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jlec 14/10/28 13:10:30 |
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|
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Modified: apbs-1.4.1-manip.patch |
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Added: apbs-1.4.1-python.patch |
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Log: |
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sci-chemistry/apbs: Link python libs completely |
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|
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(Portage version: 2.2.14/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!) |
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|
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Revision Changes Path |
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1.2 sci-chemistry/apbs/files/apbs-1.4.1-manip.patch |
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|
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch?rev=1.2&view=markup |
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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 |
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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 |
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|
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Index: apbs-1.4.1-manip.patch |
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=================================================================== |
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RCS file: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch,v |
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retrieving revision 1.1 |
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retrieving revision 1.2 |
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diff -u -r1.1 -r1.2 |
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--- apbs-1.4.1-manip.patch 21 Aug 2014 08:50:50 -0000 1.1 |
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+++ apbs-1.4.1-manip.patch 28 Oct 2014 13:10:30 -0000 1.2 |
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@@ -1,6 +1,5 @@ |
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apbs/CMakeLists.txt | 2 +- |
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apbs/tools/CMakeLists.txt | 4 ---- |
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- apbs/tools/manip/CMakeLists.txt | 4 ++-- |
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apbs/tools/mesh/CMakeLists.txt | 4 ++-- |
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4 files changed, 5 insertions(+), 9 deletions(-) |
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|
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@@ -17,18 +16,6 @@ |
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|
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list(APPEND APBS_LIBS "-lstdc++") |
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list(APPEND APBS_LIBS "-L${FETK_PATH}/lib") |
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-diff --git a/apbs/tools/CMakeLists.txt b/apbs/tools/CMakeLists.txt |
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-index 1982a3c..da3b8ee 100644 |
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---- a/apbs/tools/CMakeLists.txt |
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-+++ b/apbs/tools/CMakeLists.txt |
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-@@ -2,7 +2,3 @@ set(EXECUTABLE_OUTPUT_PATH ${TOOLS_PATH}/bin) |
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- |
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- add_subdirectory(mesh) |
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- add_subdirectory(manip) |
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-- |
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--if(ENABLE_PYTHON) |
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-- add_subdirectory(manip) |
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--endif(ENABLE_PYTHON) |
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diff --git a/apbs/tools/manip/CMakeLists.txt b/apbs/tools/manip/CMakeLists.txt |
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index 937dac7..5768cc5 100644 |
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--- a/apbs/tools/manip/CMakeLists.txt |
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|
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|
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|
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1.1 sci-chemistry/apbs/files/apbs-1.4.1-python.patch |
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|
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-chemistry/apbs/files/apbs-1.4.1-python.patch?rev=1.1&view=markup |
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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 |
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|
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Index: apbs-1.4.1-python.patch |
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=================================================================== |
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apbs/contrib/iapbs/src/apbs_driver.c | 6 +++--- |
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apbs/src/CMakeLists.txt | 1 + |
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apbs/tools/CMakeLists.txt | 2 +- |
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apbs/tools/python/CMakeLists.txt | 1 + |
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apbs/tools/python/apbslib.c | 4 ++-- |
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apbs/tools/python/apbslib.i | 4 ++-- |
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apbs/tools/python/setup.py | 16 ++++++++++++++++ |
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7 files changed, 26 insertions(+), 8 deletions(-) |
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|
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diff --git a/apbs/contrib/iapbs/src/apbs_driver.c b/apbs/contrib/iapbs/src/apbs_driver.c |
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index c9e443b..e1ad67f 100644 |
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--- a/apbs/contrib/iapbs/src/apbs_driver.c |
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+++ b/apbs/contrib/iapbs/src/apbs_driver.c |
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@@ -595,7 +595,7 @@ int apbsdrv_( |
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printPBEPARM(pbeparm); |
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|
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/* Refine mesh */ |
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- if (!preRefineFE(i, nosh, feparm, fetk)) { |
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+ if (!preRefineFE(i, feparm, fetk)) { |
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Vnm_tprint( 2, "Error pre-refining mesh!\n"); |
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VJMPERR1(0); |
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} |
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@@ -609,7 +609,7 @@ int apbsdrv_( |
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Vnm_tprint(1, " Beginning solve-estimate-refine cycle:\n"); |
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for (isolve=0; isolve<feparm->maxsolve; isolve++) { |
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Vnm_tprint(1, " Solve #%d...\n", isolve); |
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- if (!solveFE(i, nosh, pbeparm, feparm, fetk)) { |
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+ if (!solveFE(i, pbeparm, feparm, fetk)) { |
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Vnm_tprint(2, "ERROR SOLVING EQUATION!\n"); |
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VJMPERR1(0); |
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} |
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@@ -622,7 +622,7 @@ int apbsdrv_( |
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/* We're not going to refine if we've hit the max number |
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* of solves */ |
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if (isolve < (feparm->maxsolve)-1) { |
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- if (!postRefineFE(i, nosh, feparm, fetk)) break; |
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+ if (!postRefineFE(i, feparm, fetk)) break; |
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} |
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bytesTotal = Vmem_bytesTotal(); |
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highWater = Vmem_highWaterTotal(); |
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diff --git a/apbs/src/CMakeLists.txt b/apbs/src/CMakeLists.txt |
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index 44d20fa..2577343 100644 |
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--- a/apbs/src/CMakeLists.txt |
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+++ b/apbs/src/CMakeLists.txt |
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@@ -68,6 +68,7 @@ configure_file( |
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|
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if(ENABLE_iAPBS) |
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ADD_LIBRARY(apbs_routines routines.c routines.h) |
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+ target_link_libraries(apbs_routines apbs_mg apbs_fem) |
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INSTALL(TARGETS apbs_routines DESTINATION ${LIBRARY_INSTALL_PATH}) |
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INSTALL(FILES apbscfg.h DESTINATION ${HEADER_INSTALL_PATH}) |
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endif() |
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diff --git a/apbs/tools/CMakeLists.txt b/apbs/tools/CMakeLists.txt |
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index 1982a3c..4acbe68 100644 |
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--- a/apbs/tools/CMakeLists.txt |
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+++ b/apbs/tools/CMakeLists.txt |
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@@ -4,5 +4,5 @@ add_subdirectory(mesh) |
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add_subdirectory(manip) |
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|
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if(ENABLE_PYTHON) |
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- add_subdirectory(manip) |
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+ add_subdirectory(python) |
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endif(ENABLE_PYTHON) |
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diff --git a/apbs/tools/python/CMakeLists.txt b/apbs/tools/python/CMakeLists.txt |
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new file mode 100644 |
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index 0000000..8b13789 |
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--- /dev/null |
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+++ b/apbs/tools/python/CMakeLists.txt |
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@@ -0,0 +1 @@ |
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+ |
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diff --git a/apbs/tools/python/apbslib.c b/apbs/tools/python/apbslib.c |
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index fef5cc8..feaaa2c 100644 |
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--- a/apbs/tools/python/apbslib.c |
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+++ b/apbs/tools/python/apbslib.c |
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@@ -2504,8 +2504,8 @@ static swig_module_info swig_module = {swig_types, 24, 0, 0, 0, 0}; |
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#include "maloc/maloc.h" |
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#include "apbscfg.h" |
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#include "routines.h" |
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-#include "apbs/valist.h" |
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-#include "apbs/vatom.h" |
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+#include "generic/valist.h" |
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+#include "generic/vatom.h" |
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|
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|
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#include <limits.h> |
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diff --git a/apbs/tools/python/apbslib.i b/apbs/tools/python/apbslib.i |
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index 17fe521..44d05ea 100644 |
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--- a/apbs/tools/python/apbslib.i |
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+++ b/apbs/tools/python/apbslib.i |
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@@ -15,8 +15,8 @@ Header files: |
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#include "maloc/maloc.h" |
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#include "apbscfg.h" |
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#include "routines.h" |
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-#include "apbs/valist.h" |
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-#include "apbs/vatom.h" |
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+#include "generic/valist.h" |
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+#include "generic/vatom.h" |
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%} |
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|
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/* |
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diff --git a/apbs/tools/python/setup.py b/apbs/tools/python/setup.py |
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new file mode 100644 |
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index 0000000..4a20198 |
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--- /dev/null |
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+++ b/apbs/tools/python/setup.py |
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@@ -0,0 +1,16 @@ |
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+from distutils.core import setup, Extension |
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+setup(name='apbs', |
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+ version='1.4.1', |
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+ package_dir={'apbs': '', 'vgrid': 'vgrid'}, |
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+ packages=['apbs', 'vgrid'], |
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+ py_modules=['apbslib', 'main', 'noinput'], |
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+ ext_modules=[ |
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+ Extension( |
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+ '_apbslib', |
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+ ['apbslib.i'], |
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+ swig_opts=['-module', 'apbslib', '-I../include'], |
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+ include_dirs=["../../src"], |
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+ libraries=["apbs_generic", "apbs_routines"] |
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+ ) |
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+ ], |
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+ ) |
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