gentoo resync : 16.01.2021

9 files changed, 80 insertions, 15 deletions

diff --git a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.0-r1.ebuild b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.0-r1.ebuild
index 8f747a7a5acd..e6354fb05f92 100644
--- a/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.0-r1.ebuild
+++ b/sci-chemistry/GromacsWrapper/GromacsWrapper-0.8.0-r1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{7..10} )
 
 if [[ ${PV} = *9999* ]]; then
 	scm_eclass=git-r3
@@ -16,7 +16,7 @@ else
 	KEYWORDS="~amd64 ~x86"
 fi
 
-inherit eutils distutils-r1 ${scm_eclass}
+inherit distutils-r1 ${scm_eclass}
 
 DESCRIPTION="Python framework for Gromacs"
 HOMEPAGE="https://gromacswrapper.readthedocs.io"
diff --git a/sci-chemistry/GromacsWrapper/Manifest b/sci-chemistry/GromacsWrapper/Manifest
index 305cef292678..f1d8793d6285 100644
--- a/sci-chemistry/GromacsWrapper/Manifest
+++ b/sci-chemistry/GromacsWrapper/Manifest
@@ -1,4 +1,4 @@
 AUX GromacsWrapper-0.8.0-tests-package.patch 594 BLAKE2B 6b2c7c1aebebfbb5222c84e67805806aae714b8c96cbaad568b7ecb2959e38d504ea5a18a1de4bfcbfeea4488b04182d1cdbd0664511bfeb3cae2bd27534e8f7 SHA512 92b0232092ee9230050c114906ea61136d03de7b417d7267ef194c751bc801ab6f35d882681c36bb28949cddbea5e3c1c413df6ec949a073fcccd59b5433fefa
 DIST GromacsWrapper-0.8.0.tar.gz 1205837 BLAKE2B 3627e56df0dc6ba86caac67795416c7c8c187aaa4fac545600d17dcd799cb153feaab61a0f0632e051c4e9c0b4cd74f8e165156873e36bc53571bec78e5fca61 SHA512 da7215216c9a2b52094bb7e43e04f1b429c4893ba67b4bd850fe68e99f338813392fd9d0aa1b19d3398c694be964bc2badbf1b3623420da929ee4abcef18026f
-EBUILD GromacsWrapper-0.8.0-r1.ebuild 999 BLAKE2B 79622ebe01dd515f3f3697700a8493c7ddcbcf92bf64f81e61fbe7924a7ac37639dcb01794e5118e3f447bc5de3962f434610b41e3000961bd212a7261700adf SHA512 0941c46ab84522a06a6c26853ed593ca6ff315dc97d1bbbfe366d60e4aefb4221e10f2faa778030d0a19de9045a2d57ef94d37a0560f272e8ff876264dceecb0
+EBUILD GromacsWrapper-0.8.0-r1.ebuild 993 BLAKE2B fd4ce23cb8936d6dddba2443b981e14e96c762abbb00a72a9547ea5e379c64ab555b8bbf35592a7818151aa1cdaffbf3df1fd2204cad5188c36fbced83632bb4 SHA512 b8bc3c98eb64a52f6f5f6a243e4fd5d0b9d498055dceaacd6a4e518e4e4a2621f1e33b9cd1ff9aeb75693566f4588e93bc0c2400599b1753070654a429dde533
 MISC metadata.xml 483 BLAKE2B 1d8a7e888d8b95bd229ef72894ba02f583e3e3958f9cd5733ab6b466312bac0b0f5a9004135caa37a3ef137e8782fa93ff4bb90f35f31c058d8c528025b193d0 SHA512 70e5dc653ff21a0395b946e5f3548320d2abb8c63ae9f3ce04be6768e20b02ce55a612a2ad12b6c2262529ab753ca9fda02d9bdae7f6ac859bca49bbbad6f75f
diff --git a/sci-chemistry/MDAnalysis/MDAnalysis-1.0.0.ebuild b/sci-chemistry/MDAnalysis/MDAnalysis-1.0.0.ebuild
index 0b58e90489e4..1f9c2ac3aa5e 100644
--- a/sci-chemistry/MDAnalysis/MDAnalysis-1.0.0.ebuild
+++ b/sci-chemistry/MDAnalysis/MDAnalysis-1.0.0.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{7..10} )
 
 inherit distutils-r1
 
diff --git a/sci-chemistry/MDAnalysis/Manifest b/sci-chemistry/MDAnalysis/Manifest
index 58c58ab114ef..031694c2bcde 100644
--- a/sci-chemistry/MDAnalysis/Manifest
+++ b/sci-chemistry/MDAnalysis/Manifest
@@ -1,5 +1,5 @@
 DIST MDAnalysis-1.0.0.tar.gz 19552874 BLAKE2B dab625a898d71a67a37ac5b58eb23ded9487f475e3c76f6c335a0ed5b32a43785d0473d089fcfc56c07263d82248bf5ee7b50c513441b10fc97f97b49411cc5f SHA512 4a001f45695308dd5f296bd2850d5d585c065e6b0f55efca65d91e452d78c85f13fd614eca0176a8d330e14a1c9e8ccbb919c3d4ae995b1945d09dc3ad687195
 DIST MDAnalysis-2.0.0.tar.gz 3436654 BLAKE2B b29734dd61bfa1e4e1d6ead0eb9a2d00869d1adce18edf95b9368bdcc16b0d71d0d6536a7df48787034a623bf52585e1636842dcaaa9dde08a69576868c1657b SHA512 037eb3c709b9ddbdb2ba9b26a6632ff99a95331c3968176573076e4e208c8644c3ea262e1e9880f185eb080ff90180d887444cab0dfbfad04fc254d87f1ff986
-EBUILD MDAnalysis-1.0.0.ebuild 1115 BLAKE2B ab8aae2678843840557bfde1866890cbe671cab0f670d1dc253523d070e231b44268d803b8c3c03648d8536f2cf6a734affc8fbcbb9ae62956deb60d1254b19c SHA512 7099a21fcfef94938f5c2b7bc590fbebadeb94ccc35f73f36abc470038c7aa45ea5563390eb09db9162f2060a57ebba69a2c984c2c8b560247f03acb8b446c4c
+EBUILD MDAnalysis-1.0.0.ebuild 1116 BLAKE2B d0fb4a3e4aa269fa30fe3168f7611a4296c87c12d3d8dd5b5b78282d756d4d8156d53395b453ad4c24925e45547aba832afc233183f01bac4bbf57d65131f1d0 SHA512 a116ec2dfcb9256b2b6d63d67c068e0a138de788d0d5aecc60e3844058ac54cb49e34e6a79c2488b76aa447be127f5dcb9403396341a0045448eef47c94bab01
 EBUILD MDAnalysis-2.0.0.ebuild 1128 BLAKE2B e51e404e7254e614abab6856948939b5673d13940cf60d5e6dc77d08e97a401d4af00e56cf90ed9bbfca0acd319f9d328a4479c222fc5ccc0a5ddb8e41788f56 SHA512 6029cd5e527333da9aa7cb52560436eaa7424a87a3c22499f6aeb99b402525dd87a43ae7487a669df67890942f7bfd4d6d561366d002e2c0138e3f2e35f02601
 MISC metadata.xml 497 BLAKE2B ddd8c6379dfe6b6fe33160d31bda254774e0c8eb5f862cc51560097efc5c273fa972388c6fe8fb1bbedc11ab125a5487bb1d19002489be967fa3e8e209d7cc81 SHA512 03c1eb9bef1bc10d600169b221c65c87794f8b9bf8d0efb1dc6ddaa61a09d665722ed7d32087e3137b36aa7256b76371b9ce2cc92b34b1ed7d1c78ede6550287
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index d1dabc99537d..6f1cb1bf56f1 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/autodock_vina/Manifest b/sci-chemistry/autodock_vina/Manifest
index ef72e15f2c1f..89d6bcf8fc4d 100644
--- a/sci-chemistry/autodock_vina/Manifest
+++ b/sci-chemistry/autodock_vina/Manifest
@@ -3,4 +3,4 @@ AUX autodock_vina-1.1.2-boost-filesystem.patch 2936 BLAKE2B 70c55e95e9728221ba80
 AUX autodock_vina-1.1.2-missing-debug-decl.patch 365 BLAKE2B 959b46facdce27850a1f9fd6c66ecc297e4ad089e79896b9fe2127e425bd1bfcfce5d676cf2e4336c47d3a72b0e8319c791fdf1a5807f244cf5b4528de8cbb25 SHA512 ddbdca76fca16b46fd042b57eb941b7ba67f59f46c35dc18428ea6873c8ed5f03051247b8c667a08af8de40fccb0caf851848bb9082536225cacf8eb3e313c98
 DIST autodock_vina_1_1_2.tgz 67366 BLAKE2B dc754bf522795ebfbfcf89a2df4e3761d941c1f0ce05cf56898720c1e855f5dd00fd2a583f5a8d218fa2e738d37e014a9b3239b9aa989b9018a6a33f8f0bd02c SHA512 f704af322ebc192117c49d0cf8a3f217105beccb7b47d6361665470894ef7a9f91fc4b5f07cc9aff56e497bfa80953e40e39090c8394a095c61597756e333ae9
 EBUILD autodock_vina-1.1.2-r1.ebuild 951 BLAKE2B 5b7805c212b019aca0be53fe329a1a8dcb423d8e6c2516256aa37417a991b57349c0567c9cc4a4da8e31651fee0e2cc370e6ee481ae9e160c901dd44c4158b1e SHA512 2d332538c9cf9d8b6ad2f742edfb83c27f97d18bf4da23afa4d99648b4839aafc836e9b624f7508de097d3bd682b5057159e5cde3bf4234f3d326d1a5326b211
-MISC metadata.xml 1245 BLAKE2B 0a86a421bb4aea84ab3d6a5fc024cb5733f6b7cfc0664f0745b34c4dd61acf3287c56c966d529d0c5e8a1ada109cd037a61a92ff023d0fbd2d039f807b938b44 SHA512 ac8daf258641066cf4dda3bfc20830e747dfe0ab797639b3d9d2e79b5d4c81adadd136c2ef955bfc5ffd26f34e3c1f3a0eb66321eca9d13a3763115134228b88
+MISC metadata.xml 911 BLAKE2B 67eb0088781bf4f791481c993f50fa034759baf858912b50a6bd650e275e95317c2460a69aa925d7c0955fd6e3fe70bda421f656c418a6f974686b148075a37f SHA512 0614ebad142dbebe4a9577a8c4fcbd2a5b18d5267b3be92531e6c118a21a9ef71addcf972eaa5710ba88daf0257c293d769ebd7153eda200ce530685bec76f85
diff --git a/sci-chemistry/autodock_vina/metadata.xml b/sci-chemistry/autodock_vina/metadata.xml
index f603fd62c191..f29cb87a5701 100644
--- a/sci-chemistry/autodock_vina/metadata.xml
+++ b/sci-chemistry/autodock_vina/metadata.xml
@@ -17,11 +17,4 @@
 		multithreading
 		Journal of Computational Chemistry 31 (2010) 455-461
 	</longdescription>
-	<!--
-	<use>
-		<flag name='flag'>Description of how USE='flag' affects this package</flag>
-		<flag name='userland_GNU'>Description of how USERLAND='GNU' affects this package</flag>
-		<flag name='aspell'>Uses <pkg>app-text/aspell</pkg> for spell checking. Requires an installed dictionary from <cat>app-dicts</cat></flag>
-	</use>
-	-->
 </pkgmetadata>
diff --git a/sci-chemistry/votca/Manifest b/sci-chemistry/votca/Manifest
index b755470d6d3f..a6f6a9a3159b 100644
--- a/sci-chemistry/votca/Manifest
+++ b/sci-chemistry/votca/Manifest
@@ -1,4 +1,6 @@
+DIST votca-2022.tar.gz 61688862 BLAKE2B a6a8d1c34e2cd992d032730b2669c9ac5489b988fc334f730eaf1a40b275cc2fad8b24f03419510fe9fee7b0ad0bedf43f9b22b44ca1ae0178b16c9b255da53c SHA512 ea5b7405872a2c0c8d6b4b86148a605b5e83207f1953f0b7393dabbb106ac785c50b45462f6271fbfad04c0246704a92199943acc65eb30d7f1a0a6d6ee4ab83
 DIST votca-2022_rc2.tar.gz 61692061 BLAKE2B 9fdf016267ff6657bfbbd51c79c2c38cb7064635d26e80b905eeeb8326ca1780f7a9c711802491f3ec7a216dbd53b86fe08da2c969a6a10db110168a02ac0d0f SHA512 3bfd108df7499c21ad290955672ab042b9a11b7a868f0eb49fdbd94365e35ed7ffc8b8b44c9b7dd74b7504b8fd30cc6bacfed443068f2bb3702e272aad26c961
+EBUILD votca-2022.ebuild 1599 BLAKE2B 4cdcad3c29bdd25202f8940d63ec884c7b5dceb00155efe68eb73004828c40f5e05eee63029a9f5b7dcda3483ebd07ce9234beb78ed8003bb118c27ef055b3e2 SHA512 8544844fb8b91afc60e5beb4d4c5e3405356a7e627ceeed3bab2dd628cb883b03823ae53e862fb193188852afdd26a45341d841f0331b9a0a42308526cdff557
 EBUILD votca-2022_rc2.ebuild 1599 BLAKE2B 709252689e526e83d5b9f0933e44d7b83b6d2e02fd3cbae0938630e87c99a83ac2179ccc06d2d2843f7fca039305f6aff4793357ea44ef2f8db9ff2edee87f90 SHA512 9b41346126363598de2174c9e06a4c7550e82dc4ec22f2fcc0a6b8948731831ae871a2b30988dfcd5d3c5ebdd1e6a377946374bc2d3a2b25c6c3a7732b04ac71
 EBUILD votca-9999.ebuild 1599 BLAKE2B 709252689e526e83d5b9f0933e44d7b83b6d2e02fd3cbae0938630e87c99a83ac2179ccc06d2d2843f7fca039305f6aff4793357ea44ef2f8db9ff2edee87f90 SHA512 9b41346126363598de2174c9e06a4c7550e82dc4ec22f2fcc0a6b8948731831ae871a2b30988dfcd5d3c5ebdd1e6a377946374bc2d3a2b25c6c3a7732b04ac71
 MISC metadata.xml 579 BLAKE2B fc22a14bfa99c926b2c5b2071a10b6dd78baab670551c817c4c4f2e5e6a2e13c5fa216fe7a2aa455f15fbf1c8ae488a06b99960830a2d4fb6a82a6a0a277e233 SHA512 89a2c88dc5dc5e06ccd4e1830caa58e0d74f93e1742f4658ed27b6f41be3bd6924da47dc70cd7fcdce9837ceac4012dfeca39e8bf19d0451f044568d00743539
diff --git a/sci-chemistry/votca/votca-2022.ebuild b/sci-chemistry/votca/votca-2022.ebuild
new file mode 100644
index 000000000000..f59f5347f3de
--- /dev/null
+++ b/sci-chemistry/votca/votca-2022.ebuild
@@ -0,0 +1,70 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit bash-completion-r1 cmake
+
+if [[ ${PV} == *9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/votca/votca.git"
+else
+	if [[ ${PV} = *_rc[1-9] ]]; then
+		MY_PV="${PV%%_rc*}-rc.${PV##*_rc}"
+	else
+		MY_PV="${PV}"
+	fi
+	SRC_URI="https://github.com/votca/votca/archive/v${MY_PV}.tar.gz -> ${P}.tar.gz"
+	KEYWORDS="~amd64 ~x86 ~amd64-linux"
+	S="${WORKDIR}/votca-${MY_PV}"
+fi
+
+DESCRIPTION="Versatile Object-oriented Toolkit for Coarse-graining Applications"
+HOMEPAGE="https://www.votca.org/"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+IUSE="+gromacs test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+	!sci-libs/votca-tools
+	!sci-chemistry/votca-csg
+	!sci-chemistry/votca-xtp
+	app-shells/bash:*
+	>=dev-cpp/eigen-3.3
+	dev-libs/boost:=
+	dev-libs/expat
+	sci-libs/fftw:3.0=
+	dev-lang/perl
+	gromacs? ( sci-chemistry/gromacs:= )
+	sci-libs/hdf5[cxx]
+	sci-libs/libxc
+	sci-libs/libint:2
+"
+DEPEND="${RDEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+DOCS=( README.rst NOTICE.rst CHANGELOG.rst )
+
+src_configure() {
+	local mycmakeargs=(
+		-DENABLE_TESTING=$(usex test)
+		-DCMAKE_DISABLE_FIND_PACKAGE_GROMACS=$(usex !gromacs)
+		-DBUILD_CSGAPPS=ON
+		-DINSTALL_RC_FILES=OFF
+		-DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON
+	)
+	cmake_src_configure
+}
+
+pkg_postinst() {
+	einfo
+	einfo "Please read and cite:"
+	einfo "VOTCA-XTP, J. Chem. Theo. Comp. 14, 6353 (2018)"
+	einfo "https://doi.org/10.1021/acs.jctc.8b00617"
+	einfo
+	einfo "VOTCA, J. Chem. Theory Comput. 5, 3211 (2009). "
+	einfo "https://dx.doi.org/10.1021/ct900369w"
+	einfo
+}