Split python bindings into multiple pieces. Should solve PR#1905826.

scripts/Makefile.am

@@ -20,8 +20,9 @@ dist-hook:
 
 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 \
@@ -34,19 +35,17 @@ perl/openbabel_perl.cpp: openbabel-perl.i $(script_headers)
 	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 $<;
+
+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 $<;
-	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;
 
 java/openbabel_java.cpp: openbabel-java.i $(script_headers)
 	$(SWIG) -small -O -java -naturalvar -templatereduce -c++ -o $@ \

scripts/Makefile.in

@@ -34,8 +34,12 @@ host_triplet = @host@
 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 @@ LIBDL = @LIBDL@
 LIBOBJS = @LIBOBJS@
 LIBS = @LIBS@
 LIBTOOL = @LIBTOOL@
+LIPO = @LIPO@
 LN_S = @LN_S@
 LTLIBOBJS = @LTLIBOBJS@
 MAINT = @MAINT@
@@ -98,6 +103,8 @@ NM = @NM@
 NMEDIT = @NMEDIT@
 OBJDUMP = @OBJDUMP@
 OBJEXT = @OBJEXT@
+OTOOL = @OTOOL@
+OTOOL64 = @OTOOL64@
 PACKAGE = @PACKAGE@
 PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@
 PACKAGE_NAME = @PACKAGE_NAME@
@@ -173,6 +180,7 @@ sharedstatedir = @sharedstatedir@
 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 @@ EXTRA_DIST = openbabel-perl.i perl \
 # 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 \
@@ -386,19 +396,17 @@ dist-hook:
 @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@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@	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@java/openbabel_java.cpp: openbabel-java.i $(script_headers)
 @BUILD_SWIG_TRUE@@MAINTAINER_MODE_TRUE@	$(SWIG) -small -O -java -naturalvar -templatereduce -c++ -o $@ \

scripts/openbabel-python.i

@@ -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 @@ OpenBabel::OBUnitCell *toUnitCell(OpenBabel::OBGenericData *data) {
 //# %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 @@ OpenBabel::OBUnitCell *toUnitCell(OpenBabel::OBGenericData *data) {
 %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>
 

scripts/openbabel-python2.i

@@ -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);
+  }
+};    
+
+

scripts/openbabel-python3.i

@@ -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
+%}
+

scripts/perl/Makefile.PL

@@ -8,10 +8,10 @@ $CC = 'g++';
 $srcdir = '../../src';
 
 # check if we're compiling in the source directory
-$ldfrom = "\$(OBJECT) -L$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) -L$srcdir/.libs -lopenbabel -lz"
+    if (-r "$srcdir/.libs/libopenbabel.so") and (-s _) and (-B _);
 $ldfrom = "\$(OBJECT) $srcdir/.libs/libopenbabel.a -lz"
     if (-r "$srcdir/.libs/libopenbabel.a") and (-s _) and (-B _);
 

scripts/python/openbabel.py

@@ -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

scripts/python/setup.py

@@ -60,8 +60,22 @@ def find_likely_directory():
 
 OBinclude,OBlibrary = find_likely_directory()
 
-obExtension = Extension('_openbabel',
-                        ['openbabel_python.cpp'],
+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']
@@ -74,7 +88,7 @@ setup(name='openbabel',
       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',