gentoo resync : 13.10.2019

9 files changed, 413 insertions, 32 deletions

diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index b54b4bab8d9a..5207714ec30c 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -1,16 +1,19 @@
-DIST gromacs-2018.3.tar.gz 29915626 BLAKE2B 6e6eeafecdd923a25b4a2a78a8e89f793639b57ffbd63f19d133d8474302f9a381041f138a509dadb42b36e25fe508729e860efb6b0c75cdbf01d924b0a8fd83 SHA512 3c4d6eb3942d7b54d01c94c6f6f5ae706e0f5d4f9901ea11a56fde4df97b1a9112007f2cb13feea0f19f30c89f57ae80ff53a8f5203b8cdff103aa903cd0dc8f
 DIST gromacs-2018.7.tar.gz 29912662 BLAKE2B 0714b28ec2443f3201275fc2fa6db1202a059161362134d4de03a900a3a67fe9d31ba8c058d5ee971198fecd69379fcd389f03d25c61f50b8460c43ba5c564d5 SHA512 fbc3b847b70b1396f412b8f4a1b977268651f8d53a222dcf6349fe563ff6319e096484209a24351e382bc9162a949b3900591f5b469c32dd9effeb894f03c172
+DIST gromacs-2018.8.tar.gz 29913703 BLAKE2B 8780032305928067fbfe1559efe9eedc4d47e27ab2f6ab54d6dba39edfcbeefbee4673d8910009048a850620b5a08ba8feb622db652c439cfa50a149ec5f0015 SHA512 6717895942f2ab7b54019511ed2aebadadde8e96d3c4b7414bb9168ffe418432d2dee330192e199f7b9d2f665c71f5d4f1ef0911aa7243d525a2ca182ef5b122
 DIST gromacs-2019.2.tar.gz 33437869 BLAKE2B bebe4942688dace148856d4491b687b8e0fd2c86d7fbd9eecdb46824d316a0fc3854464ecafa79d8db92327ee8467be204b050c11f1e71132184efd812c3bf09 SHA512 da7ff24e8485774e22d1c2464fbe64675c3305ef0e21a3d17e363201031952e5d4a9b81f572d5284fb6f2596ed99daf62fe78d653387d9d714274f46bc750183
 DIST gromacs-2019.3.tar.gz 33441419 BLAKE2B 79319dd23982c65c7c4d8e5f633cef0c7fd99a38a4e0cc9030a3ffb0fdfc07a4fbfbcfa942896f23a143b747e044fae645498a3e6992497d1f1a7d966f80b2b0 SHA512 de9f54d095b45ea7efd1043f83a40f6c778a6e3e2067a01f48d1ce843d68d226061933ca28a3edb635b795a8ddd5ef9deb8ed1114aa3235bc8039db8ff7d0218
-DIST regressiontests-2018.3.tar.gz 67857855 BLAKE2B acd7a05ae79d1b4eb47d0c68a3fec9ee19f028a5019f39c37a033f48cf6da2a468375180ad6ceca9ac4f685a8bead38550663a47d6427b51f84c32a5c810e5f0 SHA512 57980d49efe6dcc3b3d14b5913a30c68fc1de5b679ef986fec1a149c76f67139b0299c3ee2825451461294fab5f345c7ad4f42e90f8991b81aafe9c369f3ff0b
+DIST gromacs-2019.4.tar.gz 33444527 BLAKE2B 5a01ed0e38faade037de701b72e8d52fd5a947a23228f0b5170a170dc963b00068a6b6880dd9a3f6f2a73140a3787952741dcbcc862bc357a8be8bf5640faa16 SHA512 adc6dea187b7f3a3c13fcd39445ae45248d46d56b0102fda47b1850b83ff1fb77a3fec99d4a4124b01ed04646dab6ab67749eae1bec36d1ba6f2205855cd29f8
 DIST regressiontests-2018.7.tar.gz 67856738 BLAKE2B 955ae8b5e74f90fec704cf41fbd00bd8c09d754f950551fe0adfcd407db6fdb4491a3815149ea37d36c747316c79d462e823b9f6b26f2376bf90d87aad95731b SHA512 c2ff390750bd99faebcd8d5dd8ad6dbf2b00113ed888bddddf985dbf95d7f347093adb67f3c396547b3e2990de330fddb7efe83ded91a72cf97c82a1dac7e826
+DIST regressiontests-2018.8.tar.gz 67855469 BLAKE2B 34c9b339f6229f483afbb5192ee6ba8b8f72d5c26907a853af9c53dfece0d88739e48f6b44b78d1c010f988f9385d077285300522164f533a5861e9dda879275 SHA512 3642389d27bd1942cd0f091c940ae97b197b94856a387fe581dc516b0d4169480f16551d4ba357f9282b3337d605c286d51dd38112ac87c826dda634904836bb
 DIST regressiontests-2019.2.tar.gz 67643003 BLAKE2B 4178de5d62f194a81f97e442c10f123dc59c5e63f2078f7f07135709f3f6e530e0d237bf40264b285c084519d5ace75dfcbcddc16dc740c4f17233dc33542e45 SHA512 c1f25bc770d3f0a873c887d5563c1cd88179e81211b70ce6f5015696e6fa0b6931a8da7a449f2b223f3105b9e2e7eca67248e96fbfc2a7fd5fb360ba616f22ff
 DIST regressiontests-2019.3.tar.gz 67640462 BLAKE2B ed6c176a144e0407be66585be5d6090c31c047498bc5f48f59685108de91f2f9ddb2d22b291a15e6ffa1db848aae19b94a79c8c3d34b1067680f759a179953dd SHA512 822e905fb488ce308eb9324d93f78106da5252c773c7941d49c6162e73bdff109aeca1f0d57216c6dd6536a4c41d80013fa1cee2f5206b0c4160a3e5b4a31315
-EBUILD gromacs-2018.3.ebuild 7824 BLAKE2B cc5ec314f5338c269d00bb8ec7af34f38134c59dd7009fc593cfa559cc68e69753f17bd8b77f5156f08999a83980d1e1c5684fd9ed489386af309f1babf850aa SHA512 d47c8c6e1e4c1dc5cd2429e5c77f04af822b5995cdd1f93a1331442dfe95d0192bda5565d3837575100f2fe841f1006cd38698ced727525c716d1925c0e65579
-EBUILD gromacs-2018.7.ebuild 7824 BLAKE2B cc5ec314f5338c269d00bb8ec7af34f38134c59dd7009fc593cfa559cc68e69753f17bd8b77f5156f08999a83980d1e1c5684fd9ed489386af309f1babf850aa SHA512 d47c8c6e1e4c1dc5cd2429e5c77f04af822b5995cdd1f93a1331442dfe95d0192bda5565d3837575100f2fe841f1006cd38698ced727525c716d1925c0e65579
-EBUILD gromacs-2018.9999.ebuild 7827 BLAKE2B 97a2437061a55854dd2799c8bdbec6a342586fc480785ea52de8d6b612c747ace1fba0a1fc3dbec9904cafcb3abdabd363ba0d6285cfc44f60964047c52f5b74 SHA512 975f2bcfdd93df006ec2a8f439a2a90e4c9079c58209ec2828b5647d96c29f7eef7fd0c79da844cc8d4e449b573a75884b19c951649c0028133d3fa87b03934c
-EBUILD gromacs-2019.2.ebuild 9172 BLAKE2B 9a2abe1f9e081dfa1e64e6571cce6a45815f7aadb0cc2c7e3a85b312855a1955fc66915f1e1c6ab3efc3ab7770ebc94ccbb36e32f91f69e873a66157c4a883aa SHA512 b5e0462d8dfae69545a899ddf7c7bbcfa24de4fa59a4ba7f16ae98fba994c20d715ae300ef3998406fb650b94caac9a99b3250dee8646c90129313c47b1e7479
-EBUILD gromacs-2019.3.ebuild 9175 BLAKE2B 2e26ad73b84fd5d8cce499dc77fa51122f08c6214778f327b142fce6c0790ddf68d624b264ac3b9d8c808951fbc2b9db199402a2a9c29865995df5b8a25112f1 SHA512 ab70cbfd71b180571721de010804cc53241f1888c1845ce11c6b53486a051306dfaa7b7da5bb95bf48e7fd9a7e688dedfe2168345b203e917a3d7a9aeb6caa9e
-EBUILD gromacs-2019.9999.ebuild 9175 BLAKE2B 2e26ad73b84fd5d8cce499dc77fa51122f08c6214778f327b142fce6c0790ddf68d624b264ac3b9d8c808951fbc2b9db199402a2a9c29865995df5b8a25112f1 SHA512 ab70cbfd71b180571721de010804cc53241f1888c1845ce11c6b53486a051306dfaa7b7da5bb95bf48e7fd9a7e688dedfe2168345b203e917a3d7a9aeb6caa9e
-EBUILD gromacs-9999.ebuild 8094 BLAKE2B 932061da2ed5e2e20d1ca0c1ef9000fd946bbe3720cea6d585863e4bf2d7821b7e7b934d4d33d20a4c6040865c58c61c11f5bc8ce98812ad4f946a95b1c1fb83 SHA512 e3987a36622751c20e6a5b3fa88d43c94e24a30cd513eb2e9f9375457413c9ad131ec3f3012ec94e7574d50233c00d9edd357a44413ac0873edb88df82487ba0
+DIST regressiontests-2019.4.tar.gz 67639728 BLAKE2B aba912863669a4a6a6a74e385f9b0974d0c0aa30d3aea7834d77c8bb3f4f59effcbe10a480e74e7aa31fe32d64ba6628d67703ca1894839ce7ddfc8da93902dc SHA512 45de03d368da4e6e5c647f3fea61d64defe6d1cbc1c4219eeac2db27559e3cea7f15f9acb3e56ab934b44ca3ae4ce199b4e4969f704776bb9f0b23f1a34ff56d
+EBUILD gromacs-2018.7.ebuild 7852 BLAKE2B 3c9625b06e391e1a28e804ccc9eb196cfd6adc14144867947f7a98052709cc1c400887383d164bfb1d558cf77447ca28924598e2d9b3222d00ca9930d80a2a3e SHA512 63e58f86c5ba37f5e7b52db46f7c665e77686a7f4722807658f7552fbd1f2b5f4555b2a273f9a1a74ef27966462d89a9357ab57821d3e049ff8d4dc565c9f8c8
+EBUILD gromacs-2018.8.ebuild 8787 BLAKE2B 9edbb2ae0bd3f76af41cee9971b70fdc957f22bb61ec131abd3cf44a2da56c208b0b103f72754e17cccfa054d79c1e95a9477228b0c14f4476e58bd7656b641a SHA512 c4548c8436dadf1daaf7f4f41e3c957029a10f5eb7fd11c5c8f42046d2ba38c6baf9f47e69fb8e8eeef550e0463d76bf738d6f708ffce6b4cf556e29d725ed5a
+EBUILD gromacs-2018.9999.ebuild 8787 BLAKE2B 9edbb2ae0bd3f76af41cee9971b70fdc957f22bb61ec131abd3cf44a2da56c208b0b103f72754e17cccfa054d79c1e95a9477228b0c14f4476e58bd7656b641a SHA512 c4548c8436dadf1daaf7f4f41e3c957029a10f5eb7fd11c5c8f42046d2ba38c6baf9f47e69fb8e8eeef550e0463d76bf738d6f708ffce6b4cf556e29d725ed5a
+EBUILD gromacs-2019.2.ebuild 9200 BLAKE2B d4c6bbca2dfc3d376d3c98893a273d405735a2b10ea7034622a56beb544a9c0af494e7aac71d477c4800b2d45bfea0cbae3cd8ba764ebf3f463aa0b2d613b7e4 SHA512 60170844324d3542ee5043a6ac624e9eb6838a15a16fe58e65b5f3df12a74fe1bc383c505217b2fe85183c0eb7a1b421c21e1574329a9e84bb9b86159ad90e5d
+EBUILD gromacs-2019.3.ebuild 9229 BLAKE2B 6c7f24dd45eb3d576d069b153f2af1b69eee620e7cbee9157daec43d52b32bdfc9944f9177126b8660df94191bba4191f21181862390751f955b7ba84784b26a SHA512 a32bebd21d3492b5ef30d9440e269b07c2e08010c0ae7eb83f03ebc8316efcd00c7a7b652a107fa1374673d715d3fd930848686396f128425eeeac78f19e2c22
+EBUILD gromacs-2019.4.ebuild 9234 BLAKE2B 076a2a9ff537342156ca94f138c738fbff5a0b8167b7cd34ebab388357acc2f08249675428d19b13abe4d8489aaf94afb69fb32bba1cf7658550a984319dcb30 SHA512 da0007f5e8162efd53b061a564908167f8388c4cf4288d56167e0ab313140d92641d51f1c7384d52a55998de8baf23eaf56a04d633cd20525fbc0e2c46ba4256
+EBUILD gromacs-2019.9999.ebuild 9234 BLAKE2B 076a2a9ff537342156ca94f138c738fbff5a0b8167b7cd34ebab388357acc2f08249675428d19b13abe4d8489aaf94afb69fb32bba1cf7658550a984319dcb30 SHA512 da0007f5e8162efd53b061a564908167f8388c4cf4288d56167e0ab313140d92641d51f1c7384d52a55998de8baf23eaf56a04d633cd20525fbc0e2c46ba4256
+EBUILD gromacs-9999.ebuild 8122 BLAKE2B 657e68df7563277a327984be5e23597d80b99cb3eac54c1f07037063ca1b2b7838cb07e00d4c4d41ef65f9bee622c7bba4527dea3d2792bb20b3969b8f5ea546 SHA512 97f5850567b25ca0bd11fc57331770a8d93383299d50b216e2089cd89d23b6618aad8a532d81da9f0d5cf19fc4a315c9f648e5c1dbbc5351fecb1255a02922f6
 MISC metadata.xml 1123 BLAKE2B 5e945fdf580821b62aaf40c5b4b3252b366284f2df16f02e7c3cf913e5ad498a6a8548bc2e4275d8b80373f88d9879ab59d401e619595014262dcebfe8660f9f SHA512 bac0c94aee957487d8af8a1e06323cb286c8773cef2070d91aff9fdad63eb1bd55f2678dd58dca21b33d8d3e7110d2526e280abd538e3653aee638f6de72090d
diff --git a/sci-chemistry/gromacs/gromacs-2018.7.ebuild b/sci-chemistry/gromacs/gromacs-2018.7.ebuild
index fd73db9a9811..8e5e3827188b 100644
--- a/sci-chemistry/gromacs/gromacs-2018.7.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2018.7.ebuild
@@ -65,6 +65,8 @@ REQUIRED_USE="
 
 DOCS=( AUTHORS README )
 
+RESTRICT="!test? ( test )"
+
 if [[ ${PV} != *9999 ]]; then
 	S="${WORKDIR}/${PN}-${PV/_/-}"
 fi
diff --git a/sci-chemistry/gromacs/gromacs-2018.3.ebuild b/sci-chemistry/gromacs/gromacs-2018.8.ebuild
index fd73db9a9811..4db9e9672b08 100644
--- a/sci-chemistry/gromacs/gromacs-2018.3.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2018.8.ebuild
@@ -1,7 +1,7 @@
 # Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
@@ -17,7 +17,7 @@ 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"
@@ -47,7 +47,7 @@ CDEPEND="
 	mkl? ( sci-libs/mkl )
 	mpi? ( virtual/mpi )
 	"
-DEPEND="${CDEPEND}
+BDEPEND="${CDEPEND}
 	virtual/pkgconfig
 	doc? (
 		app-doc/doxygen
@@ -65,6 +65,8 @@ REQUIRED_USE="
 
 DOCS=( AUTHORS README )
 
+RESTRICT="!test? ( test )"
+
 if [[ ${PV} != *9999 ]]; then
 	S="${WORKDIR}/${PN}-${PV/_/-}"
 fi
@@ -111,6 +113,27 @@ src_prepare() {
 	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() {
@@ -194,11 +217,13 @@ src_configure() {
 		mycmakeargs=(
 			${mycmakeargs_pre[@]} ${p}
 			-DGMX_THREAD_MPI=OFF
-			-DGMX_MPI=ON ${cuda}
+			-DGMX_MPI=ON
 			-DGMX_OPENMM=OFF
 			-DGMX_BUILD_MDRUN_ONLY=ON
 			-DBUILD_SHARED_LIBS=OFF
 			-DGMX_BUILD_MANUAL=OFF
+			"${opencl[@]}"
+			"${cuda[@]}"
 			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
 			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
 			)
@@ -249,14 +274,14 @@ src_install() {
 		doins src/external/tng_io/include/tng/*h
 	fi
 	# drop unneeded stuff
-	rm "${ED}"usr/bin/GMXRC* || die
-	for x in "${ED}"usr/bin/gmx-completion-*.bash ; do
+	rm "${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}/${n}" || die
+		cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
 		newbashcomp "${T}"/"${n}" "${n}"
 	done
-	rm "${ED}"usr/bin/gmx-completion*.bash || die
+	rm "${ED}"/usr/bin/gmx-completion*.bash || die
 	readme.gentoo_create_doc
 }
 
diff --git a/sci-chemistry/gromacs/gromacs-2018.9999.ebuild b/sci-chemistry/gromacs/gromacs-2018.9999.ebuild
index 0c57c8b32c12..4db9e9672b08 100644
--- a/sci-chemistry/gromacs/gromacs-2018.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2018.9999.ebuild
@@ -1,7 +1,7 @@
 # Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
@@ -47,7 +47,7 @@ CDEPEND="
 	mkl? ( sci-libs/mkl )
 	mpi? ( virtual/mpi )
 	"
-DEPEND="${CDEPEND}
+BDEPEND="${CDEPEND}
 	virtual/pkgconfig
 	doc? (
 		app-doc/doxygen
@@ -65,6 +65,8 @@ REQUIRED_USE="
 
 DOCS=( AUTHORS README )
 
+RESTRICT="!test? ( test )"
+
 if [[ ${PV} != *9999 ]]; then
 	S="${WORKDIR}/${PN}-${PV/_/-}"
 fi
@@ -111,6 +113,27 @@ src_prepare() {
 	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() {
@@ -194,11 +217,13 @@ src_configure() {
 		mycmakeargs=(
 			${mycmakeargs_pre[@]} ${p}
 			-DGMX_THREAD_MPI=OFF
-			-DGMX_MPI=ON ${cuda}
+			-DGMX_MPI=ON
 			-DGMX_OPENMM=OFF
 			-DGMX_BUILD_MDRUN_ONLY=ON
 			-DBUILD_SHARED_LIBS=OFF
 			-DGMX_BUILD_MANUAL=OFF
+			"${opencl[@]}"
+			"${cuda[@]}"
 			-DGMX_BINARY_SUFFIX="_mpi${suffix}"
 			-DGMX_LIBS_SUFFIX="_mpi${suffix}"
 			)
@@ -249,14 +274,14 @@ src_install() {
 		doins src/external/tng_io/include/tng/*h
 	fi
 	# drop unneeded stuff
-	rm "${ED}"usr/bin/GMXRC* || die
-	for x in "${ED}"usr/bin/gmx-completion-*.bash ; do
+	rm "${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}/${n}" || die
+		cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
 		newbashcomp "${T}"/"${n}" "${n}"
 	done
-	rm "${ED}"usr/bin/gmx-completion*.bash || die
+	rm "${ED}"/usr/bin/gmx-completion*.bash || die
 	readme.gentoo_create_doc
 }
 
diff --git a/sci-chemistry/gromacs/gromacs-2019.2.ebuild b/sci-chemistry/gromacs/gromacs-2019.2.ebuild
index 1e54e37089df..58d733d2c332 100644
--- a/sci-chemistry/gromacs/gromacs-2019.2.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2019.2.ebuild
@@ -73,6 +73,8 @@ REQUIRED_USE="
 
 DOCS=( AUTHORS README )
 
+RESTRICT="!test? ( test )"
+
 if [[ ${PV} != *9999 ]]; then
 	S="${WORKDIR}/${PN}-${PV/_/-}"
 fi
diff --git a/sci-chemistry/gromacs/gromacs-2019.3.ebuild b/sci-chemistry/gromacs/gromacs-2019.3.ebuild
index f91506d7e52c..5254b1f3f38b 100644
--- a/sci-chemistry/gromacs/gromacs-2019.3.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2019.3.ebuild
@@ -73,6 +73,8 @@ REQUIRED_USE="
 
 DOCS=( AUTHORS README )
 
+RESTRICT="!test? ( test )"
+
 if [[ ${PV} != *9999 ]]; then
 	S="${WORKDIR}/${PN}-${PV/_/-}"
 fi
@@ -233,9 +235,11 @@ src_configure() {
 		mycmakeargs=(
 			${mycmakeargs_pre[@]} ${p}
 			-DGMX_THREAD_MPI=OFF
-			-DGMX_MPI=ON ${cuda}
+			-DGMX_MPI=ON
 			-DGMX_OPENMM=OFF
 			-DGMXAPI=OFF
+			"${opencl[@]}"
+			"${cuda[@]}"
 			-DGMX_BUILD_MDRUN_ONLY=ON
 			-DBUILD_SHARED_LIBS=OFF
 			-DGMX_BUILD_MANUAL=OFF
diff --git a/sci-chemistry/gromacs/gromacs-2019.4.ebuild b/sci-chemistry/gromacs/gromacs-2019.4.ebuild
new file mode 100644
index 000000000000..a08d3ecc9027
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-2019.4.ebuild
@@ -0,0 +1,314 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+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 )
+	${PYTHON_DEPS}
+	"
+BDEPEND="${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[@]} ${p}
+			-DGMX_THREAD_MPI=OFF
+			-DGMX_MPI=ON
+			-DGMX_OPENMM=OFF
+			-DGMXAPI=OFF
+			"${opencl[@]}"
+			"${cuda[@]}"
+			-DGMX_BUILD_MDRUN_ONLY=ON
+			-DBUILD_SHARED_LIBS=OFF
+			-DGMX_BUILD_MANUAL=OFF
+			-DGMX_BINARY_SUFFIX="_mpi${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-2019.9999.ebuild b/sci-chemistry/gromacs/gromacs-2019.9999.ebuild
index f91506d7e52c..a08d3ecc9027 100644
--- a/sci-chemistry/gromacs/gromacs-2019.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2019.9999.ebuild
@@ -1,7 +1,7 @@
 # Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
@@ -51,7 +51,7 @@ CDEPEND="
 	mpi? ( virtual/mpi )
 	${PYTHON_DEPS}
 	"
-DEPEND="${CDEPEND}
+BDEPEND="${CDEPEND}
 	virtual/pkgconfig
 	doc? (
 		app-doc/doxygen
@@ -73,6 +73,8 @@ REQUIRED_USE="
 
 DOCS=( AUTHORS README )
 
+RESTRICT="!test? ( test )"
+
 if [[ ${PV} != *9999 ]]; then
 	S="${WORKDIR}/${PN}-${PV/_/-}"
 fi
@@ -233,9 +235,11 @@ src_configure() {
 		mycmakeargs=(
 			${mycmakeargs_pre[@]} ${p}
 			-DGMX_THREAD_MPI=OFF
-			-DGMX_MPI=ON ${cuda}
+			-DGMX_MPI=ON
 			-DGMX_OPENMM=OFF
 			-DGMXAPI=OFF
+			"${opencl[@]}"
+			"${cuda[@]}"
 			-DGMX_BUILD_MDRUN_ONLY=ON
 			-DBUILD_SHARED_LIBS=OFF
 			-DGMX_BUILD_MANUAL=OFF
@@ -289,14 +293,14 @@ src_install() {
 		doins src/external/tng_io/include/tng/*h
 	fi
 	# drop unneeded stuff
-	rm "${ED}"usr/bin/GMXRC* || die
-	for x in "${ED}"usr/bin/gmx-completion-*.bash ; do
+	rm "${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}/${n}" || die
+		cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
 		newbashcomp "${T}"/"${n}" "${n}"
 	done
-	rm "${ED}"usr/bin/gmx-completion*.bash || die
+	rm "${ED}"/usr/bin/gmx-completion*.bash || die
 	readme.gentoo_create_doc
 }
 
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 1fcf6ea17036..f9d980d7c0f3 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -68,6 +68,8 @@ REQUIRED_USE="
 
 DOCS=( AUTHORS README )
 
+RESTRICT="!test? ( test )"
+
 if [[ ${PV} != *9999 ]]; then
 	S="${WORKDIR}/${PN}-${PV/_/-}"
 fi