From 075fd1f8cabc5879c6eb42127fb84c3058677fde Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Sat, 18 May 2024 00:01:42 +0100 Subject: gentoo auto-resync : 18:05:2024 - 00:01:41 --- sci-chemistry/Manifest.gz | Bin 9204 -> 9202 bytes sci-chemistry/gromacs/Manifest | 4 + sci-chemistry/gromacs/gromacs-2024.2.ebuild | 335 +++++++++++++++++++++ sci-chemistry/modeller/Manifest | 5 +- .../modeller/files/modeller-10.5-fix-except.patch | 29 ++ sci-chemistry/modeller/modeller-10.5.ebuild | 148 +++++++++ sci-chemistry/modeller/modeller-9.25.ebuild | 149 --------- sci-chemistry/pymol/Manifest | 5 +- sci-chemistry/pymol/pymol-2.5.0-r3.ebuild | 100 ------ sci-chemistry/pymol/pymol-2.5.0-r5.ebuild | 108 ------- sci-chemistry/pymol/pymol-3.0.0.ebuild | 109 +++++++ 11 files changed, 630 insertions(+), 362 deletions(-) create mode 100644 sci-chemistry/gromacs/gromacs-2024.2.ebuild create mode 100644 sci-chemistry/modeller/files/modeller-10.5-fix-except.patch create mode 100644 sci-chemistry/modeller/modeller-10.5.ebuild delete mode 100644 sci-chemistry/modeller/modeller-9.25.ebuild delete mode 100644 sci-chemistry/pymol/pymol-2.5.0-r3.ebuild delete mode 100644 sci-chemistry/pymol/pymol-2.5.0-r5.ebuild create mode 100644 sci-chemistry/pymol/pymol-3.0.0.ebuild (limited to 'sci-chemistry') diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz index 7e0dbc2b816e..b6fb10d1da8a 100644 Binary files a/sci-chemistry/Manifest.gz and b/sci-chemistry/Manifest.gz differ diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index 71f6bb8fd082..05fca2bd57ec 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -7,18 +7,21 @@ DIST gromacs-2021.7.tar.gz 38028032 BLAKE2B 2dc1b15ca8692ca5cf4ad1c7a266b9e2ced0 DIST gromacs-2022.6.tar.gz 40330705 BLAKE2B fdafbd5b2a92d6022dec3e79e961fef220f1eba42850916e7cb70ef459a8d9c6ebc8c1bbe3c105f5b23161dd5c552ec00505d7c0036649b782cf52c311498743 SHA512 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27c3dfbe5423bd5e7ed6ae14976e4d0cddd4c6b138070a7b72fec6ebc0e4d56b0b3e6e5c361986b1f354788ce2e9e665999b2fdc6ff6455d7f9012860f9b80ad DIST regressiontests-2024.1.tar.gz 48136131 BLAKE2B 600b2d11916152b1a29db5b67de61752137e507d5b3634325c034b3ae16c96ca039762f74fe961912b728592d6940bb0aa1f409cc58b0b0d18e616c429e680c4 SHA512 1649a6a42be2887b4d494733d5a969df735904fba39f2532969435d99f8fc900e9234d3d0f2a34a90bc0961716c335bbbe322566d14974a9d8fb50932f6a36b0 +DIST regressiontests-2024.2.tar.gz 48131919 BLAKE2B b77592a4433df58890b343466311f21cdc3112cac5397b072666aa1fe3552f6db8ab9fa3e039961b83544c84652e739a0459a65f1e52541cbb67a4a8b27e41e7 SHA512 9fab0e0a5ca1505bf1e9ba0cf68be88a5c1a8cbd7ebe922b3a73f08766dad556ca96fab88d423ebc64715e9d6a6bb49e66dc0ce5a48275d71764878e1944b209 DIST regressiontests-2024.tar.gz 48142685 BLAKE2B e24c29c2b534f2fe42e4abc122578ba618279f3182f83be604516e6ee2a34ff037b2604b4cda7a9b7e2ea9fce0a386b3efb7c8aa0cac378d6d8c1595be884c76 SHA512 6c4a847c379603590f618a4da7c691b51bbe180ca9dc59abf885ef8599e1b66758171eb05b7d7709d968f559b209c2fa4cfec8f15cc5d072fafe952567002c2e EBUILD gromacs-2020.7-r1.ebuild 9836 BLAKE2B fddaab6e06c3a1da28f0e85f5edf03dea4ba38212e933f71f4d7f9e9efe7c042c140ef38492514b65adc4f38d341aa8ea74db5937ef22b84e0f28b1747560f98 SHA512 c3b521a32c3d0690580dfee163a9c21b016c7b7b696d617d7d5991e36de2610b32fd8f0debb05478e15e3d29c99114eeb7704c95dc13f9ff675d2e81cb1d06fb EBUILD gromacs-2021.7-r1.ebuild 10139 BLAKE2B 9611b5c6e0d22255f1faf0f5223cf013ffff2407c3f272f7e0eb932414efc63324cca3fe515fbbbaaa318b14709458d338b18b5c38b87081c1f7fb15ff33b31b SHA512 e0c00ba782790361a354d203327e80820e2c5ef9d4fc1130ece1dc6866303059e505146b8dc18e34d1690e0cd153ac9e6c6015b55e92a047ba96e9a74387301b @@ -26,6 +29,7 @@ EBUILD gromacs-2022.6.ebuild 9583 BLAKE2B 4700542f3a32bc3055617792d56fa63370438e EBUILD gromacs-2023.4.ebuild 9738 BLAKE2B af8b9cfb076d9bf0d49544cb5a7b2bcec58ccbfd20a74eb3082e818a890901d10734aa1aba3b1425aab0c0999f16afe83423a865a823e24433703380a8ed5153 SHA512 19a573be8b616440e6680a27ad4a43195d39e265142dad103f6d27d952594c8a99410c98ec2fb8792e7d1318e8a58172b0c53dfc6c494a1662793ea123cdc935 EBUILD gromacs-2023.9999.ebuild 9738 BLAKE2B af8b9cfb076d9bf0d49544cb5a7b2bcec58ccbfd20a74eb3082e818a890901d10734aa1aba3b1425aab0c0999f16afe83423a865a823e24433703380a8ed5153 SHA512 19a573be8b616440e6680a27ad4a43195d39e265142dad103f6d27d952594c8a99410c98ec2fb8792e7d1318e8a58172b0c53dfc6c494a1662793ea123cdc935 EBUILD gromacs-2024.1.ebuild 9738 BLAKE2B af8b9cfb076d9bf0d49544cb5a7b2bcec58ccbfd20a74eb3082e818a890901d10734aa1aba3b1425aab0c0999f16afe83423a865a823e24433703380a8ed5153 SHA512 19a573be8b616440e6680a27ad4a43195d39e265142dad103f6d27d952594c8a99410c98ec2fb8792e7d1318e8a58172b0c53dfc6c494a1662793ea123cdc935 +EBUILD gromacs-2024.2.ebuild 9738 BLAKE2B af8b9cfb076d9bf0d49544cb5a7b2bcec58ccbfd20a74eb3082e818a890901d10734aa1aba3b1425aab0c0999f16afe83423a865a823e24433703380a8ed5153 SHA512 19a573be8b616440e6680a27ad4a43195d39e265142dad103f6d27d952594c8a99410c98ec2fb8792e7d1318e8a58172b0c53dfc6c494a1662793ea123cdc935 EBUILD gromacs-2024.9999.ebuild 9738 BLAKE2B af8b9cfb076d9bf0d49544cb5a7b2bcec58ccbfd20a74eb3082e818a890901d10734aa1aba3b1425aab0c0999f16afe83423a865a823e24433703380a8ed5153 SHA512 19a573be8b616440e6680a27ad4a43195d39e265142dad103f6d27d952594c8a99410c98ec2fb8792e7d1318e8a58172b0c53dfc6c494a1662793ea123cdc935 EBUILD gromacs-2024.ebuild 9738 BLAKE2B af8b9cfb076d9bf0d49544cb5a7b2bcec58ccbfd20a74eb3082e818a890901d10734aa1aba3b1425aab0c0999f16afe83423a865a823e24433703380a8ed5153 SHA512 19a573be8b616440e6680a27ad4a43195d39e265142dad103f6d27d952594c8a99410c98ec2fb8792e7d1318e8a58172b0c53dfc6c494a1662793ea123cdc935 EBUILD gromacs-9999.ebuild 9738 BLAKE2B af8b9cfb076d9bf0d49544cb5a7b2bcec58ccbfd20a74eb3082e818a890901d10734aa1aba3b1425aab0c0999f16afe83423a865a823e24433703380a8ed5153 SHA512 19a573be8b616440e6680a27ad4a43195d39e265142dad103f6d27d952594c8a99410c98ec2fb8792e7d1318e8a58172b0c53dfc6c494a1662793ea123cdc935 diff --git a/sci-chemistry/gromacs/gromacs-2024.2.ebuild b/sci-chemistry/gromacs/gromacs-2024.2.ebuild new file mode 100644 index 000000000000..a3319899d419 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-2024.2.ebuild @@ -0,0 +1,335 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +PYTHON_COMPAT=( python3_{10..12} ) + +DISTUTILS_OPTIONAL=1 +DISTUTILS_USE_PEP517=no +DISTUTILS_SINGLE_IMPL=1 + +inherit bash-completion-r1 cmake cuda distutils-r1 flag-o-matic readme.gentoo-r1 toolchain-funcs xdg-utils + +if [[ ${PV} = *9999* ]]; then + EGIT_REPO_URI=" + https://gitlab.com/gromacs/gromacs.git + https://github.com/gromacs/gromacs.git + " + [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}" + inherit git-r3 +else + SRC_URI=" + https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz + doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) + test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" + # since 2022 arm support was dropped (but not arm64) + KEYWORDS="~amd64 -arm ~arm64 ~x86 ~amd64-linux ~x86-linux ~x64-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 cpu_flags_x86_avx512f cpu_flags_arm_neon" + +DESCRIPTION="The ultimate molecular dynamics simulation package" +HOMEPAGE="https://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="blas clang clang-cuda cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" + +CDEPEND=" + blas? ( virtual/blas ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-11:=[profiler] ) + opencl? ( virtual/opencl ) + fftw? ( sci-libs/fftw:3.0= ) + hwloc? ( sys-apps/hwloc:= ) + lapack? ( virtual/lapack ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi[cxx] ) + sci-libs/lmfit:= + >=dev-cpp/muParser-2.3:= + ${PYTHON_DEPS} + " +BDEPEND="${CDEPEND} + virtual/pkgconfig + clang? ( >=sys-devel/clang-6:* ) + build-manual? ( + app-text/doxygen + $(python_gen_cond_dep ' + dev-python/sphinx[${PYTHON_USEDEP}] + dev-python/sphinx-copybutton[${PYTHON_USEDEP}] + dev-python/sphinx-inline-tabs[${PYTHON_USEDEP}] + dev-python/sphinx-argparse[${PYTHON_USEDEP}] + dev-python/sphinxcontrib-autoprogram[${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 ) + doc? ( !build-manual ) + cuda? ( single-precision ) + opencl? ( single-precision ) + cuda? ( !opencl ) + clang-cuda? ( clang cuda ) + mkl? ( !blas !fftw !lapack ) + ${PYTHON_REQUIRED_USE}" + +DOCS=( AUTHORS README ) + +RESTRICT="!test? ( test )" + +if [[ ${PV} != *9999 ]]; then + S="${WORKDIR}/${PN}-${PV/_/-}" +fi + +pkg_pretend() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp +} + +pkg_setup() { + [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp + python-single-r1_pkg_setup +} + +src_unpack() { + if [[ ${PV} != *9999 ]]; then + default + else + git-r3_src_unpack + if use test; then + EGIT_REPO_URI="https://gitlab.com/gromacs/gromacs-regressiontests.git" \ + EGIT_BRANCH="${EGIT_BRANCH}" \ + EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\ + git-r3_src_unpack + fi + fi +} + +src_prepare() { + #notes/todos + # -on apple: there is framework support + + xdg_environment_reset #591952 + + # we can use clang as default + if use clang && ! tc-is-clang ; then + export CC=${CHOST}-clang + export CXX=${CHOST}-clang++ + else + tc-export CXX CC + fi + # clang-cuda need to filter mfpmath + if use clang-cuda ; then + filter-mfpmath sse + filter-mfpmath i386 + fi + + cmake_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" + if use build-manual; then + # try to create policy for imagemagik + mkdir -p "${HOME}"/.config/ImageMagick + cat >> "${HOME}"/.config/ImageMagick/policy.xml <<- EOF + + + !ATTLIST policymap xmlns CDATA #FIXED ''> + + + ]> + + + + + + + + + EOF + fi +} + +src_configure() { + local mycmakeargs_pre=( ) extra fft_opts=( ) + local acce="AUTO" + + if use custom-cflags; then + #go from slowest to fastest acceleration + acce="None" + if (use amd64 || use x86); then + 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" + use cpu_flags_x86_avx512f && acce="AVX_512" + elif (use arm); then + use cpu_flags_arm_neon && acce="ARM_NEON" + elif (use arm64); then + use cpu_flags_arm_neon && acce="ARM_NEON_ASIMD" + fi + else + strip-flags + fi + + #to create man pages, build tree binaries are executed (bug #398437) + [[ ${CHOST} = *-darwin* ]] && \ + extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF" + + if use fftw; then + fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) + elif use mkl; then + local bits=$(get_libdir) + fft_opts=( -DGMX_FFT_LIBRARY=mkl + -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)" + -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)" + ) + else + fft_opts=( -DGMX_FFT_LIBRARY=fftpack ) + fi + + mycmakeargs_pre+=( + "${fft_opts[@]}" + "${lmfit_opts[@]}" + -DGMX_USE_LMFIT=EXTERNAL + -DGMX_USE_MUPARSER=EXTERNAL + -DGMX_EXTERNAL_BLAS=$(usex blas) + -DGMX_EXTERNAL_LAPACK=$(usex lapack) + -DGMX_OPENMP=$(usex openmp) + -DGMX_COOL_QUOTES=$(usex offensive) + -DGMX_USE_TNG=$(usex tng) + -DGMX_BUILD_MANUAL=$(usex build-manual) + -DGMX_HWLOC=$(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 gpu=( "-DGMX_GPU=OFF" ) + [[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" ) + [[ ${x} = "float" ]] && use clang-cuda && gpu=( "-DGMX_GPU=CUDA" "-DGMX_CLANG_CUDA=ON" ) + use opencl && gpu=( "-DGMX_GPU=OPENCL" ) + local mycmakeargs=( + ${mycmakeargs_pre[@]} ${p} + -DGMX_MPI=$(usex mpi) + -DGMX_THREAD_MPI=$(usex threads) + -DGMXAPI=$(usex gmxapi) + -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy) + "${gpu[@]}" + "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" + -DGMX_BINARY_SUFFIX="${suffix}" + -DGMX_LIBS_SUFFIX="${suffix}" + -DGMX_PYTHON_PACKAGE=$(usex python) + ) + BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure + [[ ${CHOST} != *-darwin* ]] || \ + sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die + done +} + +src_compile() { + for x in ${GMX_DIRS}; do + einfo "Compiling for ${x} precision" + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile + if use python; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile python_packaging/all + BUILD_DIR="${WORKDIR}/${P}" \ + distutils-r1_src_compile + fi + # not 100% necessary for rel ebuilds as available from website + if use build-manual; then + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile manual + fi + done +} + +src_test() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile check + done +} + +src_install() { + for x in ${GMX_DIRS}; do + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake_src_install + if use python; then + BUILD_DIR="${WORKDIR}/${P}_${x}" \ + cmake_src_install python_packaging/install + fi + if use build-manual; then + newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf" + fi + + if use doc; then + if [[ ${PV} != *9999* ]]; then + newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf" + fi + fi + done + + if use tng; then + insinto /usr/include/tng + doins src/external/tng_io/include/tng/*h + fi + # drop unneeded stuff + rm "${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 gromacs related papers from list:" + einfo "https://www.gromacs.org/articles.html" + einfo + readme.gentoo_print_elog +} diff --git a/sci-chemistry/modeller/Manifest b/sci-chemistry/modeller/Manifest index 330cfa72107a..07dd49e6424d 100644 --- a/sci-chemistry/modeller/Manifest +++ b/sci-chemistry/modeller/Manifest @@ -1,3 +1,4 @@ -DIST modeller-9.25.tar.gz 44820658 BLAKE2B b3e8a3cc8cc70689a25bc5ed2eee294d67bef8eea9ed4b64d41aba3a27c0bc428ae58e74d734da0eaab7e4fabb213d098b9ba66b9569557159ac7d4a58244b0a SHA512 93f273aba0ec0f884cde5bbcc24769a09386bfc6bf1744d80001e41924b1a682225ba3c554fb9898ef3bfd1fd8451f9458bb92431b20f2f51b01781e79686c91 -EBUILD modeller-9.25.ebuild 3838 BLAKE2B 43569c6712ed8b26152784fdedadb440014b934517b23d9f0b7d3005313767a81e9ce9de85a8d23f7407ed2d44efab69a8d4fea15739a9e89e6cfd51a2a106b4 SHA512 bb8e488420677dbbf1e8f14ef490896d46378099e7c8b6d3faa3eb44c9dc44ed4dff765ec82ae032f1dcea47b7cedcb7299759bd53bb6e4b090cc2d8eace72c2 +AUX modeller-10.5-fix-except.patch 1494 BLAKE2B 111205f2a20df7e473340ff96d5dfd428a1e1a3edccebcb6ccf51ae9c96be28950bc7433c5ae45165b66e0ce3f8213ea4554f65036dbce783b544fad3035982b SHA512 923be1e727327321930ac9893f041bfa85079da8e1e646e79ea2efdd36581f49498ef05b55a812b06f85bf8bcccd7d5d98c98be2d5ad7a3908313daef5ef5ad6 +DIST modeller-10.5.tar.gz 38272541 BLAKE2B 9c71a9f1e4c34c91852db73ebf86f71cf355217d6889566ff6840dc6874d4906b989a36f3dd642ba4e4d1fe671c1a15753a33e7fabb53adc9182c76fe4fdb6c4 SHA512 666c5367a14084438c96b68ba0779ebd97ca831a4a6538f66e54b63657c8e13b85931c2de8300311f1df7d02907b2ec61f27f95b0704f2c6a313b6baee56febc +EBUILD modeller-10.5.ebuild 3754 BLAKE2B 31ba39d295194c676b52a0999834d1ef7dbd09e62086deda48941ed023345a557dc859e384062d10ebee9dc15b22f10ffdf68c9794bc575f389da3588d0b08c9 SHA512 402464996c584d6b648e0961a77072ba02b7a167a178441f9247b99fce0c92dd6428ae62f330f44f36739d0ef2e16ac6d773e1f4484913dbd4cc058c99f1c4e6 MISC metadata.xml 375 BLAKE2B 949d039d3cd24da52efe20f58e7da07b4371e90ef72f314d076110b4604af1c0b7a77c1241172cf5e0a1c40363a00728d14d6faf30af73d27317f24d5a6c2289 SHA512 52791b3cb6a3998676f23e16346b9c4f447f42de8a58e612eebdf8ebfd34bc724c4994c3accebf00d552187bc80d1c097f73bd02b6fd6874a84441627eb785ca diff --git a/sci-chemistry/modeller/files/modeller-10.5-fix-except.patch b/sci-chemistry/modeller/files/modeller-10.5-fix-except.patch new file mode 100644 index 000000000000..f480a8229bf9 --- /dev/null +++ b/sci-chemistry/modeller/files/modeller-10.5-fix-except.patch @@ -0,0 +1,29 @@ +--- a/modlib/modeller/top_interpreter/__init__.py 2024-03-27 15:52:04.005550025 +0300 ++++ b/modlib/modeller/top_interpreter/__init__.py 2024-03-27 15:54:00.776897686 +0300 +@@ -65,7 +65,7 @@ + if len(line) > 0: + try: + self._parse_top_ini_line(line.split(None, 4), vars) +- except TypeError, detail: # noqa: E999 ++ except (TypeError, detail): # noqa: E999 + mod_log_write("read_top__E> " + str(detail)) + mod_log_write(" top.ini line: " + line) + raise +@@ -115,7 +115,7 @@ + try: + fh = self._open_include_file( + self.variables['include_file']) +- except IOError, detail: ++ except (IOError, detail): + mod_log_write("runlines__E> " + str(detail)) + mod_log_write(" TOP Command line: " + line) + raise +@@ -162,7 +162,7 @@ + indxca = self._run_top_cmd(cmd, indxca, lines, callstack, + subrout) + _modeller.mod_top_post() +- except (IndexError, SyntaxError, TypeError), detail: ++ except (IndexError, SyntaxError, TypeError, detail): + mod_log_write("runlines__E> " + str(detail)) + mod_log_write(" TOP Command line: " + line) + raise diff --git a/sci-chemistry/modeller/modeller-10.5.ebuild b/sci-chemistry/modeller/modeller-10.5.ebuild new file mode 100644 index 000000000000..80718ec876c8 --- /dev/null +++ b/sci-chemistry/modeller/modeller-10.5.ebuild @@ -0,0 +1,148 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=setuptools +DISTUTILS_EXT=1 + +inherit distutils-r1 + +DESCRIPTION="Homology or comparative modeling of protein three-dimensional structures" +HOMEPAGE="https://salilab.org/modeller/" +SRC_URI="https://salilab.org/${PN}/${PV}/${P}.tar.gz" + +LICENSE="modeller" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples" + +RESTRICT="mirror" + +DEPEND=">=dev-lang/swig-1.3" + +PATCHES=( "${FILESDIR}/${P}-fix-except.patch" ) + +INPATH="${EPREFIX}"/opt/modeller${ver} + +QA_PREBUILT="/opt/*" + +pkg_setup() { + case ${ARCH} in + x86) + EXECTYPE="i386-intel8";; + amd64) + EXECTYPE="x86_64-intel8";; + *) + die "Your arch "${ARCH}" does not appear supported at this time.";; + esac +} + +python_prepare_all() { + sed "s:i386-intel8:${EXECTYPE}:g" -i src/swig/setup.py || die + rm -rf modlib/modeller/python_library || die + distutils-r1_python_prepare_all +} + +python_compile() { + cd src/swig || die + swig -python -keyword -nodefaultctor -nodefaultdtor -noproxy modeller.i || die + distutils-r1_python_compile +} + +python_install() { + cd src/swig || die + distutils-r1_python_install +} + +python_install_all() { + cd "${S}" || die + sed \ + -e "/^EXECUTABLE_TYPE/s:xxx:${EXECTYPE}:g" \ + -e "/MODINSTALL/s:xxx:\"${INPATH}\":g" \ + -i bin/modscript || die + + sed -e "s;@TOPDIR\@;\"${INPATH}\";" \ + -e "s;@EXETYPE\@;${EXECTYPE};" \ + bin/modpy.sh.in > "${T}/modpy.sh" + + insinto ${INPATH} + doins -r modlib + python_foreach_impl python_domodule modlib/modeller + + insinto ${INPATH}/bin + doins -r bin/{lib,*top} + + exeinto ${INPATH}/bin + doexe bin/{modscript,mod${PV}_${EXECTYPE}} "${T}"/modpy.sh + + dosym ${INPATH}/bin/modscript /opt/bin/mod${PV} + dosym ${INPATH}/bin/modpy.sh /opt/bin/modpy.sh + + exeinto ${INPATH}/lib/${EXECTYPE}/ + doexe lib/${EXECTYPE}/lib* + dosym libmodeller.so.12 ${INPATH}/lib/${EXECTYPE}/libmodeller.so + dosym ../../${INPATH}/lib/${EXECTYPE}/libmodeller.so.12 /usr/$(get_libdir)/libmodeller.so.12 + + use doc && HTML_DOCS=( doc/. ) + distutils-r1_python_install_all + + if use examples; then + insinto /usr/share/${PN}/ + doins -r examples + fi + + insinto /etc/revdep-rebuild + cat >> "${T}"/40-${PN} <<- EOF + SEARCH_DIRS_MASK="${EPREFIX}/opt/modeller/lib/" + EOF + doins "${T}"/40-${PN} +} + +pkg_postinst() { + if [[ ! -e "${INPATH}/modlib/modeller/config.py" ]]; then + echo install_dir = \"${INPATH}/\"> ${INPATH}/modlib/modeller/config.py + fi + + if grep -q license ${INPATH}/modlib/modeller/config.py; then + einfo "A license key file is already present in ${INPATH}/modlib/modeller/config.py" + else + ewarn "Obtain a license Key from" + ewarn "http://salilab.org/modeller/registration.html" + ewarn "And run this before using modeller:" + ewarn "emerge --config =${CATEGORY}/${PF}" + ewarn "That way you can [re]enter your license key." + fi +} + +pkg_postrm() { + ewarn "This package leaves a license Key file in ${INPATH}/modlib/modeller/config.py" + ewarn "that you need to remove to completely get rid of modeller." +} + +pkg_config() { + ewarn "Your license key is NOT checked for validity here." + ewarn " Make sure you type it in correctly." + eerror "If you CTRL+C out of this, modeller will not run!" + while true + do + einfo "Please enter your license key:" + read license_key1 + einfo "Please re-enter your license key:" + read license_key2 + if [[ "$license_key1" == "" ]] + then + echo "You entered a blank license key. Try again." + else + if [[ "$license_key1" == "$license_key2" ]] + then + echo license = '"'$license_key1'"' >> "${INPATH}/modlib/modeller/config.py" + einfo "Thank you!" + break + else + eerror "Your license key entries do not match. Try again." + fi + fi + done +} diff --git a/sci-chemistry/modeller/modeller-9.25.ebuild b/sci-chemistry/modeller/modeller-9.25.ebuild deleted file mode 100644 index 1401279be237..000000000000 --- a/sci-chemistry/modeller/modeller-9.25.ebuild +++ /dev/null @@ -1,149 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{9..10} ) -DISTUTILS_USE_SETUPTOOLS=no - -inherit distutils-r1 - -DESCRIPTION="Homology or comparative modeling of protein three-dimensional structures" -HOMEPAGE="https://salilab.org/modeller/" -SRC_URI="https://salilab.org/${PN}/${PV}/${P}.tar.gz" - -LICENSE="modeller" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="doc examples" -SLOT="0" - -RESTRICT="mirror" - -DEPEND=">=dev-lang/swig-1.3" -RDEPEND="" - -INPATH="${EPREFIX}"/opt/modeller${ver} - -QA_PREBUILT="/opt/*" - -pkg_setup() { - case ${ARCH} in - x86) - EXECTYPE="i386-intel8";; - amd64) - EXECTYPE="x86_64-intel8";; - *) - die "Your arch "${ARCH}" does not appear supported at this time.";; - esac -} - -python_prepare_all() { - sed "s:i386-intel8:${EXECTYPE}:g" -i src/swig/setup.py || die - rm -rf modlib/modeller/python_library || die - sed -i '1 i\#!/usr/bin/python' bin/modslave.py || die - 2to3 -w -n modlib/modeller || die - distutils-r1_python_prepare_all -} - -python_compile() { - cd src/swig || die - swig -python -keyword -nodefaultctor -nodefaultdtor -noproxy modeller.i || die - distutils-r1_python_compile -} - -python_install() { - cd src/swig || die - distutils-r1_python_install -} - -python_install_all() { - cd "${S}" || die - sed \ - -e "/^EXECUTABLE_TYPE/s:xxx:${EXECTYPE}:g" \ - -e "/MODINSTALL/s:xxx:\"${INPATH}\":g" \ - -i bin/modscript || die - - sed -e "s;@TOPDIR\@;\"${INPATH}\";" \ - -e "s;@EXETYPE\@;${EXECTYPE};" \ - bin/modpy.sh.in > "${T}/modpy.sh" - - insinto ${INPATH} - doins -r modlib - python_foreach_impl python_domodule modlib/modeller - - insinto ${INPATH}/bin - doins -r bin/{lib,*top} - - exeinto ${INPATH}/bin - doexe bin/{modscript,mod${PV}_${EXECTYPE}} "${T}"/modpy.sh - - python_foreach_impl python_doscript bin/modslave.py - dosym ${INPATH}/bin/modscript /opt/bin/mod${PV} - dosym ${INPATH}/bin/modpy.sh /opt/bin/modpy.sh - - exeinto ${INPATH}/lib/${EXECTYPE}/ - doexe lib/${EXECTYPE}/lib* - dosym libmodeller.so.12 ${INPATH}/lib/${EXECTYPE}/libmodeller.so - dosym ../../${INPATH}/lib/${EXECTYPE}/libmodeller.so.12 /usr/$(get_libdir)/libmodeller.so.12 - - use doc && HTML_DOCS=( doc/. ) - distutils-r1_python_install_all - - if use examples; then - insinto /usr/share/${PN}/ - doins -r examples - fi - - insinto /etc/revdep-rebuild - cat >> "${T}"/40-${PN} <<- EOF - SEARCH_DIRS_MASK="${EPREFIX}/opt/modeller/lib/" - EOF - doins "${T}"/40-${PN} -} - -pkg_postinst() { - if [[ ! -e "${INPATH}/modlib/modeller/config.py" ]]; then - echo install_dir = \"${INPATH}/\"> ${INPATH}/modlib/modeller/config.py - fi - - if grep -q license ${INPATH}/modlib/modeller/config.py; then - einfo "A license key file is already present in ${INPATH}/modlib/modeller/config.py" - else - ewarn "Obtain a license Key from" - ewarn "http://salilab.org/modeller/registration.html" - ewarn "And run this before using modeller:" - ewarn "emerge --config =${CATEGORY}/${PF}" - ewarn "That way you can [re]enter your license key." - fi -} - -pkg_postrm() { - ewarn "This package leaves a license Key file in ${INPATH}/modlib/modeller/config.py" - ewarn "that you need to remove to completely get rid of modeller." -} - -pkg_config() { - ewarn "Your license key is NOT checked for validity here." - ewarn " Make sure you type it in correctly." - eerror "If you CTRL+C out of this, modeller will not run!" - while true - do - einfo "Please enter your license key:" - read license_key1 - einfo "Please re-enter your license key:" - read license_key2 - if [[ "$license_key1" == "" ]] - then - echo "You entered a blank license key. Try again." - else - if [[ "$license_key1" == "$license_key2" ]] - then - echo license = '"'$license_key1'"' >> "${INPATH}/modlib/modeller/config.py" - einfo "Thank you!" - break - else - eerror "Your license key entries do not match. Try again." - fi - fi - done -} diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest index 71055d224ce1..dbc27f448a0d 100644 --- a/sci-chemistry/pymol/Manifest +++ b/sci-chemistry/pymol/Manifest @@ -1,6 +1,5 @@ AUX pymol-2.5.0-format-security.patch 562 BLAKE2B 566f653ca3abd4498f9ee5d7255e1b06d8df320bd25a569620b1ee33da0cfb6a969fd3e0a65fbce7116cd6567d9a544c57f4d6d399bec00b9effa8273a52153c SHA512 4e93a0449470abdbd2d943ef0a5fac7f302485ca42c6d9ccdf1ab9a879029d5185c3f1a3a2e237fd8b3b3bf0a306bce07db3226257360127c97546480c233c4f DIST pymol-1.8.4.0.png.xz 19528 BLAKE2B f3d23d4cedca3d8bb96b20646a548da4be570697e3346a11b01c5c3599b536ba4697be08472dfa8a4f6533167defc1a37a1de332931a73857319cb28fd42cd2b SHA512 40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c -DIST pymol-2.5.0.tar.gz 10470268 BLAKE2B ad3721432001053be93afe755f531ae47348213b042e84dae33cd79580428c9ac3d00629afa0222e4081807dc80e2dd69c3963a457666b5975b6263b988d02d9 SHA512 19f21b8f735fda5314abf202d56f3c81c7251bf6ef0df73ccee534d9c08035f4ef6155ffb68e09d7717a0fb5ba7289bbfa440691bea4cec0de7199c9e858ea91 -EBUILD pymol-2.5.0-r3.ebuild 2621 BLAKE2B 79ed22aef424c23e3269def8b7e7ea8a8a755d13699938feab9d4ff5b457551439f4aafea4bd64001c1511bf8aaaa0af4ff243578e89baf1abc70133e9341fa2 SHA512 27c27c808a4c641bb5eba7a7f4c3fb6d098e60dfc4ccc21499acae97348e1eee04615278696631870934c264dfa05bc28adc556eba6fe6873165e3953f5a3937 -EBUILD pymol-2.5.0-r5.ebuild 2830 BLAKE2B cd3ef3364dbc4c5830bc4f8f4be3ec48cb7e9063a0f834be1b74ba5dd5a2cdb4e95a91cc7cd8812c8ad0454d729de28fc68d1f9576ef2bd0a15135ab1391d62e SHA512 753b61ae2f97715f678fd665862ab912d30dbf53c77b1cde78bcc32ccac4d8805450191d214caa19ece23ca1d069ddb6400935272fd3c94ef2b579c2150ac6f8 +DIST pymol-3.0.0.tar.gz 29510174 BLAKE2B b67818e408045e386e44a203f29cd94a0ce34ec706776d29f78f1720bdc5c79d88f3b3e178882295b5a636d97fe70ff49eb1b021a9a6b96f0f4216bc392219d1 SHA512 eab05a46220339a05d8d4facdce6bfa08c6fc8a858a7b228236ef6c4054207059ef0f53a26bedebe4084a74b510015937fb4477f99612b21412cd75bf0c376a2 +EBUILD pymol-3.0.0.ebuild 2831 BLAKE2B b277127a25bc4b292238b374bd6945e372bbdfc6a7855a3e03c7855dd49fb2c75f3b064fbeb783f6dfc838f3069aeb65139a23caecc858c6557eed34a40cd79e SHA512 890933535af6f7bb0f49b554e6f9ab5fc2134a04c163ef28c61e2fb351faa5fd3c5aa166dd8bc444d649dd5688f1c5a2579acfdaeca41b8ca3f1247f24027351 MISC metadata.xml 495 BLAKE2B 32d321e92c7e7c226747660c314f5cff9aabf9ee41c8a864064432ac9554879db7bf60640993dadae6e00a9b7d1367cb8ab228b63b8797ca84e5618eeeb192cc SHA512 36ef956d111c76182c70c81a830885f540fb2710f696b2711837d4bf1055a8792226f38b827f389a3a3861f259bae1394d6da50c2b33a0ddb4e6940262e1b25d diff --git a/sci-chemistry/pymol/pymol-2.5.0-r3.ebuild b/sci-chemistry/pymol/pymol-2.5.0-r3.ebuild deleted file mode 100644 index 317350640580..000000000000 --- a/sci-chemistry/pymol/pymol-2.5.0-r3.ebuild +++ /dev/null @@ -1,100 +0,0 @@ -# Copyright 1999-2024 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{9..11} ) -DISTUTILS_USE_SETUPTOOLS=no -DISTUTILS_EXT=1 - -inherit desktop flag-o-matic xdg distutils-r1 - -DESCRIPTION="A Python-extensible molecular graphics system" -HOMEPAGE="https://www.pymol.org/" -SRC_URI=" - https://dev.gentoo.org/~pacho/${PN}/${PN}-1.8.4.0.png.xz - https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz -> ${P}.tar.gz - " -LICENSE="BitstreamVera BSD freedist HPND OFL-1.0 public-domain UoI-NCSA" #844991 -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" -IUSE="+netcdf web" - -DEPEND=" - dev-cpp/msgpack-cxx - dev-libs/mmtf-cpp - dev-python/pyopengl[${PYTHON_USEDEP}] - dev-python/PyQt5[opengl,${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pmw[${PYTHON_USEDEP}] - media-libs/freetype:2 - media-libs/glew:0= - media-libs/glm - media-libs/libpng:0= - media-video/mpeg-tools - sys-libs/zlib - netcdf? ( sci-libs/netcdf:0= ) -" -RDEPEND="${DEPEND} - sci-chemistry/chemical-mime-data -" - -S="${WORKDIR}"/${PN}-open-source-${PV} - -python_prepare_all() { - sed \ - -e "s:\"/usr:\"${EPREFIX}/usr:g" \ - -e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \ - -i setup.py || die - - sed \ - -e "s:/opt/local:${EPREFIX}/usr:g" \ - -e '/ext_comp_args/s:\[.*\]:[]:g' \ - -i setup.py || die - sed \ - -e "s:\['msgpackc'\]:\['msgpack'\]:g" \ - -i setup.py || die - - append-cxxflags -std=c++0x - - distutils-r1_python_prepare_all -} - -python_configure_all() { - use !netcdf && DISTUTILS_ARGS=( --no-vmd-plugins ) -} - -python_install() { - distutils-r1_python_install \ - --pymol-path="${EPREFIX}/usr/share/pymol" - - sed \ - -e '1i#!/usr/bin/env python' \ - "${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die - python_doscript "${T}"/${PN} -} - -python_install_all() { - distutils-r1_python_install_all - - # These environment variables should not go in the wrapper script, or else - # it will be impossible to use the PyMOL libraries from Python. - cat >> "${T}"/20pymol <<- EOF || die - 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 "${WORKDIR}"/${PN}-1.8.4.0.png ${PN}.png - make_desktop_entry "${PN} %u" 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/${PN}/LICENSE || die -} diff --git a/sci-chemistry/pymol/pymol-2.5.0-r5.ebuild b/sci-chemistry/pymol/pymol-2.5.0-r5.ebuild deleted file mode 100644 index 3e0e1d344ac6..000000000000 --- a/sci-chemistry/pymol/pymol-2.5.0-r5.ebuild +++ /dev/null @@ -1,108 +0,0 @@ -# Copyright 1999-2024 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{9..11} ) -DISTUTILS_USE_PEP517="setuptools" -DISTUTILS_EXT=1 - -inherit desktop flag-o-matic xdg distutils-r1 - -DESCRIPTION="A Python-extensible molecular graphics system" -HOMEPAGE="https://www.pymol.org/" -SRC_URI=" - https://dev.gentoo.org/~pacho/${PN}/${PN}-1.8.4.0.png.xz - https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz -> ${P}.tar.gz - " -LICENSE="BitstreamVera BSD freedist HPND OFL-1.0 public-domain UoI-NCSA" #844991 -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" -IUSE="+netcdf web" - -DEPEND=" - dev-cpp/msgpack-cxx - dev-libs/mmtf-cpp - dev-python/pyopengl[${PYTHON_USEDEP}] - dev-python/PyQt5[opengl,${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pmw[${PYTHON_USEDEP}] - media-libs/freetype:2 - media-libs/glew:0= - media-libs/glm - media-libs/libpng:0= - media-video/mpeg-tools - sys-libs/zlib - netcdf? ( sci-libs/netcdf:0= ) -" -RDEPEND="${DEPEND} - sci-chemistry/chemical-mime-data -" - -S="${WORKDIR}"/${PN}-open-source-${PV} - -PATCHES=( - "${FILESDIR}/${PN}-2.5.0-format-security.patch" -) - -python_prepare_all() { - sed \ - -e "s:\"/usr:\"${EPREFIX}/usr:g" \ - -e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \ - -i setup.py || die - - sed \ - -e "s:/opt/local:${EPREFIX}/usr:g" \ - -e '/ext_comp_args/s:\[.*\]:[]:g' \ - -i setup.py || die - sed \ - -e "s:\['msgpackc'\]:\['msgpack'\]:g" \ - -i setup.py || die - - append-cxxflags -std=c++0x - - distutils-r1_python_prepare_all -} - -python_configure_all() { - use !netcdf && DISTUTILS_ARGS=( --no-vmd-plugins ) -} - -python_install() { - distutils-r1_python_install \ - --pymol-path="${EPREFIX}/usr/share/pymol" - - sed \ - -e '1i#!/usr/bin/env python' \ - "${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die - python_doscript "${T}"/${PN} -} - -python_install_all() { - distutils-r1_python_install_all - - # Move data to correct location - dodir /usr/share/pymol - mv "${D}/$(python_get_sitedir)"/pymol/pymol_path/* "${ED}/usr/share/pymol" || die - - # These environment variables should not go in the wrapper script, or else - # it will be impossible to use the PyMOL libraries from Python. - cat >> "${T}"/20pymol <<- EOF || die - PYMOL_PATH="${EPREFIX}/usr/share/pymol" - PYMOL_DATA="${EPREFIX}/usr/share/pymol/data" - PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts" - EOF - - doenvd "${T}"/20pymol - - newicon "${WORKDIR}"/${PN}-1.8.4.0.png ${PN}.png - make_desktop_entry "${PN} %u" 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/${PN}/LICENSE || die -} diff --git a/sci-chemistry/pymol/pymol-3.0.0.ebuild b/sci-chemistry/pymol/pymol-3.0.0.ebuild new file mode 100644 index 000000000000..150f7732d930 --- /dev/null +++ b/sci-chemistry/pymol/pymol-3.0.0.ebuild @@ -0,0 +1,109 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{9..12} ) +DISTUTILS_USE_PEP517="setuptools" +DISTUTILS_EXT=1 + +inherit desktop flag-o-matic xdg distutils-r1 + +DESCRIPTION="A Python-extensible molecular graphics system" +HOMEPAGE="https://www.pymol.org/" +SRC_URI=" + https://dev.gentoo.org/~pacho/${PN}/${PN}-1.8.4.0.png.xz + https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz -> ${P}.tar.gz + " + +S="${WORKDIR}"/${PN}-open-source-${PV} + +LICENSE="BitstreamVera BSD freedist HPND OFL-1.0 public-domain UoI-NCSA" #844991 +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" +IUSE="+netcdf web" + +DEPEND=" + dev-cpp/msgpack-cxx + dev-libs/mmtf-cpp + dev-python/pyopengl[${PYTHON_USEDEP}] + dev-python/PyQt5[opengl,${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pmw[${PYTHON_USEDEP}] + media-libs/freetype:2 + media-libs/glew:0= + media-libs/glm + media-libs/libpng:0= + media-video/mpeg-tools + sys-libs/zlib + netcdf? ( sci-libs/netcdf:0= ) +" +RDEPEND="${DEPEND} + sci-chemistry/chemical-mime-data +" + +PATCHES=( + "${FILESDIR}/${PN}-2.5.0-format-security.patch" +) + +python_prepare_all() { + sed \ + -e "s:\"/usr:\"${EPREFIX}/usr:g" \ + -e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \ + -i setup.py || die + + sed \ + -e "s:/opt/local:${EPREFIX}/usr:g" \ + -e '/ext_comp_args/s:\[.*\]:[]:g' \ + -i setup.py || die + sed \ + -e "s:\['msgpackc'\]:\['msgpack'\]:g" \ + -i setup.py || die + + append-cxxflags -std=c++17 + + distutils-r1_python_prepare_all +} + +python_configure_all() { + use !netcdf && DISTUTILS_ARGS=( --no-vmd-plugins ) +} + +python_install() { + distutils-r1_python_install \ + --pymol-path="${EPREFIX}/usr/share/pymol" + + sed \ + -e '1i#!/usr/bin/env python' \ + "${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die + python_doscript "${T}"/${PN} +} + +python_install_all() { + distutils-r1_python_install_all + + # Move data to correct location + dodir /usr/share/pymol + mv "${D}/$(python_get_sitedir)"/pymol/pymol_path/* "${ED}/usr/share/pymol" || die + + # These environment variables should not go in the wrapper script, or else + # it will be impossible to use the PyMOL libraries from Python. + cat >> "${T}"/20pymol <<- EOF || die + PYMOL_PATH="${EPREFIX}/usr/share/pymol" + PYMOL_DATA="${EPREFIX}/usr/share/pymol/data" + PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts" + EOF + + doenvd "${T}"/20pymol + + newicon "${WORKDIR}"/${PN}-1.8.4.0.png ${PN}.png + make_desktop_entry "${PN} %u" 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 +} -- cgit v1.2.3