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-rw-r--r--sci-chemistry/Manifest.gzbin16708 -> 16538 bytes
-rw-r--r--sci-chemistry/burrow-owl/Manifest4
-rw-r--r--sci-chemistry/burrow-owl/burrow-owl-1.5.1.ebuild52
-rw-r--r--sci-chemistry/burrow-owl/metadata.xml11
-rw-r--r--sci-chemistry/gromacs/Manifest21
-rw-r--r--sci-chemistry/gromacs/gromacs-2018.7.ebuild2
-rw-r--r--sci-chemistry/gromacs/gromacs-2018.8.ebuild (renamed from sci-chemistry/gromacs/gromacs-2018.3.ebuild)41
-rw-r--r--sci-chemistry/gromacs/gromacs-2018.9999.ebuild39
-rw-r--r--sci-chemistry/gromacs/gromacs-2019.2.ebuild2
-rw-r--r--sci-chemistry/gromacs/gromacs-2019.3.ebuild6
-rw-r--r--sci-chemistry/gromacs/gromacs-2019.4.ebuild314
-rw-r--r--sci-chemistry/gromacs/gromacs-2019.9999.ebuild18
-rw-r--r--sci-chemistry/gromacs/gromacs-9999.ebuild2
-rw-r--r--sci-chemistry/openbabel/Manifest2
-rw-r--r--sci-chemistry/openbabel/openbabel-2.4.1-r1.ebuild101
15 files changed, 516 insertions, 99 deletions
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index c86c09617321..8e321f13b21e 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
Binary files differ
diff --git a/sci-chemistry/burrow-owl/Manifest b/sci-chemistry/burrow-owl/Manifest
deleted file mode 100644
index 6bf7bff9543f..000000000000
--- a/sci-chemistry/burrow-owl/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST burrow-demos.tar 80896000 BLAKE2B cafd01273887a30f3dadd3e0aba9b5dab22f865a2470ce779e8b94a1cd43ec34f3bea5d0909b3f106b97735c5abf3c0237490f0ecae0da2a0f81443dcc64c06a SHA512 76948846b4bff2f5c0814e41ee1745122580d6e28f8de217edbf42c4530bc64fb093dc9c96e9c0c083098755c525300b563ee1368caa12be791b2bea7015ee6b
-DIST burrow-owl-1.5.1.tar.gz 1408249 BLAKE2B 5e4581f6f1726a885d2f226e661d228353e2988e61c833a9c8c63988a2f6e26ee481dbfe630dfa3ab3d8ccdb225cb134716a6bcabe14b1b36041f8ae5fc22bf9 SHA512 38b428c8b40cdca6caabc7ed9d247118dbf67b537afaec3af14909353d6b138fdf98a33dee6241ce5224631e16c4dbce11b9aadcfe01fecf92f1aae692ce71e1
-EBUILD burrow-owl-1.5.1.ebuild 1129 BLAKE2B cd6f38b57f44182f999574fb0f010b77dd3f67c605580a0739b58ac7313b8dbcceeeca6bf4f41d35b30c07d3d72ac092f66838126c1d2c5c8d4648b0c72bf714 SHA512 e91387bd3edaf679d6e1cadac56433f6384d1cad657d1bc1ab11775f5c00cd3fcc988764915eddcbdb07b3c0b1042e8f9267f045e10cf57222ca6991e2aae28b
-MISC metadata.xml 355 BLAKE2B ebfa31389177ac700a1102dac8523b5387912b27f7d9ded0665ab22bb72aab80fda8769220954877789dd0bb173c03dc87af89c4acf765040de855e0d211157c SHA512 1bba5ea159834c137bdc08622bbd89cf895acde6b8ebce0cee6f6b5f2b754b9a5b0b01ccfb89bf6b4b03ec75925c017716773c0fc4807964c38ddad0dce79f50
diff --git a/sci-chemistry/burrow-owl/burrow-owl-1.5.1.ebuild b/sci-chemistry/burrow-owl/burrow-owl-1.5.1.ebuild
deleted file mode 100644
index 106ba29bba2e..000000000000
--- a/sci-chemistry/burrow-owl/burrow-owl-1.5.1.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools-utils virtualx
-
-DESCRIPTION="Visualize multidimensional nuclear magnetic resonance (NMR) spectra"
-HOMEPAGE="http://burrow-owl.sourceforge.net/"
-SRC_URI="
- mirror://sourceforge/${PN}/${P}.tar.gz
- examples? ( mirror://sourceforge/${PN}/burrow-demos.tar )"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc examples static-libs"
-
-RDEPEND="
- dev-libs/g-wrap
- dev-libs/glib:2
- dev-scheme/guile[networking,regex]
- dev-scheme/guile-cairo
- dev-scheme/guile-gnome-platform
- sci-libs/starparse
- x11-libs/gtk+:2"
-DEPEND="${RDEPEND}
- dev-util/indent
- virtual/pkgconfig
- doc? ( app-doc/doxygen )
-"
-
-src_configure() {
- local myeconfargs=(
- $(use_with doc doxygen doxygen)
- )
- autotools-utils_src_configure
-}
-
-src_test () {
- cd "${AUTOTOOLS_BUILD_DIR}" || die
- virtualmake -C test-suite check
-}
-
-src_install() {
- use doc && HTML_DOCS=( "${AUTOTOOLS_BUILD_DIR}/doc/api/html/." )
- autotools-utils_src_install
-
- use examples && \
- insinto /usr/share/${PN} && \
- doins -r "${WORKDIR}"/burrow-demos/*
-}
diff --git a/sci-chemistry/burrow-owl/metadata.xml b/sci-chemistry/burrow-owl/metadata.xml
deleted file mode 100644
index 776713a5da1a..000000000000
--- a/sci-chemistry/burrow-owl/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?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>
- <upstream>
- <remote-id type="sourceforge">burrow-owl</remote-id>
- </upstream>
-</pkgmetadata>
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
diff --git a/sci-chemistry/openbabel/Manifest b/sci-chemistry/openbabel/Manifest
index 4e551dea6d29..f7fb369c0129 100644
--- a/sci-chemistry/openbabel/Manifest
+++ b/sci-chemistry/openbabel/Manifest
@@ -1,5 +1,7 @@
AUX openbabel-2.3.2-gcc-6_and_7-backport.patch 635 BLAKE2B 4e98dedd149b14d5bb02fb6d2fa03e07242d100c7b41f36f749ff3d587080eeca44aa26ca095d31e0309e45f3780b67deaa97f1177ed35a9b7407bd7c33f78ff SHA512 e1b4402f34d01ced5b4caaa184b4e5544cf47893cfe7958054052b05a57dc34b4d44239a212c7d909f29b9366b83b6df74993f844a20f23748c01272ec093081
AUX openbabel-2.4.1-gcc-8.patch 706 BLAKE2B 085b2f5a1678c02a6a8efc5f760dc43ef311774a47d80c87efb75111ac750ec6bf520286fa74325eca71138eecff4b2772ab087d4de1b9b9a5f1c81806d6be87 SHA512 04884d47a9549d2c107bbeb9c36edbe18ee68a7edd447fce405f39a4297bdacf3f81ddf4c5c19e9728355f07960b836e684087573b3a2b7892225de8b7beaea1
DIST openbabel-2.4.1.tar.gz 11618304 BLAKE2B 8fc051e83add9be6456e281a109bd6bbec282a64ffc83309819f0decbf167b4914fbb7f1966e95e103f268754045b804317f51c79a952ace707c6af2bd320125 SHA512 427e678f0a911bd27b9a8a05e60b6e09f113be4e5dd180daaf80c28d06368e52b57501261755ab3817a8d31f2754db24471fd0ceee706d029386d6f70800e9c6
+DIST openbabel.png 29060 BLAKE2B 8d217d92125cc73462437411dd4e0cc05179cb0934f5ed15a307acc6b549b8ebab250a48a05ef7657f48c6df394f37da9b659de61efb1477b79b573a5b393ad3 SHA512 bbcaaa37663b526c9038ccb9edaf05ccc3ad1a861739a737f05f363098d8402a10b36e341fcc0aca636e809c6c32db99bf987b41719a0c756bf5e31444d3eb70
+EBUILD openbabel-2.4.1-r1.ebuild 2181 BLAKE2B dab9ccf7576cc1b24eb6d7566f487b4f6d6711797cb6b15800d120f2226d3fa19977908bcae3535177fb7f938365673518266bae2f3eb4eb0cbc48c6850af7d0 SHA512 4d0783e28d81d0c8f61dcf9f4d8f8acc835de48d3d7299d555ef939bd447d120c722aab97efd1981e0148485e80956632119eeb07ca6d67328a9435ce81b86ac
EBUILD openbabel-2.4.1.ebuild 2013 BLAKE2B b7fe713786600ac7efc9b4541663b8049c0145863cd6efc397dbed8a858cb006746e8ae6ddb4b9148023d5bf3a7f1cca76a4327577a5f9809c8e17d5a4f78945 SHA512 2eddc590968cb39a8c87563eb724669742b795bbf1861d85d9892e87fa9137b989f36ba435f98fe1b8151a142aa73a73df49ab5ef5ad1617e2d3875ad655ee1e
MISC metadata.xml 665 BLAKE2B 4657b85c826c006b6d69e06240dd908a72397a32cb0c0512810e22d1b02478eaa3ab460535b300eba653a334a79c81a102007da1a901d6d1dbd04fc5e795df73 SHA512 0555e7c7401dfd5fbeee339302f8eb7a104ad6538db2839d8e89c20ac5ad2184070335677671a58eb91be2780ae485467d33302f3a14d0caab4ae8c0148f03bb
diff --git a/sci-chemistry/openbabel/openbabel-2.4.1-r1.ebuild b/sci-chemistry/openbabel/openbabel-2.4.1-r1.ebuild
new file mode 100644
index 000000000000..0834c411ef29
--- /dev/null
+++ b/sci-chemistry/openbabel/openbabel-2.4.1-r1.ebuild
@@ -0,0 +1,101 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+WX_GTK_VER="3.0"
+
+inherit cmake-utils desktop eutils wxwidgets
+
+DESCRIPTION="Interconverts file formats used in molecular modeling"
+HOMEPAGE="http://openbabel.org/wiki/Main_Page"
+SRC_URI="
+ mirror://sourceforge/openbabel/${P}.tar.gz
+ https://openbabel.org/docs/dev/_static/babel130.png -> ${PN}.png
+"
+
+# See src/CMakeLists.txt for LIBRARY_VERSION
+SLOT="0/5.0.0"
+LICENSE="GPL-2"
+KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+IUSE="doc openmp test wxwidgets"
+
+RDEPEND="
+ dev-cpp/eigen:3
+ dev-libs/libxml2:2
+ sci-libs/inchi
+ sys-libs/zlib
+ wxwidgets? ( x11-libs/wxGTK:${WX_GTK_VER}[X] )
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ >=dev-util/cmake-2.4.8
+ doc? ( app-doc/doxygen )
+"
+
+DOCS=( AUTHORS NEWS.md README.md THANKS doc/dioxin.{inc,mol2} doc/README.{dioxin.pov,povray} )
+
+PATCHES=(
+ "${FILESDIR}"/${PN}-2.3.2-gcc-6_and_7-backport.patch
+ "${FILESDIR}"/${P}-gcc-8.patch
+)
+
+pkg_setup() {
+ if use openmp; then
+ if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp; then
+ ewarn "OpenMP is not available in your current selected gcc"
+ die "need openmp capable gcc"
+ fi
+ FORTRAN_NEED_OPENMP=1
+ fi
+}
+
+src_prepare() {
+ sed \
+ -e '/__GNUC__/s:== 4:>= 4:g' \
+ -i include/openbabel/shared_ptr.h || die
+ cmake-utils_src_prepare
+}
+
+src_configure() {
+ use wxwidgets && setup-wxwidgets
+ local mycmakeargs=(
+ -DOPENBABEL_USE_SYSTEM_INCHI=ON
+ -DENABLE_OPENMP=$(usex openmp)
+ -DBUILD_GUI=$(usex wxwidgets)
+ )
+
+ cmake-utils_src_configure
+}
+
+src_install() {
+ docinto html
+ dodoc doc/{*.html,*.png}
+ if use doc ; then
+ docinto html/API
+ dodoc -r doc/API/html/*
+ fi
+
+ make_desktop_entry obgui "Open Babel" "${PN}"
+ doicon "${DISTDIR}/${PN}.png"
+
+ 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
+}
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-07 22:54:51 +0000