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 6F103158094 for ; Sat, 2 Jul 2022 13:16:26 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 6C6DEE0C26; Sat, 2 Jul 2022 13:16:25 +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)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 4A5D7E0C26 for ; Sat, 2 Jul 2022 13:16:25 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (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 38BE7341C1A for ; Sat, 2 Jul 2022 13:16:24 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 6E94D526 for ; Sat, 2 Jul 2022 13:16:21 +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: <1656767761.52fc6e9547d84e09c0e13658617c46ceab10d3a1.soap@gentoo> Subject: [gentoo-commits] repo/gentoo:master commit in: sci-biology/HTSeq/ X-VCS-Repository: repo/gentoo X-VCS-Files: sci-biology/HTSeq/HTSeq-9999.ebuild X-VCS-Directories: sci-biology/HTSeq/ X-VCS-Committer: soap X-VCS-Committer-Name: David Seifert X-VCS-Revision: 52fc6e9547d84e09c0e13658617c46ceab10d3a1 X-VCS-Branch: master Date: Sat, 2 Jul 2022 13:16:21 +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: cebdbe8c-80dc-4009-80d8-2df9fafd8c24 X-Archives-Hash: f30ba8d3b0cfd897a053aaca77f060dc commit: 52fc6e9547d84e09c0e13658617c46ceab10d3a1 Author: David Seifert gentoo org> AuthorDate: Sat Jul 2 13:16:01 2022 +0000 Commit: David Seifert gentoo org> CommitDate: Sat Jul 2 13:16:01 2022 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=52fc6e95 sci-biology/HTSeq: sync live ebuild Signed-off-by: David Seifert gentoo.org> sci-biology/HTSeq/HTSeq-9999.ebuild | 49 +++++++++++++++++++++++++++++++------ 1 file changed, 42 insertions(+), 7 deletions(-) diff --git a/sci-biology/HTSeq/HTSeq-9999.ebuild b/sci-biology/HTSeq/HTSeq-9999.ebuild index 548684fd531b..678968788ff7 100644 --- a/sci-biology/HTSeq/HTSeq-9999.ebuild +++ b/sci-biology/HTSeq/HTSeq-9999.ebuild @@ -1,11 +1,12 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +DISTUTILS_IN_SOURCE_BUILD=1 +PYTHON_COMPAT=( python3_{8..10} ) -inherit distutils-r1 +inherit distutils-r1 flag-o-matic DESCRIPTION="Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files" HOMEPAGE="https://htseq.readthedocs.io/" @@ -14,7 +15,7 @@ if [[ ${PV} == *9999 ]]; then inherit git-r3 EGIT_REPO_URI="https://github.com/htseq/htseq.git" else - SRC_URI="https://github.com/htseq/htseq/archive/release_${PV}.tar.gz -> ${P}.tar.gz" + SRC_URI="https://github.com/htseq/htseq/archive/release_${PV}.tar.gz -> ${P}.gh.tar.gz" S="${WORKDIR}"/htseq-release_${PV} KEYWORDS="~amd64" @@ -22,12 +23,46 @@ fi LICENSE="GPL-3+" SLOT="0" +IUSE="test" +RESTRICT="!test? ( test )" RDEPEND=" dev-python/numpy[${PYTHON_USEDEP}] - dev-python/matplotlib[${PYTHON_USEDEP}] sci-biology/pysam[${PYTHON_USEDEP}]" -DEPEND="${RDEPEND}" +DEPEND="${RDEPEND} + test? ( + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + )" BDEPEND=" >=dev-lang/swig-3.0.8 dev-python/cython[${PYTHON_USEDEP}]" + +distutils_enable_tests pytest + +src_configure() { + # mask broken asserts in src/step_vector.h:72 + append-cppflags -DNDEBUG + + distutils-r1_src_configure +} + +python_test() { + distutils_install_for_testing + + # Due to the build directories creating a competing + # hierarchy, we move to the test/ dir to avoid implicitly + # injecting the root HTSeq/ dir into the PYTHONPATH, + # which leads the python module lookup astray: + # ${PWD} + # ├── build + # │ ├── lib + # │ │ └── HTSeq + # │ [...] + # ├── HTSeq + # └── test + cd test/ || die + ln -s ../example_data || die + epytest +}