gentoo resync : 05.02.2020

14 files changed, 31 insertions, 441 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index bf5e31657c62..11aff635982e 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/chemex/Manifest b/sci-chemistry/chemex/Manifest
index afbaeb65dddc..6992b72c5e83 100644
--- a/sci-chemistry/chemex/Manifest
+++ b/sci-chemistry/chemex/Manifest
@@ -1,3 +1,3 @@
 DIST chemex-0.6.1.tar.gz 1449216 BLAKE2B 6b7f7597b09cd43b9bec89b6359d1f650fdd7d4f3a373e706da80dafaf438417458f34af6bc378442b5b4a84cb8222103ebc8026c85583e8dece3fad0dc77204 SHA512 40f538ef9c162759c7a6863886da8d46746ac362fc19154f0a5f3dd8703f7fea7397c3f34092c86dbce486c452e0d3b09a76e4c11ae119834d7ca4912e7f3fdf
-EBUILD chemex-0.6.1-r1.ebuild 876 BLAKE2B 9eea4ff107c30077d5b8b8a62dc7c5883f3eb635f5ab38ec900b14bb7970ce0c58da7b5d6dde5fde5915d1aad816b32765967a902205f7f4f0163eccb25349b1 SHA512 fef14f301089f0ef82afee0312b8680bb17766cff97da8876063493097e778b962a08ac82856a380610b307408fec42e1ea18ea28e1e2da50a50eade8e0de823
+EBUILD chemex-0.6.1-r2.ebuild 1002 BLAKE2B 0122f5cd2ec6e61f8d24b6aa14b84e707e9344ee0dbef42eccf3a07354c36d5ac22d5be33eb390da4ff1cf9299fe47f6be4d77e1489e70fb1a9d6fd43ae89d67 SHA512 c7c5cd0a21032aa0f18ebffba48739f29a2511e387ca3ec53dc7495cac63dfb2527841a2454030179cfc217f87c29351d91b0ae2e8b038c6f87e4e644964fed7
 MISC metadata.xml 216 BLAKE2B 0fbfa16661345362ff89f87adc0bb42fc5f5c9145cdedb36f3f537b39af4023b91c4dfb0d8e83a4f9ac963141f594ba8ae678371c338d992a96e02c11fd84195 SHA512 628a69805356b7458edaa2297901224178b016477a937f77e692a78ce3e7a0b6d2d7b4c4b7e70d0185d7112e6a59a5131e07d8c950e90b9c8722471d7511afc6
diff --git a/sci-chemistry/chemex/chemex-0.6.1-r1.ebuild b/sci-chemistry/chemex/chemex-0.6.1-r2.ebuild
index 9e4f47aafc99..0b85b22ffc3d 100644
--- a/sci-chemistry/chemex/chemex-0.6.1-r1.ebuild
+++ b/sci-chemistry/chemex/chemex-0.6.1-r2.ebuild
@@ -17,12 +17,18 @@ KEYWORDS="~amd64"
 IUSE=""
 
 RDEPEND="
-	>=dev-python/matplotlib-1.1[${PYTHON_USEDEP}]
+	|| (
+		>=dev-python/matplotlib-python2-1.1[${PYTHON_USEDEP}]
+		>=dev-python/matplotlib-1.1[${PYTHON_USEDEP}]
+	)
 	|| (
 		dev-python/numpy-python2[${PYTHON_USEDEP}]
 		dev-python/numpy[${PYTHON_USEDEP}]
 	)
-	>=sci-libs/scipy-0.11[${PYTHON_USEDEP}]
+	|| (
+		>=sci-libs/scipy-python2-0.11[${PYTHON_USEDEP}]
+		>=sci-libs/scipy-0.11[${PYTHON_USEDEP}]
+	)
 "
 DEPEND="${RDEPEND}
 	dev-python/setuptools[${PYTHON_USEDEP}]
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index db87a7f4f9f2..9fb8c517a917 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -1,16 +1,13 @@
 AUX gromacs-2020_beta1-pytest.patch 630 BLAKE2B 1036e06589c24459006f0b579ee89c9d9c4623c7ca32fae90b21646db13280549a23cad717ef7481b03cbf9f2629b6804c0727d4b8c7f3274d0463d2735f976a SHA512 b5880d3a21635892d52b2ac09cbf456194a3db0fa0676bbdd2c2500964da89fbb7f4ebed7ac7843304159bf11f44e279eb505b2af8833127d2e21f10cb254c1e
 DIST gromacs-2018.8.tar.gz 29913703 BLAKE2B 8780032305928067fbfe1559efe9eedc4d47e27ab2f6ab54d6dba39edfcbeefbee4673d8910009048a850620b5a08ba8feb622db652c439cfa50a149ec5f0015 SHA512 6717895942f2ab7b54019511ed2aebadadde8e96d3c4b7414bb9168ffe418432d2dee330192e199f7b9d2f665c71f5d4f1ef0911aa7243d525a2ca182ef5b122
-DIST gromacs-2019.2.tar.gz 33437869 BLAKE2B bebe4942688dace148856d4491b687b8e0fd2c86d7fbd9eecdb46824d316a0fc3854464ecafa79d8db92327ee8467be204b050c11f1e71132184efd812c3bf09 SHA512 da7ff24e8485774e22d1c2464fbe64675c3305ef0e21a3d17e363201031952e5d4a9b81f572d5284fb6f2596ed99daf62fe78d653387d9d714274f46bc750183
 DIST gromacs-2019.5.tar.gz 33445791 BLAKE2B 1e2e2764b0c8774c878abf4f32c2fa7ddd9b46f464cf1256deb48335433d92ef1b315f5534cdec9f766ae928a71361b5a4dd4a4def638269eb260ff98dbbe8bb SHA512 fdd177e4dfd29629b72bfbb4d61ff7bcdb37279f534883a9df8fd57569212fe1e9f8b8c9cec347fcc607539f31412d604d11ee3c0eb797251960435962b1bec6
 DIST gromacs-2020.tar.gz 28928068 BLAKE2B 72d4ff8f6b383284e61df9d3b2b53c51300f6961d4c19810670c8ee9ba2f1864d2a325e2774093b9338db785cb91a94461bf93f16cdf4caf0f690298a672d51c SHA512 15f0d58cd8d217eab39ef8e3535dec34127708797eaf6575fb340292cbee2303cd25deb84b3d4417a787076f4ae7be9e4958ec3a347a3aa9aed52ef337a4587c
 DIST regressiontests-2018.8.tar.gz 67855469 BLAKE2B 34c9b339f6229f483afbb5192ee6ba8b8f72d5c26907a853af9c53dfece0d88739e48f6b44b78d1c010f988f9385d077285300522164f533a5861e9dda879275 SHA512 3642389d27bd1942cd0f091c940ae97b197b94856a387fe581dc516b0d4169480f16551d4ba357f9282b3337d605c286d51dd38112ac87c826dda634904836bb
-DIST regressiontests-2019.2.tar.gz 67643003 BLAKE2B 4178de5d62f194a81f97e442c10f123dc59c5e63f2078f7f07135709f3f6e530e0d237bf40264b285c084519d5ace75dfcbcddc16dc740c4f17233dc33542e45 SHA512 c1f25bc770d3f0a873c887d5563c1cd88179e81211b70ce6f5015696e6fa0b6931a8da7a449f2b223f3105b9e2e7eca67248e96fbfc2a7fd5fb360ba616f22ff
 DIST regressiontests-2019.5.tar.gz 67643634 BLAKE2B c4d9535d9a8a650869d67544ad5f367324f45e55325bb5074ece9b010f232f2f0dd97c9af97924d3f2368ed63015ca7330baff1cc681310e1439ec330b70ee8d SHA512 7c0917b76e7db35ab4e3271d523d268e0e2d858091e68ead863bfe6d1e56b381e30fdbf44f479f6e065c029e2eb27cfa0dbaa1b243f185144321aaf5084c55ce
 DIST regressiontests-2020.tar.gz 48536146 BLAKE2B 9511db78b5d6a5ea431fdb73782f28dde4b94655139886c0ad519888ef3e435fe81807f158d66c1a4284cb88fe730f62d039ac23549f17d0ce5984764ef35f10 SHA512 5a35aaf6fe2f3b146c7045e9c967dc1c8bf754748cc1f2a7300193ae3f206a9f5058329380ae7b03b181410303bcd434584571e6161a75f99e52bd48f8ba1821
 EBUILD gromacs-2018.8.ebuild 8784 BLAKE2B 8c08b6c4f4278ed6455a0489b765c97c748835e49973bb83b7fe8e15d9453c8c9b6c6e26cd27a2d5a927aa87a36bfdef3874020f6658c9b2dcb774043e4547e3 SHA512 b66644847daa453b9a764faaa7f3145e16f3819d0d7ffdad12c1209a398cd03dbf7c2d60e0510f514b18f6ed8c09dfadb77bca6ff2f1eb044c65632842a7499a
 EBUILD gromacs-2018.9999.ebuild 8787 BLAKE2B 9edbb2ae0bd3f76af41cee9971b70fdc957f22bb61ec131abd3cf44a2da56c208b0b103f72754e17cccfa054d79c1e95a9477228b0c14f4476e58bd7656b641a SHA512 c4548c8436dadf1daaf7f4f41e3c957029a10f5eb7fd11c5c8f42046d2ba38c6baf9f47e69fb8e8eeef550e0463d76bf738d6f708ffce6b4cf556e29d725ed5a
-EBUILD gromacs-2019.2.ebuild 9200 BLAKE2B d4c6bbca2dfc3d376d3c98893a273d405735a2b10ea7034622a56beb544a9c0af494e7aac71d477c4800b2d45bfea0cbae3cd8ba764ebf3f463aa0b2d613b7e4 SHA512 60170844324d3542ee5043a6ac624e9eb6838a15a16fe58e65b5f3df12a74fe1bc383c505217b2fe85183c0eb7a1b421c21e1574329a9e84bb9b86159ad90e5d
-EBUILD gromacs-2019.5.ebuild 9233 BLAKE2B ecc2f17bf17bdd5df1696b9877d996c44450001412bd887fff13fd53b332d3fe63556e77c01e624b0f12a445fb8a4fda688fd409f30a7c94ebfc5107ddf30f3e SHA512 e52498f36fbe36dfc33f0aaf3c4ebac0d2c643127c2c70e901d01d6223f9537889f08530db61e0167673cb6528b1b5fc2d8311b397d7cb4389cd37e7fd71259f
+EBUILD gromacs-2019.5.ebuild 9232 BLAKE2B d6983b3c0cc508e278fd5fe358d1f5351f6fb6cc028cb1ee68ffaac484b11c8d88de43ac6d2b51f64ed08c4cb73f3d17ee7bc8af3947683bd3765d6b1038212d SHA512 1ff5231b3e3e6921f65295f7baa3371dd481cb004fd045005a8f9646f54b0053645bd9eb05f2cf260482e05689d668a02e7fbb851afc4d06ff2eb139f25483a7
 EBUILD gromacs-2019.9999.ebuild 9234 BLAKE2B 076a2a9ff537342156ca94f138c738fbff5a0b8167b7cd34ebab388357acc2f08249675428d19b13abe4d8489aaf94afb69fb32bba1cf7658550a984319dcb30 SHA512 da0007f5e8162efd53b061a564908167f8388c4cf4288d56167e0ab313140d92641d51f1c7384d52a55998de8baf23eaf56a04d633cd20525fbc0e2c46ba4256
 EBUILD gromacs-2020.9999.ebuild 9793 BLAKE2B 0a689e24c71085d134e51a091d647e64a3bdfdbc9678f27cc0fb86b7caa8b4e1e4bdda4e8a379bfe593408fc0ea236141db9e8fd89e58987aadb2003054227d6 SHA512 0efe1abfcd815248f6a77d47e33867b88aae79d71c3be146da3264ae91036fd5305129515b3ae12cad757ad802c18ba79e588581c910fe06606883cacb2c9a19
 EBUILD gromacs-2020.ebuild 9793 BLAKE2B 0a689e24c71085d134e51a091d647e64a3bdfdbc9678f27cc0fb86b7caa8b4e1e4bdda4e8a379bfe593408fc0ea236141db9e8fd89e58987aadb2003054227d6 SHA512 0efe1abfcd815248f6a77d47e33867b88aae79d71c3be146da3264ae91036fd5305129515b3ae12cad757ad802c18ba79e588581c910fe06606883cacb2c9a19
diff --git a/sci-chemistry/gromacs/gromacs-2019.2.ebuild b/sci-chemistry/gromacs/gromacs-2019.2.ebuild
deleted file mode 100644
index 58d733d2c332..000000000000
--- a/sci-chemistry/gromacs/gromacs-2019.2.ebuild
+++ /dev/null
@@ -1,312 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit bash-completion-r1 cmake-utils cuda eutils multilib python-single-r1 readme.gentoo-r1 toolchain-funcs xdg-utils
-
-if [[ $PV = *9999* ]]; then
-	EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
-		https://gerrit.gromacs.org/gromacs.git
-		https://github.com/gromacs/gromacs.git
-		https://repo.or.cz/r/gromacs.git"
-	[[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
-	inherit git-r3
-else
-	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
-		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
-	KEYWORDS="amd64 arm x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-fi
-
-ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
-
-DESCRIPTION="The ultimate molecular dynamics simulation package"
-HOMEPAGE="http://www.gromacs.org/"
-
-# see COPYING for details
-# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
-#        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
-LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
-SLOT="0/${PV}"
-IUSE="X blas cuda +doc -double-precision +fftw +gmxapi +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}"
-
-CDEPEND="
-	X? (
-		x11-libs/libX11
-		x11-libs/libSM
-		x11-libs/libICE
-		)
-	blas? ( virtual/blas )
-	cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 )
-	opencl? ( virtual/opencl )
-	fftw? ( sci-libs/fftw:3.0 )
-	hwloc? ( sys-apps/hwloc )
-	lapack? ( virtual/lapack )
-	lmfit? ( sci-libs/lmfit )
-	mkl? ( sci-libs/mkl )
-	mpi? ( virtual/mpi )
-	${PYTHON_DEPS}
-	"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig
-	doc? (
-		app-doc/doxygen
-		dev-python/sphinx[${PYTHON_USEDEP}]
-		media-gfx/mscgen
-		media-gfx/graphviz
-		dev-texlive/texlive-latex
-		dev-texlive/texlive-latexextra
-		media-gfx/imagemagick
-	)"
-RDEPEND="${CDEPEND}"
-
-REQUIRED_USE="
-	|| ( single-precision double-precision )
-	cuda? ( single-precision )
-	cuda? ( !opencl )
-	mkl? ( !blas !fftw !lapack )
-	${PYTHON_REQUIRED_USE}"
-
-DOCS=( AUTHORS README )
-
-RESTRICT="!test? ( test )"
-
-if [[ ${PV} != *9999 ]]; then
-	S="${WORKDIR}/${PN}-${PV/_/-}"
-fi
-
-pkg_pretend() {
-	[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
-	use openmp && ! tc-has-openmp && \
-		die "Please switch to an openmp compatible compiler"
-}
-
-src_unpack() {
-	if [[ ${PV} != *9999 ]]; then
-		default
-	else
-		git-r3_src_unpack
-		if use test; then
-			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
-			EGIT_BRANCH="${EGIT_BRANCH}" \
-			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
-				git-r3_src_unpack
-		fi
-	fi
-}
-
-src_prepare() {
-	#notes/todos
-	# -on apple: there is framework support
-
-	xdg_environment_reset #591952
-
-	cmake-utils_src_prepare
-
-	use cuda && cuda_src_prepare
-
-	GMX_DIRS=""
-	use single-precision && GMX_DIRS+=" float"
-	use double-precision && GMX_DIRS+=" double"
-
-	if use test; then
-		for x in ${GMX_DIRS}; do
-			mkdir -p "${WORKDIR}/${P}_${x}" || die
-			cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
-		done
-	fi
-
-	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
-
-	# try to create policy for imagemagik
-	mkdir -p ${HOME}/.config/ImageMagick
-	cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF
-	<?xml version="1.0" encoding="UTF-8"?>
-	<!DOCTYPE policymap [
-	<!ELEMENT policymap (policy)+>
-	!ATTLIST policymap xmlns CDATA #FIXED ''>
-	<!ELEMENT policy EMPTY>
-	<!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
-			name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
-			stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
-	]>
-	<policymap>
-		<policy domain="coder" rights="read | write" pattern="PS" />
-		<policy domain="coder" rights="read | write" pattern="PS2" />
-		<policy domain="coder" rights="read | write" pattern="PS3" />
-		<policy domain="coder" rights="read | write" pattern="EPS" />
-		<policy domain="coder" rights="read | write" pattern="PDF" />
-		<policy domain="coder" rights="read | write" pattern="XPS" />
-	</policymap>
-	EOF
-}
-
-src_configure() {
-	local mycmakeargs_pre=( ) extra fft_opts=( )
-
-	#go from slowest to fastest acceleration
-	local acce="None"
-	use cpu_flags_x86_sse2 && acce="SSE2"
-	use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-	use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-	use cpu_flags_x86_avx && acce="AVX_256"
-	use cpu_flags_x86_avx2 && acce="AVX2_256"
-
-	#to create man pages, build tree binaries are executed (bug #398437)
-	[[ ${CHOST} = *-darwin* ]] && \
-		extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
-
-	if use fftw; then
-		fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
-	elif use mkl && has_version "=sci-libs/mkl-10*"; then
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="${MKLROOT}/include"
-			-DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
-		)
-	elif use mkl; then
-		local bits=$(get_libdir)
-		fft_opts=( -DGMX_FFT_LIBRARY=mkl
-			-DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
-			-DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
-		)
-	else
-		fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
-	fi
-
-	if use lmfit; then
-		local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL )
-	else
-		local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL )
-	fi
-
-	mycmakeargs_pre+=(
-		"${fft_opts[@]}"
-		"${lmfit_opts[@]}"
-		-DGMX_X11=$(usex X)
-		-DGMX_EXTERNAL_BLAS=$(usex blas)
-		-DGMX_EXTERNAL_LAPACK=$(usex lapack)
-		-DGMX_OPENMP=$(usex openmp)
-		-DGMX_COOL_QUOTES=$(usex offensive)
-		-DGMX_USE_TNG=$(usex tng)
-		-DGMX_BUILD_MANUAL=$(usex doc)
-		-DGMX_HWLOC=$(usex hwloc)
-		-DGMX_DEFAULT_SUFFIX=off
-		-DGMX_SIMD="$acce"
-		-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
-		-DBUILD_TESTING=$(usex test)
-		-DGMX_BUILD_UNITTESTS=$(usex test)
-		-DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}"
-		${extra}
-	)
-
-	for x in ${GMX_DIRS}; do
-		einfo "Configuring for ${x} precision"
-		local suffix=""
-		#if we build single and double - double is suffixed
-		use double-precision && use single-precision && \
-			[[ ${x} = "double" ]] && suffix="_d"
-		local p
-		[[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
-		local cuda=( "-DGMX_GPU=OFF" )
-		[[ ${x} = "float" ]] && use cuda && \
-			cuda=( "-DGMX_GPU=ON" )
-		local opencl=( "-DGMX_USE_OPENCL=OFF" )
-		use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" )
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_MPI=OFF
-			-DGMX_THREAD_MPI=$(usex threads)
-			-DGMXAPI=$(usex gmxapi)
-			"${opencl[@]}"
-			"${cuda[@]}"
-			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
-			-DGMX_BINARY_SUFFIX="${suffix}"
-			-DGMX_LIBS_SUFFIX="${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
-		use mpi || continue
-		einfo "Configuring for ${x} precision with mpi"
-		mycmakeargs=(
-			${mycmakeargs_pre[@]} ${p}
-			-DGMX_THREAD_MPI=OFF
-			-DGMX_MPI=ON ${cuda}
-			-DGMX_OPENMM=OFF
-			-DGMXAPI=OFF
-			-DGMX_BUILD_MDRUN_ONLY=ON
-			-DBUILD_SHARED_LIBS=OFF
-			-DGMX_BUILD_MANUAL=OFF
-			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
-			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
-			)
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
-		[[ ${CHOST} != *-darwin* ]] || \
-		  sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
-	done
-}
-
-src_compile() {
-	for x in ${GMX_DIRS}; do
-		einfo "Compiling for ${x} precision"
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_compile
-		# not 100% necessary for rel ebuilds as available from website
-		if use doc; then
-			BUILD_DIR="${WORKDIR}/${P}_${x}"\
-				cmake-utils_src_compile manual
-		fi
-		use mpi || continue
-		einfo "Compiling for ${x} precision with mpi"
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
-			cmake-utils_src_compile
-	done
-}
-
-src_test() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake-utils_src_make check
-	done
-}
-
-src_install() {
-	for x in ${GMX_DIRS}; do
-		BUILD_DIR="${WORKDIR}/${P}_${x}" \
-			cmake-utils_src_install
-		if use doc; then
-			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
-		fi
-		use mpi || continue
-		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
-			cmake-utils_src_install
-	done
-
-	if use tng; then
-		insinto /usr/include/tng
-		doins src/external/tng_io/include/tng/*h
-	fi
-	# drop unneeded stuff
-	rm "${ED}"usr/bin/GMXRC* || die
-	for x in "${ED}"usr/bin/gmx-completion-*.bash ; do
-		local n=${x##*/gmx-completion-}
-		n="${n%.bash}"
-		cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
-		newbashcomp "${T}"/"${n}" "${n}"
-	done
-	rm "${ED}"usr/bin/gmx-completion*.bash || die
-	readme.gentoo_create_doc
-}
-
-pkg_postinst() {
-	einfo
-	einfo  "Please read and cite:"
-	einfo  "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
-	einfo  "https://dx.doi.org/10.1021/ct700301q"
-	einfo
-	readme.gentoo_print_elog
-}
diff --git a/sci-chemistry/gromacs/gromacs-2019.5.ebuild b/sci-chemistry/gromacs/gromacs-2019.5.ebuild
index 7775143d0ae9..793ffa7a363f 100644
--- a/sci-chemistry/gromacs/gromacs-2019.5.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2019.5.ebuild
@@ -19,7 +19,7 @@ if [[ $PV = *9999* ]]; then
 else
 	SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
 		test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
-	KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+	KEYWORDS="amd64 arm x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
 fi
 
 ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
diff --git a/sci-chemistry/nmrdepaker/Manifest b/sci-chemistry/nmrdepaker/Manifest
index 0c2312658756..a3f94f72a9a2 100644
--- a/sci-chemistry/nmrdepaker/Manifest
+++ b/sci-chemistry/nmrdepaker/Manifest
@@ -1,3 +1,3 @@
 DIST nmrdepaker-1.0.tar.gz 2233765 BLAKE2B 9b638a36fc50d7c020d56833b6ca78d7079ad357f42431088c4c0735b7e9ce63a0e6318915ec751b42e6628c0da76b93ca16ffea1ffe6b311480e8d278ce1a1a SHA512 9d1a9048a85f85eacaeeb582c5550345efa673b1f517dad121e2b2e19125f93e71a26f2f8240ea9b8a06489814eb833e7b3653f882a46bad699b01fd1aa4299f
-EBUILD nmrdepaker-1.0-r1.ebuild 846 BLAKE2B 5366d7a88e40be247ddcfc6fd9e01d9da3e9c9282e58a42a53f9ac39865715fd76afaa265b89c509740d980355fedfbcdabac0bb08606c1c8444f5a2404c1e07 SHA512 c2777dc917c092e44eb0306faebdbde99e4103fa745684f936b58b4eaf8e2863079378cb34d6576cdedcbdbffd7f704d0527cf0ab659c7afd9168b53f213c238
+EBUILD nmrdepaker-1.0-r2.ebuild 920 BLAKE2B 684f7f2a3475a04abf4592da1b70033a2c7c9f29ef99be234a927555e39f3d4a3241968e4ac7ed1c23cfb37d99c97c407251e933a7bec61c0ebd7d0a38a84dd1 SHA512 f1bf2fa3827f1f161447b439d82599ee2fd7628e96aea35fba9019dd350efa6816b1a351d3e80d4182462b0e5b3ff0629edebee38f24011d9cdfe792cbec1ca4
 MISC metadata.xml 216 BLAKE2B 0fbfa16661345362ff89f87adc0bb42fc5f5c9145cdedb36f3f537b39af4023b91c4dfb0d8e83a4f9ac963141f594ba8ae678371c338d992a96e02c11fd84195 SHA512 628a69805356b7458edaa2297901224178b016477a937f77e692a78ce3e7a0b6d2d7b4c4b7e70d0185d7112e6a59a5131e07d8c950e90b9c8722471d7511afc6
diff --git a/sci-chemistry/nmrdepaker/nmrdepaker-1.0-r1.ebuild b/sci-chemistry/nmrdepaker/nmrdepaker-1.0-r2.ebuild
index 29a13632c888..043fd37324eb 100644
--- a/sci-chemistry/nmrdepaker/nmrdepaker-1.0-r1.ebuild
+++ b/sci-chemistry/nmrdepaker/nmrdepaker-1.0-r2.ebuild
@@ -17,7 +17,10 @@ KEYWORDS="~amd64"
 IUSE=""
 
 RDEPEND="
-	>=dev-python/matplotlib-0.98.5[gtk2,${PYTHON_USEDEP}]
+	|| (
+		>=dev-python/matplotlib-python2-0.98.5[gtk2,${PYTHON_USEDEP}]
+		>=dev-python/matplotlib-0.98.5[gtk2,${PYTHON_USEDEP}]
+	)
 	|| (
 		dev-python/numpy-python2[${PYTHON_USEDEP}]
 		>=dev-python/numpy-1.2[${PYTHON_USEDEP}]
diff --git a/sci-chemistry/prodecomp/Manifest b/sci-chemistry/prodecomp/Manifest
index e19bbf5f4bc4..fe180d2bdaba 100644
--- a/sci-chemistry/prodecomp/Manifest
+++ b/sci-chemistry/prodecomp/Manifest
@@ -1,3 +1,3 @@
 DIST prodecomp-3.0.tar.bz2 18377446 BLAKE2B c6b4acf20a76029fc34eaea7a0adf1a04fb727b2e246fbcad27e2fa2bea606b2e712fb986fdd3e534534b32a22acae58a00bc2a3c6bde893d5befe91696523d3 SHA512 8d23f174e125d4c7776432a37b063d2f39af8497050bd7f7ff358c67d509b1eef2c2865596efae632855fd583fb52c233b67d0e667c6c2a03ba6f5a2f2ac9b0d
-EBUILD prodecomp-3.0-r1.ebuild 1096 BLAKE2B ea880fff06ebdfc68c51aececf5064f63a6ec2fc1d183f2041d73f633c592d73282ee0635dff24a903be2e62ce2bc1307d3d6e35001d9b41009f57d1db9222fb SHA512 163404741f8cdfcc6e8c550850f79470d9a7c0accf73386351c5ce9ad2068fe0aed5316b346144b888cd5726f2b80312d1d5bcf3476c13b6009279e0c71b3362
+EBUILD prodecomp-3.0-r2.ebuild 1146 BLAKE2B fd477a14bd9e47bc8857446fc072633301f6114f30dfcc27997fc7b3d58c52a384ae8b7391bcb58f6bc23db1bbc24e0be0c7b010c971fb4d4e27c34355a38abb SHA512 b914399f357dfd514f55a82c1fb65b752725f62f0025ecdbe6524c6f0191ede74c629852d80e3c4998928649168702aa91361258c22473f499f76c3a3c4ebfc7
 MISC metadata.xml 825 BLAKE2B 6874942c301b7d68f9184de8eb7482b790d2bd51c3a853132da3ed7bb0eacf54f608f816965bbfb27b81b90fecc3eee77596d73a78f5ec67703c53ad2bc2556d SHA512 94e41d5648ac93257f11f305bf2aaf926cc103240beec884142cda42c3d4e4fae5629e26b43cd945c945af706d5b5172fcd2c30ec6cb9067b152a22cd09bddcf
diff --git a/sci-chemistry/prodecomp/prodecomp-3.0-r1.ebuild b/sci-chemistry/prodecomp/prodecomp-3.0-r2.ebuild
index ad5fb6271a2b..e66cac2b0b4f 100644
--- a/sci-chemistry/prodecomp/prodecomp-3.0-r1.ebuild
+++ b/sci-chemistry/prodecomp/prodecomp-3.0-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -20,7 +20,10 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 DEPEND="${PYTHON_DEPS}"
 RDEPEND="${DEPEND}
-	sci-libs/scipy[${PYTHON_USEDEP}]"
+	|| (
+		sci-libs/scipy-python2[${PYTHON_USEDEP}]
+		sci-libs/scipy[${PYTHON_USEDEP}]
+	)"
 
 S="${WORKDIR}"/NMRProjAnalys
 
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 3b769d6a6826..7948415a7bf8 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,6 +1,4 @@
 DIST pymol-1.8.4.0.png.xz 19528 BLAKE2B f3d23d4cedca3d8bb96b20646a548da4be570697e3346a11b01c5c3599b536ba4697be08472dfa8a4f6533167defc1a37a1de332931a73857319cb28fd42cd2b SHA512 40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c
 DIST pymol-2.3.0.tar.gz 10448674 BLAKE2B 0d508587d880ce7f2e8a0481bf664e6bfe6eb1d68b0f48b9266cde756824bd8c0144d7243e958bbc5e571d60fca9dafff125d81a8a3d32107e78ad2ff8dffc05 SHA512 e1dcea1c97bcd9045d3543e92902f240e6affbf61a38e8d2a0be04309e3dbabfe1a869847d1423b3151008978d4c305bbf3ce994fc9d453c0063ce020100c133
-DIST pymol-v1.8.4.0.tar.bz2 8717344 BLAKE2B a4cfb95eb40a3cd3da5b8cfd4acac7255997f9a3e49ef7e7e1d4c13f36e4aace462a054c326bbaadbc99f22286be878a6d5c518149760b5c939ce9362d4b8cc3 SHA512 73a810adfc31adaf0f3fa25512084882c87b0782c8af716ac0203a5b5b7f0b9fedfbce3d129bffef7b52044e92b0542e683966b2acf961c4dac17fbba72dd7fe
-EBUILD pymol-1.8.4.0-r2.ebuild 3062 BLAKE2B 98914bfee561a1f5970ca47180ae5a23ac9c547069bfa421041c4e19eaff9820ab148038406971ac8e79801f99fdd92f90e7be5249081ba1be200451efb92f30 SHA512 69714e4d11ab56af06fee425e23659b9855e2f8e39293888a57720e6c1f4dad8f823cb77f203f7bb55f3b402f899e810c73af150106621c2e8ee6cd0c4250e5f
 EBUILD pymol-2.3.0-r2.ebuild 3190 BLAKE2B a72434867a8589dda7a334f71e1aaa58f16d3caea1eb1615c44c2b813b1d0b84ed308369eb89c45251daf7bfbabed470e7d5abe42334b3fe28b484217fa29653 SHA512 5c2d08baa9407a2abe733d1753e622ea450b7c939b4f57d8e47adb5f57ac5a5e2b95264b6876698c70a5af926d378d75b6ba4ae02c85affbcfda7327d718ea14
 MISC metadata.xml 439 BLAKE2B 68df7dfc8ca3d4d4b18b419532bade69491f2e9362f10ae2397c804132b7fc9cd08dcf9703c0a89c44588c570e0c0c1bb9bffb7394d51faf1283142dbc5f70b3 SHA512 f5a3eded9b12fa715ba2e6e10b41c75d9bd823ca0dd40acbffc3f5bfc4b36c687f720b1a4e119b4540a31faf849985778cbd72b0b2cd35af8c52ca0f808d71e4
diff --git a/sci-chemistry/pymol/pymol-1.8.4.0-r2.ebuild b/sci-chemistry/pymol/pymol-1.8.4.0-r2.ebuild
deleted file mode 100644
index f60de8dcb189..000000000000
--- a/sci-chemistry/pymol/pymol-1.8.4.0-r2.ebuild
+++ /dev/null
@@ -1,111 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-PYTHON_REQ_USE="tk"
-
-inherit distutils-r1 eutils fdo-mime flag-o-matic versionator
-
-DESCRIPTION="A Python-extensible molecular graphics system"
-HOMEPAGE="https://www.pymol.org/"
-SRC_URI="
-	https://dev.gentoo.org/~jlec/distfiles/${P}.png.xz
-	mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 1-2)/${PN}-v${PV}.tar.bz2
-	"
-# git archive -v --prefix=${P}/ master -o ${P}.tar.xz
-RESTRICT="mirror"
-LICENSE="PSF-2.2"
-SLOT="0"
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
-IUSE="web"
-
-DEPEND="
-	|| (
-		dev-python/numpy-python2[${PYTHON_USEDEP}]
-		dev-python/numpy[${PYTHON_USEDEP}]
-	)
-	dev-python/pmw:py2[${PYTHON_USEDEP}]
-	dev-python/pyopengl[${PYTHON_USEDEP}]
-	media-libs/freeglut
-	media-libs/freetype:2
-	media-libs/glew:0=
-	media-libs/libpng:0=
-	media-video/mpeg-tools
-	sys-libs/zlib
-	!sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}]
-	web? ( !dev-python/webpy[${PYTHON_USEDEP}] )"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/${PN}
-
-python_prepare_all() {
-	sed \
-		-e "s:\"/usr:\"${EPREFIX}/usr:g" \
-		-e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \
-		-e "/import/s:argparse:argparseX:g" \
-		-i setup.py || die
-
-	sed \
-		-e "s:/opt/local:${EPREFIX}/usr:g" \
-		-e '/ext_comp_args/s:\[.*\]:[]:g' \
-		-i setup.py || die
-
-	append-cxxflags -std=c++0x
-
-	distutils-r1_python_prepare_all
-}
-
-python_install() {
-	distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol"
-
-	sed \
-		-e '1d' \
-		-e "/APBS_BINARY_LOCATION/s:None:\"${EPREFIX}/usr/bin/apbs\":g" \
-		-e "/APBS_PSIZE_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/src/\":g" \
-		-e "/APBS_PDB2PQR_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/\":g" \
-		-i "${D}/$(python_get_sitedir)"/pmg_tk/startup/apbs_tools.py || die
-}
-
-python_install_all() {
-	distutils-r1_python_install_all
-
-	sed \
-		-e '1i#!/usr/bin/env python' \
-		"${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die
-
-	python_foreach_impl python_doscript "${T}"/${PN}
-
-	# These environment variables should not go in the wrapper script, or else
-	# it will be impossible to use the PyMOL libraries from Python.
-	cat >> "${T}"/20pymol <<- EOF
-		PYMOL_PATH="${EPREFIX}/usr/share/pymol"
-		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
-		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
-	EOF
-
-	doenvd "${T}"/20pymol
-
-	newicon "${WORKDIR}"/${P}.png ${PN}.png
-	make_desktop_entry ${PN} PyMol ${PN} \
-		"Graphics;Education;Science;Chemistry;" \
-		"MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;"
-
-	if ! use web; then
-		rm -rf "${D}/$(python_get_sitedir)/web" || die
-	fi
-
-	rm -f "${ED}"/usr/share/${PN}/LICENSE || die
-}
-
-pkg_postinst() {
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-	optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr
-}
-
-pkg_postrm() {
-	fdo-mime_desktop_database_update
-	fdo-mime_mime_database_update
-}
diff --git a/sci-chemistry/relax/Manifest b/sci-chemistry/relax/Manifest
index 9d2df17bb325..f3b0b62ccafa 100644
--- a/sci-chemistry/relax/Manifest
+++ b/sci-chemistry/relax/Manifest
@@ -1,3 +1,3 @@
 DIST relax-4.0.0.src.tar.bz2 105659752 BLAKE2B ce5fc9b7f31787f2189e75a543f8ba6fe3cd59ce7382c6c0f79c419b9f71b2d09bd16685e7fed3c9e3205be531efa2a8dc1cce707e77e2386d2a9f7a71b4b0c1 SHA512 28b5ddab2c83f95d7e1a502d05b5d3c93337fece68a1fef95ec8978f61fccf24cb37528cfef27cb20d132033535f4120b23cc76a75f34f52b27df17116351f8e
-EBUILD relax-4.0.0-r2.ebuild 1647 BLAKE2B 47d35d0a658255c16ce7fde5c6afdf1ac80f894e9de57b4a55c7e44c61db164f50511984abbaf1b8ad98bebef132836bcbfcd07d8ddb70f7c5fe17469185df62 SHA512 88d260d222dbd1c25b327aea72e37cacb209d3dd172aefe5c15d5def95905dd7168d75d15cb707ebc4ed3863838e3c6b3a4764679e249f0ad6d689ad7cabe501
+EBUILD relax-4.0.0-r3.ebuild 1760 BLAKE2B 6ea79be4c348069a5cd54ce3f9614d145febcb47a76709b5c45c9400347d9ff035cf6138005a455e2b14c1a6a498cb8ee1fdc76d8c65aa99d82bbba966bd7d16 SHA512 c3a59cbba651f752650d840b60dfda46ceb7f6f2673607e8e1b8f1265ff3595116f64830b3e00ee42a017ecd54cf27d008c841048f302a09a2c2abb87326a204
 MISC metadata.xml 1373 BLAKE2B d5a9e36f0412ef757a23aa4991986bdc394edc035f59b0206b246affc884417eb8446a598b23054972c97dc5d883cd0242e306f9e8d61620c144939845c0bcf1 SHA512 575ccfdae744fc5d97e795a22989b377954edeacb8ec4887d987a59af813f126551743c4b29b9c2b4a26a1840f05d42fb26fd39b7ae9b38e24373fab18c0270e
diff --git a/sci-chemistry/relax/relax-4.0.0-r2.ebuild b/sci-chemistry/relax/relax-4.0.0-r3.ebuild
index 606c454f1b12..28b0f5d9da67 100644
--- a/sci-chemistry/relax/relax-4.0.0-r2.ebuild
+++ b/sci-chemistry/relax/relax-4.0.0-r3.ebuild
@@ -24,7 +24,10 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 RDEPEND="
 	${PYTHON_DEPS}
 	dev-python/Numdifftools[${PYTHON_USEDEP}]
-	dev-python/matplotlib[${PYTHON_USEDEP}]
+	|| (
+		dev-python/matplotlib-python2[${PYTHON_USEDEP}]
+		dev-python/matplotlib[${PYTHON_USEDEP}]
+	)
 	|| (
 		dev-python/numpy-python2[${PYTHON_USEDEP}]
 		dev-python/numpy[${PYTHON_USEDEP}]
@@ -35,7 +38,10 @@ RDEPEND="
 	sci-chemistry/vmd
 	>=sci-libs/bmrblib-1.0.3[${PYTHON_USEDEP}]
 	>=sci-libs/minfx-1.0.11[${PYTHON_USEDEP}]
-	sci-libs/scipy[${PYTHON_USEDEP}]
+	|| (
+		sci-libs/scipy-python2[${PYTHON_USEDEP}]
+		sci-libs/scipy[${PYTHON_USEDEP}]
+	)
 	sci-visualization/grace
 	sci-visualization/opendx
 	x11-libs/wxGTK:${WX_GTK_VER}[X]"