From patchwork Mon Dec 12 14:27:16 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Ricardo Wurmus X-Patchwork-Id: 45208 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 8403327BBEC; Mon, 12 Dec 2022 14:29:52 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS, URIBL_BLOCKED autolearn=ham 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 E643B27BBE9 for ; Mon, 12 Dec 2022 14:29:51 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1p4jnp-0006rW-HU; Mon, 12 Dec 2022 09:29:09 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1p4jnk-0006lP-5n for guix-patches@gnu.org; Mon, 12 Dec 2022 09:29:07 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1p4jnj-0006TW-U7 for guix-patches@gnu.org; Mon, 12 Dec 2022 09:29:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1p4jnj-0007Xs-Pp for guix-patches@gnu.org; Mon, 12 Dec 2022 09:29:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#60009] [PATCH 18/18] gnu: cnvkit: Update to 0.9.9. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 12 Dec 2022 14:29:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 60009 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 60009@debbugs.gnu.org Cc: Ricardo Wurmus Received: via spool by 60009-submit@debbugs.gnu.org id=B60009.167085530228967 (code B ref 60009); Mon, 12 Dec 2022 14:29:03 +0000 Received: (at 60009) by debbugs.gnu.org; 12 Dec 2022 14:28:22 +0000 Received: from localhost ([127.0.0.1]:53326 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jn3-0007X9-FH for submit@debbugs.gnu.org; Mon, 12 Dec 2022 09:28:21 -0500 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21092) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1p4jn0-0007Wx-PY for 60009@debbugs.gnu.org; Mon, 12 Dec 2022 09:28:19 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1670855296; cv=none; d=zohomail.com; s=zohoarc; b=QVBQo1u5klAa4WHw7qbzgRVS+tGwC4coDZLS1b++wDCgBTF2X4blHkBWpyE6kCiTqMoCHAGowTPD+//ylHFgT4jbaYE8KmQoscaGSet5cr7974C9JSnD1UWbKRFGGyR+DP56Tgv0WDx3fkQ/MiNVL/hxYAHaIDqyxZvE4yt8pEA= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1670855296; h=Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=0jZtos+EXI10E0GMGchAproh9ZH8+5zA0Deow8ZwCWA=; b=K8Nuwso7u4El7oHSV1ROs8QyrbpKp+/LFd0FiJ++S9D4/fyzkcZKeP3qVPM2punoFDLQ5Bo6fGkqGnEt6VHNfITXslu4VM001v0Ija7hsCrDjaKb/+Jr96kEiGYqVRGbbzz64nngWvKZrmO4TmG5xrxh40nRwVfabDcuBiU7WHQ= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1670855296; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:Message-Id:Message-Id:In-Reply-To:References:MIME-Version:Content-Transfer-Encoding:Reply-To; bh=0jZtos+EXI10E0GMGchAproh9ZH8+5zA0Deow8ZwCWA=; b=Ry3o/IfJXVliQw2TuKqbffzwdhpw3HwtRMLZG8Z4nvN0RIgSO0xEaPameT5yt0jh q1srGGoqb9qhqQNCWJIJao4gSQi3iqPq1bUeBfFCsRU0pvXBRGxIujP5ALL9f9hpD5i InwRyK677gJG0oq5V2+OppDVTGNasshUSTa4Gmo0= Received: from localhost (48-111-142-46.pool.kielnet.net [46.142.111.48]) by mx.zohomail.com with SMTPS id 1670855294432507.2421434134757; Mon, 12 Dec 2022 06:28:14 -0800 (PST) From: Ricardo Wurmus Date: Mon, 12 Dec 2022 15:27:16 +0100 Message-Id: <20221212142716.9460-18-rekado@elephly.net> X-Mailer: git-send-email 2.36.1 In-Reply-To: <20221212142716.9460-1-rekado@elephly.net> References: <87h6y03dkr.fsf@elephly.net> <20221212142716.9460-1-rekado@elephly.net> MIME-Version: 1.0 X-ZohoMailClient: External 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-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (cnvkit): Update to 0.9.9. [build-system]: Use pyproject-build-system. [arguments]: Relax restriction on python-joblib. [propagated-inputs]: Add python-pomegranate and python-scikit-learn. --- gnu/packages/bioinformatics.scm | 21 ++++++++++++++++----- 1 file changed, 16 insertions(+), 5 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e8a8ddc361..5e2e0796a0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14225,7 +14225,7 @@ (define-public nanopolish (define-public cnvkit (package (name "cnvkit") - (version "0.9.5") + (version "0.9.9") (source (origin (method git-fetch) @@ -14234,17 +14234,28 @@ (define-public cnvkit (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0g2f78k68yglmj4fsfmgs8idqv3di9aj53fg0ld0hqljg8chhh82")))) - (build-system python-build-system) + (base32 "1q4l7jhr1k135an3n9aa9wsid5lk6fwxb0hcldrr6v6y76zi4gj1")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; See upstream commit eee0f6eaec57d5c6e58142d661979f3aacc5f76a + (add-after 'unpack 'compatibility + (lambda _ + (substitute* "setup.py" + (("'joblib.*") ""))))))) (propagated-inputs (list python-biopython python-future python-matplotlib python-numpy - python-reportlab python-pandas - python-pysam + python-pomegranate python-pyfaidx + python-pysam + python-reportlab + python-scikit-learn python-scipy ;; R packages r-dnacopy))