| 1 |
|
# Copyright 1999-2018 Gentoo Foundation
|
|
1 |
# Copyright 1999-2023 Gentoo Authors
|
| 2 |
2 |
# Distributed under the terms of the GNU General Public License v2
|
| 3 |
3 |
|
| 4 |
|
EAPI=6
|
|
4 |
EAPI=8
|
| 5 |
5 |
|
| 6 |
|
WX_GTK_VER="3.0"
|
|
6 |
PYTHON_COMPAT=( python3_{9..11} )
|
|
7 |
WX_GTK_VER=3.0-gtk3
|
| 7 |
8 |
|
| 8 |
|
inherit cmake-utils eutils wxwidgets
|
|
9 |
inherit cmake desktop flag-o-matic perl-functions python-r1 toolchain-funcs wxwidgets xdg-utils
|
| 9 |
10 |
|
| 10 |
11 |
DESCRIPTION="Interconverts file formats used in molecular modeling"
|
| 11 |
|
HOMEPAGE="http://openbabel.sourceforge.net/"
|
| 12 |
|
SRC_URI="mirror://sourceforge/openbabel/${P}.tar.gz"
|
|
12 |
HOMEPAGE="https://openbabel.org/"
|
|
13 |
|
|
14 |
if [[ "${PV}" == *9999* ]]; then
|
|
15 |
inherit git-r3
|
|
16 |
EGIT_REPO_URI="https://github.com/openbabel/${PN}.git"
|
|
17 |
else
|
|
18 |
if [[ "${PV}" == *_p* ]]; then # eg., openbabel-3.1.1_p20210325
|
|
19 |
# Set to commit hash
|
|
20 |
OPENBABEL_COMMIT=08e23f39b0cc39b4eebd937a5a2ffc1a7bac3e1b
|
|
21 |
SRC_URI="https://github.com/${PN}/${PN}/archive/${OPENBABEL_COMMIT}.tar.gz -> ${P}.tar.gz"
|
|
22 |
S="${WORKDIR}/${PN}-${OPENBABEL_COMMIT}"
|
|
23 |
else
|
|
24 |
MY_P="${PN}-$(ver_rs 1- -)"
|
|
25 |
SRC_URI="https://github.com/${PN}/${PN}/archive/${MY_P}.tar.gz -> ${P}.tar.gz"
|
|
26 |
S="${WORKDIR}/${PN}-${MY_P}"
|
|
27 |
fi
|
|
28 |
KEYWORDS="amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
|
|
29 |
fi
|
|
30 |
|
|
31 |
SRC_URI="${SRC_URI}
|
|
32 |
https://openbabel.org/docs/dev/_static/babel130.png -> ${PN}.png
|
|
33 |
https://openbabel.org/OBTitle.jpg -> ${PN}.jpg"
|
| 13 |
34 |
|
| 14 |
35 |
# See src/CMakeLists.txt for LIBRARY_VERSION
|
| 15 |
|
SLOT="0/5.0.0"
|
|
36 |
SLOT="0/7.0.0"
|
| 16 |
37 |
LICENSE="GPL-2"
|
| 17 |
|
KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux ~ppc-macos"
|
| 18 |
|
IUSE="doc openmp test wxwidgets"
|
|
38 |
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"
|
| 19 |
39 |
|
| 20 |
|
RDEPEND="
|
|
40 |
RESTRICT="!test? ( test )"
|
|
41 |
|
|
42 |
# Inaccurate dependency logic upstream
|
|
43 |
REQUIRED_USE="
|
|
44 |
python? ( ${PYTHON_REQUIRED_USE} )
|
|
45 |
test? ( inchi json !minimal wxwidgets )
|
|
46 |
"
|
|
47 |
|
|
48 |
BDEPEND="
|
|
49 |
dev-lang/perl
|
|
50 |
doc? (
|
|
51 |
app-doc/doxygen
|
|
52 |
dev-texlive/texlive-latex
|
|
53 |
)
|
|
54 |
perl? ( >=dev-lang/swig-2 )
|
|
55 |
python? ( >=dev-lang/swig-2 )
|
|
56 |
test? ( dev-lang/python )
|
|
57 |
"
|
|
58 |
|
|
59 |
COMMON_DEPEND="
|
| 21 |
60 |
dev-cpp/eigen:3
|
| 22 |
61 |
dev-libs/libxml2:2
|
| 23 |
|
sci-libs/inchi
|
| 24 |
|
sys-libs/zlib
|
| 25 |
|
wxwidgets? ( x11-libs/wxGTK:${WX_GTK_VER}[X] )"
|
| 26 |
|
DEPEND="${RDEPEND}
|
| 27 |
|
>=dev-util/cmake-2.4.8
|
| 28 |
|
doc? ( app-doc/doxygen )"
|
|
62 |
sys-libs/zlib:=
|
|
63 |
inchi? ( sci-libs/inchi )
|
|
64 |
json? ( >=dev-libs/rapidjson-1.1.0 )
|
|
65 |
png? ( x11-libs/cairo )
|
|
66 |
python? ( ${PYTHON_DEPS} )
|
|
67 |
wxwidgets? ( x11-libs/wxGTK:${WX_GTK_VER}[X] )
|
|
68 |
"
|
|
69 |
|
|
70 |
DEPEND="
|
|
71 |
${COMMON_DEPEND}
|
|
72 |
perl? ( dev-lang/perl )
|
|
73 |
"
|
| 29 |
74 |
|
| 30 |
|
DOCS=( AUTHORS NEWS.md README.md THANKS doc/dioxin.{inc,mol2} doc/README.{dioxin.pov,povray} )
|
|
75 |
RDEPEND="
|
|
76 |
${COMMON_DEPEND}
|
|
77 |
perl? (
|
|
78 |
dev-lang/perl:=
|
|
79 |
!sci-chemistry/openbabel-perl
|
|
80 |
)
|
|
81 |
"
|
| 31 |
82 |
|
| 32 |
83 |
PATCHES=(
|
| 33 |
|
"${FILESDIR}"/${PN}-2.3.2-gcc-6_and_7-backport.patch
|
| 34 |
|
"${FILESDIR}"/${P}-gcc-8_and_9.patch
|
| 35 |
|
)
|
|
84 |
"${FILESDIR}"/openbabel-3.1.1-fix-time-check-cmake.patch
|
|
85 |
)
|
|
86 |
|
|
87 |
pkg_pretend() {
|
|
88 |
[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
|
|
89 |
}
|
| 36 |
90 |
|
| 37 |
91 |
pkg_setup() {
|
| 38 |
|
if use openmp; then
|
| 39 |
|
if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp; then
|
| 40 |
|
ewarn "OpenMP is not available in your current selected gcc"
|
| 41 |
|
die "need openmp capable gcc"
|
| 42 |
|
fi
|
| 43 |
|
FORTRAN_NEED_OPENMP=1
|
| 44 |
|
fi
|
|
92 |
[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
|
|
93 |
}
|
|
94 |
|
|
95 |
prepare_python_bindings() {
|
|
96 |
mkdir -p scripts/${EPYTHON} || die
|
|
97 |
# Appends to scripts/CMakeLists.txt, substituting the correct tags, for
|
|
98 |
# each valid python implementation,
|
|
99 |
cat "${FILESDIR}"/${PN}-python.cmake | \
|
|
100 |
sed -e "s|@@EPYTHON@@|${EPYTHON}|" \
|
|
101 |
-e "s|@@PYTHON_INCUDE_DIR@@|$(python_get_includedir)|" \
|
|
102 |
-e "s|@@PYTHON_LIBS@@|$(python_get_LIBS)|" \
|
|
103 |
-e "s|@@PYTHON_SITEDIR@@|$(python_get_sitedir)|" >> \
|
|
104 |
scripts/CMakeLists.txt || die
|
| 45 |
105 |
}
|
| 46 |
106 |
|
| 47 |
107 |
src_prepare() {
|
| 48 |
|
sed \
|
| 49 |
|
-e '/__GNUC__/s:== 4:>= 4:g' \
|
| 50 |
|
-i include/openbabel/shared_ptr.h || die
|
| 51 |
|
cmake-utils_src_prepare
|
|
108 |
cmake_src_prepare
|
|
109 |
|
|
110 |
if use perl; then
|
|
111 |
perl_set_version
|
|
112 |
|
|
113 |
sed -e "/\${LIB_INSTALL_DIR}\/auto/s|\${LIB_INSTALL_DIR}|${VENDOR_ARCH}|" \
|
|
114 |
-e "/\${LIB_INSTALL_DIR}\/Chemistry/s|\${LIB_INSTALL_DIR}|${VENDOR_ARCH}|" \
|
|
115 |
-i scripts/CMakeLists.txt || die
|
|
116 |
fi
|
|
117 |
|
|
118 |
if use python; then
|
|
119 |
# Skip the python bindings sections as we'll append our own
|
|
120 |
sed -e '/^if (PYTHON_BINDINGS)$/s|PYTHON_BINDINGS|false|' \
|
|
121 |
-i {scripts,test}/CMakeLists.txt || die
|
|
122 |
if use test; then
|
|
123 |
# Problems with testbindings built with -O2
|
|
124 |
local test_skip="@unittest.skip('Similar to Issue #2138')"
|
|
125 |
sed -e "/def testTemplates/s|^| ${test_skip}\\n|" \
|
|
126 |
-i test/testbindings.py || die
|
|
127 |
test_skip="@unittest.skip('Similar to Issue #2246')"
|
|
128 |
sed -e "/^def test_write_string/s|^|${test_skip}\\n|" \
|
|
129 |
-i test/testobconv_writers.py || die
|
|
130 |
fi
|
|
131 |
python_foreach_impl prepare_python_bindings
|
|
132 |
fi
|
|
133 |
|
|
134 |
# Remove dependency automagic
|
|
135 |
if ! use png; then
|
|
136 |
sed -e '/^find_package(Cairo/d' -i CMakeLists.txt || die
|
|
137 |
fi
|
|
138 |
if ! use wxwidgets; then
|
|
139 |
sed -e '/^find_package(wxWidgets/d' -i CMakeLists.txt || die
|
|
140 |
fi
|
|
141 |
if ! use inchi; then
|
|
142 |
sed -e '/^else()$/s|else\(\)|elseif\(false\)|' \
|
|
143 |
-i cmake/modules/FindInchi.cmake || die
|
|
144 |
fi
|
|
145 |
|
|
146 |
# Don't install example bins to /usr/bin
|
|
147 |
if use examples; then
|
|
148 |
sed -e "/RUNTIME DESTINATION/s|bin|share/doc/${PF}/examples|" \
|
|
149 |
-i doc/examples/CMakeLists.txt || die
|
|
150 |
fi
|
|
151 |
|
|
152 |
# boost is only used if building with gcc-3.x, which isn't supported in
|
|
153 |
# Gentoo. Still, it shouldn't look for, and include, its headers
|
|
154 |
sed -e '/find_package(Boost/d' -i {{tools,src}/,}CMakeLists.txt || die
|
| 52 |
155 |
}
|
| 53 |
156 |
|
| 54 |
157 |
src_configure() {
|
| 55 |
|
use wxwidgets && need-wxwidgets unicode
|
|
158 |
if use json; then
|
|
159 |
# -DOPTIMIZE_NATIVE=ON also forces -march=native so use
|
|
160 |
# cpu_flags to set defines instead
|
|
161 |
use cpu_flags_x86_sse2 && append-cppflags -DRAPIDJSON_SSE2
|
|
162 |
use cpu_flags_x86_sse4_2 && append-cppflags -DRAPIDJSON_SSE42
|
|
163 |
use cpu_flags_arm_neon && append-cppflags -DRAPIDJSON_NEON
|
|
164 |
fi
|
|
165 |
|
|
166 |
use wxwidgets && setup-wxwidgets
|
|
167 |
|
|
168 |
use_bindings() {
|
|
169 |
(use perl || use python) && (echo 'yes' || die) || (echo 'no' || die)
|
|
170 |
}
|
|
171 |
|
| 56 |
172 |
local mycmakeargs=(
|
| 57 |
|
-DOPENBABEL_USE_SYSTEM_INCHI=ON
|
| 58 |
|
-DOPENMP=$(usex openmp)
|
|
173 |
-DBUILD_DOCS=$(usex doc)
|
|
174 |
-DBUILD_EXAMPLES=$(usex examples)
|
| 59 |
175 |
-DBUILD_GUI=$(usex wxwidgets)
|
|
176 |
-DENABLE_OPENMP=$(usex openmp)
|
|
177 |
-DENABLE_TESTS=$(usex test)
|
|
178 |
-DMINIMAL_BUILD=$(usex minimal)
|
|
179 |
# Set this, otherwise it defaults to true and forces WITH_INCHI=true
|
|
180 |
-DOPENBABEL_USE_SYSTEM_INCHI=$(usex inchi)
|
|
181 |
-DOPTIMIZE_NATIVE=OFF
|
|
182 |
-DPERL_BINDINGS=$(usex perl)
|
|
183 |
-DPYTHON_BINDINGS=$(usex python)
|
|
184 |
-DRUN_SWIG=$(use_bindings)
|
|
185 |
-DWITH_COORDGEN=false
|
|
186 |
-DWITH_INCHI=$(usex inchi)
|
|
187 |
-DWITH_JSON=$(usex json)
|
|
188 |
-DWITH_MAEPARSER=false
|
| 60 |
189 |
)
|
| 61 |
190 |
|
| 62 |
|
cmake-utils_src_configure
|
|
191 |
if use test; then
|
|
192 |
# Help cmake find the python interpreter when dev-lang/python-exec is built
|
|
193 |
# without native-symlinks support.
|
|
194 |
python_setup
|
|
195 |
mycmakeargs+=( -DPYTHON_EXECUTABLE="${PYTHON}" )
|
|
196 |
fi
|
|
197 |
|
|
198 |
cmake_src_configure
|
|
199 |
}
|
|
200 |
|
|
201 |
src_test() {
|
|
202 |
# Wierd deadlock causes system_load to keep rising
|
|
203 |
cmake_src_test -j1
|
|
204 |
}
|
|
205 |
|
|
206 |
openbabel-optimize() {
|
|
207 |
python_optimize "${D}/$(python_get_sitedir)"/openbabel || die
|
| 63 |
208 |
}
|
| 64 |
209 |
|
| 65 |
210 |
src_install() {
|
|
211 |
cmake_src_install
|
|
212 |
|
| 66 |
213 |
docinto html
|
| 67 |
|
dodoc doc/{*.html,*.png}
|
| 68 |
|
if use doc ; then
|
|
214 |
for x in doc/*.html; do
|
|
215 |
[[ ${x} != doc/api*.html ]] && dodoc ${x}
|
|
216 |
done
|
|
217 |
# Rendered in some html pages
|
|
218 |
newdoc "${DISTDIR}"/${PN}.png babel130.png
|
|
219 |
newdoc "${DISTDIR}"/${PN}.jpg OBTitle.jpg
|
|
220 |
|
|
221 |
if use doc; then
|
|
222 |
cmake_src_install docs
|
| 69 |
223 |
docinto html/API
|
| 70 |
|
dodoc -r doc/API/html/*
|
|
224 |
dodoc -r doc/API/html/.
|
| 71 |
225 |
fi
|
| 72 |
226 |
|
| 73 |
|
cmake-utils_src_install
|
| 74 |
|
}
|
|
227 |
if use examples; then
|
|
228 |
# no compression since we want ready-to-run scripts
|
|
229 |
docompress -x /usr/share/doc/${PF}/examples
|
|
230 |
|
|
231 |
# ${PV} doesn't correspond to the internal BABEL_VERSION for
|
|
232 |
# live or patch release builds so we grep it
|
|
233 |
local babel_ver=$(
|
|
234 |
grep '^#define BABEL_VERSION' < \
|
|
235 |
"${BUILD_DIR}"/include/openbabel/babelconfig.h | \
|
|
236 |
cut -d \" -f 2 || die
|
|
237 |
)
|
|
238 |
docinto examples/povray
|
|
239 |
dodoc doc/dioxin.* doc/README*.pov*
|
|
240 |
# Needed by the povray example
|
|
241 |
dosym ../../../../${PN}/${babel_ver}/babel_povray3.inc \
|
|
242 |
/usr/share/doc/${PF}/examples/povray/babel31.inc
|
| 75 |
243 |
|
| 76 |
|
src_test() {
|
| 77 |
|
local mycmakeargs=(
|
| 78 |
|
-DOPENBABEL_USE_SYSTEM_INCHI=ON
|
| 79 |
|
-DPYTHON_EXECUTABLE=false
|
| 80 |
|
-DOPENMP=$(usex openmp)
|
| 81 |
|
-DBUILD_GUI=$(usex wxwidgets)
|
| 82 |
|
-DTESTS=$(usex test)
|
| 83 |
|
)
|
|
244 |
fi
|
|
245 |
|
|
246 |
if use perl; then
|
|
247 |
docinto /
|
|
248 |
newdoc scripts/perl/Changes Changes.perl
|
|
249 |
newdoc scripts/perl/README README.perl
|
|
250 |
if use examples; then
|
|
251 |
docinto examples/perl
|
|
252 |
dodoc -r scripts/perl/examples/.
|
|
253 |
fi
|
|
254 |
fi
|
|
255 |
|
|
256 |
if use python; then
|
|
257 |
python_foreach_impl openbabel-optimize
|
|
258 |
docinto /
|
|
259 |
newdoc scripts/python/README.rst README.python.rst
|
|
260 |
docinto html
|
|
261 |
dodoc scripts/python/*.html
|
|
262 |
if use examples; then
|
|
263 |
docinto examples/python
|
|
264 |
dodoc -r scripts/python/examples/.
|
|
265 |
fi
|
|
266 |
fi
|
| 84 |
267 |
|
| 85 |
|
cmake-utils_src_configure
|
| 86 |
|
cmake-utils_src_compile
|
| 87 |
|
cmake-utils_src_test -E py
|
|
268 |
if use wxwidgets; then
|
|
269 |
make_desktop_entry obgui "Open Babel" ${PN}
|
|
270 |
doicon "${DISTDIR}"/${PN}.png
|
|
271 |
fi
|
| 88 |
272 |
}
|
| 89 |
273 |
|
| 90 |
274 |
pkg_postinst() {
|
| 91 |
|
optfeature "perl support" sci-chemistry/openbabel-perl
|
| 92 |
|
optfeature "python support" sci-chemistry/openbabel-python
|
|
275 |
use wxwidgets && xdg_desktop_database_update
|
|
276 |
}
|
|
277 |
|
|
278 |
pkg_postrm() {
|
|
279 |
use wxwidgets && xdg_desktop_database_update
|
| 93 |
280 |
}
|
