[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/gromacs/

["Alexey Shvetsov" <alexxy@gentoo.org>]

commit:     32a93a6cf9c5d508b67d7257c940234949e58eab
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Fri Oct  4 21:45:18 2019 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Fri Oct  4 21:45:41 2019 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=32a93a6c

sci-chemistry/gromacs: Version bump for 2018.x series

Package-Manager: Portage-2.3.76, Repoman-2.3.17
Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org>

 sci-chemistry/gromacs/Manifest                     |  2 ++
 ...macs-2018.9999.ebuild => gromacs-2018.8.ebuild} | 37 ++++++++++++++++++----
 sci-chemistry/gromacs/gromacs-2018.9999.ebuild     | 37 ++++++++++++++++++----
 3 files changed, 62 insertions(+), 14 deletions(-)

diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 43ad2677e51..a3e67a7d98a 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -1,8 +1,10 @@
 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 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
 DIST regressiontests-2019.4.tar.gz 67639728 BLAKE2B aba912863669a4a6a6a74e385f9b0974d0c0aa30d3aea7834d77c8bb3f4f59effcbe10a480e74e7aa31fe32d64ba6628d67703ca1894839ce7ddfc8da93902dc SHA512 45de03d368da4e6e5c647f3fea61d64defe6d1cbc1c4219eeac2db27559e3cea7f15f9acb3e56ab934b44ca3ae4ce199b4e4969f704776bb9f0b23f1a34ff56d

diff --git a/sci-chemistry/gromacs/gromacs-2018.9999.ebuild b/sci-chemistry/gromacs/gromacs-2018.8.ebuild
similarity index 86%
copy from sci-chemistry/gromacs/gromacs-2018.9999.ebuild
copy to sci-chemistry/gromacs/gromacs-2018.8.ebuild
index 0f1504ebd16..4db9e9672b0 100644
--- a/sci-chemistry/gromacs/gromacs-2018.9999.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"
 
@@ -47,7 +47,7 @@ CDEPEND="
 	mkl? ( sci-libs/mkl )
 	mpi? ( virtual/mpi )
 	"
-DEPEND="${CDEPEND}
+BDEPEND="${CDEPEND}
 	virtual/pkgconfig
 	doc? (
 		app-doc/doxygen
@@ -113,6 +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() {
@@ -196,11 +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${suffix}"
 			)
@@ -251,14 +274,14 @@ src_install() {
 		doins src/external/tng_io/include/tng/*h
 	fi
 	# drop unneeded stuff
-	rm "${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 0f1504ebd16..4db9e9672b0 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
@@ -113,6 +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() {
@@ -196,11 +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${suffix}"
 			)
@@ -251,14 +274,14 @@ src_install() {
 		doins src/external/tng_io/include/tng/*h
 	fi
 	# drop unneeded stuff
-	rm "${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
 }