gentoo Easter resync : 12.04.2020

9 files changed, 30 insertions, 26 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index c29ffe1f8aaf..279c5e1ae791 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest
index 09afec5ba291..7c2dc6eb8a68 100644
--- a/sci-biology/bcftools/Manifest
+++ b/sci-biology/bcftools/Manifest
@@ -5,5 +5,5 @@ AUX bcftools-1.9-fix-shebangs.patch 198 BLAKE2B 9d6c365c7193c7815216be4f8034c00e
 DIST bcftools-1.5.tar.bz2 2975685 BLAKE2B 937b7db770dcaddafbd00b67c3b88501a3190564b2ca629b83e52b48b414a604dd203cd067e357e2b7d02c700387576fca458d1cab2982dafa3b2c215b528722 SHA512 66b8bc61b9fbb381679a6781f77a18f66e8105567992da011413bc573d99b619558a1cf58e9e1373ae347a8b81638dd91977802a07a4578ddc9c61fb53403233
 DIST bcftools-1.9.tar.bz2 3134355 BLAKE2B dd551b509b1ee554f70be9da28a6eaf81dfcec43fc0d1aa972d64ef846f9db47f39177345e8c1ca754d11defb9c0823976ae94d6b3e7cd99313eed4f381182ed SHA512 fd662fb0d214eb75ac04fc4494e8dbaca84d10698ca14801427341def6a5df4af99e7bd4cd873da5422ae921deb49b940cedb926da356b1eabfac525a38f806c
 EBUILD bcftools-1.5.ebuild 868 BLAKE2B acfd6758e27cb9ade023d91074724affd0fa3016af565c809819fae615be61ca8af90edf6b38eaf0a4ed5f3e9eaaa19451096b8d7c27a58c6ed0540bf7260784 SHA512 e0aacba5fc54cbf7a8d64db84e52f28baf8df36fa01c63fc167998c6ec5ef65a040c0725f445970f32888ae947b89d50d92dc2fc704fdf63a8a900762ec367e6
-EBUILD bcftools-1.9-r2.ebuild 996 BLAKE2B 27af6e1f88f2501f6b4c2a627a755e82024130f1e0b884a517322fa7181d18f00a1323fe0477f914d80c25aa0dc81152d930689e1e18870af69d8dbeb1daaeb8 SHA512 f9e052edd07c6cd9bafa338913954729bbcf0302d418426d3077685acc15128cd19991361a2737c8f56fca4069123d58446633e0ca7c881b3996a65f33fd7d0b
+EBUILD bcftools-1.9-r2.ebuild 1000 BLAKE2B eb5e7bb5f33f5ef22594eb241f3900ee6a6c125cb83b0e425732fbd6d781dac382b1664281e3256587ea8f344db578c1ec778ac2d5ae4794fa67931468cb580c SHA512 90d56585baae31be060fc8a54de5d86c1bd015da187d86a37ceee1176a685a864214e124770dfb895d568bb57e143f9a35b7f627f36598dbf4cb544119f2185d
 MISC metadata.xml 452 BLAKE2B 53a356b0569d9db1377bc1881d58b4b354d4861eb21b2c602df59b7923b175a20623cf3369695416eb08d44fabe32036f5a5ec3119c765c8f85347d3b094918a SHA512 eb656430c9ee5ffee5ec5f9f8f3c69e8b0d1ae124cd720ae4af6c3c160da5dc261838744f75e838a85935bbc9bd5201b038ee11cb41a0e1209c9df58aa85fc1a
diff --git a/sci-biology/bcftools/bcftools-1.9-r2.ebuild b/sci-biology/bcftools/bcftools-1.9-r2.ebuild
index eafe63a1ee54..0963c692fcd6 100644
--- a/sci-biology/bcftools/bcftools-1.9-r2.ebuild
+++ b/sci-biology/bcftools/bcftools-1.9-r2.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python3_6 )
+PYTHON_COMPAT=( python3_{6,7} )
 
 inherit python-single-r1
 
diff --git a/sci-biology/clustalw/Manifest b/sci-biology/clustalw/Manifest
index 9e48ef945bec..30219f3ec6ee 100644
--- a/sci-biology/clustalw/Manifest
+++ b/sci-biology/clustalw/Manifest
@@ -1,6 +1,6 @@
 AUX 1.83-as-needed.patch 388 BLAKE2B 8da98e05dcdc74ee41ff7a3d75b11590507bc769df0adb181f7c2d0a656f80d15b7363723bd760c359efb666cf962f5cf8c055abc1b7181d37203b0bfe659717 SHA512 1f66a0b539f9101a52b4117d0369294f706a048464d1908ae457def27d33ace0e5c5f9ba507f82a1406bb78ff51896ac6bb76cb03dfe8ff6bbb8ed182dc0f5ea
 DIST clustalw-2.1.tar.gz 350761 BLAKE2B 479acb42ec0b0adee8e04e99132a782c947a1261f48e674c6a11e4f38e44e5709d03f0c864f0cd3cf7eb4faf76a36b6121c3e3d3573c86ee3895971df07f1a58 SHA512 659cfe0121015dd2b84578b1a0a7f016fc944de155686b9bdef31122200a21e792203f3a6ab93a31676a50ffb70858b506ceb7ac27d921189a8381dbe0887921
 DIST clustalw1.83.UNIX.tar.gz 166863 BLAKE2B a3b1eabad8bc736cde4655f13fa8544759b7b5c50ea97fd45ee0be45ac6c361db5ced8ad21622ac2530b57c37c77dfd67657afd2c411acbfb7ff2a3ba014637e SHA512 c0cc9ebf4c8869be819065546b499b547990342c87425fae8f921a141704343f2a518ecfc2b8bfd527061902825fc5befcb2cd080c83ba887390e48338c9dc1a
-EBUILD clustalw-1.83-r4.ebuild 822 BLAKE2B a27f08c23c7ab69cdcfaa989205f47c07e46cef709d09a433d7476a7caf468ef13b76614d44d869b5e16209b32a0426487bbe147d71f2e82059e2066dc067f63 SHA512 1d4b9be166c531885a68982fcc1cecdebf60d616920306f7b716bdf0f49c42b540cf5f8398a0fd22f449bff18b2d290cb18291062b3706b1d14ae4de2e7bedc7
+EBUILD clustalw-1.83-r4.ebuild 815 BLAKE2B 9a887de5a2a1e96652d260963e13c9aca786b684ee2a9b0c02adba0b2fbfcf0f500f5edabaf4469b2e5ff13b3cf445245d59010b5f8a50e9d830d636f0f76699 SHA512 c884a8fb3029e7834299217c6db91da4f3430c738ba346dc7c3431695c235852c830151452ec534f1c1e59aaff5fbd4bb2d1030ed7779f30a675cbb30d76c218
 EBUILD clustalw-2.1-r1.ebuild 473 BLAKE2B 76c7432b4cd6d68b5dd51bdc9b4e1629d8e958f432bb9c35738373bc7ea34180e74c9d0ba498d02e5d4db3243ccd711255157490d4b42d84bc7b0b493f526234 SHA512 6cd64a7ffa784daeef1146a695e588a78e74b5b453e3cc1751907fbe09aa394eb9c962e681ecdef9eb2627d5c490a49ff58484c2c77599f169d48482521749e0
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/clustalw/clustalw-1.83-r4.ebuild b/sci-biology/clustalw/clustalw-1.83-r4.ebuild
index 6bccfd828e99..144789f4c2a3 100644
--- a/sci-biology/clustalw/clustalw-1.83-r4.ebuild
+++ b/sci-biology/clustalw/clustalw-1.83-r4.ebuild
@@ -11,7 +11,7 @@ SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/${PN}${PV}.UNIX.tar.gz"
 
 LICENSE="clustalw"
 SLOT="1"
-KEYWORDS="~alpha amd64 ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+KEYWORDS="amd64 ppc ppc64 sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
 IUSE=""
 
 S="${WORKDIR}"/${PN}${PV}
diff --git a/sci-biology/foldingathome/Manifest b/sci-biology/foldingathome/Manifest
index 64563155fe86..71fe4a3400d5 100644
--- a/sci-biology/foldingathome/Manifest
+++ b/sci-biology/foldingathome/Manifest
@@ -1,4 +1,4 @@
 AUX 7.3/folding-conf.d 339 BLAKE2B 93a0b3672777ad737ce27694aaca547634c375e180ad3c28c3adb9cae2cb1c054ff9458ee1fe04b70fe9841ae67d41198bcecfc4826d05d5de8df2759bd80910 SHA512 6fd10dc938262c05831e68176e93a24869bb6991508bcc48ece487b701788026561d073025bd347cd77ede13ca26f6b284861f30b07becf72ea77e4db22867b3
 DIST fahclient_7.5.1-64bit-release.tar.bz2 3438239 BLAKE2B 69fb60cdd5356fe4f5ad1f106b67d078baf0394c5d3c474dff2f1ac840bcb31bfd9ca9a9c6112b9ee9497dcdc223732627a21c50b455e46c096a52587d5d229b SHA512 5f6f2f882d57fe53ad0a55b48f09fc3803af6aebbbf0e92be39477d4c4da92237d6edabec61dd8183678bdcfe3923ff9b0938647a77edc2c69ce8958defcfdf1
-EBUILD foldingathome-7.5.1.ebuild 4369 BLAKE2B 23ecb21d29838bf874e4890460d020c1591e19e1c0eb61147e2b63df0b78781a9ec933c844d8ddbce02701810952988044b547946ffcb2f119da18bd3f6d6be2 SHA512 93deb4fa7f71fd331f1d08c39da54a500bbd2e32bbbbfe617c70d4fb20aaa017032ade8a2a98a6bb53605bbcb00d448926d3860acdc0e5db0f072dc9f55abefd
+EBUILD foldingathome-7.5.1-r3.ebuild 4454 BLAKE2B 9103461fe2614c5494648827b461cc488e7345f3ad12d45ccda6c44c81de7f700120d582b3ab4371974a5a25a62626b535849e8bafa13ac577c59364102cb7a3 SHA512 4c1a451a5df2e2015594f266761d51b9ac0978711ce93f4bc922937a0fa474bdead787926541ad42d554130cf6168e367f8c090648d52951ca6b7f1533c042f2
 MISC metadata.xml 360 BLAKE2B c0ef2b11cc9e6498a420dcd2e6c83ee71f7e286c3e78218257c56350bd2c0921732d48cc4207a31bcfd965a4a9dca65e9bdc4d62831dc430e86541d36fc691f8 SHA512 687f1516a8ec80270fa173b0a7d7c259f3f02ffefa69d3175b72e170bd11aeb786563edb43214390a83b6b61b1231e2734124e50bb2a523d1a564bc3b143f00b
diff --git a/sci-biology/foldingathome/foldingathome-7.5.1.ebuild b/sci-biology/foldingathome/foldingathome-7.5.1-r3.ebuild
index 08e9c15149d7..cb7ce89a604b 100644
--- a/sci-biology/foldingathome/foldingathome-7.5.1.ebuild
+++ b/sci-biology/foldingathome/foldingathome-7.5.1-r3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -25,7 +25,9 @@ RDEPEND="app-arch/bzip2
 	)
 	sys-devel/gcc
 	sys-libs/glibc
-	sys-libs/zlib"
+	sys-libs/zlib
+	acct-group/video
+"
 
 S="${WORKDIR}/fahclient_${PV}-64bit-release"
 
@@ -43,7 +45,8 @@ pkg_setup() {
 	elog "(ref: http://foldingforum.org/viewtopic.php?f=16&t=22524&p=241992#p241992 )"
 	elog ""
 
-	enewuser foldingathome -1 -1 "${EPREFIX}"/opt/foldingathome
+	enewgroup foldingathome
+	enewuser foldingathome -1 -1 "${EPREFIX}"/opt/foldingathome video
 }
 
 src_install() {
@@ -62,7 +65,7 @@ src_install() {
 	newconfd "${FILESDIR}"/7.3/folding-conf.d foldingathome
 	cat <<EOF >"${T}"/fah-init
 #!/sbin/openrc-run
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 start_stop_daemon_args="--chdir \"${EPREFIX}/opt/foldingathome\""
@@ -82,12 +85,16 @@ Documentation=https://foldingathome.org
 [Service]
 Type=simple
 User=foldingathome
+Group=foldingathome
+Nice=19
 WorkingDirectory=${EPREFIX}/opt/foldingathome
-PIDFile=/run/fahclient.pid
-ExecStart=${EPREFIX}/opt/foldingathome/FAHClient -v start
-ExecReload=${EPREFIX}/opt/foldingathome/FAHClient -v restart
-ExecStop=${EPREFIX}/opt/foldingathome/FAHClient -v stop
-KillMode=process
+ExecStart=${EPREFIX}/opt/foldingathome/FAHClient --fork=false --pid=false --respawn=false --service=false
+NoNewPrivileges=yes
+PrivateTmp=yes
+ProtectControlGroups=yes
+ProtectSystem=full
+RestrictRealtime=true
+ProtectControlGroups=yes
 
 [Install]
 WantedBy=multi-user.target
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index cb820df291ac..45ef440561f3 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -5,5 +5,5 @@ DIST samtools-1.5.tar.bz2 4190142 BLAKE2B 1d3478f9adf76925a3721e145795ce4a4caf58
 DIST samtools-1.9.tar.bz2 4440405 BLAKE2B 409265fed9ff3fcd09096c968224499750da69324eeded754e367430c0f53f9246ccc9a31e166f13ea7bc767fefab499bcfda4d008d5ac82971984c67b533aff SHA512 6c8207754615ae8dad84b278f93e7d57eb40b818efb80f6aff6aba22fde5772247724e86596e765791e3175ffbb683393dd3ddfe7681c73eef4eb4f2342bf68f
 EBUILD samtools-0.1.20-r3.ebuild 2363 BLAKE2B 6050d698f26b9962192cdbc6c3729bb812041fc92f4ba4490dc6f50e71c08853d6e2e4c6592c324c3efc3ac0da058e8b254475d6fc788f314798cdcaf85a4fc0 SHA512 f79e0f723d86e7c2060163a3b79e6624ea58d21e7c8ddeb87be40a7972cd97e60df82dacaae23b8a89cec2a0517ffdae8804ac71044685b40d5c5769f8964557
 EBUILD samtools-1.5.ebuild 1107 BLAKE2B 2088a3fcc483de227bd92c80cd9ae2bf0257af773298bebcd077d7b2385eb43a6bfde82c7fadb0e2af3400b825e5b1b3c3c4f633cc7631beb4d0dcbb39cdd2cf SHA512 2f1701695fe3aa270bd75bedc3f847b3057ea1a6d9dca386a8f420df22ab78f51b12c8e1ca80d7d2fb1221d246047a78e914022c8e4c8bae5b0b053f3b130cfd
-EBUILD samtools-1.9.ebuild 954 BLAKE2B 7019d0294f9a78d3957f56a006d0c8a401553c74c27ec14707e1eda401b9f3865089321267e873652ca8b8eff382ecb9777424b06773a4ec661ef5bd1a9267dc SHA512 4129a3ccb8e66aaa1ca1c0557acf76c27225486d1145d07fa372f48939a2c1fc30532964076e65aee5dde97c49e750f1423a0cc644966eabf0f6e54846a3bcfd
+EBUILD samtools-1.9-r1.ebuild 926 BLAKE2B a71ab1165f9fad65f0ff932880a661fb43435ebc1c72839ed8f57d3a1ee8b11d5441d53404ed650d634334a8f197d4275f82831d7332bdbbe6f110506f0d0230 SHA512 f75851ece84f8863c7352fad6133fe66299cfe94561a62f7dd4a2bf9a82d2a2400be483874d109b67b643807a25d6907d47c8310732d4b13577e27af685857bd
 MISC metadata.xml 408 BLAKE2B 28b519bf32b116c92c1a695553637a44815ff1aaf18468a5d2d5ef448d8dd53728aadf7606c6ab53ae6bb21e88fa4a48c7b443e3d0a13a5658592dc0e768ed3c SHA512 8c8d240fd37400e43637e12f008f8f2b03fcca062883dd63ccc6956bbfc46d05709f032d146a95452db35b546ff828239b108b3a331f5295ec97872d6c9478fb
diff --git a/sci-biology/samtools/samtools-1.9.ebuild b/sci-biology/samtools/samtools-1.9-r1.ebuild
index bdcd115aafee..0d0f993895fc 100644
--- a/sci-biology/samtools/samtools-1.9.ebuild
+++ b/sci-biology/samtools/samtools-1.9-r1.ebuild
@@ -1,11 +1,9 @@
-# Copyright 1999-2018 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools python-single-r1 toolchain-funcs
+inherit autotools toolchain-funcs
 
 DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
 HOMEPAGE="http://www.htslib.org/"
@@ -15,22 +13,18 @@ LICENSE="MIT"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
 IUSE="examples"
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 RDEPEND="
 	dev-lang/perl
 	=sci-libs/htslib-${PV}*
 	sys-libs/ncurses:0=
-	sys-libs/zlib:=
-	${PYTHON_DEPS}"
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
+	sys-libs/zlib:="
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
 
 src_prepare() {
 	default
 
-	python_fix_shebang misc/varfilter.py
-
 	# remove bundled htslib
 	rm -r htslib-* || die
 
@@ -45,6 +39,9 @@ src_test() {
 src_install() {
 	default
 
+	# varfilter.py has been retired upstream for being py2 only
+	rm "${ED}"/usr/bin/varfilter.py || die
+
 	if use examples; then
 		dodoc -r examples
 		docompress -x /usr/share/doc/${PF}/examples