* [gentoo-commits] gentoo-x86 commit in sci-chemistry/apbs/files: apbs-1.4.1-python.patch apbs-1.4.1-manip.patch
@ 2014-10-28 13:10 Justin Lecher (jlec)
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From: Justin Lecher (jlec) @ 2014-10-28 13:10 UTC (permalink / raw
To: gentoo-commits
jlec 14/10/28 13:10:30
Modified: apbs-1.4.1-manip.patch
Added: apbs-1.4.1-python.patch
Log:
sci-chemistry/apbs: Link python libs completely
(Portage version: 2.2.14/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)
Revision Changes Path
1.2 sci-chemistry/apbs/files/apbs-1.4.1-manip.patch
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch?rev=1.2&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch?rev=1.2&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch?r1=1.1&r2=1.2
Index: apbs-1.4.1-manip.patch
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- apbs-1.4.1-manip.patch 21 Aug 2014 08:50:50 -0000 1.1
+++ apbs-1.4.1-manip.patch 28 Oct 2014 13:10:30 -0000 1.2
@@ -1,6 +1,5 @@
apbs/CMakeLists.txt | 2 +-
apbs/tools/CMakeLists.txt | 4 ----
- apbs/tools/manip/CMakeLists.txt | 4 ++--
apbs/tools/mesh/CMakeLists.txt | 4 ++--
4 files changed, 5 insertions(+), 9 deletions(-)
@@ -17,18 +16,6 @@
list(APPEND APBS_LIBS "-lstdc++")
list(APPEND APBS_LIBS "-L${FETK_PATH}/lib")
-diff --git a/apbs/tools/CMakeLists.txt b/apbs/tools/CMakeLists.txt
-index 1982a3c..da3b8ee 100644
---- a/apbs/tools/CMakeLists.txt
-+++ b/apbs/tools/CMakeLists.txt
-@@ -2,7 +2,3 @@ set(EXECUTABLE_OUTPUT_PATH ${TOOLS_PATH}/bin)
-
- add_subdirectory(mesh)
- add_subdirectory(manip)
--
--if(ENABLE_PYTHON)
-- add_subdirectory(manip)
--endif(ENABLE_PYTHON)
diff --git a/apbs/tools/manip/CMakeLists.txt b/apbs/tools/manip/CMakeLists.txt
index 937dac7..5768cc5 100644
--- a/apbs/tools/manip/CMakeLists.txt
1.1 sci-chemistry/apbs/files/apbs-1.4.1-python.patch
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.4.1-python.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.4.1-python.patch?rev=1.1&content-type=text/plain
Index: 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/apbs/contrib/iapbs/src/apbs_driver.c b/apbs/contrib/iapbs/src/apbs_driver.c
index c9e443b..e1ad67f 100644
--- a/apbs/contrib/iapbs/src/apbs_driver.c
+++ b/apbs/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/apbs/src/CMakeLists.txt b/apbs/src/CMakeLists.txt
index 44d20fa..2577343 100644
--- a/apbs/src/CMakeLists.txt
+++ b/apbs/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/apbs/tools/CMakeLists.txt b/apbs/tools/CMakeLists.txt
index 1982a3c..4acbe68 100644
--- a/apbs/tools/CMakeLists.txt
+++ b/apbs/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/apbs/tools/python/CMakeLists.txt b/apbs/tools/python/CMakeLists.txt
new file mode 100644
index 0000000..8b13789
--- /dev/null
+++ b/apbs/tools/python/CMakeLists.txt
@@ -0,0 +1 @@
+
diff --git a/apbs/tools/python/apbslib.c b/apbs/tools/python/apbslib.c
index fef5cc8..feaaa2c 100644
--- a/apbs/tools/python/apbslib.c
+++ b/apbs/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/apbs/tools/python/apbslib.i b/apbs/tools/python/apbslib.i
index 17fe521..44d05ea 100644
--- a/apbs/tools/python/apbslib.i
+++ b/apbs/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/apbs/tools/python/setup.py b/apbs/tools/python/setup.py
new file mode 100644
index 0000000..4a20198
--- /dev/null
+++ b/apbs/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"]
+ )
+ ],
+ )
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2014-10-28 13:10 [gentoo-commits] gentoo-x86 commit in sci-chemistry/apbs/files: apbs-1.4.1-python.patch apbs-1.4.1-manip.patch Justin Lecher (jlec)
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