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(using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits)) (No client certificate requested) by bobolink.gentoo.org (Postfix) with ESMTPS id 187D21103DD for ; Mon, 19 May 2025 18:49:52 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id B4AC9340CC9 for ; Mon, 19 May 2025 18:49:51 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 52F70153E for ; Mon, 19 May 2025 18:49:50 +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: <1747680584.604da00bfc8aa75f6c2a45f431cd2a8990a0803c.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-2025.2.ebuild X-VCS-Directories: sci-chemistry/gromacs/ X-VCS-Committer: alexxy X-VCS-Committer-Name: Alexey Shvetsov X-VCS-Revision: 604da00bfc8aa75f6c2a45f431cd2a8990a0803c X-VCS-Branch: master Date: Mon, 19 May 2025 18:49:50 +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: 569049d4-87bf-423d-9668-77e7d28be7db X-Archives-Hash: 6a0b49c98457ff11d72530c79a6a99b5 commit: 604da00bfc8aa75f6c2a45f431cd2a8990a0803c Author: Alexey Shvetsov gentoo org> AuthorDate: Mon May 19 18:49:28 2025 +0000 Commit: Alexey Shvetsov gentoo org> CommitDate: Mon May 19 18:49:44 2025 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=604da00b sci-chemistry/gromacs: add 2025.2 Signed-off-by: Alexey Shvetsov gentoo.org> sci-chemistry/gromacs/Manifest | 3 + sci-chemistry/gromacs/gromacs-2025.2.ebuild | 358 ++++++++++++++++++++++++++++ 2 files changed, 361 insertions(+) diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index 65370d97cbb4..e1be89cb5e61 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -2,11 +2,14 @@ DIST gromacs-2023.5.tar.gz 42079310 BLAKE2B e50dbe76396230f4a886280bdebcf7b13150 DIST gromacs-2024.5.tar.gz 42353127 BLAKE2B c1fa6bd90390c9e13f11995ea9992902e136e15f6191ed47c9eac95384f97221533509ddd2bc4908f1d36fb790aab8a068fd1c00dd6f82e440f4719092b8ea37 SHA512 cb4f6bf4a6a53fb7ee4d8ed832d514d77d21eea3e1b86eec1bf51a4b6197a30aa8d68ca61919d7921c701af365077a9c84c12ef33d5584a1bc796b25709aa7af DIST gromacs-2025.0.tar.gz 44417653 BLAKE2B 9fb55c6c5c842faefe1811e8e2da558cae2564d81767da13fab9f23f674d6451700885269cd25d70caae6a7553d8b6fd885922bb74976e6bc9a7251e01ce696b SHA512 0d3b2684827f6f9223a954fa5df408c2e7fbe2e61f6aef2d9a8b6bdd614045ed08a08d3229f3203064dc0c6b747de1b36449afc2de0b7da7300199bbcc2be77f DIST gromacs-2025.1.tar.gz 44415202 BLAKE2B aff5ef4a1d75134573b14722007685c14f2c1195caed80ce3eaed074492aea535e290b25fc63e0479ff1ed296ffbc7985ed296b442fedb6ede8a6cbb780edeba SHA512 6affc4c36621528686e36a9f6008b82c1b552a4308a35b45e70129cb93de378f1c54473b1b8ee1a741c9ecdce963d28bc3746261f2a1a1f410733cbe0c583240 +DIST gromacs-2025.2.tar.gz 44447261 BLAKE2B 08ac9d7d0c16934c6af9f4026da49dca18676b9f0d2ced110992980bfcfda53276751300507fcf483f18235b7a134fafc55f7f5ad8229360830585963edaaa3a SHA512 72bc5b7fe7ad13190cc05619b786b576b4dd5523e7fdfdecc5be3b64843952c5a3c6d110c1503c5630522bbc71eb1615abd3c1387bf376a65bc286bf857dd209 DIST manual-2023.5.pdf 13579081 BLAKE2B 42f687ebcdb79bfc77aabac4fd382940c23ba27da380b8eff342c2e9255a58fc11a0458220d1f71f3c13ab1cf6fdabad00ac1bad741781d0b787899165bea2cc SHA512 0661f166f7a8dc24b4244c0139f366832ddfc1298129df2a6e29800b5d1567318781ab547bc7e9ee54de7a62abba4996f8e3010c91d6917c248117e5711d7dbb DIST manual-2024.5.pdf 13693341 BLAKE2B b2e94b845f04201734c0a3ef834d013c2e65be53614329166d3b7e4ffcdfb71f3d25a4e8d9f852c4a7570b776532b7d0f00f9f62b76b1cd7fa8567ce22d44540 SHA512 b33a6689f965cfd867daee26b88693ab0696bb49db86e4f411030f36ce924e29f9cedbf3df51e3b02a223b91aa54394144795edb632336b8aa9eb164da8d4ded DIST manual-2025.0.pdf 13801499 BLAKE2B 0b7a542680b3204e345a0a28a3abb8218d1d24389f0187f0bac6106b166087448382bf31abefc4d8579928f94ba52d309810ac3e66227f44db7030fb45018b49 SHA512 e16068e3357771a40970b17e8ad81407dff9e1621c7d35bb388cf74b80e0f4e7aea7069f08fe17c34eb83517dbf095efe3a96949f30a7c214a4b5d2c09ec7f1c DIST manual-2025.1.pdf 13805396 BLAKE2B f625b33e9b412c8a4343c7830defe331d1cc12233b3eca4f296a814d09552f15d59dc0052938b0e6ab96af623ee942059cb86e7488411bcefea454518b604c0f SHA512 de1abb1ac66f5f0e4f9238dfa7a2f0f44b4fc565d4527d508294dcce35858da32bf1ec9fce623d2d1a9b4c851a6c45cb44ac973ba0d53e56d1a6bc3225a3e2fc +DIST manual-2025.2.pdf 13810777 BLAKE2B 1ce1ef4619d1972a1e4212ab5684719744da821018b1d9e1e8fed9c03265ac8f1874f42d197845ab06e8c9ef45d6362da2985fa37f6c2f82816fa4dd14a18f0c SHA512 c48ad55c50f3cd8873affe6c28f187d62d8e0d06d204dd481d52f5ba459d1e38094656bf766b1f396673ab121ed011f3ebdbd5aca3ab5bd13ca14955748bcdc8 DIST regressiontests-2023.5.tar.gz 48619605 BLAKE2B f2549a34750c6866f054614a00a3360a09b82306e6bd5e5b848e18cdd3a3fabaac6203c5ca734901019403225dd47e0d662838abe9a1db7d07662f1c745b8e4f SHA512 3ccaf9db7dfba641a5e98ebff3d735cae3f679926aba443ffedec20dd6c85e67f0e9711ebad5dfa8105122d5411f5de6ded1802a7da4ddf0599657832c8c597a DIST regressiontests-2024.5.tar.gz 32776573 BLAKE2B 5e397b6c601132ac96b826325bd0304d5939b87f0edaa89ba84d672a9df27351f26dbc9fde39fdb7a177be2743db93198316663a39145231741d08f3268d67cf SHA512 8594e8365f676f18f227b4d6b87fa6a1a8ceab8301302469a626380a7d29035a2cd8667b4d923b26491d3db9298d6660a9c9bde9274dfeba278dfabdb54ef424 DIST regressiontests-2025.0.tar.gz 32653708 BLAKE2B 38d4fb66c33da1f16a8d1ed66841c9eecce900f24d8c5c7f7c26df43f35c431db9745ac1f195af7572439184a4f1d1f099f81e0a843b3ffbe6e8df0371d3bb31 SHA512 925a392926794af9067c7c385daafbd6b36b0f138d6a2354f23652b2a8f750bb9268b14d9d67579cfbacbc88543790317ec56e095bdccd9e0ed80fb9a39fd439 DIST regressiontests-2025.1.tar.gz 32653610 BLAKE2B 8301571cc10631ffa88999c56b2a30dec0543d49515193eced776ee13e10a6efa60a618100a486002b9c6deaddc0d17abd8b611cbdc49ee4dea91f722c1b73de SHA512 e104f35f83e3afeea1b47e9f54a277330a4774962ca572a0694fda49c1e8752aa80c834786eaa3d23adeee938af1203d5eb7f06134f702e500b452f580bb4701 +DIST regressiontests-2025.2.tar.gz 32653416 BLAKE2B 03c80b5dd80d8d0ed97f7faab5b56d8d9c1416d895a26ab871b46a2588d55b97386cb0c26b29f996d8c78460971a510f59b1930219b82104ca442c6d4b32b4b0 SHA512 bf067f867fed356352e492e51ed2c6e3a2a71ce0a43a9141db806a75101c9678a7f09ba1f0e5cfb63b3af6e375ae2edd41b8f78c1b587f5884e458fe8d6fe65f diff --git a/sci-chemistry/gromacs/gromacs-2025.2.ebuild b/sci-chemistry/gromacs/gromacs-2025.2.ebuild new file mode 100644 index 000000000000..b8f9ffbc8f82 --- /dev/null +++ b/sci-chemistry/gromacs/gromacs-2025.2.ebuild @@ -0,0 +1,358 @@ +# Copyright 1999-2025 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +CMAKE_MAKEFILE_GENERATOR="ninja" + +PYTHON_COMPAT=( python3_{11..13} ) + +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 + " + [[ ${PV} = 9999 ]] && EGIT_BRANCH="main" || EGIT_BRANCH="release-${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) + # since 2025 x86-32 support was dropped + KEYWORDS="~amd64 -arm ~arm64 ~riscv -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 nnpot +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 ) + openmp? ( + sys-devel/gcc[openmp] + llvm-core/clang-runtime[openmp] + ) + fftw? ( sci-libs/fftw:3.0= ) + hwloc? ( sys-apps/hwloc:= ) + lapack? ( virtual/lapack ) + mkl? ( sci-libs/mkl ) + mpi? ( virtual/mpi[cxx] ) + nnpot? ( sci-ml/caffe2[cuda=,opencl=] ) + sci-libs/lmfit:= + >=dev-cpp/muParser-2.3:= + ${PYTHON_DEPS} + " +BDEPEND="${CDEPEND} + virtual/pkgconfig + clang? ( >=llvm-core/clang-6:* ) + $(python_gen_cond_dep ' + dev-python/sphinx[${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}] + ') + 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" + local nnpot="OFF" + + if use nnpot; then + nnpot="TORCH" + fi + + 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=$(usex build-manual) + -DGMX_USE_HDF5=off + -DGMX_HWLOC=$(usex hwloc) + -DGMX_DEFAULT_SUFFIX=off + -DGMX_BUILD_HELP=$(usex doc) + -DGMX_SIMD="$acce" + -DGMX_NNPOT="$nnpot" + -DGMX_VMD_PLUGIN_PATH="${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 + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile man + if use python; then + BUILD_DIR="${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 +}