-# standard style sheet and is therefore more robust against future updates.
-# Doxygen will copy the style sheet files to the output directory.
-# Note: The order of the extra style sheet files is of importance (e.g. the last
-# style sheet in the list overrules the setting of the previous ones in the
-# list).
-# Note: Since the styling of scrollbars can currently not be overruled in
-# Webkit/Chromium, the styling will be left out of the default doxygen.css if
-# one or more extra stylesheets have been specified. So if scrollbar
-# customization is desired it has to be added explicitly. For an example see the
-# documentation.
-# This tag requires that the tag GENERATE_HTML is set to YES.
-
-HTML_EXTRA_STYLESHEET  = ${CGAL_DOC_RESOURCE_DIR}/cgal_stylesheet.css
-
 # If you want full control over the layout of the generated HTML pages it might
 # be necessary to disable the index and replace it with your own. The
 # DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top

Documentation/doc/resources/1.9.6/header.html

@@ -23,7 +23,6 @@ $search
 $mathjax
 $darkmode
 <link href="$relpath^$stylesheet" rel="stylesheet" type="text/css" />
-<!-- This should probably be an extrastylesheet instead of hardcoded. -->
 <link href="$relpath$../Manual/cgal_stylesheet.css" rel="stylesheet" type="text/css" />
 $extrastylesheet
 </head>

Documentation/doc/resources/1.9.6/header_package.html

@@ -39,7 +39,6 @@
 <script type="text/javascript" src="../Manual/search/search.js"></script>
 <!-- Manually done below. -->
 <link href="$relpath^../Manual/$stylesheet" rel="stylesheet" type="text/css" />
-<!-- This should probably be an extrastylesheet instead of hardcoded. -->
 <link href="$relpath$../Manual/cgal_stylesheet.css" rel="stylesheet" type="text/css" />
 $mathjax
 $darkmode

Documentation/doc/scripts/pkglist_filter.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import codecs
 import re
@@ -28,16 +28,10 @@ def main(argv):
             for l in pkgdesc:
                 do_print = do_print or re.match(".*cgalPkgDescriptionBegin.*", l)
                 if(do_print):
-                  if hasattr(sys.stdout, 'buffer'):
+                  sys.stdout.buffer.write(l.encode('utf-8'))
-                    sys.stdout.buffer.write(l.encode('utf-8')) #python3
-                  else:
-                    sys.stdout.write(l.encode('utf-8')) #python2
                 do_print = do_print and (not re.match(".*cgalPkgDescriptionEnd.*", l))
         else:
-          if hasattr(sys.stdout, 'buffer'):
+          sys.stdout.buffer.write(line.encode('utf-8'))
-            sys.stdout.buffer.write(line.encode('utf-8')) #python3
-          else:
-            sys.stdout.write(line.encode('utf-8')) #python2
 
 if __name__ == "__main__":
     main(sys.argv)