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 TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id 513FC13835A for ; Sun, 3 Jan 2021 06:31:05 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 85257E0802; Sun, 3 Jan 2021 06:31:03 +0000 (UTC) Received: from smtp.gentoo.org (mail.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id F27C6E07FA for ; Sun, 3 Jan 2021 06:31:02 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id B1EE4340FCB for ; Sun, 3 Jan 2021 06:31:01 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 327F7CC for ; Sun, 3 Jan 2021 06:31:00 +0000 (UTC) From: "Horea Christian" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Horea Christian" Message-ID: <1609655130.eeef69fea4f72eb2bd4400a11d80f3a5db0a3d92.chymera@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/pysam/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/pysam/metadata.xml sci-biology/pysam/pysam-0.15.3.ebuild X-VCS-Directories: sci-biology/pysam/ X-VCS-Committer: chymera X-VCS-Committer-Name: Horea Christian X-VCS-Revision: eeef69fea4f72eb2bd4400a11d80f3a5db0a3d92 X-VCS-Branch: master Date: Sun, 3 Jan 2021 06:31:00 +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: b38597b5-495d-4914-8e1b-e0d90c543fc4 X-Archives-Hash: 45257367a648f4f7526661592183b46a commit: eeef69fea4f72eb2bd4400a11d80f3a5db0a3d92 Author: Andrew Ammerlaan riseup net> AuthorDate: Sat Jan 2 13:09:32 2021 +0000 Commit: Horea Christian gmail com> CommitDate: Sun Jan 3 06:25:30 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=eeef69fe sci-biology/pysam: remove, package is in ::gentoo Package-Manager: Portage-3.0.12, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan riseup.net> Signed-off-by: Horea Christian chymera.eu> sci-biology/pysam/metadata.xml | 12 --------- sci-biology/pysam/pysam-0.15.3.ebuild | 46 ----------------------------------- 2 files changed, 58 deletions(-) diff --git a/sci-biology/pysam/metadata.xml b/sci-biology/pysam/metadata.xml deleted file mode 100644 index 6182254bd..000000000 --- a/sci-biology/pysam/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ - - - - - sci-biology@gentoo.org - Gentoo Biology Project - - - pysam - pysam-developers/pysam - - diff --git a/sci-biology/pysam/pysam-0.15.3.ebuild b/sci-biology/pysam/pysam-0.15.3.ebuild deleted file mode 100644 index 4224df0be..000000000 --- a/sci-biology/pysam/pysam-0.15.3.ebuild +++ /dev/null @@ -1,46 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 python3_6 ) - -inherit distutils-r1 - -DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format" -HOMEPAGE=" - https://github.com/pysam-developers/pysam - https://pypi.org/project/pysam/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="" - -# current code wraps 3rd-party code from htslib-1.9, samtools-1.9 and bcftools-1.9 -RDEPEND="=sci-libs/htslib-1.9*:=" -DEPEND="${RDEPEND} - dev-python/cython[${PYTHON_USEDEP}] - dev-python/setuptools[${PYTHON_USEDEP}]" - -python_prepare_all() { - # unbundle htslib - export HTSLIB_MODE="external" - export HTSLIB_INCLUDE_DIR="${EPREFIX}"/usr/include - export HTSLIB_LIBRARY_DIR="${EPREFIX}"/usr/$(get_libdir) - rm -r htslib || die - - # prevent setup.py from adding RPATHs - sed -e "/ext\.extra_link_args += \['-Wl,-rpath,\$ORIGIN'\]/d" \ - -i cy_build.py || die - sed -e '/runtime_library_dirs=htslib_library_dirs/d' \ - -i setup.py || die - - distutils-r1_python_prepare_all -} - -src_compile() { - # TODO - # empty compile, as the build system runs the whole build again in install - : -}