From patchwork Fri Nov 8 14:48:18 2024 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Navid Afkhami X-Patchwork-Id: 70123 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 2583527BBEC; Fri, 8 Nov 2024 14:49:53 +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=-7.6 required=5.0 tests=BAYES_00,DKIMWL_WL_HIGH, DKIM_SIGNED,DKIM_VALID,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, 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 B453927BBE2 for ; Fri, 8 Nov 2024 14:49:50 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1t9QIL-0008TT-J2; Fri, 08 Nov 2024 09:49:05 -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 1t9QIJ-0008Si-BJ for guix-patches@gnu.org; Fri, 08 Nov 2024 09:49:03 -0500 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1t9QIJ-0005Uk-2K for guix-patches@gnu.org; Fri, 08 Nov 2024 09:49:03 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:Date:From:To:Subject; bh=6RyvG8jl5K5iRxatfHaH4BIEB0xdHgBj0fF3vkog1ps=; b=cyaYVNdyvQZaTeY6PT3xbXzOTIgpIB4hzjKIVzJO3fBT6N956MDu9fQeoq0Pj/99AO/ZfSTUW3K9rKRPAt6ramRHx/r4VJDUN+9H8gL6Qo+9sVCDI+Af9T2v3Fz9LLm/xq/m0v9r+UirDA1mmpYZM0Ph3mrpLnhYngNqC786wYuVYV9TWAQTrhwhknZFbSduaQ8oxi9oV8jHqMQFCfs4kMOJK5ocRdV5lpK/HYwFWpmlQ77UFjGXiqVkLsxqyQksfitA5Q0Yov+SffAZtMau50BgzYbYmywAwucpBqgaTfEA/Ic5W/AjMUzqzT+quX8mLlaNlJZSo5uNXDc4JNTlhA==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1t9QII-0001xH-M4 for guix-patches@gnu.org; Fri, 08 Nov 2024 09:49:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#74259] [PATCH] gnu: Add python-harmonypy. Resent-From: Navid Afkhami Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 08 Nov 2024 14:49:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 74259 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 74259@debbugs.gnu.org Cc: Navid Afkhami X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.17310773277491 (code B ref -1); Fri, 08 Nov 2024 14:49:02 +0000 Received: (at submit) by debbugs.gnu.org; 8 Nov 2024 14:48:47 +0000 Received: from localhost ([127.0.0.1]:51672 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1t9QI3-0001wk-Eg for submit@debbugs.gnu.org; Fri, 08 Nov 2024 09:48:47 -0500 Received: from lists.gnu.org ([209.51.188.17]:59920) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1t9QI1-0001wc-IM for submit@debbugs.gnu.org; Fri, 08 Nov 2024 09:48:46 -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 1t9QI0-0006uI-MU for guix-patches@gnu.org; Fri, 08 Nov 2024 09:48:44 -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 1t9QHu-0005Rm-Jd for guix-patches@gnu.org; Fri, 08 Nov 2024 09:48:44 -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=1731077305; x=1732891706; bh=gQl00fUNIXnTHkk mx7T3iYzMZL/ws53ceBz6yakT2TI=; b=amGiq/qmymtOFJhuXb/9WBkpPAGV6Xl IPmZdkN+JegdfGKmGD7MFGQKmBu25NW3Art+TP2XUPv8/6Q9C0pkpzviJkNpNLEu tn/4vuXxn5n/eGbzIAfcedvDkNNq+2xSueTVPDcKTt5RQKpsGt+7dffEQoaNO2Iw LenoADdv4E4Q= 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 251E3A01E0 for ; Fri, 8 Nov 2024 15:48:25 +0100 (CET) Received: from localhost (141.80.121.182) 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 15.2.1544.11; Fri, 8 Nov 2024 15:48:24 +0100 From: Navid Afkhami Date: Fri, 8 Nov 2024 14:48:18 +0000 Message-ID: <965e7c3c960b7d8808a39c6d50d00dc4a268398f.1731077298.git.navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.43.0 MIME-Version: 1.0 X-Originating-IP: [141.80.121.182] X-ClientProxiedBy: SW-IT-P-EX2.mdc-berlin.net (141.80.113.60) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3223-9.1.2019-28784.000 X-TM-AS-Result: No-10--5.258300-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJNYhP20o6vOMFY9XYa1m8xAJ3y+iqiko29rIVA3IGfCC6DE DQa+uiKUQpP6/vBOuJPABo6AR1sb2oqKGmXzWdcHju2XlcEx9HRR3UkpERYmZFNJJNN/CFGz2nf Q5TtZSqi2nszPz6kZjkF0fWsfQ90fVXS3CAt+DxgarEv/I2gPylwJ057ljktmDPy/7Hbs0Dg58S arp97J84ckZT5abrxu5V3Z5DLmdVY87NISpvHKZlkrY+dGOI9nWrjfkG2JD6pCWWOpTzHg1O5er quK5lP8 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--5.258300-5.000000 X-TMASE-Version: SMEX-14.0.0.3223-9.1.2019-28784.000 X-TM-SNTS-SMTP: FD1F065F47C912A62375FA035E8A507C92D7555DA47F4B136095FE497FC58D172000: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, RCVD_IN_VALIDITY_CERTIFIED_BLOCKED=0.001, RCVD_IN_VALIDITY_RPBL_BLOCKED=0.001, SPF_HELO_PASS=-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+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 (python-harmonypy): New variable. Change-Id: Iad8be627099858776163fccfeb27c08129e6fb75 --- gnu/packages/bioinformatics.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) base-commit: 2a6d96425eea57dc6dd48a2bec16743046e32e06 prerequisite-patch-id: 8f31c5ea3685b59fb6907a9582c0ca537c9c38bd prerequisite-patch-id: e9f28e6ac20c9572b3cc53ab09c4083161bfdf8d diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 35ff96ce42..3b393acce2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2397,6 +2397,32 @@ (define-public python-doubletdetection from single-cell RNA-sequencing.") (license license:expat))) +(define-public python-harmonypy + (package + (name "python-harmonypy") + (version "0.0.10") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/slowkow/harmonypy") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "15lxgncrnsx1hapfx78pvx4rjx5d48hqixdnacdy55d84myfmrym")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-hatchling + python-numpy + python-pandas + python-scikit-learn + python-scipy)) + (native-inputs (list python-pytest)) + (home-page "https://github.com/slowkow/harmonypy") + (synopsis "Data integration algorithm") + (description + "Harmony is an algorithm for integrating multiple high-dimensional datasets.") + (license license:gpl2))) + (define-public python-hclust2 (package (name "python-hclust2")