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"] + ) + ], + )
