Moved to tree

Signed-off-by: Justin Lecher <jlec@gentoo.org>

6 files changed, 0 insertions, 359 deletions

diff --git a/sci-chemistry/openbabel-python/ChangeLog b/sci-chemistry/openbabel-python/ChangeLog
deleted file mode 100644
index aa49a851b..000000000
--- 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/Manifest b/sci-chemistry/openbabel-python/Manifest
deleted file mode 100644
index 082e5b029..000000000
--- a/sci-chemistry/openbabel-python/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-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
deleted file mode 100644
index 2e776b402..000000000
--- 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 7a0114975..000000000
--- 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 433cfe800..000000000
--- 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 f24e08453..000000000
--- 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
-}