From mboxrd@z Thu Jan 1 00:00:00 1970
Return-Path: <gentoo-commits+bounces-1489685-garchives=archives.gentoo.org@lists.gentoo.org>
Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80])
(using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)
key-exchange X25519 server-signature RSA-PSS (2048 bits))
(No client certificate requested)
by finch.gentoo.org (Postfix) with ESMTPS id B703D15802F
for <garchives@archives.gentoo.org>; Fri, 24 Feb 2023 07:30:14 +0000 (UTC)
Received: from pigeon.gentoo.org (localhost [127.0.0.1])
by pigeon.gentoo.org (Postfix) with SMTP id 0E19BE077C;
Fri, 24 Feb 2023 07:30:14 +0000 (UTC)
Received: from smtp.gentoo.org (woodpecker.gentoo.org [140.211.166.183])
(using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)
key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256)
(No client certificate requested)
by pigeon.gentoo.org (Postfix) with ESMTPS id E77B4E077C
for <gentoo-commits@lists.gentoo.org>; Fri, 24 Feb 2023 07:30:13 +0000 (UTC)
Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52])
(using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)
key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256)
(No client certificate requested)
by smtp.gentoo.org (Postfix) with ESMTPS id CD6E1335D84
for <gentoo-commits@lists.gentoo.org>; Fri, 24 Feb 2023 07:30:12 +0000 (UTC)
Received: from localhost.localdomain (localhost [IPv6:::1])
by oystercatcher.gentoo.org (Postfix) with ESMTP id 159F9807
for <gentoo-commits@lists.gentoo.org>; Fri, 24 Feb 2023 07:30:11 +0000 (UTC)
From: "Andrew Ammerlaan" <andrewammerlaan@gentoo.org>
To: gentoo-commits@lists.gentoo.org
Content-Transfer-Encoding: 8bit
Content-type: text/plain; charset=UTF-8
Reply-To: gentoo-dev@lists.gentoo.org, "Andrew Ammerlaan" <andrewammerlaan@gentoo.org>
Message-ID: <1677222627.d0d613f06aae55ab73f71229d00724034ca3c765.andrewammerlaan@gentoo>
Subject: [gentoo-commits] repo/gentoo:master commit in: sci-biology/biopython/
X-VCS-Repository: repo/gentoo
X-VCS-Files: sci-biology/biopython/Manifest sci-biology/biopython/biopython-1.81.ebuild
X-VCS-Directories: sci-biology/biopython/
X-VCS-Committer: andrewammerlaan
X-VCS-Committer-Name: Andrew Ammerlaan
X-VCS-Revision: d0d613f06aae55ab73f71229d00724034ca3c765
X-VCS-Branch: master
Date: Fri, 24 Feb 2023 07:30:11 +0000 (UTC)
Precedence: bulk
List-Post: <mailto:gentoo-commits@lists.gentoo.org>
List-Help: <mailto:gentoo-commits+help@lists.gentoo.org>
List-Unsubscribe: <mailto:gentoo-commits+unsubscribe@lists.gentoo.org>
List-Subscribe: <mailto:gentoo-commits+subscribe@lists.gentoo.org>
List-Id: Gentoo Linux mail <gentoo-commits.gentoo.org>
X-BeenThere: gentoo-commits@lists.gentoo.org
X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply
X-Archives-Salt: 9e128404-b824-4c85-9bf6-8464f3fb7b55
X-Archives-Hash: 490410ebeeea9603be5ea862835d707e
commit: d0d613f06aae55ab73f71229d00724034ca3c765
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Fri Feb 24 07:10:27 2023 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Fri Feb 24 07:10:27 2023 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d0d613f0
sci-biology/biopython: add 1.81
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/biopython/Manifest | 1 +
sci-biology/biopython/biopython-1.81.ebuild | 61 +++++++++++++++++++++++++++++
2 files changed, 62 insertions(+)
diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
index 014c48aa8401..c693a5a8a963 100644
--- a/sci-biology/biopython/Manifest
+++ b/sci-biology/biopython/Manifest
@@ -1 +1,2 @@
DIST biopython-1.79.tar.gz 16738730 BLAKE2B 8c97fc23e458f7bc98b0ed0226bd6fb42f6c6f3ce03d562b13fac66c5061451595cd5bd01cad07bbe1fc6b20f4de21b0f03766b5a20e602545da888047a57185 SHA512 81e2718f4015bb038637b4d1181e6bea48018fec1e769c5f0ab75442a769336899191f1222e82e1b9569c1fac470500d7582420e5cbe9bce0056b41751adeaaa
+DIST biopython-1.81.tar.gz 19324875 BLAKE2B be3a85f5b60638987d6186af498411b494f8d27389f24cd1b9e658bc6b1a29c799ec8b20a9ac0b955c6d4c239706f4dbb5b75f6d56908f63d731b1d56c9fd587 SHA512 1595fad6631bfb6cf4e1a92ed72e6093e2a0c24f3c0bd4182267ec9742fb03dff16099eedde139598aa6b5b8380bbac9e48246cb9ab8b44109333d60adfd00ed
diff --git a/sci-biology/biopython/biopython-1.81.ebuild b/sci-biology/biopython/biopython-1.81.ebuild
new file mode 100644
index 000000000000..8b90d610c6ae
--- /dev/null
+++ b/sci-biology/biopython/biopython-1.81.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{9..11} )
+
+inherit distutils-r1 optfeature pypi
+
+DESCRIPTION="Python modules for computational molecular biology"
+HOMEPAGE="https://www.biopython.org/ https://pypi.org/project/biopython/"
+
+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 || die
+ ln -r -s "${S}"/Bio/Align/substitution_matrices \
+ "${TEST_DIR}"/lib/Bio/Align/substitution_matrices || 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/mysqlclient
+ optfeature "PostgreSQL database support" dev-python/psycopg:2
+
+ optfeature_header "Some applications need extra packages:"
+ optfeature "EMBOSS (The European Molecular Biology Open Software Suite)" sci-biology/emboss
+}