From unknown Sat Aug 16 19:18:11 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#61382] [PATCH 1/2] gnu: Add python-scrublet. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 09 Feb 2023 08:13:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 61382 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 61382@debbugs.gnu.org X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.167593037629712 (code B ref -1); Thu, 09 Feb 2023 08:13:02 +0000 Received: (at submit) by debbugs.gnu.org; 9 Feb 2023 08:12:56 +0000 Received: from localhost ([127.0.0.1]:57354 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pQ235-0007j9-J8 for submit@debbugs.gnu.org; Thu, 09 Feb 2023 03:12:55 -0500 Received: from lists.gnu.org ([209.51.188.17]:58850) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pQ233-0007iu-Hh for submit@debbugs.gnu.org; Thu, 09 Feb 2023 03:12:54 -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 1pQ230-0006WW-Aq for guix-patches@gnu.org; Thu, 09 Feb 2023 03:12:51 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pQ22y-00012X-QZ for guix-patches@gnu.org; Thu, 09 Feb 2023 03:12:50 -0500 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=1675930366; x=1677744767; bh=e//cZ5jj09E9hX5 oponLnxssGKxZq9tZOTyGjH4ccNA=; b=J36tnVssIDnAgeQB8Ixe7NiW0GZ9q/P zffx+eXSjIzvnGUhbx/e31Hc1RjEXyvtVO/fMP9RgtTv8vBtnXy4wzLJ44rMKsT3 wnhUUq4pKvgEPlIYwLa0WvEQfhU/rvZ4ftLDtqpR6IqBKp7IM8tZ/0P+/6mHOfkc nKdbYdnE0r3Y= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 4F233A00E5 for ; Thu, 9 Feb 2023 09:12:46 +0100 (CET) Received: from localhost.localdomain (10.84.128.29) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.17; Thu, 9 Feb 2023 09:12:45 +0100 From: Navid Afkhami Date: Thu, 9 Feb 2023 09:12:34 +0100 Message-ID: <20230209081235.30512-1-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: [10.84.128.29] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27436.006 X-TM-AS-Result: No-10-0.692300-5.000000 X-TMASE-MatchedRID: 4r2MyAYFTnd6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt9GklfnQcKumwLYk+NSxc5r4qCLIu0mtIL9NdlMbI5hontU 3Lv5Rb/1Bh00zu6DygRJTjjs9yT6Yo8WMkQWv6iXBcIE78YqRWvcUt5lc1lLgKIzdZS3ou0UvU+ OKagS8dAJT1QwbGXhR+pCqRU+IB84ofghShQpram3VdrKCeQPm8uD6Y7nXL1piDRNquN7ycY5Lm YMppxFz4MJBeB13AbVZKCalsVmcQjWQPYq1JOarY9u3lK2/Yrn87HRNT0KLkg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-0.692300-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27436.006 X-TM-SNTS-SMTP: 5BA75D6F85F820B9D17541E76CE53BC0A2FEEDC0074FD0B97035C8AF4C647FB42002:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=a2062.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 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -2.3 (--) 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: -3.3 (---) * gnu/packages/bioinformatics.scm (python-scrublet): New variable. --- gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 969b978054..05a078b0b0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3459,6 +3459,32 @@ (define-public python-scikit-bio resources for bioinformatics.") (license license:bsd-3))) +(define-public python-scrublet + (package + (name "python-scrublet") + (version "0.2.3") + (source (origin + (method url-fetch) + (uri (pypi-uri "scrublet" version)) + (sha256 + (base32 + "0fk5pwk12yz9wpvwkl6j2l2g28f3x35b9r9n5bw6f0i9f0qgd191")))) + (build-system python-build-system) + (propagated-inputs (list python-annoy + python-cython + python-matplotlib + python-numba + python-numpy + python-pandas + python-scikit-image + python-scikit-learn + python-scipy + python-umap-learn)) + (home-page "https://github.com/swolock/scrublet") + (synopsis "single-cell tool to indentify and remove doublets") + (description "Tool for identifying and removing doublets in single-cell RNA-seq data.") + (license license:expat))) + (define-public cwltool (package (name "cwltool") -- 2.34.1 From unknown Sat Aug 16 19:18:11 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: Navid Afkhami Subject: bug#61382: closed ([PATCH 1/2] gnu: Add python-scrublet.) Message-ID: References: <871qmz5j1w.fsf@elephly.net> <20230209081235.30512-1-navid.afkhami@mdc-berlin.de> X-Gnu-PR-Message: they-closed 61382 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 61382@debbugs.gnu.org Date: Thu, 09 Feb 2023 08:40:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1675932002-32721-1" This is a multi-part message in MIME format... ------------=_1675932002-32721-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #61382: [PATCH 1/2] gnu: Add python-scrublet. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 61382@debbugs.gnu.org. --=20 61382: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D61382 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1675932002-32721-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 61382-done) by debbugs.gnu.org; 9 Feb 2023 08:39:50 +0000 Received: from localhost ([127.0.0.1]:57390 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pQ2T8-0008VE-Jh for submit@debbugs.gnu.org; Thu, 09 Feb 2023 03:39:50 -0500 Received: from sender3-of-o57.zoho.com ([136.143.184.57]:21739) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pQ2T4-0008V2-HS for 61382-done@debbugs.gnu.org; Thu, 09 Feb 2023 03:39:48 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1675931983; cv=none; d=zohomail.com; s=zohoarc; b=ONRkQJ1wVLEX3XHePeWyuFvk4E26DjdsWBHS1cI9qtoXA1x/9kaIZBLRKgoJzG8jUfwcxcizURCZOvrMsZ6JnpcS0o/ckOT1TgAC52MCcgVHSQkb7830CclWs5Rs5y70+OAmmYmjLWrxOLpG7zZhgbciMnwGO9lgII2/MflRZRc= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1675931983; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=wPFizuxISDdXLE8qIgIHpP1t2Iuoc4tkFYgjbCYQvcU=; b=SpLTOCiL9GjJ/ieaSamn5MtFl1g89ShnvYuK9PWd/7p8S5pOmWrHTRPylMUZCXTGAN4etqYbhyNlM94ET8afqkUMYpYADei0GI74nOeSy47gkIbwjZRFrOvzmbg94Epv4+l6xpXXvK7LbvpReApgclNWpw1KzRBHJMjdD6hMGGQ= 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=1675931983; 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=wPFizuxISDdXLE8qIgIHpP1t2Iuoc4tkFYgjbCYQvcU=; b=UT3ixZQEnzk2iqWCQ7IQbFfSv3aPgRB6+4/9PU+eIAZEydM0qiBh25lTsfNaBREi EJxisw8oPmG1OkXRsoKL+K0of5ahl+V5lPCqtaAelCXNOfClTWFkGjSiFBqhxNPvFse o9AD0Wjsrr+SrcRnTAQ4JYftWtr15Vx496cNYhmo= Received: from localhost (58-110-142-46.pool.kielnet.net [46.142.110.58]) by mx.zohomail.com with SMTPS id 1675931982446879.757916648873; Thu, 9 Feb 2023 00:39:42 -0800 (PST) User-agent: mu4e 1.8.13; emacs 28.2 From: Ricardo Wurmus To: 61382-done@debbugs.gnu.org Subject: [PATCH 1/2] gnu: Add python-scrublet. Date: Thu, 09 Feb 2023 09:38:59 +0100 X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <871qmz5j1w.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 61382-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 (-) Applied with minor changes. Thank you! -- Ricardo ------------=_1675932002-32721-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 9 Feb 2023 08:12:56 +0000 Received: from localhost ([127.0.0.1]:57354 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pQ235-0007j9-J8 for submit@debbugs.gnu.org; Thu, 09 Feb 2023 03:12:55 -0500 Received: from lists.gnu.org ([209.51.188.17]:58850) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pQ233-0007iu-Hh for submit@debbugs.gnu.org; Thu, 09 Feb 2023 03:12:54 -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 1pQ230-0006WW-Aq for guix-patches@gnu.org; Thu, 09 Feb 2023 03:12:51 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pQ22y-00012X-QZ for guix-patches@gnu.org; Thu, 09 Feb 2023 03:12:50 -0500 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=1675930366; x=1677744767; bh=e//cZ5jj09E9hX5 oponLnxssGKxZq9tZOTyGjH4ccNA=; b=J36tnVssIDnAgeQB8Ixe7NiW0GZ9q/P zffx+eXSjIzvnGUhbx/e31Hc1RjEXyvtVO/fMP9RgtTv8vBtnXy4wzLJ44rMKsT3 wnhUUq4pKvgEPlIYwLa0WvEQfhU/rvZ4ftLDtqpR6IqBKp7IM8tZ/0P+/6mHOfkc nKdbYdnE0r3Y= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS id 4F233A00E5 for ; Thu, 9 Feb 2023 09:12:46 +0100 (CET) Received: from localhost.localdomain (10.84.128.29) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.17; Thu, 9 Feb 2023 09:12:45 +0100 From: Navid Afkhami To: Subject: [PATCH 1/2] gnu: Add python-scrublet. Date: Thu, 9 Feb 2023 09:12:34 +0100 Message-ID: <20230209081235.30512-1-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: [10.84.128.29] X-ClientProxiedBy: SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-27436.006 X-TM-AS-Result: No-10-0.692300-5.000000 X-TMASE-MatchedRID: 4r2MyAYFTnd6fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt9GklfnQcKumwLYk+NSxc5r4qCLIu0mtIL9NdlMbI5hontU 3Lv5Rb/1Bh00zu6DygRJTjjs9yT6Yo8WMkQWv6iXBcIE78YqRWvcUt5lc1lLgKIzdZS3ou0UvU+ OKagS8dAJT1QwbGXhR+pCqRU+IB84ofghShQpram3VdrKCeQPm8uD6Y7nXL1piDRNquN7ycY5Lm YMppxFz4MJBeB13AbVZKCalsVmcQjWQPYq1JOarY9u3lK2/Yrn87HRNT0KLkg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-0.692300-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27436.006 X-TM-SNTS-SMTP: 5BA75D6F85F820B9D17541E76CE53BC0A2FEEDC0074FD0B97035C8AF4C647FB42002:F Received-SPF: pass client-ip=194.95.232.172; envelope-from=Navid.Afkhami@mdc-berlin.de; helo=a2062.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 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: submit 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: -3.3 (---) * gnu/packages/bioinformatics.scm (python-scrublet): New variable. --- gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 969b978054..05a078b0b0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3459,6 +3459,32 @@ (define-public python-scikit-bio resources for bioinformatics.") (license license:bsd-3))) +(define-public python-scrublet + (package + (name "python-scrublet") + (version "0.2.3") + (source (origin + (method url-fetch) + (uri (pypi-uri "scrublet" version)) + (sha256 + (base32 + "0fk5pwk12yz9wpvwkl6j2l2g28f3x35b9r9n5bw6f0i9f0qgd191")))) + (build-system python-build-system) + (propagated-inputs (list python-annoy + python-cython + python-matplotlib + python-numba + python-numpy + python-pandas + python-scikit-image + python-scikit-learn + python-scipy + python-umap-learn)) + (home-page "https://github.com/swolock/scrublet") + (synopsis "single-cell tool to indentify and remove doublets") + (description "Tool for identifying and removing doublets in single-cell RNA-seq data.") + (license license:expat))) + (define-public cwltool (package (name "cwltool") -- 2.34.1 ------------=_1675932002-32721-1--