- backport upstream patch to split Python binding (should fix #427700 for

good)
- drop no longer needed ppc64 SWIG/GCC flag hackery

openbabel-python-ppc64.patch

@@ -0,0 +1,450 @@
+Index: scripts/openbabel-python2.i
+===================================================================
+--- scripts/openbabel-python2.i	(revision 0)
++++ scripts/openbabel-python2.i	(revision 2535)
+@@ -0,0 +1,92 @@
++%module obconversion
++
++%{
++// used to set import/export for Cygwin DLLs
++#ifdef WIN32
++#define USING_OBDLL
++#endif
++
++#include <openbabel/base.h>
++
++#include <openbabel/generic.h>
++#include <openbabel/griddata.h>
++#include <openbabel/math/vector3.h>
++#include <openbabel/bitvec.h>
++
++#include <openbabel/mol.h>
++#include <openbabel/obconversion.h>
++#include <openbabel/oberror.h>
++#include <openbabel/plugin.h>
++#include <openbabel/fingerprint.h>
++#include <openbabel/descriptor.h>
++#include <openbabel/format.h>
++#include <openbabel/forcefield.h>
++#include <openbabel/op.h>
++
++%}
++
++// These methods are renamed to valid Python method names, as otherwise
++// they cannot be used from Python
++%rename(inc)   *::operator++;
++%rename(good)  *::operator bool;
++
++%import <openbabel/babelconfig.h>
++
++%import <openbabel/base.h>
++%import <openbabel/generic.h>
++%import <openbabel/griddata.h>
++
++%import <openbabel/math/vector3.h>
++%import <openbabel/bitvec.h>
++
++%import <openbabel/chains.h>
++%import <openbabel/typer.h>
++
++%include <openbabel/plugin.h>
++%include <openbabel/oberror.h>
++%include <openbabel/format.h>
++%include <openbabel/obconversion.h>
++%import <openbabel/residue.h>
++%import <openbabel/internalcoord.h>
++%import <openbabel/atom.h>
++%import <openbabel/bond.h>
++%import <openbabel/mol.h>
++%import <openbabel/ring.h>
++%import <openbabel/parsmart.h>
++
++%include <openbabel/fingerprint.h>
++%include <openbabel/descriptor.h>
++%include <openbabel/forcefield.h>
++
++%include <openbabel/op.h>
++%include <openbabel/bitvec.h>
++
++%ignore *::operator=;
++
++%include "carrays.i"
++%array_class(double, doubleArray)
++%pythoncode %{
++def double_array(mylist):
++    """Create a C array of doubles from a list."""
++    c = doubleArray(len(mylist))
++    for i,v in enumerate(mylist):
++        c[i] = v
++    return c
++%}
++
++# Functions to set the log file to std::cout and std::cerr
++       
++%ignore OBForceField::SetLogFile(std::ostream *pos);
++%extend OpenBabel::OBForceField {
++  void SetLogToStdOut() 
++  {
++    self->SetLogFile(&std::cout);
++  }
++
++  void SetLogToStdErr() 
++  {
++    self->SetLogFile(&std::cerr);
++  }
++};    
++
++
+Index: scripts/openbabel-python3.i
+===================================================================
+--- scripts/openbabel-python3.i	(revision 0)
++++ scripts/openbabel-python3.i	(revision 2535)
+@@ -0,0 +1,65 @@
++%module obtemplate
++
++%{
++// used to set import/export for Cygwin DLLs
++#ifdef WIN32
++#define USING_OBDLL
++#endif
++
++#include <openbabel/base.h>
++#include <openbabel/mol.h>
++#include <openbabel/atom.h>
++#include <openbabel/bond.h>
++#include <openbabel/residue.h>
++#include <openbabel/ring.h>
++
++%}
++
++%include "std_list.i"
++%include "std_map.i"
++%include "std_vector.i"
++%include "std_string.i"
++
++namespace std {
++%template (vectorInt)		  vector<int>;
++%template (vectorUnsignedInt)     vector<unsigned int>;
++%template (vvInt)		      vector< vector<int> >;
++%template (vectorDouble) 	vector<double>;
++%template (vectorString)		  vector<std::string>;
++%template (vVector3)		  vector<OpenBabel::vector3>;
++
++%template (vectorMol)		  vector<OpenBabel::OBMol>;
++%template (vectorBond)		vector<OpenBabel::OBBond>;
++%template (vectorResidue)	vector<OpenBabel::OBResidue>;
++%template (vectorRing)		vector<OpenBabel::OBRing>;
++%template (vectorpRing)		vector<OpenBabel::OBRing*>;
++%template (vectorData)    vector<OpenBabel::OBGenericData*>;
++}
++
++// These methods are renamed to valid Python method names, as otherwise
++// they cannot be used from Python
++%rename(inc)   *::operator++;
++%rename(good)  *::operator bool;
++
++%import <openbabel/babelconfig.h>
++
++%import <openbabel/base.h>
++%import <openbabel/residue.h>
++%import <openbabel/atom.h>
++%import <openbabel/bond.h>
++%import <openbabel/mol.h>
++%import <openbabel/ring.h>
++
++%ignore *::operator=;
++
++%include "carrays.i"
++%array_class(double, doubleArray)
++%pythoncode %{
++def double_array(mylist):
++    """Create a C array of doubles from a list."""
++    c = doubleArray(len(mylist))
++    for i,v in enumerate(mylist):
++        c[i] = v
++    return c
++%}
++
+Index: scripts/python/setup.py
+===================================================================
+--- scripts/python/setup.py	(revision 2534)
++++ scripts/python/setup.py	(revision 2535)
+@@ -60,13 +60,27 @@
+ 
+ OBinclude,OBlibrary = find_likely_directory()
+ 
+-obExtension = Extension('_openbabel',
+-                        ['openbabel_python.cpp'],
+-                        include_dirs=OBinclude,
+-                        library_dirs=OBlibrary,
+-                        libraries=['openbabel']
+-                        )
++obCore = Extension('_obcore',
++                   ['obcore.cpp'],
++                   include_dirs=OBinclude,
++                   library_dirs=OBlibrary,
++                   libraries=['openbabel']
++                   )
+ 
++obConversion = Extension('_obconversion',
++                         ['obconversion.cpp'],
++                         include_dirs=OBinclude,
++                         library_dirs=OBlibrary,
++                         libraries=['openbabel']
++                         )
++
++obTemplate = Extension('_obtemplate',
++                       ['obtemplate.cpp'],
++                       include_dirs=OBinclude,
++                       library_dirs=OBlibrary,
++                       libraries=['openbabel']
++                       )
++
+ setup(name='openbabel',
+       version='1.3',
+       author='Noel O\'Boyle',
+@@ -74,7 +88,7 @@
+       url='http://openbabel.sourceforge.net/',
+       license='http://www.gnu.org/copyleft/gpl.html',
+       py_modules=['openbabel','pybel'],
+-      ext_modules=[obExtension],
++      ext_modules=[obCore, obConversion, obTemplate],
+       description = 'openbabel: Python interface to the Open Babel chemistry library',
+       classifiers=[
+       'Development Status :: 5 - Production/Stable',
+Index: scripts/python/openbabel.py
+===================================================================
+--- scripts/python/openbabel.py	(revision 0)
++++ scripts/python/openbabel.py	(revision 2535)
+@@ -0,0 +1,11 @@
++import sys
++if sys.platform.find("linux") != -1:
++    try:
++        import dl
++    except ImportError:
++        import DLFCN as dl
++    sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)
++
++import obcore
++import obconversion
++import obtemplate
+Index: scripts/Makefile.in
+===================================================================
+--- scripts/Makefile.in	(revision 2534)
++++ scripts/Makefile.in	(revision 2535)
+@@ -34,8 +34,12 @@
+ subdir = scripts
+ DIST_COMMON = $(srcdir)/Makefile.am $(srcdir)/Makefile.in
+ ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
+-am__aclocal_m4_deps = $(top_srcdir)/acinclude.m4 \
+-	$(top_srcdir)/configure.in
++am__aclocal_m4_deps = $(top_srcdir)/autoconf/libtool.m4 \
++	$(top_srcdir)/autoconf/ltoptions.m4 \
++	$(top_srcdir)/autoconf/ltsugar.m4 \
++	$(top_srcdir)/autoconf/ltversion.m4 \
++	$(top_srcdir)/autoconf/lt~obsolete.m4 \
++	$(top_srcdir)/acinclude.m4 $(top_srcdir)/configure.in
+ am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
+ 	$(ACLOCAL_M4)
+ mkinstalldirs = $(SHELL) $(top_srcdir)/mkinstalldirs
+@@ -89,6 +93,7 @@
+ LIBOBJS = @LIBOBJS@
+ LIBS = @LIBS@
+ LIBTOOL = @LIBTOOL@
++LIPO = @LIPO@
+ LN_S = @LN_S@
+ LTLIBOBJS = @LTLIBOBJS@
+ MAINT = @MAINT@
+@@ -98,6 +103,8 @@
+ NMEDIT = @NMEDIT@
+ OBJDUMP = @OBJDUMP@
+ OBJEXT = @OBJEXT@
++OTOOL = @OTOOL@
++OTOOL64 = @OTOOL64@
+ PACKAGE = @PACKAGE@
+ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
+ PACKAGE_NAME = @PACKAGE_NAME@
+@@ -173,6 +180,7 @@
+ srcdir = @srcdir@
+ sysconfdir = @sysconfdir@
+ target_alias = @target_alias@
++top_build_prefix = @top_build_prefix@
+ top_builddir = @top_builddir@
+ top_srcdir = @top_srcdir@
+ EXTRA_DIST = openbabel-perl.i perl \
+@@ -185,9 +193,11 @@
+ # build the scripting language interfaces if --enable-maintainer-mode was set
+ # and SWIG is available -- please use the most recent version of SWIG
+ @BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@BUILT_SOURCES = perl/openbabel_perl.cpp \
+-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	python/openbabel_python.cpp \
+ @BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	java/openbabel_java.cpp \
+ @BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	csharp/openbabel_csharp.cpp \
++@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	python/obcore.cpp \
++@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	python/obconversion.cpp \
++@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	python/obtemplate.cpp \
+ @BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	$(am__append_1)
+ @BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@script_includes = $(top_srcdir)/include/openbabel
+ @BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@script_headers = $(script_includes)/mol.h $(script_includes)/obconversion.h \
+@@ -386,20 +396,18 @@
+ @BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	sed -e "s/^@EXPORT.*/& sub dl_load_flags { 0x01 }/" <perl/OpenBabel.pm >perl/OpenBabel.new;
+ @BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	mv perl/OpenBabel.new perl/OpenBabel.pm;
+ 
+-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@python/openbabel_python.cpp: openbabel-python.i $(script_headers)
++@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@python/obconversion.cpp: openbabel-python2.i $(script_headers)
+ @BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	$(SWIG) -small -O -python -templatereduce -naturalvar \
+ @BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@		-c++ -o $@ -I$(top_srcdir)/include -I$(top_builddir)/include $<;
+-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	echo "import sys" >python/ob.py;
+-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	echo "if sys.platform.find(\"linux\") != -1:"  >>python/ob.py;
+-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	echo "    try:" >>python/ob.py;
+-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	echo "        import dl" >>python/ob.py;
+-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	echo "    except ImportError:" >>python/ob.py;
+-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	echo "        import DLFCN as dl" >>python/ob.py;
+-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	echo "    sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)" >>python/ob.py;
+-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	echo >>python/ob.py;
+-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	cat python/openbabel.py >>python/ob.py;
+-@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	mv python/ob.py python/openbabel.py;
+ 
++@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@python/obtemplate.cpp: openbabel-python3.i $(script_headers)
++@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	$(SWIG) -small -O -python -templatereduce -naturalvar \
++@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@		-c++ -o $@ -I$(top_srcdir)/include -I$(top_builddir)/include $<;
++
++@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@python/obcore.cpp: openbabel-python.i $(script_headers)
++@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	$(SWIG) -small -O -python -templatereduce -naturalvar \
++@BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@		-c++ -o $@ -I$(top_srcdir)/include -I$(top_builddir)/include $<;
++
+ @BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@java/openbabel_java.cpp: openbabel-java.i $(script_headers)
+ @BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	$(SWIG) -small -O -java -naturalvar -templatereduce -c++ -o $@ \
+ @BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	-I$(top_srcdir)/include -I$(top_builddir)/include $<;
+Index: scripts/perl/Makefile.PL
+===================================================================
+--- scripts/perl/Makefile.PL	(revision 2534)
++++ scripts/perl/Makefile.PL	(revision 2535)
+@@ -9,9 +9,9 @@
+ 
+ # check if we're compiling in the source directory
+ $ldfrom = "\$(OBJECT) -L$srcdir/.libs -lopenbabel -lz"
++    if (-r "$srcdir/.libs/libopenbabel.dylib") and (-s _) and (-B _);
++$ldfrom = "\$(OBJECT) -L$srcdir/.libs -lopenbabel -lz"
+     if (-r "$srcdir/.libs/libopenbabel.so") and (-s _) and (-B _);
+-$ldfrom = "\$(OBJECT) -L$srcdir/.libs -lopenbabel -lz"
+-    if (-r "$srcdir/.libs/libopenbabel.dylib") and (-s _) and (-B _);
+ $ldfrom = "\$(OBJECT) $srcdir/.libs/libopenbabel.a -lz"
+     if (-r "$srcdir/.libs/libopenbabel.a") and (-s _) and (-B _);
+ 
+Index: scripts/Makefile.am
+===================================================================
+--- scripts/Makefile.am	(revision 2534)
++++ scripts/Makefile.am	(revision 2535)
+@@ -20,8 +20,9 @@
+ 
+ if MAINTAINER_MODE
+ if BUILD_SWIG
+-BUILT_SOURCES = perl/openbabel_perl.cpp python/openbabel_python.cpp \
+-	java/openbabel_java.cpp csharp/openbabel_csharp.cpp
++BUILT_SOURCES = perl/openbabel_perl.cpp \
++	java/openbabel_java.cpp csharp/openbabel_csharp.cpp \
++	python/obcore.cpp python/obconversion.cpp python/obtemplate.cpp
+ 
+ script_includes = $(top_srcdir)/include/openbabel
+ script_headers = $(script_includes)/mol.h $(script_includes)/obconversion.h \
+@@ -34,20 +35,18 @@
+ 	sed -e "s/^@EXPORT.*/& sub dl_load_flags { 0x01 }/" <perl/OpenBabel.pm >perl/OpenBabel.new;
+ 	mv perl/OpenBabel.new perl/OpenBabel.pm;
+ 
+-python/openbabel_python.cpp: openbabel-python.i $(script_headers)
++python/obconversion.cpp: openbabel-python2.i $(script_headers)
+ 	$(SWIG) -small -O -python -templatereduce -naturalvar \
+ 		-c++ -o $@ -I$(top_srcdir)/include -I$(top_builddir)/include $<;
+-	echo "import sys" >python/ob.py;
+-	echo "if sys.platform.find(\"linux\") != -1:"  >>python/ob.py;
+-	echo "    try:" >>python/ob.py;
+-	echo "        import dl" >>python/ob.py;
+-	echo "    except ImportError:" >>python/ob.py;
+-	echo "        import DLFCN as dl" >>python/ob.py;
+-	echo "    sys.setdlopenflags(sys.getdlopenflags() | dl.RTLD_GLOBAL)" >>python/ob.py;
+-	echo >>python/ob.py;
+-	cat python/openbabel.py >>python/ob.py;
+-	mv python/ob.py python/openbabel.py;
+ 
++python/obtemplate.cpp: openbabel-python3.i $(script_headers)
++	$(SWIG) -small -O -python -templatereduce -naturalvar \
++		-c++ -o $@ -I$(top_srcdir)/include -I$(top_builddir)/include $<;
++
++python/obcore.cpp: openbabel-python.i $(script_headers)
++	$(SWIG) -small -O -python -templatereduce -naturalvar \
++		-c++ -o $@ -I$(top_srcdir)/include -I$(top_builddir)/include $<;
++
+ java/openbabel_java.cpp: openbabel-java.i $(script_headers)
+ 	$(SWIG) -small -O -java -naturalvar -templatereduce -c++ -o $@ \
+ 	-I$(top_srcdir)/include -I$(top_builddir)/include $<;
+Index: scripts/openbabel-python.i
+===================================================================
+--- scripts/openbabel-python.i	(revision 2534)
++++ scripts/openbabel-python.i	(revision 2535)
+@@ -1,4 +1,4 @@
+-%module openbabel
++%module obcore
+ 
+ %{
+ // used to set import/export for Cygwin DLLs
+@@ -41,28 +41,6 @@
+ 
+ %}
+ 
+-%include "std_list.i"
+-%include "std_map.i"
+-%include "std_vector.i"
+-%include "std_string.i"
+-
+-namespace std {
+-%template (vectorInt)		  vector<int>;
+-%template (vectorUnsignedInt)     vector<unsigned int>;
+-%template (vvInt)		      vector< vector<int> >;
+-%template (vectorDouble) 	vector<double>;
+-%template (vectorString)		  vector<std::string>;
+-%template (vVector3)		  vector<OpenBabel::vector3>;
+-
+-%template (vectorMol)		  vector<OpenBabel::OBMol>;
+-%template (vectorBond)		vector<OpenBabel::OBBond>;
+-%template (vectorResidue)	vector<OpenBabel::OBResidue>;
+-%template (vectorRing)		vector<OpenBabel::OBRing>;
+-%template (vectorpRing)		vector<OpenBabel::OBRing*>;
+-%template (vectorData)    vector<OpenBabel::OBGenericData*>;
+-}
+-
+-
+ %inline %{
+ OpenBabel::OBPairData *toPairData(OpenBabel::OBGenericData *data) {
+ 	return (OpenBabel::OBPairData *) data;
+@@ -95,11 +73,11 @@
+ //# %import <openbabel/bitvec.h>
+ %import <openbabel/typer.h>
+ 
+-%include <openbabel/plugin.h>
++%import <openbabel/plugin.h>
+ 
+-%include <openbabel/oberror.h>
+-%include <openbabel/format.h>
+-%include <openbabel/obconversion.h>
++%import <openbabel/oberror.h>
++%import <openbabel/format.h>
++%import <openbabel/obconversion.h>
+ %include <openbabel/residue.h>
+ %include <openbabel/internalcoord.h>
+ %include <openbabel/atom.h>
+@@ -110,11 +88,11 @@
+ %include <openbabel/alias.h>
+ %include <openbabel/atomclass.h>
+ 
+-%include <openbabel/fingerprint.h>
+-%include <openbabel/descriptor.h>
+-%include <openbabel/forcefield.h>
++%import <openbabel/fingerprint.h>
++%import <openbabel/descriptor.h>
++%import <openbabel/forcefield.h>
+ 
+-%include <openbabel/op.h>
++%import <openbabel/op.h>
+ 
+ %include <openbabel/bitvec.h>
+ 

openbabel.spec

@@ -9,7 +9,7 @@
 
 Name: openbabel
 Version: 2.2.0
-Release: 0.4.%{beta_ver}%{?dist}
+Release: 0.5.%{beta_ver}%{?dist}
 Summary: Chemistry software file format converter
 License: GPLv2
 Group: Applications/File
@@ -17,6 +17,10 @@ URL: http://openbabel.sourceforge.net/
 Source: http://dl.sourceforge.net/sourceforge/openbabel/%{name}-%{version}%{beta_str}.tar.gz
 Patch: %{name}-gcc43.patch
 Patch1: %{name}-rpm.patch
+# backport upstream patch to split the huge Python binding:
+# http://openbabel.svn.sourceforge.net/viewvc/openbabel?view=rev&revision=2535
+# fixes ppc64 build (#427700)
+Patch2: openbabel-python-ppc64.patch
 BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
 BuildRequires: inchi-devel
 BuildRequires: libtool
@@ -90,16 +94,9 @@ Ruby wrapper for the Open Babel library.
 %setup -q -n %{name}-%{version}%{beta_ver}
 %patch -p1 -b .gcc43
 %patch1 -p1 -b .r
+%patch2 -p0 -b .python-ppc64
 
 %build
-%if 0%{?fedora} >= 9
-%ifarch ppc64
-# hackery to get rid of excess TOC1 entries
-sed -i -e 's/-python /-python -fastdispatch /g' scripts/Makefile.am
-export CFLAGS="$RPM_OPT_FLAGS -mno-sum-in-toc"
-export CXXFLAGS="$RPM_OPT_FLAGS -mno-sum-in-toc"
-%endif
-%endif
 # don't reference m4 include directory which isn't shipped in the tarball
 # there's also a typo ("autconf" instead of "autoconf")
 sed -i -e 's/ACLOCAL_AMFLAGS=/#ACLOCAL_AMFLAGS=/g' Makefile.am
@@ -194,6 +191,10 @@ popd
 %{ruby_sitearch}/openbabel.so
 
 %changelog
+* Fri Jun 06 2008 Kevin Kofler <Kevin@tigcc.ticalc.org> 2.2.0-0.5.b5
+- backport upstream patch to split Python binding (should fix #427700 for good)
+- drop no longer needed ppc64 SWIG/GCC flag hackery
+
 * Thu May 29 2008 Kevin Kofler <Kevin@tigcc.ticalc.org> 2.2.0-0.4.b5
 - update to 2.2.0 beta5