reinit the tree, so we can have metadata

6 files changed, 250 insertions, 0 deletions

diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest
new file mode 100644
index 000000000000..86ca7538cb5d
--- /dev/null
+++ b/sci-chemistry/openbabel/Manifest
@@ -0,0 +1,9 @@
+AUX openbabel-2.3.2-gcc-6_and_7-backport.patch 635 SHA256 49f9fc47d1c864d501a266c4d1d7251d5921ce64f1de33a7679d369938bd8490 SHA512 e1b4402f34d01ced5b4caaa184b4e5544cf47893cfe7958054052b05a57dc34b4d44239a212c7d909f29b9366b83b6df74993f844a20f23748c01272ec093081 WHIRLPOOL 8789037e71722ee28d8769eadc574edf2d7d80e8e01f6a8475b18fd4ed0314757bd02854eacf375f7c23ca20b9ec8cc9a40797b51ad3fe64921440549a49cd3d
+AUX openbabel-2.3.2-test_lib_path.patch 837 SHA256 2aa621bc05aeef47caef9a3a95922dcc6c6b819de9523ea4f0d0b4a72cbf1afb SHA512 d065eef0bb8d751d3292206feb25557394dc203e810b5f0eb7c52a28cb9e2bfaaf60f195d295ef6e58619ab9fa87d84e6b55ad822cfdefc22e02e8b5a8b49efb WHIRLPOOL 074c859d664ae00391119698f84aed2f883f06aab8182490f85faa69bb9b9d181c076d7db05e6004936493da367fb0c1fc8101e43d4c51453a66319994bde155
+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
+EBUILD openbabel-2.3.2-r1.ebuild 2061 SHA256 9de98b2a552db479eafc5c7ef1fcfb233494ad634dcbf0cada7ef23f83f31fc0 SHA512 acc8b99854f852375a19a5b6316cc439016aa258e369892bc524949e709c48412f7925e57f2b684de6a327960b09324d0327aee066560d8dd2194b279de53e0f WHIRLPOOL 0c0dd2b2aab21bff6299fca3f29914b4371dabc1c745f06300d98354c2be16842fb4d3f34a1911603d211beb7bf75998ced6f4a8fe9906b4f44cbea5719addc5
+EBUILD openbabel-2.4.1.ebuild 1981 SHA256 42ae40c260dc830d65dbee7c544f7f402890e65901f503f3965393d64daf94fd SHA512 bc0e729ed48e27b85be2c5f28f134b99247ad39493bf1fddae231161b049b765cecd183f77acc278c09a9a8fd3220fb00be84e72018df64968e6af69c8958fbe WHIRLPOOL f3db01964da09fc9c8f715be114452592c668aec14d5612bc2c2ba239ee9c50de53834dc4533f7eb3fc64ce774d824b2549b57b622ff30cd68ea2d33fd0f96b5
+MISC ChangeLog 4080 SHA256 a6e17816c99ddcbe4d1a5007227e27378860df564c2727f61973e1868c34b729 SHA512 f3b5872b3e4859359d9376fd105ee242fc72b81e558ea109b958e404823de7b430a3339b6f3a4f58a70f6c8e29888edbd3407efa6e1f0355fd6ed0dd380db484 WHIRLPOOL 7d67a816faf4561465832ccac62e5d84b8d97478ef4493060bb5c2303740394da9c2b9ab0414b0ca8d9194dfeb98f02e9712d1770ad65fdcb662bf3369e527e2
+MISC ChangeLog-2015 10475 SHA256 e40373f70624685bc366cdad53c33422e8cd239cb08dc636c10c3ec890dd4a8d SHA512 ddef7e88ca295fe84f241cfdf3bb3e69c3ec41c1030cc6a586bcbdc4eef698788b90ba9ca30c163fef66ff46727ff5cab4248be10d0d13d52c1bd15554627cc1 WHIRLPOOL 8851dc3203e35267b4ea77c34941254f8b3c913bf169352b9602847d46da4fc334fb357f55a63d0880ec377727b244c67e019a175dff9f398969d3d985567e84
+MISC metadata.xml 676 SHA256 6ea2058c7335057b66482dca5c460d664a79383350e1a2c6880218cb85f92e70 SHA512 bccb2d0f21b5186ca3b3f34a3e500afcee492326bb79f9a6143aa3fb61a3fae81581ae8d7c90f9d17cf92a0cdc5e8aab0dd8daf837509a6f3d956c3ef3434cf0 WHIRLPOOL 700f20f1d05231d8ce191551afad9ea2029412a2ac6c34650cc925c5c15865b8ee71a6045acd2350fdb9035312d221eb8db62135f3266e137c2bf21c3800bce0
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
new file mode 100644
index 000000000000..e23dc6020ee5
--- /dev/null
+++ b/sci-chemistry/openbabel/files/openbabel-2.3.2-gcc-6_and_7-backport.patch
@@ -0,0 +1,13 @@
+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 "${_gcc_version_info}")
+   # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the
+   # patch level, handle this here:
+   if (NOT _gcc_version)
diff --git a/sci-chemistry/openbabel/files/openbabel-2.3.2-test_lib_path.patch b/sci-chemistry/openbabel/files/openbabel-2.3.2-test_lib_path.patch
new file mode 100644
index 000000000000..66a796d17b7f
--- /dev/null
+++ b/sci-chemistry/openbabel/files/openbabel-2.3.2-test_lib_path.patch
@@ -0,0 +1,27 @@
+diff -ru old/openbabel-2.3.0/test/CMakeLists.txt new/openbabel-2.3.0/test/CMakeLists.txt
+--- a/test/CMakeLists.txt	2010-10-26 17:39:01.000000000 +0300
++++ b/test/CMakeLists.txt	2010-11-14 18:13:32.000000000 +0200
+@@ -2,7 +2,7 @@
+ add_definitions(-DTESTDATADIR="\\"${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 ${CMAKE_RUNTIME_OUTPUT_DIRECTORY})
+ 
diff --git a/sci-chemistry/openbabel/metadata.xml b/sci-chemistry/openbabel/metadata.xml
new file mode 100644
index 000000000000..96ded5f8a242
--- /dev/null
+++ b/sci-chemistry/openbabel/metadata.xml
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-chemistry@gentoo.org</email>
+    <name>Gentoo Chemistry Project</name>
+  </maintainer>
+  <longdescription>
+    Open Babel is a chemical toolbox designed to speak the many languages of
+	chemical data. It's an open, collaborative project allowing anyone to
+	search, convert, analyze, or store data from molecular modeling, chemistry,
+	solid-state materials, biochemistry, or related areas.
+  </longdescription>
+  <upstream>
+    <remote-id type="sourceforge">openbabel</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/sci-chemistry/openbabel/openbabel-2.3.2-r1.ebuild b/sci-chemistry/openbabel/openbabel-2.3.2-r1.ebuild
new file mode 100644
index 000000000000..9665a2ffebcb
--- /dev/null
+++ b/sci-chemistry/openbabel/openbabel-2.3.2-r1.ebuild
@@ -0,0 +1,92 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+WX_GTK_VER="3.0"
+
+inherit cmake-utils eutils wxwidgets
+
+DESCRIPTION="Interconverts file formats used in molecular modeling"
+HOMEPAGE="http://openbabel.sourceforge.net/"
+SRC_URI="mirror://sourceforge/openbabel/${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)
+		$(cmake-utils_use_enable test TESTS)"
+
+	cmake-utils_src_configure
+	cmake-utils_src_compile
+	cmake-utils_src_test -E py
+}
+
+pkg_postinst() {
+	optfeature "perl support" sci-chemistry/openbabel-perl
+	optfeature "python support" sci-chemistry/openbabel-python
+}
diff --git a/sci-chemistry/openbabel/openbabel-2.4.1.ebuild b/sci-chemistry/openbabel/openbabel-2.4.1.ebuild
new file mode 100644
index 000000000000..3719af8c81d7
--- /dev/null
+++ b/sci-chemistry/openbabel/openbabel-2.4.1.ebuild
@@ -0,0 +1,92 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+WX_GTK_VER="3.0"
+
+inherit cmake-utils eutils wxwidgets
+
+DESCRIPTION="Interconverts file formats used in molecular modeling"
+HOMEPAGE="http://openbabel.sourceforge.net/"
+SRC_URI="mirror://sourceforge/openbabel/${P}.tar.gz"
+
+# See src/CMakeLists.txt for LIBRARY_VERSION
+SLOT="0/5.0.0"
+LICENSE="GPL-2"
+KEYWORDS="amd64 ~arm 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=$(usex wxwidgets)
+	)
+
+	cmake-utils_src_configure
+}
+
+src_install() {
+	docinto html
+	dodoc doc/{*.html,*.png}
+	if use doc ; then
+		docinto html/API
+		dodoc -r doc/API/html/*
+	fi
+
+	cmake-utils_src_install
+}
+
+src_test() {
+	local mycmakeargs=(
+		-DOPENBABEL_USE_SYSTEM_INCHI=ON
+		-DPYTHON_EXECUTABLE=false
+		-DOPENMP=$(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
+}