gentoo resync : 04.01.2022

6 files changed, 0 insertions, 124 deletions

diff --git a/sci-biology/ApE/ApE-2.0.7-r1.ebuild b/sci-biology/ApE/ApE-2.0.7-r1.ebuild
deleted file mode 100644
index 273e236997ed..000000000000
--- a/sci-biology/ApE/ApE-2.0.7-r1.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit desktop
-
-DESCRIPTION="A Plasmid Editor"
-HOMEPAGE="https://jorgensen.biology.utah.edu/wayned/ape/"
-SRC_URI="https://jorgensen.biology.utah.edu/wayned/ape/Download/Linux/ApE_linux_current.zip -> ${P}.zip"
-
-LICENSE="ApE"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="app-arch/unzip"
-RDEPEND="
-	dev-lang/tcl:0
-	dev-lang/tk:0"
-
-RESTRICT="bindist mirror"
-
-S="${WORKDIR}/ApE Linux/"
-
-src_compile() { :; }
-
-src_install() {
-	cat >> "${T}/ApE" <<- "EOF"
-	#!/bin/bash
-	cmdArgs=""
-
-	# AppMain.tcl searches files relative to the directory where it resides.
-	# Add absolute path to file here, if necessary.
-	for rfpath in "$@"; do
-		afpath="$PWD/${rfpath}"
-		if test -r "${afpath}"; then
-			cmdArgs="${cmdArgs} \"${afpath}\"";
-		else
-			cmdArgs="${cmdArgs} \"${rfpath}\"";
-		fi
-	done
-
-	eval exec tclsh "\"/usr/share/ApE-2.0.7/AppMain.tcl\"" "${cmdArgs}"
-	EOF
-
-	dobin "${T}/ApE"
-	insinto "/usr/share/${P}"
-	doins -r "${WORKDIR}"/ApE\ Linux/*
-	make_desktop_entry ${PN} ${PN} \
-		"/usr/share/${P}/Accessory Files/Icons and images/monkey_icon.gif" \
-		"Science"
-}
diff --git a/sci-biology/ApE/Manifest b/sci-biology/ApE/Manifest
deleted file mode 100644
index 83055a8fbf43..000000000000
--- a/sci-biology/ApE/Manifest
+++ /dev/null
@@ -1,3 +0,0 @@
-DIST ApE-2.0.7.zip 318454 BLAKE2B 420001d298b8c6b1bc26247446aafe8c3adcf6477ebabc689219c094d46fe5e836d216a493169bac0ccd9c3b669d9421edb3b023a1a39cf74d32a81df09e66d2 SHA512 073e3f96badf4888c10a7c7eb453a3775d5bb9136b0bd836d37d1be784847f887e0c68b37325f430eebfb90c2d94021f10d4e8ede92de89b1ab1ddc1ffdbc254
-EBUILD ApE-2.0.7-r1.ebuild 1170 BLAKE2B 9156e3862ffaba5ae4141f0b35f0736fac3f5e31e57a26d4d54c09b283db9303479649a98d4de21d329834cc8baa2b96f0fbeffa29cfb8ad015eac4813d6cb44 SHA512 3bfb046677223de0bc2c3b168dcd78f6e303b15f79b0305addef98ce75060414bc7b4a1f87d8bd08ed00a2a65972b2a5da41e31dd2c9d8ef8b31261e39112127
-MISC metadata.xml 168 BLAKE2B 2e0e000b4c3b6ca04c12903fdbe278415c05a822623c52e9aa95cbbf3d50bcb1246b7edbda7d2f6b559af8950c6374e6e0a69b76319964cfe686bf50b0604a57 SHA512 4dcf45d1809e8390a2d8155c8ebfe0dd610203e392aeab0ccd8a10f42cc8532a4925eff32b35e7a6c35598a4efd288229034ec0732299dbd8cfa0acff705fed3
diff --git a/sci-biology/ApE/metadata.xml b/sci-biology/ApE/metadata.xml
deleted file mode 100644
index 115e9d64a669..000000000000
--- a/sci-biology/ApE/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<!-- maintainer-needed -->
-</pkgmetadata>
diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 90b0315f3fe9..7adf00a4e082 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
index aac147b18635..9739c4cfdbfd 100644
--- a/sci-biology/biopython/Manifest
+++ b/sci-biology/biopython/Manifest
@@ -1,5 +1,3 @@
-DIST biopython-1.77.tar.gz 16837021 BLAKE2B b5586f0ea3e476b11801dcc98039d5eea7b191e11d390192c0cf348018ded005fe2ad5dc9ba71c83aebc9cdde20c97244905dcc3aeb5436a97588da9f8c79c3e SHA512 6f4b03d46c591e1f49dd1e76bcc4ac5c9aaa2bf748c9dd37ffc5de5a613fbeed38f89b418c01601dd99c65b13b2e294bc8d81ffafc42a9ff1b309c84f840d0d5
 DIST biopython-1.79.tar.gz 16738730 BLAKE2B 8c97fc23e458f7bc98b0ed0226bd6fb42f6c6f3ce03d562b13fac66c5061451595cd5bd01cad07bbe1fc6b20f4de21b0f03766b5a20e602545da888047a57185 SHA512 81e2718f4015bb038637b4d1181e6bea48018fec1e769c5f0ab75442a769336899191f1222e82e1b9569c1fac470500d7582420e5cbe9bce0056b41751adeaaa
-EBUILD biopython-1.77.ebuild 1918 BLAKE2B 61915c04855bfa88044c7f25f36d10ab774768b8ba2df5591ce6ede34dc90a4553c0331ab85fc12139a724e6fa6a0e40e1b584892f903bcd66b038677ffd843a SHA512 13e0bd3a5bb1ef8c76d8df5d6d2d3d659b48870472c7a8a82a14e19cdae484e19bb9a3e7e2870b0e5a75c056816965e7f5e106d1c910131eefb5c206874901d1
 EBUILD biopython-1.79.ebuild 1887 BLAKE2B b3f3f50434e77dae22a744a0eeb795690a8e828167aeb0755081286de38ca4f61e661536547405cc9026ba52466c678ee1f0af291c26658eba9afec36322bb9e SHA512 74feee0feff9df45fc16f512bc48ec6c0934608783def71fd5f1373a2ad57379e77c8dd6bdd94fbe755033e5a5f9881a64e106cb1f8be738137a77584d2c83fe
 MISC metadata.xml 334 BLAKE2B 4d97c23444fdddcca57631fa2ddf4a11cfcef0accf91db65071d520f6601c0626e290e67cbf162abdefe7a74f4b410f8366a23186fc417e1fab7e9ce157d7610 SHA512 a870bd044d0e0d4e2a0c48b50f710845c6269e038790243f1d1de65b1252fd653f0f403fc55b98946df8eb27f24dfae5c84f52fcc38c969afcbdb548ccbb7a59
diff --git a/sci-biology/biopython/biopython-1.77.ebuild b/sci-biology/biopython/biopython-1.77.ebuild
deleted file mode 100644
index 1dcbc2101c45..000000000000
--- a/sci-biology/biopython/biopython-1.77.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit distutils-r1 optfeature
-
-DESCRIPTION="Python modules for computational molecular biology"
-HOMEPAGE="https://www.biopython.org/ https://pypi.org/project/biopython/"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="HPND"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-
-RDEPEND="
-	dev-python/matplotlib[${PYTHON_USEDEP}]
-	dev-python/networkx[${PYTHON_USEDEP}]
-	dev-python/numpy[${PYTHON_USEDEP}]
-	dev-python/rdflib[${PYTHON_USEDEP}]
-	dev-python/pygraphviz[${PYTHON_USEDEP}]
-	>=dev-python/reportlab-3.5.13-r1[${PYTHON_USEDEP}]
-	dev-python/pydot[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}"
-BDEPEND="sys-devel/flex"
-
-DOCS=( {CONTRIB,DEPRECATED,NEWS,README}.rst Doc/. )
-
-python_test() {
-	distutils_install_for_testing
-	cp -r {Doc,Tests} "${TEST_DIR}"/lib/ || die
-
-	# need to create symlinks for doctests
-	mkdir -p "${TEST_DIR}"/lib/Bio/Align/substitution_matrices || die
-	ln -r -s "${S}"/Bio/Align/substitution_matrices/data \
-		"${TEST_DIR}"/lib/Bio/Align/substitution_matrices/data || die
-
-	cd "${TEST_DIR}"/lib/Tests || die
-	rm test_BioSQL_{psycopg2.py,MySQLdb.py,mysql_connector.py} || die
-	"${EPYTHON}" run_tests.py --offline --verbose || die
-}
-
-python_install_all() {
-	# remove files causing ecompressdir to fail
-	rm Doc/examples/ls_orchid.gbk.{gz,bz2} || die
-
-	distutils-r1_python_install_all
-
-	dodir /usr/share/${PN}
-	cp -r --preserve=mode Scripts Tests "${ED}"/usr/share/${PN} || die
-}
-
-pkg_postinst() {
-	optfeature_header "For database support you need to install:"
-	optfeature "MySQL database support" dev-python/mysql-python
-	optfeature "PostgreSQL database support" dev-python/psycopg
-	optfeature_header "Some applications need extra packages:"
-	optfeature "EMBOSS (The European Molecular Biology Open Software Suite)" sci-biology/emboss
-}