* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/openbabel/files/, sci-chemistry/openbabel/
@ 2017-05-19 9:52 Justin Lecher
0 siblings, 0 replies; 5+ messages in thread
From: Justin Lecher @ 2017-05-19 9:52 UTC (permalink / raw
To: gentoo-commits
commit: c66f17dceb2a1745d80882ed478f2331735d4a54
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri May 19 09:18:08 2017 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri May 19 09:52:25 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c66f17dc
sci-chemistry/openbabel: Version Bump
which fixes build problems with earlier versions
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=618402
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=618414
Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=618542
Package-Manager: Portage-2.3.5, Repoman-2.3.2
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-chemistry/openbabel/Manifest | 1 +
.../files/openbabel-2.3.2-test_lib_path.patch | 4 +-
sci-chemistry/openbabel/openbabel-2.4.1.ebuild | 92 ++++++++++++++++++++++
3 files changed, 95 insertions(+), 2 deletions(-)
diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest
index 082e5b02984..3d09a5c54b9 100644
--- a/sci-chemistry/openbabel/Manifest
+++ b/sci-chemistry/openbabel/Manifest
@@ -1 +1,2 @@
DIST openbabel-2.3.2.tar.gz 20509105 SHA256 4eaca26679aa6cc85ebf96af19191472ac63ca442c36b0427b369c3a25705188 SHA512 d0e1f8b758ffdd65ec6c31d988bffe3279355e286ce69fad12c5905b3b832e2b73ee95b1061b1576aba1ee9fe4da5e31ec30350c473be17493c657dc80caf919 WHIRLPOOL 74eff18b73d24c8f702e5573a58ba6afba8402e9ce8782de95dc0568575a7d2d632dbc8e8a98b3cd25efdfa7379494f7dcd449342c81ddf73f42a387bce77aaa
+DIST openbabel-2.4.1.tar.gz 11618304 SHA256 204136582cdfe51d792000b20202de8950218d617fd9c6e18cee36706a376dfc SHA512 427e678f0a911bd27b9a8a05e60b6e09f113be4e5dd180daaf80c28d06368e52b57501261755ab3817a8d31f2754db24471fd0ceee706d029386d6f70800e9c6 WHIRLPOOL 88e333b47118449e1edba2b164af77ac7fac9c60e2965b5d6657ba8cf981845f49f6bac9427515ebbdf62668fddf38ae2422c4e107b98df46922c5bba860b216
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
index 1354f52685c..66a796d17b7 100644
--- 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
@@ -1,6 +1,6 @@
diff -ru old/openbabel-2.3.0/test/CMakeLists.txt new/openbabel-2.3.0/test/CMakeLists.txt
---- old/openbabel-2.3.0/test/CMakeLists.txt 2010-10-26 17:39:01.000000000 +0300
-+++ new/openbabel-2.3.0/test/CMakeLists.txt 2010-11-14 18:13:32.000000000 +0200
+--- 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="\\"${CMAKE_SOURCE_DIR}/test/files/\\"")
diff --git a/sci-chemistry/openbabel/openbabel-2.4.1.ebuild b/sci-chemistry/openbabel/openbabel-2.4.1.ebuild
new file mode 100644
index 00000000000..7674873aea9
--- /dev/null
+++ b/sci-chemistry/openbabel/openbabel-2.4.1.ebuild
@@ -0,0 +1,92 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+WX_GTK_VER="3.0"
+
+inherit cmake-utils eutils wxwidgets
+
+DESCRIPTION="Interconverts file formats used in molecular modeling"
+HOMEPAGE="http://openbabel.sourceforge.net/"
+SRC_URI="mirror://sourceforge/openbabel/${P}.tar.gz"
+
+# See src/CMakeLists.txt for LIBRARY_VERSION
+SLOT="0/5.0.0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~arm ~ppc ~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 NEWS.md README.md THANKS doc/dioxin.{inc,mol2} doc/README.{dioxin.pov,povray} )
+
+PATCHES=(
+ "${FILESDIR}"/${PN}-2.3.2-gcc-6_and_7-backport.patch
+ )
+
+pkg_setup() {
+ if use openmp; then
+ if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp; then
+ ewarn "OpenMP is not available in your current selected gcc"
+ die "need openmp capable gcc"
+ fi
+ FORTRAN_NEED_OPENMP=1
+ fi
+}
+
+src_prepare() {
+ sed \
+ -e '/__GNUC__/s:== 4:>= 4:g' \
+ -i include/openbabel/shared_ptr.h || die
+ cmake-utils_src_prepare
+}
+
+src_configure() {
+ use wxwidgets && need-wxwidgets unicode
+ local mycmakeargs=(
+ -DOPENBABEL_USE_SYSTEM_INCHI=ON
+ -DOPENMP=$(usex openmp)
+ -DBUILD_GUI=$(usex wxwidgets)
+ )
+
+ cmake-utils_src_configure
+}
+
+src_install() {
+ docinto html
+ dodoc doc/{*.html,*.png}
+ if use doc ; then
+ docinto html/API
+ dodoc doc/API/html/*
+ fi
+
+ cmake-utils_src_install
+}
+
+src_test() {
+ local mycmakeargs=(
+ -DOPENBABEL_USE_SYSTEM_INCHI=ON
+ -DPYTHON_EXECUTABLE=false
+ -DOPENMP=$(usex openmp)
+ -DBUILD_GUI=$(usex wxwidgets)
+ -DTESTS=$(usex test)
+ )
+
+ 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
+}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/openbabel/files/, sci-chemistry/openbabel/
@ 2018-10-14 19:41 Andreas Sturmlechner
0 siblings, 0 replies; 5+ messages in thread
From: Andreas Sturmlechner @ 2018-10-14 19:41 UTC (permalink / raw
To: gentoo-commits
commit: 5257caeccd710e6c1d27f86ebd808f14f98a120b
Author: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
AuthorDate: Sun Oct 14 19:33:19 2018 +0000
Commit: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
CommitDate: Sun Oct 14 19:33:19 2018 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5257caec
sci-chemistry/openbabel: Drop 2.3.2-r1
Signed-off-by: Andreas Sturmlechner <asturm <AT> gentoo.org>
Package-Manager: Portage-2.3.51, Repoman-2.3.11
sci-chemistry/openbabel/Manifest | 1 -
.../files/openbabel-2.3.2-test_lib_path.patch | 27 -------
sci-chemistry/openbabel/openbabel-2.3.2-r1.ebuild | 92 ----------------------
3 files changed, 120 deletions(-)
diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest
index b44e078a63a..ac268758e8c 100644
--- a/sci-chemistry/openbabel/Manifest
+++ b/sci-chemistry/openbabel/Manifest
@@ -1,2 +1 @@
-DIST openbabel-2.3.2.tar.gz 20509105 BLAKE2B d475c2da0d7171650eeb4b78a948421b783bdbb9342c81114d3dbc19d5cbb273f7303438920ffaeef5b6332e4b72606a86ded5cbd3d7e541f62b59b46483bb69 SHA512 d0e1f8b758ffdd65ec6c31d988bffe3279355e286ce69fad12c5905b3b832e2b73ee95b1061b1576aba1ee9fe4da5e31ec30350c473be17493c657dc80caf919
DIST openbabel-2.4.1.tar.gz 11618304 BLAKE2B 8fc051e83add9be6456e281a109bd6bbec282a64ffc83309819f0decbf167b4914fbb7f1966e95e103f268754045b804317f51c79a952ace707c6af2bd320125 SHA512 427e678f0a911bd27b9a8a05e60b6e09f113be4e5dd180daaf80c28d06368e52b57501261755ab3817a8d31f2754db24471fd0ceee706d029386d6f70800e9c6
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 66a796d17b7..00000000000
--- 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 ${CMAKE_RUNTIME_OUTPUT_DIRECTORY})
-
diff --git a/sci-chemistry/openbabel/openbabel-2.3.2-r1.ebuild b/sci-chemistry/openbabel/openbabel-2.3.2-r1.ebuild
deleted file mode 100644
index 9665a2ffebc..00000000000
--- a/sci-chemistry/openbabel/openbabel-2.3.2-r1.ebuild
+++ /dev/null
@@ -1,92 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-WX_GTK_VER="3.0"
-
-inherit cmake-utils eutils wxwidgets
-
-DESCRIPTION="Interconverts file formats used in molecular modeling"
-HOMEPAGE="http://openbabel.sourceforge.net/"
-SRC_URI="mirror://sourceforge/openbabel/${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)
- $(cmake-utils_use_enable test TESTS)"
-
- cmake-utils_src_configure
- cmake-utils_src_compile
- cmake-utils_src_test -E py
-}
-
-pkg_postinst() {
- optfeature "perl support" sci-chemistry/openbabel-perl
- optfeature "python support" sci-chemistry/openbabel-python
-}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/openbabel/files/, sci-chemistry/openbabel/
@ 2021-11-07 15:41 Andreas Sturmlechner
0 siblings, 0 replies; 5+ messages in thread
From: Andreas Sturmlechner @ 2021-11-07 15:41 UTC (permalink / raw
To: gentoo-commits
commit: 21c3fd3140d7a6d0804ade3b238998a1bb4f2abf
Author: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
AuthorDate: Sun Nov 7 12:15:55 2021 +0000
Commit: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
CommitDate: Sun Nov 7 15:41:41 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=21c3fd31
sci-chemistry/openbabel: Drop 2.4.1-r1
Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Andreas Sturmlechner <asturm <AT> gentoo.org>
.../openbabel-2.3.2-gcc-6_and_7-backport.patch | 13 ---
.../openbabel/files/openbabel-2.4.1-gcc-8.patch | 15 ---
sci-chemistry/openbabel/openbabel-2.4.1-r1.ebuild | 102 ---------------------
3 files changed, 130 deletions(-)
diff --git a/sci-chemistry/openbabel/files/openbabel-2.3.2-gcc-6_and_7-backport.patch b/sci-chemistry/openbabel/files/openbabel-2.3.2-gcc-6_and_7-backport.patch
deleted file mode 100644
index e23dc6020ee..00000000000
--- a/sci-chemistry/openbabel/files/openbabel-2.3.2-gcc-6_and_7-backport.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 0ee545cf..7f4b944e 100755
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -239,7 +239,7 @@ check_type_size(clock_t CLOCK_T)
- # Get the GCC version - from KDE4 cmake files
- if(CMAKE_COMPILER_IS_GNUCXX)
- exec_program(${CMAKE_C_COMPILER} ARGS --version OUTPUT_VARIABLE _gcc_version_info)
-- string(REGEX MATCH "[345]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}")
-+ string(REGEX MATCH "[34567]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}")
- # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the
- # patch level, handle this here:
- if (NOT _gcc_version)
diff --git a/sci-chemistry/openbabel/files/openbabel-2.4.1-gcc-8.patch b/sci-chemistry/openbabel/files/openbabel-2.4.1-gcc-8.patch
deleted file mode 100644
index a4aa3947f2e..00000000000
--- a/sci-chemistry/openbabel/files/openbabel-2.4.1-gcc-8.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-https://bugs.gentoo.org/654800
-Fixed-by: milan hodoscek
-diff --git a/../old/CMakeLists.txt b/CMakeLists.txt
-index dc38d1b..801207e 100644
---- a/../old/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -239,7 +239,7 @@ check_type_size(clock_t CLOCK_T)
- # Get the GCC version - from KDE4 cmake files
- if(CMAKE_COMPILER_IS_GNUCXX)
- exec_program(${CMAKE_C_COMPILER} ARGS --version OUTPUT_VARIABLE _gcc_version_info)
-- string(REGEX MATCH "[34567]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}")
-+ string(REGEX MATCH "[3456789]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}")
- # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the
- # patch level, handle this here:
- if (NOT _gcc_version)
diff --git a/sci-chemistry/openbabel/openbabel-2.4.1-r1.ebuild b/sci-chemistry/openbabel/openbabel-2.4.1-r1.ebuild
deleted file mode 100644
index db8203212fa..00000000000
--- a/sci-chemistry/openbabel/openbabel-2.4.1-r1.ebuild
+++ /dev/null
@@ -1,102 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-WX_GTK_VER="3.0"
-
-inherit cmake-utils desktop optfeature toolchain-funcs wxwidgets
-
-DESCRIPTION="Interconverts file formats used in molecular modeling"
-HOMEPAGE="http://openbabel.org/wiki/Main_Page"
-SRC_URI="
- mirror://sourceforge/openbabel/${P}.tar.gz
- https://openbabel.org/docs/dev/_static/babel130.png -> ${PN}.png
-"
-
-# See src/CMakeLists.txt for LIBRARY_VERSION
-SLOT="0/5.0.0"
-LICENSE="GPL-2"
-KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux ~ppc-macos"
-IUSE="doc openmp test wxwidgets"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
- dev-cpp/eigen:3
- dev-libs/libxml2:2
- sci-libs/inchi
- sys-libs/zlib
- wxwidgets? ( x11-libs/wxGTK:${WX_GTK_VER}[X] )
-"
-DEPEND="${RDEPEND}"
-BDEPEND="
- >=dev-util/cmake-2.4.8
- doc? ( app-doc/doxygen )
-"
-
-DOCS=( AUTHORS NEWS.md README.md THANKS doc/dioxin.{inc,mol2} doc/README.{dioxin.pov,povray} )
-
-PATCHES=(
- "${FILESDIR}"/${PN}-2.3.2-gcc-6_and_7-backport.patch
- "${FILESDIR}"/${P}-gcc-8.patch
-)
-
-pkg_setup() {
- if use openmp; then
- if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp; then
- ewarn "OpenMP is not available in your current selected gcc"
- die "need openmp capable gcc"
- fi
- FORTRAN_NEED_OPENMP=1
- fi
-}
-
-src_prepare() {
- sed \
- -e '/__GNUC__/s:== 4:>= 4:g' \
- -i include/openbabel/shared_ptr.h || die
- cmake-utils_src_prepare
-}
-
-src_configure() {
- use wxwidgets && setup-wxwidgets
- local mycmakeargs=(
- -DOPENBABEL_USE_SYSTEM_INCHI=ON
- -DENABLE_OPENMP=$(usex openmp)
- -DBUILD_GUI=$(usex wxwidgets)
- )
-
- cmake-utils_src_configure
-}
-
-src_install() {
- docinto html
- dodoc doc/{*.html,*.png}
- if use doc ; then
- docinto html/API
- dodoc -r doc/API/html/*
- fi
-
- make_desktop_entry obgui "Open Babel" "${PN}"
- doicon "${DISTDIR}/${PN}.png"
-
- cmake-utils_src_install
-}
-
-src_test() {
- local mycmakeargs=(
- -DOPENBABEL_USE_SYSTEM_INCHI=ON
- -DPYTHON_EXECUTABLE=false
- -DOPENMP=$(usex openmp)
- -DBUILD_GUI=$(usex wxwidgets)
- -DTESTS=$(usex test)
- )
-
- 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
-}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/openbabel/files/, sci-chemistry/openbabel/
@ 2022-03-07 16:28 Andreas Sturmlechner
0 siblings, 0 replies; 5+ messages in thread
From: Andreas Sturmlechner @ 2022-03-07 16:28 UTC (permalink / raw
To: gentoo-commits
commit: 3b032e0f3d0d837c2faf2051da6257844e7ced55
Author: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
AuthorDate: Mon Mar 7 15:32:02 2022 +0000
Commit: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
CommitDate: Mon Mar 7 16:28:16 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3b032e0f
sci-chemistry/openbabel: Drop 2.4.1-r2
Bug: https://bugs.gentoo.org/834115
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andreas Sturmlechner <asturm <AT> gentoo.org>
sci-chemistry/openbabel/Manifest | 1 -
.../openbabel/files/openbabel-2.4.1-gcc10.patch | 62 ------------
.../openbabel/files/openbabel-python.cmake | 104 ---------------------
sci-chemistry/openbabel/openbabel-2.4.1-r2.ebuild | 101 --------------------
4 files changed, 268 deletions(-)
diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest
index 11fe53f8f9de..a9d177301beb 100644
--- a/sci-chemistry/openbabel/Manifest
+++ b/sci-chemistry/openbabel/Manifest
@@ -1,4 +1,3 @@
-DIST openbabel-2.4.1.tar.gz 11618304 BLAKE2B 8fc051e83add9be6456e281a109bd6bbec282a64ffc83309819f0decbf167b4914fbb7f1966e95e103f268754045b804317f51c79a952ace707c6af2bd320125 SHA512 427e678f0a911bd27b9a8a05e60b6e09f113be4e5dd180daaf80c28d06368e52b57501261755ab3817a8d31f2754db24471fd0ceee706d029386d6f70800e9c6
DIST openbabel-3.1.1_p20210225.tar.gz 36674527 BLAKE2B bb82fc96f704249d211bd86c73de0cf4e7cfe5e2ba5c745aa8b4f6f19583837e2181d85101377810095f6b71fc3b91bf2f6f5636726fc8271c6905f1f8c59e7b SHA512 9ff7cb4acbfad7a9c5c8d0dd8930ac0390d0d0f2758d1a6120009071f47ffe718f92ad620d37f26f196babb14649c52b5eb7bb161c342ef36aec655e0a172de4
DIST openbabel.jpg 12159 BLAKE2B b701df2b8c29df607dc2bd3997a282aa9a726d56c789ff2db900d33234dc691f76b6af12a4c9ccda4f09984504b863c40c39e8bf91058939996714ede2dd37c7 SHA512 998ea526c8c92f87dd203527fdd9f4e001357e951409209f41ab68e0b730fe12d97f9079c12ca289be413854ea2abcf8bb691ae5af823a6f29d6a590e1a3e2b0
DIST openbabel.png 29060 BLAKE2B 8d217d92125cc73462437411dd4e0cc05179cb0934f5ed15a307acc6b549b8ebab250a48a05ef7657f48c6df394f37da9b659de61efb1477b79b573a5b393ad3 SHA512 bbcaaa37663b526c9038ccb9edaf05ccc3ad1a861739a737f05f363098d8402a10b36e341fcc0aca636e809c6c32db99bf987b41719a0c756bf5e31444d3eb70
diff --git a/sci-chemistry/openbabel/files/openbabel-2.4.1-gcc10.patch b/sci-chemistry/openbabel/files/openbabel-2.4.1-gcc10.patch
deleted file mode 100644
index 88d8c2add64a..000000000000
--- a/sci-chemistry/openbabel/files/openbabel-2.4.1-gcc10.patch
+++ /dev/null
@@ -1,62 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 2e66dd1..ef4f16b 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -1,16 +1,11 @@
- # Please ensure that any changes remain compliant with 2.4.8.
- if(NOT EMBED_OPENBABEL)
-- cmake_minimum_required(VERSION 2.4.8)
-+ cmake_minimum_required(VERSION 2.4.10)
- endif()
-
- project(openbabel)
- set(CMAKE_MODULE_PATH ${openbabel_SOURCE_DIR}/cmake/modules)
-
--# Allow loose loop constructs, i.e. no matching in if/else/endif or loops.
--# Note that this is true by default in CMake 2.6.0, but we currently only
--# require CMake 2.4.8 - remove this when the CMake requirement is bumped.
--set(CMAKE_ALLOW_LOOSE_LOOP_CONSTRUCTS 1)
--
- if(COMMAND cmake_policy)
- cmake_policy(SET CMP0003 NEW)
- cmake_policy(SET CMP0005 OLD) # add_definitions need updating to set to NEW
-@@ -20,7 +15,6 @@ if(COMMAND cmake_policy)
- endif()
-
- include (CheckCXXCompilerFlag)
--include (MacroEnsureVersion)
-
- # Version numbering - should be bumped for each release
- # Note that for "beta" releases, we should start at x.90.0 -- we've
-@@ -238,16 +232,21 @@ check_type_size(clock_t CLOCK_T)
-
- # Get the GCC version - from KDE4 cmake files
- if(CMAKE_COMPILER_IS_GNUCXX)
-- exec_program(${CMAKE_C_COMPILER} ARGS --version OUTPUT_VARIABLE _gcc_version_info)
-- string(REGEX MATCH "[345]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}")
-- # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the
-- # patch level, handle this here:
-- if (NOT _gcc_version)
-- string (REGEX REPLACE ".*\\(GCC\\).* ([34]\\.[0-9]) .*" "\\1.0" _gcc_version "${_gcc_version_info}")
-- endif ()
-- macro_ensure_version("4.0.0" "${_gcc_version}" GCC_IS_NEWER_THAN_4_0)
-- macro_ensure_version("4.1.0" "${_gcc_version}" GCC_IS_NEWER_THAN_4_1)
-- macro_ensure_version("4.2.0" "${_gcc_version}" GCC_IS_NEWER_THAN_4_2)
-+ if(NOT(${CMAKE_CXX_COMPILER_VERSION} VERSION_LESS 4.0.0))
-+ set(GCC_IS_NEWER_THAN_4_0 TRUE)
-+ else()
-+ set(GCC_IS_NEWER_THAN_4_0 FALSE)
-+ endif()
-+ if(NOT(${CMAKE_CXX_COMPILER_VERSION} VERSION_LESS 4.1.0))
-+ set(GCC_IS_NEWER_THAN_4_1 TRUE)
-+ else()
-+ set(GCC_IS_NEWER_THAN_4_1 FALSE)
-+ endif()
-+ if(NOT(${CMAKE_CXX_COMPILER_VERSION} VERSION_LESS 4.2.0))
-+ set(GCC_IS_NEWER_THAN_4_2 TRUE)
-+ else()
-+ set(GCC_IS_NEWER_THAN_4_2 FALSE)
-+ endif()
- endif()
-
- if(UNIX)
diff --git a/sci-chemistry/openbabel/files/openbabel-python.cmake b/sci-chemistry/openbabel/files/openbabel-python.cmake
deleted file mode 100644
index 425b4656a9d2..000000000000
--- a/sci-chemistry/openbabel/files/openbabel-python.cmake
+++ /dev/null
@@ -1,104 +0,0 @@
-# The following is a cmake fragment taken from scripts/CMakeLists.txt and
-# edited for Gentoo python multibuild compatibility.
-
-if (PYTHON_BINDINGS)
- # Tags should be edited to reflect the active python implementation
- set(EPYTHON @@EPYTHON@@)
- set(PYTHON_INCUDE_DIR @@PYTHON_INCUDE_DIR@@)
- set(PYTHON_LIBS @@PYTHON_LIBS@@)
- set(PYTHON_SITEDIR @@PYTHON_SITEDIR@@)
-
- include_directories(${PYTHON_INCUDE_DIR})
-
- add_custom_command(
- OUTPUT ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel-python.cpp ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel.py
- COMMAND ${SWIG_EXECUTABLE} -python -c++ -small -O -templatereduce -naturalvar -I${CMAKE_SOURCE_DIR}/include -I${CMAKE_BINARY_DIR}/include -o ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel-python.cpp ${eigen_define} -outdir ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON} ${CMAKE_SOURCE_DIR}/scripts/openbabel-python.i
- MAIN_DEPENDENCY openbabel-python.i
- VERBATIM
- )
-
- configure_file(${CMAKE_SOURCE_DIR}/scripts/python/openbabel/__init__.py.in
- ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel/__init__.py)
-
- add_library(bindings_python_${EPYTHON} MODULE ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel-python.cpp)
- target_link_libraries(bindings_python_${EPYTHON} ${PYTHON_LIBS} ${BABEL_LIBRARY})
-
- set_target_properties(bindings_python_${EPYTHON}
- PROPERTIES
- OUTPUT_NAME _openbabel
- LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel
- PREFIX ""
- SUFFIX .so )
-
- add_dependencies(bindings_python_${EPYTHON} openbabel)
-
- install(TARGETS bindings_python_${EPYTHON}
- LIBRARY DESTINATION ${PYTHON_SITEDIR}/openbabel
- COMPONENT bindings_python)
- install(FILES ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel/__init__.py
- DESTINATION ${PYTHON_SITEDIR}/openbabel
- COMPONENT bindings_python)
- install(FILES ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel.py
- DESTINATION ${PYTHON_SITEDIR}/openbabel
- COMPONENT bindings_python)
- install(FILES ${CMAKE_SOURCE_DIR}/scripts/python/openbabel/pybel.py
- DESTINATION ${PYTHON_SITEDIR}/openbabel
- COMPONENT bindings_python)
-
- if (ENABLE_TESTS)
- # Make sure all module files are together in the same directory for testing
- add_custom_command(TARGET bindings_python_${EPYTHON} POST_BUILD
- COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel.py ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel/
- COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/scripts/python/openbabel/pybel.py ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel/)
- set(TEST_SOURCE_DIR ${CMAKE_SOURCE_DIR}/test)
- # define TESTDATADIR for tests that need input files
- add_definitions(-DTESTDATADIR="${TEST_SOURCE_DIR}/files/")
- # define FORMATDIR for location of format plugin binaries
- set(FORMATDIR "${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}/")
- add_definitions(-DFORMATDIR="${FORMATDIR}/")
- include_directories(${TEST_SOURCE_DIR})
-
- # The macro is modified from cmake/modules/UsePythonTest.cmake
- MACRO(ADD_PYTHON_TEST TESTNAME FILENAME)
- GET_SOURCE_FILE_PROPERTY(loc ${FILENAME} LOCATION)
- STRING(REGEX REPLACE ";" " " wo_semicolumn "${ARGN}")
- FILE(WRITE ${CMAKE_BINARY_DIR}/test/${TESTNAME}.cmake
-"
- MESSAGE(\"${PYTHONPATH}\")
- EXECUTE_PROCESS(
- COMMAND ${EPYTHON} ${loc} ${wo_semicolumn}
- RESULT_VARIABLE import_res
- OUTPUT_VARIABLE import_output
- ERROR_VARIABLE import_output
- )
-
- # Pass the output back to ctest
- IF(import_output)
- MESSAGE(\${import_output})
- ENDIF(import_output)
- IF(import_res)
- MESSAGE(SEND_ERROR \${import_res})
- ENDIF(import_res)
-"
- )
- ADD_TEST(${TESTNAME} ${CMAKE_COMMAND} -P ${CMAKE_BINARY_DIR}/test/${TESTNAME}.cmake)
- ENDMACRO(ADD_PYTHON_TEST)
-
- set(pybindtests
- bindings
- _pybel
- example
- obconv_writers
- cdjsonformat
- pcjsonformat
- roundtrip
- )
- foreach(pybindtest ${pybindtests})
- ADD_PYTHON_TEST(pybindtest_${pybindtest}_${EPYTHON} ${TEST_SOURCE_DIR}/test${pybindtest}.py)
- set_tests_properties(pybindtest_${pybindtest}_${EPYTHON} PROPERTIES
- ENVIRONMENT "PYTHONPATH=${CMAKE_BINARY_DIR}/scripts/${EPYTHON}:${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX};LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/scripts/${EPYTHON}:${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}:\$ENV{LD_LIBRARY_PATH};BABEL_LIBDIR=${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}/;BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data"
- FAIL_REGULAR_EXPRESSION "ERROR;FAIL;Test failed"
- )
- endforeach(pybindtest ${pybindtests})
- endif (ENABLE_TESTS)
-endif(PYTHON_BINDINGS)
diff --git a/sci-chemistry/openbabel/openbabel-2.4.1-r2.ebuild b/sci-chemistry/openbabel/openbabel-2.4.1-r2.ebuild
deleted file mode 100644
index 95161d26d6d6..000000000000
--- a/sci-chemistry/openbabel/openbabel-2.4.1-r2.ebuild
+++ /dev/null
@@ -1,101 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-WX_GTK_VER="3.0-gtk3"
-
-inherit cmake-utils desktop optfeature toolchain-funcs wxwidgets
-
-DESCRIPTION="Interconverts file formats used in molecular modeling"
-HOMEPAGE="http://openbabel.org/wiki/Main_Page"
-SRC_URI="
- mirror://sourceforge/openbabel/${P}.tar.gz
- https://openbabel.org/docs/dev/_static/babel130.png -> ${PN}.png
-"
-
-# See src/CMakeLists.txt for LIBRARY_VERSION
-SLOT="0/5.0.0"
-LICENSE="GPL-2"
-KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux ~ppc-macos"
-IUSE="doc openmp test wxwidgets"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
- dev-cpp/eigen:3
- dev-libs/libxml2:2
- sci-libs/inchi
- sys-libs/zlib
- wxwidgets? ( x11-libs/wxGTK:${WX_GTK_VER}[X] )
-"
-DEPEND="${RDEPEND}"
-BDEPEND="
- >=dev-util/cmake-2.4.10
- doc? ( app-doc/doxygen )
-"
-
-DOCS=( AUTHORS NEWS.md README.md THANKS doc/dioxin.{inc,mol2} doc/README.{dioxin.pov,povray} )
-
-PATCHES=(
- "${FILESDIR}"/${P}-gcc10.patch
-)
-
-pkg_setup() {
- if use openmp; then
- if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp; then
- ewarn "OpenMP is not available in your current selected gcc"
- die "need openmp capable gcc"
- fi
- FORTRAN_NEED_OPENMP=1
- fi
-}
-
-src_prepare() {
- sed \
- -e '/__GNUC__/s:== 4:>= 4:g' \
- -i include/openbabel/shared_ptr.h || die
- cmake-utils_src_prepare
-}
-
-src_configure() {
- use wxwidgets && setup-wxwidgets
- local mycmakeargs=(
- -DOPENBABEL_USE_SYSTEM_INCHI=ON
- -DENABLE_OPENMP=$(usex openmp)
- -DBUILD_GUI=$(usex wxwidgets)
- )
-
- cmake-utils_src_configure
-}
-
-src_install() {
- docinto html
- dodoc doc/{*.html,*.png}
- if use doc ; then
- docinto html/API
- dodoc -r doc/API/html/*
- fi
-
- make_desktop_entry obgui "Open Babel" "${PN}"
- doicon "${DISTDIR}/${PN}.png"
-
- cmake-utils_src_install
-}
-
-src_test() {
- local mycmakeargs=(
- -DOPENBABEL_USE_SYSTEM_INCHI=ON
- -DPYTHON_EXECUTABLE=false
- -DOPENMP=$(usex openmp)
- -DBUILD_GUI=$(usex wxwidgets)
- -DTESTS=$(usex test)
- )
-
- 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
-}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/openbabel/files/, sci-chemistry/openbabel/
@ 2025-03-24 9:16 Sam James
0 siblings, 0 replies; 5+ messages in thread
From: Sam James @ 2025-03-24 9:16 UTC (permalink / raw
To: gentoo-commits
commit: 203d57887f27309969202417619e1fe871b6cca8
Author: Nicolas PARLANT <nicolas.parlant <AT> parhuet <DOT> fr>
AuthorDate: Thu Mar 13 15:04:20 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=203d5788
sci-chemistry/openbabel: add 3.1.1_p20241221
New snapshot to include in particular more json features.
deps :
libxml2/cairo are not required with minimal
rm openbabel-perl
replace sed :
perl LIB_INSTALL_DIR (no-op) -> set PERL_INSTDIR
PYTHON_BINDINGS (no-op for test/CMakeLists.txt due to a typo) -> not required
examples RUNTIME_DESTINATION -> patch with CMAKE_INSTALL_DOCDIR
find_package :
use DISABLE_FIND_PACKAGE for Cairo(png), wxWidgets(wxwidgets) and Boost
use ADD_INCHI_FORMAT to prevent using bundled inchi
openbabel-python-cmake :
use target_include_directories instead of include_directories to prevent
including all python_targets at the same time for each implementation.
tests :
skip two more tests with known issues
rm -O2 exclusions introduced with 1fce6e91e642ac7fe5c3b9f675c54244be423a53
It seems fixed now (checked with -O2/clang/lto/gcc15/+-openmp/+-cpu_flags).
This will require investigation if it reappears.
add py3.13 (tests passed)
Signed-off-by: Nicolas PARLANT <nicolas.parlant <AT> parhuet.fr>
Signed-off-by: Sam James <sam <AT> gentoo.org>
sci-chemistry/openbabel/Manifest | 1 +
.../files/openbabel-3.1.1_p2024-fix_examples.patch | 13 ++
.../files/openbabel-3.1.1_p2024-fix_pybind.patch | 25 +++
.../openbabel/files/openbabel-python-r2.cmake | 103 +++++++++
.../openbabel/openbabel-3.1.1_p20241221.ebuild | 236 +++++++++++++++++++++
5 files changed, 378 insertions(+)
diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest
index a9d177301beb..bb5b7ce68d7e 100644
--- a/sci-chemistry/openbabel/Manifest
+++ b/sci-chemistry/openbabel/Manifest
@@ -1,3 +1,4 @@
DIST openbabel-3.1.1_p20210225.tar.gz 36674527 BLAKE2B bb82fc96f704249d211bd86c73de0cf4e7cfe5e2ba5c745aa8b4f6f19583837e2181d85101377810095f6b71fc3b91bf2f6f5636726fc8271c6905f1f8c59e7b SHA512 9ff7cb4acbfad7a9c5c8d0dd8930ac0390d0d0f2758d1a6120009071f47ffe718f92ad620d37f26f196babb14649c52b5eb7bb161c342ef36aec655e0a172de4
+DIST openbabel-3.1.1_p20241221.tar.gz 36864825 BLAKE2B 55e6fbdd5c50a557c40fd5ffaca41753f73175b2b4eea22abe5c2b0031363e3c133acf9a8daf5b1cb362a3adb6398204497af036b9a7ba3630c1d8ccbce0f9d3 SHA512 44340c3d08b22783cf6a702c192480869b73fef21104641feaf5cbcd51f693fd17bb05ad31a3520f330aa57733d6f4be707b3c1243b3010d6ceccca8974e732f
DIST openbabel.jpg 12159 BLAKE2B b701df2b8c29df607dc2bd3997a282aa9a726d56c789ff2db900d33234dc691f76b6af12a4c9ccda4f09984504b863c40c39e8bf91058939996714ede2dd37c7 SHA512 998ea526c8c92f87dd203527fdd9f4e001357e951409209f41ab68e0b730fe12d97f9079c12ca289be413854ea2abcf8bb691ae5af823a6f29d6a590e1a3e2b0
DIST openbabel.png 29060 BLAKE2B 8d217d92125cc73462437411dd4e0cc05179cb0934f5ed15a307acc6b549b8ebab250a48a05ef7657f48c6df394f37da9b659de61efb1477b79b573a5b393ad3 SHA512 bbcaaa37663b526c9038ccb9edaf05ccc3ad1a861739a737f05f363098d8402a10b36e341fcc0aca636e809c6c32db99bf987b41719a0c756bf5e31444d3eb70
diff --git a/sci-chemistry/openbabel/files/openbabel-3.1.1_p2024-fix_examples.patch b/sci-chemistry/openbabel/files/openbabel-3.1.1_p2024-fix_examples.patch
new file mode 100644
index 000000000000..b61d3bc29b98
--- /dev/null
+++ b/sci-chemistry/openbabel/files/openbabel-3.1.1_p2024-fix_examples.patch
@@ -0,0 +1,13 @@
+prevent installation of examples in /usr/bin
+all files from examples are 'RUNTIME', no lib
+--- a/doc/examples/CMakeLists.txt
++++ b/doc/examples/CMakeLists.txt
+@@ -7,7 +7,7 @@
+ add_executable(${example} ${example}.cpp)
+ target_link_libraries(${example} ${BABEL_LIBRARY})
+ install(TARGETS ${example}
+- RUNTIME DESTINATION bin
++ RUNTIME DESTINATION ${CMAKE_INSTALL_DOCDIR}/examples
+ LIBRARY DESTINATION lib
+ ARCHIVE DESTINATION lib
+ )
diff --git a/sci-chemistry/openbabel/files/openbabel-3.1.1_p2024-fix_pybind.patch b/sci-chemistry/openbabel/files/openbabel-3.1.1_p2024-fix_pybind.patch
new file mode 100644
index 000000000000..ab1a24499306
--- /dev/null
+++ b/sci-chemistry/openbabel/files/openbabel-3.1.1_p2024-fix_pybind.patch
@@ -0,0 +1,25 @@
+--- a/scripts/CMakeLists.txt
++++ b/scripts/CMakeLists.txt
+@@ -69,13 +69,9 @@
+
+ if (DO_PYTHON_BINDINGS)
+
+- include_directories(
+- ${PYTHON_INCLUDE_PATH}
+- )
+-
+ if(RUN_SWIG)
+ add_custom_command(OUTPUT ${openbabel_SOURCE_DIR}/scripts/python/openbabel/openbabel-python.cpp ${openbabel_SOURCE_DIR}/scripts/python/openbabel/openbabel.py
+- COMMAND ${SWIG_EXECUTABLE} -python -c++ ${doxygen_switch} -small -O -templatereduce -naturalvar -I${openbabel_SOURCE_DIR}/include -I${openbabel_BINARY_DIR}/include -o ${openbabel_SOURCE_DIR}/scripts/python/openbabel/openbabel-python.cpp ${eigen_define} -outdir ${openbabel_SOURCE_DIR}/scripts/python/openbabel ${openbabel_SOURCE_DIR}/scripts/openbabel-python.i
++ COMMAND ${SWIG_EXECUTABLE} -python -c++ ${doxygen_switch} -small -O -templatereduce -naturalvar -I${PYTHON_INCLUDE_PATH} -I${openbabel_SOURCE_DIR}/include -I${openbabel_BINARY_DIR}/include -o ${openbabel_SOURCE_DIR}/scripts/python/openbabel/openbabel-python.cpp ${eigen_define} -outdir ${openbabel_SOURCE_DIR}/scripts/python/openbabel ${openbabel_SOURCE_DIR}/scripts/openbabel-python.i
+ MAIN_DEPENDENCY openbabel-python.i
+ VERBATIM
+ )
+@@ -84,6 +80,7 @@
+ configure_file(${openbabel_SOURCE_DIR}/scripts/python/openbabel/__init__.py.in
+ ${openbabel_SOURCE_DIR}/scripts/python/openbabel/__init__.py)
+ add_library(bindings_python MODULE ${openbabel_SOURCE_DIR}/scripts/python/openbabel/openbabel-python.cpp)
++ target_include_directories(bindings_python PRIVATE ${PYTHON_INCLUDE_PATH})
+
+ if(APPLE)
+ # Don't link against Python library on Mac
diff --git a/sci-chemistry/openbabel/files/openbabel-python-r2.cmake b/sci-chemistry/openbabel/files/openbabel-python-r2.cmake
new file mode 100644
index 000000000000..a16970deb0b1
--- /dev/null
+++ b/sci-chemistry/openbabel/files/openbabel-python-r2.cmake
@@ -0,0 +1,103 @@
+# The following is a cmake fragment taken from scripts/CMakeLists.txt and
+# edited for Gentoo python multibuild compatibility.
+
+if (DO_PYTHON_BINDINGS)
+ # Tags should be edited to reflect the active python implementation
+ set(EPYTHON @@EPYTHON@@)
+ set(PYTHON_INCLUDE_DIR @@PYTHON_INCLUDE_DIR@@)
+ set(PYTHON_LIBS @@PYTHON_LIBS@@)
+ set(PYTHON_SITEDIR @@PYTHON_SITEDIR@@)
+
+ add_custom_command(
+ OUTPUT ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel-python.cpp ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel.py
+ COMMAND ${SWIG_EXECUTABLE} -python -c++ -small -O -templatereduce -naturalvar -I${PYTHON_INCLUDE_DIR} -I${CMAKE_SOURCE_DIR}/include -I${CMAKE_BINARY_DIR}/include -o ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel-python.cpp ${eigen_define} -outdir ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON} ${CMAKE_SOURCE_DIR}/scripts/openbabel-python.i
+ MAIN_DEPENDENCY openbabel-python.i
+ VERBATIM
+ )
+
+ configure_file(${CMAKE_SOURCE_DIR}/scripts/python/openbabel/__init__.py.in
+ ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel/__init__.py)
+
+ add_library(bindings_python_${EPYTHON} MODULE ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel-python.cpp)
+ target_include_directories(bindings_python_${EPYTHON} PRIVATE ${PYTHON_INCLUDE_DIR})
+ target_link_libraries(bindings_python_${EPYTHON} ${PYTHON_LIBS} ${BABEL_LIBRARY})
+
+ set_target_properties(bindings_python_${EPYTHON}
+ PROPERTIES
+ OUTPUT_NAME _openbabel
+ LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel
+ PREFIX ""
+ SUFFIX .so )
+
+ add_dependencies(bindings_python_${EPYTHON} openbabel)
+
+ install(TARGETS bindings_python_${EPYTHON}
+ LIBRARY DESTINATION ${PYTHON_SITEDIR}/openbabel
+ COMPONENT bindings_python)
+ install(FILES ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel/__init__.py
+ DESTINATION ${PYTHON_SITEDIR}/openbabel
+ COMPONENT bindings_python)
+ install(FILES ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel.py
+ DESTINATION ${PYTHON_SITEDIR}/openbabel
+ COMPONENT bindings_python)
+ install(FILES ${CMAKE_SOURCE_DIR}/scripts/python/openbabel/pybel.py
+ DESTINATION ${PYTHON_SITEDIR}/openbabel
+ COMPONENT bindings_python)
+
+ if (ENABLE_TESTS)
+ # Make sure all module files are together in the same directory for testing
+ add_custom_command(TARGET bindings_python_${EPYTHON} POST_BUILD
+ COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/scripts/${EPYTHON}/openbabel.py ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel/
+ COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/scripts/python/openbabel/pybel.py ${CMAKE_BINARY_DIR}/scripts/${EPYTHON}/openbabel/)
+ set(TEST_SOURCE_DIR ${CMAKE_SOURCE_DIR}/test)
+ # define TESTDATADIR for tests that need input files
+ add_definitions(-DTESTDATADIR="${TEST_SOURCE_DIR}/files/")
+ # define FORMATDIR for location of format plugin binaries
+ set(FORMATDIR "${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}/")
+ add_definitions(-DFORMATDIR="${FORMATDIR}/")
+ include_directories(${TEST_SOURCE_DIR})
+
+ # The macro is modified from cmake/modules/UsePythonTest.cmake
+ MACRO(ADD_PYTHON_TEST TESTNAME FILENAME)
+ GET_SOURCE_FILE_PROPERTY(loc ${FILENAME} LOCATION)
+ STRING(REGEX REPLACE ";" " " wo_semicolumn "${ARGN}")
+ FILE(WRITE ${CMAKE_BINARY_DIR}/test/${TESTNAME}.cmake
+"
+ MESSAGE(\"${PYTHONPATH}\")
+ EXECUTE_PROCESS(
+ COMMAND ${EPYTHON} ${loc} ${wo_semicolumn}
+ RESULT_VARIABLE import_res
+ OUTPUT_VARIABLE import_output
+ ERROR_VARIABLE import_output
+ )
+
+ # Pass the output back to ctest
+ IF(import_output)
+ MESSAGE(\${import_output})
+ ENDIF(import_output)
+ IF(import_res)
+ MESSAGE(SEND_ERROR \${import_res})
+ ENDIF(import_res)
+"
+ )
+ ADD_TEST(${TESTNAME} ${CMAKE_COMMAND} -P ${CMAKE_BINARY_DIR}/test/${TESTNAME}.cmake)
+ ENDMACRO(ADD_PYTHON_TEST)
+
+ set(pybindtests
+ bindings
+ _pybel
+ example
+ obconv_writers
+ cdjsonformat
+ pcjsonformat
+ roundtrip
+ )
+ foreach(pybindtest ${pybindtests})
+ ADD_PYTHON_TEST(pybindtest_${pybindtest}_${EPYTHON} ${TEST_SOURCE_DIR}/test${pybindtest}.py)
+ set_tests_properties(pybindtest_${pybindtest}_${EPYTHON} PROPERTIES
+ ENVIRONMENT "PYTHONPATH=${CMAKE_BINARY_DIR}/scripts/${EPYTHON}:${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX};LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/scripts/${EPYTHON}:${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}:\$ENV{LD_LIBRARY_PATH};BABEL_LIBDIR=${CMAKE_BINARY_DIR}/lib${LIB_SUFFIX}/;BABEL_DATADIR=${CMAKE_SOURCE_DIR}/data"
+ FAIL_REGULAR_EXPRESSION "ERROR;FAIL;Test failed"
+ )
+ endforeach(pybindtest ${pybindtests})
+ endif (ENABLE_TESTS)
+endif(DO_PYTHON_BINDINGS)
diff --git a/sci-chemistry/openbabel/openbabel-3.1.1_p20241221.ebuild b/sci-chemistry/openbabel/openbabel-3.1.1_p20241221.ebuild
new file mode 100644
index 000000000000..84485db4537d
--- /dev/null
+++ b/sci-chemistry/openbabel/openbabel-3.1.1_p20241221.ebuild
@@ -0,0 +1,236 @@
+# Copyright 1999-2025 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..13} )
+WX_GTK_VER=3.2-gtk3
+
+inherit cmake desktop flag-o-matic perl-functions python-r1 toolchain-funcs wxwidgets xdg
+
+DESCRIPTION="Interconverts file formats used in molecular modeling"
+HOMEPAGE="https://openbabel.org/ https://github.com/openbabel/openbabel/"
+
+if [[ "${PV}" == *9999* ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/openbabel/${PN}.git"
+else
+ if [[ "${PV}" == *_p* ]]; then # eg., openbabel-3.1.1_p20210325
+ # Set to commit hash
+ OPENBABEL_COMMIT="889c350feb179b43aa43985799910149d4eaa2bc"
+ SRC_URI="https://github.com/${PN}/${PN}/archive/${OPENBABEL_COMMIT}.tar.gz -> ${P}.tar.gz"
+ S="${WORKDIR}/${PN}-${OPENBABEL_COMMIT}"
+ else
+ MY_P="${PN}-$(ver_rs 1- -)"
+ 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"
+fi
+
+LICENSE="GPL-2"
+# See src/CMakeLists.txt for LIBRARY_VERSION
+SLOT="0/7.0.0"
+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 )"
+REQUIRED_USE="
+ python? ( ${PYTHON_REQUIRED_USE} )
+ test? ( inchi !minimal python? ( json png ) ${PYTHON_REQUIRED_USE} )
+"
+
+RDEPEND="
+ dev-cpp/eigen:3
+ sys-libs/zlib:=
+ inchi? ( sci-libs/inchi )
+ json? ( >=dev-libs/rapidjson-1.1.0 )
+ !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="${RDEPEND}"
+BDEPEND="
+ dev-lang/perl
+ doc? (
+ app-text/doxygen
+ dev-texlive/texlive-latex
+ )
+ perl? ( dev-lang/swig )
+ python? ( dev-lang/swig )
+ test? ( dev-lang/python )
+"
+
+PATCHES=(
+ # Set include dir only for global implementation
+ "${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() {
+ [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+pkg_setup() {
+ [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+gen_python_bindings() {
+ mkdir -p scripts/${EPYTHON} || die
+ # Appends to scripts/CMakeLists.txt, substituting the correct tags, for
+ # each valid python implementation,
+ cat "${FILESDIR}"/${PN}-python-r2.cmake | \
+ sed -e "s|@@EPYTHON@@|${EPYTHON}|" \
+ -e "s|@@PYTHON_INCLUDE_DIR@@|$(python_get_includedir)|" \
+ -e "s|@@PYTHON_LIBS@@|$(python_get_LIBS)|" \
+ -e "s|@@PYTHON_SITEDIR@@|$(python_get_sitedir)|" >> \
+ scripts/CMakeLists.txt || die
+}
+
+src_prepare() {
+ cmake_src_prepare
+
+ # Prevent bundled inchi as fallback
+ rm -r include/inchi || die
+
+ use python && python_foreach_impl gen_python_bindings
+}
+
+src_configure() {
+ if use json; then
+ # -DOPTIMIZE_NATIVE=ON also forces -march=native so use
+ # cpu_flags to set defines instead
+ use cpu_flags_x86_sse2 && append-cppflags -DRAPIDJSON_SSE2
+ use cpu_flags_x86_sse4_2 && append-cppflags -DRAPIDJSON_SSE42
+ use cpu_flags_arm_neon && append-cppflags -DRAPIDJSON_NEON
+ fi
+
+ use wxwidgets && setup-wxwidgets
+
+ use_bindings() {
+ (use perl || use python) && (echo 'yes' || die) || (echo 'no' || die)
+ }
+
+ 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=$(usex minimal)
+ # All three required to comply w/ useflag and prevent bundled lib
+ -DOPENBABEL_USE_SYSTEM_INCHI=$(usex inchi)
+ -DADD_INCHI_FORMAT=$(usex inchi)
+ -DWITH_INCHI=$(usex inchi)
+ -DOPTIMIZE_NATIVE=OFF
+ -DPERL_BINDINGS=$(usex perl)
+ -DPYTHON_BINDINGS=$(usex python)
+ -DRUN_SWIG=$(use_bindings)
+ -DWITH_COORDGEN=false
+ -DWITH_JSON=$(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}"
+ )
+ fi
+
+ cmake_src_configure
+}
+
+src_test() {
+ 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
+}
+
+openbabel-optimize() {
+ python_optimize "${D}/$(python_get_sitedir)"/openbabel || die
+}
+
+src_install() {
+ cmake_src_install
+
+ docinto html
+ for x in doc/*.html; do
+ [[ ${x} != doc/api*.html ]] && dodoc ${x}
+ done
+
+ if use doc; then
+ cmake_src_install docs
+ docinto html/API
+ dodoc -r doc/API/html/.
+ fi
+
+ if use examples; then
+ # no compression since we want ready-to-run scripts
+ docompress -x /usr/share/doc/${PF}/examples
+
+ # ${PV} doesn't correspond to the internal BABEL_VERSION for
+ # live or patch release builds so we grep it
+ local babel_ver=$(
+ grep '^#define BABEL_VERSION' < \
+ "${BUILD_DIR}"/include/openbabel/babelconfig.h | \
+ cut -d \" -f 2 || die
+ )
+ docinto examples/povray
+ dodoc doc/dioxin.* doc/README*.pov*
+ # Needed by the povray example
+ dosym ../../../../${PN}/${babel_ver}/babel_povray3.inc \
+ /usr/share/doc/${PF}/examples/povray/babel31.inc
+ fi
+
+ if use perl; then
+ docinto /
+ newdoc scripts/perl/Changes Changes.perl
+ newdoc scripts/perl/README README.perl
+ if use examples; then
+ docinto examples/perl
+ dodoc -r scripts/perl/examples/.
+ fi
+ fi
+
+ if use python; then
+ python_foreach_impl openbabel-optimize
+ docinto /
+ newdoc scripts/python/README.rst README.python.rst
+ docinto html
+ dodoc scripts/python/*.html
+ if use examples; then
+ docinto examples/python
+ dodoc -r scripts/python/examples/.
+ fi
+ fi
+
+ if use wxwidgets; then
+ make_desktop_entry obgui "Open Babel" ${PN}
+ newicon "${S}"/src/GUI/babel.xpm ${PN}.xpm
+ fi
+}
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