From b8b5b64dc2e65d2b5fbebe0104cee95806063e84 Mon Sep 17 00:00:00 2001
From: Maxime Gimeno <maxime.gimeno@gmail.com>
Date: Mon, 16 Jan 2017 12:05:38 +0100
Subject: [PATCH 01/26] Add XML output

---
 Documentation/doc/resources/1.8.13/BaseDoxyfile.in | 2 +-
 Documentation/doc/resources/1.8.4/BaseDoxyfile.in  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/Documentation/doc/resources/1.8.13/BaseDoxyfile.in b/Documentation/doc/resources/1.8.13/BaseDoxyfile.in
index 6121fdf771c..18a37b7f2ee 100644
--- a/Documentation/doc/resources/1.8.13/BaseDoxyfile.in
+++ b/Documentation/doc/resources/1.8.13/BaseDoxyfile.in
@@ -1960,7 +1960,7 @@ MAN_LINKS              = NO
 # captures the structure of the code including all documentation.
 # The default value is: NO.
 
-GENERATE_XML           = NO
+GENERATE_XML           = YES
 
 # The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
 # relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
diff --git a/Documentation/doc/resources/1.8.4/BaseDoxyfile.in b/Documentation/doc/resources/1.8.4/BaseDoxyfile.in
index 972fb8ed031..2d0277784cc 100644
--- a/Documentation/doc/resources/1.8.4/BaseDoxyfile.in
+++ b/Documentation/doc/resources/1.8.4/BaseDoxyfile.in
@@ -1572,7 +1572,7 @@ MAN_LINKS              = NO
 # generate an XML file that captures the structure of
 # the code including all documentation.
 
-GENERATE_XML           = NO
+GENERATE_XML           = YES
 
 # The XML_OUTPUT tag is used to specify where the XML pages will be put.
 # If a relative path is entered the value of OUTPUT_DIRECTORY will be

From 82860688d12f6e8596626b9d83b7fac6c56eec44 Mon Sep 17 00:00:00 2001
From: Maxime Gimeno <maxime.gimeno@gmail.com>
Date: Tue, 24 Jan 2017 09:39:23 +0100
Subject: [PATCH 02/26] Fix the doc to avoid diffs between 1.8.4 and 1.8.13
 outputs

---
 AABB_tree/include/CGAL/AABB_tree.h                            | 4 ++--
 Documentation/doc/resources/1.8.13/BaseDoxyfile.in            | 4 +++-
 Documentation/doc/resources/1.8.4/BaseDoxyfile.in             | 3 ++-
 Polygon/include/CGAL/Polygon_2/Polygon_2_edge_circulator.h    | 4 ++--
 Polygon/include/CGAL/Polygon_2/Polygon_2_edge_iterator.h      | 4 ++--
 .../include/CGAL/Polygon_mesh_processing/fair.h               | 2 +-
 6 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/AABB_tree/include/CGAL/AABB_tree.h b/AABB_tree/include/CGAL/AABB_tree.h
index 0e38064d066..60a0666fb55 100644
--- a/AABB_tree/include/CGAL/AABB_tree.h
+++ b/AABB_tree/include/CGAL/AABB_tree.h
@@ -1127,7 +1127,7 @@ public:
 		this->traversal(query, traversal_traits);
 		return traversal_traits.is_intersection_found();
 	}
-
+#ifndef DOXYGEN_RUNNING //To avoid doxygen to consider definition and declaration as 2 different functions (size_type causes problems)
 	template<typename Tr>
 	template<typename Query>
 	typename AABB_tree<Tr>::size_type
@@ -1146,7 +1146,7 @@ public:
 		this->traversal(query, traversal_traits);
 		return counter;
 	}
-
+#endif
 	template<typename Tr>
 	template<typename Query, typename OutputIterator>
 	OutputIterator
diff --git a/Documentation/doc/resources/1.8.13/BaseDoxyfile.in b/Documentation/doc/resources/1.8.13/BaseDoxyfile.in
index 18a37b7f2ee..9a4fdcb9d51 100644
--- a/Documentation/doc/resources/1.8.13/BaseDoxyfile.in
+++ b/Documentation/doc/resources/1.8.13/BaseDoxyfile.in
@@ -931,7 +931,9 @@ EXCLUDE_SYMBOLS        = Tr \
                          Cb \
                          Fb \
                          K \
-                         Traits
+                         Traits \
+                         internal \
+                         internal::* \
 
 # The EXAMPLE_PATH tag can be used to specify one or more files or directories
 # that contain example code fragments that are included (see the \include
diff --git a/Documentation/doc/resources/1.8.4/BaseDoxyfile.in b/Documentation/doc/resources/1.8.4/BaseDoxyfile.in
index 2d0277784cc..3bb890c3213 100644
--- a/Documentation/doc/resources/1.8.4/BaseDoxyfile.in
+++ b/Documentation/doc/resources/1.8.4/BaseDoxyfile.in
@@ -816,7 +816,8 @@ EXCLUDE_SYMBOLS        = Tr \
                          Cb \
                          Fb \
                          K \
-                         Traits
+                         Traits \
+                         internal
 
 # The EXAMPLE_PATH tag can be used to specify one or more files or
 # directories that contain example code fragments that are included (see
diff --git a/Polygon/include/CGAL/Polygon_2/Polygon_2_edge_circulator.h b/Polygon/include/CGAL/Polygon_2/Polygon_2_edge_circulator.h
index 756fd985a1a..42fad7a69a0 100644
--- a/Polygon/include/CGAL/Polygon_2/Polygon_2_edge_circulator.h
+++ b/Polygon/include/CGAL/Polygon_2/Polygon_2_edge_circulator.h
@@ -31,9 +31,9 @@
 #include <CGAL/Polygon_2/polygon_assertions.h>
 
 namespace CGAL {
-
+#ifndef DOXYGEN_RUNNING //to avoid conflicts
 template <class _Traits, class _Container> class Polygon_2;
-
+#endif
 template <class _Traits, class _Container>
 class Polygon_2_const_edge_circulator {
   public:
diff --git a/Polygon/include/CGAL/Polygon_2/Polygon_2_edge_iterator.h b/Polygon/include/CGAL/Polygon_2/Polygon_2_edge_iterator.h
index e2d0c8d01f5..a0fe9b716d1 100644
--- a/Polygon/include/CGAL/Polygon_2/Polygon_2_edge_iterator.h
+++ b/Polygon/include/CGAL/Polygon_2/Polygon_2_edge_iterator.h
@@ -29,9 +29,9 @@
 #include <CGAL/circulator.h>
 
 namespace CGAL {
-
+#ifndef DOXYGEN_RUNNING //to avoid conflicts
 template <class Traits_, class Container_> class Polygon_2;
-
+#ifndef
 template <class Segment_>
 class Polygon_2__Segment_ptr
 {
diff --git a/Polygon_mesh_processing/include/CGAL/Polygon_mesh_processing/fair.h b/Polygon_mesh_processing/include/CGAL/Polygon_mesh_processing/fair.h
index 8d6de21215a..3a9166b4725 100644
--- a/Polygon_mesh_processing/include/CGAL/Polygon_mesh_processing/fair.h
+++ b/Polygon_mesh_processing/include/CGAL/Polygon_mesh_processing/fair.h
@@ -67,7 +67,7 @@ namespace internal {
   based on solving a linear bi-Laplacian system with boundary constraints,
   described in \cgalCite{Botsch2008OnLinearVariational}.
   The optional parameter `fairing_continuity` gives the ability to control the tangential
-  continuity C<sup>\a n</sup> of the output mesh.
+  continuity C<sup>\a n </sup>of the output mesh.
 
   The region described by `vertices` might contain multiple disconnected components.
   Note that the mesh connectivity is not altered in any way,

From 1a11ac07e7d9f13121b35f8c060cd0635b3f9a77 Mon Sep 17 00:00:00 2001
From: Maxime Gimeno <maxime.gimeno@gmail.com>
Date: Tue, 24 Jan 2017 10:55:17 +0100
Subject: [PATCH 03/26] Add scripts to compare cml outputs

---
 .../doc/scripts/compare_testsuites.sh         |  37 ++++
 .../doc/scripts/documentation_parser.py       | 179 ++++++++++++++++++
 2 files changed, 216 insertions(+)
 create mode 100644 Documentation/doc/scripts/compare_testsuites.sh
 create mode 100644 Documentation/doc/scripts/documentation_parser.py

diff --git a/Documentation/doc/scripts/compare_testsuites.sh b/Documentation/doc/scripts/compare_testsuites.sh
new file mode 100644
index 00000000000..c3ec9b43038
--- /dev/null
+++ b/Documentation/doc/scripts/compare_testsuites.sh
@@ -0,0 +1,37 @@
+#!/bin/bash
+#Path to the CGAL_Documentation_build_directory/doc_output
+PATH_TO_DOC="$1"
+#path to the repository containing the output of this script for the reference documentation.
+DOC_REF="$2"
+#output in a new directory
+mkdir -p doc_data
+cd ./doc_data
+for dir in $PATH_TO_DOC/*
+do
+  OUTPUT=$(basename $dir)
+  python ../documentation_parser.py $dir/xml > ./"$OUTPUT.txt"
+  echo "$dir done"
+done
+cd ..
+#diff the output and the reference output, ignoring the differences in whitespaces
+diff -u -w ./doc_data $DOC_REF > ./diff.txt
+
+#generate an html page showing the status of the diff
+echo "<!DOCTYPE html>" > result.html
+echo "<html>" >> result.html
+echo "    <head>" >> result.html
+echo "        <meta charset=\"utf-8\" />" >> result.html
+echo "        <title>Documentation Status</title>" >> result.html
+echo "    </head>" >> result.html
+echo "    <body>" >> result.html
+    
+#if there is a diff, give a link to show it
+if [[ -s ./diff.txt ]]
+then
+  echo " The documentation has changed ! <a href=\"diff.txt\">See logs. </a> " >> result.html
+#else just say that everything is fine
+else
+  echo " The documentation has not changed. " >> result.html
+fi
+echo "    </body>" >> result.html
+echo "</html>" >> result.html
diff --git a/Documentation/doc/scripts/documentation_parser.py b/Documentation/doc/scripts/documentation_parser.py
new file mode 100644
index 00000000000..4cbe52216bd
--- /dev/null
+++ b/Documentation/doc/scripts/documentation_parser.py
@@ -0,0 +1,179 @@
+from pyquery import PyQuery as pq
+from collections import defaultdict
+from sys import argv 
+import os.path as op
+
+def check_type(_in, args):
+  res = False;
+  for arg in args:
+    res = res or _in == arg
+  return res
+
+root_path=argv[1]
+d = pq(filename=root_path+'/index.xml', parser="xml")
+compounds=[p.text() for p in d('compound').items()]
+types=[p.attr('kind') for p in d('compound').items()]
+type_map = defaultdict(list) #map <type, name>
+dict_map = defaultdict(dict)#map <name, map<member type, member name>>
+#FOREACH compounds : fill maps
+for i in xrange(0,len(compounds)):
+  if check_type(types[i], "typedef"):
+    types[i]="type"
+  name=d('compound').children("name").eq(i).text()
+  members=[p.text() for p in d('compound').eq(i).children("member").items()]
+  m_types=[p.attr('kind') for p in d('compound').eq(i).children("member").items()]
+  if (not check_type(types[i], ['example', 'file', 'dir', 'page', 'group']) and
+      not (types[i] == "namespace" and len(members) == 0) and
+      not (types[i] == "enum" and len(members) == 0) ):
+    if (types[i] == "class"):#check if the class is a concept class
+      compound=d('compound').children("name").eq(i).text().replace('_', '__').replace('::', '_1_1')
+      filepath='class'+compound+'.xml'
+      if(op.isfile(root_path+filepath)):
+        e = pq(filename=root_path+filepath, parser="xml")
+        compoundnames=[p.text() for p in e('includes').items()]
+        if(compoundnames[0].find("Concept") != -1):
+          types[i] = 'Concept '+types[i].lower()
+    type_map[types[i]].append(name)
+
+    mtype_map = defaultdict(list)# map<member type, member name>
+
+    #FOREACH member :
+    for j in xrange(0,len(members)):
+      if(check_type(types[i], ['class', 'Concept class'])
+         and m_types[j] == "function"):
+        m_types[j]="method"
+      if(m_types[j] == "typedef"):
+        m_types[j]="type"
+      mtype_map[m_types[j]].append(members[j])
+	  #end FOREACH member
+    dict_map[name]=mtype_map
+#end FOREACH compound
+indent=""
+
+
+    
+
+#print
+#FOREACH type
+for btype in type_map:
+  out=btype
+  if btype.endswith('s'):
+    out+='e'
+  print out.title()+'s'
+  indent+="  "
+  #FOREACH name
+  for name in type_map[btype]:
+    filepath=""
+    if check_type(btype, ['class', 'Concept class']):
+      filepath='/class'+name.replace('_', '__').replace('::', '_1_1')+'.xml'
+    elif btype == 'namespace':
+      filepath='/namespace'+name.replace('_', '__').replace('::', '_1_1')+'.xml'
+    templates=[]
+    if op.isfile(root_path+filepath):
+      f=pq(filename=root_path+filepath, parser="xml")
+      templateparams=f("compounddef").children("templateparamlist").eq(0).children("param").items()
+      for param in templateparams:
+        template_type=""
+        template_name=""
+        template_defval=""
+        template_type=param.children("type").text()
+        template_name=param.children("declname").text()
+        template_defval=param.children("defval").text()
+        complete_template=""
+        if not template_type is None:
+          complete_template+=template_type+' '
+        if not template_name is None:
+          complete_template+=template_name
+        if not template_defval is None:
+          complete_template+=' = '+template_defval
+        templates.append(complete_template)        
+        if templates==[]:#if no child was found, just take param.text()
+         templates=[t.text() for t in param.items()]
+    suffix="<"
+    #as template got type, defname and declname, name is twice in template. keep only one of them.
+    to_remove=[""]
+    for template in templates:
+      suffix+=template+', '
+    if suffix == "<":
+      suffix=""
+    if suffix.endswith(', '):
+      suffix = suffix[:-2]+'>'
+    print indent+name+suffix
+
+    indent+="  "
+    #FOREACH mtype
+    for mtype in (dict_map[name]):
+      out=mtype
+      if mtype.endswith('s'):
+        out+='e'
+      print indent+out.title()+'s'
+      indent+="  "
+      #FOREACH member
+      overload_map = defaultdict(int) #contains the number of times a member has appeared (to manage the overloads)
+      templateparams=[]
+      for member in dict_map[name][mtype]:
+        templates=[]
+        args="" # will contain the arguments of the methods and functions
+        return_type="" #will contain the return type of a function/method
+        
+        #look for arguments
+        if op.isfile(root_path+filepath):
+          f=pq(filename=root_path+filepath, parser="xml")
+          index=0
+          memberdefs=[m.text() for m in f("memberdef").items()]
+          for i in xrange(0,len(memberdefs)):
+            member_names=[member_name.text() for member_name in f('memberdef').eq(i).children("name").items()]
+            if f('memberdef').eq(i).children("name").text() == member:
+              if (index < overload_map[member]):
+                index+=1
+              elif (index == overload_map[member]):
+                if check_type(mtype, ['function', 'method']):
+                  args=[f('memberdef').eq(i).children("argsstring").text()]
+                  templateparams=f('memberdef').eq(i).children("templateparamlist").children("param").items()
+                if check_type(mtype, ['function', 'method', 'type', 'variable']):
+                  return_type=[f('memberdef').eq(i).children("type").text()]
+                break;
+          #end foreach memberdef
+        arguments=""
+        for arg in args:
+          arguments+=arg
+        template_types=[]
+        template_names=[]
+        for param in templateparams:
+          template_type=""
+          template_name=""
+          template_defval=""
+          template_type=param.children("type").text()
+          template_name=param.children("declname").text()
+          template_defval=param.children("defval").text()
+          complete_template=""
+          if not template_type is None:
+            complete_template+=template_type+' '
+          if not template_name is None:
+            complete_template+=template_name
+          if not template_defval is None:
+            complete_template+=' = '+template_defval
+          templates.append(complete_template)        
+          if templates==[]:#if no child was found, just take param.text()
+           templates=[t.text() for t in param.items()]
+
+        prefix="template <"
+        for template in templates:
+          prefix+=template+', '
+        if prefix == "template <":
+          prefix=""
+        if prefix.endswith(', '):
+          prefix = prefix[:-2]+'>\n'+indent+"  "
+        for definition in return_type:
+          prefix+=definition
+        if(prefix != ""):
+          prefix+=" "
+        print indent+prefix+member+arguments
+        overload_map[member]+=1
+      #END foreach member
+      indent=indent[:-2]
+    #END foreach mtype
+    indent=indent[:-2]
+  #END foreach name
+  indent=indent[:-2]
+#END foreach type

From 60d0a39d42f3644205f5269f572567bee951097f Mon Sep 17 00:00:00 2001
From: Maxime Gimeno <maxime.gimeno@gmail.com>
Date: Tue, 24 Jan 2017 14:18:22 +0100
Subject: [PATCH 04/26] fixes

---
 .../doc/resources/1.8.13/BaseDoxyfile.in      |  5 ++-
 .../doc/resources/1.8.4/BaseDoxyfile.in       |  2 +-
 .../doc/scripts/compare_testsuites.sh         | 36 ++++++++++++++++---
 .../doc/scripts/documentation_parser.py       | 27 +++++++-------
 .../CGAL/Polygon_2/Polygon_2_edge_iterator.h  |  2 +-
 .../CGAL/Polygon_mesh_processing/fair.h       |  2 +-
 6 files changed, 52 insertions(+), 22 deletions(-)

diff --git a/Documentation/doc/resources/1.8.13/BaseDoxyfile.in b/Documentation/doc/resources/1.8.13/BaseDoxyfile.in
index 9a4fdcb9d51..73cb351a269 100644
--- a/Documentation/doc/resources/1.8.13/BaseDoxyfile.in
+++ b/Documentation/doc/resources/1.8.13/BaseDoxyfile.in
@@ -487,7 +487,7 @@ LOOKUP_CACHE_SIZE      = 0
 # normally produced when WARNINGS is set to YES.
 # The default value is: NO.
 
-EXTRACT_ALL            = YES
+EXTRACT_ALL            =
 
 #---------------------------------------------------------------------------
 # Build related configuration options
@@ -932,8 +932,7 @@ EXCLUDE_SYMBOLS        = Tr \
                          Fb \
                          K \
                          Traits \
-                         internal \
-                         internal::* \
+                         internal 
 
 # The EXAMPLE_PATH tag can be used to specify one or more files or directories
 # that contain example code fragments that are included (see the \include
diff --git a/Documentation/doc/resources/1.8.4/BaseDoxyfile.in b/Documentation/doc/resources/1.8.4/BaseDoxyfile.in
index 3bb890c3213..27f5dacb251 100644
--- a/Documentation/doc/resources/1.8.4/BaseDoxyfile.in
+++ b/Documentation/doc/resources/1.8.4/BaseDoxyfile.in
@@ -444,7 +444,7 @@ LOOKUP_CACHE_SIZE      = 0
 # Private class members and static file members will be hidden unless
 # the EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES
 
-EXTRACT_ALL            = YES
+EXTRACT_ALL            =
 
 # If the EXTRACT_PRIVATE tag is set to YES all private members of a class
 # will be included in the documentation.
diff --git a/Documentation/doc/scripts/compare_testsuites.sh b/Documentation/doc/scripts/compare_testsuites.sh
index c3ec9b43038..1efcee73542 100644
--- a/Documentation/doc/scripts/compare_testsuites.sh
+++ b/Documentation/doc/scripts/compare_testsuites.sh
@@ -1,20 +1,43 @@
 #!/bin/bash
 #Path to the CGAL_Documentation_build_directory/doc_output
 PATH_TO_DOC="$1"
+
+if ! [ -d "$PATH_TO_DOC" ] || [ $(basename $PATH_TO_DOC) != "doc_output" ]; then
+  echo "wrong path"
+  exit 1
+fi
+
 #path to the repository containing the output of this script for the reference documentation.
 DOC_REF="$2"
 #output in a new directory
 mkdir -p doc_data
 cd ./doc_data
+if [ $# -gt 2 ]; then
+  echo "too many arguments"
+  exit 1
+ fi
+
+FAILURES=()
 for dir in $PATH_TO_DOC/*
 do
   OUTPUT=$(basename $dir)
   python ../documentation_parser.py $dir/xml > ./"$OUTPUT.txt"
-  echo "$dir done"
+  if [ $? -eq 0 ]; then
+    echo "$dir OK"
+  else
+    echo "$dir FAILED"
+    FAILURES+="$dir "
+  fi
 done
 cd ..
+echo "Output generated"
+if ! [ -d "$DOC_REF" ]; then
+  echo "No reference given. Script is finished."
+  exit 2
+fi
+
 #diff the output and the reference output, ignoring the differences in whitespaces
-diff -u -w ./doc_data $DOC_REF > ./diff.txt
+diff -u -N -w ./doc_data $DOC_REF > ./diff.txt
 
 #generate an html page showing the status of the diff
 echo "<!DOCTYPE html>" > result.html
@@ -28,10 +51,15 @@ echo "    <body>" >> result.html
 #if there is a diff, give a link to show it
 if [[ -s ./diff.txt ]]
 then
-  echo " The documentation has changed ! <a href=\"diff.txt\">See logs. </a> " >> result.html
+  echo "<p> The documentation has changed ! <a href=\"diff.txt\">See logs. </a> <br /> " >> result.html
 #else just say that everything is fine
 else
-  echo " The documentation has not changed. " >> result.html
+  echo "<p> The documentation has not changed. <br /><br /> " >> result.html
 fi
+if [ "${FAILURES[0]}" != "" ]; then
+  echo " Some packages encountered problems while being parsed : <br /><br /> " >> result.html
+  echo " ${FAILURE[*]} <br /> ">> result.html
+fi
+echo "    </p>" >> result.html
 echo "    </body>" >> result.html
 echo "</html>" >> result.html
diff --git a/Documentation/doc/scripts/documentation_parser.py b/Documentation/doc/scripts/documentation_parser.py
index 4cbe52216bd..187b175bf4f 100644
--- a/Documentation/doc/scripts/documentation_parser.py
+++ b/Documentation/doc/scripts/documentation_parser.py
@@ -3,14 +3,15 @@ from collections import defaultdict
 from sys import argv 
 import os.path as op
 
+# if _in is part of args, return true.
 def check_type(_in, args):
-  res = False;
-  for arg in args:
-    res = res or _in == arg
-  return res
+  if _in in args:
+    return True
+  else:
+    return False
 
 root_path=argv[1]
-d = pq(filename=root_path+'/index.xml', parser="xml")
+d = pq(filename=op.join(op.sep, root_path,'index.xml'), parser="xml")
 compounds=[p.text() for p in d('compound').items()]
 types=[p.attr('kind') for p in d('compound').items()]
 type_map = defaultdict(list) #map <type, name>
@@ -28,10 +29,12 @@ for i in xrange(0,len(compounds)):
     if (types[i] == "class"):#check if the class is a concept class
       compound=d('compound').children("name").eq(i).text().replace('_', '__').replace('::', '_1_1')
       filepath='class'+compound+'.xml'
-      if(op.isfile(root_path+filepath)):
-        e = pq(filename=root_path+filepath, parser="xml")
+      total_path=op.join(op.sep, root_path,filepath)
+      if(op.isfile(total_path)):
+        e = pq(filename=total_path, parser="xml")
         compoundnames=[p.text() for p in e('includes').items()]
-        if(compoundnames[0].find("Concept") != -1):
+        
+        if(len(compoundnames) > 1 and compoundnames[0].find("Concept") != -1):
           types[i] = 'Concept '+types[i].lower()
     type_map[types[i]].append(name)
 
@@ -69,8 +72,8 @@ for btype in type_map:
     elif btype == 'namespace':
       filepath='/namespace'+name.replace('_', '__').replace('::', '_1_1')+'.xml'
     templates=[]
-    if op.isfile(root_path+filepath):
-      f=pq(filename=root_path+filepath, parser="xml")
+    if op.isfile(op.join(op.sep, root_path,filepath)):
+      f=pq(filename=op.join(op.sep, root_path,filepath), parser="xml")
       templateparams=f("compounddef").children("templateparamlist").eq(0).children("param").items()
       for param in templateparams:
         template_type=""
@@ -117,8 +120,8 @@ for btype in type_map:
         return_type="" #will contain the return type of a function/method
         
         #look for arguments
-        if op.isfile(root_path+filepath):
-          f=pq(filename=root_path+filepath, parser="xml")
+        if op.isfile(op.join(op.sep, root_path,filepath)):
+          f=pq(filename=op.join(op.sep, root_path,filepath), parser="xml")
           index=0
           memberdefs=[m.text() for m in f("memberdef").items()]
           for i in xrange(0,len(memberdefs)):
diff --git a/Polygon/include/CGAL/Polygon_2/Polygon_2_edge_iterator.h b/Polygon/include/CGAL/Polygon_2/Polygon_2_edge_iterator.h
index a0fe9b716d1..fc282b7fa50 100644
--- a/Polygon/include/CGAL/Polygon_2/Polygon_2_edge_iterator.h
+++ b/Polygon/include/CGAL/Polygon_2/Polygon_2_edge_iterator.h
@@ -31,7 +31,7 @@
 namespace CGAL {
 #ifndef DOXYGEN_RUNNING //to avoid conflicts
 template <class Traits_, class Container_> class Polygon_2;
-#ifndef
+#endif
 template <class Segment_>
 class Polygon_2__Segment_ptr
 {
diff --git a/Polygon_mesh_processing/include/CGAL/Polygon_mesh_processing/fair.h b/Polygon_mesh_processing/include/CGAL/Polygon_mesh_processing/fair.h
index 3a9166b4725..8978448be58 100644
--- a/Polygon_mesh_processing/include/CGAL/Polygon_mesh_processing/fair.h
+++ b/Polygon_mesh_processing/include/CGAL/Polygon_mesh_processing/fair.h
@@ -67,7 +67,7 @@ namespace internal {
   based on solving a linear bi-Laplacian system with boundary constraints,
   described in \cgalCite{Botsch2008OnLinearVariational}.
   The optional parameter `fairing_continuity` gives the ability to control the tangential
-  continuity C<sup>\a n </sup>of the output mesh.
+  continuity C<sup> n</sup> of the output mesh.
 
   The region described by `vertices` might contain multiple disconnected components.
   Note that the mesh connectivity is not altered in any way,

From 477196c52d7c734c0005bb2577aa013eaab5fad0 Mon Sep 17 00:00:00 2001
From: Maxime Gimeno <maxime.gimeno@gmail.com>
Date: Mon, 6 Feb 2017 16:31:48 +0100
Subject: [PATCH 05/26] clean-up

---
 Documentation/doc/resources/1.8.13/BaseDoxyfile.in | 4 ++--
 Documentation/doc/resources/1.8.4/BaseDoxyfile.in  | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/Documentation/doc/resources/1.8.13/BaseDoxyfile.in b/Documentation/doc/resources/1.8.13/BaseDoxyfile.in
index 73cb351a269..95c2d26b4fd 100644
--- a/Documentation/doc/resources/1.8.13/BaseDoxyfile.in
+++ b/Documentation/doc/resources/1.8.13/BaseDoxyfile.in
@@ -487,7 +487,7 @@ LOOKUP_CACHE_SIZE      = 0
 # normally produced when WARNINGS is set to YES.
 # The default value is: NO.
 
-EXTRACT_ALL            =
+EXTRACT_ALL            = YES
 
 #---------------------------------------------------------------------------
 # Build related configuration options
@@ -1961,7 +1961,7 @@ MAN_LINKS              = NO
 # captures the structure of the code including all documentation.
 # The default value is: NO.
 
-GENERATE_XML           = YES
+GENERATE_XML           =
 
 # The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
 # relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
diff --git a/Documentation/doc/resources/1.8.4/BaseDoxyfile.in b/Documentation/doc/resources/1.8.4/BaseDoxyfile.in
index 27f5dacb251..e91328518a0 100644
--- a/Documentation/doc/resources/1.8.4/BaseDoxyfile.in
+++ b/Documentation/doc/resources/1.8.4/BaseDoxyfile.in
@@ -444,7 +444,7 @@ LOOKUP_CACHE_SIZE      = 0
 # Private class members and static file members will be hidden unless
 # the EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES
 
-EXTRACT_ALL            =
+EXTRACT_ALL            = YES
 
 # If the EXTRACT_PRIVATE tag is set to YES all private members of a class
 # will be included in the documentation.
@@ -1573,7 +1573,7 @@ MAN_LINKS              = NO
 # generate an XML file that captures the structure of
 # the code including all documentation.
 
-GENERATE_XML           = YES
+GENERATE_XML           =
 
 # The XML_OUTPUT tag is used to specify where the XML pages will be put.
 # If a relative path is entered the value of OUTPUT_DIRECTORY will be

From 18d523b0693b41049f07253fe68821ba3896bad3 Mon Sep 17 00:00:00 2001
From: Maxime Gimeno <maxime.gimeno@gmail.com>
Date: Mon, 6 Feb 2017 17:22:52 +0100
Subject: [PATCH 06/26] Add a cmake option for GENERATE_XML

---
 Documentation/doc/CMakeLists.txt | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/Documentation/doc/CMakeLists.txt b/Documentation/doc/CMakeLists.txt
index 889a6d15a82..323ce63b498 100644
--- a/Documentation/doc/CMakeLists.txt
+++ b/Documentation/doc/CMakeLists.txt
@@ -78,6 +78,10 @@ function(configure_doxygen_package CGAL_PACKAGE_NAME)
   if(EXISTS "${CGAL_PACKAGE_DIR}/examples")
     file(APPEND ${CGAL_DOC_PACKAGE_DEFAULTS} "EXAMPLE_PATH = ${CGAL_PACKAGE_DIR}/examples\n")
   endif()
+  if(CGAL_GENERATE_XML)
+    file(APPEND ${CGAL_DOC_PACKAGE_DEFAULTS} "GENERATE_XML = YES\n")
+  endif()
+
   file(APPEND ${CGAL_DOC_PACKAGE_DEFAULTS} "GENERATE_TAGFILE = ${CGAL_DOC_TAG_GEN_DIR}/${CGAL_PACKAGE_NAME}.tag\n")
   file(APPEND ${CGAL_DOC_PACKAGE_DEFAULTS} "STRIP_FROM_PATH = ${CGAL_PACKAGE_DOC_DIR}/\n")
   file(APPEND ${CGAL_DOC_PACKAGE_DEFAULTS} "STRIP_FROM_PATH += ${CGAL_PACKAGE_DIR}/include/\n")

From e4f65127c284826f5d6096695a5e488c360ae75a Mon Sep 17 00:00:00 2001
From: Maxime Gimeno <maxime.gimeno@gmail.com>
Date: Mon, 13 Feb 2017 10:11:54 +0100
Subject: [PATCH 07/26] Add a script to compare to versions of doxygen

---
 .../doc/scripts/test_doxygen_versions.sh      | 56 +++++++++++++++++++
 1 file changed, 56 insertions(+)
 create mode 100644 Documentation/doc/scripts/test_doxygen_versions.sh

diff --git a/Documentation/doc/scripts/test_doxygen_versions.sh b/Documentation/doc/scripts/test_doxygen_versions.sh
new file mode 100644
index 00000000000..ba5faa4fffd
--- /dev/null
+++ b/Documentation/doc/scripts/test_doxygen_versions.sh
@@ -0,0 +1,56 @@
+#!/bin/bash
+if [ "$1" == '--help' ]; then 
+  echo "Usage: $0 <doxygen_1> [doxygen_2] "
+  echo "Compares the output of doxygen_1 and doxygen_2, "
+  echo "where  doxygen_1 and doxygen_2 are valid paths to doxygen executables."
+  echo "If doxygen_2 is not specified, the master branch of doxygen will be cloned, built and used as doxygen_2."
+  exit 0
+fi
+#build reference
+PATH_TO_1=$1
+PATH_TO_2=$2
+IS_ARG2=1
+if [ -z $PATH_TO_2 ]; then
+  IS_ARG2=0
+fi
+
+if [ -z $PATH_TO_1 ] || [ $(basename $PATH_TO_1) != "doxygen" ] || [ ! -e $PATH_TO_1 ]; then
+  echo "Please specify a valid path to a doxygen executable."
+  echo "$0 --help for more information."
+  exit 0
+fi
+mkdir ./build_doc
+cd ./build_doc
+cmake -DCGAL_GENERATE_XML=ON -DDOXYGEN_EXECUTABLE="$PATH_TO_1" ../..  &> /dev/null
+make -j7 doc  &> /dev/null
+cd ../
+bash compare_testsuites.sh $PWD/build_doc/doc_output
+mv ./doc_data ./doc_ref
+
+#download and build doxygen_master
+if [ $IS_ARG2 == 0 ] || [ $(basename $PATH_TO_2) != "doxygen" ] || [ ! -e $PATH_TO_2 ]; then
+  echo "No path to doxygen master were detected. Cloning..."
+  mkdir doxygen_master
+  git clone https://github.com/doxygen/doxygen.git doxygen_master  &> /dev/null
+  cd doxygen_master
+  mkdir build
+  cd build
+  cmake ..  &> /dev/null
+  make  &> /dev/null
+  cd ../..
+  PATH_TO_2=../doxygen_master/build/bin/doxygen
+  echo "done."
+fi
+#build doc with doxygen master
+cd ./build_doc
+cmake -DCGAL_GENERATE_XML=ON -DDOXYGEN_EXECUTABLE=$PATH_TO_2 ../..  &> /dev/null
+make -j7 doc  &> /dev/null
+cd ../
+bash ./compare_testsuites.sh $PWD/build_doc/doc_output $PWD/doc_data
+#clean-up
+rm -rf ./build_doc
+rm -rf ./doc_ref
+rm -rf ./doc_data
+if [ $IS_ARG2 == 0 ]; then
+  rm -rf ./doxygen_master
+fi

From 76553ec143f5a1df975677cd33b18fdf28085452 Mon Sep 17 00:00:00 2001
From: Maxime Gimeno <maxime.gimeno@gmail.com>
Date: Mon, 13 Feb 2017 16:39:00 +0100
Subject: [PATCH 08/26] Add date of creation in result.html

---
 Documentation/doc/scripts/compare_testsuites.sh | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/Documentation/doc/scripts/compare_testsuites.sh b/Documentation/doc/scripts/compare_testsuites.sh
index 1efcee73542..79f6fcaf474 100644
--- a/Documentation/doc/scripts/compare_testsuites.sh
+++ b/Documentation/doc/scripts/compare_testsuites.sh
@@ -49,12 +49,13 @@ echo "    </head>" >> result.html
 echo "    <body>" >> result.html
     
 #if there is a diff, give a link to show it
+DATE=`date +%Y-%m-%d`
 if [[ -s ./diff.txt ]]
 then
-  echo "<p> The documentation has changed ! <a href=\"diff.txt\">See logs. </a> <br /> " >> result.html
+  echo "<p> $DATE : The documentation has changed ! <a href=\"diff.txt\">See logs. </a> <br /> " >> result.html
 #else just say that everything is fine
 else
-  echo "<p> The documentation has not changed. <br /><br /> " >> result.html
+  echo "<p> $DATE : The documentation has not changed. <br /><br /> " >> result.html
 fi
 if [ "${FAILURES[0]}" != "" ]; then
   echo " Some packages encountered problems while being parsed : <br /><br /> " >> result.html

From 98431f49971474fc2d1c34c589fec4967cbf038e Mon Sep 17 00:00:00 2001
From: Maxime Gimeno <maxime.gimeno@gmail.com>
Date: Tue, 14 Feb 2017 12:26:53 +0100
Subject: [PATCH 09/26] Fix test_doxygen_versions.sh

---
 Documentation/doc/scripts/test_doxygen_versions.sh | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/Documentation/doc/scripts/test_doxygen_versions.sh b/Documentation/doc/scripts/test_doxygen_versions.sh
index ba5faa4fffd..13fa8b93025 100644
--- a/Documentation/doc/scripts/test_doxygen_versions.sh
+++ b/Documentation/doc/scripts/test_doxygen_versions.sh
@@ -7,8 +7,8 @@ if [ "$1" == '--help' ]; then
   exit 0
 fi
 #build reference
-PATH_TO_1=$1
-PATH_TO_2=$2
+PATH_TO_1="$1"
+PATH_TO_2="$2"
 IS_ARG2=1
 if [ -z $PATH_TO_2 ]; then
   IS_ARG2=0
@@ -42,11 +42,13 @@ if [ $IS_ARG2 == 0 ] || [ $(basename $PATH_TO_2) != "doxygen" ] || [ ! -e $PATH_
   echo "done."
 fi
 #build doc with doxygen master
+rm -rf ./build_doc
+mkdir build_doc
 cd ./build_doc
-cmake -DCGAL_GENERATE_XML=ON -DDOXYGEN_EXECUTABLE=$PATH_TO_2 ../..  &> /dev/null
+cmake -DCGAL_GENERATE_XML=ON -DDOXYGEN_EXECUTABLE="$PATH_TO_2" ../..  &> /dev/null
 make -j7 doc  &> /dev/null
 cd ../
-bash ./compare_testsuites.sh $PWD/build_doc/doc_output $PWD/doc_data
+bash ./compare_testsuites.sh $PWD/build_doc/doc_output $PWD/doc_ref
 #clean-up
 rm -rf ./build_doc
 rm -rf ./doc_ref

From 0be067d7c9781cdcd16e063a60ba67e7aaa761ee Mon Sep 17 00:00:00 2001
From: Maxime Gimeno <maxime.gimeno@gmail.com>
Date: Wed, 15 Feb 2017 11:01:45 +0100
Subject: [PATCH 10/26] Add information about CGAL and doxygen versions.

---
 .../doc/scripts/compare_testsuites.sh         | 13 ++++++----
 .../doc/scripts/test_doxygen_versions.sh      | 24 ++++++++++++++-----
 2 files changed, 26 insertions(+), 11 deletions(-)

diff --git a/Documentation/doc/scripts/compare_testsuites.sh b/Documentation/doc/scripts/compare_testsuites.sh
index 79f6fcaf474..980c7900e51 100644
--- a/Documentation/doc/scripts/compare_testsuites.sh
+++ b/Documentation/doc/scripts/compare_testsuites.sh
@@ -12,7 +12,7 @@ DOC_REF="$2"
 #output in a new directory
 mkdir -p doc_data
 cd ./doc_data
-if [ $# -gt 2 ]; then
+if [ $# -gt 5 ]; then
   echo "too many arguments"
   exit 1
  fi
@@ -40,22 +40,25 @@ fi
 diff -u -N -w ./doc_data $DOC_REF > ./diff.txt
 
 #generate an html page showing the status of the diff
+CGAL_VERSION=$3
+DATE=`date +%Y-%m-%d`
 echo "<!DOCTYPE html>" > result.html
 echo "<html>" >> result.html
 echo "    <head>" >> result.html
 echo "        <meta charset=\"utf-8\" />" >> result.html
 echo "        <title>Documentation Status</title>" >> result.html
 echo "    </head>" >> result.html
-echo "    <body>" >> result.html
+echo "    <body style=\"background-color: #C0C0D0;\"> " >> result.html
+echo "    <h1 id=\"maintitle\">Documentation Status of $CGAL_VERSION on $DATE</h1> " >> result.html
+echo "    <p> Difference between Doxygen $4 and Doxygen $5:  " >> result.html
     
 #if there is a diff, give a link to show it
-DATE=`date +%Y-%m-%d`
 if [[ -s ./diff.txt ]]
 then
-  echo "<p> $DATE : The documentation has changed ! <a href=\"diff.txt\">See logs. </a> <br /> " >> result.html
+  echo "<p> There are differences :  <a href=\"diff.txt\">See logs. </a> <br /> " >> result.html
 #else just say that everything is fine
 else
-  echo "<p> $DATE : The documentation has not changed. <br /><br /> " >> result.html
+  echo "<p> There is no difference. <br /><br /> " >> result.html
 fi
 if [ "${FAILURES[0]}" != "" ]; then
   echo " Some packages encountered problems while being parsed : <br /><br /> " >> result.html
diff --git a/Documentation/doc/scripts/test_doxygen_versions.sh b/Documentation/doc/scripts/test_doxygen_versions.sh
index 13fa8b93025..16726747786 100644
--- a/Documentation/doc/scripts/test_doxygen_versions.sh
+++ b/Documentation/doc/scripts/test_doxygen_versions.sh
@@ -1,14 +1,16 @@
 #!/bin/bash
 if [ "$1" == '--help' ]; then 
-  echo "Usage: $0 <doxygen_1> [doxygen_2] "
-  echo "Compares the output of doxygen_1 and doxygen_2, "
+  echo "Usage: $0 <doxygen_1> [doxygen_2] [CGAL_VERSION]"
+  echo "Compares the output of doxygen_1 and doxygen_2 of this CGAL version, "
   echo "where  doxygen_1 and doxygen_2 are valid paths to doxygen executables."
   echo "If doxygen_2 is not specified, the master branch of doxygen will be cloned, built and used as doxygen_2."
+  echo "CGAL_VERSION is the name that will appear on the results page. Default is CGAL-{version in cmake generated VERSION}"
   exit 0
 fi
 #build reference
 PATH_TO_1="$1"
 PATH_TO_2="$2"
+CGAL_VERSION=$3
 IS_ARG2=1
 if [ -z $PATH_TO_2 ]; then
   IS_ARG2=0
@@ -19,6 +21,15 @@ if [ -z $PATH_TO_1 ] || [ $(basename $PATH_TO_1) != "doxygen" ] || [ ! -e $PATH_
   echo "$0 --help for more information."
   exit 0
 fi
+#if no cgal version is specified, ask cmake"
+if [ -n CGAL_VERSION ]; then
+  mkdir ./shallow_build
+  cd ./shallow_build 
+  cmake ../../../.. &> /dev/null
+  CGAL_VERSION="CGAL-$(cat VERSION)"
+  cd ..
+  rm -rf ./shallow_build
+fi
 mkdir ./build_doc
 cd ./build_doc
 cmake -DCGAL_GENERATE_XML=ON -DDOXYGEN_EXECUTABLE="$PATH_TO_1" ../..  &> /dev/null
@@ -30,15 +41,14 @@ mv ./doc_data ./doc_ref
 #download and build doxygen_master
 if [ $IS_ARG2 == 0 ] || [ $(basename $PATH_TO_2) != "doxygen" ] || [ ! -e $PATH_TO_2 ]; then
   echo "No path to doxygen master were detected. Cloning..."
-  mkdir doxygen_master
   git clone https://github.com/doxygen/doxygen.git doxygen_master  &> /dev/null
   cd doxygen_master
   mkdir build
   cd build
   cmake ..  &> /dev/null
-  make  &> /dev/null
+  make -j7 &> /dev/null
   cd ../..
-  PATH_TO_2=../doxygen_master/build/bin/doxygen
+  PATH_TO_2="$PWD/doxygen_master/build/bin/doxygen"
   echo "done."
 fi
 #build doc with doxygen master
@@ -48,7 +58,9 @@ cd ./build_doc
 cmake -DCGAL_GENERATE_XML=ON -DDOXYGEN_EXECUTABLE="$PATH_TO_2" ../..  &> /dev/null
 make -j7 doc  &> /dev/null
 cd ../
-bash ./compare_testsuites.sh $PWD/build_doc/doc_output $PWD/doc_ref
+DOXYGEN_1=$($PATH_TO_1 --version)
+DOXYGEN_2=$($PATH_TO_2 --version)
+bash ./compare_testsuites.sh $PWD/build_doc/doc_output $PWD/doc_ref $CGAL_VERSION $DOXYGEN_1 $DOXYGEN_2
 #clean-up
 rm -rf ./build_doc
 rm -rf ./doc_ref

From a27436d393e6bdd54381fa5c6d87bafa92d3eac2 Mon Sep 17 00:00:00 2001
From: Maxime Gimeno <maxime.gimeno@gmail.com>
Date: Fri, 17 Feb 2017 17:07:52 +0100
Subject: [PATCH 11/26] Change testsuite.py to integrate a diff to the
 overview.

---
 Documentation/doc/scripts/testsuite.py | 23 +++++++++++++++++++----
 1 file changed, 19 insertions(+), 4 deletions(-)

diff --git a/Documentation/doc/scripts/testsuite.py b/Documentation/doc/scripts/testsuite.py
index ffc64689fb6..6bdef902738 100755
--- a/Documentation/doc/scripts/testsuite.py
+++ b/Documentation/doc/scripts/testsuite.py
@@ -116,6 +116,7 @@ def main():
     parser.add_argument('--publish', metavar='/path/to/publish', help='Specify this argument if the results should be published.')
     parser.add_argument('--doc-log-dir', default='.', metavar='/path/to/cgal/build/dir/doc_log', help='The path of the documentation logs.')
     parser.add_argument('--output-dir', default='.', metavar='/path/to/cgal/build/dir/doc_output', help='The path to the build documentation')
+    parser.add_argument('--diff', metavar='/path/to/diff', help='The path to the diff file.')
     parser.add_argument('--cgal-version', help='Path to a version.h file from the current release. If not specified use git hash instead.')
     parser.add_argument('--version-to-keep', help='indicates the number of release testsuites that should be kept at the publishing location.')
     parser.add_argument('--do-copy-results', action="store_true", help='Specify this argument if you want to copy the generated documentation into the publishing location.')
@@ -135,7 +136,14 @@ def main():
     title=d('#maintitle')
     title.text(title.text() + ' for ' + version_string)
     write_out_html(d, './index.html')
-    
+
+    # does the diff exist ?
+    diff='n/a'
+    if args.diff:
+        diff_file=args.diff
+        if not os.path.isfile(diff_file):
+            sys.stderr.write('Diff file ' + diff_file + ' is not a file. Cannot diff.\n')
+            sys.exit(1)    
     if args.publish:
         if args.publish.endswith('/'):
             publish_dir=args.publish
@@ -156,6 +164,13 @@ def main():
             with open(publish_dir + 'index.html') as f: pass
         except IOError as e:
             print('No index.html in the publish directory found. Writing a skeleton.')
+            shutil.copyfile(diff_file, publish_dir+'diff.txt')
+            with open(diff_file, 'r') as myfile:
+                diff=myfile.read()
+            if not diff:
+                diff='none'
+            else:
+                diff='<a href=\"diff.txt\">See diff. </a>'
             with open(publish_dir + 'index.html', 'w') as f:
                 f.write('''<!DOCTYPE html>
 <style type="text/css">
@@ -167,12 +182,12 @@ body  {color: black; background-color: #C0C0D0; font-family: sans-serif;}
 <html><head><title>Manual Testsuite Overview</title></head>
 <body><h1>Overviewpage of the Doxygen Manual Testsuite</h1>
 <table  border="1" cellspacing="2" cellpadding="5" id="revisions" class="rev-table">
-<tr><th>Revision</th><th>Date</th><th>Warnings</th><th>Errors</th></tr></table></body></html>''')
+<tr><th>Revision</th><th>Date</th><th>Warnings</th><th>Errors</th><th>Diff</th></tr></table></body></html>''')
 
         d=pq(filename=publish_dir + 'index.html',parser="html")
         revs=d('#revisions tr')
-        new_row='<tr><td><a href="{revision}/index.html">{revision}</a></td><td>{date}</td><td>{warnings}</td><td>{errors}</td></tr>'.format(
-            revision=version_string, date=version_date, warnings=sum[0], errors=sum[1])
+        new_row='<tr><td><a href="{revision}/index.html">{revision}</a></td><td>{date}</td><td>{warnings}</td><td>{errors}</td><td>{diffs}</td></tr>'.format(
+            revision=version_string, date=version_date, warnings=sum[0], errors=sum[1], diffs=diff)
         revs.eq(0).after(new_row)
         if args.version_to_keep:
           nb_items=len(revs)

From 02971d09555aed71bcbfd216f0fbe9a6987c0ebe Mon Sep 17 00:00:00 2001
From: Maxime Gimeno <maxime.gimeno@gmail.com>
Date: Fri, 17 Feb 2017 17:07:52 +0100
Subject: [PATCH 12/26] Change testsuite.py to integrate a diff to the
 overview.

---
 Documentation/doc/scripts/test_doxygen_versions.sh | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/Documentation/doc/scripts/test_doxygen_versions.sh b/Documentation/doc/scripts/test_doxygen_versions.sh
index 16726747786..14b625b17cd 100644
--- a/Documentation/doc/scripts/test_doxygen_versions.sh
+++ b/Documentation/doc/scripts/test_doxygen_versions.sh
@@ -1,10 +1,11 @@
 #!/bin/bash
 if [ "$1" == '--help' ]; then 
-  echo "Usage: $0 <doxygen_1> [doxygen_2] [CGAL_VERSION]"
+  echo "Usage: $0 <doxygen_1> [doxygen_2] [CGAL_VERSION][publish_dir]"
   echo "Compares the output of doxygen_1 and doxygen_2 of this CGAL version, "
   echo "where  doxygen_1 and doxygen_2 are valid paths to doxygen executables."
   echo "If doxygen_2 is not specified, the master branch of doxygen will be cloned, built and used as doxygen_2."
   echo "CGAL_VERSION is the name that will appear on the results page. Default is CGAL-{version in cmake generated VERSION}"
+  echo "publish_dir is the path to the dir where the testsuite results are kept"
   exit 0
 fi
 #build reference
@@ -12,6 +13,7 @@ PATH_TO_1="$1"
 PATH_TO_2="$2"
 CGAL_VERSION=$3
 IS_ARG2=1
+PUBLISH_DIR="$4"
 if [ -z $PATH_TO_2 ]; then
   IS_ARG2=0
 fi
@@ -32,7 +34,8 @@ if [ -n CGAL_VERSION ]; then
 fi
 mkdir ./build_doc
 cd ./build_doc
-cmake -DCGAL_GENERATE_XML=ON -DDOXYGEN_EXECUTABLE="$PATH_TO_1" ../..  &> /dev/null
+cmake -DCGAL_GENERATE_XML=ON -DCGAL_DOC_CREATE_LOGS=true -DDOXYGEN_EXECUTABLE="$PATH_TO_1" ../..  &> /dev/null
+make -j7 doc  &> /dev/null
 make -j7 doc  &> /dev/null
 cd ../
 bash compare_testsuites.sh $PWD/build_doc/doc_output
@@ -52,7 +55,7 @@ if [ $IS_ARG2 == 0 ] || [ $(basename $PATH_TO_2) != "doxygen" ] || [ ! -e $PATH_
   echo "done."
 fi
 #build doc with doxygen master
-rm -rf ./build_doc
+mv ./build_doc ./doc_dir
 mkdir build_doc
 cd ./build_doc
 cmake -DCGAL_GENERATE_XML=ON -DDOXYGEN_EXECUTABLE="$PATH_TO_2" ../..  &> /dev/null
@@ -61,8 +64,13 @@ cd ../
 DOXYGEN_1=$($PATH_TO_1 --version)
 DOXYGEN_2=$($PATH_TO_2 --version)
 bash ./compare_testsuites.sh $PWD/build_doc/doc_output $PWD/doc_ref $CGAL_VERSION $DOXYGEN_1 $DOXYGEN_2
+
+#update overview
+python ./testsuite.py --output-dir $PWD/doc_dir/doc_output/ --doc-log-dir $PWD/doc_dir/doc_log/ --publish $PUBLISH_DIR --diff $PWD/diff.txt
+
 #clean-up
 rm -rf ./build_doc
+rm -rf ./doc_dir
 rm -rf ./doc_ref
 rm -rf ./doc_data
 if [ $IS_ARG2 == 0 ]; then

From 1f2ba45635a9336024c1fbef7cbf80a3f9d19f69 Mon Sep 17 00:00:00 2001
From: Maxime Gimeno <maxime.gimeno@gmail.com>
Date: Mon, 20 Feb 2017 09:42:01 +0100
Subject: [PATCH 13/26] Move the diff in the revision directory

---
 Documentation/doc/scripts/test_doxygen_versions.sh |  8 ++++----
 Documentation/doc/scripts/testsuite.py             | 14 +++++++-------
 2 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/Documentation/doc/scripts/test_doxygen_versions.sh b/Documentation/doc/scripts/test_doxygen_versions.sh
index 14b625b17cd..aeb62187817 100644
--- a/Documentation/doc/scripts/test_doxygen_versions.sh
+++ b/Documentation/doc/scripts/test_doxygen_versions.sh
@@ -37,20 +37,20 @@ cd ./build_doc
 cmake -DCGAL_GENERATE_XML=ON -DCGAL_DOC_CREATE_LOGS=true -DDOXYGEN_EXECUTABLE="$PATH_TO_1" ../..  &> /dev/null
 make -j7 doc  &> /dev/null
 make -j7 doc  &> /dev/null
-cd ../
+cd ../ #scripts
 bash compare_testsuites.sh $PWD/build_doc/doc_output
 mv ./doc_data ./doc_ref
 
 #download and build doxygen_master
 if [ $IS_ARG2 == 0 ] || [ $(basename $PATH_TO_2) != "doxygen" ] || [ ! -e $PATH_TO_2 ]; then
-  echo "No path to doxygen master were detected. Cloning..."
+  echo "No second path detected. Cloning Doxygen master branch..."
   git clone https://github.com/doxygen/doxygen.git doxygen_master  &> /dev/null
   cd doxygen_master
   mkdir build
   cd build
   cmake ..  &> /dev/null
   make -j7 &> /dev/null
-  cd ../..
+  cd ../.. #scripts
   PATH_TO_2="$PWD/doxygen_master/build/bin/doxygen"
   echo "done."
 fi
@@ -60,7 +60,7 @@ mkdir build_doc
 cd ./build_doc
 cmake -DCGAL_GENERATE_XML=ON -DDOXYGEN_EXECUTABLE="$PATH_TO_2" ../..  &> /dev/null
 make -j7 doc  &> /dev/null
-cd ../
+cd ../ #scripts
 DOXYGEN_1=$($PATH_TO_1 --version)
 DOXYGEN_2=$($PATH_TO_2 --version)
 bash ./compare_testsuites.sh $PWD/build_doc/doc_output $PWD/doc_ref $CGAL_VERSION $DOXYGEN_1 $DOXYGEN_2
diff --git a/Documentation/doc/scripts/testsuite.py b/Documentation/doc/scripts/testsuite.py
index 6bdef902738..b4ac1c679fd 100755
--- a/Documentation/doc/scripts/testsuite.py
+++ b/Documentation/doc/scripts/testsuite.py
@@ -158,19 +158,18 @@ def main():
             sys.stderr.write('Logs for this revision have already been publish under: ' 
                              + publish_dir + 'log' + version_string + ' Cannot publish.\n')
             sys.exit(1)
-
+        log_target=publish_dir + version_string
         # does the index file exist? if not write out a skeleton
         try:
             with open(publish_dir + 'index.html') as f: pass
         except IOError as e:
-            print('No index.html in the publish directory found. Writing a skeleton.')
-            shutil.copyfile(diff_file, publish_dir+'diff.txt')
+            print('No index.html in the publish directory found. Writing a skeleton.')               
             with open(diff_file, 'r') as myfile:
-                diff=myfile.read()
+              diff=myfile.read()
             if not diff:
-                diff='none'
+              diff='none'
             else:
-                diff='<a href=\"diff.txt\">See diff. </a>'
+              diff='<a href=\"{log_path}/diff.txt\">See diff. </a>'.format(log_path=version_string)
             with open(publish_dir + 'index.html', 'w') as f:
                 f.write('''<!DOCTYPE html>
 <style type="text/css">
@@ -199,10 +198,11 @@ body  {color: black; background-color: #C0C0D0; font-family: sans-serif;}
                 sys.stderr.write("Warning: the directory " + publish_dir + dir_to_remove + " does not exist or is not writable!\n")
             revs.eq(k).remove()
         write_out_html(d, publish_dir + 'index.html')
-        log_target=publish_dir + version_string
         try:
           #copy log files
           shutil.copytree('.', log_target)
+          #copy diff
+          shutil.copyfile(diff_file, log_target+'/diff.txt')
           try:
             #copy documentation
             if args.do_copy_results:

From a77063109c934e84101e7e7b20b533f88974a360 Mon Sep 17 00:00:00 2001
From: Maxime Gimeno <maxime.gimeno@gmail.com>
Date: Mon, 20 Feb 2017 12:46:20 +0100
Subject: [PATCH 14/26] Fix testsuite.py

---
 Documentation/doc/scripts/testsuite.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/Documentation/doc/scripts/testsuite.py b/Documentation/doc/scripts/testsuite.py
index b4ac1c679fd..1c32d2438b6 100755
--- a/Documentation/doc/scripts/testsuite.py
+++ b/Documentation/doc/scripts/testsuite.py
@@ -164,12 +164,6 @@ def main():
             with open(publish_dir + 'index.html') as f: pass
         except IOError as e:
             print('No index.html in the publish directory found. Writing a skeleton.')               
-            with open(diff_file, 'r') as myfile:
-              diff=myfile.read()
-            if not diff:
-              diff='none'
-            else:
-              diff='<a href=\"{log_path}/diff.txt\">See diff. </a>'.format(log_path=version_string)
             with open(publish_dir + 'index.html', 'w') as f:
                 f.write('''<!DOCTYPE html>
 <style type="text/css">
@@ -181,8 +175,14 @@ body  {color: black; background-color: #C0C0D0; font-family: sans-serif;}
 <html><head><title>Manual Testsuite Overview</title></head>
 <body><h1>Overviewpage of the Doxygen Manual Testsuite</h1>
 <table  border="1" cellspacing="2" cellpadding="5" id="revisions" class="rev-table">
-<tr><th>Revision</th><th>Date</th><th>Warnings</th><th>Errors</th><th>Diff</th></tr></table></body></html>''')
+<tr><th>Revision</th><th>Date</th><th>Warnings</th><th>Errors</th><th>Diff with doxygen master</th></tr></table></body></html>''')
 
+        with open(diff_file, 'r') as myfile:
+          diff=myfile.read()
+        if not diff:
+          diff='none'
+        else:
+          diff='<a href="{log_path}/diff.txt">Diff</a>'.format(log_path=version_string)
         d=pq(filename=publish_dir + 'index.html',parser="html")
         revs=d('#revisions tr')
         new_row='<tr><td><a href="{revision}/index.html">{revision}</a></td><td>{date}</td><td>{warnings}</td><td>{errors}</td><td>{diffs}</td></tr>'.format(

From 85b04e4919d23a50dc4eaac80659dfd09789bede Mon Sep 17 00:00:00 2001
From: Maxime Gimeno <maxime.gimeno@gmail.com>
Date: Mon, 20 Feb 2017 12:53:51 +0100
Subject: [PATCH 15/26] clean-up

---
 .../doc/scripts/compare_testsuites.sh         | 29 -------------------
 .../doc/scripts/test_doxygen_versions.sh      | 16 ++--------
 2 files changed, 3 insertions(+), 42 deletions(-)

diff --git a/Documentation/doc/scripts/compare_testsuites.sh b/Documentation/doc/scripts/compare_testsuites.sh
index 980c7900e51..1afd0b672e1 100644
--- a/Documentation/doc/scripts/compare_testsuites.sh
+++ b/Documentation/doc/scripts/compare_testsuites.sh
@@ -38,32 +38,3 @@ fi
 
 #diff the output and the reference output, ignoring the differences in whitespaces
 diff -u -N -w ./doc_data $DOC_REF > ./diff.txt
-
-#generate an html page showing the status of the diff
-CGAL_VERSION=$3
-DATE=`date +%Y-%m-%d`
-echo "<!DOCTYPE html>" > result.html
-echo "<html>" >> result.html
-echo "    <head>" >> result.html
-echo "        <meta charset=\"utf-8\" />" >> result.html
-echo "        <title>Documentation Status</title>" >> result.html
-echo "    </head>" >> result.html
-echo "    <body style=\"background-color: #C0C0D0;\"> " >> result.html
-echo "    <h1 id=\"maintitle\">Documentation Status of $CGAL_VERSION on $DATE</h1> " >> result.html
-echo "    <p> Difference between Doxygen $4 and Doxygen $5:  " >> result.html
-    
-#if there is a diff, give a link to show it
-if [[ -s ./diff.txt ]]
-then
-  echo "<p> There are differences :  <a href=\"diff.txt\">See logs. </a> <br /> " >> result.html
-#else just say that everything is fine
-else
-  echo "<p> There is no difference. <br /><br /> " >> result.html
-fi
-if [ "${FAILURES[0]}" != "" ]; then
-  echo " Some packages encountered problems while being parsed : <br /><br /> " >> result.html
-  echo " ${FAILURE[*]} <br /> ">> result.html
-fi
-echo "    </p>" >> result.html
-echo "    </body>" >> result.html
-echo "</html>" >> result.html
diff --git a/Documentation/doc/scripts/test_doxygen_versions.sh b/Documentation/doc/scripts/test_doxygen_versions.sh
index aeb62187817..71ef370e2a6 100644
--- a/Documentation/doc/scripts/test_doxygen_versions.sh
+++ b/Documentation/doc/scripts/test_doxygen_versions.sh
@@ -1,17 +1,15 @@
 #!/bin/bash
 if [ "$1" == '--help' ]; then 
-  echo "Usage: $0 <doxygen_1> [doxygen_2] [CGAL_VERSION][publish_dir]"
+  echo "Usage: $0 <doxygen_1> [doxygen_2] [publish_dir]"
   echo "Compares the output of doxygen_1 and doxygen_2 of this CGAL version, "
   echo "where  doxygen_1 and doxygen_2 are valid paths to doxygen executables."
   echo "If doxygen_2 is not specified, the master branch of doxygen will be cloned, built and used as doxygen_2."
-  echo "CGAL_VERSION is the name that will appear on the results page. Default is CGAL-{version in cmake generated VERSION}"
   echo "publish_dir is the path to the dir where the testsuite results are kept"
   exit 0
 fi
 #build reference
 PATH_TO_1="$1"
 PATH_TO_2="$2"
-CGAL_VERSION=$3
 IS_ARG2=1
 PUBLISH_DIR="$4"
 if [ -z $PATH_TO_2 ]; then
@@ -23,15 +21,7 @@ if [ -z $PATH_TO_1 ] || [ $(basename $PATH_TO_1) != "doxygen" ] || [ ! -e $PATH_
   echo "$0 --help for more information."
   exit 0
 fi
-#if no cgal version is specified, ask cmake"
-if [ -n CGAL_VERSION ]; then
-  mkdir ./shallow_build
-  cd ./shallow_build 
-  cmake ../../../.. &> /dev/null
-  CGAL_VERSION="CGAL-$(cat VERSION)"
-  cd ..
-  rm -rf ./shallow_build
-fi
+
 mkdir ./build_doc
 cd ./build_doc
 cmake -DCGAL_GENERATE_XML=ON -DCGAL_DOC_CREATE_LOGS=true -DDOXYGEN_EXECUTABLE="$PATH_TO_1" ../..  &> /dev/null
@@ -63,7 +53,7 @@ make -j7 doc  &> /dev/null
 cd ../ #scripts
 DOXYGEN_1=$($PATH_TO_1 --version)
 DOXYGEN_2=$($PATH_TO_2 --version)
-bash ./compare_testsuites.sh $PWD/build_doc/doc_output $PWD/doc_ref $CGAL_VERSION $DOXYGEN_1 $DOXYGEN_2
+bash ./compare_testsuites.sh $PWD/build_doc/doc_output $PWD/doc_ref $DOXYGEN_1 $DOXYGEN_2
 
 #update overview
 python ./testsuite.py --output-dir $PWD/doc_dir/doc_output/ --doc-log-dir $PWD/doc_dir/doc_log/ --publish $PUBLISH_DIR --diff $PWD/diff.txt

From f027bbbab6b3d16559c78ae635408cad0a3f9ebf Mon Sep 17 00:00:00 2001
From: Maxime Gimeno <maxime.gimeno@gmail.com>
Date: Mon, 27 Feb 2017 15:36:22 +0100
Subject: [PATCH 16/26] Fix doc_tags

---
 Documentation/doc/scripts/test_doxygen_versions.sh | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/Documentation/doc/scripts/test_doxygen_versions.sh b/Documentation/doc/scripts/test_doxygen_versions.sh
index 71ef370e2a6..50ddea8fbb5 100644
--- a/Documentation/doc/scripts/test_doxygen_versions.sh
+++ b/Documentation/doc/scripts/test_doxygen_versions.sh
@@ -26,7 +26,6 @@ mkdir ./build_doc
 cd ./build_doc
 cmake -DCGAL_GENERATE_XML=ON -DCGAL_DOC_CREATE_LOGS=true -DDOXYGEN_EXECUTABLE="$PATH_TO_1" ../..  &> /dev/null
 make -j7 doc  &> /dev/null
-make -j7 doc  &> /dev/null
 cd ../ #scripts
 bash compare_testsuites.sh $PWD/build_doc/doc_output
 mv ./doc_data ./doc_ref
@@ -54,7 +53,14 @@ cd ../ #scripts
 DOXYGEN_1=$($PATH_TO_1 --version)
 DOXYGEN_2=$($PATH_TO_2 --version)
 bash ./compare_testsuites.sh $PWD/build_doc/doc_output $PWD/doc_ref $DOXYGEN_1 $DOXYGEN_2
-
+#rebuild doc with Doxygen_1 to get the right doc_tags
+rm -rf ./doc_dir
+mkdir ./doc_dir
+cd ./doc_dir
+cmake -DCGAL_GENERATE_XML=ON -DCGAL_DOC_CREATE_LOGS=true -DDOXYGEN_EXECUTABLE="$PATH_TO_1" ../..  &> /dev/null
+make -j7 doc  &> /dev/null
+make -j7 doc  &> /dev/null
+cd ..
 #update overview
 python ./testsuite.py --output-dir $PWD/doc_dir/doc_output/ --doc-log-dir $PWD/doc_dir/doc_log/ --publish $PUBLISH_DIR --diff $PWD/diff.txt
 

From 305807ef6d7996ae17441cc80bcf4172ffee8272 Mon Sep 17 00:00:00 2001
From: Maxime Gimeno <maxime.gimeno@gmail.com>
Date: Thu, 13 Apr 2017 10:31:24 +0200
Subject: [PATCH 17/26] add cgal version

---
 Documentation/doc/resources/1.8.13/BaseDoxyfile.in | 2 +-
 Documentation/doc/resources/1.8.4/BaseDoxyfile.in  | 2 +-
 Documentation/doc/scripts/test_doxygen_versions.sh | 9 ++++++++-
 3 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/Documentation/doc/resources/1.8.13/BaseDoxyfile.in b/Documentation/doc/resources/1.8.13/BaseDoxyfile.in
index 95c2d26b4fd..448bae7be6f 100644
--- a/Documentation/doc/resources/1.8.13/BaseDoxyfile.in
+++ b/Documentation/doc/resources/1.8.13/BaseDoxyfile.in
@@ -1961,7 +1961,7 @@ MAN_LINKS              = NO
 # captures the structure of the code including all documentation.
 # The default value is: NO.
 
-GENERATE_XML           =
+GENERATE_XML           = NO
 
 # The XML_OUTPUT tag is used to specify where the XML pages will be put. If a
 # relative path is entered the value of OUTPUT_DIRECTORY will be put in front of
diff --git a/Documentation/doc/resources/1.8.4/BaseDoxyfile.in b/Documentation/doc/resources/1.8.4/BaseDoxyfile.in
index e91328518a0..03daafc1db4 100644
--- a/Documentation/doc/resources/1.8.4/BaseDoxyfile.in
+++ b/Documentation/doc/resources/1.8.4/BaseDoxyfile.in
@@ -1573,7 +1573,7 @@ MAN_LINKS              = NO
 # generate an XML file that captures the structure of
 # the code including all documentation.
 
-GENERATE_XML           =
+GENERATE_XML           = NO
 
 # The XML_OUTPUT tag is used to specify where the XML pages will be put.
 # If a relative path is entered the value of OUTPUT_DIRECTORY will be
diff --git a/Documentation/doc/scripts/test_doxygen_versions.sh b/Documentation/doc/scripts/test_doxygen_versions.sh
index 50ddea8fbb5..e19e9b08c51 100644
--- a/Documentation/doc/scripts/test_doxygen_versions.sh
+++ b/Documentation/doc/scripts/test_doxygen_versions.sh
@@ -22,6 +22,7 @@ if [ -z $PATH_TO_1 ] || [ $(basename $PATH_TO_1) != "doxygen" ] || [ ! -e $PATH_
   exit 0
 fi
 
+ROOT=$PWD
 mkdir ./build_doc
 cd ./build_doc
 cmake -DCGAL_GENERATE_XML=ON -DCGAL_DOC_CREATE_LOGS=true -DDOXYGEN_EXECUTABLE="$PATH_TO_1" ../..  &> /dev/null
@@ -61,8 +62,14 @@ cmake -DCGAL_GENERATE_XML=ON -DCGAL_DOC_CREATE_LOGS=true -DDOXYGEN_EXECUTABLE="$
 make -j7 doc  &> /dev/null
 make -j7 doc  &> /dev/null
 cd ..
+#get VERSION.h
+cd $ROOT
+mkdir ./build && cd ./build
+cmake ..
+PATH_TO_VERSION=$PWD/VESRION
 #update overview
-python ./testsuite.py --output-dir $PWD/doc_dir/doc_output/ --doc-log-dir $PWD/doc_dir/doc_log/ --publish $PUBLISH_DIR --diff $PWD/diff.txt
+cd $ROOT
+python ./testsuite.py --output-dir $PWD/doc_dir/doc_output/ --doc-log-dir $PWD/doc_dir/doc_log/ --publish $PUBLISH_DIR --diff $PWD/diff.txt --cgal-version $PATH_TO_VERSION
 
 #clean-up
 rm -rf ./build_doc

From 64915b1232d4ac1465dcd5faa11baf6e741ab89a Mon Sep 17 00:00:00 2001
From: Maxime Gimeno <maxime.gimeno@gmail.com>
Date: Thu, 13 Apr 2017 10:49:46 +0200
Subject: [PATCH 18/26] addlink to master documentation

---
 Documentation/doc/scripts/test_doxygen_versions.sh |  5 +++--
 Documentation/doc/scripts/testsuite.py             | 13 ++++++++++++-
 2 files changed, 15 insertions(+), 3 deletions(-)

diff --git a/Documentation/doc/scripts/test_doxygen_versions.sh b/Documentation/doc/scripts/test_doxygen_versions.sh
index e19e9b08c51..077eae52292 100644
--- a/Documentation/doc/scripts/test_doxygen_versions.sh
+++ b/Documentation/doc/scripts/test_doxygen_versions.sh
@@ -55,7 +55,7 @@ DOXYGEN_1=$($PATH_TO_1 --version)
 DOXYGEN_2=$($PATH_TO_2 --version)
 bash ./compare_testsuites.sh $PWD/build_doc/doc_output $PWD/doc_ref $DOXYGEN_1 $DOXYGEN_2
 #rebuild doc with Doxygen_1 to get the right doc_tags
-rm -rf ./doc_dir
+mv ./doc_dir ./doc_dir_2
 mkdir ./doc_dir
 cd ./doc_dir
 cmake -DCGAL_GENERATE_XML=ON -DCGAL_DOC_CREATE_LOGS=true -DDOXYGEN_EXECUTABLE="$PATH_TO_1" ../..  &> /dev/null
@@ -69,11 +69,12 @@ cmake ..
 PATH_TO_VERSION=$PWD/VESRION
 #update overview
 cd $ROOT
-python ./testsuite.py --output-dir $PWD/doc_dir/doc_output/ --doc-log-dir $PWD/doc_dir/doc_log/ --publish $PUBLISH_DIR --diff $PWD/diff.txt --cgal-version $PATH_TO_VERSION
+python ./testsuite.py --output-dir $PWD/doc_dir/doc_output/ --doc-log-dir $PWD/doc_dir/doc_log/ --publish $PUBLISH_DIR --diff $PWD/diff.txt --output2-dir $PWD/doc_dir_2/doc_output/ --cgal-version $PATH_TO_VERSION
 
 #clean-up
 rm -rf ./build_doc
 rm -rf ./doc_dir
+rm -rf ./doc_dir_2
 rm -rf ./doc_ref
 rm -rf ./doc_data
 if [ $IS_ARG2 == 0 ]; then
diff --git a/Documentation/doc/scripts/testsuite.py b/Documentation/doc/scripts/testsuite.py
index 1c32d2438b6..7a8f6854755 100755
--- a/Documentation/doc/scripts/testsuite.py
+++ b/Documentation/doc/scripts/testsuite.py
@@ -115,6 +115,7 @@ def main():
 
     parser.add_argument('--publish', metavar='/path/to/publish', help='Specify this argument if the results should be published.')
     parser.add_argument('--doc-log-dir', default='.', metavar='/path/to/cgal/build/dir/doc_log', help='The path of the documentation logs.')
+    parser.add_argument('--master-dir', default='.', metavar='/path/to/cgal/build/master_dir/doc_output', help='The path to the master build documentation.')
     parser.add_argument('--output-dir', default='.', metavar='/path/to/cgal/build/dir/doc_output', help='The path to the build documentation')
     parser.add_argument('--diff', metavar='/path/to/diff', help='The path to the diff file.')
     parser.add_argument('--cgal-version', help='Path to a version.h file from the current release. If not specified use git hash instead.')
@@ -175,7 +176,7 @@ body  {color: black; background-color: #C0C0D0; font-family: sans-serif;}
 <html><head><title>Manual Testsuite Overview</title></head>
 <body><h1>Overviewpage of the Doxygen Manual Testsuite</h1>
 <table  border="1" cellspacing="2" cellpadding="5" id="revisions" class="rev-table">
-<tr><th>Revision</th><th>Date</th><th>Warnings</th><th>Errors</th><th>Diff with doxygen master</th></tr></table></body></html>''')
+<tr><th>Revision</th><th>Date</th><th>Warnings</th><th>Errors</th><th>Diff with doxygen master</th><th>Documentation from doxygen master</th></tr></table></body></html>''')
 
         with open(diff_file, 'r') as myfile:
           diff=myfile.read()
@@ -212,6 +213,16 @@ body  {color: black; background-color: #C0C0D0; font-family: sans-serif;}
           except:
             sys.stderr.write("Error while copying documentation\n")
             raise
+          try:
+            #copy documentation from master
+            if args.do_copy_results:
+              tgt=os.path.join(log_target, 'master')
+              shutil.copytree(args.master_dir, tgt, symlinks=True)
+              os.symlink("../MathJax", os.path.join(log_target, 'MathJax'))
+          except:
+            sys.stderr.write("Error while copying master documentation\n")
+            raise
+
         except:
           sys.stderr.write("Error while writing to "+log_target+". Does it already exists?\n")
           raise

From 66ba81722436b8359d793e49453f38d7e8e7ac77 Mon Sep 17 00:00:00 2001
From: Maxime Gimeno <maxime.gimeno@gmail.com>
Date: Thu, 13 Apr 2017 12:27:47 +0200
Subject: [PATCH 19/26] fix ROOT

---
 Documentation/doc/scripts/test_doxygen_versions.sh | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/Documentation/doc/scripts/test_doxygen_versions.sh b/Documentation/doc/scripts/test_doxygen_versions.sh
index 077eae52292..7b54b5738d2 100644
--- a/Documentation/doc/scripts/test_doxygen_versions.sh
+++ b/Documentation/doc/scripts/test_doxygen_versions.sh
@@ -22,7 +22,7 @@ if [ -z $PATH_TO_1 ] || [ $(basename $PATH_TO_1) != "doxygen" ] || [ ! -e $PATH_
   exit 0
 fi
 
-ROOT=$PWD
+ROOT=$PWD/../../..
 mkdir ./build_doc
 cd ./build_doc
 cmake -DCGAL_GENERATE_XML=ON -DCGAL_DOC_CREATE_LOGS=true -DDOXYGEN_EXECUTABLE="$PATH_TO_1" ../..  &> /dev/null
@@ -66,10 +66,10 @@ cd ..
 cd $ROOT
 mkdir ./build && cd ./build
 cmake ..
-PATH_TO_VERSION=$PWD/VESRION
+PATH_TO_VERSION=$PWD/VERSION
 #update overview
-cd $ROOT
-python ./testsuite.py --output-dir $PWD/doc_dir/doc_output/ --doc-log-dir $PWD/doc_dir/doc_log/ --publish $PUBLISH_DIR --diff $PWD/diff.txt --output2-dir $PWD/doc_dir_2/doc_output/ --cgal-version $PATH_TO_VERSION
+cd $ROOT/Documentation/doc/scripts
+python ./testsuite.py --output-dir $PWD/doc_dir/doc_output/ --doc-log-dir $PWD/doc_dir/doc_log/ --publish $PUBLISH_DIR --diff $PWD/diff.txt --master-dir $PWD/doc_dir_2/doc_output/ --cgal-version $PATH_TO_VERSION
 
 #clean-up
 rm -rf ./build_doc

From 14941fd75961b19e0ca1b382a90579081ef75829 Mon Sep 17 00:00:00 2001
From: Maxime Gimeno <maxime.gimeno@gmail.com>
Date: Thu, 13 Apr 2017 14:09:38 +0200
Subject: [PATCH 20/26] Add a link to the doxygen master documentation

---
 Documentation/doc/scripts/test_doxygen_versions.sh | 11 ++++++-----
 Documentation/doc/scripts/testsuite.py             |  6 +++---
 2 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/Documentation/doc/scripts/test_doxygen_versions.sh b/Documentation/doc/scripts/test_doxygen_versions.sh
index 7b54b5738d2..966aef2890a 100644
--- a/Documentation/doc/scripts/test_doxygen_versions.sh
+++ b/Documentation/doc/scripts/test_doxygen_versions.sh
@@ -55,26 +55,27 @@ DOXYGEN_1=$($PATH_TO_1 --version)
 DOXYGEN_2=$($PATH_TO_2 --version)
 bash ./compare_testsuites.sh $PWD/build_doc/doc_output $PWD/doc_ref $DOXYGEN_1 $DOXYGEN_2
 #rebuild doc with Doxygen_1 to get the right doc_tags
-mv ./doc_dir ./doc_dir_2
+mv ./build_doc ./doc_master
+rm -rf ./doc_dir
 mkdir ./doc_dir
 cd ./doc_dir
 cmake -DCGAL_GENERATE_XML=ON -DCGAL_DOC_CREATE_LOGS=true -DDOXYGEN_EXECUTABLE="$PATH_TO_1" ../..  &> /dev/null
 make -j7 doc  &> /dev/null
 make -j7 doc  &> /dev/null
 cd ..
-#get VERSION.h
+#get VERSION's content
 cd $ROOT
 mkdir ./build && cd ./build
 cmake ..
-PATH_TO_VERSION=$PWD/VERSION
+CGAL_NAME="$(cat $PWD/VERSION)"
 #update overview
 cd $ROOT/Documentation/doc/scripts
-python ./testsuite.py --output-dir $PWD/doc_dir/doc_output/ --doc-log-dir $PWD/doc_dir/doc_log/ --publish $PUBLISH_DIR --diff $PWD/diff.txt --master-dir $PWD/doc_dir_2/doc_output/ --cgal-version $PATH_TO_VERSION
+python ./testsuite.py --output-dir $PWD/doc_dir/doc_output/ --doc-log-dir $PWD/doc_dir/doc_log/ --publish $PUBLISH_DIR --diff $PWD/diff.txt --master-dir $PWD/doc_master/doc_output/ --cgal-version $CGAL_NAME --do-copy-results 
 
 #clean-up
 rm -rf ./build_doc
 rm -rf ./doc_dir
-rm -rf ./doc_dir_2
+#rm -rf ./doc_master
 rm -rf ./doc_ref
 rm -rf ./doc_data
 if [ $IS_ARG2 == 0 ]; then
diff --git a/Documentation/doc/scripts/testsuite.py b/Documentation/doc/scripts/testsuite.py
index 7a8f6854755..879a87d1765 100755
--- a/Documentation/doc/scripts/testsuite.py
+++ b/Documentation/doc/scripts/testsuite.py
@@ -85,7 +85,8 @@ body  {color: black; background-color: #C0C0D0; font-family: sans-serif;}
     
     if args.publish and args.do_copy_results:
       link="\nLink to this <a href=output/Manual/index.html>documentation</a>\n"
-      d = pq(page_header+link+page_footer)
+      link_master="\nLink to <a href=master/Manual/index.html>master documentation</a>\n"
+      d = pq(page_header+link+"   "+link_master+page_footer)
     else:
       d = pq(page_header+page_footer)
     logs=sorted(glob.glob('./*.log'))
@@ -176,7 +177,7 @@ body  {color: black; background-color: #C0C0D0; font-family: sans-serif;}
 <html><head><title>Manual Testsuite Overview</title></head>
 <body><h1>Overviewpage of the Doxygen Manual Testsuite</h1>
 <table  border="1" cellspacing="2" cellpadding="5" id="revisions" class="rev-table">
-<tr><th>Revision</th><th>Date</th><th>Warnings</th><th>Errors</th><th>Diff with doxygen master</th><th>Documentation from doxygen master</th></tr></table></body></html>''')
+<tr><th>Revision</th><th>Date</th><th>Warnings</th><th>Errors</th><th>Diff with doxygen master</th></tr></table></body></html>''')
 
         with open(diff_file, 'r') as myfile:
           diff=myfile.read()
@@ -218,7 +219,6 @@ body  {color: black; background-color: #C0C0D0; font-family: sans-serif;}
             if args.do_copy_results:
               tgt=os.path.join(log_target, 'master')
               shutil.copytree(args.master_dir, tgt, symlinks=True)
-              os.symlink("../MathJax", os.path.join(log_target, 'MathJax'))
           except:
             sys.stderr.write("Error while copying master documentation\n")
             raise

From fa4bac968971da796a0bf9210be23a2335288625 Mon Sep 17 00:00:00 2001
From: Maxime Gimeno <maxime.gimeno@gmail.com>
Date: Fri, 14 Apr 2017 13:19:19 +0200
Subject: [PATCH 21/26] Add info about doxygen versions and change default
 resources directory.

---
 Documentation/doc/CMakeLists.txt                   |  2 +-
 Documentation/doc/scripts/test_doxygen_versions.sh | 14 +++++++++-----
 Documentation/doc/scripts/testsuite.py             | 12 ++++++++++--
 3 files changed, 20 insertions(+), 8 deletions(-)

diff --git a/Documentation/doc/CMakeLists.txt b/Documentation/doc/CMakeLists.txt
index 323ce63b498..144461b8c65 100644
--- a/Documentation/doc/CMakeLists.txt
+++ b/Documentation/doc/CMakeLists.txt
@@ -203,7 +203,7 @@ 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 "${CMAKE_CURRENT_LIST_DIR}/resources/1.8.4")
+set(CGAL_DOC_RESOURCE_DIR_DEFAULT "${CMAKE_CURRENT_LIST_DIR}/resources/1.8.13")
 
 #  first look if resources for the specific doxygen version is available, fallback
 #  on the default otherwise
diff --git a/Documentation/doc/scripts/test_doxygen_versions.sh b/Documentation/doc/scripts/test_doxygen_versions.sh
index 966aef2890a..b859cababca 100644
--- a/Documentation/doc/scripts/test_doxygen_versions.sh
+++ b/Documentation/doc/scripts/test_doxygen_versions.sh
@@ -36,6 +36,7 @@ if [ $IS_ARG2 == 0 ] || [ $(basename $PATH_TO_2) != "doxygen" ] || [ ! -e $PATH_
   echo "No second path detected. Cloning Doxygen master branch..."
   git clone https://github.com/doxygen/doxygen.git doxygen_master  &> /dev/null
   cd doxygen_master
+  MASTER_DESCRIBE=$(git describe --tags)
   mkdir build
   cd build
   cmake ..  &> /dev/null
@@ -59,23 +60,26 @@ mv ./build_doc ./doc_master
 rm -rf ./doc_dir
 mkdir ./doc_dir
 cd ./doc_dir
-cmake -DCGAL_GENERATE_XML=ON -DCGAL_DOC_CREATE_LOGS=true -DDOXYGEN_EXECUTABLE="$PATH_TO_1" ../..  &> /dev/null
+cmake -DCGAL_GENERATE_XML=ON -DCGAL_DOC_CREATE_LOGS=true -DDOXYGEN_EXECUTABLE="$PATH_TO_1" -DCGAL_DOC_RESOURCE_DIR=$ROOT/Documentation/doc/resources/1.8.13 ../..  &> /dev/null
 make -j7 doc  &> /dev/null
 make -j7 doc  &> /dev/null
 cd ..
 #get VERSION's content
 cd $ROOT
-mkdir ./build && cd ./build
+mkdir -p ./build && cd ./build
 cmake ..
-CGAL_NAME="$(cat $PWD/VERSION)"
+CGAL_NAME="$(cat $PWD/VERSION) with Doxygen $DOXYGEN_1"
+
 #update overview
 cd $ROOT/Documentation/doc/scripts
-python ./testsuite.py --output-dir $PWD/doc_dir/doc_output/ --doc-log-dir $PWD/doc_dir/doc_log/ --publish $PUBLISH_DIR --diff $PWD/diff.txt --master-dir $PWD/doc_master/doc_output/ --cgal-version $CGAL_NAME --do-copy-results 
+python ./testsuite.py --output-dir $PWD/doc_dir/doc_output/ --doc-log-dir $PWD/doc_dir/doc_log/ \
+  --publish $PUBLISH_DIR --diff $PWD/diff.txt --master-dir $PWD/doc_master/doc_output/ \
+  --cgal-version "$CGAL_NAME" --do-copy-results --doxygen-version "$DOXYGEN_1" --master-describe "$MASTER_DESCRIBE"
 
 #clean-up
 rm -rf ./build_doc
 rm -rf ./doc_dir
-#rm -rf ./doc_master
+rm -rf ./doc_master
 rm -rf ./doc_ref
 rm -rf ./doc_data
 if [ $IS_ARG2 == 0 ]; then
diff --git a/Documentation/doc/scripts/testsuite.py b/Documentation/doc/scripts/testsuite.py
index 879a87d1765..7bf00eac8ad 100755
--- a/Documentation/doc/scripts/testsuite.py
+++ b/Documentation/doc/scripts/testsuite.py
@@ -84,8 +84,14 @@ body  {color: black; background-color: #C0C0D0; font-family: sans-serif;}
 </table></body></html>'''
     
     if args.publish and args.do_copy_results:
-      link="\nLink to this <a href=output/Manual/index.html>documentation</a>\n"
-      link_master="\nLink to <a href=master/Manual/index.html>master documentation</a>\n"
+      suffix=''
+      if args.doxygen_version:
+        suffix = "built with Doxygen "+args.doxygen_version
+      link="\nLink to this <a href=output/Manual/index.html>documentation {_suffix}</a>\n".format(_suffix=suffix)
+      suffix = ''
+      if args.master_describe:
+        suffix=args.master_describe
+      link_master="\nLink to <a href=master/Manual/index.html> documentation compiled with Doxygen Master {_suffix}</a>\n".format(_suffix=suffix)
       d = pq(page_header+link+"   "+link_master+page_footer)
     else:
       d = pq(page_header+page_footer)
@@ -122,6 +128,8 @@ def main():
     parser.add_argument('--cgal-version', help='Path to a version.h file from the current release. If not specified use git hash instead.')
     parser.add_argument('--version-to-keep', help='indicates the number of release testsuites that should be kept at the publishing location.')
     parser.add_argument('--do-copy-results', action="store_true", help='Specify this argument if you want to copy the generated documentation into the publishing location.')
+    parser.add_argument('--doxygen-version', default ='', help='Specify this argument if you want to add a version number to the name of the link to the documentation.')
+    parser.add_argument('--master-describe', default ='', help='Specify this argument if you want to add a suffix to the name of the link to the doxygen master documentation.')
     
     args = parser.parse_args()
     

From 9b222903135ae0b53968b7e8b88dd5e30b2f4ae2 Mon Sep 17 00:00:00 2001
From: Maxime Gimeno <maxime.gimeno@gmail.com>
Date: Tue, 18 Apr 2017 10:37:24 +0200
Subject: [PATCH 22/26] Suppress warnings from GENERATE_XML in the logs

---
 Documentation/doc/scripts/test_doxygen_versions.sh | 7 ++++---
 Documentation/doc/scripts/testsuite.py             | 2 +-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/Documentation/doc/scripts/test_doxygen_versions.sh b/Documentation/doc/scripts/test_doxygen_versions.sh
index b859cababca..7bf24275589 100644
--- a/Documentation/doc/scripts/test_doxygen_versions.sh
+++ b/Documentation/doc/scripts/test_doxygen_versions.sh
@@ -25,7 +25,7 @@ fi
 ROOT=$PWD/../../..
 mkdir ./build_doc
 cd ./build_doc
-cmake -DCGAL_GENERATE_XML=ON -DCGAL_DOC_CREATE_LOGS=true -DDOXYGEN_EXECUTABLE="$PATH_TO_1" ../..  &> /dev/null
+cmake -DCGAL_GENERATE_XML=ON -DDOXYGEN_EXECUTABLE="$PATH_TO_1" ../..  &> /dev/null
 make -j7 doc  &> /dev/null
 cd ../ #scripts
 bash compare_testsuites.sh $PWD/build_doc/doc_output
@@ -55,12 +55,13 @@ cd ../ #scripts
 DOXYGEN_1=$($PATH_TO_1 --version)
 DOXYGEN_2=$($PATH_TO_2 --version)
 bash ./compare_testsuites.sh $PWD/build_doc/doc_output $PWD/doc_ref $DOXYGEN_1 $DOXYGEN_2
-#rebuild doc with Doxygen_1 to get the right doc_tags
+#rebuild doc with Doxygen_1 to get the right doc_tags without GENERATE_XML because it ignores the EXCLUDE_SYMBOLS, 
+#which disrupts the logs
 mv ./build_doc ./doc_master
 rm -rf ./doc_dir
 mkdir ./doc_dir
 cd ./doc_dir
-cmake -DCGAL_GENERATE_XML=ON -DCGAL_DOC_CREATE_LOGS=true -DDOXYGEN_EXECUTABLE="$PATH_TO_1" -DCGAL_DOC_RESOURCE_DIR=$ROOT/Documentation/doc/resources/1.8.13 ../..  &> /dev/null
+cmake -DCGAL_DOC_CREATE_LOGS=true -DDOXYGEN_EXECUTABLE="$PATH_TO_1" -DCGAL_DOC_RESOURCE_DIR=$ROOT/Documentation/doc/resources/1.8.13 ../..  &> /dev/null
 make -j7 doc  &> /dev/null
 make -j7 doc  &> /dev/null
 cd ..
diff --git a/Documentation/doc/scripts/testsuite.py b/Documentation/doc/scripts/testsuite.py
index 7bf00eac8ad..caf9e10f57f 100755
--- a/Documentation/doc/scripts/testsuite.py
+++ b/Documentation/doc/scripts/testsuite.py
@@ -91,7 +91,7 @@ body  {color: black; background-color: #C0C0D0; font-family: sans-serif;}
       suffix = ''
       if args.master_describe:
         suffix=args.master_describe
-      link_master="\nLink to <a href=master/Manual/index.html> documentation compiled with Doxygen Master {_suffix}</a>\n".format(_suffix=suffix)
+      link_master="\n<br>Link to <a href=master/Manual/index.html> documentation built with Doxygen Master {_suffix}</a>\n".format(_suffix=suffix)
       d = pq(page_header+link+"   "+link_master+page_footer)
     else:
       d = pq(page_header+page_footer)

From 7745ed842389a76c1dd1843dc67bdb08abac0b39 Mon Sep 17 00:00:00 2001
From: Maxime Gimeno <maxime.gimeno@gmail.com>
Date: Tue, 18 Apr 2017 12:59:26 +0200
Subject: [PATCH 23/26] Modify run_doxygen_testsuite to use the new doxygen
 testsuite.

---
 .../doc/scripts/test_doxygen_versions.sh      |  2 +-
 .../test_doxygen_versions_from_release.sh     | 86 +++++++++++++++++++
 .../developer_scripts/run_doxygen_testsuite   | 17 +---
 3 files changed, 89 insertions(+), 16 deletions(-)
 create mode 100644 Documentation/doc/scripts/test_doxygen_versions_from_release.sh

diff --git a/Documentation/doc/scripts/test_doxygen_versions.sh b/Documentation/doc/scripts/test_doxygen_versions.sh
index 7bf24275589..8948334370d 100644
--- a/Documentation/doc/scripts/test_doxygen_versions.sh
+++ b/Documentation/doc/scripts/test_doxygen_versions.sh
@@ -61,7 +61,7 @@ mv ./build_doc ./doc_master
 rm -rf ./doc_dir
 mkdir ./doc_dir
 cd ./doc_dir
-cmake -DCGAL_DOC_CREATE_LOGS=true -DDOXYGEN_EXECUTABLE="$PATH_TO_1" -DCGAL_DOC_RESOURCE_DIR=$ROOT/Documentation/doc/resources/1.8.13 ../..  &> /dev/null
+cmake -DCGAL_DOC_CREATE_LOGS=true -DDOXYGEN_EXECUTABLE="$PATH_TO_1" ../..  &> /dev/null
 make -j7 doc  &> /dev/null
 make -j7 doc  &> /dev/null
 cd ..
diff --git a/Documentation/doc/scripts/test_doxygen_versions_from_release.sh b/Documentation/doc/scripts/test_doxygen_versions_from_release.sh
new file mode 100644
index 00000000000..08525369e06
--- /dev/null
+++ b/Documentation/doc/scripts/test_doxygen_versions_from_release.sh
@@ -0,0 +1,86 @@
+#!/bin/bash
+if [ "$1" == '--help' ]; then 
+  echo "Usage: $0 <doxygen_1> [doxygen_2] [publish_dir]"
+  echo "Compares the output of doxygen_1 and doxygen_2 of this CGAL version, "
+  echo "where  doxygen_1 and doxygen_2 are valid paths to doxygen executables."
+  echo "If doxygen_2 is not specified, the master branch of doxygen will be cloned, built and used as doxygen_2."
+  echo "publish_dir is the path to the dir where the testsuite results are kept"
+  exit 0
+fi
+#build reference
+PATH_TO_1="$1"
+PATH_TO_2="$2"
+IS_ARG2=1
+PUBLISH_DIR="$4"
+if [ -z $PATH_TO_2 ]; then
+  IS_ARG2=0
+fi
+
+if [ -z $PATH_TO_1 ] || [ $(basename $PATH_TO_1) != "doxygen" ] || [ ! -e $PATH_TO_1 ]; then
+  echo "Please specify a valid path to a doxygen executable."
+  echo "$0 --help for more information."
+  exit 0
+fi
+
+ROOT=/home/cgal-testsuite
+mkdir ./build_doc
+cd ./build_doc
+cmake -DCGAL_GENERATE_XML=ON -DDOXYGEN_EXECUTABLE="$PATH_TO_1" ../..  &> /dev/null
+make -j7 doc  &> /dev/null
+cd ../ #scripts
+bash compare_testsuites.sh $PWD/build_doc/doc_output
+mv ./doc_data ./doc_ref
+
+#download and build doxygen_master
+if [ $IS_ARG2 == 0 ] || [ $(basename $PATH_TO_2) != "doxygen" ] || [ ! -e $PATH_TO_2 ]; then
+  echo "No second path detected. Cloning Doxygen master branch..."
+  git clone https://github.com/doxygen/doxygen.git doxygen_master  &> /dev/null
+  cd doxygen_master
+  MASTER_DESCRIBE=$(git describe --tags)
+  mkdir build
+  cd build
+  cmake ..  &> /dev/null
+  make -j7 &> /dev/null
+  cd ../.. #scripts
+  PATH_TO_2="$PWD/doxygen_master/build/bin/doxygen"
+  echo "done."
+fi
+#build doc with doxygen master
+mv ./build_doc ./doc_dir
+mkdir build_doc
+cd ./build_doc
+cmake -DCGAL_GENERATE_XML=ON -DDOXYGEN_EXECUTABLE="$PATH_TO_2" ../..  &> /dev/null
+make -j7 doc  &> /dev/null
+cd ../ #scripts
+DOXYGEN_1=$($PATH_TO_1 --version)
+DOXYGEN_2=$($PATH_TO_2 --version)
+bash ./compare_testsuites.sh $PWD/build_doc/doc_output $PWD/doc_ref $DOXYGEN_1 $DOXYGEN_2
+#rebuild doc with Doxygen_1 to get the right doc_tags without GENERATE_XML because it ignores the EXCLUDE_SYMBOLS, 
+#which disrupts the logs
+mv ./build_doc ./doc_master
+rm -rf ./doc_dir
+mkdir ./doc_dir
+cd ./doc_dir
+cmake -DCGAL_DOC_CREATE_LOGS=true -DDOXYGEN_EXECUTABLE="$PATH_TO_1" ../..  &> /dev/null
+make -j7 doc  &> /dev/null
+make -j7 doc  &> /dev/null
+cd ..
+#get VERSION's content
+cd $ROOT
+CGAL_NAME="$(cat $PWD/VERSION) with Doxygen $DOXYGEN_1"
+
+#update overview
+cd $ROOT/doc/scripts
+python ./testsuite.py --output-dir $PWD/doc_dir/doc_output/ --doc-log-dir $PWD/doc_dir/doc_log/ \
+  --publish $PUBLISH_DIR --diff $PWD/diff.txt --master-dir $PWD/doc_master/doc_output/ \
+  --cgal-version "$CGAL_NAME" --do-copy-results --version-to-keep 10 --doxygen-version "$DOXYGEN_1" --master-describe "$MASTER_DESCRIBE"
+
+#clean-up
+rm -rf ./build_doc
+rm -rf ./doc_dir
+rm -rf ./doc_master
+rm -rf ./doc_ref
+rm -rf ./doc_data
+if [ $IS_ARG2 == 0 ]; then
+  rm -rf ./doxygen_master
+fi
diff --git a/Scripts/developer_scripts/run_doxygen_testsuite b/Scripts/developer_scripts/run_doxygen_testsuite
index 25e1b28b743..b2862d85d74 100755
--- a/Scripts/developer_scripts/run_doxygen_testsuite
+++ b/Scripts/developer_scripts/run_doxygen_testsuite
@@ -62,21 +62,8 @@ PYTHONPATH=/home/cgal-testsuite/.local/lib/python2.6/site-packages
 export PYTHONPATH
 PATH=/home/cgal-testsuite/local/bin:$PATH
 export PATH
-
-cmake \
-    -DBUILD_DOC:BOOL=ON \
-    -DCGAL_DOC_CREATE_LOGS:bool=ON \
-    -DCGAL_DOC_MATHJAX_LOCATION:STRING=../../MathJax \
-    -DCGAL_DOC_RELEASE:BOOL=TRUE \
-    -DCGAL_DOC_PUBLISH_DIR=/srv/CGAL/www/Members/Manual_doxygen_test \
-    -DDOXYGEN_EXECUTABLE:FILEPATH=/home/cgal-testsuite/local/bin/doxygen \
-    -DPYTHON_EXECUTABLE:FILEPATH=/home/cgal-testsuite/local/bin/python2 \
-    . 2>&1 || error "exit code $? returned by CMake"
-# Note that -DCGAL_DOC_RELEASE:BOOL=TRUE should be only for master-only
-# internal releases, and not for integration releases.
-
-make doc 2>&1 || error "exit code $? returned by the command 'make doc'"
-make doc_and_publish_testsuite 2>&1 || error "exit code $? returned by the command 'make doc_and_publish_testsuite'"
+cd "$PWD/doc/scripts"
+bash ./test_doxygen_versions_from_release.sh /home/cgal-testsuite/local/bin/doxygen '' '' /srv/CGAL/www/Members/Manual_doxygen_test
 case "$CGAL_RELEASE_ID" in
     *-I-*) ln -snf "../Manual_doxygen_test/$CGAL_RELEASE_ID/output" /srv/CGAL/www/doc/master
            ;;

From 33cd8fda21aa39efb800da839eeb3ea92e78abc9 Mon Sep 17 00:00:00 2001
From: Maxime Gimeno <maxime.gimeno@gmail.com>
Date: Wed, 10 May 2017 15:32:53 +0200
Subject: [PATCH 24/26] Last adjustments for the text of the links.

---
 Documentation/doc/scripts/test_doxygen_versions.sh             | 2 +-
 .../doc/scripts/test_doxygen_versions_from_release.sh          | 2 +-
 Documentation/doc/scripts/testsuite.py                         | 3 ++-
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/Documentation/doc/scripts/test_doxygen_versions.sh b/Documentation/doc/scripts/test_doxygen_versions.sh
index 8948334370d..46afe71e114 100644
--- a/Documentation/doc/scripts/test_doxygen_versions.sh
+++ b/Documentation/doc/scripts/test_doxygen_versions.sh
@@ -69,7 +69,7 @@ cd ..
 cd $ROOT
 mkdir -p ./build && cd ./build
 cmake ..
-CGAL_NAME="$(cat $PWD/VERSION) with Doxygen $DOXYGEN_1"
+CGAL_NAME="$(cat $PWD/VERSION)"
 
 #update overview
 cd $ROOT/Documentation/doc/scripts
diff --git a/Documentation/doc/scripts/test_doxygen_versions_from_release.sh b/Documentation/doc/scripts/test_doxygen_versions_from_release.sh
index 08525369e06..e975ef06971 100644
--- a/Documentation/doc/scripts/test_doxygen_versions_from_release.sh
+++ b/Documentation/doc/scripts/test_doxygen_versions_from_release.sh
@@ -67,7 +67,7 @@ make -j7 doc  &> /dev/null
 cd ..
 #get VERSION's content
 cd $ROOT
-CGAL_NAME="$(cat $PWD/VERSION) with Doxygen $DOXYGEN_1"
+CGAL_NAME="$(cat $PWD/VERSION)"
 
 #update overview
 cd $ROOT/doc/scripts
diff --git a/Documentation/doc/scripts/testsuite.py b/Documentation/doc/scripts/testsuite.py
index caf9e10f57f..d39711727a8 100755
--- a/Documentation/doc/scripts/testsuite.py
+++ b/Documentation/doc/scripts/testsuite.py
@@ -192,7 +192,8 @@ body  {color: black; background-color: #C0C0D0; font-family: sans-serif;}
         if not diff:
           diff='none'
         else:
-          diff='<a href="{log_path}/diff.txt">Diff</a>'.format(log_path=version_string)
+          diff='<a href="{log_path}/diff.txt">Diff between {test_version} and {master version}.</a>'.format(
+          log_path=version_string, test_version=args.doxygen_version, master_version=args.master_describe)
         d=pq(filename=publish_dir + 'index.html',parser="html")
         revs=d('#revisions tr')
         new_row='<tr><td><a href="{revision}/index.html">{revision}</a></td><td>{date}</td><td>{warnings}</td><td>{errors}</td><td>{diffs}</td></tr>'.format(

From 82d26e2ab3fddfaebd420a0f1df28d0cdba09437 Mon Sep 17 00:00:00 2001
From: Maxime Gimeno <maxime.gimeno@gmail.com>
Date: Tue, 6 Jun 2017 15:20:57 +0200
Subject: [PATCH 25/26] If not args.master_dir, don't copy doxygen masters
 documentation

---
 Documentation/doc/scripts/testsuite.py | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/Documentation/doc/scripts/testsuite.py b/Documentation/doc/scripts/testsuite.py
index d39711727a8..6c5af94a0eb 100755
--- a/Documentation/doc/scripts/testsuite.py
+++ b/Documentation/doc/scripts/testsuite.py
@@ -223,14 +223,15 @@ body  {color: black; background-color: #C0C0D0; font-family: sans-serif;}
           except:
             sys.stderr.write("Error while copying documentation\n")
             raise
-          try:
-            #copy documentation from master
-            if args.do_copy_results:
-              tgt=os.path.join(log_target, 'master')
-              shutil.copytree(args.master_dir, tgt, symlinks=True)
-          except:
-            sys.stderr.write("Error while copying master documentation\n")
-            raise
+          if args.master_dir:
+            try:
+              #copy documentation from master
+              if args.do_copy_results:
+                tgt=os.path.join(log_target, 'master')
+                shutil.copytree(args.master_dir, tgt, symlinks=True)
+            except:
+              sys.stderr.write("Error while copying master documentation\n")
+              raise
 
         except:
           sys.stderr.write("Error while writing to "+log_target+". Does it already exists?\n")

From 36d1a39bfc9b7dbeea91e0926feacf42a6708bc1 Mon Sep 17 00:00:00 2001
From: Maxime Gimeno <maxime.gimeno@gmail.com>
Date: Wed, 7 Jun 2017 13:58:48 +0200
Subject: [PATCH 26/26] Optimisations :

 - Fix path problems
 - Unify test_doxygens.sh
 - use th emax number of cores available for make calls
 - fix doc of the scripts
---
 .../doc/scripts/compare_testsuites.sh         |  7 ++
 .../doc/scripts/test_doxygen_versions.sh      | 64 +++++++++-----
 .../test_doxygen_versions_from_release.sh     | 86 -------------------
 .../developer_scripts/run_doxygen_testsuite   |  2 +-
 4 files changed, 49 insertions(+), 110 deletions(-)
 delete mode 100644 Documentation/doc/scripts/test_doxygen_versions_from_release.sh

diff --git a/Documentation/doc/scripts/compare_testsuites.sh b/Documentation/doc/scripts/compare_testsuites.sh
index 1afd0b672e1..ec4e941e451 100644
--- a/Documentation/doc/scripts/compare_testsuites.sh
+++ b/Documentation/doc/scripts/compare_testsuites.sh
@@ -1,4 +1,11 @@
 #!/bin/bash
+if [ "$1" == '--help' ]; then
+  echo "Usage: $0 <doc 1> [doc 2]"
+  exho "doc 1 and doc 2 are paths to doxygen outputs (doc_output)."
+  echo "Parse the xml output of doc 1 and creates a directory with organized text files."
+  echo "Then, if doc_2 is specified, do the same for its xml output and make the diff between them."
+  exit 0
+fi
 #Path to the CGAL_Documentation_build_directory/doc_output
 PATH_TO_DOC="$1"
 
diff --git a/Documentation/doc/scripts/test_doxygen_versions.sh b/Documentation/doc/scripts/test_doxygen_versions.sh
index 46afe71e114..1b435c88d77 100644
--- a/Documentation/doc/scripts/test_doxygen_versions.sh
+++ b/Documentation/doc/scripts/test_doxygen_versions.sh
@@ -1,20 +1,18 @@
 #!/bin/bash
-if [ "$1" == '--help' ]; then 
+if [ "$1" == '--help' ]; then
   echo "Usage: $0 <doxygen_1> [doxygen_2] [publish_dir]"
   echo "Compares the output of doxygen_1 and doxygen_2 of this CGAL version, "
   echo "where  doxygen_1 and doxygen_2 are valid paths to doxygen executables."
   echo "If doxygen_2 is not specified, the master branch of doxygen will be cloned, built and used as doxygen_2."
   echo "publish_dir is the path to the dir where the testsuite results are kept"
+  echo "$0 must be called from doc/scripts"
   exit 0
 fi
 #build reference
 PATH_TO_1="$1"
 PATH_TO_2="$2"
-IS_ARG2=1
-PUBLISH_DIR="$4"
-if [ -z $PATH_TO_2 ]; then
-  IS_ARG2=0
-fi
+PUBLISH_DIR="$3"
+NB_CORES="$(grep -c ^processor /proc/cpuinfo)"
 
 if [ -z $PATH_TO_1 ] || [ $(basename $PATH_TO_1) != "doxygen" ] || [ ! -e $PATH_TO_1 ]; then
   echo "Please specify a valid path to a doxygen executable."
@@ -22,17 +20,30 @@ if [ -z $PATH_TO_1 ] || [ $(basename $PATH_TO_1) != "doxygen" ] || [ ! -e $PATH_
   exit 0
 fi
 
-ROOT=$PWD/../../..
+#Find the CGAL directory. If there is a directory called Documentation, this is a branch build.
+#Else it is from a release.
+TEMP=$PWD
+IS_RELEASE=1
+cd $PWD/../..
+if [ "$(basename $PWD)" = 'Documentation' ]; then
+  ROOT=$PWD/..
+  IS_RELEASE=0
+else
+  ROOT=$PWD
+fi
+cd $TEMP #scripts
+
+
 mkdir ./build_doc
 cd ./build_doc
 cmake -DCGAL_GENERATE_XML=ON -DDOXYGEN_EXECUTABLE="$PATH_TO_1" ../..  &> /dev/null
-make -j7 doc  &> /dev/null
+make -j$NB_CORES doc  &> /dev/null
 cd ../ #scripts
 bash compare_testsuites.sh $PWD/build_doc/doc_output
 mv ./doc_data ./doc_ref
 
 #download and build doxygen_master
-if [ $IS_ARG2 == 0 ] || [ $(basename $PATH_TO_2) != "doxygen" ] || [ ! -e $PATH_TO_2 ]; then
+if [ -z $PATH_TO_2 ] || [ $(basename $PATH_TO_2) != "doxygen" ] || [ ! -e $PATH_TO_2 ]; then
   echo "No second path detected. Cloning Doxygen master branch..."
   git clone https://github.com/doxygen/doxygen.git doxygen_master  &> /dev/null
   cd doxygen_master
@@ -40,7 +51,7 @@ if [ $IS_ARG2 == 0 ] || [ $(basename $PATH_TO_2) != "doxygen" ] || [ ! -e $PATH_
   mkdir build
   cd build
   cmake ..  &> /dev/null
-  make -j7 &> /dev/null
+  make -j$NB_CORES &> /dev/null
   cd ../.. #scripts
   PATH_TO_2="$PWD/doxygen_master/build/bin/doxygen"
   echo "done."
@@ -50,32 +61,39 @@ mv ./build_doc ./doc_dir
 mkdir build_doc
 cd ./build_doc
 cmake -DCGAL_GENERATE_XML=ON -DDOXYGEN_EXECUTABLE="$PATH_TO_2" ../..  &> /dev/null
-make -j7 doc  &> /dev/null
+make -j$NB_CORES doc  &> /dev/null
 cd ../ #scripts
 DOXYGEN_1=$($PATH_TO_1 --version)
 DOXYGEN_2=$($PATH_TO_2 --version)
-bash ./compare_testsuites.sh $PWD/build_doc/doc_output $PWD/doc_ref $DOXYGEN_1 $DOXYGEN_2
-#rebuild doc with Doxygen_1 to get the right doc_tags without GENERATE_XML because it ignores the EXCLUDE_SYMBOLS, 
+bash ./compare_testsuites.sh $PWD/build_doc/doc_output $PWD/doc_ref
+#rebuild doc with Doxygen_1 to get the right doc_tags without GENERATE_XML because it ignores the EXCLUDE_SYMBOLS,
 #which disrupts the logs
 mv ./build_doc ./doc_master
 rm -rf ./doc_dir
 mkdir ./doc_dir
 cd ./doc_dir
 cmake -DCGAL_DOC_CREATE_LOGS=true -DDOXYGEN_EXECUTABLE="$PATH_TO_1" ../..  &> /dev/null
-make -j7 doc  &> /dev/null
-make -j7 doc  &> /dev/null
-cd ..
+make -j$NB_CORES doc  &> /dev/null
+make -j$NB_CORES doc  &> /dev/null
+cd .. #scripts
 #get VERSION's content
-cd $ROOT
-mkdir -p ./build && cd ./build
-cmake ..
-CGAL_NAME="$(cat $PWD/VERSION)"
+if [ $IS_RELEASE = 0 ]; then
+  cd $ROOT
+  mkdir -p ./build && cd ./build
+  cmake ..
+  CGAL_NAME="$(cat $PWD/VERSION)"
+  cd ..$ROOT
+  rm -rf ./build
+  cd $ROOT/Documentation/doc/scripts
+else
+  CGAL_NAME="$(cat $ROOT/VERSION)"
+fi
 
 #update overview
-cd $ROOT/Documentation/doc/scripts
+
 python ./testsuite.py --output-dir $PWD/doc_dir/doc_output/ --doc-log-dir $PWD/doc_dir/doc_log/ \
   --publish $PUBLISH_DIR --diff $PWD/diff.txt --master-dir $PWD/doc_master/doc_output/ \
-  --cgal-version "$CGAL_NAME" --do-copy-results --doxygen-version "$DOXYGEN_1" --master-describe "$MASTER_DESCRIBE"
+  --cgal-version "$CGAL_NAME" --do-copy-results --version-to-keep 10 --doxygen-version "$DOXYGEN_1" --master-describe "$MASTER_DESCRIBE"
 
 #clean-up
 rm -rf ./build_doc
@@ -83,6 +101,6 @@ rm -rf ./doc_dir
 rm -rf ./doc_master
 rm -rf ./doc_ref
 rm -rf ./doc_data
-if [ $IS_ARG2 == 0 ]; then
+if [ -z $PATH_TO_2 ]; then
   rm -rf ./doxygen_master
 fi
diff --git a/Documentation/doc/scripts/test_doxygen_versions_from_release.sh b/Documentation/doc/scripts/test_doxygen_versions_from_release.sh
deleted file mode 100644
index e975ef06971..00000000000
--- a/Documentation/doc/scripts/test_doxygen_versions_from_release.sh
+++ /dev/null
@@ -1,86 +0,0 @@
-#!/bin/bash
-if [ "$1" == '--help' ]; then 
-  echo "Usage: $0 <doxygen_1> [doxygen_2] [publish_dir]"
-  echo "Compares the output of doxygen_1 and doxygen_2 of this CGAL version, "
-  echo "where  doxygen_1 and doxygen_2 are valid paths to doxygen executables."
-  echo "If doxygen_2 is not specified, the master branch of doxygen will be cloned, built and used as doxygen_2."
-  echo "publish_dir is the path to the dir where the testsuite results are kept"
-  exit 0
-fi
-#build reference
-PATH_TO_1="$1"
-PATH_TO_2="$2"
-IS_ARG2=1
-PUBLISH_DIR="$4"
-if [ -z $PATH_TO_2 ]; then
-  IS_ARG2=0
-fi
-
-if [ -z $PATH_TO_1 ] || [ $(basename $PATH_TO_1) != "doxygen" ] || [ ! -e $PATH_TO_1 ]; then
-  echo "Please specify a valid path to a doxygen executable."
-  echo "$0 --help for more information."
-  exit 0
-fi
-
-ROOT=/home/cgal-testsuite
-mkdir ./build_doc
-cd ./build_doc
-cmake -DCGAL_GENERATE_XML=ON -DDOXYGEN_EXECUTABLE="$PATH_TO_1" ../..  &> /dev/null
-make -j7 doc  &> /dev/null
-cd ../ #scripts
-bash compare_testsuites.sh $PWD/build_doc/doc_output
-mv ./doc_data ./doc_ref
-
-#download and build doxygen_master
-if [ $IS_ARG2 == 0 ] || [ $(basename $PATH_TO_2) != "doxygen" ] || [ ! -e $PATH_TO_2 ]; then
-  echo "No second path detected. Cloning Doxygen master branch..."
-  git clone https://github.com/doxygen/doxygen.git doxygen_master  &> /dev/null
-  cd doxygen_master
-  MASTER_DESCRIBE=$(git describe --tags)
-  mkdir build
-  cd build
-  cmake ..  &> /dev/null
-  make -j7 &> /dev/null
-  cd ../.. #scripts
-  PATH_TO_2="$PWD/doxygen_master/build/bin/doxygen"
-  echo "done."
-fi
-#build doc with doxygen master
-mv ./build_doc ./doc_dir
-mkdir build_doc
-cd ./build_doc
-cmake -DCGAL_GENERATE_XML=ON -DDOXYGEN_EXECUTABLE="$PATH_TO_2" ../..  &> /dev/null
-make -j7 doc  &> /dev/null
-cd ../ #scripts
-DOXYGEN_1=$($PATH_TO_1 --version)
-DOXYGEN_2=$($PATH_TO_2 --version)
-bash ./compare_testsuites.sh $PWD/build_doc/doc_output $PWD/doc_ref $DOXYGEN_1 $DOXYGEN_2
-#rebuild doc with Doxygen_1 to get the right doc_tags without GENERATE_XML because it ignores the EXCLUDE_SYMBOLS, 
-#which disrupts the logs
-mv ./build_doc ./doc_master
-rm -rf ./doc_dir
-mkdir ./doc_dir
-cd ./doc_dir
-cmake -DCGAL_DOC_CREATE_LOGS=true -DDOXYGEN_EXECUTABLE="$PATH_TO_1" ../..  &> /dev/null
-make -j7 doc  &> /dev/null
-make -j7 doc  &> /dev/null
-cd ..
-#get VERSION's content
-cd $ROOT
-CGAL_NAME="$(cat $PWD/VERSION)"
-
-#update overview
-cd $ROOT/doc/scripts
-python ./testsuite.py --output-dir $PWD/doc_dir/doc_output/ --doc-log-dir $PWD/doc_dir/doc_log/ \
-  --publish $PUBLISH_DIR --diff $PWD/diff.txt --master-dir $PWD/doc_master/doc_output/ \
-  --cgal-version "$CGAL_NAME" --do-copy-results --version-to-keep 10 --doxygen-version "$DOXYGEN_1" --master-describe "$MASTER_DESCRIBE"
-
-#clean-up
-rm -rf ./build_doc
-rm -rf ./doc_dir
-rm -rf ./doc_master
-rm -rf ./doc_ref
-rm -rf ./doc_data
-if [ $IS_ARG2 == 0 ]; then
-  rm -rf ./doxygen_master
-fi
diff --git a/Scripts/developer_scripts/run_doxygen_testsuite b/Scripts/developer_scripts/run_doxygen_testsuite
index b2862d85d74..f533e2d5f36 100755
--- a/Scripts/developer_scripts/run_doxygen_testsuite
+++ b/Scripts/developer_scripts/run_doxygen_testsuite
@@ -63,7 +63,7 @@ export PYTHONPATH
 PATH=/home/cgal-testsuite/local/bin:$PATH
 export PATH
 cd "$PWD/doc/scripts"
-bash ./test_doxygen_versions_from_release.sh /home/cgal-testsuite/local/bin/doxygen '' '' /srv/CGAL/www/Members/Manual_doxygen_test
+bash ./test_doxygen_versions.sh /home/cgal-testsuite/local/bin/doxygen '' /srv/CGAL/www/Members/Manual_doxygen_test
 case "$CGAL_RELEASE_ID" in
     *-I-*) ln -snf "../Manual_doxygen_test/$CGAL_RELEASE_ID/output" /srv/CGAL/www/doc/master
            ;;