gentoo-overlay/sci-chemistry/apbs/files/apbs-1.4.1-python.patch

 apbs/contrib/iapbs/src/apbs_driver.c |  6 +++---
 apbs/src/CMakeLists.txt              |  1 +
 apbs/tools/CMakeLists.txt            |  2 +-
 apbs/tools/python/CMakeLists.txt     |  1 +
 apbs/tools/python/apbslib.c          |  4 ++--
 apbs/tools/python/apbslib.i          |  4 ++--
 apbs/tools/python/setup.py           | 16 ++++++++++++++++
 7 files changed, 26 insertions(+), 8 deletions(-)

diff --git a/contrib/iapbs/src/apbs_driver.c b/contrib/iapbs/src/apbs_driver.c
index c9e443b..e1ad67f 100644
--- a/contrib/iapbs/src/apbs_driver.c
+++ b/contrib/iapbs/src/apbs_driver.c
@@ -595,7 +595,7 @@ int apbsdrv_(
 		printPBEPARM(pbeparm);
 
 		/* Refine mesh */
-		if (!preRefineFE(i, nosh, feparm, fetk)) {
+		if (!preRefineFE(i, feparm, fetk)) {
 		    Vnm_tprint( 2, "Error pre-refining mesh!\n");
 		    VJMPERR1(0);
 		}
@@ -609,7 +609,7 @@ int apbsdrv_(
 		Vnm_tprint(1, "  Beginning solve-estimate-refine cycle:\n");
 		for (isolve=0; isolve<feparm->maxsolve; isolve++) {
 		    Vnm_tprint(1, "    Solve #%d...\n", isolve);
-		    if (!solveFE(i, nosh, pbeparm, feparm, fetk)) {
+		    if (!solveFE(i, pbeparm, feparm, fetk)) {
 			Vnm_tprint(2, "ERROR SOLVING EQUATION!\n");
 			VJMPERR1(0);
 		    }
@@ -622,7 +622,7 @@ int apbsdrv_(
 		    /* We're not going to refine if we've hit the max number
 		     * of solves */
 		    if (isolve < (feparm->maxsolve)-1) {
-			if (!postRefineFE(i, nosh, feparm, fetk)) break;
+			if (!postRefineFE(i, feparm, fetk)) break;
 		    }
 		    bytesTotal = Vmem_bytesTotal();
 		    highWater = Vmem_highWaterTotal();
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 44d20fa..2577343 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -68,6 +68,7 @@ configure_file(
 
 if(ENABLE_iAPBS)
     ADD_LIBRARY(apbs_routines routines.c routines.h)
+    target_link_libraries(apbs_routines apbs_mg apbs_fem)
     INSTALL(TARGETS apbs_routines DESTINATION ${LIBRARY_INSTALL_PATH})
     INSTALL(FILES apbscfg.h DESTINATION ${HEADER_INSTALL_PATH})
 endif()
diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt
index 1982a3c..4acbe68 100644
--- a/tools/CMakeLists.txt
+++ b/tools/CMakeLists.txt
@@ -4,5 +4,5 @@ add_subdirectory(mesh)
 add_subdirectory(manip)
 
 if(ENABLE_PYTHON)
-    add_subdirectory(manip)
+    add_subdirectory(python)
 endif(ENABLE_PYTHON)
diff --git a/tools/python/CMakeLists.txt b/tools/python/CMakeLists.txt
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/tools/python/CMakeLists.txt
@@ -0,0 +1 @@
+
diff --git a/tools/python/apbslib.c b/tools/python/apbslib.c
index fef5cc8..feaaa2c 100644
--- a/tools/python/apbslib.c
+++ b/tools/python/apbslib.c
@@ -2504,8 +2504,8 @@ static swig_module_info swig_module = {swig_types, 24, 0, 0, 0, 0};
 #include "maloc/maloc.h"
 #include "apbscfg.h" 
 #include "routines.h"
-#include "apbs/valist.h"
-#include "apbs/vatom.h"
+#include "generic/valist.h"
+#include "generic/vatom.h"
 
 
 #include <limits.h>
diff --git a/tools/python/apbslib.i b/tools/python/apbslib.i
index 17fe521..44d05ea 100644
--- a/tools/python/apbslib.i
+++ b/tools/python/apbslib.i
@@ -15,8 +15,8 @@ Header files:
 #include "maloc/maloc.h"
 #include "apbscfg.h" 
 #include "routines.h"
-#include "apbs/valist.h"
-#include "apbs/vatom.h"
+#include "generic/valist.h"
+#include "generic/vatom.h"
 %} 
 
 /* 
diff --git a/tools/python/setup.py b/tools/python/setup.py
new file mode 100644
index 0000000..4a20198
--- /dev/null
+++ b/tools/python/setup.py
@@ -0,0 +1,16 @@
+from distutils.core import setup, Extension
+setup(name='apbs',
+    version='1.4.1',
+    package_dir={'apbs': '', 'vgrid': 'vgrid'},
+    packages=['apbs', 'vgrid'],
+    py_modules=['apbslib', 'main', 'noinput'],
+    ext_modules=[
+        Extension(
+            '_apbslib',
+            ['apbslib.i'],
+            swig_opts=['-module', 'apbslib', '-I../include'],
+            include_dirs=["../../src"],
+            libraries=["apbs_generic", "apbs_routines"]
+            )
+        ],
+    )