From patchwork Wed Mar 16 11:37:35 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Efraim Flashner X-Patchwork-Id: 37855 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 61AC727BBEA; Wed, 16 Mar 2022 11:39:45 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.9 required=5.0 tests=BAYES_00,MAILING_LIST_MULTI, RCVD_IN_MSPIKE_H5,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 203C127BBE9 for ; Wed, 16 Mar 2022 11:39:45 +0000 (GMT) Received: from localhost ([::1]:36308 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nUS0G-00048z-8V for patchwork@mira.cbaines.net; Wed, 16 Mar 2022 07:39:44 -0400 Received: from eggs.gnu.org ([209.51.188.92]:41196) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nURzc-00047n-9c for guix-patches@gnu.org; Wed, 16 Mar 2022 07:39:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:56497) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1nURza-0000vV-Mq for guix-patches@gnu.org; Wed, 16 Mar 2022 07:39:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1nURza-0008Pe-J7 for guix-patches@gnu.org; Wed, 16 Mar 2022 07:39:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#54419] [PATCH] gnu: Add python-scikit-allel. Resent-From: Efraim Flashner Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 16 Mar 2022 11:39:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 54419 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 54419@debbugs.gnu.org Cc: Efraim Flashner X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.164743073932324 (code B ref -1); Wed, 16 Mar 2022 11:39:02 +0000 Received: (at submit) by debbugs.gnu.org; 16 Mar 2022 11:38:59 +0000 Received: from localhost ([127.0.0.1]:50394 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nURzR-0008PA-NN for submit@debbugs.gnu.org; Wed, 16 Mar 2022 07:38:59 -0400 Received: from lists.gnu.org ([209.51.188.17]:41934) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nURzP-0008P2-Fr for submit@debbugs.gnu.org; Wed, 16 Mar 2022 07:38:52 -0400 Received: from eggs.gnu.org ([209.51.188.92]:41180) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nURzP-00045N-0n for guix-patches@gnu.org; Wed, 16 Mar 2022 07:38:51 -0400 Received: from flashner.co.il ([178.62.234.194]:38838) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nURzI-0000rf-M5 for guix-patches@gnu.org; Wed, 16 Mar 2022 07:38:46 -0400 Received: from localhost (unknown [31.210.181.186]) by flashner.co.il (Postfix) with ESMTPSA id 182F2400B7; Wed, 16 Mar 2022 11:38:11 +0000 (UTC) From: Efraim Flashner Date: Wed, 16 Mar 2022 13:37:35 +0200 Message-Id: <856daf639aa2f6dee3f09e242179ba2fccaf22d8.1647430620.git.efraim@flashner.co.il> X-Mailer: git-send-email 2.34.0 MIME-Version: 1.0 Received-SPF: pass client-ip=178.62.234.194; envelope-from=efraim@flashner.co.il; helo=flashner.co.il X-Spam_score_int: -18 X-Spam_score: -1.9 X-Spam_bar: - X-Spam_report: (-1.9 / 5.0 requ) BAYES_00=-1.9, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/python-science.scm (python-scikit-allel): New variable. --- gnu/packages/python-science.scm | 51 ++++++++++++++++++++++++++++++++- 1 file changed, 50 insertions(+), 1 deletion(-) base-commit: 53d986215f629f461651e3181af0689ef5f418a2 diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index e3e874dac2..bb25386094 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2015 Federico Beffa ;;; Copyright © 2016 Ben Woodcroft ;;; Copyright © 2016 Hartmut Goebel -;;; Copyright © 2016 Efraim Flashner +;;; Copyright © 2016, 2022 Efraim Flashner ;;; Copyright © 2016-2020, 2022 Marius Bakke ;;; Copyright © 2019 Tobias Geerinckx-Rice ;;; Copyright © 2019, 2021 Maxim Cournoyer @@ -35,6 +35,7 @@ (define-module (gnu packages python-science) #:use-module ((guix licenses) #:prefix license:) #:use-module (gnu packages) #:use-module (gnu packages base) + #:use-module (gnu packages bioinformatics) #:use-module (gnu packages boost) #:use-module (gnu packages check) #:use-module (gnu packages cpp) @@ -307,6 +308,54 @@ (define-public python-scikit-image "Scikit-image is a collection of algorithms for image processing.") (license license:bsd-3))) +(define-public python-scikit-allel + (package + (name "python-scikit-allel") + (version "1.3.5") + (source + (origin + (method url-fetch) + (uri (pypi-uri "scikit-allel" version)) + (sha256 + (base32 "1vg88ng6gd175gzk39iz1drxig5l91dyx398w2kbw3w8036zv8gj")))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python" "setup.py" "build_ext" "--inplace") + (invoke "python" "-m" "pytest" "-v" "allel" + ;; AttributeError: 'Dataset' object has no attribute 'asstr' + "-k" (string-append + "not test_vcf_to_hdf5" + " and not test_vcf_to_hdf5_exclude" + " and not test_vcf_to_hdf5_rename" + " and not test_vcf_to_hdf5_group" + " and not test_vcf_to_hdf5_ann")))))))) + (propagated-inputs + (list python-dask + python-numpy)) + (native-inputs + (list python-cython + ;; The following are all needed for the tests + htslib + python-h5py + python-hmmlearn + python-numexpr + python-pytest + python-scipy + python-setuptools-scm + python-zarr)) + (home-page "https://github.com/cggh/scikit-allel") + (synopsis "Explore and analyze genetic variation data") + (description + "This package provides utilities for exploratory analysis of large scale +genetic variation data.") + (license license:expat))) + (define-public python-sgp4 (package (name "python-sgp4")