From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-chemistry/openbabel-perl/Manifest | 10 ++ .../files/openbabel-perl-2.3.2-bindings_only.patch | 108 +++++++++++++++++++++ ...openbabel-perl-2.3.2-gcc-6_and_7-backport.patch | 13 +++ .../files/openbabel-perl-2.3.2-trunk_cmake.patch | 41 ++++++++ sci-chemistry/openbabel-perl/metadata.xml | 18 ++++ .../openbabel-perl/openbabel-perl-2.3.2.ebuild | 72 ++++++++++++++ .../openbabel-perl/openbabel-perl-2.4.1.ebuild | 70 +++++++++++++ 7 files changed, 332 insertions(+) create mode 100644 sci-chemistry/openbabel-perl/Manifest create mode 100644 sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-bindings_only.patch create mode 100644 sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-gcc-6_and_7-backport.patch create mode 100644 sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-trunk_cmake.patch create mode 100644 sci-chemistry/openbabel-perl/metadata.xml create mode 100644 sci-chemistry/openbabel-perl/openbabel-perl-2.3.2.ebuild create mode 100644 sci-chemistry/openbabel-perl/openbabel-perl-2.4.1.ebuild (limited to 'sci-chemistry/openbabel-perl') diff --git a/sci-chemistry/openbabel-perl/Manifest b/sci-chemistry/openbabel-perl/Manifest new file mode 100644 index 000000000000..430fc44ecbdd --- /dev/null +++ b/sci-chemistry/openbabel-perl/Manifest @@ -0,0 +1,10 @@ +AUX openbabel-perl-2.3.2-bindings_only.patch 4557 SHA256 5ccb04d28bcbaf190275581fb66729b6a06c59b2e4a10e288bd90251f06f66a5 SHA512 475600513f188f2e3dee711ab2073954511b7d71c0af222dc9fe121bcbd4821d0ab32934d5035452ad4820d0dd750899995696c20504769b25cad7ef2d27aa5e WHIRLPOOL c573a123b43c67324b04a1283b2b567ed589f619dc2a22c1f4937edab82a2da40d74f56e52cb2d9418477c7713fd1f450dfd2f6b4563f745717a5a417a67975b +AUX openbabel-perl-2.3.2-gcc-6_and_7-backport.patch 635 SHA256 49f9fc47d1c864d501a266c4d1d7251d5921ce64f1de33a7679d369938bd8490 SHA512 e1b4402f34d01ced5b4caaa184b4e5544cf47893cfe7958054052b05a57dc34b4d44239a212c7d909f29b9366b83b6df74993f844a20f23748c01272ec093081 WHIRLPOOL 8789037e71722ee28d8769eadc574edf2d7d80e8e01f6a8475b18fd4ed0314757bd02854eacf375f7c23ca20b9ec8cc9a40797b51ad3fe64921440549a49cd3d +AUX openbabel-perl-2.3.2-trunk_cmake.patch 2335 SHA256 20692e07e436c610b0d18f6a28ebaef342b43053b3b1dd57cc23b0c87fe5dedf SHA512 9f42cb3c8aff7eb765790fd3a7f259d8076ebce11f3c2e324a9568a94d948583455db90a8714cdcbd6b6a74087167ada9ec19261862233823d0792bc79302f30 WHIRLPOOL 766f7f1eec840021cc7fe29e94a45a839966bb4726578c72d341dcb9047bb71eec50df72de1072888d158b4ff69b7ee2c8c88a97e1569fb4f4024c8de3d26213 +DIST openbabel-2.3.2.tar.gz 20509105 SHA256 4eaca26679aa6cc85ebf96af19191472ac63ca442c36b0427b369c3a25705188 SHA512 d0e1f8b758ffdd65ec6c31d988bffe3279355e286ce69fad12c5905b3b832e2b73ee95b1061b1576aba1ee9fe4da5e31ec30350c473be17493c657dc80caf919 WHIRLPOOL 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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 ${LIB_INSTALL_DIR}/Chemistry/ ++ COMPONENT bindings_perl) + + endif (DO_PERL_BINDINGS) + diff --git a/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-gcc-6_and_7-backport.patch b/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-gcc-6_and_7-backport.patch new file mode 100644 index 000000000000..e23dc6020ee5 --- /dev/null +++ b/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-gcc-6_and_7-backport.patch @@ -0,0 +1,13 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 0ee545cf..7f4b944e 100755 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -239,7 +239,7 @@ check_type_size(clock_t CLOCK_T) + # Get the GCC version - from KDE4 cmake files + if(CMAKE_COMPILER_IS_GNUCXX) + exec_program(${CMAKE_C_COMPILER} ARGS --version OUTPUT_VARIABLE _gcc_version_info) +- string(REGEX MATCH "[345]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}") ++ string(REGEX MATCH "[34567]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}") + # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the + # patch level, handle this here: + if (NOT _gcc_version) 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 000000000000..b72a622a3afb --- /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} ${BABEL_LIBRARY}) +- set_target_properties(bindings_perl PROPERTIES +- OUTPUT_NAME openbabel_perl ) +- endif(NOT MSVC) +- + endif (DO_PERL_BINDINGS) + + ################### diff --git a/sci-chemistry/openbabel-perl/metadata.xml b/sci-chemistry/openbabel-perl/metadata.xml new file mode 100644 index 000000000000..e549fb694ab7 --- /dev/null +++ b/sci-chemistry/openbabel-perl/metadata.xml @@ -0,0 +1,18 @@ + + + + + sci-chemistry@gentoo.org + Gentoo Chemistry Project + + +OpenBabel is a chemical toolbox designed to speak the many languages of +chemical data. It's an open, collaborative project allowing anyone to +search, convert, analyze, or store data from molecular modeling, chemistry, +solid-state materials, biochemistry, or related areas. +This package enables to access OpenBabel library from Perl programs. + + + openbabel + + diff --git a/sci-chemistry/openbabel-perl/openbabel-perl-2.3.2.ebuild b/sci-chemistry/openbabel-perl/openbabel-perl-2.3.2.ebuild new file mode 100644 index 000000000000..1f6b5d8005a2 --- /dev/null +++ b/sci-chemistry/openbabel-perl/openbabel-perl-2.3.2.ebuild @@ -0,0 +1,72 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +inherit cmake-utils eutils perl-module + +DESCRIPTION="Perl bindings for OpenBabel" +HOMEPAGE="http://openbabel.sourceforge.net/" +SRC_URI="mirror://sourceforge/openbabel/openbabel-${PV}.tar.gz" + +KEYWORDS="amd64 ~arm 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}" + +PATCHES=( + "${FILESDIR}"/${P}-trunk_cmake.patch + "${FILESDIR}"/${P}-bindings_only.patch + "${FILESDIR}"/${P}-gcc-6_and_7-backport.patch +) + +src_prepare() { + sed \ + -e '/__GNUC__/s:== 4:>= 4:g' \ + -i include/openbabel/shared_ptr.h || die + epatch "${PATCHES[@]}" + perl_set_version +} + +src_configure() { + local mycmakeargs=( + -DCMAKE_INSTALL_RPATH= + -DBINDINGS_ONLY=ON + -DBABEL_SYSTEM_LIBRARY="${EPREFIX}/usr/$(get_libdir)/libopenbabel.so" + -DOB_MODULE_PATH="${EPREFIX}/usr/$(get_libdir)/openbabel/${PV}" + -DLIB_INSTALL_DIR="${D}/${VENDOR_ARCH}" + -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 + einfo "Running test: ${i}" + perl -I"${CMAKE_BUILD_DIR}/$(get_libdir)" "${i}" || die + done +} + +src_install() { + cd "${CMAKE_BUILD_DIR}" + cmake -DCOMPONENT=bindings_perl -P cmake_install.cmake +} diff --git a/sci-chemistry/openbabel-perl/openbabel-perl-2.4.1.ebuild b/sci-chemistry/openbabel-perl/openbabel-perl-2.4.1.ebuild new file mode 100644 index 000000000000..1e01e9007b7b --- /dev/null +++ b/sci-chemistry/openbabel-perl/openbabel-perl-2.4.1.ebuild @@ -0,0 +1,70 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit cmake-utils perl-module + +DESCRIPTION="Perl bindings for OpenBabel" +HOMEPAGE="http://openbabel.sourceforge.net/" +SRC_URI="mirror://sourceforge/openbabel/openbabel-${PV}.tar.gz" + +KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux" +SLOT="0/5" +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}" + +PATCHES=( + "${FILESDIR}"/${PN}-2.3.2-gcc-6_and_7-backport.patch +) + +src_prepare() { + sed \ + -e '/__GNUC__/s:== 4:>= 4:g' \ + -i include/openbabel/shared_ptr.h || die + default + perl_set_version +} + +src_configure() { + local mycmakeargs=( + -DCMAKE_INSTALL_RPATH= + -DBINDINGS_ONLY=ON + -DBABEL_SYSTEM_LIBRARY="${EPREFIX}/usr/$(get_libdir)/libopenbabel.so" + -DOB_MODULE_PATH="${EPREFIX}/usr/$(get_libdir)/openbabel/${PV}" + -DLIB_INSTALL_DIR="${D}/${VENDOR_ARCH}" + -DPERL_BINDINGS=ON + -DRUN_SWIG=ON + ) + + cmake-utils_src_configure +} + +src_compile() { + cmake-utils_src_compile bindings_perl +} + +src_test() { + mkdir "${CMAKE_BUILD_DIR}/$(get_libdir)/Chemistry" || die + cp \ + "${CMAKE_USE_DIR}/scripts/perl/OpenBabel.pm" \ + "${CMAKE_BUILD_DIR}/$(get_libdir)/Chemistry/" || die + for i in "${CMAKE_USE_DIR}"/scripts/perl/t/*; do + einfo "Running test: ${i}" + perl -I"${CMAKE_BUILD_DIR}/$(get_libdir)" "${i}" || die + done +} + +src_install() { + cd "${CMAKE_BUILD_DIR}" || die + cmake -DCOMPONENT=bindings_perl -P cmake_install.cmake +} -- cgit v1.2.3