sci-libs/chemkit: Unbundle what is possible to unbundle

Package-Manager: portage-2.2.8/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

4 files changed, 296 insertions, 15 deletions

diff --git a/sci-libs/chemkit/ChangeLog b/sci-libs/chemkit/ChangeLog
index e6c8e42d0bce..077021dfecc4 100644
--- a/sci-libs/chemkit/ChangeLog
+++ b/sci-libs/chemkit/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-libs/chemkit
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/chemkit/ChangeLog,v 1.2 2014/01/13 14:28:56 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/chemkit/ChangeLog,v 1.3 2014/01/13 18:17:59 jlec Exp $
+
+*chemkit-0.1-r1 (13 Jan 2014)
+
+  13 Jan 2014; Justin Lecher <jlec@gentoo.org> +chemkit-0.1-r1.ebuild,
+  +files/chemkit-0.1-unbundle.patch:
+  Unbundle what is possible to unbundle
 
   13 Jan 2014; Justin Lecher <jlec@gentoo.org> chemkit-0.1.ebuild:
   Updated deps
diff --git a/sci-libs/chemkit/Manifest b/sci-libs/chemkit/Manifest
index 0ed2d1e12cdc..5af15ac3817c 100644
--- a/sci-libs/chemkit/Manifest
+++ b/sci-libs/chemkit/Manifest
@@ -2,24 +2,26 @@
 Hash: SHA512
 
 AUX chemkit-0.1-multilib.patch 4694 SHA256 9c9402535a1afc727d96d6415dcf16780c0f29998ea7bac3e1e4c3b89ecf3af2 SHA512 dedde9e5db14f088e5a70ebfcd9f46b6fbb2d60b1800a61ece1f7afef24caac502f129573823807caec050ba1515ad402a3615953b903a239c5287a5b96aa8b8 WHIRLPOOL 4e86024cc5dd39af48133c43f477ca4c69fa21d88498fb7af95f1565c6785e2fac39cd1724129db1c390cbdb723a8deee9fab82e6aceae8ed6dfcae0e0a3a646
+AUX chemkit-0.1-unbundle.patch 6103 SHA256 0fb331b49205fc55e00404dec5dbbfc70f5d80b5a64ae06c6aeb7a6971f42552 SHA512 9edd39008763b56eb7697562536c4c4d476880a414ae1a305d1af64cee04e4ccb82585cfd15d2f7608b5200e39863a9a97c2a152110b28e501fbd055737ce015 WHIRLPOOL 1bfe931e706d7259dbf2a5527b1e75cbfa1ca09148fffd25c4e4cc986112fd1cb18730b462c29fcae553b6bbdefcb5c895934b96fb5e141a307fa67eb0becc23
 DIST chemkit-0.1.tar.gz 5842235 SHA256 bec718ce4ae2fcb4cda63004d05a6e6bf65c1887179f665fcee118cbe7bec11b SHA512 0273f8735333000b04007ccd7adc58f0c4809a570fa5a72e4161652d72e8953bf89cad0893c20ecbb3484d6c13a8828c92f12366dddeedaf591815c35f6ef011 WHIRLPOOL 30c73d5d2bb7e946204d3dcdd87b82fa3e5278e799b06df523557f46ca4c71ae7d5b9c37d82af8dcdee48bb83f8840c5f2900b4331c3cf643c323ef20abc1883
+EBUILD chemkit-0.1-r1.ebuild 1911 SHA256 45559fba5ca854080a7478d7a8bf5a952c764de64838cc0ae12ae33314b596e0 SHA512 b052cb47aeb082d6463d5db20aa2a2097d7ab95908931a1e96d53278cb66358b6bc036fa7483f39626e2cab15decb4ffe05727bd2621bff3a64ee363dd84d32b WHIRLPOOL 88722ce5e7bfaf848264967afc6fddb2a88a9167560a62e3b99acba059aa62643dddba048c074722a8dbd9cb14f9f2aeaf27f804dbeb5a79a26c3443c0f6d0db
 EBUILD chemkit-0.1.ebuild 1551 SHA256 02475f9aee0ab7e5a63d7c9da158508b34cdc2bd2b94b6b3a689245b3de08f51 SHA512 d8f95d2cca1b819260ae8e4224e5a7c47e36ac6e75dc73d1acd9f7f93c4b2b372d86a414c801e2acc14a0b8cad9382792c5ba225401e6604e387026d438b60e4 WHIRLPOOL 5c309942f1cfe9b848566855501d096b3c2666126ac4302162a59b43c3356add2b9691f531d38ee924b1cbfe09b58948dce31f8305541c64ddc9198816e9b89d
-MISC ChangeLog 810 SHA256 e16a5a1fdce617042f2c748778b5aeb15a5edd47548a7af16c7aebabddb07d4e SHA512 78d42c9f10a85730cc5aa992081f985ec28f7e460796e46e2fc6cd757d075f60c556420ce3b42d554e0d19b2d2d3bc1e26077de0e1a494617d8937d273c3f460 WHIRLPOOL aea6c7eaa78bbfd43222cf34021ac563b34e419d23445841715e6c21ff85aaa8fdfdc6240e3314ad53041c853e65c4e1f953eabcc6925dacd9c6bee622de617e
+MISC ChangeLog 990 SHA256 d37645ab389e4140c5e0530951425a1fa0179a314658bff6230d41c2ddf919e2 SHA512 2e7377579e458f1e33077f9c4a9103466d0354aba2cf15001826bff8b81866a212c3bc8723786fc57c0b3fe88167822d31e535e6b095d1699e0afd48f8499864 WHIRLPOOL 23670deac9bd0918cae6dd0540d3d724f848788f514f4850b6e921b0d5b4d9f3e3dcad2e2568e8d51c122020b1c735c5a3856fd067b18fa28f650ac3203f92d7
 MISC metadata.xml 335 SHA256 42901825111b3e532c90541fef71de935df027d060984cee36f92df57a156ccf SHA512 4aa3708c472f54fbda19512be60cd0e46aab8a70bee50e90c1b8c9399589a45b1009cb33fd72e99e6be25559f84f3f4946452a013e3e1fe0f85798224a9a0efe WHIRLPOOL 4df3f28e5909f68d99773df15b491ff19966df1bd93e13a9500051e7835a27befa75d5620544f165118fb7a9cf464600d37b605bb51462bd7a121d34bf8efa74
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diff --git a/sci-libs/chemkit/chemkit-0.1-r1.ebuild b/sci-libs/chemkit/chemkit-0.1-r1.ebuild
new file mode 100644
index 000000000000..cec8b4813f97
--- /dev/null
+++ b/sci-libs/chemkit/chemkit-0.1-r1.ebuild
@@ -0,0 +1,82 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/chemkit/chemkit-0.1-r1.ebuild,v 1.1 2014/01/13 18:17:58 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit cmake-utils multilib python-single-r1 virtualx
+
+DESCRIPTION="Library for chemistry applications"
+HOMEPAGE="http://www.chemkit.org/"
+SRC_URI="mirror://sourceforge/project/${PN}/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD PSF-2.2"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="applications examples python test"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}
+	test? ( applications python )"
+
+RDEPEND="
+	dev-libs/boost
+	dev-libs/rapidxml
+	dev-cpp/eigen:3
+	dev-qt/qtcore:4
+	dev-qt/qtgui:4
+	dev-qt/qtopengl:4
+	media-libs/glu
+	sci-libs/inchi
+	sci-libs/lemon
+	virtual/opengl
+	examples? (
+		x11-libs/libX11
+		x11-libs/libXext
+	)
+	python? ( ${PYTHON_DEPS} )
+"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}"/${PN}
+
+PATCHES=(
+	"${FILESDIR}"/${P}-multilib.patch
+	"${FILESDIR}"/${P}-unbundle.patch
+	)
+
+src_prepare() {
+	# jsoncpp API change
+	# xdrf != xdrfile
+	rm -rvf src/3rdparty/{inchi,khronos,lemon,rapidxml} || die
+	cmake-utils_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DCHEMKIT_BUILD_PLUGIN_BABEL=on
+		-DUSE_SYSTEM_INCHI=ON
+		-DUSE_SYSTEM_JSONCPP=OFF
+		-DUSE_SYSTEM_RAPIDXML=ON
+		-DUSE_SYSTEM_XDRF=OFF
+		$(cmake-utils_use applications CHEMKIT_BUILD_APPS)
+		$(cmake-utils_use applications CHEMKIT_BUILD_QT_DESIGNER_PLUGINS)
+		$(cmake-utils_use examples CHEMKIT_BUILD_EXAMPLES)
+		$(cmake-utils_use examples CHEMKIT_BUILD_DEMOS)
+		$(cmake-utils_use python CHEMKIT_BUILD_BINDINGS_PYTHON)
+		$(cmake-utils_use test CHEMKIT_BUILD_TESTS)
+	)
+	cmake-utils_src_configure
+}
+
+src_test() {
+	VIRTUALX_COMMAND="cmake-utils_src_test"
+	virtualmake
+}
+
+src_install() {
+	use examples && dobin demos/*-viewer/*-viewer examples/uff-energy/uff-energy
+
+	cmake-utils_src_install
+}
diff --git a/sci-libs/chemkit/files/chemkit-0.1-unbundle.patch b/sci-libs/chemkit/files/chemkit-0.1-unbundle.patch
new file mode 100644
index 000000000000..e8c9d18dca6e
--- /dev/null
+++ b/sci-libs/chemkit/files/chemkit-0.1-unbundle.patch
@@ -0,0 +1,191 @@
+ CMakeLists.txt                              | 21 +++++++++++++++++++++
+ src/plugins/chemjson/CMakeLists.txt         |  6 +++++-
+ src/plugins/chemjson/chemjsonfileformat.cpp |  4 ++++
+ src/plugins/cml/cmlfileformat.h             |  4 ++++
+ src/plugins/inchi/CMakeLists.txt            |  4 +++-
+ src/plugins/inchi/inchikeylineformat.cpp    |  4 ++++
+ src/plugins/inchi/inchilineformat.cpp       |  4 ++++
+ src/plugins/pdb/pdbmlfileformat.cpp         |  4 ++++
+ src/plugins/xtc/CMakeLists.txt              |  9 +++++++--
+ src/plugins/xtc/xtcfileformat.cpp           |  4 ++++
+ 10 files changed, 60 insertions(+), 4 deletions(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index e531be4..622ea9d 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -55,6 +55,27 @@ configure_file(
+ # export the Chemkit package
+ export(PACKAGE Chemkit)
+ 
++option(USE_SYSTEM_INCHI "Use inchi installed in system" OFF)
++option(USE_SYSTEM_JSONCPP "Use json cpp installed in system" OFF)
++option(USE_SYSTEM_RAPIXML "Use rapidxml installed in system" OFF)
++option(USE_SYSTEM_XDRF "Use xdrflib installed in system" OFF)
++
++if(USE_SYSTEM_INCHI)
++	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DSYSTEM_INCHI")
++endif()
++
++if(USE_SYSTEM_JSONCPP)
++	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DSYSTEM_JSONCPP")
++endif()
++
++if(USE_SYSTEM_RAPIDXML)
++	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DSYSTEM_RAPIDXML")
++endif()
++
++if(USE_SYSTEM_XDRF)
++	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DSYSTEM_XDRF")
++endif()
++
+ # build options
+ option(CHEMKIT_WITH_GRAPHICS "Build the chemkit-graphics library." ON)
+ option(CHEMKIT_WITH_IO "Build the chemkit-io library." ON)
+diff --git a/src/plugins/chemjson/CMakeLists.txt b/src/plugins/chemjson/CMakeLists.txt
+index 0e115b5..a5e6f48 100644
+--- a/src/plugins/chemjson/CMakeLists.txt
++++ b/src/plugins/chemjson/CMakeLists.txt
+@@ -10,7 +10,11 @@ set(SOURCES
+   chemjsonplugin.cpp
+ )
+ 
+-aux_source_directory(../../3rdparty/jsoncpp/ JSONCPP_SOURCES)
++if(NOT USE_SYSTEM_JSONCPP)
++	aux_source_directory(../../3rdparty/jsoncpp/ JSONCPP_SOURCES)
++else()
++	target_link_libraries(chemjson jsoncpp)
++endif()
+ 
+ add_chemkit_plugin(chemjson ${SOURCES} ${JSONCPP_SOURCES})
+ target_link_libraries(chemjson ${CHEMKIT_LIBRARIES})
+diff --git a/src/plugins/chemjson/chemjsonfileformat.cpp b/src/plugins/chemjson/chemjsonfileformat.cpp
+index a0d271e..3cd5827 100644
+--- a/src/plugins/chemjson/chemjsonfileformat.cpp
++++ b/src/plugins/chemjson/chemjsonfileformat.cpp
+@@ -43,7 +43,11 @@
+ #include <chemkit/molecule.h>
+ #include <chemkit/moleculefile.h>
+ 
++#ifdef SYSTEM_JSONCPP
++#include <jsoncpp/json/json.h>
++#else
+ #include "../../3rdparty/jsoncpp/json/json.h"
++#endif
+ 
+ namespace {
+ 
+diff --git a/src/plugins/cml/cmlfileformat.h b/src/plugins/cml/cmlfileformat.h
+index e813223..61a547d 100644
+--- a/src/plugins/cml/cmlfileformat.h
++++ b/src/plugins/cml/cmlfileformat.h
+@@ -38,7 +38,11 @@
+ 
+ #include <chemkit/moleculefileformat.h>
+ 
++#ifdef SYSTEM_RAPIDXML
++#include <rapidxml/rapidxml.hpp>
++#else
+ #include "../../3rdparty/rapidxml/rapidxml.hpp"
++#endif
+ 
+ class CmlFileFormat : public chemkit::MoleculeFileFormat
+ {
+diff --git a/src/plugins/inchi/CMakeLists.txt b/src/plugins/inchi/CMakeLists.txt
+index 2b25d9b..5f45f8a 100644
+--- a/src/plugins/inchi/CMakeLists.txt
++++ b/src/plugins/inchi/CMakeLists.txt
+@@ -7,7 +7,9 @@ set(SOURCES
+   inchiplugin.cpp
+ )
+ 
+-aux_source_directory(../../3rdparty/inchi/ IUPAC_INCHI_SOURCES)
++if(NOT USE_SYSTEM_INCHI)
++	aux_source_directory(../../3rdparty/inchi/ IUPAC_INCHI_SOURCES)
++endif()
+ 
+ add_chemkit_plugin(inchi ${SOURCES} ${IUPAC_INCHI_SOURCES})
+ target_link_libraries(inchi ${CHEMKIT_LIBRARIES})
+diff --git a/src/plugins/inchi/inchikeylineformat.cpp b/src/plugins/inchi/inchikeylineformat.cpp
+index 2682f95..cec0a17 100644
+--- a/src/plugins/inchi/inchikeylineformat.cpp
++++ b/src/plugins/inchi/inchikeylineformat.cpp
+@@ -38,7 +38,11 @@
+ #include <boost/format.hpp>
+ 
+ #include "inchilineformat.h"
++#ifdef SYSTEM_INCHI
++#include <inchi_api.h>
++#else
+ #include "../../3rdparty/inchi/inchi_api.h"
++#endif
+ 
+ InchiKeyLineFormat::InchiKeyLineFormat()
+     : chemkit::LineFormat("inchikey")
+diff --git a/src/plugins/inchi/inchilineformat.cpp b/src/plugins/inchi/inchilineformat.cpp
+index 5b9bc42..ea5977c 100644
+--- a/src/plugins/inchi/inchilineformat.cpp
++++ b/src/plugins/inchi/inchilineformat.cpp
+@@ -42,7 +42,11 @@
+ 
+ #include <boost/algorithm/string.hpp>
+ 
++#ifdef SYSTEM_INCHI
++#include <inchi_api.h>
++#else
+ #include "../../3rdparty/inchi/inchi_api.h"
++#endif
+ 
+ #include <chemkit/atom.h>
+ #include <chemkit/bond.h>
+diff --git a/src/plugins/pdb/pdbmlfileformat.cpp b/src/plugins/pdb/pdbmlfileformat.cpp
+index 081a4ec..2ca4269 100644
+--- a/src/plugins/pdb/pdbmlfileformat.cpp
++++ b/src/plugins/pdb/pdbmlfileformat.cpp
+@@ -35,7 +35,11 @@
+ 
+ #include "pdbmlfileformat.h"
+ 
++#ifdef SYSTEM_RAPIDXML
++#include <rapidxml/rapidxml.hpp>
++#else
+ #include "../../3rdparty/rapidxml/rapidxml.hpp"
++#endif
+ 
+ #include <chemkit/atom.h>
+ #include <chemkit/polymer.h>
+diff --git a/src/plugins/xtc/CMakeLists.txt b/src/plugins/xtc/CMakeLists.txt
+index 98d8ba7..8c09e64 100644
+--- a/src/plugins/xtc/CMakeLists.txt
++++ b/src/plugins/xtc/CMakeLists.txt
+@@ -13,7 +13,12 @@ set(SOURCES
+   xtcplugin.cpp
+ )
+ 
+-aux_source_directory(../../3rdparty/xdrf/ XDRF_SOURCES)
++
++if(USE_SYSTEM_XDRF)
++	find_library(XDRF_LIBRARY NAMES xdrfile libxdrfile)
++else()
++	aux_source_directory(../../3rdparty/xdrf/ XDRF_SOURCES)
++endif()
+ 
+ add_chemkit_plugin(xtc ${SOURCES} ${XDRF_SOURCES})
+-target_link_libraries(xtc ${CHEMKIT_LIBRARIES} ${Boost_LIBRARIES})
++target_link_libraries(xtc ${CHEMKIT_LIBRARIES} ${Boost_LIBRARIES} ${XDRF_LIBRARY} )
+diff --git a/src/plugins/xtc/xtcfileformat.cpp b/src/plugins/xtc/xtcfileformat.cpp
+index 0f00cb6..f8659ca 100644
+--- a/src/plugins/xtc/xtcfileformat.cpp
++++ b/src/plugins/xtc/xtcfileformat.cpp
+@@ -47,7 +47,11 @@
+ #include <chemkit/trajectoryframe.h>
+ #include <chemkit/cartesiancoordinates.h>
+ 
++#ifdef SYSTEM_XDRF
++#include <xdrfile/xdrfile.h>
++#else
+ #include "../../3rdparty/xdrf/xdrf.h"
++#endif
+ 
+ XtcFileFormat::XtcFileFormat()
+     : chemkit::TrajectoryFileFormat("xtc")