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 30D35158093 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 3D749E0BF9; Sat, 2 Jul 2022 13:16:25 +0000 (UTC) Received: from smtp.gentoo.org (dev.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (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 24F4AE0BF9 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 37DDE341C16 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 5B395525 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: <1656767760.45b11a00d7dd6f99521af35a08cc4c7214656751.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-2.0.2.ebuild sci-biology/HTSeq/Manifest X-VCS-Directories: sci-biology/HTSeq/ X-VCS-Committer: soap X-VCS-Committer-Name: David Seifert X-VCS-Revision: 45b11a00d7dd6f99521af35a08cc4c7214656751 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: e87cdfd5-3e83-4bef-a060-087882b55921 X-Archives-Hash: be1f7a7ea2230c776ee47c120b72759a commit: 45b11a00d7dd6f99521af35a08cc4c7214656751 Author: David Seifert gentoo org> AuthorDate: Sat Jul 2 13:16:00 2022 +0000 Commit: David Seifert gentoo org> CommitDate: Sat Jul 2 13:16:00 2022 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=45b11a00 sci-biology/HTSeq: add 2.0.2 Bug: https://bugs.gentoo.org/809662 Bug: https://bugs.gentoo.org/846221 Signed-off-by: David Seifert gentoo.org> sci-biology/HTSeq/HTSeq-2.0.2.ebuild | 68 ++++++++++++++++++++++++++++++++++++ sci-biology/HTSeq/Manifest | 1 + 2 files changed, 69 insertions(+) diff --git a/sci-biology/HTSeq/HTSeq-2.0.2.ebuild b/sci-biology/HTSeq/HTSeq-2.0.2.ebuild new file mode 100644 index 000000000000..678968788ff7 --- /dev/null +++ b/sci-biology/HTSeq/HTSeq-2.0.2.ebuild @@ -0,0 +1,68 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_IN_SOURCE_BUILD=1 +PYTHON_COMPAT=( python3_{8..10} ) + +inherit distutils-r1 flag-o-matic + +DESCRIPTION="Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files" +HOMEPAGE="https://htseq.readthedocs.io/" + +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 -> ${P}.gh.tar.gz" + + S="${WORKDIR}"/htseq-release_${PV} + KEYWORDS="~amd64" +fi + +LICENSE="GPL-3+" +SLOT="0" +IUSE="test" +RESTRICT="!test? ( test )" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + sci-biology/pysam[${PYTHON_USEDEP}]" +DEPEND="${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 +} diff --git a/sci-biology/HTSeq/Manifest b/sci-biology/HTSeq/Manifest index 92258c60174f..fbb304f1410e 100644 --- a/sci-biology/HTSeq/Manifest +++ b/sci-biology/HTSeq/Manifest @@ -1 +1,2 @@ DIST HTSeq-0.12.4.tar.gz 36187218 BLAKE2B 27be4e8783f9e32c10e23ae812069b489eb11dfa4058db43b5db4b8089792351901255103e4d4de1bcf866da3acd13e742adf8d35a9b70305aa156c70dde0837 SHA512 ec4a1a7e9177f103465840ffa9f936a5e887ffd17760b99d4cbdfd5a88e2ab44275fadfcbee153aadc6e828de7be205ed7a07f3a0548457b7c66826341c3ca64 +DIST HTSeq-2.0.2.gh.tar.gz 48468261 BLAKE2B c68ec67906f3cf78954e94214b82fd51bc19e0c505f994a3df4bfc682d804fa26f4883e9a8fa1e8ddf1e4f8ba8690d605705ebdd2d1695470984c2f04b6a19ce SHA512 96c0b4de6c9cfa9e405f02e366ecfed63bb0dba0ab76fe872f6f48b52a4956b08fa75efa4b1e4c6e4560e34b4e2921bf1ec9671831226ad415ed421a88ec3f6d