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commit: 730740b74ec2c133b225870c4f6ee620b3f3dab5 |
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Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
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AuthorDate: Thu Jan 2 20:21:16 2020 +0000 |
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Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> |
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CommitDate: Thu Jan 2 20:21:16 2020 +0000 |
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URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=730740b7 |
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|
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sci-chemistry/gromacs: Version bump |
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|
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Package-Manager: Portage-2.3.83, Repoman-2.3.20 |
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Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org> |
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|
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sci-chemistry/gromacs/Manifest | 4 +- |
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...cs-2020_rc1.ebuild => gromacs-2020.9999.ebuild} | 2 +- |
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...gromacs-2020_rc1.ebuild => gromacs-2020.ebuild} | 2 +- |
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sci-chemistry/gromacs/gromacs-9999.ebuild | 75 ++++++++++++++++++---- |
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4 files changed, 67 insertions(+), 16 deletions(-) |
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|
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diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest |
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index 867bba59978..68cba940949 100644 |
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--- a/sci-chemistry/gromacs/Manifest |
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+++ b/sci-chemistry/gromacs/Manifest |
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@@ -1,8 +1,8 @@ |
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DIST gromacs-2018.8.tar.gz 29913703 BLAKE2B 8780032305928067fbfe1559efe9eedc4d47e27ab2f6ab54d6dba39edfcbeefbee4673d8910009048a850620b5a08ba8feb622db652c439cfa50a149ec5f0015 SHA512 6717895942f2ab7b54019511ed2aebadadde8e96d3c4b7414bb9168ffe418432d2dee330192e199f7b9d2f665c71f5d4f1ef0911aa7243d525a2ca182ef5b122 |
| 25 |
DIST gromacs-2019.2.tar.gz 33437869 BLAKE2B bebe4942688dace148856d4491b687b8e0fd2c86d7fbd9eecdb46824d316a0fc3854464ecafa79d8db92327ee8467be204b050c11f1e71132184efd812c3bf09 SHA512 da7ff24e8485774e22d1c2464fbe64675c3305ef0e21a3d17e363201031952e5d4a9b81f572d5284fb6f2596ed99daf62fe78d653387d9d714274f46bc750183 |
| 26 |
DIST gromacs-2019.5.tar.gz 33445791 BLAKE2B 1e2e2764b0c8774c878abf4f32c2fa7ddd9b46f464cf1256deb48335433d92ef1b315f5534cdec9f766ae928a71361b5a4dd4a4def638269eb260ff98dbbe8bb SHA512 fdd177e4dfd29629b72bfbb4d61ff7bcdb37279f534883a9df8fd57569212fe1e9f8b8c9cec347fcc607539f31412d604d11ee3c0eb797251960435962b1bec6 |
| 27 |
-DIST gromacs-2020-rc1.tar.gz 29077110 BLAKE2B 5d5e6e63bd6b4dd03b688913b2da923547daddb270bca1a7d6ab8e625c26fb1031eea65330bd2e772f958e72e5a096c662633fbc71e7ee32ad83d99dcfb09170 SHA512 9dac945c5de9be2dc79bdde4d5f4afa3f2818334437ef8b4d1c57e46bdb80a0623ed7b16e1a8100395820b7eec367ea14195d420d3564f0f4eef0c88c52e78f9 |
| 28 |
+DIST gromacs-2020.tar.gz 28928068 BLAKE2B 72d4ff8f6b383284e61df9d3b2b53c51300f6961d4c19810670c8ee9ba2f1864d2a325e2774093b9338db785cb91a94461bf93f16cdf4caf0f690298a672d51c SHA512 15f0d58cd8d217eab39ef8e3535dec34127708797eaf6575fb340292cbee2303cd25deb84b3d4417a787076f4ae7be9e4958ec3a347a3aa9aed52ef337a4587c |
| 29 |
DIST regressiontests-2018.8.tar.gz 67855469 BLAKE2B 34c9b339f6229f483afbb5192ee6ba8b8f72d5c26907a853af9c53dfece0d88739e48f6b44b78d1c010f988f9385d077285300522164f533a5861e9dda879275 SHA512 3642389d27bd1942cd0f091c940ae97b197b94856a387fe581dc516b0d4169480f16551d4ba357f9282b3337d605c286d51dd38112ac87c826dda634904836bb |
| 30 |
DIST regressiontests-2019.2.tar.gz 67643003 BLAKE2B 4178de5d62f194a81f97e442c10f123dc59c5e63f2078f7f07135709f3f6e530e0d237bf40264b285c084519d5ace75dfcbcddc16dc740c4f17233dc33542e45 SHA512 c1f25bc770d3f0a873c887d5563c1cd88179e81211b70ce6f5015696e6fa0b6931a8da7a449f2b223f3105b9e2e7eca67248e96fbfc2a7fd5fb360ba616f22ff |
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DIST regressiontests-2019.5.tar.gz 67643634 BLAKE2B c4d9535d9a8a650869d67544ad5f367324f45e55325bb5074ece9b010f232f2f0dd97c9af97924d3f2368ed63015ca7330baff1cc681310e1439ec330b70ee8d SHA512 7c0917b76e7db35ab4e3271d523d268e0e2d858091e68ead863bfe6d1e56b381e30fdbf44f479f6e065c029e2eb27cfa0dbaa1b243f185144321aaf5084c55ce |
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-DIST regressiontests-2020-rc1.tar.gz 48537816 BLAKE2B f9f4cde7a29691459d36e5f3fac91e75f4ebc6d95302c760722f4731a63a5e0695c8bc5106d38bb7b7266f6bac19bcb988496b572dca3f500f6c323c72615c60 SHA512 fb082479a3f3e03aaac4653682680ba8409f42a47f6e64e2a67e497467fce28e013b4fed8f9d3a1ce2db52237eb0e92e6e5c8de9be33beb7324d855de20b6ec7 |
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+DIST regressiontests-2020.tar.gz 48536146 BLAKE2B 9511db78b5d6a5ea431fdb73782f28dde4b94655139886c0ad519888ef3e435fe81807f158d66c1a4284cb88fe730f62d039ac23549f17d0ce5984764ef35f10 SHA512 5a35aaf6fe2f3b146c7045e9c967dc1c8bf754748cc1f2a7300193ae3f206a9f5058329380ae7b03b181410303bcd434584571e6161a75f99e52bd48f8ba1821 |
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|
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diff --git a/sci-chemistry/gromacs/gromacs-2020_rc1.ebuild b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild |
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similarity index 99% |
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copy from sci-chemistry/gromacs/gromacs-2020_rc1.ebuild |
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copy to sci-chemistry/gromacs/gromacs-2020.9999.ebuild |
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index 162d64c983f..859628fa107 100644 |
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--- a/sci-chemistry/gromacs/gromacs-2020_rc1.ebuild |
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+++ b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild |
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@@ -1,4 +1,4 @@ |
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-# Copyright 1999-2019 Gentoo Authors |
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+# Copyright 1999-2020 Gentoo Authors |
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# Distributed under the terms of the GNU General Public License v2 |
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|
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EAPI=7 |
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|
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diff --git a/sci-chemistry/gromacs/gromacs-2020_rc1.ebuild b/sci-chemistry/gromacs/gromacs-2020.ebuild |
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similarity index 99% |
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rename from sci-chemistry/gromacs/gromacs-2020_rc1.ebuild |
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rename to sci-chemistry/gromacs/gromacs-2020.ebuild |
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index 162d64c983f..859628fa107 100644 |
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--- a/sci-chemistry/gromacs/gromacs-2020_rc1.ebuild |
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+++ b/sci-chemistry/gromacs/gromacs-2020.ebuild |
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@@ -1,4 +1,4 @@ |
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-# Copyright 1999-2019 Gentoo Authors |
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+# Copyright 1999-2020 Gentoo Authors |
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# Distributed under the terms of the GNU General Public License v2 |
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|
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EAPI=7 |
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|
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diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild |
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index f9d980d7c0f..859628fa107 100644 |
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--- a/sci-chemistry/gromacs/gromacs-9999.ebuild |
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+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild |
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@@ -1,11 +1,15 @@ |
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-# Copyright 1999-2019 Gentoo Authors |
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+# Copyright 1999-2020 Gentoo Authors |
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# Distributed under the terms of the GNU General Public License v2 |
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|
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-EAPI=6 |
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+EAPI=7 |
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|
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CMAKE_MAKEFILE_GENERATOR="ninja" |
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|
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-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils |
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+PYTHON_COMPAT=( python3_{5,6,7} ) |
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+ |
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+DISTUTILS_SINGLE_IMPL=1 |
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+ |
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+inherit bash-completion-r1 cmake-utils cuda distutils-r1 eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils |
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|
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if [[ $PV = *9999* ]]; then |
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EGIT_REPO_URI="git://git.gromacs.org/gromacs.git |
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@@ -30,7 +34,7 @@ HOMEPAGE="http://www.gromacs.org/" |
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# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib |
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LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" |
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SLOT="0/${PV}" |
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-IUSE="X blas cuda +doc -double-precision +fftw +gmxapi +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +single-precision test +threads +tng ${ACCE_IUSE}" |
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+IUSE="X blas cuda +doc -double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" |
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|
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CDEPEND=" |
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X? ( |
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@@ -47,13 +51,16 @@ CDEPEND=" |
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lmfit? ( sci-libs/lmfit ) |
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mkl? ( sci-libs/mkl ) |
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mpi? ( virtual/mpi ) |
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+ ${PYTHON_DEPS} |
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+ !sci-chemistry/gmxapi |
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" |
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-DEPEND="${CDEPEND} |
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+BDEPEND="${CDEPEND} |
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virtual/pkgconfig |
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doc? ( |
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app-doc/doxygen |
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- dev-python/sphinx |
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+ dev-python/sphinx[${PYTHON_USEDEP}] |
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media-gfx/mscgen |
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+ media-gfx/graphviz |
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dev-texlive/texlive-latex |
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dev-texlive/texlive-latexextra |
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media-gfx/imagemagick |
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@@ -64,7 +71,8 @@ REQUIRED_USE=" |
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|| ( single-precision double-precision ) |
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cuda? ( single-precision ) |
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cuda? ( !opencl ) |
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- mkl? ( !blas !fftw !lapack )" |
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+ mkl? ( !blas !fftw !lapack ) |
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+ ${PYTHON_REQUIRED_USE}" |
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|
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DOCS=( AUTHORS README ) |
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|
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@@ -74,12 +82,18 @@ if [[ ${PV} != *9999 ]]; then |
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S="${WORKDIR}/${PN}-${PV/_/-}" |
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fi |
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|
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+PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" ) |
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+ |
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pkg_pretend() { |
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[[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" |
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use openmp && ! tc-has-openmp && \ |
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die "Please switch to an openmp compatible compiler" |
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} |
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|
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+pkg_setup() { |
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+ python-single-r1_pkg_setup |
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+} |
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+ |
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src_unpack() { |
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if [[ ${PV} != *9999 ]]; then |
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default |
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@@ -116,6 +130,28 @@ src_prepare() { |
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fi |
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|
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DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" |
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+ |
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+ # try to create policy for imagemagik |
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+ mkdir -p ${HOME}/.config/ImageMagick |
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+ cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF |
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+ <?xml version="1.0" encoding="UTF-8"?> |
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+ <!DOCTYPE policymap [ |
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+ <!ELEMENT policymap (policy)+> |
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+ !ATTLIST policymap xmlns CDATA #FIXED ''> |
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+ <!ELEMENT policy EMPTY> |
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+ <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED |
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+ name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED |
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+ stealth NMTOKEN #IMPLIED value CDATA #IMPLIED> |
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+ ]> |
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+ <policymap> |
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+ <policy domain="coder" rights="read | write" pattern="PS" /> |
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+ <policy domain="coder" rights="read | write" pattern="PS2" /> |
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+ <policy domain="coder" rights="read | write" pattern="PS3" /> |
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+ <policy domain="coder" rights="read | write" pattern="EPS" /> |
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+ <policy domain="coder" rights="read | write" pattern="PDF" /> |
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+ <policy domain="coder" rights="read | write" pattern="XPS" /> |
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+ </policymap> |
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+ EOF |
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} |
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|
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src_configure() { |
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@@ -172,6 +208,7 @@ src_configure() { |
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-DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" |
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-DBUILD_TESTING=$(usex test) |
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-DGMX_BUILD_UNITTESTS=$(usex test) |
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+ -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" |
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${extra} |
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) |
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|
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@@ -193,11 +230,13 @@ src_configure() { |
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-DGMX_MPI=OFF |
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-DGMX_THREAD_MPI=$(usex threads) |
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-DGMXAPI=$(usex gmxapi) |
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+ -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) |
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"${opencl[@]}" |
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"${cuda[@]}" |
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"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" |
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-DGMX_BINARY_SUFFIX="${suffix}" |
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-DGMX_LIBS_SUFFIX="${suffix}" |
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+ -DGMX_PYTHON_PACKAGE=$(usex python) |
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) |
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BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure |
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[[ ${CHOST} != *-darwin* ]] || \ |
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@@ -207,9 +246,11 @@ src_configure() { |
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mycmakeargs=( |
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${mycmakeargs_pre[@]} ${p} |
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-DGMX_THREAD_MPI=OFF |
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- -DGMX_MPI=ON ${cuda} |
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+ -DGMX_MPI=ON |
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-DGMX_OPENMM=OFF |
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-DGMXAPI=OFF |
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+ "${opencl[@]}" |
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+ "${cuda[@]}" |
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-DGMX_BUILD_MDRUN_ONLY=ON |
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-DBUILD_SHARED_LIBS=OFF |
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-DGMX_BUILD_MANUAL=OFF |
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@@ -227,6 +268,12 @@ src_compile() { |
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einfo "Compiling for ${x} precision" |
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BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
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cmake-utils_src_compile |
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+ if use python; then |
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+ BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
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+ cmake-utils_src_compile python_packaging/all |
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+ BUILD_DIR="${WORKDIR}/${P}" \ |
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+ distutils-r1_src_compile |
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+ fi |
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# not 100% necessary for rel ebuilds as available from website |
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if use doc; then |
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BUILD_DIR="${WORKDIR}/${P}_${x}"\ |
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@@ -250,6 +297,10 @@ src_install() { |
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for x in ${GMX_DIRS}; do |
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BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
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cmake-utils_src_install |
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+ if use python; then |
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+ BUILD_DIR="${WORKDIR}/${P}_${x}" \ |
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+ cmake-utils_src_install python_packaging/install |
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+ fi |
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if use doc; then |
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newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" |
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fi |
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@@ -263,14 +314,14 @@ src_install() { |
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doins src/external/tng_io/include/tng/*h |
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fi |
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# drop unneeded stuff |
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- rm "${ED}"usr/bin/GMXRC* || die |
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- for x in "${ED}"usr/bin/gmx-completion-*.bash ; do |
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+ rm "${ED}"/usr/bin/GMXRC* || die |
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+ for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do |
| 239 |
local n=${x##*/gmx-completion-} |
| 240 |
n="${n%.bash}" |
| 241 |
- cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
| 242 |
+ cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die |
| 243 |
newbashcomp "${T}"/"${n}" "${n}" |
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done |
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- rm "${ED}"usr/bin/gmx-completion*.bash || die |
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+ rm "${ED}"/usr/bin/gmx-completion*.bash || die |
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readme.gentoo_create_doc |
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} |
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