From 29aabba0ea759c6a2864ff5631735b67ee38e5e0 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Wed, 5 Feb 2020 18:44:56 +0000 Subject: gentoo resync : 05.02.2020 --- sci-chemistry/Manifest.gz | Bin 15357 -> 15352 bytes sci-chemistry/chemex/Manifest | 2 +- sci-chemistry/chemex/chemex-0.6.1-r1.ebuild | 35 --- sci-chemistry/chemex/chemex-0.6.1-r2.ebuild | 41 +++ sci-chemistry/gromacs/Manifest | 5 +- sci-chemistry/gromacs/gromacs-2019.2.ebuild | 312 ---------------------- sci-chemistry/gromacs/gromacs-2019.5.ebuild | 2 +- sci-chemistry/nmrdepaker/Manifest | 2 +- sci-chemistry/nmrdepaker/nmrdepaker-1.0-r1.ebuild | 36 --- sci-chemistry/nmrdepaker/nmrdepaker-1.0-r2.ebuild | 39 +++ sci-chemistry/prodecomp/Manifest | 2 +- sci-chemistry/prodecomp/prodecomp-3.0-r1.ebuild | 48 ---- sci-chemistry/prodecomp/prodecomp-3.0-r2.ebuild | 51 ++++ sci-chemistry/pymol/Manifest | 2 - sci-chemistry/pymol/pymol-1.8.4.0-r2.ebuild | 111 -------- sci-chemistry/relax/Manifest | 2 +- sci-chemistry/relax/relax-4.0.0-r2.ebuild | 75 ------ sci-chemistry/relax/relax-4.0.0-r3.ebuild | 81 ++++++ 18 files changed, 218 insertions(+), 628 deletions(-) delete mode 100644 sci-chemistry/chemex/chemex-0.6.1-r1.ebuild create mode 100644 sci-chemistry/chemex/chemex-0.6.1-r2.ebuild delete mode 100644 sci-chemistry/gromacs/gromacs-2019.2.ebuild delete mode 100644 sci-chemistry/nmrdepaker/nmrdepaker-1.0-r1.ebuild create mode 100644 sci-chemistry/nmrdepaker/nmrdepaker-1.0-r2.ebuild delete mode 100644 sci-chemistry/prodecomp/prodecomp-3.0-r1.ebuild create mode 100644 sci-chemistry/prodecomp/prodecomp-3.0-r2.ebuild delete mode 100644 sci-chemistry/pymol/pymol-1.8.4.0-r2.ebuild delete mode 100644 sci-chemistry/relax/relax-4.0.0-r2.ebuild create mode 100644 sci-chemistry/relax/relax-4.0.0-r3.ebuild (limited to 'sci-chemistry') diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz index bf5e31657c62..11aff635982e 100644 Binary files a/sci-chemistry/Manifest.gz and b/sci-chemistry/Manifest.gz differ diff --git a/sci-chemistry/chemex/Manifest b/sci-chemistry/chemex/Manifest index afbaeb65dddc..6992b72c5e83 100644 --- a/sci-chemistry/chemex/Manifest +++ b/sci-chemistry/chemex/Manifest @@ -1,3 +1,3 @@ DIST chemex-0.6.1.tar.gz 1449216 BLAKE2B 6b7f7597b09cd43b9bec89b6359d1f650fdd7d4f3a373e706da80dafaf438417458f34af6bc378442b5b4a84cb8222103ebc8026c85583e8dece3fad0dc77204 SHA512 40f538ef9c162759c7a6863886da8d46746ac362fc19154f0a5f3dd8703f7fea7397c3f34092c86dbce486c452e0d3b09a76e4c11ae119834d7ca4912e7f3fdf -EBUILD chemex-0.6.1-r1.ebuild 876 BLAKE2B 9eea4ff107c30077d5b8b8a62dc7c5883f3eb635f5ab38ec900b14bb7970ce0c58da7b5d6dde5fde5915d1aad816b32765967a902205f7f4f0163eccb25349b1 SHA512 fef14f301089f0ef82afee0312b8680bb17766cff97da8876063493097e778b962a08ac82856a380610b307408fec42e1ea18ea28e1e2da50a50eade8e0de823 +EBUILD chemex-0.6.1-r2.ebuild 1002 BLAKE2B 0122f5cd2ec6e61f8d24b6aa14b84e707e9344ee0dbef42eccf3a07354c36d5ac22d5be33eb390da4ff1cf9299fe47f6be4d77e1489e70fb1a9d6fd43ae89d67 SHA512 c7c5cd0a21032aa0f18ebffba48739f29a2511e387ca3ec53dc7495cac63dfb2527841a2454030179cfc217f87c29351d91b0ae2e8b038c6f87e4e644964fed7 MISC metadata.xml 216 BLAKE2B 0fbfa16661345362ff89f87adc0bb42fc5f5c9145cdedb36f3f537b39af4023b91c4dfb0d8e83a4f9ac963141f594ba8ae678371c338d992a96e02c11fd84195 SHA512 628a69805356b7458edaa2297901224178b016477a937f77e692a78ce3e7a0b6d2d7b4c4b7e70d0185d7112e6a59a5131e07d8c950e90b9c8722471d7511afc6 diff --git a/sci-chemistry/chemex/chemex-0.6.1-r1.ebuild b/sci-chemistry/chemex/chemex-0.6.1-r1.ebuild deleted file mode 100644 index 9e4f47aafc99..000000000000 --- a/sci-chemistry/chemex/chemex-0.6.1-r1.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 -DISTUTILS_SINGLE_IMPL="yes" -PYTHON_COMPAT=( python2_7 ) - -inherit distutils-r1 - -DESCRIPTION="Program to fit chemical exchange induced shift and relaxation data" -HOMEPAGE="https://github.com/gbouvignies/chemex" -SRC_URI="https://github.com/gbouvignies/chemex/archive/${PV}.tar.gz -> ${P}.tar.gz" - -SLOT="0" -LICENSE="BSD" -KEYWORDS="~amd64" -IUSE="" - -RDEPEND=" - >=dev-python/matplotlib-1.1[${PYTHON_USEDEP}] - || ( - dev-python/numpy-python2[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - ) - >=sci-libs/scipy-0.11[${PYTHON_USEDEP}] -" -DEPEND="${RDEPEND} - dev-python/setuptools[${PYTHON_USEDEP}] -" - -src_prepare() { - # Fix quotes to detect the version properly - sed -i -e 's/matplotlib>=1.3.1/matplotlib>="1.3.1"/' setup.py || die - distutils-r1_python_prepare_all -} diff --git a/sci-chemistry/chemex/chemex-0.6.1-r2.ebuild b/sci-chemistry/chemex/chemex-0.6.1-r2.ebuild new file mode 100644 index 000000000000..0b85b22ffc3d --- /dev/null +++ b/sci-chemistry/chemex/chemex-0.6.1-r2.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 +DISTUTILS_SINGLE_IMPL="yes" +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +DESCRIPTION="Program to fit chemical exchange induced shift and relaxation data" +HOMEPAGE="https://github.com/gbouvignies/chemex" +SRC_URI="https://github.com/gbouvignies/chemex/archive/${PV}.tar.gz -> ${P}.tar.gz" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64" +IUSE="" + +RDEPEND=" + || ( + >=dev-python/matplotlib-python2-1.1[${PYTHON_USEDEP}] + >=dev-python/matplotlib-1.1[${PYTHON_USEDEP}] + ) + || ( + dev-python/numpy-python2[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + ) + || ( + >=sci-libs/scipy-python2-0.11[${PYTHON_USEDEP}] + >=sci-libs/scipy-0.11[${PYTHON_USEDEP}] + ) +" +DEPEND="${RDEPEND} + dev-python/setuptools[${PYTHON_USEDEP}] +" + +src_prepare() { + # Fix quotes to detect the version properly + sed -i -e 's/matplotlib>=1.3.1/matplotlib>="1.3.1"/' setup.py || die + distutils-r1_python_prepare_all +} diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index db87a7f4f9f2..9fb8c517a917 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -1,16 +1,13 @@ AUX gromacs-2020_beta1-pytest.patch 630 BLAKE2B 1036e06589c24459006f0b579ee89c9d9c4623c7ca32fae90b21646db13280549a23cad717ef7481b03cbf9f2629b6804c0727d4b8c7f3274d0463d2735f976a SHA512 b5880d3a21635892d52b2ac09cbf456194a3db0fa0676bbdd2c2500964da89fbb7f4ebed7ac7843304159bf11f44e279eb505b2af8833127d2e21f10cb254c1e 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.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.tar.gz 48536146 BLAKE2B 9511db78b5d6a5ea431fdb73782f28dde4b94655139886c0ad519888ef3e435fe81807f158d66c1a4284cb88fe730f62d039ac23549f17d0ce5984764ef35f10 SHA512 5a35aaf6fe2f3b146c7045e9c967dc1c8bf754748cc1f2a7300193ae3f206a9f5058329380ae7b03b181410303bcd434584571e6161a75f99e52bd48f8ba1821 EBUILD gromacs-2018.8.ebuild 8784 BLAKE2B 8c08b6c4f4278ed6455a0489b765c97c748835e49973bb83b7fe8e15d9453c8c9b6c6e26cd27a2d5a927aa87a36bfdef3874020f6658c9b2dcb774043e4547e3 SHA512 b66644847daa453b9a764faaa7f3145e16f3819d0d7ffdad12c1209a398cd03dbf7c2d60e0510f514b18f6ed8c09dfadb77bca6ff2f1eb044c65632842a7499a EBUILD gromacs-2018.9999.ebuild 8787 BLAKE2B 9edbb2ae0bd3f76af41cee9971b70fdc957f22bb61ec131abd3cf44a2da56c208b0b103f72754e17cccfa054d79c1e95a9477228b0c14f4476e58bd7656b641a SHA512 c4548c8436dadf1daaf7f4f41e3c957029a10f5eb7fd11c5c8f42046d2ba38c6baf9f47e69fb8e8eeef550e0463d76bf738d6f708ffce6b4cf556e29d725ed5a -EBUILD gromacs-2019.2.ebuild 9200 BLAKE2B d4c6bbca2dfc3d376d3c98893a273d405735a2b10ea7034622a56beb544a9c0af494e7aac71d477c4800b2d45bfea0cbae3cd8ba764ebf3f463aa0b2d613b7e4 SHA512 60170844324d3542ee5043a6ac624e9eb6838a15a16fe58e65b5f3df12a74fe1bc383c505217b2fe85183c0eb7a1b421c21e1574329a9e84bb9b86159ad90e5d -EBUILD gromacs-2019.5.ebuild 9233 BLAKE2B ecc2f17bf17bdd5df1696b9877d996c44450001412bd887fff13fd53b332d3fe63556e77c01e624b0f12a445fb8a4fda688fd409f30a7c94ebfc5107ddf30f3e SHA512 e52498f36fbe36dfc33f0aaf3c4ebac0d2c643127c2c70e901d01d6223f9537889f08530db61e0167673cb6528b1b5fc2d8311b397d7cb4389cd37e7fd71259f +EBUILD gromacs-2019.5.ebuild 9232 BLAKE2B d6983b3c0cc508e278fd5fe358d1f5351f6fb6cc028cb1ee68ffaac484b11c8d88de43ac6d2b51f64ed08c4cb73f3d17ee7bc8af3947683bd3765d6b1038212d SHA512 1ff5231b3e3e6921f65295f7baa3371dd481cb004fd045005a8f9646f54b0053645bd9eb05f2cf260482e05689d668a02e7fbb851afc4d06ff2eb139f25483a7 EBUILD gromacs-2019.9999.ebuild 9234 BLAKE2B 076a2a9ff537342156ca94f138c738fbff5a0b8167b7cd34ebab388357acc2f08249675428d19b13abe4d8489aaf94afb69fb32bba1cf7658550a984319dcb30 SHA512 da0007f5e8162efd53b061a564908167f8388c4cf4288d56167e0ab313140d92641d51f1c7384d52a55998de8baf23eaf56a04d633cd20525fbc0e2c46ba4256 EBUILD gromacs-2020.9999.ebuild 9793 BLAKE2B 0a689e24c71085d134e51a091d647e64a3bdfdbc9678f27cc0fb86b7caa8b4e1e4bdda4e8a379bfe593408fc0ea236141db9e8fd89e58987aadb2003054227d6 SHA512 0efe1abfcd815248f6a77d47e33867b88aae79d71c3be146da3264ae91036fd5305129515b3ae12cad757ad802c18ba79e588581c910fe06606883cacb2c9a19 EBUILD gromacs-2020.ebuild 9793 BLAKE2B 0a689e24c71085d134e51a091d647e64a3bdfdbc9678f27cc0fb86b7caa8b4e1e4bdda4e8a379bfe593408fc0ea236141db9e8fd89e58987aadb2003054227d6 SHA512 0efe1abfcd815248f6a77d47e33867b88aae79d71c3be146da3264ae91036fd5305129515b3ae12cad757ad802c18ba79e588581c910fe06606883cacb2c9a19 diff --git a/sci-chemistry/gromacs/gromacs-2019.2.ebuild b/sci-chemistry/gromacs/gromacs-2019.2.ebuild deleted file mode 100644 index 58d733d2c332..000000000000 --- a/sci-chemistry/gromacs/gromacs-2019.2.ebuild +++ /dev/null @@ -1,312 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -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 ) - ${PYTHON_DEPS} - " -DEPEND="${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 - - - !ATTLIST policymap xmlns CDATA #FIXED ''> - - - ]> - - - - - - - - - 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 ${cuda} - -DGMX_OPENMM=OFF - -DGMXAPI=OFF - -DGMX_BUILD_MDRUN_ONLY=ON - -DBUILD_SHARED_LIBS=OFF - -DGMX_BUILD_MANUAL=OFF - -DGMX_BINARY_SUFFIX="_mpi${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-2019.5.ebuild b/sci-chemistry/gromacs/gromacs-2019.5.ebuild index 7775143d0ae9..793ffa7a363f 100644 --- a/sci-chemistry/gromacs/gromacs-2019.5.ebuild +++ b/sci-chemistry/gromacs/gromacs-2019.5.ebuild @@ -19,7 +19,7 @@ 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" diff --git a/sci-chemistry/nmrdepaker/Manifest b/sci-chemistry/nmrdepaker/Manifest index 0c2312658756..a3f94f72a9a2 100644 --- a/sci-chemistry/nmrdepaker/Manifest +++ b/sci-chemistry/nmrdepaker/Manifest @@ -1,3 +1,3 @@ DIST nmrdepaker-1.0.tar.gz 2233765 BLAKE2B 9b638a36fc50d7c020d56833b6ca78d7079ad357f42431088c4c0735b7e9ce63a0e6318915ec751b42e6628c0da76b93ca16ffea1ffe6b311480e8d278ce1a1a SHA512 9d1a9048a85f85eacaeeb582c5550345efa673b1f517dad121e2b2e19125f93e71a26f2f8240ea9b8a06489814eb833e7b3653f882a46bad699b01fd1aa4299f -EBUILD nmrdepaker-1.0-r1.ebuild 846 BLAKE2B 5366d7a88e40be247ddcfc6fd9e01d9da3e9c9282e58a42a53f9ac39865715fd76afaa265b89c509740d980355fedfbcdabac0bb08606c1c8444f5a2404c1e07 SHA512 c2777dc917c092e44eb0306faebdbde99e4103fa745684f936b58b4eaf8e2863079378cb34d6576cdedcbdbffd7f704d0527cf0ab659c7afd9168b53f213c238 +EBUILD nmrdepaker-1.0-r2.ebuild 920 BLAKE2B 684f7f2a3475a04abf4592da1b70033a2c7c9f29ef99be234a927555e39f3d4a3241968e4ac7ed1c23cfb37d99c97c407251e933a7bec61c0ebd7d0a38a84dd1 SHA512 f1bf2fa3827f1f161447b439d82599ee2fd7628e96aea35fba9019dd350efa6816b1a351d3e80d4182462b0e5b3ff0629edebee38f24011d9cdfe792cbec1ca4 MISC metadata.xml 216 BLAKE2B 0fbfa16661345362ff89f87adc0bb42fc5f5c9145cdedb36f3f537b39af4023b91c4dfb0d8e83a4f9ac963141f594ba8ae678371c338d992a96e02c11fd84195 SHA512 628a69805356b7458edaa2297901224178b016477a937f77e692a78ce3e7a0b6d2d7b4c4b7e70d0185d7112e6a59a5131e07d8c950e90b9c8722471d7511afc6 diff --git a/sci-chemistry/nmrdepaker/nmrdepaker-1.0-r1.ebuild b/sci-chemistry/nmrdepaker/nmrdepaker-1.0-r1.ebuild deleted file mode 100644 index 29a13632c888..000000000000 --- a/sci-chemistry/nmrdepaker/nmrdepaker-1.0-r1.ebuild +++ /dev/null @@ -1,36 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 -DISTUTILS_SINGLE_IMPL="yes" -PYTHON_COMPAT=( python2_7 ) - -inherit desktop distutils-r1 - -DESCRIPTION="Program to perform NMR spectra 'De-Pake-ing' and moment calculation" -HOMEPAGE="https://launchpad.net/nmrdepaker" -SRC_URI="https://launchpad.net/${PN}/${PV}/${PV}/+download/${P}.tar.gz" - -SLOT="0" -LICENSE="GPL-3+" -KEYWORDS="~amd64" -IUSE="" - -RDEPEND=" - >=dev-python/matplotlib-0.98.5[gtk2,${PYTHON_USEDEP}] - || ( - dev-python/numpy-python2[${PYTHON_USEDEP}] - >=dev-python/numpy-1.2[${PYTHON_USEDEP}] - ) - >=dev-python/pygtk-2.12:2[${PYTHON_USEDEP}] -" -DEPEND="${RDEPEND}" - -S="${WORKDIR}/nmrdpaker-${PV}" - -src_install() { - distutils-r1_src_install - - newicon lib/data/images/unused/nmrfriend-buddy.svg ${PN}.svg - make_desktop_entry ${PN} -} diff --git a/sci-chemistry/nmrdepaker/nmrdepaker-1.0-r2.ebuild b/sci-chemistry/nmrdepaker/nmrdepaker-1.0-r2.ebuild new file mode 100644 index 000000000000..043fd37324eb --- /dev/null +++ b/sci-chemistry/nmrdepaker/nmrdepaker-1.0-r2.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 +DISTUTILS_SINGLE_IMPL="yes" +PYTHON_COMPAT=( python2_7 ) + +inherit desktop distutils-r1 + +DESCRIPTION="Program to perform NMR spectra 'De-Pake-ing' and moment calculation" +HOMEPAGE="https://launchpad.net/nmrdepaker" +SRC_URI="https://launchpad.net/${PN}/${PV}/${PV}/+download/${P}.tar.gz" + +SLOT="0" +LICENSE="GPL-3+" +KEYWORDS="~amd64" +IUSE="" + +RDEPEND=" + || ( + >=dev-python/matplotlib-python2-0.98.5[gtk2,${PYTHON_USEDEP}] + >=dev-python/matplotlib-0.98.5[gtk2,${PYTHON_USEDEP}] + ) + || ( + dev-python/numpy-python2[${PYTHON_USEDEP}] + >=dev-python/numpy-1.2[${PYTHON_USEDEP}] + ) + >=dev-python/pygtk-2.12:2[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/nmrdpaker-${PV}" + +src_install() { + distutils-r1_src_install + + newicon lib/data/images/unused/nmrfriend-buddy.svg ${PN}.svg + make_desktop_entry ${PN} +} diff --git a/sci-chemistry/prodecomp/Manifest b/sci-chemistry/prodecomp/Manifest index e19bbf5f4bc4..fe180d2bdaba 100644 --- a/sci-chemistry/prodecomp/Manifest +++ b/sci-chemistry/prodecomp/Manifest @@ -1,3 +1,3 @@ DIST prodecomp-3.0.tar.bz2 18377446 BLAKE2B c6b4acf20a76029fc34eaea7a0adf1a04fb727b2e246fbcad27e2fa2bea606b2e712fb986fdd3e534534b32a22acae58a00bc2a3c6bde893d5befe91696523d3 SHA512 8d23f174e125d4c7776432a37b063d2f39af8497050bd7f7ff358c67d509b1eef2c2865596efae632855fd583fb52c233b67d0e667c6c2a03ba6f5a2f2ac9b0d -EBUILD prodecomp-3.0-r1.ebuild 1096 BLAKE2B ea880fff06ebdfc68c51aececf5064f63a6ec2fc1d183f2041d73f633c592d73282ee0635dff24a903be2e62ce2bc1307d3d6e35001d9b41009f57d1db9222fb SHA512 163404741f8cdfcc6e8c550850f79470d9a7c0accf73386351c5ce9ad2068fe0aed5316b346144b888cd5726f2b80312d1d5bcf3476c13b6009279e0c71b3362 +EBUILD prodecomp-3.0-r2.ebuild 1146 BLAKE2B fd477a14bd9e47bc8857446fc072633301f6114f30dfcc27997fc7b3d58c52a384ae8b7391bcb58f6bc23db1bbc24e0be0c7b010c971fb4d4e27c34355a38abb SHA512 b914399f357dfd514f55a82c1fb65b752725f62f0025ecdbe6524c6f0191ede74c629852d80e3c4998928649168702aa91361258c22473f499f76c3a3c4ebfc7 MISC metadata.xml 825 BLAKE2B 6874942c301b7d68f9184de8eb7482b790d2bd51c3a853132da3ed7bb0eacf54f608f816965bbfb27b81b90fecc3eee77596d73a78f5ec67703c53ad2bc2556d SHA512 94e41d5648ac93257f11f305bf2aaf926cc103240beec884142cda42c3d4e4fae5629e26b43cd945c945af706d5b5172fcd2c30ec6cb9067b152a22cd09bddcf diff --git a/sci-chemistry/prodecomp/prodecomp-3.0-r1.ebuild b/sci-chemistry/prodecomp/prodecomp-3.0-r1.ebuild deleted file mode 100644 index ad5fb6271a2b..000000000000 --- a/sci-chemistry/prodecomp/prodecomp-3.0-r1.ebuild +++ /dev/null @@ -1,48 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) -PYTHON_REQ_USE="tk" - -inherit python-single-r1 - -DESCRIPTION="Decomposition-based analysis of NMR projections" -HOMEPAGE="http://www.lundberg.gu.se/nmr/software.php?program=PRODECOMP" -SRC_URI="mirror://gentoo/${P}.tar.bz2" - -SLOT="0" -LICENSE="GPL-2" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="examples" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -DEPEND="${PYTHON_DEPS}" -RDEPEND="${DEPEND} - sci-libs/scipy[${PYTHON_USEDEP}]" - -S="${WORKDIR}"/NMRProjAnalys - -src_install() { - python_export - if use examples; then - insinto /usr/share/${PN} - doins -r ExampleData Results - fi - - dodoc ProjTools/Manual.pdf - rm -rf ProjTools/Manual.pdf ProdecompOutput || die - - python_moduleinto ${PN} - python_domodule ProjTools/. - python_optimize - - cat >> "${T}"/${PN} <<- EOF - #!/bin/bash - ${PYTHON} -O $(python_get_sitedir)/${PN}/ProjAnalys.py \$@ - EOF - dobin "${T}"/${PN} - - dosym ../../../../share/doc/${PF}/Manual.pdf "${PYTHON_SITEDIR##${EPREFIX}}"/${PN}/Manual.pdf -} diff --git a/sci-chemistry/prodecomp/prodecomp-3.0-r2.ebuild b/sci-chemistry/prodecomp/prodecomp-3.0-r2.ebuild new file mode 100644 index 000000000000..e66cac2b0b4f --- /dev/null +++ b/sci-chemistry/prodecomp/prodecomp-3.0-r2.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +PYTHON_REQ_USE="tk" + +inherit python-single-r1 + +DESCRIPTION="Decomposition-based analysis of NMR projections" +HOMEPAGE="http://www.lundberg.gu.se/nmr/software.php?program=PRODECOMP" +SRC_URI="mirror://gentoo/${P}.tar.bz2" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +DEPEND="${PYTHON_DEPS}" +RDEPEND="${DEPEND} + || ( + sci-libs/scipy-python2[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] + )" + +S="${WORKDIR}"/NMRProjAnalys + +src_install() { + python_export + if use examples; then + insinto /usr/share/${PN} + doins -r ExampleData Results + fi + + dodoc ProjTools/Manual.pdf + rm -rf ProjTools/Manual.pdf ProdecompOutput || die + + python_moduleinto ${PN} + python_domodule ProjTools/. + python_optimize + + cat >> "${T}"/${PN} <<- EOF + #!/bin/bash + ${PYTHON} -O $(python_get_sitedir)/${PN}/ProjAnalys.py \$@ + EOF + dobin "${T}"/${PN} + + dosym ../../../../share/doc/${PF}/Manual.pdf "${PYTHON_SITEDIR##${EPREFIX}}"/${PN}/Manual.pdf +} diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest index 3b769d6a6826..7948415a7bf8 100644 --- a/sci-chemistry/pymol/Manifest +++ b/sci-chemistry/pymol/Manifest @@ -1,6 +1,4 @@ DIST pymol-1.8.4.0.png.xz 19528 BLAKE2B f3d23d4cedca3d8bb96b20646a548da4be570697e3346a11b01c5c3599b536ba4697be08472dfa8a4f6533167defc1a37a1de332931a73857319cb28fd42cd2b SHA512 40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c DIST pymol-2.3.0.tar.gz 10448674 BLAKE2B 0d508587d880ce7f2e8a0481bf664e6bfe6eb1d68b0f48b9266cde756824bd8c0144d7243e958bbc5e571d60fca9dafff125d81a8a3d32107e78ad2ff8dffc05 SHA512 e1dcea1c97bcd9045d3543e92902f240e6affbf61a38e8d2a0be04309e3dbabfe1a869847d1423b3151008978d4c305bbf3ce994fc9d453c0063ce020100c133 -DIST pymol-v1.8.4.0.tar.bz2 8717344 BLAKE2B a4cfb95eb40a3cd3da5b8cfd4acac7255997f9a3e49ef7e7e1d4c13f36e4aace462a054c326bbaadbc99f22286be878a6d5c518149760b5c939ce9362d4b8cc3 SHA512 73a810adfc31adaf0f3fa25512084882c87b0782c8af716ac0203a5b5b7f0b9fedfbce3d129bffef7b52044e92b0542e683966b2acf961c4dac17fbba72dd7fe -EBUILD pymol-1.8.4.0-r2.ebuild 3062 BLAKE2B 98914bfee561a1f5970ca47180ae5a23ac9c547069bfa421041c4e19eaff9820ab148038406971ac8e79801f99fdd92f90e7be5249081ba1be200451efb92f30 SHA512 69714e4d11ab56af06fee425e23659b9855e2f8e39293888a57720e6c1f4dad8f823cb77f203f7bb55f3b402f899e810c73af150106621c2e8ee6cd0c4250e5f EBUILD pymol-2.3.0-r2.ebuild 3190 BLAKE2B a72434867a8589dda7a334f71e1aaa58f16d3caea1eb1615c44c2b813b1d0b84ed308369eb89c45251daf7bfbabed470e7d5abe42334b3fe28b484217fa29653 SHA512 5c2d08baa9407a2abe733d1753e622ea450b7c939b4f57d8e47adb5f57ac5a5e2b95264b6876698c70a5af926d378d75b6ba4ae02c85affbcfda7327d718ea14 MISC metadata.xml 439 BLAKE2B 68df7dfc8ca3d4d4b18b419532bade69491f2e9362f10ae2397c804132b7fc9cd08dcf9703c0a89c44588c570e0c0c1bb9bffb7394d51faf1283142dbc5f70b3 SHA512 f5a3eded9b12fa715ba2e6e10b41c75d9bd823ca0dd40acbffc3f5bfc4b36c687f720b1a4e119b4540a31faf849985778cbd72b0b2cd35af8c52ca0f808d71e4 diff --git a/sci-chemistry/pymol/pymol-1.8.4.0-r2.ebuild b/sci-chemistry/pymol/pymol-1.8.4.0-r2.ebuild deleted file mode 100644 index f60de8dcb189..000000000000 --- a/sci-chemistry/pymol/pymol-1.8.4.0-r2.ebuild +++ /dev/null @@ -1,111 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) -PYTHON_REQ_USE="tk" - -inherit distutils-r1 eutils fdo-mime flag-o-matic versionator - -DESCRIPTION="A Python-extensible molecular graphics system" -HOMEPAGE="https://www.pymol.org/" -SRC_URI=" - https://dev.gentoo.org/~jlec/distfiles/${P}.png.xz - mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 1-2)/${PN}-v${PV}.tar.bz2 - " -# git archive -v --prefix=${P}/ master -o ${P}.tar.xz -RESTRICT="mirror" -LICENSE="PSF-2.2" -SLOT="0" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos" -IUSE="web" - -DEPEND=" - || ( - dev-python/numpy-python2[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - ) - dev-python/pmw:py2[${PYTHON_USEDEP}] - dev-python/pyopengl[${PYTHON_USEDEP}] - media-libs/freeglut - media-libs/freetype:2 - media-libs/glew:0= - media-libs/libpng:0= - media-video/mpeg-tools - sys-libs/zlib - !sci-chemistry/pymol-apbs-plugin[${PYTHON_USEDEP}] - web? ( !dev-python/webpy[${PYTHON_USEDEP}] )" -RDEPEND="${DEPEND}" - -S="${WORKDIR}"/${PN} - -python_prepare_all() { - sed \ - -e "s:\"/usr:\"${EPREFIX}/usr:g" \ - -e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \ - -e "/import/s:argparse:argparseX:g" \ - -i setup.py || die - - sed \ - -e "s:/opt/local:${EPREFIX}/usr:g" \ - -e '/ext_comp_args/s:\[.*\]:[]:g' \ - -i setup.py || die - - append-cxxflags -std=c++0x - - distutils-r1_python_prepare_all -} - -python_install() { - distutils-r1_python_install --pymol-path="${EPREFIX}/usr/share/pymol" - - sed \ - -e '1d' \ - -e "/APBS_BINARY_LOCATION/s:None:\"${EPREFIX}/usr/bin/apbs\":g" \ - -e "/APBS_PSIZE_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/src/\":g" \ - -e "/APBS_PDB2PQR_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/\":g" \ - -i "${D}/$(python_get_sitedir)"/pmg_tk/startup/apbs_tools.py || die -} - -python_install_all() { - distutils-r1_python_install_all - - sed \ - -e '1i#!/usr/bin/env python' \ - "${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die - - python_foreach_impl python_doscript "${T}"/${PN} - - # These environment variables should not go in the wrapper script, or else - # it will be impossible to use the PyMOL libraries from Python. - cat >> "${T}"/20pymol <<- EOF - PYMOL_PATH="${EPREFIX}/usr/share/pymol" - PYMOL_DATA="${EPREFIX}/usr/share/pymol/data" - PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts" - EOF - - doenvd "${T}"/20pymol - - newicon "${WORKDIR}"/${P}.png ${PN}.png - make_desktop_entry ${PN} PyMol ${PN} \ - "Graphics;Education;Science;Chemistry;" \ - "MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;" - - if ! use web; then - rm -rf "${D}/$(python_get_sitedir)/web" || die - fi - - rm -f "${ED}"/usr/share/${PN}/LICENSE || die -} - -pkg_postinst() { - fdo-mime_desktop_database_update - fdo-mime_mime_database_update - optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr -} - -pkg_postrm() { - fdo-mime_desktop_database_update - fdo-mime_mime_database_update -} diff --git a/sci-chemistry/relax/Manifest b/sci-chemistry/relax/Manifest index 9d2df17bb325..f3b0b62ccafa 100644 --- a/sci-chemistry/relax/Manifest +++ b/sci-chemistry/relax/Manifest @@ -1,3 +1,3 @@ DIST relax-4.0.0.src.tar.bz2 105659752 BLAKE2B ce5fc9b7f31787f2189e75a543f8ba6fe3cd59ce7382c6c0f79c419b9f71b2d09bd16685e7fed3c9e3205be531efa2a8dc1cce707e77e2386d2a9f7a71b4b0c1 SHA512 28b5ddab2c83f95d7e1a502d05b5d3c93337fece68a1fef95ec8978f61fccf24cb37528cfef27cb20d132033535f4120b23cc76a75f34f52b27df17116351f8e -EBUILD relax-4.0.0-r2.ebuild 1647 BLAKE2B 47d35d0a658255c16ce7fde5c6afdf1ac80f894e9de57b4a55c7e44c61db164f50511984abbaf1b8ad98bebef132836bcbfcd07d8ddb70f7c5fe17469185df62 SHA512 88d260d222dbd1c25b327aea72e37cacb209d3dd172aefe5c15d5def95905dd7168d75d15cb707ebc4ed3863838e3c6b3a4764679e249f0ad6d689ad7cabe501 +EBUILD relax-4.0.0-r3.ebuild 1760 BLAKE2B 6ea79be4c348069a5cd54ce3f9614d145febcb47a76709b5c45c9400347d9ff035cf6138005a455e2b14c1a6a498cb8ee1fdc76d8c65aa99d82bbba966bd7d16 SHA512 c3a59cbba651f752650d840b60dfda46ceb7f6f2673607e8e1b8f1265ff3595116f64830b3e00ee42a017ecd54cf27d008c841048f302a09a2c2abb87326a204 MISC metadata.xml 1373 BLAKE2B d5a9e36f0412ef757a23aa4991986bdc394edc035f59b0206b246affc884417eb8446a598b23054972c97dc5d883cd0242e306f9e8d61620c144939845c0bcf1 SHA512 575ccfdae744fc5d97e795a22989b377954edeacb8ec4887d987a59af813f126551743c4b29b9c2b4a26a1840f05d42fb26fd39b7ae9b38e24373fab18c0270e diff --git a/sci-chemistry/relax/relax-4.0.0-r2.ebuild b/sci-chemistry/relax/relax-4.0.0-r2.ebuild deleted file mode 100644 index 606c454f1b12..000000000000 --- a/sci-chemistry/relax/relax-4.0.0-r2.ebuild +++ /dev/null @@ -1,75 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -WX_GTK_VER="3.0" - -inherit eutils multiprocessing python-single-r1 scons-utils toolchain-funcs wxwidgets virtualx - -DESCRIPTION="Molecular dynamics by NMR data analysis" -HOMEPAGE="https://www.nmr-relax.com/" -SRC_URI="http://download.gna.org/relax/${P}.src.tar.bz2" - -SLOT="0" -LICENSE="GPL-2" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="test" -RESTRICT="!test? ( test )" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - ${PYTHON_DEPS} - dev-python/Numdifftools[${PYTHON_USEDEP}] - dev-python/matplotlib[${PYTHON_USEDEP}] - || ( - dev-python/numpy-python2[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - ) - dev-python/wxpython:${WX_GTK_VER}[${PYTHON_USEDEP}] - sci-chemistry/molmol - sci-chemistry/pymol[${PYTHON_USEDEP}] - sci-chemistry/vmd - >=sci-libs/bmrblib-1.0.3[${PYTHON_USEDEP}] - >=sci-libs/minfx-1.0.11[${PYTHON_USEDEP}] - sci-libs/scipy[${PYTHON_USEDEP}] - sci-visualization/grace - sci-visualization/opendx - x11-libs/wxGTK:${WX_GTK_VER}[X]" -DEPEND="${RDEPEND} - media-gfx/pngcrush - test? ( ${RDEPEND} ) - " - -pkg_setup() { - python-single-r1_pkg_setup -} - -src_prepare() { - rm -rf minfx bmrblib extern/numdifftools || die - tc-export CC - need-wxwidgets unicode -} - -src_compile() { - escons -} - -src_test() { - VIRTUALX_COMMAND="${EPYTHON} ./${PN}.py -x --traceback" - virtualmake -} - -src_install() { - dodoc README docs/{CHANGES,COMMITTERS,JOBS,relax.pdf} - - python_moduleinto ${PN} - python_domodule * - - rm ${PN} README || die - - make_wrapper ${PN}-nmr "${EPYTHON} $(python_get_sitedir)/${PN}/${PN}.py $@" -} diff --git a/sci-chemistry/relax/relax-4.0.0-r3.ebuild b/sci-chemistry/relax/relax-4.0.0-r3.ebuild new file mode 100644 index 000000000000..28b0f5d9da67 --- /dev/null +++ b/sci-chemistry/relax/relax-4.0.0-r3.ebuild @@ -0,0 +1,81 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +WX_GTK_VER="3.0" + +inherit eutils multiprocessing python-single-r1 scons-utils toolchain-funcs wxwidgets virtualx + +DESCRIPTION="Molecular dynamics by NMR data analysis" +HOMEPAGE="https://www.nmr-relax.com/" +SRC_URI="http://download.gna.org/relax/${P}.src.tar.bz2" + +SLOT="0" +LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test" +RESTRICT="!test? ( test )" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND=" + ${PYTHON_DEPS} + dev-python/Numdifftools[${PYTHON_USEDEP}] + || ( + dev-python/matplotlib-python2[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + ) + || ( + dev-python/numpy-python2[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + ) + dev-python/wxpython:${WX_GTK_VER}[${PYTHON_USEDEP}] + sci-chemistry/molmol + sci-chemistry/pymol[${PYTHON_USEDEP}] + sci-chemistry/vmd + >=sci-libs/bmrblib-1.0.3[${PYTHON_USEDEP}] + >=sci-libs/minfx-1.0.11[${PYTHON_USEDEP}] + || ( + sci-libs/scipy-python2[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] + ) + sci-visualization/grace + sci-visualization/opendx + x11-libs/wxGTK:${WX_GTK_VER}[X]" +DEPEND="${RDEPEND} + media-gfx/pngcrush + test? ( ${RDEPEND} ) + " + +pkg_setup() { + python-single-r1_pkg_setup +} + +src_prepare() { + rm -rf minfx bmrblib extern/numdifftools || die + tc-export CC + need-wxwidgets unicode +} + +src_compile() { + escons +} + +src_test() { + VIRTUALX_COMMAND="${EPYTHON} ./${PN}.py -x --traceback" + virtualmake +} + +src_install() { + dodoc README docs/{CHANGES,COMMITTERS,JOBS,relax.pdf} + + python_moduleinto ${PN} + python_domodule * + + rm ${PN} README || die + + make_wrapper ${PN}-nmr "${EPYTHON} $(python_get_sitedir)/${PN}/${PN}.py $@" +} -- cgit v1.2.3