openbabel-python: Version bump to 2.3.2

6 files changed, 349 insertions, 0 deletions

diff --git a/sci-chemistry/openbabel-python/ChangeLog b/sci-chemistry/openbabel-python/ChangeLog
new file mode 100644
index 000000000..51e3bf640
--- /dev/null
+++ b/sci-chemistry/openbabel-python/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-chemistry/openbabel-python
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*openbabel-python-2.3.2 (19 Oct 2012)
+
+  19 Oct 2012; Reinis Danne <rei4dan@gmail.com> +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/Manifest b/sci-chemistry/openbabel-python/Manifest
new file mode 100644
index 000000000..082e5b029
--- /dev/null
+++ b/sci-chemistry/openbabel-python/Manifest
@@ -0,0 +1 @@
+DIST openbabel-2.3.2.tar.gz 20509105 SHA256 4eaca26679aa6cc85ebf96af19191472ac63ca442c36b0427b369c3a25705188 SHA512 d0e1f8b758ffdd65ec6c31d988bffe3279355e286ce69fad12c5905b3b832e2b73ee95b1061b1576aba1ee9fe4da5e31ec30350c473be17493c657dc80caf919 WHIRLPOOL 74eff18b73d24c8f702e5573a58ba6afba8402e9ce8782de95dc0568575a7d2d632dbc8e8a98b3cd25efdfa7379494f7dcd449342c81ddf73f42a387bce77aaa
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
new file mode 100644
index 000000000..2e776b402
--- /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 000000000..7a0114975
--- /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/metadata.xml b/sci-chemistry/openbabel-python/metadata.xml
new file mode 100644
index 000000000..433cfe800
--- /dev/null
+++ b/sci-chemistry/openbabel-python/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 Python programs.
+	</longdescription>
+</pkgmetadata>
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 000000000..df2c15baf
--- /dev/null
+++ b/sci-chemistry/openbabel-python/openbabel-python-2.3.2.ebuild
@@ -0,0 +1,88 @@
+# 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-${PV}.tar.gz"
+
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+SLOT="0"
+LICENSE="GPL-2"
+IUSE=""
+
+RDEPEND="
+	!sci-chemistry/babel
+	~sci-chemistry/openbabel-${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() {
+	python_foreach_impl cmake -DCOMPONENT=bindings_python -P cmake_install.cmake
+}