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 2F7F1158018 for ; Sun, 3 Oct 2021 17:41:51 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 23984E0898; Sun, 3 Oct 2021 17:41:50 +0000 (UTC) Received: from smtp.gentoo.org (woodpecker.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (using TLSv1.2 with cipher ECDHE-RSA-CHACHA20-POLY1305 (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 02362E0898 for ; Sun, 3 Oct 2021 17:41:49 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher ECDHE-RSA-CHACHA20-POLY1305 (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 16BE4342F1E for ; Sun, 3 Oct 2021 17:41:49 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id A448A12F for ; Sun, 3 Oct 2021 17:41:47 +0000 (UTC) From: "David Seifert" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "David Seifert" Message-ID: <1633282899.938a340079ee1b725936dad3e441faf8cc3420cd.soap@gentoo> Subject: [gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/ X-VCS-Repository: repo/gentoo X-VCS-Files: sci-biology/pysam/Manifest sci-biology/pysam/pysam-0.17.0.ebuild X-VCS-Directories: sci-biology/pysam/ X-VCS-Committer: soap X-VCS-Committer-Name: David Seifert X-VCS-Revision: 938a340079ee1b725936dad3e441faf8cc3420cd X-VCS-Branch: master Date: Sun, 3 Oct 2021 17:41:47 +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: ecbfa3a2-603e-4a52-8083-cda2bfe96286 X-Archives-Hash: 0e503c5896c234808d4147df31a96b20 commit: 938a340079ee1b725936dad3e441faf8cc3420cd Author: David Seifert gentoo org> AuthorDate: Sun Oct 3 17:41:39 2021 +0000 Commit: David Seifert gentoo org> CommitDate: Sun Oct 3 17:41:39 2021 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=938a3400 sci-biology/pysam: add 0.17.0 Signed-off-by: David Seifert gentoo.org> sci-biology/pysam/Manifest | 1 + sci-biology/pysam/pysam-0.17.0.ebuild | 66 +++++++++++++++++++++++++++++++++++ 2 files changed, 67 insertions(+) diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest index f349d8ddc8a..1e305c998da 100644 --- a/sci-biology/pysam/Manifest +++ b/sci-biology/pysam/Manifest @@ -1 +1,2 @@ DIST pysam-0.16.0.1.tar.gz 3294073 BLAKE2B 8df1c9b061b0d4b3962ff4b0e30f1589e02d7df41ce362bff861596d3599bf800bb16b2fa4de326fc07102dc7801b48c6b821e5d47e694a3536bec2c5b1cfece SHA512 5cebb9f3bc8dc6186a629e91423a3c8cb802af6529b943fcd880e056661ec6ee2a00de789cf144c9e40b9d1ef2459c0e06ce27a1b9eab8e2875d2087f275af28 +DIST pysam-0.17.0.tar.gz 3579324 BLAKE2B 6b88fe771350f20fa7c90a4c02c60fefd6a34d979c687fce1e34a17e1ff203c7d2d07e36b64f7a73f99676b805334df7f049932ce15e26362a5214da03435d64 SHA512 16740f08fb68a1f24656454b834dd9ac52ad9f864f307564566fc244bbd2efb7cb17107b2e85ca5c56af817918a138d1c071533de1b80e5bba42b01bbad7f552 diff --git a/sci-biology/pysam/pysam-0.17.0.ebuild b/sci-biology/pysam/pysam-0.17.0.ebuild new file mode 100644 index 00000000000..afdc4777e20 --- /dev/null +++ b/sci-biology/pysam/pysam-0.17.0.ebuild @@ -0,0 +1,66 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{8..10} ) + +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="https://github.com/pysam-developers/pysam/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND="=sci-libs/htslib-1.13*:=" +DEPEND="${RDEPEND} + dev-python/cython[${PYTHON_USEDEP}] + dev-python/setuptools[${PYTHON_USEDEP}]" +BDEPEND=" + test? ( + =sci-biology/bcftools-1.13* + =sci-biology/samtools-1.13* + )" + +distutils_enable_tests pytest + +DISTUTILS_IN_SOURCE_BUILD=1 + +EPYTEST_DESELECT=( + # only work with bundled htslib + 'tests/tabix_test.py::TestRemoteFileHTTP' + 'tests/tabix_test.py::TestRemoteFileHTTPWithHeader' +) + +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 (except $ORIGIN) + sed -e '/runtime_library_dirs=htslib_library_dirs/d' \ + -i setup.py || die + + if use test; then + einfo "Building test data" + emake -C tests/pysam_data + emake -C tests/cbcf_data + fi + + distutils-r1_python_prepare_all +} + +python_compile() { + # breaks with parallel build + # need to avoid dropping .so plugins into + # build-lib, which breaks tests + esetup.py build_ext --inplace -j1 + distutils-r1_python_compile -j1 +}