From d7317f4eb68c357fde8a4cb334e224b34f67365a Mon Sep 17 00:00:00 2001
From: Richard Roberts <richard.jw.roberts@gmail.com>
Date: Tue, 10 Jan 2012 22:25:12 +0000
Subject: [PATCH] doxygen documentation no longer build with autotools, added
 makedoc.sh to build it in top-level directory

---
 Doxyfile     | 16 ++++++++--------
 Makefile.am  |  6 +++---
 aminclude.am |  6 +++---
 configure.ac | 18 +++++++++---------
 makedoc.sh   | 13 +++++++++++++
 5 files changed, 36 insertions(+), 23 deletions(-)
 create mode 100755 makedoc.sh

diff --git a/Doxyfile b/Doxyfile
index 341ae16dd..2ecf956f5 100644
--- a/Doxyfile
+++ b/Doxyfile
@@ -567,7 +567,7 @@ FILE_VERSION_FILTER    =
 # You can optionally specify a file name after the option, if omitted 
 # DoxygenLayout.xml will be used as the name of the layout file.
 
-LAYOUT_FILE            = $(SRCDIR)/DoxygenLayout.xml
+LAYOUT_FILE            = DoxygenLayout.xml
 
 # The CITE_BIB_FILES tag can be used to specify one or more bib files 
 # containing the references data. This must be a list of .bib files. The 
@@ -638,13 +638,13 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories 
 # with spaces.
 
-INPUT                  = $(SRCDIR)/gtsam/base \
-                         $(SRCDIR)/gtsam/geometry \
-                         $(SRCDIR)/gtsam/inference \
-                         $(SRCDIR)/gtsam/linear \
-                         $(SRCDIR)/gtsam/nonlinear \
-                         $(SRCDIR)/gtsam/slam \
-                         $(SRCDIR)/gtsam
+INPUT                  = gtsam/base \
+                         gtsam/geometry \
+                         gtsam/inference \
+                         gtsam/linear \
+                         gtsam/nonlinear \
+                         gtsam/slam \
+                         gtsam
 
 # This tag can be used to specify the character encoding of the source files 
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is 
diff --git a/Makefile.am b/Makefile.am
index 28ff05ae9..8e68e7d6d 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -11,7 +11,7 @@ ACLOCAL_AMFLAGS = -I m4
 AUTOMAKE_OPTIONS = foreign nostdinc
 
 # For Doxygen integration
-include aminclude.am
+#include aminclude.am
 
 # All the sub-directories that need to be built
 SUBDIRS = CppUnitLite gtsam tests examples
@@ -24,8 +24,8 @@ endif
 EXTRA_DIST = autogen.sh configure.ac COPYING INSTALL LGPL LICENSE README THANKS USAGE doc
 
 # For Doxygen integration
-MOSTLYCLEANFILES = $(DX_CLEANFILES)
-EXTRA_DIST += $(DX_CONFIG)
+#MOSTLYCLEANFILES = $(DX_CLEANFILES)
+#EXTRA_DIST += $(DX_CONFIG)
 
 # Remove .svn directories from dist
 dist-hook:
diff --git a/aminclude.am b/aminclude.am
index 420049eca..09e6bf065 100644
--- a/aminclude.am
+++ b/aminclude.am
@@ -5,7 +5,7 @@
 # are controlled by the various DX_COND_??? conditionals set by autoconf.
 #
 # The provided goals are:
-# doxygen-doc: Generate all doxygen documentation.
+# doc:         Generate all doxygen documentation.
 # doxygen-run: Run doxygen, which will generate some of the documentation
 #              (HTML, CHM, CHI, MAN, RTF, XML) but will not do the post
 #              processing required for the rest of it (PS, PDF, and some MAN).
@@ -158,13 +158,13 @@ DX_CLEAN_LATEX = @DX_DOCDIR@/latex
 
 endif DX_COND_latex
 
-.PHONY: doxygen-run doxygen-doc $(DX_PS_GOAL) $(DX_PDF_GOAL)
+.PHONY: doxygen-run doc $(DX_PS_GOAL) $(DX_PDF_GOAL)
 
 .INTERMEDIATE: doxygen-run $(DX_PS_GOAL) $(DX_PDF_GOAL)
 
 doxygen-run: @DX_DOCDIR@/@PACKAGE@.tag
 
-doxygen-doc: doxygen-run $(DX_PS_GOAL) $(DX_PDF_GOAL)
+doc: doxygen-run $(DX_PS_GOAL) $(DX_PDF_GOAL)
 
 @DX_DOCDIR@/@PACKAGE@.tag: $(DX_CONFIG) $(pkginclude_HEADERS)
 	rm -rf @DX_DOCDIR@
diff --git a/configure.ac b/configure.ac
index 5929b22ee..6bcbfe015 100644
--- a/configure.ac
+++ b/configure.ac
@@ -19,15 +19,15 @@ AC_CONFIG_SRCDIR([examples/SimpleRotation.cpp])
 AC_CONFIG_SRCDIR([gtsam/3rdparty/Makefile.am])
 
 # For doxygen support
-DX_HTML_FEATURE(ON)
-DX_CHM_FEATURE(OFF)
-DX_CHI_FEATURE(OFF)
-DX_MAN_FEATURE(OFF)
-DX_RTF_FEATURE(OFF)
-DX_XML_FEATURE(OFF)
-DX_PDF_FEATURE(OFF)
-DX_PS_FEATURE(OFF)
-DX_INIT_DOXYGEN(gtsam)
+#DX_HTML_FEATURE(ON)
+#DX_CHM_FEATURE(OFF)
+#DX_CHI_FEATURE(OFF)
+#DX_MAN_FEATURE(OFF)
+#DX_RTF_FEATURE(OFF)
+#DX_XML_FEATURE(OFF)
+#DX_PDF_FEATURE(OFF)
+#DX_PS_FEATURE(OFF)
+#DX_INIT_DOXYGEN(gtsam, Doxyfile, doc)
 
 # Check for OS
 # needs to be called at some point earlier
diff --git a/makedoc.sh b/makedoc.sh
new file mode 100755
index 000000000..5acbd3d87
--- /dev/null
+++ b/makedoc.sh
@@ -0,0 +1,13 @@
+#!/bin/sh
+
+# Add to PATH the default install path for doxygen on Mac OS X
+
+PATH=$PATH:/Applications/Doxygen.app/Contents/Resources
+
+
+# Run doxygen from the gtsam directory even if this script is run from another
+# directory, so that the output 'doc' goes in the gtsam directory.
+
+GTSAM_DIR=$(dirname "$0")
+cd $GTSAM_DIR
+doxygen
\ No newline at end of file