From unknown Sat Jun 21 03:27:08 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#66847 <66847@debbugs.gnu.org> To: bug#66847 <66847@debbugs.gnu.org> Subject: Status: [PATCH] gnu: python-baltica: Update to 1.1.2. Reply-To: bug#66847 <66847@debbugs.gnu.org> Date: Sat, 21 Jun 2025 10:27:08 +0000 retitle 66847 [PATCH] gnu: python-baltica: Update to 1.1.2. reassign 66847 guix-patches submitter 66847 "Afkhami, Navid" severity 66847 normal tag 66847 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Tue Oct 31 10:02:39 2023 Received: (at submit) by debbugs.gnu.org; 31 Oct 2023 14:02:39 +0000 Received: from localhost ([127.0.0.1]:48892 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qxpKJ-0005Jo-Cz for submit@debbugs.gnu.org; Tue, 31 Oct 2023 10:02:39 -0400 Received: from lists.gnu.org ([2001:470:142::17]:40828) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qxpKF-0005JY-07 for submit@debbugs.gnu.org; Tue, 31 Oct 2023 10:02:37 -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 1qxpJZ-00022S-MZ for guix-patches@gnu.org; Tue, 31 Oct 2023 10:01:54 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qxpJW-0001zw-N7 for guix-patches@gnu.org; Tue, 31 Oct 2023 10:01:52 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received; s=mdc; t=1698760890; x=1700575291; bh=HVmhqg0cArtbs5b rux1msn+TdF6ZeAw82nOW4lxS32A=; b=W+qQpmtMMx98jdk0DqDCIXQNXZuT8Kf vIyqAuC9eybBp2gMmAjL99LhDUSKT/tmezChfC6wNGV0e1YV/UVK97pu5zKRO7lA fZOtGeCmqzf0w2rUHMqroKXUo8ZaFLgGnlao7ckjgJiSDedrCI97Hystjt6gx0eZ CgFezxAxFDSI= Received: from SW-IT-P-EX2.mdc-berlin.net (mgw2.mdc-berlin.de [141.80.113.60]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id 8125F160171 for ; Tue, 31 Oct 2023 15:01:30 +0100 (CET) Received: from localhost (141.80.218.27) by SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.34; Tue, 31 Oct 2023 15:01:29 +0100 From: "Afkhami, Navid" To: Subject: [PATCH] gnu: python-baltica: Update to 1.1.2. Date: Tue, 31 Oct 2023 14:01:22 +0000 Message-ID: <777b97bec88e9beb56d7d57738eb9aba9956566e.1698760882.git.Navid.Afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.34.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.218.27] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27970.000 X-TM-AS-Result: No-10--8.241500-5.000000 X-TMASE-MatchedRID: d2m5lHDXR73RTAZ5iUYfyfSG/+sPtZVkcV3n4J/0zUPAuQ0xDMaXkH4q tYI9sRE/4K9FmervsqXuNT8xdcEnQwE+dA3RWUSvnVTWWiNp+v/BDDo09qAAYmtEzrC9eANpKWF xEPEOC9uESVL06fzYO439fs3HQurh0sb2unTQdoWOjIrMSa2sR9hQO8CvZj/XtDgmvV2H8PlFmB b8AoJ5ymFAfS5PD9X1CAsjrwMzmsYRC3tpysE8ADU9EK4+H8U1JsfRAseVNgUPa94jf+HCb0p9E X9Zh2FufS0Ip2eEHnyFh/DzryTTljOrHoO19Vm29xS3mVzWUuCgZHIBpyeFpiqau3IvSUQEcCFx GhggrFxCYbXo5Au6wAyEcDukNi6JftwZ3X11IV0= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--8.241500-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27970.000 X-TM-SNTS-SMTP: 0214D26EE695EF40FD652BD12988DCFBFA221716AE99DA519246136BB0ACE59C2000:F Received-SPF: pass client-ip=194.95.234.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=b2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 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, RCVD_IN_DNSWL_MED=-2.3, 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-Spam-Score: 0.9 (/) X-Debbugs-Envelope-To: submit Cc: "Afkhami, Navid" 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: -0.1 (/) * gnu/packages/bioinformatics.scm (python-baltica): Update to 1.1.2. [propagated-inputs]: Add r-yaml, r-rsamtools, r-biocmanager, r-here, r-genomicranges, r-readr, r-tidyr, r-stringr, r-optparse, r-openxlsx, r-dplyr, and r-upsetr. Change-Id: I8c1bb556048b406b95e081155a46da17a6be5676 --- gnu/packages/bioinformatics.scm | 76 +++++++++++++++++++-------------- 1 file changed, 43 insertions(+), 33 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a47e84bc33..66d1a21ffe 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5130,47 +5130,57 @@ (define-public python-baltica (package (name "python-baltica") (version "1.1.2") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/dieterich-lab/Baltica") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "001ac03v9pbqqzf9pv7v8gf0296ksa4f0v3wdmpa6m9701skqi4r")))) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/dieterich-lab/Baltica") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "001ac03v9pbqqzf9pv7v8gf0296ksa4f0v3wdmpa6m9701skqi4r")))) (build-system pyproject-build-system) (arguments (list - #:phases - '(modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - ;; The tests need to be run from elsewhere... - (mkdir-p "/tmp/test") - (copy-recursively ".tests" "/tmp/test") - (with-directory-excursion "/tmp/test" - (invoke "pytest" "-v" "--doctest-modules")))))))) - (propagated-inputs - (list gunicorn - python-anndata - python-click - python-flask - python-flask-wtf - python-h5py - python-numpy - python-psutil - python-pysam - python-pyyaml - python-scipy - snakemake-7)) + #:phases '(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; The tests need to be run from elsewhere... + (mkdir-p "/tmp/test") + (copy-recursively ".tests" "/tmp/test") + (with-directory-excursion "/tmp/test" + (invoke "pytest" "-v" "--doctest-modules")))))))) + (propagated-inputs (list gunicorn + python-anndata + python-click + python-flask + python-flask-wtf + python-h5py + python-numpy + python-psutil + python-pysam + python-pyyaml + python-scipy + r-yaml + r-rsamtools + r-biocmanager + r-here + r-genomicranges + r-readr + r-tidyr + r-stringr + r-optparse + r-openxlsx + r-dplyr + r-upsetr + snakemake-7)) (native-inputs (list python-cython python-pyfakefs python-pytest)) (home-page "https://github.com/dieterich-lab/Baltica") (synopsis "Integrated splice junction usage analysis") (description "This framework facilitates the execution of @dfn{differential junction -usage} (DJU) methods. Additionally, it enables the integration of results from +usage} (DJU) methods. Additionally, it enables the integration of results from multiple DJU methods.") (license license:expat))) base-commit: c0895371c5759c7d9edb330774e90f192cc4cf2c -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Oct 31 17:06:53 2023 Received: (at 66847-done) by debbugs.gnu.org; 31 Oct 2023 21:06:53 +0000 Received: from localhost ([127.0.0.1]:49400 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qxvwq-0007eR-Ve for submit@debbugs.gnu.org; Tue, 31 Oct 2023 17:06:53 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21160) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qxvwl-0007e9-Dn for 66847-done@debbugs.gnu.org; Tue, 31 Oct 2023 17:06:51 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1698786369; cv=none; d=zohomail.com; s=zohoarc; b=IKa4v2y/IzanL7vuMBE2g+vvAu3WFj0l5pn1wWvLF+p4mdg0UaeE1O/EkaYIRneQvcWtyi99vLSeLmPph+HlEvYOgsH77mdKg3GZxvlPq8E3S787HCeUc/VpGvXFcoZo8mjWF7EG9LOI9w9cxCKZEP6Ksy/HHdVkr/8OHh/PH50= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1698786369; h=Content-Type:Date:Date:From:From:MIME-Version:Message-ID:Subject:Subject:To:To:Message-Id:Reply-To:Cc; bh=BflOoLOwAXRKf7ogSXDvzjQUOa6LZifFXuPXucGRekY=; b=R2Q5kZhvX5SZwAJz9m6d56pSWd7lvgOC0qocotntJrdaDNgRknR17V5ZKHtWx7gGvUePurbW58sghpWWYB1Y/3diKghnnnmyAmGMV9tZVqLHpkdbK1Xw47t4okH7cCmT0oSfrh7eAu/jaCCc0IzGe1QLRv2ggZ+9Hxq45BIgO8c= 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=1698786369; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To:Cc; bh=BflOoLOwAXRKf7ogSXDvzjQUOa6LZifFXuPXucGRekY=; b=gWAT6Ug/ddJ0p+6z/H0+Wl+N6bb7Vf1SCwCT4UIlngtnAZGaOlbFowBoRa6Ary8b QRTPOzIIIQ3E9I5+dY3/ib8v36u/fMnwxmpkQTiWNEVnIVUEZKIqhnLGQ+JOg7ZNJDc +2JPykRKmzKBRYqkghDPIdU/uxhihxk/6j7opxYU= Received: from localhost (215-110-142-46.pool.kielnet.net [46.142.110.215]) by mx.zohomail.com with SMTPS id 1698786367582720.1947613991096; Tue, 31 Oct 2023 14:06:07 -0700 (PDT) User-agent: mu4e 1.10.7; emacs 29.1 From: Ricardo Wurmus To: 66847-done@debbugs.gnu.org Subject: [PATCH] gnu: python-baltica: Update to 1.1.2. Date: Tue, 31 Oct 2023 22:05:29 +0100 Message-ID: <875y2mv6wz.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 66847-done 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 (-) Thanks for the patch. I changed the commit message and reduced the number of changes to the essential. Pushed! -- Ricardo From unknown Sat Jun 21 03:27:08 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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