first try at a nicer Doxygen implementation

Makefile.am

@@ -1,5 +1,7 @@
 # additional include paths necessary to compile the C++ library
 SUBDIRS = lib benchmarks tests
 
+include $(top_srcdir)/doxygen.inc
+
 AM_CXXFLAGS += -I$(top_builddir)/include
 ACLOCAL_AMFLAGS = -I m4

configure.ac

@@ -250,12 +250,17 @@ esac
 AM_CONDITIONAL(BUILD_CHROMA_REGRESSION,[ test "X${ac_CHROMA}X" == "XyesX" ])
 
 ############### Doxygen
-AC_PROG_DOXYGEN
-
-if test -n "$DOXYGEN"
-then
-AC_CONFIG_FILES([docs/doxy.cfg])
-fi
+DX_DOXYGEN_FEATURE([OFF])
+DX_DOT_FEATURE([OFF])
+DX_HTML_FEATURE([ON])
+DX_CHM_FEATURE([OFF])
+DX_CHI_FEATURE([OFF])
+DX_MAN_FEATURE([OFF])
+DX_RTF_FEATURE([OFF])
+DX_XML_FEATURE([OFF])
+DX_PDF_FEATURE([OFF])
+DX_PS_FEATURE([OFF])
+DX_INIT_DOXYGEN([$PACKAGE_NAME], [doxygen.cfg])
 
 ############### Ouput
 cwd=`pwd -P`; cd ${srcdir}; abs_srcdir=`pwd -P`; cd ${cwd}

lib/algorithms/iterative/ImplicitlyRestartedLanczos.h

@@ -1076,10 +1076,10 @@ say con = 2
 **/
 
 template<class T>
-static void Lock(DenseMatrix<T> &H, 	///Hess mtx	
-		 DenseMatrix<T> &Q, 	///Lock Transform
-		 T val, 		///value to be locked
-		 int con, 	///number already locked
+static void Lock(DenseMatrix<T> &H, 	// Hess mtx	
+		 DenseMatrix<T> &Q, 	// Lock Transform
+		 T val, 		// value to be locked
+		 int con, 	// number already locked
 		 RealD small,
 		 int dfg,
 		 bool herm)

lib/simd/Grid_avx512.h

@@ -27,15 +27,6 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
     See the full license in the file "LICENSE" in the top level distribution directory
     *************************************************************************************/
     /*  END LEGAL */
-//----------------------------------------------------------------------
-/*! @file Grid_knc.h
-  @brief Optimization libraries for AVX512 instructions set for KNC
-
-  Using intrinsics
-*/
-// Time-stamp: <2015-06-09 14:27:28 neo>
-//----------------------------------------------------------------------
-
 #include <immintrin.h>
 
 

lib/simd/Grid_imci.h

@@ -26,14 +26,6 @@ Author: paboyle <paboyle@ph.ed.ac.uk>
     See the full license in the file "LICENSE" in the top level distribution directory
     *************************************************************************************/
     /*  END LEGAL */
-//----------------------------------------------------------------------
-/*! @file Grid_knc.h
-  @brief Optimization libraries for AVX512 instructions set for KNC
-
-  Using intrinsics
-*/
-// Time-stamp: <2015-06-09 14:27:28 neo>
-//----------------------------------------------------------------------
 
 #include <immintrin.h>
 #include <zmmintrin.h>

m4/ac_prog_doxygen.m4

@@ -1,54 +0,0 @@
-dnl Check for doxygen to create API docs
-dnl
-AC_DEFUN([AC_PROG_DOXYGEN],
-[
-AC_ARG_ENABLE(doxygen,
-AS_HELP_STRING([--enable-doxygen],[enable documentation generation with doxygen (auto)]))
-
-AC_ARG_ENABLE(dot,
-AS_HELP_STRING([--enable-dot],[use 'dot' to generate graphs in doxygen (auto)]))              
-AC_ARG_ENABLE(html-docs,
-AS_HELP_STRING([--enable-html-docs],[enable HTML generation with doxygen (yes)]),
-[],[ enable_html_docs=yes])              
-AC_ARG_ENABLE(latex-docs,
-AS_HELP_STRING([--enable-latex-docs],
-[enable LaTeX documentation generation with doxygen (no)]),[],[enable_latex_docs=no])              
-
-if test "x$enable_doxygen" = xno; then
- enable_doc=no	
-else 
- AC_CHECK_PROG(DOXYGEN, doxygen, doxygen)
- if test x$DOXYGEN = x; then
-  if test "x$enable_doxygen" = xyes; then
-   AC_MSG_ERROR([could not find doxygen])
-  fi
-  enable_doc=no
- else
-  doxy_ver=`doxygen --version`
-  doxy_major=`expr "$doxy_ver" : '\(@<:@0-9@:>@\)\..*'`
-  doxy_minor=`expr "$doxy_ver" : '@<:@0-9@:>@\.\(@<:@0-9@:>@\).*'`
-  if test $doxy_major -eq "1" -a $doxy_minor -ge "3" ; then
-   enable_doc=yes
-   AC_CHECK_PROG(DOT, dot, dot)
-  else
-   AC_MSG_WARN([doxygen version $doxy_ver too old, doxygen will not be used.])
-   enable_doc=no
-  fi
- fi
-fi
-
-AM_CONDITIONAL(DOXYGEN_DOC, test x$enable_doc = xyes)
-
-if test x$DOT = x; then
- if test "x$enable_dot" = xyes; then
-  AC_MSG_ERROR([could not find dot])
- fi
- enable_dot=no
-else
- enable_dot=yes
-fi
-
-AC_SUBST(enable_dot)
-AC_SUBST(enable_html_docs)
-AC_SUBST(enable_latex_docs)
-])