From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id 0F495138334 for ; Thu, 2 Jan 2020 20:21:35 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 2C7CAE0A5D; Thu, 2 Jan 2020 20:21:34 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id E4BF2E0A5D for ; Thu, 2 Jan 2020 20:21:33 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 42FDF34DDEE for ; Thu, 2 Jan 2020 20:21:32 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 2536174 for ; Thu, 2 Jan 2020 20:21:30 +0000 (UTC) From: "Alexey Shvetsov" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Alexey Shvetsov" Message-ID: <1577996476.730740b74ec2c133b225870c4f6ee620b3f3dab5.alexxy@gentoo> Subject: [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/gromacs/ X-VCS-Repository: repo/gentoo X-VCS-Files: sci-chemistry/gromacs/Manifest sci-chemistry/gromacs/gromacs-2020.9999.ebuild sci-chemistry/gromacs/gromacs-2020.ebuild sci-chemistry/gromacs/gromacs-2020_rc1.ebuild sci-chemistry/gromacs/gromacs-9999.ebuild X-VCS-Directories: sci-chemistry/gromacs/ X-VCS-Committer: alexxy X-VCS-Committer-Name: Alexey Shvetsov X-VCS-Revision: 730740b74ec2c133b225870c4f6ee620b3f3dab5 X-VCS-Branch: master Date: Thu, 2 Jan 2020 20:21:30 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: dbbeb2c4-8903-46a3-bb27-895f6d8ee3cf X-Archives-Hash: 962e22ed6d65d9dd85d59c9366f8f611 commit: 730740b74ec2c133b225870c4f6ee620b3f3dab5 Author: Alexey Shvetsov gentoo org> AuthorDate: Thu Jan 2 20:21:16 2020 +0000 Commit: Alexey Shvetsov gentoo org> CommitDate: Thu Jan 2 20:21:16 2020 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=730740b7 sci-chemistry/gromacs: Version bump Package-Manager: Portage-2.3.83, Repoman-2.3.20 Signed-off-by: Alexey Shvetsov gentoo.org> sci-chemistry/gromacs/Manifest | 4 +- ...cs-2020_rc1.ebuild => gromacs-2020.9999.ebuild} | 2 +- ...gromacs-2020_rc1.ebuild => gromacs-2020.ebuild} | 2 +- sci-chemistry/gromacs/gromacs-9999.ebuild | 75 ++++++++++++++++++---- 4 files changed, 67 insertions(+), 16 deletions(-) diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index 867bba59978..68cba940949 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -1,8 +1,8 @@ DIST gromacs-2018.8.tar.gz 29913703 BLAKE2B 8780032305928067fbfe1559efe9eedc4d47e27ab2f6ab54d6dba39edfcbeefbee4673d8910009048a850620b5a08ba8feb622db652c439cfa50a149ec5f0015 SHA512 6717895942f2ab7b54019511ed2aebadadde8e96d3c4b7414bb9168ffe418432d2dee330192e199f7b9d2f665c71f5d4f1ef0911aa7243d525a2ca182ef5b122 DIST gromacs-2019.2.tar.gz 33437869 BLAKE2B bebe4942688dace148856d4491b687b8e0fd2c86d7fbd9eecdb46824d316a0fc3854464ecafa79d8db92327ee8467be204b050c11f1e71132184efd812c3bf09 SHA512 da7ff24e8485774e22d1c2464fbe64675c3305ef0e21a3d17e363201031952e5d4a9b81f572d5284fb6f2596ed99daf62fe78d653387d9d714274f46bc750183 DIST gromacs-2019.5.tar.gz 33445791 BLAKE2B 1e2e2764b0c8774c878abf4f32c2fa7ddd9b46f464cf1256deb48335433d92ef1b315f5534cdec9f766ae928a71361b5a4dd4a4def638269eb260ff98dbbe8bb SHA512 fdd177e4dfd29629b72bfbb4d61ff7bcdb37279f534883a9df8fd57569212fe1e9f8b8c9cec347fcc607539f31412d604d11ee3c0eb797251960435962b1bec6 -DIST gromacs-2020-rc1.tar.gz 29077110 BLAKE2B 5d5e6e63bd6b4dd03b688913b2da923547daddb270bca1a7d6ab8e625c26fb1031eea65330bd2e772f958e72e5a096c662633fbc71e7ee32ad83d99dcfb09170 SHA512 9dac945c5de9be2dc79bdde4d5f4afa3f2818334437ef8b4d1c57e46bdb80a0623ed7b16e1a8100395820b7eec367ea14195d420d3564f0f4eef0c88c52e78f9 +DIST gromacs-2020.tar.gz 28928068 BLAKE2B 72d4ff8f6b383284e61df9d3b2b53c51300f6961d4c19810670c8ee9ba2f1864d2a325e2774093b9338db785cb91a94461bf93f16cdf4caf0f690298a672d51c SHA512 15f0d58cd8d217eab39ef8e3535dec34127708797eaf6575fb340292cbee2303cd25deb84b3d4417a787076f4ae7be9e4958ec3a347a3aa9aed52ef337a4587c DIST regressiontests-2018.8.tar.gz 67855469 BLAKE2B 34c9b339f6229f483afbb5192ee6ba8b8f72d5c26907a853af9c53dfece0d88739e48f6b44b78d1c010f988f9385d077285300522164f533a5861e9dda879275 SHA512 3642389d27bd1942cd0f091c940ae97b197b94856a387fe581dc516b0d4169480f16551d4ba357f9282b3337d605c286d51dd38112ac87c826dda634904836bb DIST regressiontests-2019.2.tar.gz 67643003 BLAKE2B 4178de5d62f194a81f97e442c10f123dc59c5e63f2078f7f07135709f3f6e530e0d237bf40264b285c084519d5ace75dfcbcddc16dc740c4f17233dc33542e45 SHA512 c1f25bc770d3f0a873c887d5563c1cd88179e81211b70ce6f5015696e6fa0b6931a8da7a449f2b223f3105b9e2e7eca67248e96fbfc2a7fd5fb360ba616f22ff DIST regressiontests-2019.5.tar.gz 67643634 BLAKE2B c4d9535d9a8a650869d67544ad5f367324f45e55325bb5074ece9b010f232f2f0dd97c9af97924d3f2368ed63015ca7330baff1cc681310e1439ec330b70ee8d SHA512 7c0917b76e7db35ab4e3271d523d268e0e2d858091e68ead863bfe6d1e56b381e30fdbf44f479f6e065c029e2eb27cfa0dbaa1b243f185144321aaf5084c55ce -DIST regressiontests-2020-rc1.tar.gz 48537816 BLAKE2B f9f4cde7a29691459d36e5f3fac91e75f4ebc6d95302c760722f4731a63a5e0695c8bc5106d38bb7b7266f6bac19bcb988496b572dca3f500f6c323c72615c60 SHA512 fb082479a3f3e03aaac4653682680ba8409f42a47f6e64e2a67e497467fce28e013b4fed8f9d3a1ce2db52237eb0e92e6e5c8de9be33beb7324d855de20b6ec7 +DIST regressiontests-2020.tar.gz 48536146 BLAKE2B 9511db78b5d6a5ea431fdb73782f28dde4b94655139886c0ad519888ef3e435fe81807f158d66c1a4284cb88fe730f62d039ac23549f17d0ce5984764ef35f10 SHA512 5a35aaf6fe2f3b146c7045e9c967dc1c8bf754748cc1f2a7300193ae3f206a9f5058329380ae7b03b181410303bcd434584571e6161a75f99e52bd48f8ba1821 diff --git a/sci-chemistry/gromacs/gromacs-2020_rc1.ebuild b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild similarity index 99% copy from sci-chemistry/gromacs/gromacs-2020_rc1.ebuild copy to sci-chemistry/gromacs/gromacs-2020.9999.ebuild index 162d64c983f..859628fa107 100644 --- a/sci-chemistry/gromacs/gromacs-2020_rc1.ebuild +++ b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 diff --git a/sci-chemistry/gromacs/gromacs-2020_rc1.ebuild b/sci-chemistry/gromacs/gromacs-2020.ebuild similarity index 99% rename from sci-chemistry/gromacs/gromacs-2020_rc1.ebuild rename to sci-chemistry/gromacs/gromacs-2020.ebuild index 162d64c983f..859628fa107 100644 --- a/sci-chemistry/gromacs/gromacs-2020_rc1.ebuild +++ b/sci-chemistry/gromacs/gromacs-2020.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild index f9d980d7c0f..859628fa107 100644 --- a/sci-chemistry/gromacs/gromacs-9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-9999.ebuild @@ -1,11 +1,15 @@ -# Copyright 1999-2019 Gentoo Authors +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 CMAKE_MAKEFILE_GENERATOR="ninja" -inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils +PYTHON_COMPAT=( python3_{5,6,7} ) + +DISTUTILS_SINGLE_IMPL=1 + +inherit bash-completion-r1 cmake-utils cuda distutils-r1 eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils if [[ $PV = *9999* ]]; then EGIT_REPO_URI="git://git.gromacs.org/gromacs.git @@ -30,7 +34,7 @@ HOMEPAGE="http://www.gromacs.org/" # base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" SLOT="0/${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}" +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}" CDEPEND=" X? ( @@ -47,13 +51,16 @@ CDEPEND=" lmfit? ( sci-libs/lmfit ) mkl? ( sci-libs/mkl ) mpi? ( virtual/mpi ) + ${PYTHON_DEPS} + !sci-chemistry/gmxapi " -DEPEND="${CDEPEND} +BDEPEND="${CDEPEND} virtual/pkgconfig doc? ( app-doc/doxygen - dev-python/sphinx + dev-python/sphinx[${PYTHON_USEDEP}] media-gfx/mscgen + media-gfx/graphviz dev-texlive/texlive-latex dev-texlive/texlive-latexextra media-gfx/imagemagick @@ -64,7 +71,8 @@ REQUIRED_USE=" || ( single-precision double-precision ) cuda? ( single-precision ) cuda? ( !opencl ) - mkl? ( !blas !fftw !lapack )" + mkl? ( !blas !fftw !lapack ) + ${PYTHON_REQUIRED_USE}" DOCS=( AUTHORS README ) @@ -74,12 +82,18 @@ if [[ ${PV} != *9999 ]]; then S="${WORKDIR}/${PN}-${PV/_/-}" fi +PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" ) + 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" } +pkg_setup() { + python-single-r1_pkg_setup +} + src_unpack() { if [[ ${PV} != *9999 ]]; then default @@ -116,6 +130,28 @@ 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 >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF + + + !ATTLIST policymap xmlns CDATA #FIXED ''> + + + ]> + + + + + + + + + EOF } src_configure() { @@ -172,6 +208,7 @@ src_configure() { -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" -DBUILD_TESTING=$(usex test) -DGMX_BUILD_UNITTESTS=$(usex test) + -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}" ${extra} ) @@ -193,11 +230,13 @@ src_configure() { -DGMX_MPI=OFF -DGMX_THREAD_MPI=$(usex threads) -DGMXAPI=$(usex gmxapi) + -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) "${opencl[@]}" "${cuda[@]}" "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" -DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" + -DGMX_PYTHON_PACKAGE=$(usex python) ) BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure [[ ${CHOST} != *-darwin* ]] || \ @@ -207,9 +246,11 @@ 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 @@ -227,6 +268,12 @@ src_compile() { einfo "Compiling for ${x} precision" BUILD_DIR="${WORKDIR}/${P}_${x}"\ cmake-utils_src_compile + if use python; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake-utils_src_compile python_packaging/all + BUILD_DIR="${WORKDIR}/${P}" \ + distutils-r1_src_compile + fi # not 100% necessary for rel ebuilds as available from website if use doc; then BUILD_DIR="${WORKDIR}/${P}_${x}"\ @@ -250,6 +297,10 @@ src_install() { for x in ${GMX_DIRS}; do BUILD_DIR="${WORKDIR}/${P}_${x}" \ cmake-utils_src_install + if use python; then + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake-utils_src_install python_packaging/install + fi if use doc; then newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" fi @@ -263,14 +314,14 @@ 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 }