From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id 114151381F3 for ; Thu, 6 Dec 2012 17:20:27 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 79AAD21C019; Thu, 6 Dec 2012 17:20:09 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 87D6B21C013 for ; Thu, 6 Dec 2012 17:20:08 +0000 (UTC) Received: from hornbill.gentoo.org (hornbill.gentoo.org [94.100.119.163]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 6AB2433DA3E for ; Thu, 6 Dec 2012 17:20:07 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by hornbill.gentoo.org (Postfix) with ESMTP id 03A0FE5449 for ; Thu, 6 Dec 2012 17:20:06 +0000 (UTC) From: "Justin Lecher" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Justin Lecher" Message-ID: <1354813818.4768fca0773e1e1783a9c023f131d8a86c6c7e59.jlec@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-chemistry/openbabel-python/files/, sci-chemistry/openbabel-python/ X-VCS-Repository: proj/sci X-VCS-Files: sci-chemistry/openbabel-python/ChangeLog sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-bindings_only.patch sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-testpybel.patch sci-chemistry/openbabel-python/metadata.xml sci-chemistry/openbabel-python/openbabel-python-2.3.2.ebuild X-VCS-Directories: sci-chemistry/openbabel-python/files/ sci-chemistry/openbabel-python/ X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: 4768fca0773e1e1783a9c023f131d8a86c6c7e59 X-VCS-Branch: master Date: Thu, 6 Dec 2012 17:20:06 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: defaa9d8-2ee9-4149-a9dc-6804654a8ac0 X-Archives-Hash: 8f3b5d093f2b57ce7c39da4b1f388b2f commit: 4768fca0773e1e1783a9c023f131d8a86c6c7e59 Author: Justin Lecher gentoo org> AuthorDate: Thu Dec 6 17:10:18 2012 +0000 Commit: Justin Lecher gentoo org> CommitDate: Thu Dec 6 17:10:18 2012 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4768fca0 Moved to tree Signed-off-by: Justin Lecher gentoo.org> --- sci-chemistry/openbabel-python/ChangeLog | 15 -- .../openbabel-python-2.3.2-bindings_only.patch | 209 -------------------- .../files/openbabel-python-2.3.2-testpybel.patch | 28 --- sci-chemistry/openbabel-python/metadata.xml | 12 -- .../openbabel-python/openbabel-python-2.3.2.ebuild | 94 --------- 5 files changed, 0 insertions(+), 358 deletions(-) diff --git a/sci-chemistry/openbabel-python/ChangeLog b/sci-chemistry/openbabel-python/ChangeLog deleted file mode 100644 index aa49a85..0000000 --- a/sci-chemistry/openbabel-python/ChangeLog +++ /dev/null @@ -1,15 +0,0 @@ -# ChangeLog for sci-chemistry/openbabel-python -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 10 Nov 2012; Reinis Danne openbabel-python-2.3.2.ebuild: - python-r1.eclass doesn't enter BUILD_DIR in python_foreach_impl, do it - manually where necessary. - -*openbabel-python-2.3.2 (19 Oct 2012) - - 19 Oct 2012; Reinis Danne +openbabel-python-2.3.2.ebuild, - +files/openbabel-python-2.3.2-bindings_only.patch, - +files/openbabel-python-2.3.2-testpybel.patch, +metadata.xml: - Bump to 2.3.2. - diff --git a/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-bindings_only.patch b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-bindings_only.patch deleted file mode 100644 index 2e776b4..0000000 --- a/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-bindings_only.patch +++ /dev/null @@ -1,209 +0,0 @@ -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 deleted file mode 100644 index 7a01149..0000000 --- a/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-testpybel.patch +++ /dev/null @@ -1,28 +0,0 @@ -From b34edb6de512e5735d87cb0893804a4abd14f9b7 Mon Sep 17 00:00:00 2001 -From: baoilleach -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/metadata.xml b/sci-chemistry/openbabel-python/metadata.xml deleted file mode 100644 index 433cfe8..0000000 --- a/sci-chemistry/openbabel-python/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ - - - - sci-chemistry - - 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 Python programs. - - diff --git a/sci-chemistry/openbabel-python/openbabel-python-2.3.2.ebuild b/sci-chemistry/openbabel-python/openbabel-python-2.3.2.ebuild deleted file mode 100644 index f24e084..0000000 --- a/sci-chemistry/openbabel-python/openbabel-python-2.3.2.ebuild +++ /dev/null @@ -1,94 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -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} - -src_prepare() { - epatch "${FILESDIR}/${P}-testpybel.patch" - epatch "${FILESDIR}/${P}-bindings_only.patch" - - 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="${BUILD_DIR}" - ln -s "${EPREFIX}/usr/bin/babel" bin/babel - ln -s "${EPREFIX}/usr/bin/obabel" bin/obabel - - cmake-utils_src_test -R py - } - - python_foreach_impl my_impl_src_test -} - -src_install() { - my_impl_src_install() { - cd "${BUILD_DIR}" - - cmake -DCOMPONENT=bindings_python -P cmake_install.cmake - } - - python_foreach_impl my_impl_src_install -}