sci-chemistry/vesta: add new package

since there is a behavior change from 3.5.6, it is necessary
to preserve an old version.

licenses/VESTA

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+VESTA LICENSE
+Version 3
+Copyright (C) 2006-2021, Koichi Momma and Fujio Izumi
+
+This software is distributed free of charge for academic, scientific, educational, and noncommercial users. Users belonging to commercial enterprises may also use this software at no cost until a license for business users is established. Permission to use this software is hereby granted under the following conditions:
+
+1) Drawings produced by VESTA may be used in any publications provided that its use is explicitly acknowledged. A suitable reference for VESTA is:
+K. Momma and F. Izumi, "VESTA 3 for three-dimensional visualization of crystal, volumetric and morphology data," J. Appl. Crystallogr., 44, 1272-1276 (2011).
+2) You should not redistribute any copy of the distributed files unless you have a written permission from us.
+
+Part of these terms may be changed without any prior announcement.
+This software is provided "as is" without any express or implied warranty.

sci-chemistry/vesta/Manifest

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+DIST vesta-3.5.5.tar.bz2 25990320 BLAKE2B e00532b5f542b2c9d76b20f91556978fc4948d093a64786d68001f0d44404bb3688541d41eda45d1bfc5b82f7526d4d242208bcca141e91092d1bbe5d04f8a05 SHA512 090560e4953f8b2771bbf2fa44131a1b9193430902d2ed93c499436cbbe9298199e0774cbf7346ab4fa758820dd13ba2fed14e97fbea1350d0da3baaca258d33
+DIST vesta-3.5.7.tar.bz2 25021115 BLAKE2B 11ed4c4788ed0bf1841b46c74537036f9e00d57ae02345f308386068cf7e6317a67ffbfd42f683848732e8c79ba7f8b2753d3620a430da98988715021fcb821e SHA512 95a803bd403cab0e374f18870392264756a8a970d5178c91408e2fcd7ce490ebefbb2f3a51e1cc3edc9aff4b810093f4444544c7bbcaccea2160a071e815de11

sci-chemistry/vesta/files/VESTA.desktop

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+[Desktop Entry]
+Name=VESTA
+Exec=/opt/bin/VESTA %F
+Type=Application
+Categories=Science
+Terminal=false
+StartupNotify=false
+Icon=/opt/VESTA/img/logo.png
+GenericName="Visualization for Electronic and STructural Analysis"
+Comment="Crystal structure visualization program"
+MimeType=application/x-vesta;

sci-chemistry/vesta/metadata.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>chn@chn.moe</email>
+		<name>Haonan Chen</name>
+	</maintainer>
+</pkgmetadata>

sci-chemistry/vesta/vesta-3.5.5.ebuild

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+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit desktop xdg
+
+DESCRIPTION="Visualization for Electronic and STructural Analysis"
+HOMEPAGE="https://jp-minerals.org/vesta"
+SRC_URI="https://jp-minerals.org/vesta/archives/${PV}/VESTA-gtk3.tar.bz2 -> ${PN}-${PV}.tar.bz2"
+
+LICENSE="VESTA"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+RESTRICT="mirror strip"
+
+DEPEND=""
+RDEPEND="
+	x11-libs/gtk+
+	virtual/glu
+	dev-util/desktop-file-utils
+	x11-libs/libXtst
+	virtual/jdk
+	${DEPEND}"
+BDEPEND=""
+
+S="${WORKDIR}/VESTA-gtk3"
+
+QA_PREBUILD="*"
+
+src_install() {
+	insinto /opt/VESTA
+	doins -r *
+	fperms +x /opt/VESTA/VESTA
+	fperms +x /opt/VESTA/VESTA-gui
+
+	domenu "${FILESDIR}/VESTA.desktop"
+
+	dosym ../VESTA/VESTA /opt/bin/VESTA
+	dosym ../VESTA/VESTA /opt/bin/vesta
+}
+
+pkg_postinst() {
+	xdg_desktop_database_update
+
+	elog "If you meet any abnormal behavior while using VESTA after upgrade or downgrade,"
+	elog "try remove ~/.VESTA and restart VESTA. Note that this will make you lost"
+	elog "all your saved configs."
+}
+
+pkg_postrm() {
+	xdg_desktop_database_update
+}

sci-chemistry/vesta/vesta-3.5.7.ebuild

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+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit desktop xdg
+
+DESCRIPTION="Visualization for Electronic and STructural Analysis"
+HOMEPAGE="https://jp-minerals.org/vesta"
+SRC_URI="https://jp-minerals.org/vesta/archives/${PV}/VESTA-gtk3.tar.bz2 -> ${PN}-${PV}.tar.bz2"
+
+LICENSE="VESTA"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+RESTRICT="mirror strip"
+
+DEPEND=""
+RDEPEND="
+	x11-libs/gtk+
+	virtual/glu
+	dev-util/desktop-file-utils
+	x11-libs/libXtst
+	virtual/jdk
+	${DEPEND}"
+BDEPEND=""
+
+S="${WORKDIR}/VESTA-gtk3"
+
+QA_PREBUILD="*"
+
+src_install() {
+	insinto /opt/VESTA
+	doins -r *
+	fperms +x /opt/VESTA/VESTA
+	fperms +x /opt/VESTA/VESTA-gui
+
+	domenu "${FILESDIR}/VESTA.desktop"
+
+	dosym ../VESTA/VESTA /opt/bin/VESTA
+	dosym ../VESTA/VESTA /opt/bin/vesta
+}
+
+pkg_postinst() {
+	xdg_desktop_database_update
+
+	elog "Since version 3.5.6, a behavior change has been made, which may cause deleted atoms appear again."
+	elog "See: https://groups.google.com/g/vesta-discuss/c/y7TCMRe1HlA"
+	elog "To restore the previous behavior, please install version 3.5.5 or earlier."
+
+	elog "If you meet any abnormal behavior while using VESTA after upgrade or downgrade,"
+	elog "try remove ~/.VESTA and restart VESTA. Note that this will make you lost"
+	elog "all your saved configs."
+}
+
+pkg_postrm() {
+	xdg_desktop_database_update
+}