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

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* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2020-09-17 20:58 Pacho Ramos
  0 siblings, 0 replies; 23+ 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] 23+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2024-12-26 17:50 Ionen Wolkens
  0 siblings, 0 replies; 23+ messages in thread
From: Ionen Wolkens @ 2024-12-26 17:50 UTC (permalink / raw
  To: gentoo-commits

commit:     fc5107437cc612cada0a3222a250d19375f11ea0
Author:     Ionen Wolkens <ionen <AT> gentoo <DOT> org>
AuthorDate: Thu Dec 26 08:41:42 2024 +0000
Commit:     Ionen Wolkens <ionen <AT> gentoo <DOT> org>
CommitDate: Thu Dec 26 17:48:34 2024 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=fc510743

sci-chemistry/vmd: add binding := to fltk, soname changed

Also cleanup lower bound, 1.1 is extremely ancient.

Untested with fltk-1.4 given have not bothered getting the
fetch restricted distfile. If there's any issues, note that
fixes are typically easy (often IWYU missing headers or
misnamed headers that relied on compat symlinks) and should
avoid a upper bound if possible.

Signed-off-by: Ionen Wolkens <ionen <AT> gentoo.org>

 .../vmd/{vmd-1.9.4_alpha57.ebuild => vmd-1.9.4_alpha57-r2.ebuild}       | 2 +-
 .../vmd/{vmd-1.9.4_alpha57-r1.ebuild => vmd-1.9.4_alpha57-r3.ebuild}    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha57.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha57-r2.ebuild
similarity index 99%
rename from sci-chemistry/vmd/vmd-1.9.4_alpha57.ebuild
rename to sci-chemistry/vmd/vmd-1.9.4_alpha57-r2.ebuild
index e0628f111574..9addf38da980 100644
--- a/sci-chemistry/vmd/vmd-1.9.4_alpha57.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.4_alpha57-r2.ebuild
@@ -35,7 +35,7 @@ CDEPEND="${PYTHON_DEPS}
 	dev-libs/expat
 	sci-libs/netcdf:0=
 	virtual/opengl
-	>=x11-libs/fltk-1.1.10-r2:1
+	x11-libs/fltk:1=
 	x11-libs/libXft
 	x11-libs/libXi
 	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= )

diff --git a/sci-chemistry/vmd/vmd-1.9.4_alpha57-r1.ebuild b/sci-chemistry/vmd/vmd-1.9.4_alpha57-r3.ebuild
similarity index 99%
rename from sci-chemistry/vmd/vmd-1.9.4_alpha57-r1.ebuild
rename to sci-chemistry/vmd/vmd-1.9.4_alpha57-r3.ebuild
index 18bdb88a4c0c..cc5a157bf69a 100644
--- a/sci-chemistry/vmd/vmd-1.9.4_alpha57-r1.ebuild
+++ b/sci-chemistry/vmd/vmd-1.9.4_alpha57-r3.ebuild
@@ -35,7 +35,7 @@ CDEPEND="${PYTHON_DEPS}
 	dev-libs/expat
 	sci-libs/netcdf:0=
 	virtual/opengl
-	>=x11-libs/fltk-1.1.10-r2:1
+	x11-libs/fltk:1=
 	x11-libs/libXft
 	x11-libs/libXi
 	cuda? ( >=dev-util/nvidia-cuda-toolkit-4.2.9-r1:= )


^ permalink raw reply related	[flat|nested] 23+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2024-07-11 11:42 Pacho Ramos
  0 siblings, 0 replies; 23+ 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] 23+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2024-06-05 17:27 Alexey Shvetsov
  0 siblings, 0 replies; 23+ 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] 23+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2023-05-02 18:42 Pacho Ramos
  0 siblings, 0 replies; 23+ 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] 23+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2023-05-02 18:42 Pacho Ramos
  0 siblings, 0 replies; 23+ 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] 23+ messages in thread

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

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2022-05-20 19:30 Pacho Ramos
  0 siblings, 0 replies; 23+ 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] 23+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2022-05-20 19:30 Pacho Ramos
  0 siblings, 0 replies; 23+ 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] 23+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2021-11-11 11:03 Pacho Ramos
  0 siblings, 0 replies; 23+ 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] 23+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2021-02-12 12:31 Pacho Ramos
  0 siblings, 0 replies; 23+ 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] 23+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2020-12-06 17:19 Pacho Ramos
  0 siblings, 0 replies; 23+ 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] 23+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2020-09-12 22:32 Pacho Ramos
  0 siblings, 0 replies; 23+ 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] 23+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2020-02-09 16:36 Michał Górny
  0 siblings, 0 replies; 23+ 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] 23+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2020-01-22 21:50 Michał Górny
  0 siblings, 0 replies; 23+ 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] 23+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2020-01-16  6:39 Michał Górny
  0 siblings, 0 replies; 23+ 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] 23+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2019-05-30 11:15 Pacho Ramos
  0 siblings, 0 replies; 23+ 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] 23+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2019-02-04 21:56 Ben Kohler
  0 siblings, 0 replies; 23+ 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] 23+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2018-12-24 22:39 Zac Medico
  0 siblings, 0 replies; 23+ 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] 23+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2018-11-10 11:06 Pacho Ramos
  0 siblings, 0 replies; 23+ 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] 23+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2018-06-20 15:31 Alexey Shvetsov
  0 siblings, 0 replies; 23+ 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] 23+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2017-12-08 14:37 Alexey Shvetsov
  0 siblings, 0 replies; 23+ 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] 23+ messages in thread

* [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/
@ 2016-12-28 11:58 Pacho Ramos
  0 siblings, 0 replies; 23+ 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] 23+ messages in thread

end of thread, other threads:[~2024-12-26 17:50 UTC | newest]

Thread overview: 23+ messages (download: mbox.gz follow: Atom feed
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2020-09-17 20:58 [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/vmd/ Pacho Ramos
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2024-12-26 17:50 Ionen Wolkens
2024-07-11 11:42 Pacho Ramos
2024-06-05 17:27 Alexey Shvetsov
2023-05-02 18:42 Pacho Ramos
2023-05-02 18:42 Pacho Ramos
2022-10-15 23:26 Sam James
2022-05-20 19:30 Pacho Ramos
2022-05-20 19:30 Pacho Ramos
2021-11-11 11:03 Pacho Ramos
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2020-12-06 17:19 Pacho Ramos
2020-09-12 22:32 Pacho Ramos
2020-02-09 16:36 Michał Górny
2020-01-22 21:50 Michał Górny
2020-01-16  6:39 Michał Górny
2019-05-30 11:15 Pacho Ramos
2019-02-04 21:56 Ben Kohler
2018-12-24 22:39 Zac Medico
2018-11-10 11:06 Pacho Ramos
2018-06-20 15:31 Alexey Shvetsov
2017-12-08 14:37 Alexey Shvetsov
2016-12-28 11:58 Pacho Ramos

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