sci-chemistry/apbs: Link python libs completely

(Portage version: 2.2.14/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

4 files changed, 162 insertions, 19 deletions

diff --git a/sci-chemistry/apbs/ChangeLog b/sci-chemistry/apbs/ChangeLog
index 530323b8bf51..d189a27f63ee 100644
--- a/sci-chemistry/apbs/ChangeLog
+++ b/sci-chemistry/apbs/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-chemistry/apbs
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/ChangeLog,v 1.67 2014/10/24 11:38:49 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/ChangeLog,v 1.68 2014/10/28 13:10:30 jlec Exp $
+
+*apbs-1.4.1-r1 (28 Oct 2014)
+
+  28 Oct 2014; Justin Lecher <jlec@gentoo.org> -apbs-1.4.1.ebuild,
+  +apbs-1.4.1-r1.ebuild, files/apbs-1.4.1-manip.patch,
+  +files/apbs-1.4.1-python.patch:
+  Link python libs completely
 
   24 Oct 2014; Justin Lecher <jlec@gentoo.org> apbs-1.4.1.ebuild:
   Add missing requiered use
diff --git a/sci-chemistry/apbs/apbs-1.4.1.ebuild b/sci-chemistry/apbs/apbs-1.4.1-r1.ebuild
index acbe367af4c8..61461b25cfef 100644
--- a/sci-chemistry/apbs/apbs-1.4.1.ebuild
+++ b/sci-chemistry/apbs/apbs-1.4.1-r1.ebuild
@@ -1,12 +1,12 @@
 # Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/apbs-1.4.1.ebuild,v 1.4 2014/10/24 11:38:49 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/apbs/apbs-1.4.1-r1.ebuild,v 1.1 2014/10/28 13:10:30 jlec Exp $
 
 EAPI=5
 
 PYTHON_COMPAT=( python2_7 )
 
-inherit cmake-utils flag-o-matic multilib python-single-r1 toolchain-funcs
+inherit cmake-utils distutils-r1 flag-o-matic multilib toolchain-funcs
 
 GITHUB_REV="74fcb8676de69ed04ddab8976a8b05a6caaf4d65"
 
@@ -22,7 +22,7 @@ IUSE="debug doc examples fast +fetk mpi openmp python tools"
 
 REQUIRED_USE="
 	mpi? ( !python )
-	${PYTHON_REQUIRED_USE}"
+	python? ( tools fetk ${PYTHON_REQUIRED_USE} )"
 
 RDEPEND="
 	dev-cpp/eigen:3
@@ -48,6 +48,7 @@ S="${WORKDIR}"/${PN}-pdb2pqr-${GITHUB_REV}/${PN}
 PATCHES=(
 	"${FILESDIR}"/${P}-multilib.patch
 	"${FILESDIR}"/${P}-manip.patch
+	"${FILESDIR}"/${P}-python.patch
 )
 
 src_prepare() {
@@ -56,12 +57,19 @@ src_prepare() {
 
 	sed \
 		-e "s:-lblas:$($(tc-getPKG_CONFIG) --libs blas):g" \
+		-e "/TOOLS_PATH/d" \
 		-i CMakeLists.txt || die
 	use doc && MAKEOPTS+=" -j1"
+	if use python; then
+		unset PATCHES || die
+		cd tools/python && distutils-r1_src_prepare
+	fi
 }
 
 src_configure() {
 	local mycmakeargs=(
+		-DCMAKE_SKIP_RPATH=ON
+		-DTOOLS_PATH="${ED}"/usr
 		-DSYS_LIBPATHS="${EPREFIX}"/usr/$(get_libdir)
 		-DLIBRARY_INSTALL_PATH=$(get_libdir)
 		-DFETK_PATH="${EPREFIX}"/usr/
@@ -78,11 +86,21 @@ src_configure() {
 		$(cmake-utils_use_enable mpi MPI)
 		$(cmake-utils_use_enable python PYTHON)
 # ENABLE_TINKER: Enable TINKER support
-		$(cmake-utils_use_enable python PYTHON)
 # ENABLE_iAPBS: Enable iAPBS
+		-DENABLE_iAPBS=ON
 # MAX_MEMORY: Set the maximum memory (in MB) to be used for a job
 	)
 	cmake-utils_src_configure
+	if use python; then
+		cd tools/python && distutils-r1_src_configure
+	fi
+}
+
+src_compile(){
+	cmake-utils_src_compile
+	if use python; then
+		cd tools/python && distutils-r1_src_compile
+	fi
 }
 
 src_test() {
@@ -92,6 +110,15 @@ src_test() {
 }
 
 src_install() {
+	dodir /usr/bin
 	cmake-utils_src_install
-	python_optimize "${ED}"
+	local i
+	for i in "${ED}"/usr/bin/*; do
+		if [[ ! "${i}" =~ .*apbs$ ]]; then
+			mv "${i}" "${i}-apbs" || die
+		fi
+	done
+	if use python; then
+		cd tools/python && distutils-r1_src_install
+	fi
 }
diff --git a/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch b/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch
index edfeb75b886c..378223397594 100644
--- a/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch
+++ b/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch
@@ -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 @@ index 8917fc4..5152008 100644
  
      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
diff --git a/sci-chemistry/apbs/files/apbs-1.4.1-python.patch b/sci-chemistry/apbs/files/apbs-1.4.1-python.patch
new file mode 100644
index 000000000000..db9f86ba120a
--- /dev/null
+++ b/sci-chemistry/apbs/files/apbs-1.4.1-python.patch
@@ -0,0 +1,122 @@
+ 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"]
++            )
++        ],
++    )