xraylib release 2.13.0

Final commit before merge into master branch

Changelog

@@ -17,7 +17,8 @@ imaginary parts of the refractive index of a given compound.
 -Numerous bugfixes: an important one would be the restoration of IDL support
 on Mac OS X Snow Leopard
 -Creation of IDL bindings rpm
--Added Java bindings (requires Sun JAVA compiler)
+-Added Java bindings (requires Sun JAVA compiler): works on Linux and Mac Os X
+-Verified support on FreeBSD 8.0 64-bit
 
 Version 2.12.1 Tom Schoonjans
 

INSTALL

@@ -39,16 +39,17 @@ Platforms known to compile and run xraylib
 	Solaris 10 (32-bit/64-bit)
 	Mac OS X (32-bit/64-bit)
 	Windows (Cygwin, static version only)
+	FreeBSD (64-bit)
 
 Not all bindings have been tested on each of these platforms. The following table summarizes the current status.
 
-	 | Linux | Mac OS X | Solaris | Cygwin |
-------------------------------------------------
- Fortran |   x   |     x    |    x    |    x   |
-  Perl   |   x   |     x    |    x    |    x   |
- Python  |   x   |     x    |         |    x   |
-   IDL   |   x   |     x    |         |        |
-
+	 | Linux | Mac OS X | Solaris | Cygwin | FreeBSD |
+----------------------------------------------------------
+ Fortran |   x   |     x    |    x    |    x   |    x    |
+  Perl   |   x   |     x    |    x    |    x   |    x    |
+ Python  |   x   |     x    |         |    x   |         |
+   IDL   |   x   |     x    |         |        |         |
+  Java   |   x   |     x    |    ?    |    ?   |         |
 
 
 		-----------------------------------------------
@@ -83,7 +84,7 @@ on the PATH.  A typical PATH should include the directories
 For example,
 
   $ PATH=/opt/SUNWspro/bin:/usr/ccs/bin:/usr/ucb:$PATH
-  $ ./configure CC=cc CFLAGS=-O
+  $ ./configure CC=cc 
 
 Use gmake instead of make. To do this, invoke:
 

Makefile.am

@@ -21,6 +21,6 @@ if ENABLE_FORTRAN
 endif
 
 
-EXTRA_DIST = idl doc xraylib.spec.in xraylib.spec
+EXTRA_DIST = idl doc xraylib.spec.in 
 
 

configure.ac

@@ -541,7 +541,11 @@ AM_CONDITIONAL([ENABLE_JAVA],[test x$VALID_JAVA = xyes])
 
 #C++ example
 AC_PROG_CXX
-if test $CXX ; then
+AC_PROG_CXXCPP
+AC_LANG_PUSH([C++])
+AC_CHECK_HEADERS([cstdio cstdlib], ,[CXX=""])
+AC_LANG_POP([C++])
+if test x$CXX != x ; then
 	AC_MSG_NOTICE([C++ example enabled])
 	AC_SUBST(CXX)
 fi

example/xrlexample6.cpp

@@ -21,41 +21,41 @@ int main()
   //if something goes wrong, the test will end with EXIT_FAILURE
   SetHardExit(1);
 
-  printf("Example of C++ program using xraylib\n");
-  printf("Ca K-alpha Fluorescence Line Energy: %f\n",
+  std::printf("Example of C++ program using xraylib\n");
+  std::printf("Ca K-alpha Fluorescence Line Energy: %f\n",
 	 LineEnergy(20,KA_LINE));
-  printf("Fe partial photoionization cs of L3 at 6.0 keV: %f\n",CS_Photo_Partial(26,L3_SHELL,6.0));
-  printf("Zr L1 edge energy: %f\n",EdgeEnergy(40,L1_SHELL));
-  printf("Pb Lalpha XRF production cs at 20.0 keV (jump approx): %f\n",CS_FluorLine(82,LA_LINE,20.0));
-  printf("Pb Lalpha XRF production cs at 20.0 keV (Kissel): %f\n",CS_FluorLine_Kissel(82,LA_LINE,20.0));
-  printf("Bi M1N2 radiative rate: %f\n",RadRate(83,M1N2_LINE));
-  printf("U M3O3 Fluorescence Line Energy: %f\n",LineEnergy(92,M3O3_LINE));
+  std::printf("Fe partial photoionization cs of L3 at 6.0 keV: %f\n",CS_Photo_Partial(26,L3_SHELL,6.0));
+  std::printf("Zr L1 edge energy: %f\n",EdgeEnergy(40,L1_SHELL));
+  std::printf("Pb Lalpha XRF production cs at 20.0 keV (jump approx): %f\n",CS_FluorLine(82,LA_LINE,20.0));
+  std::printf("Pb Lalpha XRF production cs at 20.0 keV (Kissel): %f\n",CS_FluorLine_Kissel(82,LA_LINE,20.0));
+  std::printf("Bi M1N2 radiative rate: %f\n",RadRate(83,M1N2_LINE));
+  std::printf("U M3O3 Fluorescence Line Energy: %f\n",LineEnergy(92,M3O3_LINE));
   //parser test for Ca(HCO3)2 (calcium bicarbonate)
   struct compoundData cdtest;
   if (CompoundParser("Ca(HCO3)2",&cdtest) == 0)
 	return 1;
   int i;
-  printf("Ca(HCO3)2 contains %i atoms and %i elements\n",cdtest.nAtomsAll,cdtest.nElements);
+  std::printf("Ca(HCO3)2 contains %i atoms and %i elements\n",cdtest.nAtomsAll,cdtest.nElements);
   for (i = 0 ; i < cdtest.nElements ; i++)
-    printf("Element %i: %lf %%\n",cdtest.Elements[i],cdtest.massFractions[i]*100.0);
+    std::printf("Element %i: %lf %%\n",cdtest.Elements[i],cdtest.massFractions[i]*100.0);
 
   FREE_COMPOUND_DATA(cdtest)
 
   //parser test for SiO2 (quartz)
   if (CompoundParser("SiO2",&cdtest) == 0)
 	return 1;
 
-  printf("SiO2 contains %i atoms and %i elements\n",cdtest.nAtomsAll,cdtest.nElements);
+  std::printf("SiO2 contains %i atoms and %i elements\n",cdtest.nAtomsAll,cdtest.nElements);
   for (i = 0 ; i < cdtest.nElements ; i++)
-    printf("Element %i: %lf %%\n",cdtest.Elements[i],cdtest.massFractions[i]*100.0);
+    std::printf("Element %i: %lf %%\n",cdtest.Elements[i],cdtest.massFractions[i]*100.0);
 
   FREE_COMPOUND_DATA(cdtest)
 
-  printf("Ca(HCO3)2 Rayleigh cs at 10.0 keV: %f\n",CS_Rayl_CP("Ca(HCO3)2",10.0) );
+  std::printf("Ca(HCO3)2 Rayleigh cs at 10.0 keV: %f\n",CS_Rayl_CP("Ca(HCO3)2",10.0) );
 
-  printf("CS2 Refractive Index at 10.0 keV : %g - %g i\n",Refractive_Index_Re("CS2",10.0,1.261),Refractive_Index_Im("CS2",10.0,1.261));
-  printf("C16H14O3 Refractive Index at 1 keV : %g - %g i\n",Refractive_Index_Re("C16H14O3",1.0,1.2),Refractive_Index_Im("C16H14O3",1.0,1.2));
-  printf("SiO2 Refractive Index at 5 keV : %g - %g i\n",Refractive_Index_Re("SiO2",5.0,2.65),Refractive_Index_Im("SiO2",5.0,2.65));
+  std::printf("CS2 Refractive Index at 10.0 keV : %g - %g i\n",Refractive_Index_Re("CS2",10.0,1.261),Refractive_Index_Im("CS2",10.0,1.261));
+  std::printf("C16H14O3 Refractive Index at 1 keV : %g - %g i\n",Refractive_Index_Re("C16H14O3",1.0,1.2),Refractive_Index_Im("C16H14O3",1.0,1.2));
+  std::printf("SiO2 Refractive Index at 5 keV : %g - %g i\n",Refractive_Index_Re("SiO2",5.0,2.65),Refractive_Index_Im("SiO2",5.0,2.65));
 
 
 }

include/xraylib-parser.h

@@ -60,9 +60,13 @@ struct compoundData {
  * in a compoundData structure
  */
 
-#define FREE_COMPOUND_DATA(cd) free(cd.Elements);\
+#ifdef __cplusplus
+	#define FREE_COMPOUND_DATA(cd) std::free(cd.Elements);\
+				std::free(cd.massFractions);
+#else
+	#define FREE_COMPOUND_DATA(cd) free(cd.Elements);\
 				free(cd.massFractions);
-
+#endif
 /*
  * The CompoundParser function will parse a string and will put the results in
  * a compoundData structure pointed to by cd. If successful, the function

m4/m4-ax_prog_javah.m4

@@ -33,7 +33,9 @@ if test "x$ac_cv_path_JAVAH" != x ; then
     if test -L $ac_cv_path_JAVAH ; then
 	while test -L $ac_cv_path_JAVAH 
 	 do 
-	 ac_cv_path_JAVAH=`readlink $ac_cv_path_JAVAH`
+dnl	 ac_cv_path_JAVAH=`readlink $ac_cv_path_JAVAH`
+dnl 	since readlink doesn't appear on all systems (I hate Solaris...), let's use an awk trick
+ 	 ac_cv_path_JAVAH=`ls -l $ac_cv_path_JAVAH | awk -F\> '{print $NF}'` 
 	 done
     fi
     ac_save_CPPFLAGS="$CPPFLAGS"

src/xraylib_idl.c

@@ -565,8 +565,6 @@ XRL_4SFFF(DCSPb_Rayl_CP)
 XRL_4SFFF(DCSPb_Compt_CP)
 XRL_2SF(CS_Photo_Total_CP)
 XRL_2SF(CSb_Photo_Total_CP)
-XRL_3SIF(CS_Photo_Partial_CP)
-XRL_3SIF(CSb_Photo_Partial_CP)
 XRL_2SF(CS_Total_Kissel_CP)
 XRL_2SF(CSb_Total_Kissel_CP)
 XRL_3SFF(Refractive_Index_Re)

xraylib.spec.in

@@ -80,7 +80,11 @@ This rpm package provides the IDL bindings of xraylib.
 
 
 %build
-%configure --disable-perl FC=gfortran 
+%configure --disable-perl --disable-java --enable-idl --enable-fortran2003 --enable-python FC=gfortran 
+#necessary to fix rpath issues during rpmbuild
+sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' libtool
+sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool
+
 make 
 
 
@@ -117,6 +121,7 @@ rm -rf $RPM_BUILD_ROOT
 
 %postun -p /sbin/ldconfig
 
+
 %files
 %defattr(-,root,root)