gentoo resync : 06.04.2022

12 files changed, 0 insertions, 252 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 934bbd878063..ddccaf21679d 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/mm-align/Manifest b/sci-chemistry/mm-align/Manifest
deleted file mode 100644
index 86393b5285e8..000000000000
--- a/sci-chemistry/mm-align/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-AUX CMakeLists.txt 142 BLAKE2B 43a1c754ff92fa7b11a2cbe8616626b97dfe12b2ada84f6fe9882bc0386df6ead6b00aaff897f958001e0ac2fded9fe87b3d9e7da559cc3b6c0ff2d79c66e921 SHA512 edeaeed165d8b89edaf0f8e1e50870c61fa1446e3b8febb367451cf93d160679e042131256e3a5d52406a4f1731f94414550cacb8dc023246dbda12c6586a00c
-DIST MM-align-20120321.tar.xz 20072 BLAKE2B be53cff43b220c9c44bbd600e4e2870e3987da25744a4bf3da0bc8cf7bc2619c93839e27327d23b5ef3bfbf9aca86b865717c48eb5d91a9da7b977909fb3bc39 SHA512 193c3b16b2d9fb0aaacf18b203fcf0240de7b11b4c0ce99fc571c277aa6e624b7b8b4df625e34433a5dec4349bb5bf6ae0368609c1738337923cf3b4d06428bc
-EBUILD mm-align-20120321.ebuild 512 BLAKE2B c59652bc65df34ce0a26f8781b4794bf26a55838a66a27e93a36d2091b2f0668043a56cb5899c09e85c017ae23ef0d8db02d672c47cf47db5ab8bfdfeeb122ce SHA512 0da84f046c7aaa3023a0512397f09b298a5d99ea8623126aa1a4c2a18e3fc9b93eab635253a424e149013d39c47e1ab608edb68b540edb40fc3db7e055fdded8
-MISC metadata.xml 1451 BLAKE2B 9f5071f4eb82f5a49b9b3dd690c4105f8b56b80fda035544f864ff3062ac5fdf4d6b2c16a2e42eacc3bf4cbc64b3ad27d090ffd635506ce3789556fb7e023284 SHA512 908da672d7cf091949b7f1120764a3ea93a67b48edd2e391e66d4ca1d5ce39a25acecdee723a0444c680b4e835e197197cef56e85e1bd6018999df1bc330d797
diff --git a/sci-chemistry/mm-align/files/CMakeLists.txt b/sci-chemistry/mm-align/files/CMakeLists.txt
deleted file mode 100644
index 635ffdd67418..000000000000
--- a/sci-chemistry/mm-align/files/CMakeLists.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-cmake_minimum_required (VERSION 2.6)
-project (MM-align Fortran)
-add_executable(MMalign MM-align.f)
-
-install (TARGETS MMalign DESTINATION bin)
diff --git a/sci-chemistry/mm-align/metadata.xml b/sci-chemistry/mm-align/metadata.xml
deleted file mode 100644
index 03c48e987ffb..000000000000
--- a/sci-chemistry/mm-align/metadata.xml
+++ /dev/null
@@ -1,26 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-  <longdescription>
-MM-align is an algorithm for structurally aligning multiple-chain 
-protein-protein complexes. The algorithm is built on a heuristic 
-iteration of a modified Needleman-Wunsch dynamic programming (DP) 
-algorithm, with the alignment score specified by the inter-complex residue 
-distances. The multiple chains in each complex are first joined, in every 
-possible order, and then simultaneously aligned with cross-chain alignments 
-prevented. The alignments of interface residues are enhanced by an 
-interface-specific weighting factor. An optimal alignment between two complexes,
-as well as the overall TM-score, will be reported for each comparison.
-What is the difference between TM-align and MM-align? TM-align is for aligning 
-monomer protein structures while MM-align is designed for aligning 
-multiple-chain protein complex structures. Although one can still use TM-align 
-to align protein complexes after manually joining the chains, this will lead 
-to suboptimal alignments with unphysical cross alignments. Therefore, the 
-best result will be obtained if one uses TM-align to monomer structures and 
-MM-align for multimer structures.
-</longdescription>
-</pkgmetadata>
diff --git a/sci-chemistry/mm-align/mm-align-20120321.ebuild b/sci-chemistry/mm-align/mm-align-20120321.ebuild
deleted file mode 100644
index d2b42fe2547e..000000000000
--- a/sci-chemistry/mm-align/mm-align-20120321.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils fortran-2
-
-DESCRIPTION="Protein Complex Structural Alignment"
-HOMEPAGE="http://zhanglab.ccmb.med.umich.edu/MM-align/"
-SRC_URI="https://dev.gentoo.org/~jlec/distfiles/MM-align-${PV}.tar.xz"
-
-SLOT="0"
-LICENSE="tm-align"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-S="${WORKDIR}"
-
-src_prepare() {
-	cp "${FILESDIR}"/CMakeLists.txt . || die
-
-	cmake-utils_src_prepare
-}
diff --git a/sci-chemistry/openbabel-perl/Manifest b/sci-chemistry/openbabel-perl/Manifest
deleted file mode 100644
index fb62a44827f6..000000000000
--- a/sci-chemistry/openbabel-perl/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-AUX openbabel-perl-2.3.2-gcc-6_and_7-backport.patch 635 BLAKE2B 4e98dedd149b14d5bb02fb6d2fa03e07242d100c7b41f36f749ff3d587080eeca44aa26ca095d31e0309e45f3780b67deaa97f1177ed35a9b7407bd7c33f78ff SHA512 e1b4402f34d01ced5b4caaa184b4e5544cf47893cfe7958054052b05a57dc34b4d44239a212c7d909f29b9366b83b6df74993f844a20f23748c01272ec093081
-DIST openbabel-2.4.1.tar.gz 11618304 BLAKE2B 8fc051e83add9be6456e281a109bd6bbec282a64ffc83309819f0decbf167b4914fbb7f1966e95e103f268754045b804317f51c79a952ace707c6af2bd320125 SHA512 427e678f0a911bd27b9a8a05e60b6e09f113be4e5dd180daaf80c28d06368e52b57501261755ab3817a8d31f2754db24471fd0ceee706d029386d6f70800e9c6
-EBUILD openbabel-perl-2.4.1.ebuild 1583 BLAKE2B 233459caeea67df903f80dff500cce8fc1e4a99cc13124d8cee60fecd59261979c62ee0f5072f955d2c95043722c98450ad27187f7d0443c8ecc4a27f4c9ffee SHA512 6336a34a6d5dca6d573a62276cccf34cee37e95c31704f52a178366910d5267353b49fb981c1dce07ea935cac0e7887aad60df77468f7d4838ca18b901998651
-MISC metadata.xml 736 BLAKE2B d5039a999403b341b01d33f9791afacebc5aaf9ae66ae49b39c5933e92ca0d0bbfcc556d0e6c86de4574bfcc3cac273ecd00a75297969d9a95ea0badb0c561c9 SHA512 f83097e7a6ba608939b69248b23f72a4eeb8f32b01a52588a27265627bdb251cbc27e6188e9376041dffebc51cfb664acca11cbfca0018bde7208c374794ed49
diff --git a/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-gcc-6_and_7-backport.patch b/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-gcc-6_and_7-backport.patch
deleted file mode 100644
index e23dc6020ee5..000000000000
--- a/sci-chemistry/openbabel-perl/files/openbabel-perl-2.3.2-gcc-6_and_7-backport.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 0ee545cf..7f4b944e 100755
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -239,7 +239,7 @@ check_type_size(clock_t CLOCK_T)
- # Get the GCC version - from KDE4 cmake files
- if(CMAKE_COMPILER_IS_GNUCXX)
-   exec_program(${CMAKE_C_COMPILER} ARGS --version OUTPUT_VARIABLE _gcc_version_info)
--  string(REGEX MATCH "[345]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}")
-+  string(REGEX MATCH "[34567]\\.[0-9]\\.[0-9]" _gcc_version "${_gcc_version_info}")
-   # gcc on mac just reports: "gcc (GCC) 3.3 20030304 ..." without the
-   # patch level, handle this here:
-   if (NOT _gcc_version)
diff --git a/sci-chemistry/openbabel-perl/metadata.xml b/sci-chemistry/openbabel-perl/metadata.xml
deleted file mode 100644
index 74da65eec81e..000000000000
--- a/sci-chemistry/openbabel-perl/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-chemistry@gentoo.org</email>
-    <name>Gentoo Chemistry Project</name>
-  </maintainer>
-  <longdescription>
-OpenBabel is a chemical toolbox designed to speak the many languages of
-chemical data. It's an open, collaborative project allowing anyone to
-search, convert, analyze, or store data from molecular modeling, chemistry,
-solid-state materials, biochemistry, or related areas.
-This package enables to access OpenBabel library from Perl programs.
-</longdescription>
-  <upstream>
-    <remote-id type="sourceforge">openbabel</remote-id>
-  </upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/openbabel-perl/openbabel-perl-2.4.1.ebuild b/sci-chemistry/openbabel-perl/openbabel-perl-2.4.1.ebuild
deleted file mode 100644
index 6a3ef89b0e13..000000000000
--- a/sci-chemistry/openbabel-perl/openbabel-perl-2.4.1.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit cmake-utils perl-module
-
-DESCRIPTION="Perl bindings for OpenBabel"
-HOMEPAGE="http://openbabel.sourceforge.net/"
-SRC_URI="mirror://sourceforge/openbabel/openbabel-${PV}.tar.gz"
-
-KEYWORDS="amd64 ~arm x86 ~amd64-linux ~x86-linux"
-SLOT="0/5"
-LICENSE="GPL-2"
-IUSE=""
-
-RDEPEND="
-	dev-lang/perl:=
-	~sci-chemistry/openbabel-${PV}"
-DEPEND="${RDEPEND}
-	>=dev-util/cmake-2.4.8
-	>=dev-lang/swig-2"
-
-S="${WORKDIR}/openbabel-${PV}"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-2.3.2-gcc-6_and_7-backport.patch
-)
-
-src_prepare() {
-	sed \
-		-e '/__GNUC__/s:== 4:>= 4:g' \
-		-i include/openbabel/shared_ptr.h || die
-	cmake-utils_src_prepare
-	perl_set_version
-}
-
-src_configure() {
-	local mycmakeargs=(
-		-DCMAKE_INSTALL_RPATH=
-		-DBINDINGS_ONLY=ON
-		-DBABEL_SYSTEM_LIBRARY="${EPREFIX}/usr/$(get_libdir)/libopenbabel.so"
-		-DOB_MODULE_PATH="${EPREFIX}/usr/$(get_libdir)/openbabel/${PV}"
-		-DLIB_INSTALL_DIR="${D}/${VENDOR_ARCH}"
-		-DPERL_BINDINGS=ON
-		-DRUN_SWIG=ON
-	)
-
-	cmake-utils_src_configure
-}
-
-src_compile() {
-	cmake-utils_src_compile bindings_perl
-}
-
-src_test() {
-	mkdir "${CMAKE_BUILD_DIR}/$(get_libdir)/Chemistry" || die
-	cp \
-		"${CMAKE_USE_DIR}/scripts/perl/OpenBabel.pm" \
-		"${CMAKE_BUILD_DIR}/$(get_libdir)/Chemistry/" || die
-	for i in "${CMAKE_USE_DIR}"/scripts/perl/t/*; do
-		einfo "Running test: ${i}"
-		perl -I"${CMAKE_BUILD_DIR}/$(get_libdir)" "${i}" || die
-	done
-}
-
-src_install() {
-	cd "${CMAKE_BUILD_DIR}" || die
-	cmake -DCOMPONENT=bindings_perl -P cmake_install.cmake
-}
diff --git a/sci-chemistry/votca-ctp/Manifest b/sci-chemistry/votca-ctp/Manifest
deleted file mode 100644
index 007ab7ec3548..000000000000
--- a/sci-chemistry/votca-ctp/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST votca-ctp-1.5.1.tar.gz 1345994 BLAKE2B 6e927c5d57abfff335412bdac085c9dd81696503310e58a89bf2207b07f9d9900d11d20176a11fbde6d6cdfa97f50faa5e877889e35201ad9ed5dd93dbc158cb SHA512 686d7193cdd6a763197dd4f332554c9c6c2022c539191d0a243e70450aa2a4c7048fff3c06636aee09525516fb3717fe49934d5daf2dfcdcbc08be416cc4b6c0
-DIST votca-ctp-manual-1.5.1.pdf 948647 BLAKE2B 4afec48d0e6bb29dc86d4d22fce74a8d2197d6b7a1ed35a5b09af84c5bbc0fc49b91e045c85e5b5ab79beb5a7de1db78a15e395a1a5faf4c11cc1b58c1ffca97 SHA512 b4ae79b2da0037cc325fdff3b0fd8d142d6bfdad5bc11991cee314f40f105bcdcb1189d17679a84eb37da7a9bb686d0c5ee57c7796a0c6b787b70d53222dbc17
-EBUILD votca-ctp-1.5.1-r1.ebuild 1515 BLAKE2B 634ed349161b15dfc152ffbfe0ad3a24f0544c470c597f30fcf8c1ed4a198e4db4f95c41aa71db0db1bd3faecb71ad8fc437b4ec9793d2e8def8dc12489ecd11 SHA512 f2e0cbf730a44aabd0fe5d34626781dc43977023e6a1d7a98604563430f28a18e79214b1dda818f8b5c25827db8ca4dafac587c064f75d4278916af6668791a2
-MISC metadata.xml 454 BLAKE2B fc74a3b0be617a1298d983dd1f63d59b4022af9a9762d78c4647ae4fe7402e0f37392e0c9c213adff4c71c21741cbe002bef6b4bf19843e1d41810bec572b390 SHA512 3a6dc400309fc883c76fc93004f31b8a34126287acee999b345cb607147f457e3cfd7ebe5d5b17507211813b90fd3bbbffe8d56d235528cf465e994a2a6d7524
diff --git a/sci-chemistry/votca-ctp/metadata.xml b/sci-chemistry/votca-ctp/metadata.xml
deleted file mode 100644
index a77179a479f6..000000000000
--- a/sci-chemistry/votca-ctp/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>junghans@gentoo.org</email>
-		<name>Christoph Junghans</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-chemistry@gentoo.org</email>
-		<name>Gentoo Chemistry Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="github">votca/ctp</remote-id>
-	</upstream>
-</pkgmetadata>
diff --git a/sci-chemistry/votca-ctp/votca-ctp-1.5.1-r1.ebuild b/sci-chemistry/votca-ctp/votca-ctp-1.5.1-r1.ebuild
deleted file mode 100644
index ace4787f199b..000000000000
--- a/sci-chemistry/votca-ctp/votca-ctp-1.5.1-r1.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-CMAKE_MAKEFILE_GENERATOR="ninja"
-
-inherit cmake-utils multilib
-
-IUSE="doc"
-if [ "${PV}" != "9999" ]; then
-	SRC_URI="https://github.com/${PN/-//}/archive/v${PV}.tar.gz -> ${P}.tar.gz
-		doc? ( https://github.com/${PN/-//}/releases/download/v${PV}/${PN}-manual-${PV}.pdf )"
-	KEYWORDS="~amd64 ~x86 ~amd64-linux"
-	S="${WORKDIR}/${P#votca-}"
-else
-	inherit git-r3
-	EGIT_REPO_URI="https://github.com/${PN/-//}.git"
-fi
-
-DESCRIPTION="Votca charge transport module"
-HOMEPAGE="http://www.votca.org"
-
-LICENSE="Apache-2.0"
-SLOT="0"
-
-RDEPEND="
-	~sci-libs/votca-tools-${PV}[sqlite]
-	>=dev-cpp/eigen-3.3
-	sci-libs/gsl:=
-	~sci-chemistry/votca-csg-${PV}"
-
-DEPEND="${RDEPEND}
-	virtual/pkgconfig"
-
-if [ "${PV}" != "9999" ]; then
-	DEPEND="${DEPEND}
-	doc? (
-		app-doc/doxygen[dot]
-		dev-texlive/texlive-latexextra
-		virtual/latex-base
-		dev-tex/pgf
-	)"
-fi
-
-DOCS=( README.md NOTICE CHANGELOG.md )
-
-src_configure() {
-	[[ ${PV} = *9999* ]] && mycmakeargs=(
-		-DBUILD_XTP_MANUAL=$(usex doc)
-	)
-	cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-	if use doc; then
-		[[ ${PV} != *9999* ]] && dodoc "${DISTDIR}/${PN}-manual-${PV}.pdf"
-		cmake-utils_src_make -C "${CMAKE_BUILD_DIR}" html
-		dodoc -r "${CMAKE_BUILD_DIR}"/share/doc/html
-	fi
-}
-
-pkg_postinst() {
-	einfo
-	einfo "Please read and cite:"
-	einfo "VOTCA-CTP, J. Chem. Theo. Comp. 7, 3335-3345 (2011)"
-	einfo "https://dx.doi.org/10.1021/ct200388s"
-	einfo
-}