diff --git a/sci-chemistry/openbabel-python/Manifest b/sci-chemistry/openbabel-python/Manifest new file mode 100644 index 000000000..ac268758e --- /dev/null +++ b/sci-chemistry/openbabel-python/Manifest @@ -0,0 +1 @@ +DIST openbabel-2.4.1.tar.gz 11618304 BLAKE2B 8fc051e83add9be6456e281a109bd6bbec282a64ffc83309819f0decbf167b4914fbb7f1966e95e103f268754045b804317f51c79a952ace707c6af2bd320125 SHA512 427e678f0a911bd27b9a8a05e60b6e09f113be4e5dd180daaf80c28d06368e52b57501261755ab3817a8d31f2754db24471fd0ceee706d029386d6f70800e9c6 diff --git a/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-gcc-6_and_7-backport.patch b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-gcc-6_and_7-backport.patch new file mode 100644 index 000000000..e23dc6020 --- /dev/null +++ b/sci-chemistry/openbabel-python/files/openbabel-python-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-python/files/openbabel-python-2.4.1-fix_cmake.patch b/sci-chemistry/openbabel-python/files/openbabel-python-2.4.1-fix_cmake.patch new file mode 100644 index 000000000..3147723b3 --- /dev/null +++ b/sci-chemistry/openbabel-python/files/openbabel-python-2.4.1-fix_cmake.patch @@ -0,0 +1,199 @@ +From 00120f89cf62b121c30d0b2a891b159e19b53624 Mon Sep 17 00:00:00 2001 +From: David Hall +Date: Mon, 4 Sep 2017 00:30:10 +0000 +Subject: [PATCH] Compiler version parsing and comparison from CMake 2.8 + +Fix for #1624 by using CMake's version parsing. Also move to using +CMake's internal version comparison operators. +--- + CMakeLists.txt | 35 ++++---- + cmake/modules/MacroEnsureVersion.cmake | 117 ------------------------- + 2 files changed, 17 insertions(+), 135 deletions(-) + delete mode 100644 cmake/modules/MacroEnsureVersion.cmake + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index b28ca09ce..1c3adfee7 100755 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -1,16 +1,11 @@ +-# Please ensure that any changes remain compliant with 2.4.8. ++# Please ensure that any changes remain compliant with 2.8.10. + if(NOT EMBED_OPENBABEL) +- cmake_minimum_required(VERSION 2.4.8) ++ cmake_minimum_required(VERSION 2.8.10) + endif() + + project(openbabel) + set(CMAKE_MODULE_PATH ${openbabel_SOURCE_DIR}/cmake/modules) + +-# Allow loose loop constructs, i.e. no matching in if/else/endif or loops. +-# Note that this is true by default in CMake 2.6.0, but we currently only +-# require CMake 2.4.8 - remove this when the CMake requirement is bumped. +-set(CMAKE_ALLOW_LOOSE_LOOP_CONSTRUCTS 1) +- + if(COMMAND cmake_policy) + cmake_policy(SET CMP0003 NEW) + cmake_policy(SET CMP0005 OLD) # add_definitions need updating to set to NEW +@@ -20,7 +15,6 @@ if(COMMAND cmake_policy) + endif() + + include (CheckCXXCompilerFlag) +-include (MacroEnsureVersion) + + # Version numbering - should be bumped for each release + # Note that for "beta" releases, we should start at x.90.0 -- we've +@@ -239,16 +233,21 @@ check_type_size(clock_t CLOCK_T) + + # Get the GCC version - from KDE4 cmake files + if(CMAKE_COMPILER_IS_GNUCXX) +- exec_program(${CMAKE_C_COMPILER} ARGS --version OUTPUT_VARIABLE _gcc_version_info) +- string(REGEX MATCH "[34567]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}") +- # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the +- # patch level, handle this here: +- if (NOT _gcc_version) +- string (REGEX REPLACE ".*\\(GCC\\).* ([34]\\.[0-9]) .*" "\\1.0" _gcc_version "${_gcc_version_info}") +- endif () +- macro_ensure_version("4.0.0" "${_gcc_version}" GCC_IS_NEWER_THAN_4_0) +- macro_ensure_version("4.1.0" "${_gcc_version}" GCC_IS_NEWER_THAN_4_1) +- macro_ensure_version("4.2.0" "${_gcc_version}" GCC_IS_NEWER_THAN_4_2) ++ if(NOT(${CMAKE_CXX_COMPILER_VERSION} VERSION_LESS 4.0.0)) ++ set(GCC_IS_NEWER_THAN_4_0 TRUE) ++ else() ++ set(GCC_IS_NEWER_THAN_4_0 FALSE) ++ endif() ++ if(NOT(${CMAKE_CXX_COMPILER_VERSION} VERSION_LESS 4.1.0)) ++ set(GCC_IS_NEWER_THAN_4_1 TRUE) ++ else() ++ set(GCC_IS_NEWER_THAN_4_1 FALSE) ++ endif() ++ if(NOT(${CMAKE_CXX_COMPILER_VERSION} VERSION_LESS 4.2.0)) ++ set(GCC_IS_NEWER_THAN_4_2 TRUE) ++ else() ++ set(GCC_IS_NEWER_THAN_4_2 FALSE) ++ endif() + endif() + + if(UNIX) +diff --git a/cmake/modules/MacroEnsureVersion.cmake b/cmake/modules/MacroEnsureVersion.cmake +deleted file mode 100644 +index 6797e5b7d..000000000 +--- a/cmake/modules/MacroEnsureVersion.cmake ++++ /dev/null +@@ -1,117 +0,0 @@ +-# This file defines the following macros for developers to use in ensuring +-# that installed software is of the right version: +-# +-# MACRO_ENSURE_VERSION - test that a version number is greater than +-# or equal to some minimum +-# MACRO_ENSURE_VERSION_RANGE - test that a version number is greater than +-# or equal to some minimum and less than some +-# maximum +-# MACRO_ENSURE_VERSION2 - deprecated, do not use in new code +-# +- +-# MACRO_ENSURE_VERSION +-# This macro compares version numbers of the form "x.y.z" or "x.y" +-# MACRO_ENSURE_VERSION( FOO_MIN_VERSION FOO_VERSION_FOUND FOO_VERSION_OK) +-# will set FOO_VERSION_OK to true if FOO_VERSION_FOUND >= FOO_MIN_VERSION +-# Leading and trailing text is ok, e.g. +-# MACRO_ENSURE_VERSION( "2.5.31" "flex 2.5.4a" VERSION_OK) +-# which means 2.5.31 is required and "flex 2.5.4a" is what was found on the system +- +-# Copyright (c) 2006, David Faure, +-# Copyright (c) 2007, Will Stephenson +-# +-# Redistribution and use is allowed according to the terms of the BSD license. +-# For details see the accompanying COPYING-CMAKE-SCRIPTS file. +- +-# MACRO_ENSURE_VERSION_RANGE +-# This macro ensures that a version number of the form +-# "x.y.z" or "x.y" falls within a range defined by +-# min_version <= found_version < max_version. +-# If this expression holds, FOO_VERSION_OK will be set TRUE +-# +-# Example: MACRO_ENSURE_VERSION_RANGE3( "0.1.0" ${FOOCODE_VERSION} "0.7.0" FOO_VERSION_OK ) +-# +-# This macro will break silently if any of x,y,z are greater than 100. +-# +-# Copyright (c) 2007, Will Stephenson +-# +-# Redistribution and use is allowed according to the terms of the BSD license. +-# For details see the accompanying COPYING-CMAKE-SCRIPTS file. +- +-# NORMALIZE_VERSION +-# Helper macro to convert version numbers of the form "x.y.z" +-# to an integer equal to 10^4 * x + 10^2 * y + z +-# +-# This macro will break silently if any of x,y,z are greater than 100. +-# +-# Copyright (c) 2006, David Faure, +-# Copyright (c) 2007, Will Stephenson +-# +-# Redistribution and use is allowed according to the terms of the BSD license. +-# For details see the accompanying COPYING-CMAKE-SCRIPTS file. +- +-# CHECK_RANGE_INCLUSIVE_LOWER +-# Helper macro to check whether x <= y < z +-# +-# Copyright (c) 2007, Will Stephenson +-# +-# Redistribution and use is allowed according to the terms of the BSD license. +-# For details see the accompanying COPYING-CMAKE-SCRIPTS file. +- +- +-MACRO(NORMALIZE_VERSION _requested_version _normalized_version) +- STRING(REGEX MATCH "[^0-9]*[0-9]+\\.[0-9]+\\.[0-9]+.*" _threePartMatch "${_requested_version}") +- if (_threePartMatch) +- # parse the parts of the version string +- STRING(REGEX REPLACE "[^0-9]*([0-9]+)\\.[0-9]+\\.[0-9]+.*" "\\1" _major_vers "${_requested_version}") +- STRING(REGEX REPLACE "[^0-9]*[0-9]+\\.([0-9]+)\\.[0-9]+.*" "\\1" _minor_vers "${_requested_version}") +- STRING(REGEX REPLACE "[^0-9]*[0-9]+\\.[0-9]+\\.([0-9]+).*" "\\1" _patch_vers "${_requested_version}") +- else (_threePartMatch) +- STRING(REGEX REPLACE "([0-9]+)\\.[0-9]+" "\\1" _major_vers "${_requested_version}") +- STRING(REGEX REPLACE "[0-9]+\\.([0-9]+)" "\\1" _minor_vers "${_requested_version}") +- set(_patch_vers "0") +- endif (_threePartMatch) +- +- # compute an overall version number which can be compared at once +- MATH(EXPR ${_normalized_version} "${_major_vers}*10000 + ${_minor_vers}*100 + ${_patch_vers}") +-ENDMACRO(NORMALIZE_VERSION) +- +-MACRO(MACRO_CHECK_RANGE_INCLUSIVE_LOWER _lower_limit _value _upper_limit _ok) +- if (${_value} LESS ${_lower_limit}) +- set( ${_ok} FALSE ) +- elseif (${_value} EQUAL ${_lower_limit}) +- set( ${_ok} TRUE ) +- elseif (${_value} EQUAL ${_upper_limit}) +- set( ${_ok} FALSE ) +- elseif (${_value} GREATER ${_upper_limit}) +- set( ${_ok} FALSE ) +- else (${_value} LESS ${_lower_limit}) +- set( ${_ok} TRUE ) +- endif (${_value} LESS ${_lower_limit}) +-ENDMACRO(MACRO_CHECK_RANGE_INCLUSIVE_LOWER) +- +-MACRO(MACRO_ENSURE_VERSION requested_version found_version var_too_old) +- NORMALIZE_VERSION( ${requested_version} req_vers_num ) +- NORMALIZE_VERSION( ${found_version} found_vers_num ) +- +- if (found_vers_num LESS req_vers_num) +- set( ${var_too_old} FALSE ) +- else (found_vers_num LESS req_vers_num) +- set( ${var_too_old} TRUE ) +- endif (found_vers_num LESS req_vers_num) +- +-ENDMACRO(MACRO_ENSURE_VERSION) +- +-MACRO(MACRO_ENSURE_VERSION2 requested_version2 found_version2 var_too_old2) +- MACRO_ENSURE_VERSION( ${requested_version2} ${found_version2} ${var_too_old2}) +-ENDMACRO(MACRO_ENSURE_VERSION2) +- +-MACRO(MACRO_ENSURE_VERSION_RANGE min_version found_version max_version var_ok) +- NORMALIZE_VERSION( ${min_version} req_vers_num ) +- NORMALIZE_VERSION( ${found_version} found_vers_num ) +- NORMALIZE_VERSION( ${max_version} max_vers_num ) +- +- MACRO_CHECK_RANGE_INCLUSIVE_LOWER( ${req_vers_num} ${found_vers_num} ${max_vers_num} ${var_ok}) +-ENDMACRO(MACRO_ENSURE_VERSION_RANGE) +- +- diff --git a/sci-chemistry/openbabel-python/metadata.xml b/sci-chemistry/openbabel-python/metadata.xml new file mode 100644 index 000000000..06fa4d239 --- /dev/null +++ b/sci-chemistry/openbabel-python/metadata.xml @@ -0,0 +1,18 @@ + + + + + sci-chemistry@gentoo.org + Gentoo Chemistry Project + + +OpenBabel is a chemical toolbox designed to speak the many languages of +chemical data. It's an open, collaborative project allowing anyone to +search, convert, analyze, or store data from molecular modeling, chemistry, +solid-state materials, biochemistry, or related areas. This package enables +to access OpenBabel library from Python programs. + + + openbabel + + diff --git a/sci-chemistry/openbabel-python/openbabel-python-2.4.1-r2.ebuild b/sci-chemistry/openbabel-python/openbabel-python-2.4.1-r2.ebuild new file mode 100644 index 000000000..0800a01e0 --- /dev/null +++ b/sci-chemistry/openbabel-python/openbabel-python-2.4.1-r2.ebuild @@ -0,0 +1,92 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +PYTHON_COMPAT=( python2_7 python3_{4,5,6} ) + +inherit cmake-utils python-r1 + +DESCRIPTION="Python bindings for OpenBabel (including Pybel)" +HOMEPAGE="http://openbabel.sourceforge.net/" +SRC_URI="mirror://sourceforge/openbabel/openbabel-${PV}.tar.gz" + +KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux" +SLOT="0/5" +LICENSE="GPL-2" +IUSE="" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS} + ~sci-chemistry/openbabel-${PV} + sys-libs/zlib" +DEPEND="${RDEPEND} + >=dev-lang/swig-2" + +S="${WORKDIR}"/openbabel-${PV} + +PATCHES=( + "${FILESDIR}"/${PN}-2.3.2-gcc-6_and_7-backport.patch + "${FILESDIR}"/${PN}-2.4.1-fix_cmake.patch + ) + +src_prepare() { + cmake-utils_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" + sed \ + -e '/__GNUC__/s:== 4:>= 4:g' \ + -i include/openbabel/shared_ptr.h || die +} + +src_configure() { + my_impl_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}$(python_get_sitedir)" + -DPYTHON_BINDINGS=ON + -DPYTHON_EXECUTABLE=${PYTHON} + -DPYTHON_INCLUDE_DIR="$(python_get_includedir)" + -DPYTHON_INCLUDE_PATH="$(python_get_includedir)" + -DPYTHON_LIBRARY="$(python_get_library_path)" + -DENABLE_TESTS=ON + -DCMAKE_INSTALL_PREFIX="${ED%/}/usr" + ) + + cmake-utils_src_configure + } + + python_foreach_impl my_impl_src_configure +} + +src_compile() { + python_foreach_impl cmake-utils_src_make bindings_python +} + +src_test() { + python_foreach_impl cmake-utils_src_test -R py +} + +src_install() { + my_impl_src_install() { + cd "${BUILD_DIR}" || die + + cmake -DCOMPONENT=bindings_python -P cmake_install.cmake + + python_optimize + } + + python_foreach_impl my_impl_src_install +}