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sci-chemistry/openbabel: sync live
sync with last version Signed-off-by: Nicolas PARLANT <nicolas.parlant@parhuet.fr> Closes: https://github.com/gentoo/gentoo/pull/41087 Signed-off-by: Sam James <sam@gentoo.org>
This commit is contained in:
Nicolas PARLANT
committed by
Sam James
Sam James
parent
203d57887f
commit
714bdc8b5b
@@ -1,12 +1,12 @@
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# Copyright 1999-2024 Gentoo Authors
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# Copyright 1999-2025 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=8
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PYTHON_COMPAT=( python3_{10..12} )
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PYTHON_COMPAT=( python3_{10..13} )
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WX_GTK_VER=3.2-gtk3
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inherit cmake desktop flag-o-matic perl-functions python-r1 toolchain-funcs wxwidgets xdg-utils
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inherit cmake desktop flag-o-matic perl-functions python-r1 toolchain-funcs wxwidgets xdg
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DESCRIPTION="Interconverts file formats used in molecular modeling"
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HOMEPAGE="https://openbabel.org/ https://github.com/openbabel/openbabel/"
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@@ -17,7 +17,7 @@ if [[ "${PV}" == *9999* ]]; then
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else
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if [[ "${PV}" == *_p* ]]; then # eg., openbabel-3.1.1_p20210325
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# Set to commit hash
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OPENBABEL_COMMIT=08e23f39b0cc39b4eebd937a5a2ffc1a7bac3e1b
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OPENBABEL_COMMIT="889c350feb179b43aa43985799910149d4eaa2bc"
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SRC_URI="https://github.com/${PN}/${PN}/archive/${OPENBABEL_COMMIT}.tar.gz -> ${P}.tar.gz"
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S="${WORKDIR}/${PN}-${OPENBABEL_COMMIT}"
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else
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@@ -25,63 +25,49 @@ else
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SRC_URI="https://github.com/${PN}/${PN}/archive/${MY_P}.tar.gz -> ${P}.tar.gz"
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S="${WORKDIR}/${PN}-${MY_P}"
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fi
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KEYWORDS="amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
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KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
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fi
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SRC_URI="${SRC_URI}
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https://openbabel.org/docs/dev/_static/babel130.png -> ${PN}.png
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https://openbabel.org/OBTitle.jpg -> ${PN}.jpg"
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LICENSE="GPL-2"
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# See src/CMakeLists.txt for LIBRARY_VERSION
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SLOT="0/7.0.0"
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LICENSE="GPL-2"
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IUSE="cpu_flags_arm_neon cpu_flags_x86_sse2 cpu_flags_x86_sse4_2 doc examples +inchi json minimal openmp perl png python test wxwidgets"
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RESTRICT="!test? ( test )"
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# Inaccurate dependency logic upstream
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REQUIRED_USE="
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python? ( ${PYTHON_REQUIRED_USE} )
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test? ( inchi json !minimal wxwidgets )
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test? ( inchi !minimal python? ( json png ) ${PYTHON_REQUIRED_USE} )
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"
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RDEPEND="
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dev-cpp/eigen:3
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sys-libs/zlib:=
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inchi? ( sci-libs/inchi )
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json? ( >=dev-libs/rapidjson-1.1.0 )
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!minimal? (
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dev-libs/libxml2:2
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png? ( x11-libs/cairo )
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)
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perl? ( dev-lang/perl:= )
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python? ( ${PYTHON_DEPS} )
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wxwidgets? ( x11-libs/wxGTK:${WX_GTK_VER}[X] )
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"
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DEPEND="${RDEPEND}"
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BDEPEND="
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dev-lang/perl
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doc? (
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app-text/doxygen
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dev-texlive/texlive-latex
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)
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perl? ( >=dev-lang/swig-2 )
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python? ( >=dev-lang/swig-2 )
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perl? ( dev-lang/swig )
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python? ( dev-lang/swig )
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test? ( dev-lang/python )
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"
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COMMON_DEPEND="
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dev-cpp/eigen:3
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dev-libs/libxml2:2
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sys-libs/zlib:=
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inchi? ( sci-libs/inchi )
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json? ( >=dev-libs/rapidjson-1.1.0 )
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png? ( x11-libs/cairo )
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python? ( ${PYTHON_DEPS} )
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wxwidgets? ( x11-libs/wxGTK:${WX_GTK_VER}[X] )
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"
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DEPEND="
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${COMMON_DEPEND}
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perl? ( dev-lang/perl )
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"
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RDEPEND="
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${COMMON_DEPEND}
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perl? (
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dev-lang/perl:=
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!sci-chemistry/openbabel-perl
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)
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"
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PATCHES=(
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"${FILESDIR}"/openbabel-3.1.1-fix-time-check-cmake.patch
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# Set include dir only for global implementation
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"${FILESDIR}"/${PN}-3.1.1_p2024-fix_pybind.patch
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# prevent installation of examples in /usr/bin
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"${FILESDIR}"/${PN}-3.1.1_p2024-fix_examples.patch
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)
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pkg_pretend() {
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@@ -92,13 +78,13 @@ pkg_setup() {
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[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
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}
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prepare_python_bindings() {
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gen_python_bindings() {
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mkdir -p scripts/${EPYTHON} || die
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# Appends to scripts/CMakeLists.txt, substituting the correct tags, for
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# each valid python implementation,
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cat "${FILESDIR}"/${PN}-python.cmake | \
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cat "${FILESDIR}"/${PN}-python-r2.cmake | \
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sed -e "s|@@EPYTHON@@|${EPYTHON}|" \
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-e "s|@@PYTHON_INCUDE_DIR@@|$(python_get_includedir)|" \
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-e "s|@@PYTHON_INCLUDE_DIR@@|$(python_get_includedir)|" \
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-e "s|@@PYTHON_LIBS@@|$(python_get_LIBS)|" \
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-e "s|@@PYTHON_SITEDIR@@|$(python_get_sitedir)|" >> \
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scripts/CMakeLists.txt || die
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@@ -107,51 +93,10 @@ prepare_python_bindings() {
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src_prepare() {
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cmake_src_prepare
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if use perl; then
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perl_set_version
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# Prevent bundled inchi as fallback
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rm -r include/inchi || die
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sed -e "/\${LIB_INSTALL_DIR}\/auto/s|\${LIB_INSTALL_DIR}|${VENDOR_ARCH}|" \
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-e "/\${LIB_INSTALL_DIR}\/Chemistry/s|\${LIB_INSTALL_DIR}|${VENDOR_ARCH}|" \
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-i scripts/CMakeLists.txt || die
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fi
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if use python; then
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# Skip the python bindings sections as we'll append our own
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sed -e '/^if (PYTHON_BINDINGS)$/s|PYTHON_BINDINGS|false|' \
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-i {scripts,test}/CMakeLists.txt || die
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if use test; then
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# Problems with testbindings built with -O2
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local test_skip="@unittest.skip('Similar to Issue #2138')"
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sed -e "/def testTemplates/s|^| ${test_skip}\\n|" \
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-i test/testbindings.py || die
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test_skip="@unittest.skip('Similar to Issue #2246')"
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sed -e "/^def test_write_string/s|^|${test_skip}\\n|" \
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-i test/testobconv_writers.py || die
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fi
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python_foreach_impl prepare_python_bindings
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fi
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# Remove dependency automagic
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if ! use png; then
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sed -e '/^find_package(Cairo/d' -i CMakeLists.txt || die
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fi
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if ! use wxwidgets; then
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sed -e '/^find_package(wxWidgets/d' -i CMakeLists.txt || die
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fi
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if ! use inchi; then
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sed -e '/^else()$/s|else\(\)|elseif\(false\)|' \
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-i cmake/modules/FindInchi.cmake || die
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fi
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# Don't install example bins to /usr/bin
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if use examples; then
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sed -e "/RUNTIME DESTINATION/s|bin|share/doc/${PF}/examples|" \
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-i doc/examples/CMakeLists.txt || die
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fi
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# boost is only used if building with gcc-3.x, which isn't supported in
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# Gentoo. Still, it shouldn't look for, and include, its headers
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sed -e '/find_package(Boost/d' -i {{tools,src}/,}CMakeLists.txt || die
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use python && python_foreach_impl gen_python_bindings
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}
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src_configure() {
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@@ -170,36 +115,59 @@ src_configure() {
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}
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local mycmakeargs=(
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$(cmake_use_find_package png Cairo)
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$(cmake_use_find_package wxwidgets wxWidgets)
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-DCMAKE_SKIP_RPATH=ON
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-DBUILD_DOCS=$(usex doc)
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-DBUILD_EXAMPLES=$(usex examples)
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-DBUILD_GUI=$(usex wxwidgets)
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-DENABLE_OPENMP=$(usex openmp)
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-DENABLE_TESTS=$(usex test)
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-DMINIMAL_BUILD=$(usex minimal)
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# Set this, otherwise it defaults to true and forces WITH_INCHI=true
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# All three required to comply w/ useflag and prevent bundled lib
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-DOPENBABEL_USE_SYSTEM_INCHI=$(usex inchi)
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-DADD_INCHI_FORMAT=$(usex inchi)
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-DWITH_INCHI=$(usex inchi)
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-DOPTIMIZE_NATIVE=OFF
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-DPERL_BINDINGS=$(usex perl)
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-DPYTHON_BINDINGS=$(usex python)
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-DRUN_SWIG=$(use_bindings)
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-DWITH_COORDGEN=false
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-DWITH_INCHI=$(usex inchi)
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-DWITH_JSON=$(usex json)
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# MEAPARSER
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-DCMAKE_DISABLE_FIND_PACKAGE_Boost=ON
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-DWITH_MAEPARSER=false
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)
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if use perl; then
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perl_set_version
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mycmakeargs+=(
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-DPERL_INSTDIR="${VENDOR_ARCH}"
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)
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fi
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if use test; then
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# Help cmake find the python interpreter when dev-lang/python-exec is built
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# without native-symlinks support.
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python_setup
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mycmakeargs+=( -DPYTHON_EXECUTABLE="${PYTHON}" )
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mycmakeargs+=(
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-DPYTHON_EXECUTABLE="${PYTHON}"
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)
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fi
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cmake_src_configure
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}
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src_test() {
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# Wierd deadlock causes system_load to keep rising
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local CMAKE_SKIP_TESTS=(
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# https://github.com/openbabel/openbabel/issues/2766
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test_align_{4,5}
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)
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! use wxwidgets && CMAKE_SKIP_TESTS+=(
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test_tautomer_{22,27}
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)
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# Weird deadlock causes system_load to keep rising
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cmake_src_test -j1
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}
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@@ -214,9 +182,6 @@ src_install() {
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for x in doc/*.html; do
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[[ ${x} != doc/api*.html ]] && dodoc ${x}
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done
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# Rendered in some html pages
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newdoc "${DISTDIR}"/${PN}.png babel130.png
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newdoc "${DISTDIR}"/${PN}.jpg OBTitle.jpg
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if use doc; then
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cmake_src_install docs
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@@ -240,7 +205,6 @@ src_install() {
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# Needed by the povray example
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dosym ../../../../${PN}/${babel_ver}/babel_povray3.inc \
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/usr/share/doc/${PF}/examples/povray/babel31.inc
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fi
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if use perl; then
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@@ -267,14 +231,6 @@ src_install() {
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if use wxwidgets; then
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make_desktop_entry obgui "Open Babel" ${PN}
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doicon "${DISTDIR}"/${PN}.png
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newicon "${S}"/src/GUI/babel.xpm ${PN}.xpm
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fi
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}
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pkg_postinst() {
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use wxwidgets && xdg_desktop_database_update
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}
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pkg_postrm() {
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use wxwidgets && xdg_desktop_database_update
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}
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