From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: 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 E7A5B1581C1 for ; Fri, 19 Jul 2024 12:43:56 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id EE334E2ACC; Fri, 19 Jul 2024 12:43:55 +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 D179EE2ACC for ; Fri, 19 Jul 2024 12:43:55 +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)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id A1154342FF8 for ; Fri, 19 Jul 2024 12:43:54 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 408D11E44 for ; Fri, 19 Jul 2024 12:43:53 +0000 (UTC) From: "Andrew Ammerlaan" 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" Message-ID: <1721392507.acafe6e0405a9bcd41829884a04736f8d94e4d8c.andrewammerlaan@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/gffutils/gffutils-0.11.1.ebuild sci-biology/gffutils/gffutils-0.13.ebuild sci-biology/gffutils/metadata.xml X-VCS-Directories: sci-biology/gffutils/ X-VCS-Committer: andrewammerlaan X-VCS-Committer-Name: Andrew Ammerlaan X-VCS-Revision: acafe6e0405a9bcd41829884a04736f8d94e4d8c X-VCS-Branch: master Date: Fri, 19 Jul 2024 12:43:53 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: eacbdb9d-6d14-46da-8b03-dd507f14152c X-Archives-Hash: f871ec7bfca2bbe484afde0a918c1416 commit: acafe6e0405a9bcd41829884a04736f8d94e4d8c Author: Michael Schubert gmail com> AuthorDate: Fri Jul 12 11:44:16 2024 +0000 Commit: Andrew Ammerlaan gentoo org> CommitDate: Fri Jul 19 12:35:07 2024 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=acafe6e0 sci-bioloy/gffutils: version bump 0.13; fix tests Signed-off-by: Michael Schubert gmail.com> Signed-off-by: Andrew Ammerlaan gentoo.org> sci-biology/gffutils/gffutils-0.11.1.ebuild | 42 ----------------------------- sci-biology/gffutils/gffutils-0.13.ebuild | 32 ++++++++++++++++++++++ sci-biology/gffutils/metadata.xml | 4 --- 3 files changed, 32 insertions(+), 46 deletions(-) diff --git a/sci-biology/gffutils/gffutils-0.11.1.ebuild b/sci-biology/gffutils/gffutils-0.11.1.ebuild deleted file mode 100644 index 8ee8fd4b5..000000000 --- a/sci-biology/gffutils/gffutils-0.11.1.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{10..11} ) - -inherit distutils-r1 - -DESCRIPTION="GFF and GTF file manipulation and interconversion" -HOMEPAGE="https://gffutils.readthedocs.io/en/latest/" -SRC_URI="https://github.com/daler/gffutils/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="test" -# Nose tests no longer supported, migration on next release -#RESTRICT="test" -RESTRICT="!test? ( test )" - -RDEPEND=" - dev-python/simplejson[${PYTHON_USEDEP}] - dev-python/argh[${PYTHON_USEDEP}] - dev-python/argcomplete[${PYTHON_USEDEP}] - sci-biology/biopython[${PYTHON_USEDEP}] - sci-biology/pybedtools[${PYTHON_USEDEP}] - sci-biology/pyfaidx[${PYTHON_USEDEP}] -" -DEPEND="${RDEPEND}" - -python_prepare_all() { - if use test; then - sed -i -e "s:/tmp/gffutils-test:${T}:g" gffutils/test/test.py || die - fi - distutils-r1_python_prepare_all -} - -python_test() { - distutils_install_for_testing - nosetests -v -x --with-doctest -a '!slow' || die -} diff --git a/sci-biology/gffutils/gffutils-0.13.ebuild b/sci-biology/gffutils/gffutils-0.13.ebuild new file mode 100644 index 000000000..fbd90b6d9 --- /dev/null +++ b/sci-biology/gffutils/gffutils-0.13.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="GFF and GTF file manipulation and interconversion" +HOMEPAGE="https://gffutils.readthedocs.io/en/latest/" +SRC_URI="https://github.com/daler/gffutils/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-python/simplejson[${PYTHON_USEDEP}] + dev-python/argh[${PYTHON_USEDEP}] + dev-python/argcomplete[${PYTHON_USEDEP}] + dev-python/pyfaidx[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" + +# https://github.com/daler/gffutils/issues/233 + cli not installed yet +EPYTEST_DESELECT=( + gffutils/test/test_biopython_integration.py::test_roundtrip + gffutils/test/test_cli.py::test_issue_224 +) + +distutils_enable_tests pytest diff --git a/sci-biology/gffutils/metadata.xml b/sci-biology/gffutils/metadata.xml index c9fe23ced..dc2c60220 100644 --- a/sci-biology/gffutils/metadata.xml +++ b/sci-biology/gffutils/metadata.xml @@ -5,10 +5,6 @@ mschu.dev@gmail.com Michael Schubert - - sci-biology@gentoo.org - Gentoo Biology Project - daler/gffutils