sci-chemistry/openbabel: support gcc-9

* https://bugs.gentoo.org/664506

sci-chemistry/openbabel/Manifest

@@ -0,0 +1 @@
+DIST openbabel-2.4.1.tar.gz 11618304 BLAKE2B 8fc051e83add9be6456e281a109bd6bbec282a64ffc83309819f0decbf167b4914fbb7f1966e95e103f268754045b804317f51c79a952ace707c6af2bd320125 SHA512 427e678f0a911bd27b9a8a05e60b6e09f113be4e5dd180daaf80c28d06368e52b57501261755ab3817a8d31f2754db24471fd0ceee706d029386d6f70800e9c6

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)

sci-chemistry/openbabel/files/openbabel-2.4.1-gcc-8_and_9.patch

@@ -0,0 +1,15 @@
+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)

sci-chemistry/openbabel/openbabel-2.4.1-r2.ebuild

@@ -0,0 +1,93 @@
+# Copyright 1999-2018 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}"/${PN}-2.3.2-gcc-6_and_7-backport.patch
+	"${FILESDIR}"/${P}-gcc-8_and_9.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
+}