gentoo resync : 08.10.2021

6 files changed, 37 insertions, 4 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 5a44c21e64d0..a0b7688fa224 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/dssp/Manifest b/sci-chemistry/dssp/Manifest
index d07091f553d9..ba167e11628e 100644
--- a/sci-chemistry/dssp/Manifest
+++ b/sci-chemistry/dssp/Manifest
@@ -4,8 +4,10 @@ AUX dssp-2.2.1-boost-1.65-tr1-removal.patch 2126 BLAKE2B dc59d21a6be26ee96b636c1
 DIST dssp-2.2.1.tgz 47141 BLAKE2B 34d8b2db8797a8c23763766c0214337f03584c4be52c1bc820a0df0db6a5f78ac0229aafdd47a60b8fd6f4832abf0399663c53f9e898c75f08ecbe22b141c8da SHA512 4a273714d6b3230daea166caa7f4117d5ccb225bea0cf1bc2eb61539b6cc8e227d0ba19047d61f0ad0d1d6bc2efdec9c193bd44341e15ef0950acb4a22498811
 DIST dssp-3.0.11.tar.gz 168085 BLAKE2B e1c42fd22cfb2287f10b5deae48b56a4583d4a67737a3485dcbd160d1597a15c2d5105c3794c875d8001abede1c014efb4f7f5b7c250f867bdf9ed95a0860217 SHA512 a0cfe44e517ff1f909ef2928b62ae2c639c6bddfd8a0fb538883f647fd2771e00da68e0fd2521aa02ba3c6d1b0c9b784b7fe142392af3a3abf6ea89f1546bd9d
 DIST dssp-4.0.1_p20210831.tar.gz 121793 BLAKE2B 1e028b086b418772a93db350f8084d1786996ff6ea935d236b1431d8f4a07c0b33ebf374a4c4d5d4d243952f3f56e29a548ce09763863a1e0c529755fba6c211 SHA512 62f1ac781dd3d6f3436e6c155ae1a470d0baf6a6d9f6d6729034a7a5ef41550f76d0473c688d235279336306c9f3598377c056cddd6d00a89a826fbb04c1bfb3
+DIST dssp-4.0.3.tar.gz 122872 BLAKE2B f88c330370645b4bd4e89656ad676e443a33c38d7882145bc60e329f823eb761777713df6c7ae44550d10bcd22256ac16db358587cadd39efd6268dd869655d4 SHA512 31ca481b097c9c59f407e35eb8175638b5e4102991007090b5b4ea30db0b076f97cff45d0aa9ae01a826f7673258464b572d68714f00e210db26020cea4be094
 EBUILD dssp-2.2.1-r2.ebuild 962 BLAKE2B 4badf2ae8647aab9c5e359d9e0763d051388afe3bf5763c8eeb99cb21b30283d72ace619f1b65c5ee248c42f8264cb31c2c1c079f75eacda1568cc4352cec5e3 SHA512 4a599b6e7cd068175bd89f4ea948ad1267df783c240ab46d3c6109bf3f2853de714ecf1e5776722309688599f28af545287fe5cb98d8b7a5f46d319df953b926
-EBUILD dssp-2.2.1-r3.ebuild 882 BLAKE2B d95025d549b3114107e3e52292e6ae086141436c23bfcbfe3604c59c971fc360de84a621e3415d26a6b2faf5c51810e9e3e7441641af9967b38534178ace62a7 SHA512 29f0c7cf76f6029146668d08d992380147f698ae2bb00cee76777936217f27e329cfe25f41c58c07906b881d40385d134d51f34e14f80c0836c78cf50f1bf37a
+EBUILD dssp-2.2.1-r3.ebuild 880 BLAKE2B 057a862fbc9ff19fbf487f9df0faf661a7db5406c28e6cb91d5e38dfaa2e9d24eead9ba78d4e92b5b5022e2be5c69b30ff6c386aeac8160062b5f7f35b449889 SHA512 747ac74fd95400759569e657db85c3dc5c5a7ee0753761bc4b4927f4d119d168f0d5dcbd9ca16f37486358e7117e773d812034fb07953aae88c63ac1e706f8f7
 EBUILD dssp-3.0.11.ebuild 825 BLAKE2B 020ea517127ffc1167cbff3a9362e5ff255b25664769ef2ac8f7f3060e34e0bec29e965df46e65bab8943cbf5fb11175d70b1b9f9e7d71bdbf92a4c54a903367 SHA512 b81dbe1cb9f7b66c5268485dc262bb705b12d250e2ec778c80fddbc584a38e36b64cb93e92385c178fdeca0e593c45ce25aef16480bfa9eb230bdd2b8a82fa53
 EBUILD dssp-4.0.1_p20210831.ebuild 849 BLAKE2B 0d6089c63608b85c98f67136cfd275098272985f689ac0e6338c7ee6cd158a851901815d0dab988a2ab65ff63a1bfbcd689577daa98c2c91bc04c95f2a95420b SHA512 35d5e67754a7a7b3d3021c16d57d1b4e5c8a2316606b7ebed08bb543e647794d87b64e4ba04db3d86d34f13999e04af08b4df8cbe4d8d5843c1f3f26c491b0b0
+EBUILD dssp-4.0.3.ebuild 769 BLAKE2B 406a817ed8545b7b85524cd36a0f7016b75639a0dd15971639eba0e55a2eb78b68817d0892149d8b6781d6b4ed9a767d7e508d236023a1bd16663fc289bc6399 SHA512 2dbd1aa4e76d6bc58a42ed4dc848c7e87afd3079d5f2bd21652288b38ef7ad0d5c5804a52532e33cd2519652d3a94cc2f9fc462e8488aee42309edb2a40dc156
 MISC metadata.xml 217 BLAKE2B f8189b02494f180dac078dcd5c275d3c795f20f360f8b172c66065a2d937e396b24b8631bba4cd8567d60285ce89fc77b9539f2233bf33899c820613c48c33ba SHA512 f0c9e5b3d281fecd21b1e23a6f44c94c1c0b3220de46a177d35932111b7f1ab4399061c42833ac1ee9bd0324b139fc8db66e0d2890224d607bd3be38ae469be9
diff --git a/sci-chemistry/dssp/dssp-2.2.1-r3.ebuild b/sci-chemistry/dssp/dssp-2.2.1-r3.ebuild
index 8697005fc2cd..208f006e4f5b 100644
--- a/sci-chemistry/dssp/dssp-2.2.1-r3.ebuild
+++ b/sci-chemistry/dssp/dssp-2.2.1-r3.ebuild
@@ -11,7 +11,7 @@ SRC_URI="ftp://ftp.cmbi.ru.nl/pub/molbio/software/dssp-2/${P}.tgz"
 
 LICENSE="Boost-1.0"
 SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
 IUSE=""
 
 RDEPEND="dev-libs/boost:=[bzip2,zlib,threads(+)]"
diff --git a/sci-chemistry/dssp/dssp-4.0.3.ebuild b/sci-chemistry/dssp/dssp-4.0.3.ebuild
new file mode 100644
index 000000000000..d9d8a5740c8d
--- /dev/null
+++ b/sci-chemistry/dssp/dssp-4.0.3.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+inherit cmake
+
+DESCRIPTION="The protein secondary structure standard"
+HOMEPAGE="https://swift.cmbi.umcn.nl/gv/dssp/ https://github.com/PDB-REDO/dssp"
+
+SRC_URI="https://github.com/PDB-REDO/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+BDEPEND="
+	>=dev-libs/boost-1.70.0:=[zlib,threads(+)]
+	>=sci-libs/libcifpp-2.0.0
+"
+DEPEND=""
+RDEPEND="${BDEPEND}"
+
+pkg_postinst() {
+	if has_version sci-chemistry/gromacs; then
+		ewarn "DSSP > 3.0.x is not compatible with gmx do_dssp:"
+		ewarn "https://gitlab.com/gromacs/gromacs/-/issues/4129"
+		ewarn
+		ewarn "Feel free to mask newer versions if needed."
+	fi
+}
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index aafd837a6016..11c5547a7590 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -23,7 +23,7 @@ EBUILD gromacs-2019.6.ebuild 7264 BLAKE2B 6196f750a81562c82f1004ba3e4be05193aa91
 EBUILD gromacs-2020.4.ebuild 10134 BLAKE2B efc77b2cb0981ebf3f90fbe531d54020be2e82b464dace3ab8d07d41cae060c5e073a8a3f641b4bb0431ec2717a5f990a2a6f08ceed6a805bde82742b9eba487 SHA512 f7af8d31c43abe23b9c92ce6afd0dbea4219fe48dad3d91bf19f50f80a520cb0ab98949d4f2653679de751853755e793fd0e84ad73ebf13bef17fc255d693001
 EBUILD gromacs-2020.6.ebuild 10137 BLAKE2B e5f058493f7757ffcff53c892445a3ea2dd15ebb83bbd7fd186a56d85e785be75277e8329487a182d27e23f7756b02618c227ef40c2aaf0243f2a1fbeda232c6 SHA512 37df9d310ab597ce4bb69bd3d77ec20d4b6e0b825b341e5fe78b139164fd02a43b5e3d012530fd9a62500d4a63d2efa05fcbc1219ef5edcb93bf232d563af821
 EBUILD gromacs-2021.2.ebuild 10361 BLAKE2B 925ad220aa14d1e0ec8ad0bc2a1b5f887c2dc7e3e419ef54b009026fa8dd251ef91821acd82e12a3126a065d709dde9a9df14f026323373d0b2909b750795b50 SHA512 15e159486ff136633fc6de6f32a5efd14b7d7276197db7bd0e83dfdf8c57ecc2374c8021783726de9b0d99512ccb8f0980506ceb53cdaaee1cecd847a699caf0
-EBUILD gromacs-2021.3.ebuild 10271 BLAKE2B 3f8c197fa70a2cace08d0852186920eb7953a25fe650262f994c78ef7cd27610c907c86deb8d031c465d5abf57154fcc2eebb48203d59c45a030dcfe85aa6f42 SHA512 7f6ac310f3a3057d3c595ff8d4f0fa275ac6d820ec445fc9f7d01e71b5da445b59ba60a0fd508dab696fe023e86eaaa15b35789de7115d4ff6e55c34e0ba682c
+EBUILD gromacs-2021.3.ebuild 10269 BLAKE2B 90f318b96a6a5a4ce24753d6ea610dabe2cbd59670db5f4ee61c9d9b282fd79e6db0d2e758834fdb563c8c3b27876f63c619306f8c25a669ac9fa8153d71b0fc SHA512 7eaeff9d5468e3c51d7277b18588250aedae6c5c023793c91f0d9583608c85ee11da6278e293a0597d29ea408b7a86d17448c118f7f52c6b575be9ec137b4d5a
 EBUILD gromacs-2021.9999.ebuild 10271 BLAKE2B 59d6173d1c82cfa1c084528edf2e9cf9bab8e6eefb5e3cc7c05fc43654c7be9463a24cd62a8c764afcddb9fe29fad2643cf60222608f0cdbe72eedd6c41337f2 SHA512 8434cfaf918264c8ad1e0c87f2876c6531a70d330c1205378ac65f537a562e2a72208cffca41bc85773ff1f2eb73653a4c5b1cb992f007c03bab125aa13ae4f6
 EBUILD gromacs-9999.ebuild 10271 BLAKE2B 59d6173d1c82cfa1c084528edf2e9cf9bab8e6eefb5e3cc7c05fc43654c7be9463a24cd62a8c764afcddb9fe29fad2643cf60222608f0cdbe72eedd6c41337f2 SHA512 8434cfaf918264c8ad1e0c87f2876c6531a70d330c1205378ac65f537a562e2a72208cffca41bc85773ff1f2eb73653a4c5b1cb992f007c03bab125aa13ae4f6
 MISC metadata.xml 1224 BLAKE2B dc6de7f135e5cbd7bdb94bc630d3c7344f5f5387305ada4f3f0fd3f027f9fa4e2c5e44120c8eab8e983fcda314680ac3d140ab61873ab21b839f912a52b21dde SHA512 d036cffac5fd3c4b8d26efdee0f4b4db8d3520f771754a0859f8e99f64d558795b6cab1efba1d4f1700027707a05a724ae96a7e257434d3894ef5fa6eed7ccba
diff --git a/sci-chemistry/gromacs/gromacs-2021.3.ebuild b/sci-chemistry/gromacs/gromacs-2021.3.ebuild
index 6d851074d36b..e77091aa53d1 100644
--- a/sci-chemistry/gromacs/gromacs-2021.3.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2021.3.ebuild
@@ -24,7 +24,7 @@ else
 		http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
 		doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
 		test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
-	KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+	KEYWORDS="amd64 arm ~x86 ~amd64-linux ~x86-linux ~x64-macos"
 fi
 
 ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon"