From: "Sam James" <sam@gentoo.org>
To: gentoo-commits@lists.gentoo.org
Subject: [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/openbabel/
Date: Mon, 24 Mar 2025 09:16:21 +0000 (UTC) [thread overview]
Message-ID: <1742807754.714bdc8b5ba99e156a92fd2f4025a41e157e5a20.sam@gentoo> (raw)
commit: 714bdc8b5ba99e156a92fd2f4025a41e157e5a20
Author: Nicolas PARLANT <nicolas.parlant <AT> parhuet <DOT> fr>
AuthorDate: Thu Mar 13 15:04:29 2025 +0000
Commit: Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Mon Mar 24 09:15:54 2025 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=714bdc8b
sci-chemistry/openbabel: sync live
sync with last version
Signed-off-by: Nicolas PARLANT <nicolas.parlant <AT> parhuet.fr>
Closes: https://github.com/gentoo/gentoo/pull/41087
Signed-off-by: Sam James <sam <AT> gentoo.org>
sci-chemistry/openbabel/openbabel-9999.ebuild | 164 ++++++++++----------------
1 file changed, 60 insertions(+), 104 deletions(-)
diff --git a/sci-chemistry/openbabel/openbabel-9999.ebuild b/sci-chemistry/openbabel/openbabel-9999.ebuild
index fc4d6cab575e..84485db4537d 100644
--- a/sci-chemistry/openbabel/openbabel-9999.ebuild
+++ b/sci-chemistry/openbabel/openbabel-9999.ebuild
@@ -1,12 +1,12 @@
-# Copyright 1999-2024 Gentoo Authors
+# Copyright 1999-2025 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
-PYTHON_COMPAT=( python3_{10..12} )
+PYTHON_COMPAT=( python3_{10..13} )
WX_GTK_VER=3.2-gtk3
-inherit cmake desktop flag-o-matic perl-functions python-r1 toolchain-funcs wxwidgets xdg-utils
+inherit cmake desktop flag-o-matic perl-functions python-r1 toolchain-funcs wxwidgets xdg
DESCRIPTION="Interconverts file formats used in molecular modeling"
HOMEPAGE="https://openbabel.org/ https://github.com/openbabel/openbabel/"
@@ -17,7 +17,7 @@ if [[ "${PV}" == *9999* ]]; then
else
if [[ "${PV}" == *_p* ]]; then # eg., openbabel-3.1.1_p20210325
# Set to commit hash
- OPENBABEL_COMMIT=08e23f39b0cc39b4eebd937a5a2ffc1a7bac3e1b
+ OPENBABEL_COMMIT="889c350feb179b43aa43985799910149d4eaa2bc"
SRC_URI="https://github.com/${PN}/${PN}/archive/${OPENBABEL_COMMIT}.tar.gz -> ${P}.tar.gz"
S="${WORKDIR}/${PN}-${OPENBABEL_COMMIT}"
else
@@ -25,63 +25,49 @@ else
SRC_URI="https://github.com/${PN}/${PN}/archive/${MY_P}.tar.gz -> ${P}.tar.gz"
S="${WORKDIR}/${PN}-${MY_P}"
fi
- KEYWORDS="amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+ KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
fi
-SRC_URI="${SRC_URI}
- https://openbabel.org/docs/dev/_static/babel130.png -> ${PN}.png
- https://openbabel.org/OBTitle.jpg -> ${PN}.jpg"
-
+LICENSE="GPL-2"
# See src/CMakeLists.txt for LIBRARY_VERSION
SLOT="0/7.0.0"
-LICENSE="GPL-2"
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"
-
RESTRICT="!test? ( test )"
-
-# Inaccurate dependency logic upstream
REQUIRED_USE="
python? ( ${PYTHON_REQUIRED_USE} )
- test? ( inchi json !minimal wxwidgets )
-"
-
-BDEPEND="
- dev-lang/perl
- doc? (
- app-text/doxygen
- dev-texlive/texlive-latex
- )
- perl? ( >=dev-lang/swig-2 )
- python? ( >=dev-lang/swig-2 )
- test? ( dev-lang/python )
+ test? ( inchi !minimal python? ( json png ) ${PYTHON_REQUIRED_USE} )
"
-COMMON_DEPEND="
+RDEPEND="
dev-cpp/eigen:3
- dev-libs/libxml2:2
sys-libs/zlib:=
inchi? ( sci-libs/inchi )
json? ( >=dev-libs/rapidjson-1.1.0 )
- png? ( x11-libs/cairo )
+ !minimal? (
+ dev-libs/libxml2:2
+ png? ( x11-libs/cairo )
+ )
+ perl? ( dev-lang/perl:= )
python? ( ${PYTHON_DEPS} )
wxwidgets? ( x11-libs/wxGTK:${WX_GTK_VER}[X] )
"
-
-DEPEND="
- ${COMMON_DEPEND}
- perl? ( dev-lang/perl )
-"
-
-RDEPEND="
- ${COMMON_DEPEND}
- perl? (
- dev-lang/perl:=
- !sci-chemistry/openbabel-perl
+DEPEND="${RDEPEND}"
+BDEPEND="
+ dev-lang/perl
+ doc? (
+ app-text/doxygen
+ dev-texlive/texlive-latex
)
+ perl? ( dev-lang/swig )
+ python? ( dev-lang/swig )
+ test? ( dev-lang/python )
"
PATCHES=(
- "${FILESDIR}"/openbabel-3.1.1-fix-time-check-cmake.patch
+ # Set include dir only for global implementation
+ "${FILESDIR}"/${PN}-3.1.1_p2024-fix_pybind.patch
+ # prevent installation of examples in /usr/bin
+ "${FILESDIR}"/${PN}-3.1.1_p2024-fix_examples.patch
)
pkg_pretend() {
@@ -92,13 +78,13 @@ pkg_setup() {
[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
}
-prepare_python_bindings() {
+gen_python_bindings() {
mkdir -p scripts/${EPYTHON} || die
# Appends to scripts/CMakeLists.txt, substituting the correct tags, for
# each valid python implementation,
- cat "${FILESDIR}"/${PN}-python.cmake | \
+ cat "${FILESDIR}"/${PN}-python-r2.cmake | \
sed -e "s|@@EPYTHON@@|${EPYTHON}|" \
- -e "s|@@PYTHON_INCUDE_DIR@@|$(python_get_includedir)|" \
+ -e "s|@@PYTHON_INCLUDE_DIR@@|$(python_get_includedir)|" \
-e "s|@@PYTHON_LIBS@@|$(python_get_LIBS)|" \
-e "s|@@PYTHON_SITEDIR@@|$(python_get_sitedir)|" >> \
scripts/CMakeLists.txt || die
@@ -107,51 +93,10 @@ prepare_python_bindings() {
src_prepare() {
cmake_src_prepare
- if use perl; then
- perl_set_version
-
- sed -e "/\${LIB_INSTALL_DIR}\/auto/s|\${LIB_INSTALL_DIR}|${VENDOR_ARCH}|" \
- -e "/\${LIB_INSTALL_DIR}\/Chemistry/s|\${LIB_INSTALL_DIR}|${VENDOR_ARCH}|" \
- -i scripts/CMakeLists.txt || die
- fi
-
- if use python; then
- # Skip the python bindings sections as we'll append our own
- sed -e '/^if (PYTHON_BINDINGS)$/s|PYTHON_BINDINGS|false|' \
- -i {scripts,test}/CMakeLists.txt || die
- if use test; then
- # Problems with testbindings built with -O2
- local test_skip="@unittest.skip('Similar to Issue #2138')"
- sed -e "/def testTemplates/s|^| ${test_skip}\\n|" \
- -i test/testbindings.py || die
- test_skip="@unittest.skip('Similar to Issue #2246')"
- sed -e "/^def test_write_string/s|^|${test_skip}\\n|" \
- -i test/testobconv_writers.py || die
- fi
- python_foreach_impl prepare_python_bindings
- fi
-
- # Remove dependency automagic
- if ! use png; then
- sed -e '/^find_package(Cairo/d' -i CMakeLists.txt || die
- fi
- if ! use wxwidgets; then
- sed -e '/^find_package(wxWidgets/d' -i CMakeLists.txt || die
- fi
- if ! use inchi; then
- sed -e '/^else()$/s|else\(\)|elseif\(false\)|' \
- -i cmake/modules/FindInchi.cmake || die
- fi
-
- # Don't install example bins to /usr/bin
- if use examples; then
- sed -e "/RUNTIME DESTINATION/s|bin|share/doc/${PF}/examples|" \
- -i doc/examples/CMakeLists.txt || die
- fi
+ # Prevent bundled inchi as fallback
+ rm -r include/inchi || die
- # boost is only used if building with gcc-3.x, which isn't supported in
- # Gentoo. Still, it shouldn't look for, and include, its headers
- sed -e '/find_package(Boost/d' -i {{tools,src}/,}CMakeLists.txt || die
+ use python && python_foreach_impl gen_python_bindings
}
src_configure() {
@@ -170,36 +115,59 @@ src_configure() {
}
local mycmakeargs=(
+ $(cmake_use_find_package png Cairo)
+ $(cmake_use_find_package wxwidgets wxWidgets)
+ -DCMAKE_SKIP_RPATH=ON
-DBUILD_DOCS=$(usex doc)
-DBUILD_EXAMPLES=$(usex examples)
-DBUILD_GUI=$(usex wxwidgets)
-DENABLE_OPENMP=$(usex openmp)
-DENABLE_TESTS=$(usex test)
-DMINIMAL_BUILD=$(usex minimal)
- # Set this, otherwise it defaults to true and forces WITH_INCHI=true
+ # All three required to comply w/ useflag and prevent bundled lib
-DOPENBABEL_USE_SYSTEM_INCHI=$(usex inchi)
+ -DADD_INCHI_FORMAT=$(usex inchi)
+ -DWITH_INCHI=$(usex inchi)
-DOPTIMIZE_NATIVE=OFF
-DPERL_BINDINGS=$(usex perl)
-DPYTHON_BINDINGS=$(usex python)
-DRUN_SWIG=$(use_bindings)
-DWITH_COORDGEN=false
- -DWITH_INCHI=$(usex inchi)
-DWITH_JSON=$(usex json)
+ # MEAPARSER
+ -DCMAKE_DISABLE_FIND_PACKAGE_Boost=ON
-DWITH_MAEPARSER=false
)
+ if use perl; then
+ perl_set_version
+ mycmakeargs+=(
+ -DPERL_INSTDIR="${VENDOR_ARCH}"
+ )
+ fi
+
if use test; then
# Help cmake find the python interpreter when dev-lang/python-exec is built
# without native-symlinks support.
python_setup
- mycmakeargs+=( -DPYTHON_EXECUTABLE="${PYTHON}" )
+ mycmakeargs+=(
+ -DPYTHON_EXECUTABLE="${PYTHON}"
+ )
fi
cmake_src_configure
}
src_test() {
- # Wierd deadlock causes system_load to keep rising
+ local CMAKE_SKIP_TESTS=(
+ # https://github.com/openbabel/openbabel/issues/2766
+ test_align_{4,5}
+ )
+ ! use wxwidgets && CMAKE_SKIP_TESTS+=(
+ test_tautomer_{22,27}
+ )
+
+ # Weird deadlock causes system_load to keep rising
cmake_src_test -j1
}
@@ -214,9 +182,6 @@ src_install() {
for x in doc/*.html; do
[[ ${x} != doc/api*.html ]] && dodoc ${x}
done
- # Rendered in some html pages
- newdoc "${DISTDIR}"/${PN}.png babel130.png
- newdoc "${DISTDIR}"/${PN}.jpg OBTitle.jpg
if use doc; then
cmake_src_install docs
@@ -240,7 +205,6 @@ src_install() {
# Needed by the povray example
dosym ../../../../${PN}/${babel_ver}/babel_povray3.inc \
/usr/share/doc/${PF}/examples/povray/babel31.inc
-
fi
if use perl; then
@@ -267,14 +231,6 @@ src_install() {
if use wxwidgets; then
make_desktop_entry obgui "Open Babel" ${PN}
- doicon "${DISTDIR}"/${PN}.png
+ newicon "${S}"/src/GUI/babel.xpm ${PN}.xpm
fi
}
-
-pkg_postinst() {
- use wxwidgets && xdg_desktop_database_update
-}
-
-pkg_postrm() {
- use wxwidgets && xdg_desktop_database_update
-}
next reply other threads:[~2025-03-24 9:16 UTC|newest]
Thread overview: 31+ messages / expand[flat|nested] mbox.gz Atom feed top
2025-03-24 9:16 Sam James [this message]
-- strict thread matches above, loose matches on Subject: below --
2024-07-30 21:13 [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/openbabel/ Pacho Ramos
2024-07-30 21:13 Pacho Ramos
2024-06-29 18:08 Andreas Sturmlechner
2024-04-11 17:52 Arthur Zamarin
2023-11-24 14:31 Pacho Ramos
2023-02-23 13:20 Andrew Ammerlaan
2022-05-16 8:12 David Seifert
2022-03-10 21:12 Sam James
2022-03-07 14:33 Jakov Smolić
2022-03-07 14:33 Jakov Smolić
2021-12-15 10:09 Andrew Ammerlaan
2021-12-15 10:09 Andrew Ammerlaan
2021-03-28 11:00 Sam James
2021-03-28 10:00 Agostino Sarubbo
2021-01-18 10:14 David Seifert
2020-12-18 10:48 Agostino Sarubbo
2020-12-02 3:06 Thomas Deutschmann
2020-09-07 8:55 David Seifert
2019-09-29 11:26 Pacho Ramos
2017-10-05 12:05 Michael Palimaka
2017-09-12 22:58 Matt Turner
2017-07-31 11:36 Tobias Klausmann
2017-06-03 8:39 Justin Lecher
2015-11-07 9:09 Justin Lecher
2015-11-04 19:28 Justin Lecher
2015-11-04 15:17 Agostino Sarubbo
2015-11-01 13:49 Mikle Kolyada
2015-10-30 9:18 Agostino Sarubbo
2015-10-27 18:04 Justin Lecher
2015-10-25 10:31 Pacho Ramos
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