From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from smtp.gentoo.org (woodpecker.gentoo.org [140.211.166.183]) (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 finch.gentoo.org (Postfix) with ESMTPS id 3ADC61581EE for ; Tue, 08 Apr 2025 16:23:27 +0000 (UTC) Received: from lists.gentoo.org (bobolink.gentoo.org [140.211.166.189]) (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) (Authenticated sender: relay-lists.gentoo.org@gentoo.org) by smtp.gentoo.org (Postfix) with ESMTPSA id 2222B34311A for ; Tue, 08 Apr 2025 16:23:27 +0000 (UTC) Received: from bobolink.gentoo.org (localhost [127.0.0.1]) by bobolink.gentoo.org (Postfix) with ESMTP id 3139B1104B8; Tue, 08 Apr 2025 16:23:22 +0000 (UTC) Received: from smtp.gentoo.org (woodpecker.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by bobolink.gentoo.org (Postfix) with ESMTPS id 2712B1104B8 for ; Tue, 08 Apr 2025 16:23:22 +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) server-digest SHA256) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id C659C3430C1 for ; Tue, 08 Apr 2025 16:23:21 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 2B1BB2777 for ; Tue, 08 Apr 2025 16:23:20 +0000 (UTC) From: "Pacho Ramos" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Pacho Ramos" Message-ID: <1744129296.c72ffc755c1bd51ddc7bfe8b11e382f6e46592b2.pacho@gentoo> Subject: [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/ X-VCS-Repository: repo/gentoo X-VCS-Files: sci-chemistry/vmd/vmd-1.9.4_alpha57-r2.ebuild X-VCS-Directories: sci-chemistry/vmd/ X-VCS-Committer: pacho X-VCS-Committer-Name: Pacho Ramos X-VCS-Revision: c72ffc755c1bd51ddc7bfe8b11e382f6e46592b2 X-VCS-Branch: master Date: Tue, 08 Apr 2025 16:23:20 +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: 53f363c0-cd8b-4bc3-aafc-2a57b2b53f93 X-Archives-Hash: 8881971b84776676759af28708e0f720 commit: c72ffc755c1bd51ddc7bfe8b11e382f6e46592b2 Author: Pacho Ramos gentoo org> AuthorDate: Tue Apr 8 16:20:57 2025 +0000 Commit: Pacho Ramos gentoo org> CommitDate: Tue Apr 8 16:21:36 2025 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c72ffc75 sci-chemistry/vmd: drop 1.9.4_alpha57-r2 Signed-off-by: Pacho Ramos gentoo.org> sci-chemistry/vmd/vmd-1.9.4_alpha57-r2.ebuild | 267 -------------------------- 1 file changed, 267 deletions(-) diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha57-r2.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha57-r2.ebuild deleted file mode 100644 index 9addf38da980..000000000000 --- a/sci-chemistry/vmd/vmd-1.9.4_alpha57-r2.ebuild +++ /dev/null @@ -1,267 +0,0 @@ -# Copyright 1999-2024 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 -PYTHON_COMPAT=( python3_{10..12} ) - -inherit cuda desktop prefix python-single-r1 toolchain-funcs xdg - -DESCRIPTION="Visual Molecular Dynamics" -HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/" - -MY_PV="${PV/_alpha/a}" -MY_P="${PN}-${MY_PV}" -SRC_URI=" - ${MY_P}.src.tar.gz - fetch+https://dev.gentoo.org/~pacho/${PN}/${PN}-1.9.4_alpha57-gentoo-patches.tar.xz -" -S="${WORKDIR}/${MY_P}" -LICENSE="vmd" - -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" - -IUSE="cuda gromacs msms povray sqlite tachyon xinerama" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RESTRICT="fetch" - -CDEPEND="${PYTHON_DEPS} - $(python_gen_cond_dep ' - dev-python/numpy[${PYTHON_USEDEP}] - ') - >=dev-lang/tk-8.6.1:0= - dev-lang/perl - dev-libs/expat - sci-libs/netcdf:0= - virtual/opengl - x11-libs/fltk:1= - x11-libs/libXft - x11-libs/libXi - cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= ) - gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1:0=[tng] ) - sqlite? ( dev-db/sqlite:3= ) - tachyon? ( >=media-gfx/tachyon-0.99_beta6 ) - xinerama? ( x11-libs/libXinerama ) -" -DEPEND="${CDEPEND}" -BDEPEND=" - virtual/pkgconfig - dev-lang/swig -" -RDEPEND="${CDEPEND} - sci-biology/stride - sci-chemistry/chemical-mime-data - sci-chemistry/surf - x11-misc/xdg-utils - x11-terms/xterm - msms? ( sci-chemistry/msms-bin ) - povray? ( media-gfx/povray ) -" -VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD" - -# Binary only plugin -QA_PREBUILT="usr/lib*/vmd/plugins/LINUX/tcl/intersurf/bin/intersurf.so" -QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil/volutil" -QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil/volutil" - -pkg_nofetch() { - elog "Please download ${MY_P}.src.tar.gz from" - elog "${VMD_DOWNLOAD}" - elog "after agreeing to the license." - elog "Place it into your DISTDIR directory." -} - -src_prepare() { - # Apply user patches from ${WORKDIR} to allow patching on patches - # subdir too - cd "${WORKDIR}" - default - - # https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32121.html - # https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32116.html - eapply "${WORKDIR}"/${PN}-patches/${PN}-1.9.4a51-gentoo-plugins.patch - - use cuda && cuda_sanitize - - # Prepare plugins - cd plugins || die - - sed '/^.SILENT/d' -i $(find -name Makefile) - - sed \ - -e "s:CC = gcc:CC = $(tc-getCC):" \ - -e "s:CXX = g++:CXX = $(tc-getCXX):" \ - -e "s:COPTO =.*\":COPTO = -fPIC -o \":" \ - -e "s:LOPTO = .*\":LOPTO = ${LDFLAGS} -fPIC -o \":" \ - -e "s:CCFLAGS =.*\":CCFLAGS = ${CFLAGS}\":" \ - -e "s:CXXFLAGS =.*\":CXXFLAGS = ${CXXFLAGS}\":" \ - -e "s:SHLD = gcc:SHLD = $(tc-getCC) -shared:" \ - -e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX) -shared:" \ - -e "s:-ltcl8.5:-ltcl:" \ - -i Make-arch || die "Failed to set up plugins Makefile" - - sed \ - -e '/^AR /s:=:?=:g' \ - -e '/^RANLIB /s:=:?=:g' \ - -i ../plugins/*/Makefile || die - - tc-export AR RANLIB - - sed \ - -e "s:\$(CXXFLAGS)::g" \ - -i hesstrans/Makefile || die - - # prepare vmd itself - cd "${S}" || die - - eapply "${WORKDIR}"/${PN}-patches/${PN}-1.9.4a51-gentoo-paths.patch - - # https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/32122.html - eapply "${WORKDIR}"/${PN}-patches/${PN}-1.9.4-tmpdir.patch - - # PREFIX - sed \ - -e "s:/usr/include/:${EPREFIX}/usr/include:g" \ - -i configure || die - - sed \ - -e "s:gentoo-bindir:${ED}/usr/bin:g" \ - -e "s:gentoo-libdir:${ED}/usr/$(get_libdir):g" \ - -e "s:gentoo-opengl-include:${EPREFIX}/usr/include/GL:g" \ - -e "s:gentoo-opengl-libs:${EPREFIX}/usr/$(get_libdir):g" \ - -e "s:gentoo-gcc:$(tc-getCC):g" \ - -e "s:gentoo-g++:$(tc-getCXX):g" \ - -e "s:gentoo-nvcc:${EPREFIX}/opt/cuda/bin/nvcc:g" \ - -e "s:gentoo-cflags:${CFLAGS}:g" \ - -e "s:gentoo-cxxflags:${CXXFLAGS}:g" \ - -e "s:gentoo-nvflags::g" \ - -e "s:gentoo-ldflags:${LDFLAGS}:g" \ - -e "s:gentoo-plugindir:${WORKDIR}/plugins:g" \ - -e "s:gentoo-fltk-include:$(fltk-config --includedir):g" \ - -e "s:gentoo-fltk-libs:$(dirname $(fltk-config --libs)) -Wl,-rpath,$(dirname $(fltk-config --libs)):g" \ - -e "s:gentoo-libtachyon-include:${EPREFIX}/usr/include/tachyon:g" \ - -e "s:gentoo-libtachyon-libs:${EPREFIX}/usr/$(get_libdir):g" \ - -e "s:gentoo-netcdf-include:${EPREFIX}/usr/include:g" \ - -e "s:gentoo-netcdf-libs:${EPREFIX}/usr/$(get_libdir):g" \ - -i configure || die - - if use cuda; then - sed \ - -e "s:gentoo-cuda-lib:${EPREFIX}/opt/cuda/$(get_libdir):g" \ - -e "/NVCCFLAGS/s:=:= ${NVCCFLAGS}:g" \ - -i configure src/Makefile || die - sed \ - -e '/compute_/d' \ - -i configure || die - sed \ - -e 's:-gencode .*code=sm_..::' \ - -i src/Makefile || die - fi - - sed \ - -e "s:LINUXPPC:LINUX:g" \ - -e "s:LINUXALPHA:LINUX:g" \ - -e "s:LINUXAMD64:LINUX:g" \ - -e "s:gentoo-stride:${EPREFIX}/usr/bin/stride:g" \ - -e "s:gentoo-surf:${EPREFIX}/usr/bin/surf:g" \ - -e "s:gentoo-tachyon:${EPREFIX}/usr/bin/tachyon:g" \ - -i "${S}"/bin/vmd.sh || die "failed setting up vmd wrapper script" - - EMAKEOPTS=( - TCLINC="-I${EPREFIX}/usr/include" - TCLLIB="-L${EPREFIX}/usr/$(get_libdir)" - TCLLDFLAGS="-shared" - NETCDFLIB="$($(tc-getPKG_CONFIG) --libs-only-L netcdf)${EPREFIX}/usr/$(get_libdir)/libnetcdf.so" - NETCDFINC="$($(tc-getPKG_CONFIG) --cflags-only-I netcdf)${EPREFIX}/usr/include" - NETCDFLDFLAGS="$($(tc-getPKG_CONFIG) --libs netcdf)" - NETCDFDYNAMIC=1 - EXPATINC="-I${EPREFIX}/usr/include" - EXPATLIB="$($(tc-getPKG_CONFIG) --libs expat)" - EXPATLDFLAGS="-shared" - EXPATDYNAMIC=1 - ) - if use gromacs; then - EMAKEOPTS+=( - TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)" - TNGINC="-I${EPREFIX}/usr/include" - TNGLDFLAGS="-shared" - TNGDYNAMIC=1 - ) - fi - if use sqlite; then - EMAKEOPTS+=( - SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)" - SQLITEINC="-I${EPREFIX}/usr/include" - SQLITELDFLAGS="-shared" - SQLITEDYNAMIC=1 - ) - fi -} - -src_configure() { - local myconf="OPENGL OPENGLPBUFFER COLVARS FLTK TK TCL PTHREADS PYTHON IMD NETCDF NUMPY NOSILENT XINPUT" - rm -f configure.options && echo $myconf >> configure.options - - use cuda && myconf+=" CUDA" -# use mpi && myconf+=" MPI" - use tachyon && myconf+=" LIBTACHYON" - use xinerama && myconf+=" XINERAMA" - - export \ - PYTHON_INCLUDE_DIR="$(python_get_includedir)" \ - PYTHON_LIBRARY_DIR="$(python_get_library_path)" \ - PYTHON_LIBRARY="$(python_get_LIBS)" \ - NUMPY_INCLUDE_DIR="$(python_get_sitedir)/numpy/core/include" \ - NUMPY_LIBRARY_DIR="$(python_get_sitedir)/numpy/core/include" - - perl ./configure LINUX \ - ${myconf} || die -} - -src_compile() { - # build plugins - cd "${WORKDIR}"/plugins || die - - emake \ - ${EMAKEOPTS[@]} \ - LINUX - - # build vmd - cd "${S}"/src || die - emake -} - -src_install() { - # install plugins - cd "${WORKDIR}"/plugins || die - emake \ - PLUGINDIR="${ED}/usr/$(get_libdir)/${PN}/plugins" \ - distrib - - # install vmd - cd "${S}"/src || die - emake install - - # install docs - cd "${S}" || die - dodoc Announcement README doc/ig.pdf doc/ug.pdf - - # remove some of the things we don't want and need in - # /usr/lib - cd "${ED}"/usr/$(get_libdir)/vmd || die - rm -fr doc README Announcement LICENSE || \ - die "failed to clean up /usr/lib/vmd directory" - - # adjust path in vmd wrapper - sed \ - -e "s:${ED}::" -i "${ED}"/usr/bin/${PN} \ - -e "/^defaultvmddir/s:^.*$:defaultvmddir=\"${EPREFIX}/usr/$(get_libdir)/${PN}\":g" \ - || die "failed to set up vmd wrapper script" - - # install icon and generate desktop entry - insinto /usr/share/pixmaps - doins "${WORKDIR}"/vmd-patches/vmd.png - eprefixify "${WORKDIR}"/vmd-patches/vmd.desktop - domenu "${WORKDIR}"/vmd-patches/vmd.desktop -}