sci-chemistry/apbs: EAPI-6 bump

Package-Manager: Portage-2.3.52, Repoman-2.3.12
Signed-off-by: Andreas Sturmlechner <asturm@gentoo.org>

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

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")

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',