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Resent-From: Simon Tournier Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 08 Apr 2024 12:51:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 70276 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 70276@debbugs.gnu.org Cc: Simon Tournier X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.17125806312740 (code B ref -1); Mon, 08 Apr 2024 12:51:01 +0000 Received: (at submit) by debbugs.gnu.org; 8 Apr 2024 12:50:31 +0000 Received: from localhost ([127.0.0.1]:45569 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rtoSE-0000i7-49 for submit@debbugs.gnu.org; Mon, 08 Apr 2024 08:50:30 -0400 Received: from lists.gnu.org ([2001:470:142::17]:44706) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rtoSA-0000h7-HR for submit@debbugs.gnu.org; Mon, 08 Apr 2024 08:50:28 -0400 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 1rtoRw-0007lg-Ix for guix-patches@gnu.org; Mon, 08 Apr 2024 08:50:12 -0400 Received: from mail-wm1-x32c.google.com ([2a00:1450:4864:20::32c]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1rtoRt-0004Ki-NW for guix-patches@gnu.org; Mon, 08 Apr 2024 08:50:12 -0400 Received: by mail-wm1-x32c.google.com with SMTP id 5b1f17b1804b1-416463e82fbso2075745e9.1 for ; Mon, 08 Apr 2024 05:50:09 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20230601; t=1712580605; x=1713185405; darn=gnu.org; h=content-transfer-encoding:mime-version:message-id:date:subject:cc :to:from:from:to:cc:subject:date:message-id:reply-to; bh=Jvq5v1nqdx+HZ9utU5n6OwHW9V5PxnGHlRD3HId3raY=; b=e0r1OZQPFntOxoLDYB1r9+kwqqvYom09FwVJjCrTOoVmOmEXC0Z1y3b8ta7ptjeZnY W/cuGg3s44jBrhIvQPmjF3EyST+/1i/jDAfh6jvBvBEO20yTUfI68yoHf1PcasSxj151 Kd7Hayk9jbKjsbIaZfw3ymmUaWvUb3RRuInWiNLtnSUFOsu6cR5zb7fD421l80xxPIq4 5A3d5Km+6F1scoFZi+O1R60U86IXEK7FfntY/E5cuLQ5/a5s+ZhEl2EpGLVxbnb/8nAe d1nnVNuDfAWan8Zb2Y7U0YhONn2FYYfbbJPzQBoejMxgoBjeMLqTMzF7Uq2ZSJf+l4/q xUaA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20230601; t=1712580605; x=1713185405; h=content-transfer-encoding:mime-version:message-id:date:subject:cc :to:from:x-gm-message-state:from:to:cc:subject:date:message-id :reply-to; bh=Jvq5v1nqdx+HZ9utU5n6OwHW9V5PxnGHlRD3HId3raY=; b=U7MsyVT8cvac3QNmLHMkKacGmJr8Yb9BKVR9vnSaQCYkE3A+1roiqVGYQMNkK8eZGM R5LpdFguXin7LdZ4EesNNxGIAJ1/UeUxvMKKjwubdspTxG3seKiUwIE5kZ4a1fHGnta+ SrZJw+nqf4CQ/D4Eknho+OwGP0DvUEoaZMLfwMefp76eoso1gA7gJf+oQBBOj2rQM+QV iJKTE9T7aumjC0WUR2RtOXJCzApwa2tq2/QrM3J6h9Rsn7qAwxln49xJOGFuo4R4IL+p VsJm2rlUcyOwAKZpqh377m65WK9Cia8EItoT13sYXjV2iiJJ+M4Dl/cq1C1PVBq6rtUn Cbww== X-Gm-Message-State: AOJu0YzW9PpiEVrypvi11LHRkd0r56xQze/pzW8i5mcxnGF46kp7bMEU H8ZhTRxiz6RhgLFqYQLIfBPW9FCyFhUbwB6SXnlqo1Xqx//uLbZ2ZdgXaGYh X-Google-Smtp-Source: AGHT+IFKaLXjHWVPRtXkY2XC+PX3qa6OHOQVHZWHp4hYgvMfZiLxtOkGaZ4lpQrSxObP8+QBT5Q8Pg== X-Received: by 2002:a05:600c:354f:b0:416:80b1:6a31 with SMTP id i15-20020a05600c354f00b0041680b16a31mr1164408wmq.0.1712580605295; Mon, 08 Apr 2024 05:50:05 -0700 (PDT) Received: from localhost.localdomain ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id b3-20020a05600c4e0300b00416920ca56csm665621wmq.42.2024.04.08.05.50.04 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 08 Apr 2024 05:50:04 -0700 (PDT) From: Simon Tournier Date: Mon, 8 Apr 2024 14:49:56 +0200 Message-ID: <7ce52e967f67a161bbfc172e6494863a3355f8ab.1712580113.git.zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.41.0 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=2a00:1450:4864:20::32c; envelope-from=zimon.toutoune@gmail.com; helo=mail-wm1-x32c.google.com X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 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+larch=yhetil.org@gnu.org Sender: guix-patches-bounces+larch=yhetil.org@gnu.org X-Migadu-Flow: FLOW_IN X-Migadu-Country: US X-Spam-Score: -4.77 X-Migadu-Queue-Id: 214A7692EB X-Migadu-Spam-Score: -4.77 X-Migadu-Scanner: mx10.migadu.com X-TUID: pUALXzy1N2iH * gnu/packages/bioinformatics.scm (python-deeptools): Update to 3.5.5. [build-system]: Replace by pyproject-build-system. [arguments]: Add phase that fixes 'test/test_tools.py'. Change-Id: Ibb51939275c96df2c4a1e248a03d683f2f4904ac --- gnu/packages/bioinformatics.scm | 23 +++++++++++++++++++---- 1 file changed, 19 insertions(+), 4 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7861987704..452ec1d829 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4615,7 +4615,7 @@ (define-public python-deeptoolsintervals (define-public python-deeptools (package (name "python-deeptools") - (version "3.4.3") + (version "3.5.5") (source (origin (method git-fetch) (uri (git-reference @@ -4624,8 +4624,23 @@ (define-public python-deeptools (file-name (git-file-name name version)) (sha256 (base32 - "0l09vyynz6s6w7fnyd94rpys4a6aja6kp4gli64pngdxdz3md1nl")))) - (build-system python-build-system) + "0mgcs03amrd5157drbm6ikdg0m0szrn9xbflariz2zrrnqpsai6s")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-test + (lambda _ + (substitute* "deeptools/test/test_tools.py" + (("e_ver = _p") + "e_ver = \".\" + _p + \"-real\"")) + (substitute* "deeptools/multiBigwigSummary.py" + (("version='multiBigwigSummary") + "version='%(prog)s")) + (substitute* "deeptools/plotCoverage.py" + (("version='plotCoverage") + "version='%(prog)s"))))))) (native-inputs (list python-mock python-nose)) (propagated-inputs @@ -4637,7 +4652,7 @@ (define-public python-deeptools python-pysam python-scipy python-deeptoolsintervals - python-plotly-2.4.1)) + python-plotly)) (home-page "https://pypi.org/project/deepTools/") (synopsis "Useful tools for exploring deep sequencing data") (description "This package addresses the challenge of handling large amounts base-commit: cd45294d576975a3bff2f755764a3f46f09ea6f9 -- 2.41.0