gentoo resync : 02.06.2019

5 files changed, 35 insertions, 272 deletions

diff --git a/sci-chemistry/molmol/Manifest b/sci-chemistry/molmol/Manifest
index 3fb7f463629c..d8afb6a89cc3 100644
--- a/sci-chemistry/molmol/Manifest
+++ b/sci-chemistry/molmol/Manifest
@@ -1,8 +1,6 @@
 DIST molmol-2k.2.0-doc.tar.gz 1062297 BLAKE2B 082d4eea5544bab52ffc1ff6364c50304348f76759dd3125cd74d02e629383d4a566f28ac77ab89ecf5e17a82617b8f61525e6f454689840b27899827399d866 SHA512 131f747a5762859398ebe9b676a07df56c82c8864ecc035ec914f1dea74dafcd67f87993421dfe5899c640470c7e1e1ef03ae262b04a9b360ae329eb19a331fe
 DIST molmol-2k.2.0-src.tar.gz 1088805 BLAKE2B cd649604f6ee491d3a4485391ecdaa48dc1bc4bcd82865cd4a01ca460a6653f8cbba636050bfab9027b9b95dbefa28a8deeff7065b9b461f518001242af4a849 SHA512 6ab01a6fd3d19752634a2cf22919a20e43d195768bd4bdacd5f0bbe016c3058c94915bad4c7fa64dcd86576be39cad0ae112cb62f5e69ffb10041518101e7a9b
 DIST molmol-patches.tbz2 17528 BLAKE2B b91270a980f290edc169be00639e86b3272281c9fe237750f5778eab1605ed482c09bdaf90660a5edf74bd04b3e31adc755e77e39aea6c75d88b6db9bf47a6d6 SHA512 bd94baf0a378f40f854f396963edd9b9e4afc5c56462ee6f8b68889290afdb4c5d9b10878aa5619d0a70153453fe6ee8e7540064522c6db0291ae9162bba9287
-EBUILD molmol-2k_p2-r2.ebuild 1786 BLAKE2B eda77c9e82f6b48eb38c5f47dfdd74d5916f376cc2d07fe54542fef4c1c7ecffd90ec3af82f4abd8453b15ea2044f56280dfa14274aa3d8a549136153f43c709 SHA512 cffa98ccf69382a64b4005d8971e6ecd1ed02d4199d8b494819d62439daa74b50244f6cb599c7ea73231d60f2d45d1aa49543121fc07b0e7d2ae30da044b7240
-EBUILD molmol-2k_p2-r3.ebuild 1918 BLAKE2B 134be8d8f1c11b60117c701a9b19c5f857dc554d8cd3221eae63d8f8f2d1e7d6382da8071c1d10f08294823bb1e8acabe7c3018d4817ecc9e62959f1fb204c22 SHA512 a1442eb74cc7aaa49ca81765601d1272138ed2ca3d7cebdadedd3bee4f561abf340bcfeabe4556d893df8d1be7983ac488b8773661ffc74a93a379fd503ebf0d
-EBUILD molmol-2k_p2-r4.ebuild 1935 BLAKE2B f0efe15c919180becacbd408e9974b7699276c31307773865c78ba4a2c2d122dee693af69d3aac14f3f58417410cfc0c0701207870bd474e0cda546dceab24d9 SHA512 3a59f7e5df34e0762289e6156a24bbaa7f1853c54c8db3436beae457f1c4f7e49656234f843d529099d9e2ad79ade7aff6f463f12fd5495c58265f538156c180
-EBUILD molmol-2k_p2-r5.ebuild 1947 BLAKE2B 85d1f2c7dde895f466fa334f5163be3b21eca7cc06cadb1fa15598351ea5f4bc0400680f92ed69e42031e3bfbe6a7ffcb85d9460e55055d3760eed5429360038 SHA512 6c0b9db7453acb3a14d762317548ace5a88143d9d3add2104acab0c7c2a7c6901b2086edf5bd5c48caa5fa1059664cf2c24304a88ba28e26ff77f895c1f03084
+DIST molmol.png 509 BLAKE2B 981217602d128da2eb3765ca07580ed58164a4aa8c2d3e016cd54d9f5133418a7c87bbf0f8a83bcbd5d60ad568bf4938ce680eea315716166592e37f815b5aab SHA512 233d3be0c2e2759a8b064b4cf3708f96817f34eb2a397d5122b26a902864a0f1dca1762f8bcc6981cd030e2644cbedef9eb20c7756016fcf27565e3ed586c271
+EBUILD molmol-2k_p2-r5.ebuild 2222 BLAKE2B 701c748446929618b42916e94b2742969d7b66acb055dab37834463bd5420f22e2d0119440dd58685236054a61745a36d8cd385dfd1593217595a48f9978111b SHA512 49dafa2d8a771ec2f8e3ff76f16790d61de84419037f7132581ef5de3f7c2ba12aedaf2ec778139420996d610788aef4c23ee8ac4339a8fe81cba4d36f99ebf8
 MISC metadata.xml 271 BLAKE2B a446884cbe7a6789e0bcd82759f57bf1ab7b29c5ab714057ffa821c90f799d1fa9f9310c187ee4c3a8ae2476f6ea9d15f368045779f1581e68d02802c61c884c SHA512 3e6e6047a29e07123b81279cae1de17bc4bd4c3d7d8a8d26560114a18185f473d038fc220fa81c7213fa203ce197bad8b1c272d9b7e41cd770a953fa6308ff92
diff --git a/sci-chemistry/molmol/molmol-2k_p2-r2.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r2.ebuild
deleted file mode 100644
index 888c738d4f15..000000000000
--- a/sci-chemistry/molmol/molmol-2k_p2-r2.ebuild
+++ /dev/null
@@ -1,80 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-inherit eutils multilib prefix toolchain-funcs
-
-MY_PV="${PV/_p/.}.0"
-MY_P="${PN}-${MY_PV}"
-
-DESCRIPTION="Publication-quality molecular visualization package"
-HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html"
-SRC_URI="
-	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz
-	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz
-	https://dev.gentoo.org/~soap/distfiles/${PN}-patches.tbz2"
-
-LICENSE="molmol"
-SLOT="0"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-DEPEND="
-	|| (
-		(	media-libs/mesa
-			x11-libs/libGLw )
-		media-libs/mesa[motif] )
-	media-libs/libpng:0
-	media-libs/tiff:0
-	sys-libs/zlib
-	virtual/glu
-	virtual/jpeg
-	x11-libs/libXpm
-	x11-libs/motif:0
-	x11-apps/xdpyinfo"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"
-
-MAKEOPTS="${MAKEOPTS} -j1"
-
-pkg_setup() {
-	MMDIR="/usr/$(get_libdir)/molmol"
-}
-
-src_prepare() {
-	rm -rf tiff*
-	# Patch from http://pjf.net/science/molmol.html, where src.rpm is provided
-	epatch "${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff
-
-	epatch "${WORKDIR}"/patches/prefix.patch
-	eprefixify molmol
-
-	epatch "${WORKDIR}"/patches/ldflags.patch
-
-	ln -s makedef.lnx "${S}"/makedef || die
-
-	sed \
-		-e "s:/bin/ksh:${EPREFIX}/bin/sh:" \
-		-e "s:^MOLMOLHOME.*:MOLMOLHOME=${EPREFIX}/${MMDIR}:" \
-		-i "${S}"/molmol || die
-	sed \
-		-e "s:^MCFLAGS.*:MCFLAGS = ${CFLAGS}:" \
-		-e "s:^CC.*:CC = $(tc-getCC):" \
-		-i "${S}"/makedef || die
-
-	epatch "${WORKDIR}"/patches/cast.patch
-	epatch "${WORKDIR}"/patches/libpng15.patch
-}
-
-src_install() {
-	dobin molmol
-
-	exeinto ${MMDIR}
-	newexe src/main/molmol molmol.lnx
-	insinto ${MMDIR}
-	doins -r auxil help macros man setup tips
-
-	dodoc HISTORY README
-}
diff --git a/sci-chemistry/molmol/molmol-2k_p2-r3.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r3.ebuild
deleted file mode 100644
index 22f3e6a03bdf..000000000000
--- a/sci-chemistry/molmol/molmol-2k_p2-r3.ebuild
+++ /dev/null
@@ -1,84 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=4
-
-inherit eutils multilib prefix toolchain-funcs
-
-MY_PV="${PV/_p/.}.0"
-MY_P="${PN}-${MY_PV}"
-
-DESCRIPTION="Publication-quality molecular visualization package"
-HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html"
-SRC_URI="
-	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz
-	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz
-	https://dev.gentoo.org/~soap/distfiles/${PN}-patches.tbz2"
-
-LICENSE="molmol"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-DEPEND="
-	|| (
-		(	media-libs/mesa
-			x11-libs/libGLw )
-		media-libs/mesa[motif] )
-	media-libs/libpng:0
-	media-libs/tiff:0
-	sys-libs/zlib
-	virtual/glu
-	virtual/jpeg
-	x11-libs/libXpm
-	x11-libs/motif:0
-	x11-apps/xdpyinfo"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"
-
-MAKEOPTS="${MAKEOPTS} -j1"
-
-pkg_setup() {
-	MMDIR="/usr/$(get_libdir)/molmol"
-}
-
-src_prepare() {
-	rm -rf tiff*
-	# Patch from http://pjf.net/science/molmol.html, where src.rpm is provided
-	epatch "${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff
-
-	epatch "${WORKDIR}"/patches/prefix.patch
-	eprefixify molmol
-
-	epatch "${WORKDIR}"/patches/ldflags.patch
-
-	ln -s makedef.lnx "${S}"/makedef || die
-
-	sed \
-		-e "s:/bin/ksh:${EPREFIX}/bin/sh:" \
-		-e "s:^MOLMOLHOME.*:MOLMOLHOME=${EPREFIX}/${MMDIR}:" \
-		-i "${S}"/molmol || die
-	sed \
-		-e "s:^MCFLAGS.*:MCFLAGS = ${CFLAGS}:" \
-		-e "s:^CC.*:CC = $(tc-getCC):" \
-		-i "${S}"/makedef || die
-
-	epatch "${WORKDIR}"/patches/cast.patch
-	epatch "${WORKDIR}"/patches/libpng15.patch
-
-	# patch from fink
-	# fixes numerous bad bracings and hopefully the OGL bug 429974
-	epatch "${WORKDIR}"/patches/${P}-fink.patch
-}
-
-src_install() {
-	dobin molmol
-
-	exeinto ${MMDIR}
-	newexe src/main/molmol molmol.lnx
-	insinto ${MMDIR}
-	doins -r auxil help macros man setup tips
-
-	dodoc HISTORY README
-}
diff --git a/sci-chemistry/molmol/molmol-2k_p2-r4.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r4.ebuild
deleted file mode 100644
index 26a294922182..000000000000
--- a/sci-chemistry/molmol/molmol-2k_p2-r4.ebuild
+++ /dev/null
@@ -1,86 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils multilib prefix toolchain-funcs
-
-MY_PV="${PV/_p/.}.0"
-MY_P="${PN}-${MY_PV}"
-
-DESCRIPTION="Publication-quality molecular visualization package"
-HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html"
-SRC_URI="
-	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz
-	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz
-	https://dev.gentoo.org/~soap/distfiles/${PN}-patches.tbz2"
-
-LICENSE="molmol"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-DEPEND="
-	|| (
-		(	media-libs/mesa
-			x11-libs/libGLw )
-		media-libs/mesa[motif] )
-	media-libs/libpng:0
-	media-libs/tiff:0
-	sys-libs/zlib
-	virtual/glu
-	virtual/jpeg:0
-	x11-libs/libXpm
-	x11-libs/motif:0
-	x11-apps/xdpyinfo"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"
-
-MAKEOPTS="${MAKEOPTS} -j1"
-
-pkg_setup() {
-	MMDIR="/usr/$(get_libdir)/molmol"
-}
-
-src_prepare() {
-	rm -rf tiff*
-	# Patch from http://pjf.net/science/molmol.html, where src.rpm is provided
-	epatch "${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff
-
-	epatch "${WORKDIR}"/patches/prefix.patch
-	eprefixify molmol
-
-	epatch "${WORKDIR}"/patches/ldflags.patch
-
-	ln -s makedef.lnx "${S}"/makedef || die
-
-	sed \
-		-e "s:/bin/ksh:${EPREFIX}/bin/sh:" \
-		-e "s:^MOLMOLHOME.*:MOLMOLHOME=${EPREFIX}/${MMDIR}:" \
-		-i "${S}"/molmol || die
-	sed \
-		-e "s:^MCFLAGS.*:MCFLAGS = ${CFLAGS}:" \
-		-e "s:^CC.*:CC = $(tc-getCC):" \
-		-i "${S}"/makedef || die
-
-	epatch "${WORKDIR}"/patches/cast.patch
-	epatch "${WORKDIR}"/patches/libpng15.patch
-
-	# patch from fink
-	# fixes numerous bad bracings and hopefully the OGL bug 429974
-	epatch "${WORKDIR}"/patches/${P}-fink.patch
-
-	tc-export AR
-}
-
-src_install() {
-	dobin molmol
-
-	exeinto ${MMDIR}
-	newexe src/main/molmol molmol.lnx
-	insinto ${MMDIR}
-	doins -r auxil help macros man setup tips
-
-	dodoc HISTORY README
-}
diff --git a/sci-chemistry/molmol/molmol-2k_p2-r5.ebuild b/sci-chemistry/molmol/molmol-2k_p2-r5.ebuild
index 41b041609f2f..a09bfe07847b 100644
--- a/sci-chemistry/molmol/molmol-2k_p2-r5.ebuild
+++ b/sci-chemistry/molmol/molmol-2k_p2-r5.ebuild
@@ -1,39 +1,48 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
-
-inherit eutils multilib prefix toolchain-funcs
+EAPI=7
+inherit desktop prefix toolchain-funcs
 
 MY_PV="${PV/_p/.}.0"
 MY_P="${PN}-${MY_PV}"
 
 DESCRIPTION="Publication-quality molecular visualization package"
-HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html"
+
+# Original page dead
+#HOMEPAGE="http://hugin.ethz.ch/wuthrich/software/molmol/index.html"
+HOMEPAGE="
+	http://www.csb.yale.edu/userguides/graphics/molmol/molmol_descrip.html
+	http://pjf.net/science/molmol.html
+"
 SRC_URI="
 	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-src.tar.gz
 	ftp://ftp.mol.biol.ethz.ch/software/MOLMOL/unix-gzip/${MY_P}-doc.tar.gz
-	https://dev.gentoo.org/~soap/distfiles/${PN}-patches.tbz2"
+	https://dev.gentoo.org/~soap/distfiles/${PN}-patches.tbz2
+	https://dev.gentoo.org/~pacho/${PN}/${PN}.png
+"
 
 LICENSE="molmol"
 SLOT="0"
 KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
 IUSE=""
 
-DEPEND="
+RDEPEND="
 	|| (
 		(	media-libs/mesa
 			x11-libs/libGLw )
 		media-libs/mesa[motif] )
-	media-libs/libpng:0
+	media-libs/libpng:0=
 	media-libs/tiff:0
 	sys-libs/zlib
 	virtual/glu
 	virtual/jpeg:0
 	x11-libs/libXpm
 	x11-libs/motif:0
-	x11-apps/xdpyinfo"
-RDEPEND="${DEPEND}"
+	x11-apps/xdpyinfo
+"
+DEPEND="${RDEPEND}"
+BDEPEND=""
 
 S="${WORKDIR}"
 
@@ -44,12 +53,14 @@ pkg_setup() {
 }
 
 src_prepare() {
+	default
+
 	rm -rf tiff*
 	# Patch from http://pjf.net/science/molmol.html, where src.rpm is provided
-	epatch "${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff
+	eapply "${WORKDIR}"/patches/pjf_RH9_molmol2k2.diff
 
-	epatch "${WORKDIR}"/patches/ldflags.patch
-	epatch "${WORKDIR}"/patches/opengl.patch
+	eapply "${WORKDIR}"/patches/ldflags.patch
+	eapply "${WORKDIR}"/patches/opengl.patch
 
 	ln -s makedef.lnx "${S}"/makedef || die
 
@@ -62,14 +73,14 @@ src_prepare() {
 		-e "s:^CC.*:CC = $(tc-getCC):" \
 		-i "${S}"/makedef || die
 
-	epatch "${WORKDIR}"/patches/cast.patch
-	epatch "${WORKDIR}"/patches/libpng15.patch
+	eapply "${WORKDIR}"/patches/cast.patch
+	eapply -p0 "${WORKDIR}"/patches/libpng15.patch
 
 	# patch from fink
 	# fixes numerous bad bracings and hopefully the OGL bug 429974
-	epatch "${WORKDIR}"/patches/${P}-fink.patch
+	eapply "${WORKDIR}"/patches/${P}-fink.patch
 
-	epatch "${WORKDIR}"/patches/wild.patch
+	eapply "${WORKDIR}"/patches/wild.patch
 	tc-export AR
 }
 
@@ -81,5 +92,9 @@ src_install() {
 	insinto ${MMDIR}
 	doins -r auxil help macros man setup tips
 
-	dodoc HISTORY README
+	make_desktop_entry "${PN}"
+	doicon "${DISTDIR}/${PN}.png"
+
+	einstalldocs
+	dodoc HISTORY
 }