[gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/

["Sam James" <sam@gentoo.org>]

commit:     374f6ec5091a7208d1d75948caa7a18c7b1dca54
Author:     Sam James <sam <AT> gentoo <DOT> org>
AuthorDate: Sat Oct 15 15:35:32 2022 +0000
Commit:     Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Sat Oct 15 23:26:17 2022 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=374f6ec5

sci-chemistry/vmd: drop 1.9.4_alpha55

Signed-off-by: Sam James <sam <AT> gentoo.org>

 sci-chemistry/vmd/Manifest                 |   2 -
 sci-chemistry/vmd/vmd-1.9.4_alpha55.ebuild | 269 -----------------------------
 2 files changed, 271 deletions(-)

diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index b37c5944d2a0..a736ed9ed3ca 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -1,4 +1,2 @@
-DIST vmd-1.9.4_alpha51-gentoo-patches.tar.xz 14604 BLAKE2B f8621956785d365cc056ba53373120d8f99da1476ab9789af6bb8ef00b8dd8c2a4c3599d75e13eba2fc5630b291aed966ce64f7f408504b079e3e994e45da243 SHA512 c57fd81e667e405ab1208a4e4a1d63710e593c07f554420c32980becd3547c2df98fbf6e439a53a626121fc361559f1ba53ab7b7235c97422bba61ece59d23bc
 DIST vmd-1.9.4_alpha57-gentoo-patches.tar.xz 14612 BLAKE2B e50a2fc734038207174dd5cc525f01824ce324a65b8ce604f83862ce50be6b1950d199188a717e2368b2b050256a4705662009e3530d621b19c52bb109b6a844 SHA512 6283076e47dfcd780bbc94f9ca2b044a028a472c09d78616d373813d81ec764bf1697e56a8f487f9f0999cf409c0f141bf248156f60851073347d1b640a6953c
-DIST vmd-1.9.4a55.src.tar.gz 43049895 BLAKE2B 311fdbf8742647d1dbba8346e8559d26b19ec445bb5df4b23f684c5769997e2261e200b8118668d296654f59ab340fc150f5aa33fc808ad55f2e78ce7030960b SHA512 1be5f50555423120fd8c5c335a346a40253fb80cc352f08907d864f6b34d3debe28d9a3fbf821c3a6c7c86c615fd09735c05aadf1b4503722075e9ab0b946378
 DIST vmd-1.9.4a57.src.tar.gz 43155120 BLAKE2B de0da96f6681c24e7b1d38890f109088187198cbdddb3d86d783322e837b7a71224085699f3addf2833cf293ab2689f06ab47df284b8fbe080162740094ae844 SHA512 0a3726d8fa279ac62c368cd18724cd09535618454ff6e299d147291ef5d4198ad9d58a94f0b05699ec8a23128753c55e7397c95a5ce194e36d3fabef1bcf454c

diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha55.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha55.ebuild
deleted file mode 100644
index 28638554552f..000000000000
--- a/sci-chemistry/vmd/vmd-1.9.4_alpha55.ebuild
+++ /dev/null
@@ -1,269 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-PYTHON_COMPAT=( python3_{8..10} )
-
-inherit cuda desktop flag-o-matic 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}/${PN}-1.9.4_alpha51-gentoo-patches.tar.xz
-"
-
-SLOT="0"
-LICENSE="vmd"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-IUSE="cuda gromacs msms povray sqlite tachyon xinerama"
-REQUIRED_USE="${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-1.1.10-r2:1
-	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 )
-"
-
-S="${WORKDIR}/${MY_P}"
-
-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
-}