diff options
| author |   Justin Lecher <jlec@gentoo.org> | 2012-12-06 17:09:31 +0000 |
|---|---|---|
| committer | Justin Lecher <jlec@gentoo.org> | 2012-12-06 17:09:31 +0000 |
| commit | ca9c9a9b7cf6a7335986006f7c034900d91dbe81 (patch) | |
| tree | 92b742cee9e746cbf5d7bf50536b7396e35bb862 /sci-chemistry/openbabel-python | |
| parent | Add bug number. (diff) | |
| download | historical-ca9c9a9b7cf6a7335986006f7c034900d91dbe81.tar.gz historical-ca9c9a9b7cf6a7335986006f7c034900d91dbe81.tar.bz2 historical-ca9c9a9b7cf6a7335986006f7c034900d91dbe81.zip | |
sci-chemistry/openbabel-python: Version Bump prepared by Reinis Danne, #439434
Package-Manager: portage-2.2.0_alpha144/cvs/Linux x86_64
Manifest-Sign-Key: 0x70EB7916
Diffstat (limited to 'sci-chemistry/openbabel-python')
5 files changed, 361 insertions, 17 deletions
diff --git a/sci-chemistry/openbabel-python/ChangeLog b/sci-chemistry/openbabel-python/ChangeLog index 473ee2d91087..57faf7b391e6 100644 --- a/sci-chemistry/openbabel-python/ChangeLog +++ b/sci-chemistry/openbabel-python/ChangeLog @@ -1,6 +1,13 @@ # ChangeLog for sci-chemistry/openbabel-python # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/openbabel-python/ChangeLog,v 1.8 2012/03/04 10:29:38 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/openbabel-python/ChangeLog,v 1.9 2012/12/06 17:09:30 jlec Exp $ + +*openbabel-python-2.3.2 (06 Dec 2012) + + 06 Dec 2012; Justin Lecher <jlec@gentoo.org> +openbabel-python-2.3.2.ebuild, + +files/openbabel-python-2.3.2-bindings_only.patch, + +files/openbabel-python-2.3.2-testpybel.patch: + Version Bump prepared by Reinis Danne, #439434 *openbabel-python-2.3.1 (04 Mar 2012) diff --git a/sci-chemistry/openbabel-python/Manifest b/sci-chemistry/openbabel-python/Manifest index be9cd54d23a8..7e91c146ca5c 100644 --- a/sci-chemistry/openbabel-python/Manifest +++ b/sci-chemistry/openbabel-python/Manifest @@ -1,21 +1,25 @@ -----BEGIN PGP SIGNED MESSAGE----- -Hash: SHA512 +Hash: SHA256 -AUX openbabel-python-2.3.0-py3_iterator.patch 346 RMD160 56692e9ab5ce307736a217e2c34121d055fcc5b9 SHA1 6e7dcffa4aa4d6c789b968598f97cc0ebb2165dd SHA256 d138acc218e006e5f5f2defb24c9183f8feae48a5d775788badde21fef77d68e -AUX openbabel-python-2.3.0-swig.patch 887 RMD160 5fa3e9f6ee70c4f7ec542840cdf861a7b6b8acd5 SHA1 eaf1d9b79787a82734195433bf2ef29f81e0a10c SHA256 2cb191078d1280325ab2eea473be8800e5989e33d0d11a673702436a65954a4e -AUX openbabel-python-2.3.0-system_openbabel.patch 529 RMD160 a1fd4653ad351cdd8b828497d63d9e80b33a9bd4 SHA1 c7bf439c46a912b78b9dcf3e5f7ac8b052677c0f SHA256 c8ae97e253ae2431418a2f06f0cb86c495ea05434062c391c09866af51ea609c -AUX openbabel-python-2.3.0-wrap_OBInternalCoord.patch 391 RMD160 d998f3b0cf238fdc925f5f1637630645232e956e SHA1 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b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-bindings_only.patch new file mode 100644 index 000000000000..2e776b4029ec --- /dev/null +++ b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-bindings_only.patch @@ -0,0 +1,209 @@ +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..ecd2295 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 ${LIB_INSTALL_DIR} ++ COMPONENT bindings_python) + else(NOT WIN32) + set_target_properties(bindings_python PROPERTIES + OUTPUT_NAME _openbabel +diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt +index 7841782..6f3495f 100644 +--- a/test/CMakeLists.txt ++++ b/test/CMakeLists.txt +@@ -2,7 +2,12 @@ + add_definitions(-DTESTDATADIR="\\"${CMAKE_SOURCE_DIR}/test/files/\\"") + + # define FORMATDIR for location of format plugin binaries +-add_definitions(-DFORMATDIR="\\"${openbabel_BINARY_DIR}/lib/\\"") ++if(BINDINGS_ONLY) ++ set(FORMATDIR "${OB_MODULE_PATH}/") ++else() ++ set(FORMATDIR "${openbabel_BINARY_DIR}/lib${LIB_SUFFIX}/") ++endif() ++add_definitions(-DFORMATDIR="\\"${FORMATDIR}/\\"") + + ########################################################### + # new tests using obtest.h +@@ -89,7 +94,7 @@ foreach(test ${tests}) + add_test(${test}_Test ${TEST_PATH}/test_${test}) + set_tests_properties(${test}_Test PROPERTIES + FAIL_REGULAR_EXPRESSION "ERROR;FAIL;Test failed" +- ENVIRONMENT "BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data;LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib") ++ ENVIRONMENT "BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data;LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}") + endforeach(test ${tests}) + + ############################################################ +@@ -152,7 +157,7 @@ if(WITH_INCHI) + ${TEST_PATH}/test_inchiwrite ${inchidata}/${test} ${inchidata}/${test}.txt) + set_tests_properties(inchi${test}_Test PROPERTIES + FAIL_REGULAR_EXPRESSION "Not ok" +- ENVIRONMENT "BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data;LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib" ++ ENVIRONMENT "BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data;LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}" + ) + endforeach(test ${inchitests}) + endif(WITH_INCHI) +@@ -166,7 +171,7 @@ foreach(test ${old_tests}) + add_test(${test}_Test ${TEST_PATH}/test_${test}) + set_tests_properties(${test}_Test PROPERTIES + FAIL_REGULAR_EXPRESSION "not ok" +- ENVIRONMENT "BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data;LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib" ++ ENVIRONMENT "BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data;LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}" + ) + endforeach(test ${old_tests}) + +@@ -181,8 +186,8 @@ if(NOT BUILD_SHARED AND NOT BUILD_MIXED) + endif() + install(TARGETS roundtrip + RUNTIME DESTINATION bin +- LIBRARY DESTINATION lib +- ARCHIVE DESTINATION lib ++ LIBRARY DESTINATION lib${LIB_SUFFIX} ++ ARCHIVE DESTINATION lib${LIB_SUFFIX} + ) + + ########################### +@@ -199,10 +204,10 @@ if(NOT MINGW AND NOT CYGWIN) + babel sym smartssym fastsearch unique kekule) + foreach(pytest ${pytests}) + SET_SOURCE_FILES_PROPERTIES(test${pytest}.py PROPERTIES +- PYTHONPATH "${CMAKE_SOURCE_DIR}/scripts/python:${CMAKE_BINARY_DIR}/lib" +- BABEL_LIBDIR "${CMAKE_BINARY_DIR}/lib" ++ PYTHONPATH "${CMAKE_SOURCE_DIR}/scripts/python:${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}" ++ BABEL_LIBDIR "${FORMATDIR}" + BABEL_DATADIR "${CMAKE_SOURCE_DIR}/data" +- LD_LIBRARY_PATH "${CMAKE_BINARY_DIR}/lib" ++ LD_LIBRARY_PATH "${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}" + ) + ADD_PYTHON_TEST(pytest_${pytest} test${pytest}.py) + set_tests_properties(pytest_${pytest} PROPERTIES +@@ -221,10 +226,10 @@ if (PYTHON_BINDINGS) + bindings _pybel example) + foreach(pybindtest ${pybindtests}) + SET_SOURCE_FILES_PROPERTIES(test${pybindtest}.py PROPERTIES +- PYTHONPATH "${CMAKE_SOURCE_DIR}/scripts/python:${CMAKE_BINARY_DIR}/lib" +- BABEL_LIBDIR "${CMAKE_BINARY_DIR}/lib" ++ PYTHONPATH "${CMAKE_SOURCE_DIR}/scripts/python:${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}" ++ BABEL_LIBDIR "${FORMATDIR}" + BABEL_DATADIR "${CMAKE_SOURCE_DIR}/data" +- LD_LIBRARY_PATH "${CMAKE_BINARY_DIR}/lib" ++ LD_LIBRARY_PATH "${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}" + ) + if(MSVC) + SET_SOURCE_FILES_PROPERTIES(test${pybindtest}.py PROPERTIES +diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt +index 1f547bf..fb98441 100644 +--- a/tools/CMakeLists.txt ++++ b/tools/CMakeLists.txt +@@ -38,8 +38,8 @@ if(BUILD_SHARED) + target_link_libraries(${tool} ${BABEL_LIBRARY}) + install(TARGETS ${tool} + RUNTIME DESTINATION bin +- LIBRARY DESTINATION lib +- ARCHIVE DESTINATION lib ++ LIBRARY DESTINATION lib${LIB_SUFFIX} ++ ARCHIVE DESTINATION lib${LIB_SUFFIX} + ) + endforeach(tool) + +@@ -53,8 +53,8 @@ if(BUILD_SHARED) + target_link_libraries(obspectrophore ${BABEL_LIBRARY}) + install(TARGETS obspectrophore + RUNTIME DESTINATION bin +- LIBRARY DESTINATION lib +- ARCHIVE DESTINATION lib ++ LIBRARY DESTINATION lib${LIB_SUFFIX} ++ ARCHIVE DESTINATION lib${LIB_SUFFIX} + ) + + # obgrep -- requires getopt +@@ -66,8 +66,8 @@ if(BUILD_SHARED) + target_link_libraries(obgrep ${BABEL_LIBRARY}) + install(TARGETS obgrep + RUNTIME DESTINATION bin +- LIBRARY DESTINATION lib +- ARCHIVE DESTINATION lib ++ LIBRARY DESTINATION lib${LIB_SUFFIX} ++ ARCHIVE DESTINATION lib${LIB_SUFFIX} + ) + endif(NOT MINIMAL_BUILD) + +@@ -146,7 +146,7 @@ else(BUILD_SHARED) + + install(TARGETS babel + RUNTIME DESTINATION bin +- LIBRARY DESTINATION lib +- ARCHIVE DESTINATION lib) ++ LIBRARY DESTINATION lib${LIB_SUFFIX} ++ ARCHIVE DESTINATION lib${LIB_SUFFIX}) + + endif(BUILD_SHARED) diff --git a/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-testpybel.patch b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-testpybel.patch new file mode 100644 index 000000000000..7a0114975fff --- /dev/null +++ b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-testpybel.patch @@ -0,0 +1,28 @@ +From b34edb6de512e5735d87cb0893804a4abd14f9b7 Mon Sep 17 00:00:00 2001 +From: baoilleach <baoilleach@71e0b675-c112-0410-beda-96664073b5c2> +Date: Mon, 1 Oct 2012 20:40:36 +0000 +Subject: [PATCH] scripts/python/testpybel.py: Minor fix to enable failing + test to pass. Failures due to the new MOL Chiral Flag data + that I stored a while ago. + +git-svn-id: https://openbabel.svn.sourceforge.net/svnroot/openbabel/openbabel/trunk@5022 71e0b675-c112-0410-beda-96664073b5c2 +--- + scripts/python/examples/testpybel.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/scripts/python/examples/testpybel.py b/scripts/python/examples/testpybel.py +index aa5fcd4..7951851 100644 +--- a/scripts/python/examples/testpybel.py ++++ b/scripts/python/examples/testpybel.py +@@ -336,7 +336,7 @@ class TestPybel(TestToolkit): + tpsaname = "TPSA" + Nbits = 3 + Nfpbits = 32 +- datakeys = ['NSC', 'Comment', 'OpenBabel Symmetry Classes'] ++ datakeys = ['NSC', 'Comment', 'OpenBabel Symmetry Classes', 'MOL Chiral Flag'] + + def testFP_FP3(self): + "Checking the results from FP3" +-- +1.7.12.3 + diff --git a/sci-chemistry/openbabel-python/openbabel-python-2.3.2.ebuild b/sci-chemistry/openbabel-python/openbabel-python-2.3.2.ebuild new file mode 100644 index 000000000000..e94d2f4a8343 --- /dev/null +++ b/sci-chemistry/openbabel-python/openbabel-python-2.3.2.ebuild @@ -0,0 +1,96 @@ +# Copyright 1999-2012 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/openbabel-python/openbabel-python-2.3.2.ebuild,v 1.1 2012/12/06 17:09:30 jlec Exp $ + +EAPI=5 + +PYTHON_COMPAT=(python2_6 python2_7 python3_1 python3_2) + +inherit cmake-utils eutils multilib python-r1 + +DESCRIPTION="Python bindings for OpenBabel (including Pybel)" +HOMEPAGE="http://openbabel.sourceforge.net/" +SRC_URI="mirror://sourceforge/openbabel/openbabel-${PV}.tar.gz" + +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +SLOT="0" +LICENSE="GPL-2" +IUSE="" + +RDEPEND="${PYTHON_DEPS} + !sci-chemistry/babel + ~sci-chemistry/openbabel-${PV} + sys-libs/zlib" +DEPEND="${RDEPEND} + >=dev-util/cmake-2.4.8 + >=dev-lang/swig-2" + +S="${WORKDIR}"/openbabel-${PV} + +PATCHES=( + "${FILESDIR}/${P}-testpybel.patch" + "${FILESDIR}/${P}-bindings_only.patch" ) + +src_prepare() { + base_src_prepare + sed \ + -e "s:\"\.\.\":\"${EPREFIX}/usr\":g" \ + -i test/testbabel.py || die + swig -python -c++ -small -O -templatereduce -naturalvar \ + -I"${EPREFIX}/usr/include/openbabel-2.0" \ + -o scripts/python/openbabel-python.cpp \ + -DHAVE_EIGEN \ + -outdir scripts/python \ + scripts/openbabel-python.i \ + || die "Regeneration of openbabel-python.cpp failed" +} + +src_configure() { + my_impl_src_configure() { + CMAKE_BUILD_DIR="${BUILD_DIR}" + local mycmakeargs="${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}/usr/$(get_libdir)/${EPYTHON}/site-packages" + -DPYTHON_BINDINGS=ON + -DPYTHON_EXECUTABLE=${PYTHON} + -DPYTHON_INCLUDE_DIR="${EPREFIX}/usr/include/${EPYTHON}" + -DPYTHON_LIBRARY="${EPREFIX}/usr/$(get_libdir)/lib${EPYTHON}.so" + -DENABLE_TESTS=ON" + + cmake-utils_src_configure + } + + python_foreach_impl my_impl_src_configure +} + +src_compile() { + my_impl_src_compile() { + CMAKE_BUILD_DIR="${BUILD_DIR}" + + cmake-utils_src_make bindings_python + } + + python_foreach_impl my_impl_src_compile +} + +src_test() { + my_impl_src_test() { + CMAKE_BUILD_DIR="${BUILD_DIR}" + cmake-utils_src_test -R py + } + + python_foreach_impl my_impl_src_test +} + +src_install() { + my_impl_src_install() { + cd "${BUILD_DIR}" + + cmake -DCOMPONENT=bindings_python -P cmake_install.cmake + } + + python_foreach_impl my_impl_src_install +} |