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-rw-r--r--sci-chemistry/Manifest.gzbin17559 -> 17568 bytes
-rw-r--r--sci-chemistry/apbs/Manifest2
-rw-r--r--sci-chemistry/apbs/apbs-1.4.1-r2.ebuild24
-rw-r--r--sci-chemistry/openbabel-perl/Manifest4
-rw-r--r--sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-bindings_only.patch108
-rw-r--r--sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-trunk_cmake.patch41
-rw-r--r--sci-chemistry/openbabel-perl/openbabel-perl-2.3.2.ebuild72
-rw-r--r--sci-chemistry/openbabel-python/Manifest5
-rw-r--r--sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-bindings_only.patch209
-rw-r--r--sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-swig-3.0.3.patch97
-rw-r--r--sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-testpybel.patch28
-rw-r--r--sci-chemistry/openbabel-python/openbabel-python-2.3.2.ebuild93
-rw-r--r--sci-chemistry/openbabel/Manifest3
-rw-r--r--sci-chemistry/openbabel/files/openbabel-2.3.2-test_lib_path.patch27
-rw-r--r--sci-chemistry/openbabel/openbabel-2.3.2-r1.ebuild92
-rw-r--r--sci-chemistry/tm-align/Manifest2
-rw-r--r--sci-chemistry/tm-align/tm-align-20150914.ebuild10
17 files changed, 21 insertions, 796 deletions
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 1be75c4273c8..dd8fa32bf085 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
Binary files differ
diff --git a/sci-chemistry/apbs/Manifest b/sci-chemistry/apbs/Manifest
index 912658bff2af..d83109851ca0 100644
--- a/sci-chemistry/apbs/Manifest
+++ b/sci-chemistry/apbs/Manifest
@@ -2,5 +2,5 @@ AUX apbs-1.4.1-manip.patch 1522 BLAKE2B 4a30aadc2d80fef5d813ea29f20073b6c4d1cefe
AUX apbs-1.4.1-multilib.patch 3301 BLAKE2B 4268a21ec878d780c7a1efe433bf2c82ef2e72f49a6071b6df695bf672ee999be9c29fed06e949b80cc230333d8deca1094c946662ec657d31e3b6f86e873969 SHA512 cdd72fd23a57ee8413f72bf674ae246543b1c9f326727ff07c3b8848d59f98ab7d2daf28677460cb4726f919832079c1d280bcdc86a8bef5c0875583c789b7c0
AUX apbs-1.4.1-python.patch 4109 BLAKE2B 25193eb227ab9d34f3f636b6264bdbaecdbe48747220582b39798c5c6631bdc7731645f66096dbf659c9eea7f31c8e20c0944796f8f89d995a4cd2712be91a3b SHA512 369c0fa08187ba80d8ce72542fc2942f28426beed39619dd6a90a9ef8dfecb47ea6dc7aa20994629a69d63b55d72d1f837c442744bf5499a942bf312f6723092
DIST apbs-1.4.1.zip 37999283 BLAKE2B 2301deb7ab4eb2f20098cf63df180bb53189e42a89cd5559357cdcf08e84d27a44eafe8557bb460574802d24d29741ad4606dc3bd7f32911d0d0f2c7453d6470 SHA512 3a127af3940054e5a43b3c0c620507f4f9baa69049e5a0933d8e8825458ad2faba840392752de49fe68d91e2054fb1394cf87bb5bb1c0b48305368e2f404cf6a
-EBUILD apbs-1.4.1-r2.ebuild 3117 BLAKE2B 0d5b38d97ab3c9917b4b4ced1cd5a5ff20dc03522bbedc3492ff2276b59f41b48a3b48cc97a660144afda07fc677f131e56293b8467a27cc3bab70cef0a7bfa3 SHA512 e8f20517537119640c8f12accdcc37a2f25b30d3b25923f54a5bff3c88b679219f029b49ae96ac66acf04599877f1b33289e1ce15462a0e7a6a4cd5f979ac3fc
+EBUILD apbs-1.4.1-r2.ebuild 3140 BLAKE2B b31ecbf8ddb9e8824917cb7c79ba5239957e1723c56a60b9b20aa6d818a0140ce0e4ace7691ac9663d0e38f99b5d851b529b1355b965d071d7e6b65566763bf9 SHA512 e97100de2ed58f60b414cead8aea44d53178f2b28ca016c9fa4a783993b3be0c66a53eb541e4679f58bc3054e18ab8866bef1a31b817cf62031b65ad3044e1a5
MISC metadata.xml 1048 BLAKE2B 53a61bd7e05e53b294f0cbd1a21b86f391429ad5f23a545e7cbb27625b152589247a08db06c5d7f6658425de032be970fae0230ad1ac14ac4f6de42663d6c97c SHA512 7d68049cb9b044676430fe879890cc4cd869b99f85696f579d9cbf3b156081301792fd7f03205a9b9d429d71c9a35b4815f4236573f68d3ef6b4718e6e1f0bb3
diff --git a/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild b/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild
index aecbcd3ce745..108e43bf904b 100644
--- a/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild
+++ b/sci-chemistry/apbs/apbs-1.4.1-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -11,7 +11,7 @@ inherit cmake-utils distutils-r1 flag-o-matic multilib toolchain-funcs
GITHUB_REV="74fcb8676de69ed04ddab8976a8b05a6caaf4d65"
DESCRIPTION="Evaluation of electrostatic properties of nanoscale biomolecular systems"
-HOMEPAGE="http://www.poissonboltzmann.org/apbs/"
+HOMEPAGE="https://www.poissonboltzmann.org/apbs/"
#SRC_URI="mirror://sourceforge/${PN}/${P}-source.tar.gz"
SRC_URI="https://github.com/Electrostatics/apbs-pdb2pqr/archive/${GITHUB_REV}.zip -> ${P}.zip"
@@ -28,18 +28,18 @@ REQUIRED_USE="
RDEPEND="
dev-cpp/eigen:3
dev-libs/maloc[mpi=]
- virtual/blas
sys-libs/readline
+ virtual/blas
fetk? (
- sci-libs/fetk
sci-libs/amd
- sci-libs/umfpack
+ sci-libs/fetk
sci-libs/superlu
+ sci-libs/umfpack
)
mpi? ( virtual/mpi )
python? ( ${PYTHON_DEPS} )
"
-DEPEND="${DEPEND}
+DEPEND="${RDEPEND}
virtual/pkgconfig
doc? ( app-doc/doxygen )
"
@@ -63,7 +63,8 @@ src_prepare() {
use doc && MAKEOPTS+=" -j1"
if use python; then
unset PATCHES || die
- cd tools/python && distutils-r1_src_prepare
+ cd tools/python || die
+ distutils-r1_src_prepare
fi
}
@@ -92,7 +93,8 @@ src_configure() {
)
cmake-utils_src_configure
if use python; then
- cd tools/python && distutils-r1_src_configure
+ cd tools/python || die
+ distutils-r1_src_configure
fi
}
@@ -100,7 +102,8 @@ src_compile(){
cmake-utils_src_compile
if use python; then
append-ldflags -L"${S}"/lib
- cd tools/python && distutils-r1_src_compile
+ cd tools/python || die
+ distutils-r1_src_compile
fi
}
@@ -121,7 +124,8 @@ src_install() {
fi
done
if use python; then
- cd tools/python && distutils-r1_src_install
+ cd tools/python || die
+ distutils-r1_src_install
rm -rf "${ED}"/usr/share/apbs/tools/python || die
fi
}
diff --git a/sci-chemistry/openbabel-perl/Manifest b/sci-chemistry/openbabel-perl/Manifest
index 3a0ffb6f92bb..079b42b9f50f 100644
--- a/sci-chemistry/openbabel-perl/Manifest
+++ b/sci-chemistry/openbabel-perl/Manifest
@@ -1,8 +1,4 @@
-AUX openbabel-perl-2.3.2-bindings_only.patch 4557 BLAKE2B 3549bc5f6d0c02ace76d8f26e5669c83ea6dc1912f28433bec54f837c2a8276ee243f4311fd65766b0e5af4bb5d6a6a627ba5ef42c0aa919d842c945aa6db9bc SHA512 475600513f188f2e3dee711ab2073954511b7d71c0af222dc9fe121bcbd4821d0ab32934d5035452ad4820d0dd750899995696c20504769b25cad7ef2d27aa5e
AUX openbabel-perl-2.3.2-gcc-6_and_7-backport.patch 635 BLAKE2B 4e98dedd149b14d5bb02fb6d2fa03e07242d100c7b41f36f749ff3d587080eeca44aa26ca095d31e0309e45f3780b67deaa97f1177ed35a9b7407bd7c33f78ff SHA512 e1b4402f34d01ced5b4caaa184b4e5544cf47893cfe7958054052b05a57dc34b4d44239a212c7d909f29b9366b83b6df74993f844a20f23748c01272ec093081
-AUX openbabel-perl-2.3.2-trunk_cmake.patch 2335 BLAKE2B 5e829c555d8a06bf9524b5008c21dfd6830b1c95a40834f248d4b4d875fcd8cd64f664ab93a5f37f614201c106277bc0ae75bbd5f4cd392517e9d8f198e39946 SHA512 9f42cb3c8aff7eb765790fd3a7f259d8076ebce11f3c2e324a9568a94d948583455db90a8714cdcbd6b6a74087167ada9ec19261862233823d0792bc79302f30
-DIST openbabel-2.3.2.tar.gz 20509105 BLAKE2B d475c2da0d7171650eeb4b78a948421b783bdbb9342c81114d3dbc19d5cbb273f7303438920ffaeef5b6332e4b72606a86ded5cbd3d7e541f62b59b46483bb69 SHA512 d0e1f8b758ffdd65ec6c31d988bffe3279355e286ce69fad12c5905b3b832e2b73ee95b1061b1576aba1ee9fe4da5e31ec30350c473be17493c657dc80caf919
DIST openbabel-2.4.1.tar.gz 11618304 BLAKE2B 8fc051e83add9be6456e281a109bd6bbec282a64ffc83309819f0decbf167b4914fbb7f1966e95e103f268754045b804317f51c79a952ace707c6af2bd320125 SHA512 427e678f0a911bd27b9a8a05e60b6e09f113be4e5dd180daaf80c28d06368e52b57501261755ab3817a8d31f2754db24471fd0ceee706d029386d6f70800e9c6
-EBUILD openbabel-perl-2.3.2.ebuild 1638 BLAKE2B 01039ea5f28d080cc2dd47dd2c13260644be996eb9f2f7bfe4db73dabfd6c3e0ed2136a69040e4ed1ce868f21e0fafff647ad16fa995ca2f7a7967c2d0622e0d SHA512 73cb5637922195122ed9cc75092b03b34a595763baa81d8edb4ad323c4381a68593d22b023cb1ad004329b7d54e126b0227bf4211845468811711e374ff0c7ae
EBUILD openbabel-perl-2.4.1.ebuild 1583 BLAKE2B 233459caeea67df903f80dff500cce8fc1e4a99cc13124d8cee60fecd59261979c62ee0f5072f955d2c95043722c98450ad27187f7d0443c8ecc4a27f4c9ffee SHA512 6336a34a6d5dca6d573a62276cccf34cee37e95c31704f52a178366910d5267353b49fb981c1dce07ea935cac0e7887aad60df77468f7d4838ca18b901998651
MISC metadata.xml 735 BLAKE2B de3dbec049667c35b29293f9c27e81b0e0ffade4c57ffa519c013c788409f310dac834fd92f0d72c05281bf76317b3c7fc2b429b8644a7d350020caf425185c0 SHA512 62052b0e677a52adba98961185e5b83525c652e260ebad1b820ed19b071a1f6476cca550ec0c570a5faf0cbad7189cadb78ac8d6de077fbf15e346b7c66e4cf7
diff --git a/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-bindings_only.patch b/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-bindings_only.patch
deleted file mode 100644
index 92e126a77d86..000000000000
--- a/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-bindings_only.patch
+++ /dev/null
@@ -1,108 +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..8f92e91 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
-@@ -231,13 +245,25 @@ if (DO_PERL_BINDINGS)
- endif (RUN_SWIG)
-
- add_library(bindings_perl MODULE ${openbabel_SOURCE_DIR}/scripts/perl/openbabel-perl.cpp)
-- target_link_libraries(bindings_perl ${PERL_LIBRARY} ${BABEL_LIBRARY} ${PERL_EXTRA_LINK_FLAGS})
-+ if(BINDINGS_ONLY)
-+ target_link_libraries(bindings_perl ${PERL_LIBRARY} ${BABEL_SYSTEM_LIBRARY} ${PERL_EXTRA_LINK_FLAGS})
-+ else()
-+ target_link_libraries(bindings_perl ${PERL_LIBRARY} ${BABEL_LIBRARY} ${PERL_EXTRA_LINK_FLAGS})
-+ endif()
-+
- set_target_properties(bindings_perl PROPERTIES
- PREFIX ""
- OUTPUT_NAME OpenBabel)
-- add_dependencies(bindings_perl openbabel)
-- install(TARGETS bindings_perl LIBRARY DESTINATION ${LIB_INSTALL_DIR})
-- install(FILES ${openbabel_SOURCE_DIR}/scripts/perl/OpenBabel.pm DESTINATION ${LIB_INSTALL_DIR})
-+ if(NOT BINDINGS_ONLY)
-+ add_dependencies(bindings_perl openbabel)
-+ endif()
-+
-+ install(TARGETS bindings_perl
-+ LIBRARY DESTINATION ${LIB_INSTALL_DIR}/auto/Chemistry/OpenBabel/
-+ COMPONENT bindings_perl)
-+ install(FILES ${openbabel_SOURCE_DIR}/scripts/perl/OpenBabel.pm
-+ DESTINATION ${LIB_INSTALL_DIR}/Chemistry/
-+ COMPONENT bindings_perl)
-
- endif (DO_PERL_BINDINGS)
-
diff --git a/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-trunk_cmake.patch b/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-trunk_cmake.patch
deleted file mode 100644
index b72a622a3afb..000000000000
--- a/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-trunk_cmake.patch
+++ /dev/null
@@ -1,41 +0,0 @@
-diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt
-index e7298ce..16e9000 100644
---- a/scripts/CMakeLists.txt
-+++ b/scripts/CMakeLists.txt
-@@ -231,36 +239,6 @@ if (DO_PERL_BINDINGS)
- install(TARGETS bindings_perl LIBRARY DESTINATION ${LIB_INSTALL_DIR})
- install(FILES ${openbabel_SOURCE_DIR}/scripts/perl/OpenBabel.pm DESTINATION ${LIB_INSTALL_DIR})
-
-- set(PERL_INSTALLDIRS_TEXT "")
-- if (OBPERL_INSTALLDIRS)
-- set(PERL_INSTALLDIRS_TEXT "INSTALLDIRS=${OBPERL_INSTALLDIRS}")
-- endif (OBPERL_INSTALLDIRS)
--
-- if (NOT MSVC)
-- add_custom_target(pre_bindings_perl ALL
-- # Create the scripts/perl directory; we cannot do this inside
-- # bindings_perl as the WORKING_DIRECTORY needs to already exist!
-- COMMAND ${CMAKE_COMMAND} -E make_directory ${openbabel_BINARY_DIR}/scripts/perl
-- )
-- add_custom_target(bindings_perl ALL
-- COMMAND ${CMAKE_COMMAND} -E copy ${openbabel_SOURCE_DIR}/scripts/perl/Makefile.PL ${openbabel_BINARY_DIR}/scripts/perl
-- COMMAND ${CMAKE_COMMAND} -E copy ${openbabel_SOURCE_DIR}/scripts/perl/OpenBabel.pm ${openbabel_BINARY_DIR}/scripts/perl
-- COMMAND ${CMAKE_COMMAND} -E copy ${openbabel_SOURCE_DIR}/scripts/perl/openbabel-perl.cpp ${openbabel_BINARY_DIR}/scripts/perl
-- COMMAND PERL5LIB=${openbabel_SOURCE_DIR}/scripts/perl/inc SRC_DIR=${openbabel_SOURCE_DIR} OBJ_DIR=${openbabel_BINARY_DIR} ${PERL_EXECUTABLE} ${openbabel_BINARY_DIR}/scripts/perl/Makefile.PL ${PERL_PREFIX_TEXT} ${PERL_INSTALLDIRS_TEXT}
-- COMMAND PERL5LIB=${openbabel_SOURCE_DIR}/scripts/perl/inc make
-- DEPENDS openbabel ${openbabel_SOURCE_DIR}/scripts/perl/openbabel-perl.cpp
-- WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts/perl
-- )
-- add_dependencies(bindings_perl pre_bindings_perl openbabel)
-- install(CODE "execute_process(COMMAND make install DESTDIR=\$ENV{DESTDIR} WORKING_DIRECTORY ${openbabel_BINARY_DIR}/scripts/perl)")
--
-- else (NOT MSVC)
-- add_library(bindings_perl MODULE ${openbabel_SOURCE_DIR}/scripts/perl/openbabel-perl.cpp)
-- target_link_libraries(bindings_perl ${PERL_LIBRARY} ${BABEL_LIBRARY})
-- set_target_properties(bindings_perl PROPERTIES
-- OUTPUT_NAME openbabel_perl )
-- endif(NOT MSVC)
--
- endif (DO_PERL_BINDINGS)
-
- ###################
diff --git a/sci-chemistry/openbabel-perl/openbabel-perl-2.3.2.ebuild b/sci-chemistry/openbabel-perl/openbabel-perl-2.3.2.ebuild
deleted file mode 100644
index 25a87bc1b7ef..000000000000
--- a/sci-chemistry/openbabel-perl/openbabel-perl-2.3.2.ebuild
+++ /dev/null
@@ -1,72 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit cmake-utils eutils perl-module
-
-DESCRIPTION="Perl bindings for OpenBabel"
-HOMEPAGE="http://openbabel.sourceforge.net/"
-SRC_URI="mirror://sourceforge/openbabel/openbabel-${PV}.tar.gz"
-
-KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux"
-SLOT="0"
-LICENSE="GPL-2"
-IUSE=""
-
-RDEPEND="
- dev-lang/perl:=
- ~sci-chemistry/openbabel-${PV}"
-DEPEND="${RDEPEND}
- >=dev-util/cmake-2.4.8
- >=dev-lang/swig-2"
-
-S="${WORKDIR}/openbabel-${PV}"
-
-PATCHES=(
- "${FILESDIR}"/${P}-trunk_cmake.patch
- "${FILESDIR}"/${P}-bindings_only.patch
- "${FILESDIR}"/${P}-gcc-6_and_7-backport.patch
-)
-
-src_prepare() {
- sed \
- -e '/__GNUC__/s:== 4:>= 4:g' \
- -i include/openbabel/shared_ptr.h || die
- cmake-utils_src_prepare
- perl_set_version
-}
-
-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}/${VENDOR_ARCH}"
- -DPERL_BINDINGS=ON
- -DRUN_SWIG=ON
- )
-
- cmake-utils_src_configure
-}
-
-src_compile() {
- cmake-utils_src_compile bindings_perl
-}
-
-src_test() {
- mkdir "${CMAKE_BUILD_DIR}/$(get_libdir)/Chemistry"
- cp \
- "${CMAKE_USE_DIR}/scripts/perl/OpenBabel.pm" \
- "${CMAKE_BUILD_DIR}/$(get_libdir)/Chemistry/"
- for i in "${CMAKE_USE_DIR}"/scripts/perl/t/*; do
- einfo "Running test: ${i}"
- perl -I"${CMAKE_BUILD_DIR}/$(get_libdir)" "${i}" || die
- done
-}
-
-src_install() {
- cd "${CMAKE_BUILD_DIR}"
- cmake -DCOMPONENT=bindings_perl -P cmake_install.cmake
-}
diff --git a/sci-chemistry/openbabel-python/Manifest b/sci-chemistry/openbabel-python/Manifest
index 0431b6bcd93d..fb43c0117165 100644
--- a/sci-chemistry/openbabel-python/Manifest
+++ b/sci-chemistry/openbabel-python/Manifest
@@ -1,9 +1,4 @@
-AUX openbabel-python-2.3.2-bindings_only.patch 8843 BLAKE2B 55661b83b40d440c3c442e84a75baa0c7c7cfe697626fd9e51b00975959438304dfb6220684edfd4cc3a12f20ac1a608a9bc1d8aa606159591a44da3d4987c1c SHA512 c933ac9f0c2370ceb305ebb831ab81e3d66dc9233d175f2b31f0e6ca0cc91dce591c46478ef5d5ccc118cfa8f6d82459331d5e7885bffa904ad486215c657333
AUX openbabel-python-2.3.2-gcc-6_and_7-backport.patch 635 BLAKE2B 4e98dedd149b14d5bb02fb6d2fa03e07242d100c7b41f36f749ff3d587080eeca44aa26ca095d31e0309e45f3780b67deaa97f1177ed35a9b7407bd7c33f78ff SHA512 e1b4402f34d01ced5b4caaa184b4e5544cf47893cfe7958054052b05a57dc34b4d44239a212c7d909f29b9366b83b6df74993f844a20f23748c01272ec093081
-AUX openbabel-python-2.3.2-swig-3.0.3.patch 4138 BLAKE2B c029caf309007de63c13f876c7e26f30078b8171cbf171f025d0a18267128b0e44faf1b503c38f88774ffc2f2a67669463513f3cca46bb78375bd04a2d89f2d4 SHA512 ac454d8f8a8e6d8942d493ee648ad190e275d616bea99cc16bede97e00733d4aa6522cf43a80707b3aa59a78ba68731ccdf748beb76fb2b69267b3b060a5e96f
-AUX openbabel-python-2.3.2-testpybel.patch 1105 BLAKE2B a73e76780b0d3c3d0e2f16e5e90c2a6bd1ed83186955eb7e2ead3d9196ed684a447fb17ed71b544f45f03e9c42ae516309d4c755ad1933d766953f9a1c0df168 SHA512 65df0351fc626ba9d88c06c7f9e84e5707585f302baea4b4885faa3b190c29483b0016d7390e23c2d2444e83c39ad525ba52d7b8d22faed89d82beb480c5b469
-DIST openbabel-2.3.2.tar.gz 20509105 BLAKE2B d475c2da0d7171650eeb4b78a948421b783bdbb9342c81114d3dbc19d5cbb273f7303438920ffaeef5b6332e4b72606a86ded5cbd3d7e541f62b59b46483bb69 SHA512 d0e1f8b758ffdd65ec6c31d988bffe3279355e286ce69fad12c5905b3b832e2b73ee95b1061b1576aba1ee9fe4da5e31ec30350c473be17493c657dc80caf919
DIST openbabel-2.4.1.tar.gz 11618304 BLAKE2B 8fc051e83add9be6456e281a109bd6bbec282a64ffc83309819f0decbf167b4914fbb7f1966e95e103f268754045b804317f51c79a952ace707c6af2bd320125 SHA512 427e678f0a911bd27b9a8a05e60b6e09f113be4e5dd180daaf80c28d06368e52b57501261755ab3817a8d31f2754db24471fd0ceee706d029386d6f70800e9c6
-EBUILD openbabel-python-2.3.2.ebuild 2249 BLAKE2B 9ebd9593daa4d35cca9192e6cc83e46deaecbcc724ec1ead9a60101b7adc25abf108c8280c9be88c4efb9e083c62a3e6e2f86d95429edfe70436150e0c14c476 SHA512 5cda71fe2a54d46eb8d7d68e03c0791866172466a54769a032a03e3ab7327ad3c5dac96a937416dd576635528f6b1c0602f753fc13a3f44e8d79579620279fe7
EBUILD openbabel-python-2.4.1-r1.ebuild 2175 BLAKE2B a940a18ee6b73bd62143546a9a1bee6f8d06637af8f366cbfdde1a6827ea8e2ac707df4c354cf6a782282bf008befb92e903f40b8289ec19f5c131d0071bf711 SHA512 a4174ac5fabedd91719a7adba9bfac803ca231e223243a32eff6bfd98a95d6d21e0ab7c9ac0457f43b064866bb5876fb684449f6389764afa2365a83aa749ae2
MISC metadata.xml 737 BLAKE2B 9a5fe97df44ce22c6ee27133bbc6144132ee3775db77440adcd6c3e9c44b87cefbace4ebe17906af87f841e07deef5183e451a8c193232d2a6ca7da05c7a0ed7 SHA512 7ff97ef3f6752a8fed578676aa2cb9706b7d68e31ee22d26e90d4bbb01c10ff410b66da20a91b078293add3bcb3a3711ad180d5174368e0d588ea718ad297d7e
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 2e776b4029ec..000000000000
--- 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-swig-3.0.3.patch b/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-swig-3.0.3.patch
deleted file mode 100644
index d30efd55bd92..000000000000
--- a/sci-chemistry/openbabel-python/files/openbabel-python-2.3.2-swig-3.0.3.patch
+++ /dev/null
@@ -1,97 +0,0 @@
- scripts/openbabel-python.i | 34 +++++++++++++++++-----------------
- 1 file changed, 17 insertions(+), 17 deletions(-)
-
-diff --git a/scripts/openbabel-python.i b/scripts/openbabel-python.i
-index 7cb8f24..d893129 100644
---- a/scripts/openbabel-python.i
-+++ b/scripts/openbabel-python.i
-@@ -227,7 +227,7 @@ CAST_GENERICDATA_TO(SquarePlanarStereo)
- %include <openbabel/math/transform3d.h>
- %include <openbabel/math/spacegroup.h>
-
--# CloneData should be used instead of the following method
-+// CloneData should be used instead of the following method
- %ignore OpenBabel::OBBase::SetData;
- %include <openbabel/base.h>
-
-@@ -289,7 +289,7 @@ OBMol.BeginResidues = OBMol.EndResidues = OBMol.BeginResidue = OBMol.EndResidue
- %ignore OpenBabel::OBDescriptor::LessThan;
- %include <openbabel/descriptor.h>
-
--# Ignore shadowed methods
-+// Ignore shadowed methods
- %ignore OpenBabel::OBForceField::VectorSubtract(const double *const, const double *const, double *);
- %ignore OpenBabel::OBForceField::VectorMultiply(const double *const, const double, double *);
- %include <openbabel/forcefield.h>
-@@ -310,7 +310,7 @@ OBMol.BeginResidues = OBMol.EndResidues = OBMol.BeginResidue = OBMol.EndResidue
-
- %warnfilter(503) OpenBabel::OBBitVec; // Not wrapping any of the overloaded operators
- %include <openbabel/bitvec.h>
--# Ignore shadowed method
-+// Ignore shadowed method
- %ignore OpenBabel::OBRotor::GetRotAtoms() const;
- %include <openbabel/rotor.h>
- %ignore OpenBabel::Swab;
-@@ -321,13 +321,13 @@ OBMol.BeginResidues = OBMol.EndResidues = OBMol.BeginResidue = OBMol.EndResidue
- %include <openbabel/math/align.h>
- #endif
-
--# The following %ignores avoid warning messages due to shadowed classes.
--# This does not imply a loss of functionality as (in this case)
--# the shadowed class is identical (from the point of view of SWIG) to
--# the shadowing class.
--# This is because C++ references (&) are transformed by SWIG back into
--# pointers, so that OBAtomIter(OBMol &) would be treated the same as
--# OBAtomIter(OBMol *).
-+// The following %ignores avoid warning messages due to shadowed classes.
-+// This does not imply a loss of functionality as (in this case)
-+// the shadowed class is identical (from the point of view of SWIG) to
-+// the shadowing class.
-+// This is because C++ references (&) are transformed by SWIG back into
-+// pointers, so that OBAtomIter(OBMol &) would be treated the same as
-+// OBAtomIter(OBMol *).
-
- %ignore OBAtomAtomIter(OBAtom &);
- %ignore OBAtomBondIter(OBAtom &);
-@@ -346,9 +346,9 @@ OBMol.BeginResidues = OBMol.EndResidues = OBMol.BeginResidue = OBMol.EndResidue
- %ignore OBResidueIter(OBMol &);
- %ignore OBResidueAtomIter(OBResidue &);
-
--# These classes are renamed so that they can be replaced by Python
--# classes of the same name which provide Pythonic iterators
--# (see %pythoncode section below)
-+// These classes are renamed so that they can be replaced by Python
-+// classes of the same name which provide Pythonic iterators
-+// (see %pythoncode section below)
-
- %rename(_OBAtomAtomIter) OpenBabel::OBAtomAtomIter;
- %rename(_OBAtomBondIter) OpenBabel::OBAtomBondIter;
-@@ -367,8 +367,8 @@ OBMol.BeginResidues = OBMol.EndResidues = OBMol.BeginResidue = OBMol.EndResidue
-
- %include <openbabel/obiter.h>
-
--# The following class, OBiter, is subclassed to provide Python iterators
--# equivalent to the C++ iterators in obiter.h and the plugin iterators
-+// The following class, OBiter, is subclassed to provide Python iterators
-+// equivalent to the C++ iterators in obiter.h and the plugin iterators
-
- %pythoncode %{
- class OBIter(object):
-@@ -459,7 +459,7 @@ def double_array(mylist):
- return c
- %}
-
--# Copy some of the global variables in cvar into the openbabel namespace
-+// Copy some of the global variables in cvar into the openbabel namespace
-
- %pythoncode %{
- obErrorLog = cvar.obErrorLog
-@@ -470,7 +470,7 @@ atomtyper = cvar.atomtyper
- aromtyper = cvar.aromtyper
- %}
-
--# Functions to set the log file to std::cout and std::cerr
-+// Functions to set the log file to std::cout and std::cerr
-
- %ignore OBForceField::SetLogFile(std::ostream *pos);
- %extend OpenBabel::OBForceField {
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 7a0114975fff..000000000000
--- 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/openbabel-python-2.3.2.ebuild b/sci-chemistry/openbabel-python/openbabel-python-2.3.2.ebuild
deleted file mode 100644
index 999a73bc7948..000000000000
--- a/sci-chemistry/openbabel-python/openbabel-python-2.3.2.ebuild
+++ /dev/null
@@ -1,93 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 python3_4 )
-
-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 ~arm x86 ~amd64-linux ~x86-linux"
-SLOT="0"
-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=(
- "${FILESDIR}"/${P}-testpybel.patch
- "${FILESDIR}"/${P}-bindings_only.patch
- "${FILESDIR}"/${P}-swig-3.0.3.patch
- "${FILESDIR}"/${P}-gcc-6_and_7-backport.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="$(python_get_library_path)"
- -DENABLE_TESTS=ON
- )
-
- cmake-utils_src_configure
- }
-
- python_foreach_impl my_impl_src_configure
-}
-
-src_compile() {
- python_foreach_impl cmake-utils_src_make bindings_python
-}
-
-src_test() {
- python_foreach_impl cmake-utils_src_test -R py
-}
-
-src_install() {
- my_impl_src_install() {
- cd "${BUILD_DIR}" || die
-
- cmake -DCOMPONENT=bindings_python -P cmake_install.cmake
-
- python_optimize
- }
-
- python_foreach_impl my_impl_src_install
-}
diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest
index 970eee422e6d..4e551dea6d29 100644
--- a/sci-chemistry/openbabel/Manifest
+++ b/sci-chemistry/openbabel/Manifest
@@ -1,8 +1,5 @@
AUX openbabel-2.3.2-gcc-6_and_7-backport.patch 635 BLAKE2B 4e98dedd149b14d5bb02fb6d2fa03e07242d100c7b41f36f749ff3d587080eeca44aa26ca095d31e0309e45f3780b67deaa97f1177ed35a9b7407bd7c33f78ff SHA512 e1b4402f34d01ced5b4caaa184b4e5544cf47893cfe7958054052b05a57dc34b4d44239a212c7d909f29b9366b83b6df74993f844a20f23748c01272ec093081
-AUX openbabel-2.3.2-test_lib_path.patch 837 BLAKE2B 1d6e1c26cd794cef61bde2c2821b937cf0aa2f0a6e812579a44f65bc787b63cb8e85e0979cf945c2892cbd4a39ffaddb8464f93b0a08f6751b8fc062495b42a4 SHA512 d065eef0bb8d751d3292206feb25557394dc203e810b5f0eb7c52a28cb9e2bfaaf60f195d295ef6e58619ab9fa87d84e6b55ad822cfdefc22e02e8b5a8b49efb
AUX openbabel-2.4.1-gcc-8.patch 706 BLAKE2B 085b2f5a1678c02a6a8efc5f760dc43ef311774a47d80c87efb75111ac750ec6bf520286fa74325eca71138eecff4b2772ab087d4de1b9b9a5f1c81806d6be87 SHA512 04884d47a9549d2c107bbeb9c36edbe18ee68a7edd447fce405f39a4297bdacf3f81ddf4c5c19e9728355f07960b836e684087573b3a2b7892225de8b7beaea1
-DIST openbabel-2.3.2.tar.gz 20509105 BLAKE2B d475c2da0d7171650eeb4b78a948421b783bdbb9342c81114d3dbc19d5cbb273f7303438920ffaeef5b6332e4b72606a86ded5cbd3d7e541f62b59b46483bb69 SHA512 d0e1f8b758ffdd65ec6c31d988bffe3279355e286ce69fad12c5905b3b832e2b73ee95b1061b1576aba1ee9fe4da5e31ec30350c473be17493c657dc80caf919
DIST openbabel-2.4.1.tar.gz 11618304 BLAKE2B 8fc051e83add9be6456e281a109bd6bbec282a64ffc83309819f0decbf167b4914fbb7f1966e95e103f268754045b804317f51c79a952ace707c6af2bd320125 SHA512 427e678f0a911bd27b9a8a05e60b6e09f113be4e5dd180daaf80c28d06368e52b57501261755ab3817a8d31f2754db24471fd0ceee706d029386d6f70800e9c6
-EBUILD openbabel-2.3.2-r1.ebuild 2061 BLAKE2B 292e860a5ae8eac6de4d273fe4030965ac4f710224127b2aa5155dd12e7452fe3204ffb49388d290555574124fc004930cd0af38028c30c73aa99fa4cf802dfa SHA512 acc8b99854f852375a19a5b6316cc439016aa258e369892bc524949e709c48412f7925e57f2b684de6a327960b09324d0327aee066560d8dd2194b279de53e0f
EBUILD openbabel-2.4.1.ebuild 2013 BLAKE2B b7fe713786600ac7efc9b4541663b8049c0145863cd6efc397dbed8a858cb006746e8ae6ddb4b9148023d5bf3a7f1cca76a4327577a5f9809c8e17d5a4f78945 SHA512 2eddc590968cb39a8c87563eb724669742b795bbf1861d85d9892e87fa9137b989f36ba435f98fe1b8151a142aa73a73df49ab5ef5ad1617e2d3875ad655ee1e
MISC metadata.xml 665 BLAKE2B 4657b85c826c006b6d69e06240dd908a72397a32cb0c0512810e22d1b02478eaa3ab460535b300eba653a334a79c81a102007da1a901d6d1dbd04fc5e795df73 SHA512 0555e7c7401dfd5fbeee339302f8eb7a104ad6538db2839d8e89c20ac5ad2184070335677671a58eb91be2780ae485467d33302f3a14d0caab4ae8c0148f03bb
diff --git a/sci-chemistry/openbabel/files/openbabel-2.3.2-test_lib_path.patch b/sci-chemistry/openbabel/files/openbabel-2.3.2-test_lib_path.patch
deleted file mode 100644
index 66a796d17b7f..000000000000
--- a/sci-chemistry/openbabel/files/openbabel-2.3.2-test_lib_path.patch
+++ /dev/null
@@ -1,27 +0,0 @@
-diff -ru old/openbabel-2.3.0/test/CMakeLists.txt new/openbabel-2.3.0/test/CMakeLists.txt
---- a/test/CMakeLists.txt 2010-10-26 17:39:01.000000000 +0300
-+++ b/test/CMakeLists.txt 2010-11-14 18:13:32.000000000 +0200
-@@ -2,7 +2,7 @@
- add_definitions(-DTESTDATADIR="\\"${CMAKE_SOURCE_DIR}/test/files/\\"")
-
- # define FORMATDIR for location of format plugin binaries
--add_definitions(-DFORMATDIR="\\"${openbabel_BINARY_DIR}/lib/\\"")
-+add_definitions(-DFORMATDIR="\\"${openbabel_BINARY_DIR}/lib${LIB_SUFFIX}/\\"")
-
- ###########################################################
- # new tests using obtest.h
-@@ -32,12 +35,12 @@ set(tests
- uniqueid
- )
-
--if (EIGEN2_FOUND)
-+if(EIGEN2_FOUND OR EIGEN3_FOUND)
- set(tests
- align
- ${tests}
- )
--endif (EIGEN2_FOUND)
-+endif()
-
- set(TEST_PATH ${CMAKE_RUNTIME_OUTPUT_DIRECTORY})
-
diff --git a/sci-chemistry/openbabel/openbabel-2.3.2-r1.ebuild b/sci-chemistry/openbabel/openbabel-2.3.2-r1.ebuild
deleted file mode 100644
index 9665a2ffebcb..000000000000
--- a/sci-chemistry/openbabel/openbabel-2.3.2-r1.ebuild
+++ /dev/null
@@ -1,92 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-WX_GTK_VER="3.0"
-
-inherit cmake-utils eutils wxwidgets
-
-DESCRIPTION="Interconverts file formats used in molecular modeling"
-HOMEPAGE="http://openbabel.sourceforge.net/"
-SRC_URI="mirror://sourceforge/openbabel/${P}.tar.gz"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux ~ppc-macos"
-IUSE="doc openmp test wxwidgets"
-
-RDEPEND="
- dev-cpp/eigen:3
- dev-libs/libxml2:2
- sci-libs/inchi
- sys-libs/zlib
- wxwidgets? ( x11-libs/wxGTK:${WX_GTK_VER}[X] )"
-DEPEND="${RDEPEND}
- >=dev-util/cmake-2.4.8
- doc? ( app-doc/doxygen )"
-
-DOCS="AUTHORS ChangeLog NEWS README THANKS doc/*.inc doc/README* doc/*.mol2"
-
-PATCHES=(
- "${FILESDIR}"/${P}-test_lib_path.patch
- "${FILESDIR}"/${P}-gcc-6_and_7-backport.patch
- )
-
-pkg_setup() {
- if use openmp; then
- if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp; then
- ewarn "OpenMP is not available in your current selected gcc"
- die "need openmp capable gcc"
- fi
- FORTRAN_NEED_OPENMP=1
- fi
-}
-
-src_prepare() {
- sed \
- -e '/__GNUC__/s:== 4:>= 4:g' \
- -i include/openbabel/shared_ptr.h || die
- cmake-utils_src_prepare
-}
-
-src_configure() {
- use wxwidgets && need-wxwidgets unicode
- local mycmakeargs=()
- mycmakeargs+=(
- -DOPENBABEL_USE_SYSTEM_INCHI=ON
- $(cmake-utils_use_enable openmp OPENMP)
- $(cmake-utils_use wxwidgets BUILD_GUI)
- )
-
- cmake-utils_src_configure
-}
-
-src_install() {
- dohtml doc/{*.html,*.png}
- if use doc ; then
- insinto /usr/share/doc/${PF}/API/html
- doins doc/API/html/*
- fi
-
- cmake-utils_src_install
-}
-
-src_test() {
- local mycmakeargs=""
- mycmakeargs="${mycmakeargs}
- -DOPENBABEL_USE_SYSTEM_INCHI=ON
- -DPYTHON_EXECUTABLE=false
- $(cmake-utils_use_enable openmp OPENMP)
- $(cmake-utils_use wxwidgets BUILD_GUI)
- $(cmake-utils_use_enable test TESTS)"
-
- cmake-utils_src_configure
- cmake-utils_src_compile
- cmake-utils_src_test -E py
-}
-
-pkg_postinst() {
- optfeature "perl support" sci-chemistry/openbabel-perl
- optfeature "python support" sci-chemistry/openbabel-python
-}
diff --git a/sci-chemistry/tm-align/Manifest b/sci-chemistry/tm-align/Manifest
index 59bbb7ff261d..8260fae5754a 100644
--- a/sci-chemistry/tm-align/Manifest
+++ b/sci-chemistry/tm-align/Manifest
@@ -2,5 +2,5 @@ AUX CMakeLists.txt 182 BLAKE2B a6bd5aedcbeb2b8019d59123da91cf668c3717a3e41c2259b
DIST TMtools20140601.tar.gz 934391 BLAKE2B 4dfe18501bfd26b0c12f734175b908f65e97cea9cf2c620c100aa2f68f10fb288c8973c71c9fc6364a635f0275d3a04d7eaffdd5833345dda57e7a318e7c4e5f SHA512 99b90425ff051c836e19225601ddfb1576bec9c8f233aafeba96075f924a3c0892b5b1cfef36254ff5ef468a6dbf64f7fcc9a3ce24a0d869b3c1eb87c0149765
DIST TMtools20150914.tar.gz 982948 BLAKE2B 788f43040c1262c7e9eae2b47b0035d320a30fe7194e340d682b78e5961b82e46eef2b0a43d1ae458b9d5da6570f9c0ec0aca51b6ec3e25f0447fd43d629f592 SHA512 5fda29f6437ac9b0216a037496a01502de07e5a36736815833cb09217158a959370e750b75c55a54a49c733e4bd28be53b2dcbb25d71e2897273a4280ed3b530
EBUILD tm-align-20140601.ebuild 720 BLAKE2B 169462fabc7fb255e1746ae1f692b6f989591787ca53023ded771f56489c4c8a2407d40d45186b8fa89ba3750d51e45ab889e4ca6b4f768fa28f1f8eea004f4b SHA512 04d20ceb4a1a33277af7cee7ec49e1902eceb5cb33361020a56f6b9bad62b0c423867104fb6b4bda8b0197d3b7d0a0e057cea87907ab43d69cf10961ca082543
-EBUILD tm-align-20150914.ebuild 724 BLAKE2B 1b14b8ee35ebc27c8d30f6d458b15bfb90d4024bf99cbe547afd70da46f9b475cf34ee09c67f4583002210d8e80b8fd5e501c37dcb737a8a17c1c18f4e9b7b07 SHA512 dde3650a7d1361c46fe93d99ea1b8df3bc40f0a067f3df8cc79b1187d6c44f588e228ff60e0c4fa9702160d310b439cdae901db5ed6067ce81b934d280af4714
+EBUILD tm-align-20150914.ebuild 719 BLAKE2B 085ff1781394ded54c8f8759c5dcb3c74f92283cfe94ab6f6f85b5d6f8e09eeb84d539aacfe998384870db0f7f34f7cb3c560d316eb55ffb9628d6cfb343dbbf SHA512 e725f7d70953c620a4082049e435647d2ead74359912e0028ef065d6fb428e4ac885f8c13f7c4d72fbe91367853066b2451d351c4aa0a4ab82339bac85608ef0
MISC metadata.xml 1294 BLAKE2B 7972c0f1c379a3929c3d561756099a2071ddc9a6ff35a905a30807f1d724100aa39e98bf549ab4614a7f7b95628246fde7f44d655dceebb0e8f4a4f70686123d SHA512 e1b90b61682c3c1099c3b2d5d5fad166e408b14aca67e49521f470b2df1c746aa4c1eeae06f4f67fe6ccf8ded94c5fbe7a194a441fae8fab450f69acdcb49663
diff --git a/sci-chemistry/tm-align/tm-align-20150914.ebuild b/sci-chemistry/tm-align/tm-align-20150914.ebuild
index 6732f611eaad..a19b8da0b4c1 100644
--- a/sci-chemistry/tm-align/tm-align-20150914.ebuild
+++ b/sci-chemistry/tm-align/tm-align-20150914.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=6
inherit cmake-utils flag-o-matic fortran-2
@@ -11,15 +11,15 @@ SRC_URI="http://zhanglab.ccmb.med.umich.edu/TM-align/TMtools${PV}.tar.gz"
LICENSE="tm-align"
SLOT="0"
-KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="static custom-cflags"
+KEYWORDS="~amd64 ppc ppc64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="custom-cflags static"
S="${WORKDIR}"
src_prepare() {
+ cp "${FILESDIR}"/CMakeLists.txt . || die
cmake-utils_src_prepare
- cp "${FILESDIR}"/CMakeLists.txt . || die
use static && append-fflags -static && append-ldflags -static
# recommended by upstream
use custom-cflags || replace-flags -O* -O3 && append-fflags -ffast-math
generated by cgit v1.2.3 (git 2.25.1) at 2024-12-27 17:13:18 +0000