[gentoo-commits] proj/sci:master commit in: sci-chemistry/openbabel-perl/, sci-chemistry/openbabel-perl/files/

["Reinis Danne" <rei4dan@gmail.com>]

commit:     7c91da989c0f06c156cb2241b438a709316b4ff0
Author:     Reinis Danne <rei4dan <AT> gmail <DOT> com>
AuthorDate: Fri Oct 19 16:41:37 2012 +0000
Commit:     Reinis Danne <rei4dan <AT> gmail <DOT> com>
CommitDate: Fri Oct 19 16:41:37 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7c91da98

openbabel-perl: Version bump to 2.3.2

---
 sci-chemistry/openbabel-perl/ChangeLog             |   11 ++
 .../files/openbabel-perl-2.3.2-bindings_only.patch |  108 ++++++++++++++++++++
 .../files/openbabel-perl-2.3.2-trunk_cmake.patch   |   41 ++++++++
 sci-chemistry/openbabel-perl/metadata.xml          |   12 ++
 .../openbabel-perl/openbabel-perl-2.3.2.ebuild     |   66 ++++++++++++
 5 files changed, 238 insertions(+), 0 deletions(-)

diff --git a/sci-chemistry/openbabel-perl/ChangeLog b/sci-chemistry/openbabel-perl/ChangeLog
new file mode 100644
index 0000000..f1cb357
--- /dev/null
+++ b/sci-chemistry/openbabel-perl/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-chemistry/openbabel-perl
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*openbabel-perl-2.3.2 (19 Oct 2012)
+
+  19 Oct 2012; Reinis Danne <rei4dan@gmail.com> +openbabel-perl-2.3.2.ebuild,
+  +files/openbabel-perl-2.3.2-bindings_only.patch,
+  +files/openbabel-perl-2.3.2-trunk_cmake.patch, +metadata.xml:
+  Bump to 2.3.2.
+

diff --git a/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-bindings_only.patch b/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-bindings_only.patch
new file mode 100644
index 0000000..92e126a
--- /dev/null
+++ b/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-bindings_only.patch
@@ -0,0 +1,108 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 449f4b4..1c9ad00 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -252,7 +252,8 @@ if(NOT MSVC)
+     }
+    " SCANDIR_NEEDS_CONST)
+ 
+-  set(OB_MODULE_PATH "${CMAKE_INSTALL_PREFIX}/${OB_PLUGIN_INSTALL_DIR}")
++  set(OB_MODULE_PATH "${CMAKE_INSTALL_PREFIX}/${OB_PLUGIN_INSTALL_DIR}"
++      CACHE PATH "Set to system install for bindings only build")
+   add_definitions(-DOB_MODULE_PATH="\\"${OB_MODULE_PATH}\\"")
+ 
+   # Add some visibility support when using GCC
+@@ -380,7 +381,8 @@ if(UNIX AND BUILD_SHARED)
+   if(APPLE)
+     set(CMAKE_INSTALL_NAME_DIR ${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR})
+   else()
+-    set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}")
++    set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}"
++        CACHE PATH "Set sane rpath")
+     set(CMAKE_SKIP_BUILD_RPATH FALSE)
+     set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
+     set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
+@@ -477,6 +479,13 @@ endif()
+ # Should the language bindings be regenereted?
+ option(RUN_SWIG "Generate language bindings with SWIG" OFF)
+ 
++# Build bindings only
++option(BINDINGS_ONLY "Build bindings only" OFF)
++
++# Point to library if building bindings only
++set(BABEL_SYSTEM_LIBRARY ${BABEL_LIBRARY}
++    CACHE PATH "Point to openbabel library if building bindings only")
++
+ # Should all bindings be built?
+ option(ALL_BINDINGS "Build all languages bindings" OFF)
+ 
+diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt
+index 16e9000..8f92e91 100644
+--- a/scripts/CMakeLists.txt
++++ b/scripts/CMakeLists.txt
+@@ -92,16 +92,30 @@ if (DO_PYTHON_BINDINGS)
+     endif(RUN_SWIG)
+ 
+     add_library(bindings_python MODULE ${openbabel_SOURCE_DIR}/scripts/python/openbabel-python.cpp)
+-    target_link_libraries(bindings_python ${PYTHON_LIBRARIES} ${BABEL_LIBRARY})
++    if(BINDINGS_ONLY)
++        target_link_libraries(bindings_python ${PYTHON_LIBRARIES} ${BABEL_SYSTEM_LIBRARY})
++    else()
++        target_link_libraries(bindings_python ${PYTHON_LIBRARIES} ${BABEL_LIBRARY})
++    endif()
++
+     if(NOT WIN32)
+         set_target_properties(bindings_python PROPERTIES
+             OUTPUT_NAME _openbabel
+             PREFIX ""
+             SUFFIX .so )
+-        add_dependencies(bindings_python openbabel)
+-        install(TARGETS bindings_python LIBRARY DESTINATION ${LIB_INSTALL_DIR})
+-        install(FILES ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py DESTINATION ${LIB_INSTALL_DIR})
+-        install(FILES ${openbabel_SOURCE_DIR}/scripts/python/pybel.py DESTINATION ${LIB_INSTALL_DIR})
++        if(NOT BINDINGS_ONLY)
++            add_dependencies(bindings_python openbabel)
++        endif()
++
++        install(TARGETS bindings_python
++                LIBRARY DESTINATION ${LIB_INSTALL_DIR}
++                COMPONENT bindings_python)
++        install(FILES ${openbabel_SOURCE_DIR}/scripts/python/openbabel.py
++                DESTINATION ${LIB_INSTALL_DIR}
++                COMPONENT bindings_python)
++        install(FILES ${openbabel_SOURCE_DIR}/scripts/python/pybel.py
++                DESTINATION ${LIB_INSTALL_DIR}
++                COMPONENT bindings_python)
+     else(NOT WIN32)
+         set_target_properties(bindings_python PROPERTIES
+             OUTPUT_NAME _openbabel
+@@ -231,13 +245,25 @@ if (DO_PERL_BINDINGS)
+     endif (RUN_SWIG)
+ 
+     add_library(bindings_perl MODULE ${openbabel_SOURCE_DIR}/scripts/perl/openbabel-perl.cpp)
+-    target_link_libraries(bindings_perl ${PERL_LIBRARY} ${BABEL_LIBRARY} ${PERL_EXTRA_LINK_FLAGS})
++    if(BINDINGS_ONLY)
++      target_link_libraries(bindings_perl ${PERL_LIBRARY} ${BABEL_SYSTEM_LIBRARY} ${PERL_EXTRA_LINK_FLAGS})
++    else()
++      target_link_libraries(bindings_perl ${PERL_LIBRARY} ${BABEL_LIBRARY} ${PERL_EXTRA_LINK_FLAGS})
++    endif()
++
+     set_target_properties(bindings_perl PROPERTIES
+         PREFIX ""
+         OUTPUT_NAME OpenBabel)
+-    add_dependencies(bindings_perl openbabel)
+-    install(TARGETS bindings_perl LIBRARY DESTINATION ${LIB_INSTALL_DIR})
+-    install(FILES ${openbabel_SOURCE_DIR}/scripts/perl/OpenBabel.pm DESTINATION ${LIB_INSTALL_DIR})
++    if(NOT BINDINGS_ONLY)
++      add_dependencies(bindings_perl openbabel)
++    endif()
++
++    install(TARGETS bindings_perl
++            LIBRARY DESTINATION ${LIB_INSTALL_DIR}/auto/Chemistry/OpenBabel/
++            COMPONENT bindings_perl)
++    install(FILES ${openbabel_SOURCE_DIR}/scripts/perl/OpenBabel.pm
++            DESTINATION ${LIB_INSTALL_DIR}/Chemistry/
++            COMPONENT bindings_perl)
+ 
+ endif (DO_PERL_BINDINGS)
+ 

diff --git a/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-trunk_cmake.patch b/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-trunk_cmake.patch
new file mode 100644
index 0000000..b72a622
--- /dev/null
+++ b/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-trunk_cmake.patch
@@ -0,0 +1,41 @@
+diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt
+index e7298ce..16e9000 100644
+--- a/scripts/CMakeLists.txt
++++ b/scripts/CMakeLists.txt
+@@ -231,36 +239,6 @@ if (DO_PERL_BINDINGS)
+     install(TARGETS bindings_perl LIBRARY DESTINATION ${LIB_INSTALL_DIR})
+     install(FILES ${openbabel_SOURCE_DIR}/scripts/perl/OpenBabel.pm DESTINATION ${LIB_INSTALL_DIR})
+ 
+-    set(PERL_INSTALLDIRS_TEXT "")
+-    if (OBPERL_INSTALLDIRS)
+-      set(PERL_INSTALLDIRS_TEXT "INSTALLDIRS=${OBPERL_INSTALLDIRS}")
+-    endif (OBPERL_INSTALLDIRS)
+-
+-    if (NOT MSVC)
+-      add_custom_target(pre_bindings_perl ALL
+-        # Create the scripts/perl directory; we cannot do this inside
+-        # bindings_perl as the WORKING_DIRECTORY needs to already exist!
+-        COMMAND ${CMAKE_COMMAND} -E make_directory ${openbabel_BINARY_DIR}/scripts/perl
+-        )
+-      add_custom_target(bindings_perl ALL
+-        COMMAND ${CMAKE_COMMAND} -E copy ${openbabel_SOURCE_DIR}/scripts/perl/Makefile.PL ${openbabel_BINARY_DIR}/scripts/perl
+-        COMMAND ${CMAKE_COMMAND} -E copy ${openbabel_SOURCE_DIR}/scripts/perl/OpenBabel.pm ${openbabel_BINARY_DIR}/scripts/perl
+-        COMMAND ${CMAKE_COMMAND} -E copy ${openbabel_SOURCE_DIR}/scripts/perl/openbabel-perl.cpp ${openbabel_BINARY_DIR}/scripts/perl
+-        COMMAND PERL5LIB=${openbabel_SOURCE_DIR}/scripts/perl/inc SRC_DIR=${openbabel_SOURCE_DIR} OBJ_DIR=${openbabel_BINARY_DIR} ${PERL_EXECUTABLE} ${openbabel_BINARY_DIR}/scripts/perl/Makefile.PL ${PERL_PREFIX_TEXT} ${PERL_INSTALLDIRS_TEXT}
+-        COMMAND PERL5LIB=${openbabel_SOURCE_DIR}/scripts/perl/inc make
+-            DEPENDS openbabel ${openbabel_SOURCE_DIR}/scripts/perl/openbabel-perl.cpp
+-            WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts/perl
+-        )
+-      add_dependencies(bindings_perl pre_bindings_perl openbabel)
+-      install(CODE "execute_process(COMMAND make install DESTDIR=\$ENV{DESTDIR} WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts/perl)")
+-
+-    else (NOT MSVC)
+-      add_library(bindings_perl MODULE ${openbabel_SOURCE_DIR}/scripts/perl/openbabel-perl.cpp)
+-      target_link_libraries(bindings_perl ${PERL_LIBRARY} ${BABEL_LIBRARY})
+-      set_target_properties(bindings_perl PROPERTIES
+-          OUTPUT_NAME openbabel_perl )
+-    endif(NOT MSVC)
+-
+ endif (DO_PERL_BINDINGS)
+ 
+ ###################

diff --git a/sci-chemistry/openbabel-perl/metadata.xml b/sci-chemistry/openbabel-perl/metadata.xml
new file mode 100644
index 0000000..8bbdbef
--- /dev/null
+++ b/sci-chemistry/openbabel-perl/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci-chemistry</herd>
+	<longdescription>
+		OpenBabel is a chemical toolbox designed to speak the many languages of
+		chemical data. It's an open, collaborative project allowing anyone to
+		search, convert, analyze, or store data from molecular modeling, chemistry,
+		solid-state materials, biochemistry, or related areas. This package enables
+		to access OpenBabel library from Perl programs.
+	</longdescription>
+</pkgmetadata>

diff --git a/sci-chemistry/openbabel-perl/openbabel-perl-2.3.2.ebuild b/sci-chemistry/openbabel-perl/openbabel-perl-2.3.2.ebuild
new file mode 100644
index 0000000..605184e
--- /dev/null
+++ b/sci-chemistry/openbabel-perl/openbabel-perl-2.3.2.ebuild
@@ -0,0 +1,66 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit cmake-utils eutils #perl-module
+
+DESCRIPTION="Perl bindings for OpenBabel"
+HOMEPAGE="http://openbabel.sourceforge.net/"
+SRC_URI="mirror://sourceforge/openbabel/openbabel-${PV}.tar.gz"
+
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+SLOT="0"
+LICENSE="GPL-2"
+IUSE=""
+
+RDEPEND="
+	dev-lang/perl
+	~sci-chemistry/openbabel-${PV}"
+DEPEND="${RDEPEND}
+	>=dev-util/cmake-2.4.8
+	>=dev-lang/swig-2"
+
+S="${WORKDIR}/openbabel-${PV}"
+
+src_prepare() {
+	epatch "${FILESDIR}/${P}-trunk_cmake.patch"
+	epatch "${FILESDIR}/${P}-bindings_only.patch"
+}
+
+src_configure() {
+	#perl-module_src_configure
+	eval "$(${EPREFIX}/usr/bin/perl -V:installvendorarch)"
+	local mycmakeargs="${mycmakeargs}
+		-DCMAKE_INSTALL_RPATH=
+		-DBINDINGS_ONLY=ON
+		-DBABEL_SYSTEM_LIBRARY=${EPREFIX}/usr/$(get_libdir)/libopenbabel.so
+		-DOB_MODULE_PATH=${EPREFIX}/usr/$(get_libdir)/openbabel/${PV}
+		-DLIB_INSTALL_DIR=${ED}/${installvendorarch}
+		-DPERL_BINDINGS=ON
+		-DRUN_SWIG=ON"
+
+	cmake-utils_src_configure
+}
+
+src_compile() {
+	cmake-utils_src_compile bindings_perl
+}
+
+src_test() {
+	mkdir "${CMAKE_BUILD_DIR}/$(get_libdir)/Chemistry"
+	cp \
+		"${CMAKE_USE_DIR}/scripts/perl/OpenBabel.pm" \
+		"${CMAKE_BUILD_DIR}/$(get_libdir)/Chemistry/"
+	for i in "${CMAKE_USE_DIR}"/scripts/perl/t/*
+	do
+		echo ${i}
+		"${EPREFIX}"/usr/bin/perl -I"${CMAKE_BUILD_DIR}/$(get_libdir)" "${i}" || die
+	done
+}
+
+src_install() {
+	cd "${CMAKE_BUILD_DIR}"
+	cmake -DCOMPONENT=bindings_perl -P cmake_install.cmake
+}