From unknown Sat Jul 26 23:55:40 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#70276 <70276@debbugs.gnu.org> To: bug#70276 <70276@debbugs.gnu.org> Subject: Status: [PATCH] gnu: python-deeptools: Update to 3.5.5. Reply-To: bug#70276 <70276@debbugs.gnu.org> Date: Sun, 27 Jul 2025 06:55:40 +0000 retitle 70276 [PATCH] gnu: python-deeptools: Update to 3.5.5. reassign 70276 guix-patches submitter 70276 Simon Tournier severity 70276 normal tag 70276 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Mon Apr 08 08:50:31 2024 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 To: guix-patches@gnu.org Subject: [PATCH] gnu: python-deeptools: Update to 3.5.5. 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-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: submit Cc: Simon Tournier X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.0 (/) * 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 From debbugs-submit-bounces@debbugs.gnu.org Tue Apr 09 13:15:32 2024 Received: (at 70276-done) by debbugs.gnu.org; 9 Apr 2024 17:15:33 +0000 Received: from localhost ([127.0.0.1]:51373 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ruF4G-00033Y-Mf for submit@debbugs.gnu.org; Tue, 09 Apr 2024 13:15:32 -0400 Received: from mira.cbaines.net ([2a01:7e00:e000:2f8:fd4d:b5c7:13fb:3d27]:39753) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ruF4E-00033Q-LP for 70276-done@debbugs.gnu.org; Tue, 09 Apr 2024 13:15:30 -0400 Received: from localhost (unknown [212.132.255.10]) by mira.cbaines.net (Postfix) with ESMTPSA id 187D927BBE2; Tue, 9 Apr 2024 18:15:22 +0100 (BST) Received: from felis (localhost.lan [127.0.0.1]) by localhost (OpenSMTPD) with ESMTP id 0b515738; Tue, 9 Apr 2024 17:15:21 +0000 (UTC) From: Christopher Baines To: Simon Tournier Subject: Re: [bug#70276] [PATCH] gnu: python-deeptools: Update to 3.5.5. In-Reply-To: <7ce52e967f67a161bbfc172e6494863a3355f8ab.1712580113.git.zimon.toutoune@gmail.com> (Simon Tournier's message of "Mon, 8 Apr 2024 14:49:56 +0200") References: <7ce52e967f67a161bbfc172e6494863a3355f8ab.1712580113.git.zimon.toutoune@gmail.com> User-Agent: mu4e 1.12.2; emacs 29.3 Date: Tue, 09 Apr 2024 18:15:21 +0100 Message-ID: <87h6gacv9y.fsf@cbaines.net> MIME-Version: 1.0 Content-Type: multipart/signed; boundary="=-=-="; micalg=pgp-sha512; protocol="application/pgp-signature" X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 70276-done Cc: 70276-done@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) --=-=-= Content-Type: text/plain Simon Tournier writes: > * 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(-) Looks good to me, I've pushed this to master as cf29c427e90bd82556addf67885c276e067ce121. Chris --=-=-= Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQKlBAEBCgCPFiEEPonu50WOcg2XVOCyXiijOwuE9XcFAmYVd6lfFIAAAAAALgAo aXNzdWVyLWZwckBub3RhdGlvbnMub3BlbnBncC5maWZ0aGhvcnNlbWFuLm5ldDNF ODlFRUU3NDU4RTcyMEQ5NzU0RTBCMjVFMjhBMzNCMEI4NEY1NzcRHG1haWxAY2Jh aW5lcy5uZXQACgkQXiijOwuE9XdnMg/9EwKsNMfpOFLoIKkeNw9Dv6iTYa7RYNtZ SwLhl+OOccuBPeW7YBfH3DmJZdk4N3d9x1RJPvw2ua2byxfTg2BxER+Z3BiGizNC 0cWJV6HBd4RvKmDtCDr28RIPPzRqVMV4Cfz/mhpNtOiOR6pvGQ1Mna/EmCUukhUF SJ9nj0+WPmTR26glOwrUb0LqrCQQOvDhLK5/S2DLIw4546Af3/8+6pBhFewacAnd ONdxEkIyp6EwJpqeqa4mDvkK21vCVTblRoyL/2B9idF4ReVrjDOqFbbqbAG5AfFB la3ER5FlgK1f49bSDUcrft80aJopnzVvSX0NBe9sIExG46FBrR83oyn/0qDDSJAt TrPin25n2rkHikh6XcqXfvQ1yJXTytvyRtBOJAbKB3364vPi/F/5R/5sIzpLY8z/ PhNy1z+nAhujLjt5LtPLHWUfnwM9mX536Acs+/j5HHimbZsuZWdE8eE9FEAIG8sj 21Rkhv3lCSZUCLNt4hEuWbWxVNzT2Y/Gomg5MjcdmuuoqV8RwfqFGLd5n1vsTcYV 2dEuERVRQz6ChaiPXiZ2eLeWhseD0DgwoyZNSKpamIyIzK3yZ69TEogvGW1WNzir 0IYhkkGGp2u4sSFU2QdPOoAU6aqi64V7oF/meFH7TGVK4sd9Y8rgzGgMHoV35AEI FCl2HWeIZBc= =MjK+ -----END PGP SIGNATURE----- --=-=-=-- From unknown Sat Jul 26 23:55:40 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. 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