gentoo resync : 12.01.2019

4 files changed, 46 insertions, 48 deletions

diff --git a/sci-chemistry/apbs/Manifest b/sci-chemistry/apbs/Manifest
index d83109851ca0..1b33c2abb01e 100644
--- a/sci-chemistry/apbs/Manifest
+++ b/sci-chemistry/apbs/Manifest
@@ -1,6 +1,6 @@
-AUX apbs-1.4.1-manip.patch 1522 BLAKE2B 4a30aadc2d80fef5d813ea29f20073b6c4d1cefe24578624faca4fef19418bca64768653b5c3ba7ff935f79885432480b46f7a5fef407d8951be76386e5a62c2 SHA512 b2517b86b688091a9ae6a78132e8cd5a451eff6150211459dae6919bf2ee61edcf2cf1b95d8b2922050a3a7a3aaaa9ce8e2be6766116a1e66d413339b291326b
+AUX apbs-1.4.1-manip.patch 1462 BLAKE2B f4559008a1fc4dc367bc770ed29b7fa9ae9489ab57cfc8dd6e5cff358e27e2ac71b1e786bf9a4e3d96dfb4eea3596305beb5078746324769b582abf8a702a1c5 SHA512 70679623621fb56eeffc79166aa6fd35b5fa2fec828f6800a27b795a4e94c9eee673a7ba5f872c3266c9e78af8935d684fb5c4679b57da6a969189ce45e31468
 AUX apbs-1.4.1-multilib.patch 3301 BLAKE2B 4268a21ec878d780c7a1efe433bf2c82ef2e72f49a6071b6df695bf672ee999be9c29fed06e949b80cc230333d8deca1094c946662ec657d31e3b6f86e873969 SHA512 cdd72fd23a57ee8413f72bf674ae246543b1c9f326727ff07c3b8848d59f98ab7d2daf28677460cb4726f919832079c1d280bcdc86a8bef5c0875583c789b7c0
-AUX apbs-1.4.1-python.patch 4109 BLAKE2B 25193eb227ab9d34f3f636b6264bdbaecdbe48747220582b39798c5c6631bdc7731645f66096dbf659c9eea7f31c8e20c0944796f8f89d995a4cd2712be91a3b SHA512 369c0fa08187ba80d8ce72542fc2942f28426beed39619dd6a90a9ef8dfecb47ea6dc7aa20994629a69d63b55d72d1f837c442744bf5499a942bf312f6723092
+AUX apbs-1.4.1-python.patch 3979 BLAKE2B b21633655df329f5d445c4e53140367b0a8a6cfbfafccba8943206ed9bae46839bae532e3efd19d75e89bc70a1fa59d05f3ed977b1a59f949649d3e89b887a96 SHA512 a38ca3bbf692f42268d192aff61949ece95d9b043ac10b4eec33e383773beec1c60425a12e84843a602e828528f6cf0ed6b8c90e99aeea679c5abc8c093c68ae
 DIST apbs-1.4.1.zip 37999283 BLAKE2B 2301deb7ab4eb2f20098cf63df180bb53189e42a89cd5559357cdcf08e84d27a44eafe8557bb460574802d24d29741ad4606dc3bd7f32911d0d0f2c7453d6470 SHA512 3a127af3940054e5a43b3c0c620507f4f9baa69049e5a0933d8e8825458ad2faba840392752de49fe68d91e2054fb1394cf87bb5bb1c0b48305368e2f404cf6a
-EBUILD apbs-1.4.1-r2.ebuild 3140 BLAKE2B b31ecbf8ddb9e8824917cb7c79ba5239957e1723c56a60b9b20aa6d818a0140ce0e4ace7691ac9663d0e38f99b5d851b529b1355b965d071d7e6b65566763bf9 SHA512 e97100de2ed58f60b414cead8aea44d53178f2b28ca016c9fa4a783993b3be0c66a53eb541e4679f58bc3054e18ab8866bef1a31b817cf62031b65ad3044e1a5
+EBUILD apbs-1.4.1-r2.ebuild 3038 BLAKE2B 52199b0b53f146f7ed915b0cf65e48de40b39e5df10fde56ab89fb43324e3d98e66ba9d09a85d4cc209427d0cd0fc24f7472bc55393703b4c8aa2a13c3d23cdd SHA512 d5b3e8008db4f59618dc08d7e5289929a4852856aea51e2b08e6151d8530f6dab882a0b7229b079afd4ef336023b0f0a0ff19accce91f980fe2a6aea71a6399c
 MISC metadata.xml 1048 BLAKE2B 53a61bd7e05e53b294f0cbd1a21b86f391429ad5f23a545e7cbb27625b152589247a08db06c5d7f6658425de032be970fae0230ad1ac14ac4f6de42663d6c97c SHA512 7d68049cb9b044676430fe879890cc4cd869b99f85696f579d9cbf3b156081301792fd7f03205a9b9d429d71c9a35b4815f4236573f68d3ef6b4718e6e1f0bb3
diff --git a/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild b/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild
index 108e43bf904b..b3c4f192894b 100644
--- a/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild
+++ b/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild
@@ -1,19 +1,17 @@
 # Copyright 1999-2018 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=6
 
 PYTHON_COMPAT=( python2_7 )
 DISTUTILS_SINGLE_IMPL=true
-
-inherit cmake-utils distutils-r1 flag-o-matic multilib toolchain-funcs
-
-GITHUB_REV="74fcb8676de69ed04ddab8976a8b05a6caaf4d65"
+COMMIT="74fcb8676de69ed04ddab8976a8b05a6caaf4d65"
+inherit cmake-utils distutils-r1 flag-o-matic toolchain-funcs
 
 DESCRIPTION="Evaluation of electrostatic properties of nanoscale biomolecular systems"
 HOMEPAGE="https://www.poissonboltzmann.org/apbs/"
 #SRC_URI="mirror://sourceforge/${PN}/${P}-source.tar.gz"
-SRC_URI="https://github.com/Electrostatics/apbs-pdb2pqr/archive/${GITHUB_REV}.zip -> ${P}.zip"
+SRC_URI="https://github.com/Electrostatics/apbs-pdb2pqr/archive/${COMMIT}.zip -> ${P}.zip"
 
 SLOT="0"
 LICENSE="BSD"
@@ -44,7 +42,7 @@ DEPEND="${RDEPEND}
 	doc? ( app-doc/doxygen )
 "
 
-S="${WORKDIR}"/${PN}-pdb2pqr-${GITHUB_REV}/${PN}
+S="${WORKDIR}"/${PN}-pdb2pqr-${COMMIT}/${PN}
 
 PATCHES=(
 	"${FILESDIR}"/${P}-multilib.patch
@@ -71,24 +69,24 @@ src_prepare() {
 src_configure() {
 	local mycmakeargs=(
 		-DCMAKE_SKIP_RPATH=ON
-		-DTOOLS_PATH="${ED}"/usr
+		-DTOOLS_PATH="${ED%/}"/usr
 		-DSYS_LIBPATHS="${EPREFIX}"/usr/$(get_libdir)
 		-DLIBRARY_INSTALL_PATH=$(get_libdir)
 		-DFETK_PATH="${EPREFIX}"/usr/
 		-DBUILD_SHARED_LIBS=ON
 		-DENABLE_QUIT=OFF
-		$(cmake-utils_use_build doc DOC)
-		$(cmake-utils_use_build tools TOOLS)
+		-DBUILD_DOC=$(usex doc)
+		-DBUILD_TOOLS=$(usex tools)
 		-DENABLE_BEM=OFF
 # ENABLE_BEM: Boundary element method using TABIPB
-		$(cmake-utils_use_enable debug DEBUG)
-		$(cmake-utils_use_enable debug VERBOSE_DEBUG)
-		$(cmake-utils_use_enable fast FAST)
-		$(cmake-utils_use_enable fetk FETK)
-		$(cmake-utils_use_enable mpi MPI)
-		$(cmake-utils_use_enable python PYTHON)
+		-DENABLE_DEBUG=$(usex debug)
+		-DENABLE_VERBOSE_DEBUG=$(usex debug)
+		-DENABLE_FAST=$(usex fast)
+		-DENABLE_FETK=$(usex fetk)
+		-DENABLE_MPI=$(usex mpi)
+		-DENABLE_PYTHON=$(usex python)
 # ENABLE_TINKER: Enable TINKER support
-		$(cmake-utils_use_enable iapbs iAPBS)
+		-DENABLE_iAPBS=$(usex iapbs)
 # MAX_MEMORY: Set the maximum memory (in MB) to be used for a job
 	)
 	cmake-utils_src_configure
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 378223397594..090a27d8a5a6 100644
--- a/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch
+++ b/sci-chemistry/apbs/files/apbs-1.4.1-manip.patch
@@ -3,10 +3,10 @@
  apbs/tools/mesh/CMakeLists.txt  | 4 ++--
  4 files changed, 5 insertions(+), 9 deletions(-)
 
-diff --git a/apbs/CMakeLists.txt b/apbs/CMakeLists.txt
+diff --git a/CMakeLists.txt b/CMakeLists.txt
 index 8917fc4..5152008 100644
---- a/apbs/CMakeLists.txt
-+++ b/apbs/CMakeLists.txt
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
 @@ -293,7 +293,7 @@ option(ENABLE_FETK "Enable the finite element solver" OFF)
  
  if(ENABLE_FETK)
@@ -16,10 +16,10 @@ index 8917fc4..5152008 100644
  
      list(APPEND APBS_LIBS "-lstdc++")
      list(APPEND APBS_LIBS "-L${FETK_PATH}/lib")
-diff --git a/apbs/tools/manip/CMakeLists.txt b/apbs/tools/manip/CMakeLists.txt
+diff --git a/tools/manip/CMakeLists.txt b/tools/manip/CMakeLists.txt
 index 937dac7..5768cc5 100644
---- a/apbs/tools/manip/CMakeLists.txt
-+++ b/apbs/tools/manip/CMakeLists.txt
+--- a/tools/manip/CMakeLists.txt
++++ b/tools/manip/CMakeLists.txt
 @@ -4,9 +4,9 @@ set(LIBS "")
  list(APPEND LIBS "apbs_generic")
  list(APPEND LIBS "apbs_mg")
@@ -32,10 +32,10 @@ index 937dac7..5768cc5 100644
  
  message(STATUS "libraries: ${LIBS}")
  
-diff --git a/apbs/tools/mesh/CMakeLists.txt b/apbs/tools/mesh/CMakeLists.txt
+diff --git a/tools/mesh/CMakeLists.txt b/tools/mesh/CMakeLists.txt
 index 1406377..6e6dfb9 100644
---- a/apbs/tools/mesh/CMakeLists.txt
-+++ b/apbs/tools/mesh/CMakeLists.txt
+--- a/tools/mesh/CMakeLists.txt
++++ b/tools/mesh/CMakeLists.txt
 @@ -4,9 +4,9 @@ set(LIBS "")
  list(APPEND LIBS "apbs_generic")
  list(APPEND LIBS "apbs_mg")
diff --git a/sci-chemistry/apbs/files/apbs-1.4.1-python.patch b/sci-chemistry/apbs/files/apbs-1.4.1-python.patch
index db9f86ba120a..5ad6613615f2 100644
--- a/sci-chemistry/apbs/files/apbs-1.4.1-python.patch
+++ b/sci-chemistry/apbs/files/apbs-1.4.1-python.patch
@@ -7,10 +7,10 @@
  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
+diff --git a/contrib/iapbs/src/apbs_driver.c b/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
+--- a/contrib/iapbs/src/apbs_driver.c
++++ b/contrib/iapbs/src/apbs_driver.c
 @@ -595,7 +595,7 @@ int apbsdrv_(
  		printPBEPARM(pbeparm);
  
@@ -38,10 +38,10 @@ index c9e443b..e1ad67f 100644
  		    }
  		    bytesTotal = Vmem_bytesTotal();
  		    highWater = Vmem_highWaterTotal();
-diff --git a/apbs/src/CMakeLists.txt b/apbs/src/CMakeLists.txt
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
 index 44d20fa..2577343 100644
---- a/apbs/src/CMakeLists.txt
-+++ b/apbs/src/CMakeLists.txt
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
 @@ -68,6 +68,7 @@ configure_file(
  
  if(ENABLE_iAPBS)
@@ -50,10 +50,10 @@ index 44d20fa..2577343 100644
      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
+diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt
 index 1982a3c..4acbe68 100644
---- a/apbs/tools/CMakeLists.txt
-+++ b/apbs/tools/CMakeLists.txt
+--- a/tools/CMakeLists.txt
++++ b/tools/CMakeLists.txt
 @@ -4,5 +4,5 @@ add_subdirectory(mesh)
  add_subdirectory(manip)
  
@@ -61,17 +61,17 @@ index 1982a3c..4acbe68 100644
 -    add_subdirectory(manip)
 +    add_subdirectory(python)
  endif(ENABLE_PYTHON)
-diff --git a/apbs/tools/python/CMakeLists.txt b/apbs/tools/python/CMakeLists.txt
+diff --git a/tools/python/CMakeLists.txt b/tools/python/CMakeLists.txt
 new file mode 100644
 index 0000000..8b13789
 --- /dev/null
-+++ b/apbs/tools/python/CMakeLists.txt
++++ b/tools/python/CMakeLists.txt
 @@ -0,0 +1 @@
 +
-diff --git a/apbs/tools/python/apbslib.c b/apbs/tools/python/apbslib.c
+diff --git a/tools/python/apbslib.c b/tools/python/apbslib.c
 index fef5cc8..feaaa2c 100644
---- a/apbs/tools/python/apbslib.c
-+++ b/apbs/tools/python/apbslib.c
+--- 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" 
@@ -83,10 +83,10 @@ index fef5cc8..feaaa2c 100644
  
  
  #include <limits.h>
-diff --git a/apbs/tools/python/apbslib.i b/apbs/tools/python/apbslib.i
+diff --git a/tools/python/apbslib.i b/tools/python/apbslib.i
 index 17fe521..44d05ea 100644
---- a/apbs/tools/python/apbslib.i
-+++ b/apbs/tools/python/apbslib.i
+--- a/tools/python/apbslib.i
++++ b/tools/python/apbslib.i
 @@ -15,8 +15,8 @@ Header files:
  #include "maloc/maloc.h"
  #include "apbscfg.h" 
@@ -98,11 +98,11 @@ index 17fe521..44d05ea 100644
  %} 
  
  /* 
-diff --git a/apbs/tools/python/setup.py b/apbs/tools/python/setup.py
+diff --git a/tools/python/setup.py b/tools/python/setup.py
 new file mode 100644
 index 0000000..4a20198
 --- /dev/null
-+++ b/apbs/tools/python/setup.py
++++ b/tools/python/setup.py
 @@ -0,0 +1,16 @@
 +from distutils.core import setup, Extension
 +setup(name='apbs',