* [gentoo-commits] proj/sci:master commit in: sci-chemistry/openbabel-python/files/, sci-chemistry/openbabel-python/
@ 2011-03-25 19:04 Reinis Danne
0 siblings, 0 replies; 4+ messages in thread
From: Reinis Danne @ 2011-03-25 19:04 UTC (permalink / raw
To: gentoo-commits
commit: 24be5fc2eaedf8e9c69db19b563251d42a487415
Author: Reinis Danne <rei4dan <AT> gmail <DOT> com>
AuthorDate: Fri Mar 25 18:59:39 2011 +0000
Commit: Reinis Danne <rei4dan <AT> gmail <DOT> com>
CommitDate: Fri Mar 25 18:59:39 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=24be5fc2
openbabel-python: Add Python3 iterator and wrap OBInternalCoord patches
---
sci-chemistry/openbabel-python/ChangeLog | 7 +++++++
.../openbabel-python-2.3.0-py3_iterator.patch | 12 ++++++++++++
...enbabel-python-2.3.0-wrap_OBInternalCoord.patch | 10 ++++++++++
.../openbabel-python/openbabel-python-2.3.0.ebuild | 10 +++++++++-
4 files changed, 38 insertions(+), 1 deletions(-)
diff --git a/sci-chemistry/openbabel-python/ChangeLog b/sci-chemistry/openbabel-python/ChangeLog
index b568ab5..2d92edd 100644
--- a/sci-chemistry/openbabel-python/ChangeLog
+++ b/sci-chemistry/openbabel-python/ChangeLog
@@ -2,6 +2,13 @@
# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 25 Mar 2011; Reinis Danne <rei4dan@gmail.com>
+ openbabel-python-2.3.0.ebuild,
+ +files/openbabel-python-2.3.0-py3_iterator.patch,
+ +files/openbabel-python-2.3.0-wrap_OBInternalCoord.patch:
+ Add Python3 iterator and wrap OBInternalCoord patches, upstream r4399,
+ r4400
+
25 Mar 2011; Justin Lecher <jlec@gentoo.org> openbabel-python-2.3.0.ebuild,
metadata.xml:
Cleaned ebuild
diff --git a/sci-chemistry/openbabel-python/files/openbabel-python-2.3.0-py3_iterator.patch b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.0-py3_iterator.patch
new file mode 100644
index 0000000..7efc0ca
--- /dev/null
+++ b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.0-py3_iterator.patch
@@ -0,0 +1,12 @@
+--- scripts/openbabel-python.i 2010-08-16 15:05:20.000000000 +0300
++++ scripts/openbabel-python.i 2011-02-27 14:18:17.000000000 +0200
+@@ -316,6 +316,9 @@
+ def __iter__(self):
+ return self
+
++ def __next__(self):
++ return self.next()
++
+ def next(self):
+ if not self.finished:
+ b = self.iter.__ref__()
diff --git a/sci-chemistry/openbabel-python/files/openbabel-python-2.3.0-wrap_OBInternalCoord.patch b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.0-wrap_OBInternalCoord.patch
new file mode 100644
index 0000000..9346189
--- /dev/null
+++ b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.0-wrap_OBInternalCoord.patch
@@ -0,0 +1,10 @@
+--- scripts/openbabel-python.i 2010-08-16 15:05:20.000000000 +0300
++++ scripts/openbabel-python.i 2011-02-25 22:46:08.000000000 +0200
+@@ -120,6 +120,7 @@
+ VECTORTEMPLATE_WRAP(OBRing, OpenBabel::OBRing)
+ VECTORTEMPLATE_WRAP(pOBRing, OpenBabel::OBRing*)
+ VECTORTEMPLATE_WRAP(pOBGenericData, OpenBabel::OBGenericData*)
++VECTORTEMPLATE_WRAP(pOBInternalCoord, OpenBabel::OBInternalCoord*)
+
+ }
+
diff --git a/sci-chemistry/openbabel-python/openbabel-python-2.3.0.ebuild b/sci-chemistry/openbabel-python/openbabel-python-2.3.0.ebuild
index 463ab69..c5abbeb 100644
--- a/sci-chemistry/openbabel-python/openbabel-python-2.3.0.ebuild
+++ b/sci-chemistry/openbabel-python/openbabel-python-2.3.0.ebuild
@@ -24,6 +24,7 @@ RDEPEND="
dev-libs/libxml2:2
!sci-chemistry/babel
~sci-chemistry/openbabel-${PV}
+ =dev-lang/swig-2.0.1
sys-libs/zlib"
DEPEND="${RDEPEND}
dev-util/cmake"
@@ -32,13 +33,20 @@ S="${WORKDIR}"/openbabel-${PV}
DISTUTILS_SETUP_FILES="${WORKDIR}/openbabel-${PV}/scripts/python/setup.py"
+src_prepare() {
+ epatch "${FILESDIR}/${P}-wrap_OBInternalCoord.patch"
+ epatch "${FILESDIR}/${P}-py3_iterator.patch"
+}
+
src_configure() {
local mycmakeargs="-DPYTHON_BINDINGS=ON"
+ mycmakeargs="${mycmakeargs}
+ -DRUN_SWIG=ON"
cmake-utils_src_configure
}
src_compile() {
- #cmake-utils_src_compile _openbabel
+ cmake-utils_src_compile _openbabel
cd "${WORKDIR}/${P}_build/scripts"
distutils_src_compile
}
^ permalink raw reply related [flat|nested] 4+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-chemistry/openbabel-python/files/, sci-chemistry/openbabel-python/
@ 2011-11-10 13:48 Reinis Danne
0 siblings, 0 replies; 4+ messages in thread
From: Reinis Danne @ 2011-11-10 13:48 UTC (permalink / raw
To: gentoo-commits
commit: 34930b2d5b1ff70d13924571c3fa53363893fb21
Author: Reinis Danne <rei4dan <AT> gmail <DOT> com>
AuthorDate: Thu Nov 10 13:35:47 2011 +0000
Commit: Reinis Danne <rei4dan <AT> gmail <DOT> com>
CommitDate: Thu Nov 10 13:35:47 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=34930b2d
openbabel-python: Version bump to 2.3.1
---
sci-chemistry/openbabel-python/ChangeLog | 10 ++++
.../openbabel-python-2.3.1-system_openbabel.patch | 15 ++++++
sci-chemistry/openbabel-python/metadata.xml | 12 +++++
.../openbabel-python/openbabel-python-2.3.1.ebuild | 53 ++++++++++++++++++++
4 files changed, 90 insertions(+), 0 deletions(-)
diff --git a/sci-chemistry/openbabel-python/ChangeLog b/sci-chemistry/openbabel-python/ChangeLog
new file mode 100644
index 0000000..0378f55
--- /dev/null
+++ b/sci-chemistry/openbabel-python/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-chemistry/openbabel-python
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*openbabel-python-2.3.1 (10 Nov 2011)
+
+ 10 Nov 2011; Reinis Danne <rei4dan@gmail.com> +openbabel-python-2.3.1.ebuild,
+ +files/openbabel-python-2.3.1-system_openbabel.patch, +metadata.xml:
+ Version bump to 2.3.1
+
diff --git a/sci-chemistry/openbabel-python/files/openbabel-python-2.3.1-system_openbabel.patch b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.1-system_openbabel.patch
new file mode 100644
index 0000000..6420bba
--- /dev/null
+++ b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.1-system_openbabel.patch
@@ -0,0 +1,15 @@
+--- scripts/python/setup.py
++++ scripts/python/setup.py
+@@ -15,11 +15,7 @@
+
+ obExtension = Extension('_openbabel',
+ [os.path.join(srcdir, "openbabel-python.cpp")],
+- include_dirs=[os.path.join(srcdir, "..", "..", "include"),
+- os.path.join("..", "include")],
+- library_dirs=[os.path.join(srcdir, "..", "..", "lib"),
+- os.path.join(srcdir, "..", "..", "lib64"),
+- os.path.join("..", "lib")],
++ include_dirs=[os.path.join("/usr", "include", "openbabel-2.0")],
+ libraries=['openbabel']
+ )
+
diff --git a/sci-chemistry/openbabel-python/metadata.xml b/sci-chemistry/openbabel-python/metadata.xml
new file mode 100644
index 0000000..433cfe8
--- /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-2.3.1.ebuild b/sci-chemistry/openbabel-python/openbabel-python-2.3.1.ebuild
new file mode 100644
index 0000000..0da030f
--- /dev/null
+++ b/sci-chemistry/openbabel-python/openbabel-python-2.3.1.ebuild
@@ -0,0 +1,53 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/openbabel-python/openbabel-python-2.3.0.ebuild,v 1.7 2011/09/14 05:06:41 jlec Exp $
+
+EAPI="3"
+
+PYTHON_DEPEND="2"
+SUPPORT_PYTHON_ABIS="1"
+RESTRICT_PYTHON_ABIS="*-jython"
+PYTHON_MODNAME="openbabel.py pybel.py"
+
+inherit distutils eutils flag-o-matic
+
+DESCRIPTION="Python bindings for OpenBabel (including Pybel)"
+HOMEPAGE="http://openbabel.sourceforge.net/"
+SRC_URI="mirror://sourceforge/openbabel/openbabel-${PV}.tar.gz"
+
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+SLOT="0"
+LICENSE="GPL-2"
+IUSE=""
+
+RDEPEND="
+ dev-cpp/eigen:2
+ dev-libs/libxml2:2
+ !sci-chemistry/babel
+ ~sci-chemistry/openbabel-${PV}
+ sys-libs/zlib"
+DEPEND="${RDEPEND}
+ >=dev-lang/swig-2"
+
+S="${WORKDIR}"/openbabel-${PV}
+
+DISTUTILS_SETUP_FILES=("scripts|python/setup.py")
+
+src_prepare() {
+ epatch \
+ "${FILESDIR}"/${P}-system_openbabel.patch
+
+ sed \
+ -e "s:/usr:${EPREFIX}/usr:g" \
+ -i ./scripts/python/setup.py || die
+
+ swig -python -c++ -small -O -templatereduce -naturalvar \
+ -I"${EPREFIX}/usr/include/openbabel-2.0" \
+ -o scripts/python/openbabel-python.cpp \
+ -DHAVE_EIGEN2 \
+ -outdir scripts/python \
+ scripts/openbabel-python.i \
+ || die "Regeneration of openbabel-python.cpp failed"
+
+ append-cxxflags "$(pkg-config --cflags-only-I eigen2)"
+}
^ permalink raw reply related [flat|nested] 4+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-chemistry/openbabel-python/files/, sci-chemistry/openbabel-python/
@ 2012-10-19 17:04 Reinis Danne
0 siblings, 0 replies; 4+ messages in thread
From: Reinis Danne @ 2012-10-19 17:04 UTC (permalink / raw
To: gentoo-commits
commit: 8a1221408b74d21b8c5a28e2822d2d69e672dce4
Author: Reinis Danne <rei4dan <AT> gmail <DOT> com>
AuthorDate: Fri Oct 19 16:50:07 2012 +0000
Commit: Reinis Danne <rei4dan <AT> gmail <DOT> com>
CommitDate: Fri Oct 19 16:50:07 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8a122140
openbabel-python: Version bump to 2.3.2
---
sci-chemistry/openbabel-python/ChangeLog | 11 +
.../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 | 88 ++++++++
5 files changed, 348 insertions(+), 0 deletions(-)
diff --git a/sci-chemistry/openbabel-python/ChangeLog b/sci-chemistry/openbabel-python/ChangeLog
new file mode 100644
index 0000000..51e3bf6
--- /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/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 0000000..2e776b4
--- /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 0000000..7a01149
--- /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 0000000..433cfe8
--- /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 0000000..df2c15b
--- /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
+}
^ permalink raw reply related [flat|nested] 4+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-chemistry/openbabel-python/files/, sci-chemistry/openbabel-python/
@ 2012-12-06 17:20 Justin Lecher
0 siblings, 0 replies; 4+ messages in thread
From: Justin Lecher @ 2012-12-06 17:20 UTC (permalink / raw
To: gentoo-commits
commit: 4768fca0773e1e1783a9c023f131d8a86c6c7e59
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Dec 6 17:10:18 2012 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> 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 <jlec <AT> 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 <rei4dan@gmail.com> 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 <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/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 <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
deleted file mode 100644
index 433cfe8..0000000
--- a/sci-chemistry/openbabel-python/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?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
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
-}
^ permalink raw reply related [flat|nested] 4+ messages in thread
end of thread, other threads:[~2012-12-06 17:20 UTC | newest]
Thread overview: 4+ messages (download: mbox.gz follow: Atom feed
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2011-03-25 19:04 [gentoo-commits] proj/sci:master commit in: sci-chemistry/openbabel-python/files/, sci-chemistry/openbabel-python/ Reinis Danne
-- strict thread matches above, loose matches on Subject: below --
2011-11-10 13:48 Reinis Danne
2012-10-19 17:04 Reinis Danne
2012-12-06 17:20 Justin Lecher
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