sci-chemistry/ball: Fix Swig bug, qualify std::isnan

Gentoo-Bug: 583932
* EAPI=6
* Also fix GCC warning pollution due to
  misplaced attributes
* Add subslot operator for dev-libs/boost
* Remove USE=webkit, as webkit is no longer supported

Package-Manager: portage-2.3.0_rc1

5 files changed, 133 insertions, 14 deletions

diff --git a/sci-chemistry/ball/ball-1.4.2.ebuild b/sci-chemistry/ball/ball-1.4.2-r1.ebuild
index bc1005204c0b..635e8b4989ab 100644
--- a/sci-chemistry/ball/ball-1.4.2.ebuild
+++ b/sci-chemistry/ball/ball-1.4.2-r1.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=5
+EAPI=6
 
 PYTHON_COMPAT=( python2_7 )
 
@@ -15,13 +15,13 @@ SRC_URI="http://www.ball-project.org/Downloads/v${PV}/BALL-${PV}.tar.xz"
 SLOT="0"
 LICENSE="LGPL-2 GPL-3"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="cuda mpi +python sql test +threads +webkit"
+IUSE="cuda mpi +python sql test +threads"
 
 REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
 
 RDEPEND="
 	dev-cpp/eigen:3
-	dev-libs/boost
+	dev-libs/boost:=
 	dev-qt/qtcore:4
 	dev-qt/qtgui:4
 	dev-qt/qtopengl:4
@@ -37,8 +37,7 @@ RDEPEND="
 	cuda? ( dev-util/nvidia-cuda-toolkit )
 	mpi? ( virtual/mpi )
 	python? ( ${PYTHON_DEPS} )
-	sql? ( dev-qt/qtsql:4 )
-	webkit? ( dev-qt/qtwebkit:4 )"
+	sql? ( dev-qt/qtsql:4 )"
 DEPEND="${RDEPEND}
 	dev-python/sip
 	sys-devel/bison
@@ -54,7 +53,10 @@ PATCHES=(
 	"${FILESDIR}"/${PN}-1.4.1-BondOrder.xml.patch
 	"${FILESDIR}"/${P}-Fix-compilation-of-sipModularWidget.patch
 	"${FILESDIR}"/${P}-underlinking.patch
-	)
+	"${FILESDIR}"/${P}-fix-python-bindings.patch
+	"${FILESDIR}"/${P}-std-namespace-isnan.patch
+	"${FILESDIR}"/${P}-struct-swap-attribute.patch
+)
 
 pkg_setup() {
 	use python && python-single-r1_pkg_setup
@@ -62,14 +64,14 @@ pkg_setup() {
 
 src_configure() {
 	local mycmakeargs=(
-		$(cmake-utils_use_use threads FFTW_THREADS)
-		$(cmake-utils_use cuda MT_ENABLE_CUDA)
-		$(cmake-utils_use mpi MT_ENABLE_MPI)
-		$(cmake-utils_use sql BALL_HAS_QTSQL)
-		$(cmake-utils_use_use webkit USE_QTWEBKIT)
-		$(cmake-utils_use python BALL_PYTHON_SUPPORT)
+		-DUSE_FFTW_THREADS=$(usex threads)
+		-DMT_ENABLE_CUDA=$(usex cuda)
+		-DMT_ENABLE_MPI=$(usex mpi)
+		-DBALL_HAS_QTSQL=$(usex sql)
+		-DBALL_PYTHON_SUPPORT=$(usex python)
 	)
 	cmake-utils_src_configure
+
 	local i
 	for i in "${S}"/data/*; do
 		ln -sf "${i}" "${BUILD_DIR}"/source/TEST/ || die
diff --git a/sci-chemistry/ball/files/ball-1.4.2-fix-python-bindings.patch b/sci-chemistry/ball/files/ball-1.4.2-fix-python-bindings.patch
new file mode 100644
index 000000000000..a13ea2f36ec0
--- /dev/null
+++ b/sci-chemistry/ball/files/ball-1.4.2-fix-python-bindings.patch
@@ -0,0 +1,22 @@
+From 38a955ad9588817073a330c79d4b4476afcf69d5 Mon Sep 17 00:00:00 2001
+From: Daniel Stoeckel <dstoeckel@bioinf.uni-sb.de>
+Date: Thu, 14 Apr 2016 19:30:04 +0200
+Subject: [PATCH] Fix Python bindings for Box
+
+---
+ source/PYTHON/EXTENSIONS/VIEW/box.sip | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/source/PYTHON/EXTENSIONS/VIEW/box.sip b/source/PYTHON/EXTENSIONS/VIEW/box.sip
+index 341b1a4..592765e 100644
+--- a/source/PYTHON/EXTENSIONS/VIEW/box.sip
++++ b/source/PYTHON/EXTENSIONS/VIEW/box.sip
+@@ -6,7 +6,7 @@
+ 
+ class Box
+ 	: GeometricObject,
+-		Vertex2
++	  Box3
+ {
+ %TypeHeaderCode
+ 	#include <BALL/VIEW/PRIMITIVES/box.h>
diff --git a/sci-chemistry/ball/files/ball-1.4.2-std-namespace-isnan.patch b/sci-chemistry/ball/files/ball-1.4.2-std-namespace-isnan.patch
new file mode 100644
index 000000000000..cea6377b6a20
--- /dev/null
+++ b/sci-chemistry/ball/files/ball-1.4.2-std-namespace-isnan.patch
@@ -0,0 +1,16 @@
+Fix C++11 changes to isnan():
+* /var/tmp/portage/sci-chemistry/ball-1.4.2/work/BALL-1.4.2/source/MOLMEC/MINIMIZATION/shiftedLVMM.C:769:46:   required from here
+* /var/tmp/portage/sci-chemistry/ball-1.4.2/work/BALL-1.4.2/include/BALL/MATHS/common.h:175:18: error: ‘isnan’ was not declared in this scope, and no declarations were found by argument-dependent lookup at the point of instantiation [-fpermissive]
+*      return (isnan(t) != 0);
+
+--- BALL-1.4.2/include/BALL/MATHS/common.h
++++ BALL-1.4.2/include/BALL/MATHS/common.h
+@@ -172,7 +172,7 @@
+ 			#elif  defined(BALL_OS_DARWIN)
+ 				return ( __inline_isnand(t) != 0);
+ 			#else
+-				return (isnan(t) != 0);
++				return (std::isnan(t) != 0);
+ 			#endif
+ 		}
+ 
diff --git a/sci-chemistry/ball/files/ball-1.4.2-struct-swap-attribute.patch b/sci-chemistry/ball/files/ball-1.4.2-struct-swap-attribute.patch
new file mode 100644
index 000000000000..da334915f410
--- /dev/null
+++ b/sci-chemistry/ball/files/ball-1.4.2-struct-swap-attribute.patch
@@ -0,0 +1,80 @@
+Silence warning pollution due to misplaced attributes:
+* /var/tmp/portage/sci-chemistry/ball-1.4.2/work/BALL-1.4.2/include/BALL/COMMON/logStream.h:165:22: note: attribute for ‘struct BALL::LogStreamBuf::StreamStruct’ must follow the ‘struct’ keyword
+
+--- BALL-1.4.2/include/BALL/COMMON/logStream.h
++++ BALL-1.4.2/include/BALL/COMMON/logStream.h
+@@ -162,7 +162,7 @@
+ 		virtual int overflow(int c = -1);
+ 		//@}
+ 
+-		BALL_EXPORT struct StreamStruct
++		struct BALL_EXPORT StreamStruct
+ 		{
+ 			std::ostream*				stream;
+ 			string							prefix;
+--- BALL-1.4.2/include/BALL/FORMAT/MOL2File.h
++++ BALL-1.4.2/include/BALL/FORMAT/MOL2File.h
+@@ -33,7 +33,7 @@
+ 		public:
+ 
+ 		/// A class used for storing TRIPOS sets
+-		BALL_EXPORT struct SetStruct
++		struct BALL_EXPORT SetStruct
+ 		{
+ 			String			name;
+ 			bool				is_static;
+@@ -136,7 +136,7 @@
+ 
+ 		bool containsAtomChilds_(AtomContainerConstIterator& frag_it);
+ 
+-		BALL_EXPORT struct AtomStruct
++		struct BALL_EXPORT AtomStruct
+ 		{
+ 			String		name;
+ 			Vector3		position;
+@@ -146,14 +146,14 @@
+ 			float			charge;
+ 		};
+ 
+-		BALL_EXPORT struct BondStruct
++		struct BALL_EXPORT BondStruct
+ 		{
+ 			Position	atom1;
+ 			Position	atom2;
+ 			String		type;
+ 		};
+ 
+-		BALL_EXPORT struct MoleculeStruct
++		struct BALL_EXPORT MoleculeStruct
+ 		{
+ 			String			name;
+ 			Size				number_of_atoms;
+@@ -166,7 +166,7 @@
+ 			String			comment;
+ 		};
+ 
+-		BALL_EXPORT struct SubstructureStruct
++		struct BALL_EXPORT SubstructureStruct
+ 		{
+ 			String			name;
+ 			Size				root_atom;
+@@ -178,7 +178,7 @@
+ 			String			comment;
+ 		};
+ 
+-		BALL_EXPORT struct CommentStruct
++		struct BALL_EXPORT CommentStruct
+ 		{
+ 			String name;
+ 			String value;
+--- BALL-1.4.2/include/BALL/FORMAT/MOLFile.h
++++ BALL-1.4.2/include/BALL/FORMAT/MOLFile.h
+@@ -41,7 +41,7 @@
+ 				@see PropertyManager::setProperty
+ 				@see PropertyManager::getProperty
+ 		*/
+-		BALL_EXPORT struct Property
++		struct BALL_EXPORT Property
+ 		{
+ 			///
+ 			static const String ATOM_MASS_DIFFERENCE;
diff --git a/sci-chemistry/ball/metadata.xml b/sci-chemistry/ball/metadata.xml
index a4d9afb7efb3..72d683b18460 100644
--- a/sci-chemistry/ball/metadata.xml
+++ b/sci-chemistry/ball/metadata.xml
@@ -27,6 +27,5 @@ integrated user-friendly GUI.
   <use>
     <flag name="sql">Include SQL database support</flag>
     <flag name="cuda">Include cuda support</flag>
-    <flag name="webkit">Uses <pkg>dev-qt/qtwebkit</pkg> for drawing</flag>
   </use>
 </pkgmetadata>