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

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* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2016-12-28 11:58 Pacho Ramos
  0 siblings, 0 replies; 22+ messages in thread
From: Pacho Ramos @ 2016-12-28 11:58 UTC (permalink / raw
  To: gentoo-commits

commit:     836b5ca891fcae762875a927afe65d1e6de9a99a
Author:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Wed Dec 28 11:35:27 2016 +0000
Commit:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Wed Dec 28 11:58:04 2016 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=836b5ca8

sci-chemistry/vmd: Needs to be rebuilt with netcdf subslot bumps

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-chemistry/vmd/vmd-1.9.2.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/vmd/vmd-1.9.2.ebuild b/sci-chemistry/vmd/vmd-1.9.2.ebuild
index c9647a1..cbad14c 100644
--- a/sci-chemistry/vmd/vmd-1.9.2.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -28,7 +28,7 @@ CDEPEND="
 	dev-lang/perl
 	dev-libs/expat
 	dev-python/numpy[${PYTHON_USEDEP}]
-	sci-libs/netcdf
+	sci-libs/netcdf:0=
 	virtual/opengl
 	>=x11-libs/fltk-1.1.10-r2:1
 	x11-libs/libXft


^ permalink raw reply related	[flat|nested] 22+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2017-12-08 14:37 Alexey Shvetsov
  0 siblings, 0 replies; 22+ messages in thread
From: Alexey Shvetsov @ 2017-12-08 14:37 UTC (permalink / raw
  To: gentoo-commits

commit:     446a9f633b7faf69bf1c6b8624f8f2e965b7dc74
Author:     Alexey Shvetsov <alexxy <AT> omrb <DOT> pnpi <DOT> spb <DOT> ru>
AuthorDate: Fri Dec  8 14:37:27 2017 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Fri Dec  8 14:37:27 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=446a9f63

sci-chemistry/vmd: Version bump

Package-Manager: Portage-2.3.16, Repoman-2.3.6

 sci-chemistry/vmd/Manifest         |   6 +-
 sci-chemistry/vmd/vmd-1.9.3.ebuild | 250 +++++++++++++++++++++++++++++++++++++
 2 files changed, 254 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index 8f003565998..49868a8280d 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -1,2 +1,4 @@
-DIST vmd-1.9.2-gentoo-patches.tar.xz 14896 SHA256 91508b384cb0a8aab8d8cfc31c1e7e0bc4225dbd7cdb36fbaefcfe8baca9442c SHA512 0516b9e57b256ce822a64df420ebf3ab7391722757caeaa7e615526242043e9375fee8f4ee86fb4eb8de7a50d5cfc8f8d973ace5fa082e6f9010eb692cd6ee51 WHIRLPOOL 3f87d24ad0ca7eb60e0ae3d561da7c61e0caa9fe8bb71cd3a06731228926d4c16ee03699d80adf02e2c9b263f96ea8d5b096e64e3e94b0208b1cb618c8a8a7ca
-DIST vmd-1.9.2.src.tar.gz 34903084 SHA256 870ee1e483ad23eb7f3bb6ac816cb7be5df893879dddc0bda8423a011993ccdb SHA512 b232b743d4ea97dcf76e3005e1c8716d7138602edc078c4846026ab67759c8559af956182cb1acf3c85890db10b6f658ac9c269d432f2595612cf376d6d505ef WHIRLPOOL e2489b4bd8f28359ee959d6ebec3a9e775fbaf7a25baa1324c99dd04c7768e002924c671c11830ec6e9589ecc9de4864f2bcf3dfaf9eb36f5a1d03d5e5841f17
+DIST vmd-1.9.2-gentoo-patches.tar.xz 14896 BLAKE2B eb7c7fb982602f37bd8374bf8458a0a2ea2202161248caffd0d4e0f8124d627755304bb778976e1cf5598b6bfbbe5d8c8e6016c9ec562204d6782aaaf179b185 SHA512 0516b9e57b256ce822a64df420ebf3ab7391722757caeaa7e615526242043e9375fee8f4ee86fb4eb8de7a50d5cfc8f8d973ace5fa082e6f9010eb692cd6ee51
+DIST vmd-1.9.2.src.tar.gz 34903084 BLAKE2B f7f7048ef7bb72a8b0dcae955c7f90691085158c38a59229d5b929a4b52d3148bdb2f40084cf8c4544f01cb8bcb57de1d98a90bd17568a07c4ebb8f6985cec9b SHA512 b232b743d4ea97dcf76e3005e1c8716d7138602edc078c4846026ab67759c8559af956182cb1acf3c85890db10b6f658ac9c269d432f2595612cf376d6d505ef
+DIST vmd-1.9.3-gentoo-patches.tar.xz 14804 BLAKE2B 64e5df40ed88c23c924d32636495f0383590f91dbb714e64c73551072bb50d72b4e5f188fb2da58d32e84b4bc96ff0297d7ff1bf02b0481198901c4e12e4ee59 SHA512 5d506d4df5ca4a3edb33d77aeeb440fcb4750a250c77103b99f385f356eb9d71d954173b981d3a50f7a714cfc872587e5040868904e50fa1f6fd69d7e4d9f1b1
+DIST vmd-1.9.3.src.tar 129566720 BLAKE2B 848f3280d51765dcd18722dd233e0cdee3b7c0ac3dd48324260ebe1604ba781ca0a1fe4cae6652501d23d5d41712020e17dbb6bc21a1856eb3289a4aab6b774b SHA512 0502df1e8b60c570ca88b779b4153acfaa599a78df53fa96fca36301bab902864118332b5524ae7d170d3a9e429cf1e13d69e1197268b5e841afc0bb56a737ba

diff --git a/sci-chemistry/vmd/vmd-1.9.3.ebuild b/sci-chemistry/vmd/vmd-1.9.3.ebuild
new file mode 100644
index 00000000000..81ebf51d9c2
--- /dev/null
+++ b/sci-chemistry/vmd/vmd-1.9.3.ebuild
@@ -0,0 +1,250 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit cuda eutils flag-o-matic multilib prefix python-single-r1 toolchain-funcs
+
+DESCRIPTION="Visual Molecular Dynamics"
+HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"
+SRC_URI="
+	https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz
+	${P}.src.tar"
+
+SLOT="0"
+LICENSE="vmd"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="cuda gromacs msms povray sqlite tachyon xinerama"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RESTRICT="fetch"
+
+# currently, tk-8.5* with USE=truetype breaks some
+# tk apps such as Sequence Viewer or Timeline.
+CDEPEND="
+	>=dev-lang/tk-8.6.1
+	dev-lang/perl
+	dev-libs/expat
+	dev-python/numpy[${PYTHON_USEDEP}]
+	sci-libs/netcdf:0=
+	virtual/opengl
+	>=x11-libs/fltk-1.1.10-r2:1
+	x11-libs/libXft
+	x11-libs/libXi
+	${PYTHON_DEPS}
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= )
+	gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1[tng] )
+	sqlite? ( dev-db/sqlite:3= )
+	tachyon? ( >=media-gfx/tachyon-0.99_beta6 )
+	xinerama? ( x11-libs/libXinerama )"
+DEPEND="${CDEPEND}
+	virtual/pkgconfig
+	dev-lang/swig"
+RDEPEND="${CDEPEND}
+	sci-biology/stride
+	sci-chemistry/surf
+	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/intersurf1.1/bin/intersurf.so"
+QA_FLAGS_IGNORED_amd64=" usr/lib64/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
+QA_FLAGS_IGNORED_x86=" usr/lib/vmd/plugins/LINUX/tcl/volutil1.3/volutil"
+
+pkg_nofetch() {
+	elog "Please download ${P}.src.tar.gz from"
+	elog "${VMD_DOWNLOAD}"
+	elog "after agreeing to the license and get"
+	elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz"
+	elog "Place both in ${DISTDIR}"
+}
+
+src_prepare() {
+	use cuda && cuda_sanitize
+
+	epatch "${FILESDIR}"/${PN}-1.9.1-cuda-device_ptr.patch
+
+	cd "${WORKDIR}"/plugins || die
+
+	epatch \
+		"${WORKDIR}"/${P}-gentoo-plugins.patch
+
+	[[ ${SILENT} == yes ]] || 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
+
+	epatch "${WORKDIR}"/${P}-gentoo-base.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 $(fltk-config --libs)):g" \
+		-e "s:gentoo-netcdf-include:${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 $myconf >> configure.options
+
+	use cuda && myconf+=" CUDA"
+#	use mpi && myconf+=" MPI"
+	use tachyon && myconf+=" LIBTACHYON" && append-cflags -I"${EPREFIX}/usr/include/tachyon"
+	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.png
+	eprefixify "${WORKDIR}"/vmd.desktop
+	sed -i '/^Path/d' "${WORKDIR}"/vmd.desktop || die
+	domenu "${WORKDIR}"/vmd.desktop
+}


^ permalink raw reply related	[flat|nested] 22+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2018-06-20 15:31 Alexey Shvetsov
  0 siblings, 0 replies; 22+ messages in thread
From: Alexey Shvetsov @ 2018-06-20 15:31 UTC (permalink / raw
  To: gentoo-commits

commit:     a8911a91543c296a03ce97876bb058494bf71754
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Wed Jun 20 15:30:49 2018 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Wed Jun 20 15:30:49 2018 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a8911a91

sci-chemistry/vmd: Update metadata

Closes: https://bugs.gentoo.org/653520
Package-Manager: Portage-2.3.40, Repoman-2.3.9

 sci-chemistry/vmd/metadata.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-chemistry/vmd/metadata.xml b/sci-chemistry/vmd/metadata.xml
index 1b24082830f..6bcabe5b79d 100644
--- a/sci-chemistry/vmd/metadata.xml
+++ b/sci-chemistry/vmd/metadata.xml
@@ -12,7 +12,7 @@
   <use>
     <flag name="cuda">Use nvidia cuda toolkit for speeding up computations</flag>
     <flag name="gromacs">Add support for TNG file format</flag>
-    <flag name="msms">Add support for MSMS SAS calcualtion tool</flag>
+    <flag name="msms">Add support for MSMS SES calcualtion tool</flag>
     <flag name="povray">Add support for povray raytracer for HQ	images</flag>
     <flag name="tachyon">Add support for tachyon raytracer for HQ images</flag>
   </use>


^ permalink raw reply related	[flat|nested] 22+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2018-11-10 11:06 Pacho Ramos
  0 siblings, 0 replies; 22+ messages in thread
From: Pacho Ramos @ 2018-11-10 11:06 UTC (permalink / raw
  To: gentoo-commits

commit:     7bcb5fd26701788546a1ab3c6e71d7683652d330
Author:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Sat Nov 10 10:45:27 2018 +0000
Commit:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Sat Nov 10 11:06:20 2018 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7bcb5fd2

sci-chemistry/vmd: Needs to be rebuilt with gromacs updates

Signed-off-by: Pacho Ramos <pacho <AT> gentoo.org>
Package-Manager: Portage-2.3.51, Repoman-2.3.11

 sci-chemistry/vmd/vmd-1.9.3.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/vmd/vmd-1.9.3.ebuild b/sci-chemistry/vmd/vmd-1.9.3.ebuild
index 81ebf51d9c2..9a92a88134e 100644
--- a/sci-chemistry/vmd/vmd-1.9.3.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -35,7 +35,7 @@ CDEPEND="
 	x11-libs/libXi
 	${PYTHON_DEPS}
 	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= )
-	gromacs? ( >=sci-chemistry/gromacs-5.0.4-r1[tng] )
+	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 )"


^ permalink raw reply related	[flat|nested] 22+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2018-12-24 22:39 Zac Medico
  0 siblings, 0 replies; 22+ messages in thread
From: Zac Medico @ 2018-12-24 22:39 UTC (permalink / raw
  To: gentoo-commits

commit:     c7f0e7452ecc8115dc8cff36621cd3c336c82d48
Author:     Marty E. Plummer <hanetzer <AT> startmail <DOT> com>
AuthorDate: Sat Dec 15 01:28:14 2018 +0000
Commit:     Zac Medico <zmedico <AT> gentoo <DOT> org>
CommitDate: Mon Dec 24 22:39:22 2018 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c7f0e745

sci-chemistry/vmd: fix mixed use of tabs and spaces

Closes: https://github.com/gentoo/gentoo/pull/10643
Package-Manager: Portage-2.3.52, Repoman-2.3.12
Signed-off-by: Marty E. Plummer <hanetzer <AT> startmail.com>
Signed-off-by: Zac Medico <zmedico <AT> gentoo.org>

 sci-chemistry/vmd/metadata.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-chemistry/vmd/metadata.xml b/sci-chemistry/vmd/metadata.xml
index 6bcabe5b79d..25e17d0a8ff 100644
--- a/sci-chemistry/vmd/metadata.xml
+++ b/sci-chemistry/vmd/metadata.xml
@@ -13,7 +13,7 @@
     <flag name="cuda">Use nvidia cuda toolkit for speeding up computations</flag>
     <flag name="gromacs">Add support for TNG file format</flag>
     <flag name="msms">Add support for MSMS SES calcualtion tool</flag>
-    <flag name="povray">Add support for povray raytracer for HQ	images</flag>
+    <flag name="povray">Add support for povray raytracer for HQ images</flag>
     <flag name="tachyon">Add support for tachyon raytracer for HQ images</flag>
   </use>
 </pkgmetadata>


^ permalink raw reply related	[flat|nested] 22+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2019-02-04 21:56 Ben Kohler
  0 siblings, 0 replies; 22+ messages in thread
From: Ben Kohler @ 2019-02-04 21:56 UTC (permalink / raw
  To: gentoo-commits

commit:     c0e8a7d550dbb94fa1dc74bfe31cad0051860cff
Author:     Ben Kohler <bkohler <AT> gentoo <DOT> org>
AuthorDate: Mon Feb  4 21:43:41 2019 +0000
Commit:     Ben Kohler <bkohler <AT> gentoo <DOT> org>
CommitDate: Mon Feb  4 21:43:41 2019 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c0e8a7d5

sci-chemistry/vmd: don't reference ${DISTDIR} in pkg_nofetch

Closes: https://bugs.gentoo.org/663224
Package-Manager: Portage-2.3.59, Repoman-2.3.12
Signed-off-by: Ben Kohler <bkohler <AT> gentoo.org>

 sci-chemistry/vmd/vmd-1.9.2.ebuild | 4 ++--
 sci-chemistry/vmd/vmd-1.9.3.ebuild | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/sci-chemistry/vmd/vmd-1.9.2.ebuild b/sci-chemistry/vmd/vmd-1.9.2.ebuild
index 347a8c9a751..4bc9360f009 100644
--- a/sci-chemistry/vmd/vmd-1.9.2.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -61,7 +61,7 @@ pkg_nofetch() {
 	elog "${VMD_DOWNLOAD}"
 	elog "after agreeing to the license and get"
 	elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz"
-	elog "Place both in ${DISTDIR}"
+	elog "Place both into your DISTDIR directory"
 }
 
 src_prepare() {

diff --git a/sci-chemistry/vmd/vmd-1.9.3.ebuild b/sci-chemistry/vmd/vmd-1.9.3.ebuild
index 9a92a88134e..c1480738aa4 100644
--- a/sci-chemistry/vmd/vmd-1.9.3.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Authors
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -61,7 +61,7 @@ pkg_nofetch() {
 	elog "${VMD_DOWNLOAD}"
 	elog "after agreeing to the license and get"
 	elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz"
-	elog "Place both in ${DISTDIR}"
+	elog "Place both into your DISTDIR directory"
 }
 
 src_prepare() {


^ permalink raw reply related	[flat|nested] 22+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2019-05-30 11:15 Pacho Ramos
  0 siblings, 0 replies; 22+ messages in thread
From: Pacho Ramos @ 2019-05-30 11:15 UTC (permalink / raw
  To: gentoo-commits

commit:     17886825b13dd8039f5b8abaed7f52a329d8f334
Author:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Thu May 30 11:15:23 2019 +0000
Commit:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Thu May 30 11:15:23 2019 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=17886825

sci-chemistry/vmd: Make repoman more happy

Package-Manager: Portage-2.3.66, Repoman-2.3.12
Signed-off-by: Pacho Ramos <pacho <AT> gentoo.org>

 sci-chemistry/vmd/vmd-1.9.3-r1.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild
index 392e380ece1..3f24f85d627 100644
--- a/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild
@@ -81,7 +81,7 @@ src_prepare() {
 
 	cd "${WORKDIR}"/plugins || die
 
-	eapply -p2 "${WORKDIR}"/${P}-gentoo-plugins.patch	
+	eapply -p2 "${WORKDIR}"/${P}-gentoo-plugins.patch
 
 	[[ ${SILENT} == yes ]] || sed '/^.SILENT/d' -i $(find -name Makefile)
 


^ permalink raw reply related	[flat|nested] 22+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2020-01-16  6:39 Michał Górny
  0 siblings, 0 replies; 22+ messages in thread
From: Michał Górny @ 2020-01-16  6:39 UTC (permalink / raw
  To: gentoo-commits

commit:     2ea12cd580ee77a8b6571ecb80b6ac2481904a2d
Author:     Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 16 06:28:38 2020 +0000
Commit:     Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Thu Jan 16 06:38:07 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2ea12cd5

sci-chemistry/vmd: Permit numpy-python2

Signed-off-by: Michał Górny <mgorny <AT> gentoo.org>

 sci-chemistry/vmd/vmd-1.9.2.ebuild    | 7 +++++--
 sci-chemistry/vmd/vmd-1.9.3-r1.ebuild | 7 +++++--
 sci-chemistry/vmd/vmd-1.9.3-r2.ebuild | 7 +++++--
 sci-chemistry/vmd/vmd-1.9.3.ebuild    | 7 +++++--
 4 files changed, 20 insertions(+), 8 deletions(-)

diff --git a/sci-chemistry/vmd/vmd-1.9.2.ebuild b/sci-chemistry/vmd/vmd-1.9.2.ebuild
index 4bc9360f009..2cee984cdd4 100644
--- a/sci-chemistry/vmd/vmd-1.9.2.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -27,7 +27,10 @@ CDEPEND="
 	>=dev-lang/tk-8.6.1
 	dev-lang/perl
 	dev-libs/expat
-	dev-python/numpy[${PYTHON_USEDEP}]
+	|| (
+		dev-python/numpy-python2[${PYTHON_USEDEP}]
+		dev-python/numpy[${PYTHON_USEDEP}]
+	)
 	sci-libs/netcdf:0=
 	virtual/opengl
 	>=x11-libs/fltk-1.1.10-r2:1

diff --git a/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild
index 3f24f85d627..abf5d03202f 100644
--- a/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -27,7 +27,10 @@ CDEPEND="
 	>=dev-lang/tk-8.6.1:0=
 	dev-lang/perl
 	dev-libs/expat
-	dev-python/numpy[${PYTHON_USEDEP}]
+	|| (
+		dev-python/numpy-python2[${PYTHON_USEDEP}]
+		dev-python/numpy[${PYTHON_USEDEP}]
+	)
 	sci-libs/netcdf:0=
 	virtual/opengl
 	>=x11-libs/fltk-1.1.10-r2:1

diff --git a/sci-chemistry/vmd/vmd-1.9.3-r2.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r2.ebuild
index 02ad806afbe..8d8897a57f8 100644
--- a/sci-chemistry/vmd/vmd-1.9.3-r2.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.3-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -27,7 +27,10 @@ CDEPEND="
 	>=dev-lang/tk-8.6.1:0=
 	dev-lang/perl
 	dev-libs/expat
-	dev-python/numpy[${PYTHON_USEDEP}]
+	|| (
+		dev-python/numpy-python2[${PYTHON_USEDEP}]
+		dev-python/numpy[${PYTHON_USEDEP}]
+	)
 	sci-libs/netcdf:0=
 	virtual/opengl
 	>=x11-libs/fltk-1.1.10-r2:1

diff --git a/sci-chemistry/vmd/vmd-1.9.3.ebuild b/sci-chemistry/vmd/vmd-1.9.3.ebuild
index c1480738aa4..01098a723de 100644
--- a/sci-chemistry/vmd/vmd-1.9.3.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -27,7 +27,10 @@ CDEPEND="
 	>=dev-lang/tk-8.6.1
 	dev-lang/perl
 	dev-libs/expat
-	dev-python/numpy[${PYTHON_USEDEP}]
+	|| (
+		dev-python/numpy-python2[${PYTHON_USEDEP}]
+		dev-python/numpy[${PYTHON_USEDEP}]
+	)
 	sci-libs/netcdf:0=
 	virtual/opengl
 	>=x11-libs/fltk-1.1.10-r2:1


^ permalink raw reply related	[flat|nested] 22+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2020-01-22 21:50 Michał Górny
  0 siblings, 0 replies; 22+ messages in thread
From: Michał Górny @ 2020-01-22 21:50 UTC (permalink / raw
  To: gentoo-commits

commit:     787aa04ebb58d6e4f06e8b49890d022d6e06ff2b
Author:     Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Wed Jan 22 21:43:32 2020 +0000
Commit:     Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Wed Jan 22 21:49:52 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=787aa04e

sci-chemistry/vmd: Revbump post dep change

Signed-off-by: Michał Górny <mgorny <AT> gentoo.org>

 sci-chemistry/vmd/{vmd-1.9.3-r2.ebuild => vmd-1.9.3-r3.ebuild} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/sci-chemistry/vmd/vmd-1.9.3-r2.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r3.ebuild
similarity index 100%
rename from sci-chemistry/vmd/vmd-1.9.3-r2.ebuild
rename to sci-chemistry/vmd/vmd-1.9.3-r3.ebuild


^ permalink raw reply	[flat|nested] 22+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2020-02-09 16:36 Michał Górny
  0 siblings, 0 replies; 22+ messages in thread
From: Michał Górny @ 2020-02-09 16:36 UTC (permalink / raw
  To: gentoo-commits

commit:     8ba9e5b982ef7fd97b46b4b0f20c93ea71f6c103
Author:     Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Fri Feb  7 18:01:42 2020 +0000
Commit:     Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Sun Feb  9 16:35:21 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8ba9e5b9

sci-chemistry/vmd: Switch to PYTHON_MULTI_USEDEP API

Signed-off-by: Michał Górny <mgorny <AT> gentoo.org>

 sci-chemistry/vmd/vmd-1.9.2.ebuild                             | 10 ++++++----
 sci-chemistry/vmd/vmd-1.9.3-r1.ebuild                          | 10 ++++++----
 sci-chemistry/vmd/{vmd-1.9.3-r3.ebuild => vmd-1.9.3-r4.ebuild} | 10 ++++++----
 sci-chemistry/vmd/vmd-1.9.3.ebuild                             | 10 ++++++----
 4 files changed, 24 insertions(+), 16 deletions(-)

diff --git a/sci-chemistry/vmd/vmd-1.9.2.ebuild b/sci-chemistry/vmd/vmd-1.9.2.ebuild
index 2cee984cdd4..92daf030477 100644
--- a/sci-chemistry/vmd/vmd-1.9.2.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.2.ebuild
@@ -27,10 +27,12 @@ CDEPEND="
 	>=dev-lang/tk-8.6.1
 	dev-lang/perl
 	dev-libs/expat
-	|| (
-		dev-python/numpy-python2[${PYTHON_USEDEP}]
-		dev-python/numpy[${PYTHON_USEDEP}]
-	)
+	$(python_gen_cond_dep '
+		|| (
+			dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}]
+			dev-python/numpy[${PYTHON_MULTI_USEDEP}]
+		)
+	')
 	sci-libs/netcdf:0=
 	virtual/opengl
 	>=x11-libs/fltk-1.1.10-r2:1

diff --git a/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild
index abf5d03202f..f42cb4d104f 100644
--- a/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.3-r1.ebuild
@@ -27,10 +27,12 @@ CDEPEND="
 	>=dev-lang/tk-8.6.1:0=
 	dev-lang/perl
 	dev-libs/expat
-	|| (
-		dev-python/numpy-python2[${PYTHON_USEDEP}]
-		dev-python/numpy[${PYTHON_USEDEP}]
-	)
+	$(python_gen_cond_dep '
+		|| (
+			dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}]
+			dev-python/numpy[${PYTHON_MULTI_USEDEP}]
+		)
+	')
 	sci-libs/netcdf:0=
 	virtual/opengl
 	>=x11-libs/fltk-1.1.10-r2:1

diff --git a/sci-chemistry/vmd/vmd-1.9.3-r3.ebuild b/sci-chemistry/vmd/vmd-1.9.3-r4.ebuild
similarity index 98%
rename from sci-chemistry/vmd/vmd-1.9.3-r3.ebuild
rename to sci-chemistry/vmd/vmd-1.9.3-r4.ebuild
index 8d8897a57f8..39e7a9751ce 100644
--- a/sci-chemistry/vmd/vmd-1.9.3-r3.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.3-r4.ebuild
@@ -27,10 +27,12 @@ CDEPEND="
 	>=dev-lang/tk-8.6.1:0=
 	dev-lang/perl
 	dev-libs/expat
-	|| (
-		dev-python/numpy-python2[${PYTHON_USEDEP}]
-		dev-python/numpy[${PYTHON_USEDEP}]
-	)
+	$(python_gen_cond_dep '
+		|| (
+			dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}]
+			dev-python/numpy[${PYTHON_MULTI_USEDEP}]
+		)
+	')
 	sci-libs/netcdf:0=
 	virtual/opengl
 	>=x11-libs/fltk-1.1.10-r2:1

diff --git a/sci-chemistry/vmd/vmd-1.9.3.ebuild b/sci-chemistry/vmd/vmd-1.9.3.ebuild
index 01098a723de..88394af1970 100644
--- a/sci-chemistry/vmd/vmd-1.9.3.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.3.ebuild
@@ -27,10 +27,12 @@ CDEPEND="
 	>=dev-lang/tk-8.6.1
 	dev-lang/perl
 	dev-libs/expat
-	|| (
-		dev-python/numpy-python2[${PYTHON_USEDEP}]
-		dev-python/numpy[${PYTHON_USEDEP}]
-	)
+	$(python_gen_cond_dep '
+		|| (
+			dev-python/numpy-python2[${PYTHON_MULTI_USEDEP}]
+			dev-python/numpy[${PYTHON_MULTI_USEDEP}]
+		)
+	')
 	sci-libs/netcdf:0=
 	virtual/opengl
 	>=x11-libs/fltk-1.1.10-r2:1


^ permalink raw reply related	[flat|nested] 22+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2020-09-12 22:32 Pacho Ramos
  0 siblings, 0 replies; 22+ messages in thread
From: Pacho Ramos @ 2020-09-12 22:32 UTC (permalink / raw
  To: gentoo-commits

commit:     83ad69352b99be7362c95935706182b66fca3df4
Author:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Sat Sep 12 22:31:29 2020 +0000
Commit:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Sat Sep 12 22:32:26 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=83ad6935

sci-chemistry/vmd: Fix pkg_nofetch message

Bug: https://bugs.gentoo.org/735462
Package-Manager: Portage-3.0.6, Repoman-3.0.1
Signed-off-by: Pacho Ramos <pacho <AT> gentoo.org>

 sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild
index 29d0417b34e..6ff1210c542 100644
--- a/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild
@@ -65,16 +65,16 @@ 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 ${P}.src.tar from"
+	elog "Please download ${MY_P}.src.tar from"
 	elog "${VMD_DOWNLOAD}"
 	elog "after agreeing to the license and get"
-	elog "https://dev.gentoo.org/~jlec/distfiles/${P}-gentoo-patches.tar.xz"
+	elog "https://dev.gentoo.org/~jlec/distfiles/${PN}-1.9.3-gentoo-patches.tar.xz"
 	elog "Place both into your DISTDIR directory"
 	elog
 	elog "Due to an upstream bug (https://bugs.gentoo.org/640440) sources"
 	elog "file may get downloaded as a compressed tarball or not. In that case"
 	elog "you will need to ensure you uncompress the file and rename it"
-	elog "as ${P}.src.tar"
+	elog "to ${MY_P}.src.tar"
 }
 
 src_prepare() {


^ permalink raw reply related	[flat|nested] 22+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2020-09-17 20:58 Pacho Ramos
  0 siblings, 0 replies; 22+ messages in thread
From: Pacho Ramos @ 2020-09-17 20:58 UTC (permalink / raw
  To: gentoo-commits

commit:     2b8ca2477464d99ddabb7c1da6df8138d44917e7
Author:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Thu Sep 17 20:58:33 2020 +0000
Commit:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Thu Sep 17 20:58:33 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2b8ca247

sci-chemistry/vmd: Allow to apply user patches in plugins

Bug: https://bugs.gentoo.org/show_bug.cgi?id=741978
Package-Manager: Portage-3.0.7, Repoman-3.0.1
Signed-off-by: Pacho Ramos <pacho <AT> gentoo.org>

 sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild
index 6ff1210c542..8ffb5a09007 100644
--- a/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild
@@ -78,11 +78,15 @@ pkg_nofetch() {
 }
 
 src_prepare() {
+	# Apply user patches from ${WORKDIR} to allow patching on patches
+	# subdir too
+	cd "${WORKDIR}"
 	xdg_src_prepare
 
 	use cuda && cuda_sanitize
 
-	cd "${WORKDIR}"/plugins || die
+	# Prepare plugins
+	cd plugins || die
 
 	sed '/^.SILENT/d' -i $(find -name Makefile)
 


^ permalink raw reply related	[flat|nested] 22+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2020-12-06 17:19 Pacho Ramos
  0 siblings, 0 replies; 22+ messages in thread
From: Pacho Ramos @ 2020-12-06 17:19 UTC (permalink / raw
  To: gentoo-commits

commit:     40cc1efe632ae9c6fb0a5d165b87a76bf133a1dd
Author:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Sun Dec  6 17:19:36 2020 +0000
Commit:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Sun Dec  6 17:19:49 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=40cc1efe

sci-chemistry/vmd: Update fetch restriction message

Package-Manager: Portage-3.0.11, Repoman-3.0.2
Signed-off-by: Pacho Ramos <pacho <AT> gentoo.org>

 sci-chemistry/vmd/Manifest                 | 2 +-
 sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index e2e670e4391..60415a0181f 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -1,3 +1,3 @@
 DIST vmd-1.9.3-gentoo-patches.tar.xz 14804 BLAKE2B 64e5df40ed88c23c924d32636495f0383590f91dbb714e64c73551072bb50d72b4e5f188fb2da58d32e84b4bc96ff0297d7ff1bf02b0481198901c4e12e4ee59 SHA512 5d506d4df5ca4a3edb33d77aeeb440fcb4750a250c77103b99f385f356eb9d71d954173b981d3a50f7a714cfc872587e5040868904e50fa1f6fd69d7e4d9f1b1
-DIST vmd-1.9.4a43.src.tar 123955200 BLAKE2B a99ee2bce1024613ad951fc97f4cd4b6f6ad114aea67a0a6644f687c69eae488eb862fd5ea5bff31e12f01a95f6f60be04dad2a82879603b9b457443267bb18f SHA512 3e3d5d7b0d220f070d4978940ff5ab8af531e507a224cdd15e4871e263de64b4ba24e9d964cb680b31f376afbdc08f46cb4070e3cd4a474b9bfe0732c7b3cff0
 DIST vmd-1.9.4-gentoo-plugins.patch 24618 BLAKE2B 6fbcf2e3bb59765e0980a5ed46f02e29d7b72a313865849c15891f2398d2aaf9afe6069f993a61257572d031556ce523c622858e29611ca6795be6030f4bb186 SHA512 9b8675811992d6392e9ec49cdcbcfd0da99dce1e164be4f8bf9bd07e0582b6b1e1d25f3e90fbc91cad7f94984bd091e644713c136628d0e4cc60e782a855fb63
+DIST vmd-1.9.4a43.src.tar 123955200 BLAKE2B a99ee2bce1024613ad951fc97f4cd4b6f6ad114aea67a0a6644f687c69eae488eb862fd5ea5bff31e12f01a95f6f60be04dad2a82879603b9b457443267bb18f SHA512 3e3d5d7b0d220f070d4978940ff5ab8af531e507a224cdd15e4871e263de64b4ba24e9d964cb680b31f376afbdc08f46cb4070e3cd4a474b9bfe0732c7b3cff0

diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild
index d449af190b4..895f18b3607 100644
--- a/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.4_alpha43.ebuild
@@ -70,7 +70,8 @@ pkg_nofetch() {
 	elog "${VMD_DOWNLOAD}"
 	elog "after agreeing to the license and get"
 	elog "https://dev.gentoo.org/~jlec/distfiles/${PN}-1.9.3-gentoo-patches.tar.xz"
-	elog "Place both into your DISTDIR directory"
+	elog "https://dev.gentoo.org/~juippis/distfiles/tmp/vmd-1.9.4-gentoo-plugins.patch"
+	elog "Place them into your DISTDIR directory"
 	elog
 	elog "Due to an upstream bug (https://bugs.gentoo.org/640440) sources"
 	elog "file may get downloaded as a compressed tarball or not. In that case"


^ permalink raw reply related	[flat|nested] 22+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2021-02-12 12:31 Pacho Ramos
  0 siblings, 0 replies; 22+ messages in thread
From: Pacho Ramos @ 2021-02-12 12:31 UTC (permalink / raw
  To: gentoo-commits

commit:     3b1941d5039ebc6b665882de5bca60934b366814
Author:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Fri Feb 12 12:30:59 2021 +0000
Commit:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Fri Feb 12 12:30:59 2021 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3b1941d5

sci-chemistry/vmd: Bump to 1.9.4_alpha51

Also stop pushing people to play with tar vs tar.gz file as most web
browsers properly download tar.gz file at present time, bug #640440

Closes: https://bugs.gentoo.org/640440
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Pacho Ramos <pacho <AT> gentoo.org>

 sci-chemistry/vmd/Manifest                 |   2 +
 sci-chemistry/vmd/vmd-1.9.4_alpha51.ebuild | 270 +++++++++++++++++++++++++++++
 2 files changed, 272 insertions(+)

diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index 60415a0181f..a94593a65fc 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -1,3 +1,5 @@
 DIST vmd-1.9.3-gentoo-patches.tar.xz 14804 BLAKE2B 64e5df40ed88c23c924d32636495f0383590f91dbb714e64c73551072bb50d72b4e5f188fb2da58d32e84b4bc96ff0297d7ff1bf02b0481198901c4e12e4ee59 SHA512 5d506d4df5ca4a3edb33d77aeeb440fcb4750a250c77103b99f385f356eb9d71d954173b981d3a50f7a714cfc872587e5040868904e50fa1f6fd69d7e4d9f1b1
 DIST vmd-1.9.4-gentoo-plugins.patch 24618 BLAKE2B 6fbcf2e3bb59765e0980a5ed46f02e29d7b72a313865849c15891f2398d2aaf9afe6069f993a61257572d031556ce523c622858e29611ca6795be6030f4bb186 SHA512 9b8675811992d6392e9ec49cdcbcfd0da99dce1e164be4f8bf9bd07e0582b6b1e1d25f3e90fbc91cad7f94984bd091e644713c136628d0e4cc60e782a855fb63
+DIST vmd-1.9.4_alpha51-gentoo-patches.tar.xz 14604 BLAKE2B f8621956785d365cc056ba53373120d8f99da1476ab9789af6bb8ef00b8dd8c2a4c3599d75e13eba2fc5630b291aed966ce64f7f408504b079e3e994e45da243 SHA512 c57fd81e667e405ab1208a4e4a1d63710e593c07f554420c32980becd3547c2df98fbf6e439a53a626121fc361559f1ba53ab7b7235c97422bba61ece59d23bc
 DIST vmd-1.9.4a43.src.tar 123955200 BLAKE2B a99ee2bce1024613ad951fc97f4cd4b6f6ad114aea67a0a6644f687c69eae488eb862fd5ea5bff31e12f01a95f6f60be04dad2a82879603b9b457443267bb18f SHA512 3e3d5d7b0d220f070d4978940ff5ab8af531e507a224cdd15e4871e263de64b4ba24e9d964cb680b31f376afbdc08f46cb4070e3cd4a474b9bfe0732c7b3cff0
+DIST vmd-1.9.4a51.src.tar.gz 42826371 BLAKE2B 239d87f975c41a71096083028c1db8bf40cc058fc687fd9fff3c14c97c9b12bd68818d4c2eaeefd8c95c661409f1f056bce42178d0ba9271aa344fdce6f81ea9 SHA512 b42af6a4a7b1d2f0d242f89bff3a1c25a608ff59b9902b90154ba82a40439afb802a2d319363fa388a5211420fdaf0ee9bfd1f0a0e6e85d89d1dd506b373ba40

diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha51.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha51.ebuild
new file mode 100644
index 00000000000..732d96f97bd
--- /dev/null
+++ b/sci-chemistry/vmd/vmd-1.9.4_alpha51.ebuild
@@ -0,0 +1,270 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+PYTHON_COMPAT=( python3_{7..9} )
+
+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="
+	${MY_P}.src.tar.gz
+	https://dev.gentoo.org/~pacho/${PN}/${P}-gentoo-patches.tar.xz
+"
+
+SLOT="0"
+LICENSE="vmd"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+IUSE="cuda gromacs msms povray sqlite tachyon xinerama"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RESTRICT="fetch"
+
+CDEPEND="${PYTHON_DEPS}
+	$(python_gen_cond_dep '
+		dev-python/numpy[${PYTHON_MULTI_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 and get"
+	elog "https://dev.gentoo.org/~pacho/${PN}/${P}-gentoo-patches.tar.xz"
+	elog "Place them into your DISTDIR directory."
+}
+
+src_prepare() {
+	# Apply user patches from ${WORKDIR} to allow patching on patches
+	# subdir too
+	cd "${WORKDIR}"
+	xdg_src_prepare
+
+	# 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
+}


^ permalink raw reply related	[flat|nested] 22+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2021-11-11 11:03 Pacho Ramos
  0 siblings, 0 replies; 22+ messages in thread
From: Pacho Ramos @ 2021-11-11 11:03 UTC (permalink / raw
  To: gentoo-commits

commit:     dd5c2486af46f8cd775a04a2b3364e504fed3dc0
Author:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Thu Nov 11 11:02:24 2021 +0000
Commit:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Thu Nov 11 11:02:57 2021 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=dd5c2486

sci-chemistry/vmd: Bump to alpha55

Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Pacho Ramos <pacho <AT> gentoo.org>

 sci-chemistry/vmd/Manifest                 |   1 +
 sci-chemistry/vmd/vmd-1.9.4_alpha55.ebuild | 269 +++++++++++++++++++++++++++++
 2 files changed, 270 insertions(+)

diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index dbb4249c928..584d38bd84a 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -1,2 +1,3 @@
 DIST vmd-1.9.4_alpha51-gentoo-patches.tar.xz 14604 BLAKE2B f8621956785d365cc056ba53373120d8f99da1476ab9789af6bb8ef00b8dd8c2a4c3599d75e13eba2fc5630b291aed966ce64f7f408504b079e3e994e45da243 SHA512 c57fd81e667e405ab1208a4e4a1d63710e593c07f554420c32980becd3547c2df98fbf6e439a53a626121fc361559f1ba53ab7b7235c97422bba61ece59d23bc
 DIST vmd-1.9.4a51.src.tar.gz 42826371 BLAKE2B 239d87f975c41a71096083028c1db8bf40cc058fc687fd9fff3c14c97c9b12bd68818d4c2eaeefd8c95c661409f1f056bce42178d0ba9271aa344fdce6f81ea9 SHA512 b42af6a4a7b1d2f0d242f89bff3a1c25a608ff59b9902b90154ba82a40439afb802a2d319363fa388a5211420fdaf0ee9bfd1f0a0e6e85d89d1dd506b373ba40
+DIST vmd-1.9.4a55.src.tar.gz 43049895 BLAKE2B 311fdbf8742647d1dbba8346e8559d26b19ec445bb5df4b23f684c5769997e2261e200b8118668d296654f59ab340fc150f5aa33fc808ad55f2e78ce7030960b SHA512 1be5f50555423120fd8c5c335a346a40253fb80cc352f08907d864f6b34d3debe28d9a3fbf821c3a6c7c86c615fd09735c05aadf1b4503722075e9ab0b946378

diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha55.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha55.ebuild
new file mode 100644
index 00000000000..28638554552
--- /dev/null
+++ b/sci-chemistry/vmd/vmd-1.9.4_alpha55.ebuild
@@ -0,0 +1,269 @@
+# 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
+}


^ permalink raw reply related	[flat|nested] 22+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2022-05-20 19:30 Pacho Ramos
  0 siblings, 0 replies; 22+ messages in thread
From: Pacho Ramos @ 2022-05-20 19:30 UTC (permalink / raw
  To: gentoo-commits

commit:     7d374e6585c28845b4370683b4eb3ad266436b60
Author:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Fri May 20 19:28:06 2022 +0000
Commit:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Fri May 20 19:30:24 2022 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7d374e65

sci-chemistry/vmd: add 1.9.4_alpha57

Signed-off-by: Pacho Ramos <pacho <AT> gentoo.org>

 sci-chemistry/vmd/Manifest                 |   2 +
 sci-chemistry/vmd/vmd-1.9.4_alpha57.ebuild | 269 +++++++++++++++++++++++++++++
 2 files changed, 271 insertions(+)

diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index 584d38bd84a5..0cc49d841bd2 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -1,3 +1,5 @@
 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-1.9.4a51.src.tar.gz 42826371 BLAKE2B 239d87f975c41a71096083028c1db8bf40cc058fc687fd9fff3c14c97c9b12bd68818d4c2eaeefd8c95c661409f1f056bce42178d0ba9271aa344fdce6f81ea9 SHA512 b42af6a4a7b1d2f0d242f89bff3a1c25a608ff59b9902b90154ba82a40439afb802a2d319363fa388a5211420fdaf0ee9bfd1f0a0e6e85d89d1dd506b373ba40
 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_alpha57.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha57.ebuild
new file mode 100644
index 000000000000..d4c354c5bd35
--- /dev/null
+++ b/sci-chemistry/vmd/vmd-1.9.4_alpha57.ebuild
@@ -0,0 +1,269 @@
+# Copyright 1999-2022 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}/${PN}-1.9.4_alpha57-gentoo-patches.tar.xz
+"
+
+SLOT="0"
+LICENSE="vmd"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+IUSE="cuda gromacs msms povray sqlite tachyon xinerama"
+REQUIRED_USE="${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
+}


^ permalink raw reply related	[flat|nested] 22+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2022-05-20 19:30 Pacho Ramos
  0 siblings, 0 replies; 22+ messages in thread
From: Pacho Ramos @ 2022-05-20 19:30 UTC (permalink / raw
  To: gentoo-commits

commit:     0b747add2f74c816412a868cbf82ac1f4f2eb92e
Author:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Fri May 20 19:28:19 2022 +0000
Commit:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Fri May 20 19:30:24 2022 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0b747add

sci-chemistry/vmd: drop 1.9.4_alpha51

Signed-off-by: Pacho Ramos <pacho <AT> gentoo.org>

 sci-chemistry/vmd/Manifest                 |   1 -
 sci-chemistry/vmd/vmd-1.9.4_alpha51.ebuild | 270 -----------------------------
 2 files changed, 271 deletions(-)

diff --git a/sci-chemistry/vmd/Manifest b/sci-chemistry/vmd/Manifest
index 0cc49d841bd2..b37c5944d2a0 100644
--- a/sci-chemistry/vmd/Manifest
+++ b/sci-chemistry/vmd/Manifest
@@ -1,5 +1,4 @@
 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-1.9.4a51.src.tar.gz 42826371 BLAKE2B 239d87f975c41a71096083028c1db8bf40cc058fc687fd9fff3c14c97c9b12bd68818d4c2eaeefd8c95c661409f1f056bce42178d0ba9271aa344fdce6f81ea9 SHA512 b42af6a4a7b1d2f0d242f89bff3a1c25a608ff59b9902b90154ba82a40439afb802a2d319363fa388a5211420fdaf0ee9bfd1f0a0e6e85d89d1dd506b373ba40
 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_alpha51.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha51.ebuild
deleted file mode 100644
index f4678f8d788b..000000000000
--- a/sci-chemistry/vmd/vmd-1.9.4_alpha51.ebuild
+++ /dev/null
@@ -1,270 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-PYTHON_COMPAT=( python3_{8..9} )
-
-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="
-	${MY_P}.src.tar.gz
-	https://dev.gentoo.org/~pacho/${PN}/${P}-gentoo-patches.tar.xz
-"
-
-SLOT="0"
-LICENSE="vmd"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-IUSE="cuda gromacs msms povray sqlite tachyon xinerama"
-REQUIRED_USE="${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 and get"
-	elog "https://dev.gentoo.org/~pacho/${PN}/${P}-gentoo-patches.tar.xz"
-	elog "Place them into your DISTDIR directory."
-}
-
-src_prepare() {
-	# Apply user patches from ${WORKDIR} to allow patching on patches
-	# subdir too
-	cd "${WORKDIR}"
-	xdg_src_prepare
-
-	# 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
-}


^ permalink raw reply related	[flat|nested] 22+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2022-10-15 23:26 Sam James
  0 siblings, 0 replies; 22+ messages in thread
From: Sam James @ 2022-10-15 23:26 UTC (permalink / raw
  To: gentoo-commits

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
-}


^ permalink raw reply related	[flat|nested] 22+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2023-05-02 18:42 Pacho Ramos
  0 siblings, 0 replies; 22+ messages in thread
From: Pacho Ramos @ 2023-05-02 18:42 UTC (permalink / raw
  To: gentoo-commits

commit:     126bd93d9cd0e5087c57feb1d5ab36ee097cd4f3
Author:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Tue May  2 18:35:07 2023 +0000
Commit:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Tue May  2 18:42:46 2023 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=126bd93d

sci-chemistry/vmd: flag-o_matic.eclass is not used

Signed-off-by: Pacho Ramos <pacho <AT> gentoo.org>

 sci-chemistry/vmd/vmd-1.9.4_alpha57.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha57.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha57.ebuild
index f9ae461b0bc8..af9f38835c45 100644
--- a/sci-chemistry/vmd/vmd-1.9.4_alpha57.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.4_alpha57.ebuild
@@ -4,7 +4,7 @@
 EAPI=8
 PYTHON_COMPAT=( python3_{9..11} )
 
-inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs xdg
+inherit cuda desktop prefix python-single-r1 toolchain-funcs xdg
 
 DESCRIPTION="Visual Molecular Dynamics"
 HOMEPAGE="http://www.ks.uiuc.edu/Research/vmd/"


^ permalink raw reply related	[flat|nested] 22+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2023-05-02 18:42 Pacho Ramos
  0 siblings, 0 replies; 22+ messages in thread
From: Pacho Ramos @ 2023-05-02 18:42 UTC (permalink / raw
  To: gentoo-commits

commit:     9e05d8b3c631e019d8b69db903c82ab881cce403
Author:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Tue May  2 18:33:51 2023 +0000
Commit:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Tue May  2 18:42:46 2023 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9e05d8b3

sci-chemistry/vmd: enable py3.11

Closes: https://bugs.gentoo.org/897204
Signed-off-by: Pacho Ramos <pacho <AT> gentoo.org>

 sci-chemistry/vmd/vmd-1.9.4_alpha57.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha57.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha57.ebuild
index 5dba4060a94b..f9ae461b0bc8 100644
--- a/sci-chemistry/vmd/vmd-1.9.4_alpha57.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.4_alpha57.ebuild
@@ -2,7 +2,7 @@
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
-PYTHON_COMPAT=( python3_{9..10} )
+PYTHON_COMPAT=( python3_{9..11} )
 
 inherit cuda desktop flag-o-matic prefix python-single-r1 toolchain-funcs xdg
 


^ permalink raw reply related	[flat|nested] 22+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2024-06-05 17:27 Alexey Shvetsov
  0 siblings, 0 replies; 22+ messages in thread
From: Alexey Shvetsov @ 2024-06-05 17:27 UTC (permalink / raw
  To: gentoo-commits

commit:     435b1efde5f64e20abd52bfe53f3636c4088bce6
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Wed Jun  5 17:27:32 2024 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Wed Jun  5 17:27:32 2024 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=435b1efd

sci-chemistry/vmd: enable py3.12

Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org>

 sci-chemistry/vmd/vmd-1.9.4_alpha57.ebuild | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha57.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha57.ebuild
index af9f38835c45..e0628f111574 100644
--- a/sci-chemistry/vmd/vmd-1.9.4_alpha57.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.4_alpha57.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2023 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
-PYTHON_COMPAT=( python3_{9..11} )
+PYTHON_COMPAT=( python3_{10..12} )
 
 inherit cuda desktop prefix python-single-r1 toolchain-funcs xdg
 
@@ -15,9 +15,10 @@ 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"
-LICENSE="vmd"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 
 IUSE="cuda gromacs msms povray sqlite tachyon xinerama"
@@ -57,9 +58,6 @@ RDEPEND="${CDEPEND}
 	msms? ( sci-chemistry/msms-bin )
 	povray? ( media-gfx/povray )
 "
-
-S="${WORKDIR}/${MY_P}"
-
 VMD_DOWNLOAD="http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD"
 
 # Binary only plugin


^ permalink raw reply related	[flat|nested] 22+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2024-07-11 11:42 Pacho Ramos
  0 siblings, 0 replies; 22+ messages in thread
From: Pacho Ramos @ 2024-07-11 11:42 UTC (permalink / raw
  To: gentoo-commits

commit:     8762ad972d826ad2be59344e68b67b1bbfefe760
Author:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
AuthorDate: Thu Jul 11 11:39:53 2024 +0000
Commit:     Pacho Ramos <pacho <AT> gentoo <DOT> org>
CommitDate: Thu Jul 11 11:42:13 2024 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8762ad97

sci-chemistry/vmd: Fix compat with numpy-2 and don't mess with linking

Ebuild forcing linking flags break some utils, point to new location for
numpy2 include files

Closes: https://bugs.gentoo.org/929763
Thanks-to: he.ousia
Closes: https://bugs.gentoo.org/835604
Thanks-to: Hypoon
Signed-off-by: Pacho Ramos <pacho <AT> gentoo.org>

 sci-chemistry/vmd/vmd-1.9.4_alpha57-r1.ebuild | 263 ++++++++++++++++++++++++++
 1 file changed, 263 insertions(+)

diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha57-r1.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha57-r1.ebuild
new file mode 100644
index 000000000000..18bdb88a4c0c
--- /dev/null
+++ b/sci-chemistry/vmd/vmd-1.9.4_alpha57-r1.ebuild
@@ -0,0 +1,263 @@
+# 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}
+	$(python_gen_cond_dep '
+		>=dev-python/numpy-2[${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 )
+"
+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):" \
+		-e "s:SHXXLD = g++:SHXXLD = $(tc-getCXX):" \
+		-e "s:-ltcl8.5:-ltcl:" \
+		-i Make-arch || die "Failed to set up plugins Makefile"
+
+	sed \
+		-e '/^AR /s:=:?=:g' \
+		-e '/^RANLIB /s:=:?=:g' \
+		-i ../plugins/*/Makefile || die
+
+	tc-export AR RANLIB
+
+	sed \
+		-e "s:\$(CXXFLAGS)::g" \
+		-i hesstrans/Makefile || die
+
+	# prepare vmd itself
+	cd "${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)"
+		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)"
+		EXPATDYNAMIC=1
+	)
+	if use gromacs; then
+		EMAKEOPTS+=(
+			TNGLIB="$($(tc-getPKG_CONFIG) --libs libgromacs)"
+			TNGINC="-I${EPREFIX}/usr/include"
+			TNGDYNAMIC=1
+		)
+	fi
+	if use sqlite; then
+		EMAKEOPTS+=(
+			SQLITELIB="$($(tc-getPKG_CONFIG) --libs sqlite3)"
+			SQLITEINC="-I${EPREFIX}/usr/include"
+			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
+}


^ permalink raw reply related	[flat|nested] 22+ messages in thread

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Thread overview: 22+ messages (download: mbox.gz follow: Atom feed
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2016-12-28 11:58 [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/ Pacho Ramos
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2017-12-08 14:37 Alexey Shvetsov
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2018-11-10 11:06 Pacho Ramos
2018-12-24 22:39 Zac Medico
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2020-01-16  6:39 Michał Górny
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2020-09-12 22:32 Pacho Ramos
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