From 4b9cf91eb7fe68977c283d258a6000c4d331407b Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Tue, 3 Jun 2014 00:15:51 +0100
Subject: [PATCH] Improved devel doxyfile

---
 developer-doc/.gitignore                | 1 -
 developer-doc/{Doxyfile.in => Doxyfile} | 5 ++---
 developer-doc/Makefile                  | 4 ++--
 developer-doc/extract                   | 3 ---
 developer-doc/go-doxygen                | 9 +++++++++
 5 files changed, 13 insertions(+), 9 deletions(-)
 rename developer-doc/{Doxyfile.in => Doxyfile} (99%)
 create mode 100755 developer-doc/go-doxygen

diff --git a/developer-doc/.gitignore b/developer-doc/.gitignore
index ad4cccefa..9a6b15381 100644
--- a/developer-doc/.gitignore
+++ b/developer-doc/.gitignore
@@ -4,5 +4,4 @@
 /automatic
 /*PP.txt
 /links-to-user-manual.txt
-/Doxyfile
 
diff --git a/developer-doc/Doxyfile.in b/developer-doc/Doxyfile
similarity index 99%
rename from developer-doc/Doxyfile.in
rename to developer-doc/Doxyfile
index 540425126..4ca478d7e 100644
--- a/developer-doc/Doxyfile.in
+++ b/developer-doc/Doxyfile
@@ -738,7 +738,6 @@ INPUT                  = ./Intro.txt \
                          ./plmdIntro.txt \
                          ./usingDoxygen.txt \
                          ./parsing.txt \
-                         @SRCDIR@ \
                          ./links-to-user-manual.txt \
                          ./AddingAColvar.txt \
                          ./AddingAFunction.txt \
@@ -911,13 +910,13 @@ STRIP_CODE_COMMENTS    = NO
 # function all documented functions referencing it will be listed.
 # The default value is: NO.
 
-REFERENCED_BY_RELATION = @MAYBE@
+REFERENCED_BY_RELATION = NO
 
 # If the REFERENCES_RELATION tag is set to YES then for each documented function
 # all documented entities called/used by that function will be listed.
 # The default value is: NO.
 
-REFERENCES_RELATION    = @MAYBE@
+REFERENCES_RELATION    = NO
 
 # If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set
 # to YES, then the hyperlinks from functions in REFERENCES_RELATION and
diff --git a/developer-doc/Makefile b/developer-doc/Makefile
index 4cae983e1..5a3d7730a 100644
--- a/developer-doc/Makefile
+++ b/developer-doc/Makefile
@@ -3,8 +3,8 @@
 
 all:
 	./extract
-	doxygen
+	./go-doxygen
 	cp Octocat.png html/
 
 clean:
-	rm -fr automatic html latex *~ links-to-user-manual.txt Doxyfile
+	rm -fr automatic html latex *~ links-to-user-manual.txt
diff --git a/developer-doc/extract b/developer-doc/extract
index 19a519c20..b2b803f18 100755
--- a/developer-doc/extract
+++ b/developer-doc/extract
@@ -1,8 +1,5 @@
 #!/bin/bash
 
-sed s:@SRCDIR@:"$(echo ../src/*/ ../src/*/*/)": Doxyfile.in|
-sed s:@MAYBE@:NO: > Doxyfile
-
 cat ../src/*/*cpp |
 awk '
   /PLUMED_REGISTER_ACTION/{print}
diff --git a/developer-doc/go-doxygen b/developer-doc/go-doxygen
new file mode 100755
index 000000000..776ad8b84
--- /dev/null
+++ b/developer-doc/go-doxygen
@@ -0,0 +1,9 @@
+#! /bin/bash
+
+{
+  cat Doxyfile
+  echo "PROJECT_NUMBER = \"$(plumed info --version)\""
+  echo "INPUT+=" ../src/*/ ../src/*/*/
+  echo "REFERENCES_RELATION=NO"
+  echo "REFERENCED_BY_RELATION=NO"
+} | doxygen -
-- 
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