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Reply-To: bug#63849 <63849@debbugs.gnu.org> Date: Sun, 22 Jun 2025 18:35:27 +0000 retitle 63849 [PATCH] gnu: Add python-cell2cell. reassign 63849 guix-patches submitter 63849 Navid Afkhami severity 63849 normal tag 63849 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Fri Jun 02 11:24:09 2023 Received: (at submit) by debbugs.gnu.org; 2 Jun 2023 15:24:09 +0000 Received: from localhost ([127.0.0.1]:40660 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q56dN-0001W3-6d for submit@debbugs.gnu.org; Fri, 02 Jun 2023 11:24:09 -0400 Received: from lists.gnu.org ([209.51.188.17]:41458) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q56dK-0001Vv-G7 for submit@debbugs.gnu.org; Fri, 02 Jun 2023 11:24:08 -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 1q56dK-0001rr-6u for guix-patches@gnu.org; Fri, 02 Jun 2023 11:24:06 -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 1q56dG-0005wC-DE for guix-patches@gnu.org; Fri, 02 Jun 2023 11:24:05 -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=1685719428; x=1687533829; bh=zw6rI9UQOJQ1jYD ge1y1RLV43p9yrbJ143g74lrgv+Q=; b=qMXi6J3whVLP046rdf6pQSFlHr82XDV X+hiSgOpuyWRzOZFnxKNPhEyh8hQplied6muS75faWkTwMv/9uQRfdk27fSs6owi H/X85B56fBoZYTiWmlm869L3B4PjBQr4L1b+NpDf7D9SP52zV5pyzJ1/V+3gcfrR KtPTbEk7uO/I= Received-SPF: Pass (mailfrom) identity=mailfrom; client-ip=141.80.113.62; helo=sw-it-p-ex4.mdc-berlin.net; envelope-from=navid.afkhami@mdc-berlin.de; receiver= Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS id 4042716013D for ; Fri, 2 Jun 2023 17:23:48 +0200 (CEST) Received: from localhost (141.80.218.27) 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 15.1.2507.23; Fri, 2 Jun 2023 17:23:47 +0200 From: Navid Afkhami To: Subject: [PATCH] gnu: Add python-cell2cell. Date: Fri, 2 Jun 2023 15:23:43 +0000 Message-ID: <13266f60b98b4632c6b7fa2c4e5cacdc3a0840f7.1685719423.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-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-14.0.0.3092-9.0.1002-27668.000 X-TM-AS-Result: No-10--4.137400-5.000000 X-TMASE-MatchedRID: NGDYxnKYxb16fjezFKxXHArcxrzwsv5uwTlc9CcHMZerwqxtE531VIPc XuILVCbaRRa406V/YwyBUGewL2YXt10ieHN50/kHxi///JpaHQO/yN2q8U674kz5vzLEGq8DoHy 0bASrKBp06UCnKOpkwpw6kSS19ACeU3mQhmdh4RiqFx2c/3V5ccXSSNhWWhyhZQbp9tWWMvoQRH 1F2WksnV/2DAzeeU3rtWKNR2epAFaCWMXx8ovaCeLzNWBegCW2xl8lw85EaVQLbigRnpKlKTpcQ TtiHDgWeZW/uHJhhEDVNaRzz0mpxhZeoJXhK2rbhs9OdGWLupUwmNGMka2UWA4WQ6lJFZDQNwEb WM03DKGs/XbeKVMHjQC4uxuSReCAt0oQIuj+SVeFEVfQxs3N6ZDgmt8QekvB5maCeNv/LIzVGQd qwsDiEg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.137400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27668.000 X-TM-SNTS-SMTP: 522FFF86708B4ED725A6ED2E98FC96E119E832855F1EFB324E1FBF19893C3EEB2002: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: -1.4 (-) X-Debbugs-Envelope-To: submit Cc: Navid Afkhami 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: -2.4 (--) * gnu/packages/bioinformatics.scm (python-cell2cell): New variable. --- gnu/packages/bioinformatics.scm | 64 +++++++++++++++++++++++++++++++++ 1 file changed, 64 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 89f8041d56..6dbbc26eac 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1298,6 +1298,70 @@ (define-public python-biofluff experiments.") (license license:expat))) +(define-public python-cell2cell + (package + (name "python-cell2cell") + (version "0.6.8") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/earmingol/cell2cell") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1hwww0rcv8sc4k312n4d0jhbyix1jjqgv5djg25bw8127q5iym3s")) + (modules '((guix build utils))) + (snippet '(begin + (substitute* "cell2cell/plotting/factor_plot.py" + (("from statannotations.Annotator import Annotator") + "") + (("if statistical_test is not None") + "if False")) + (substitute* "setup.py" + (("'statannotations',") + "")) + (substitute* "setup.py" + (("matplotlib >= 3.2.0,<=3.5.1") + "")) + (substitute* "setup.py" + (("'gseapy == 1.0.3'") + "'gseapy'")))))) + (build-system pyproject-build-system) + (arguments + (list #:tests? #f ;There are no tests + #:phases '(modify-phases %standard-phases + ;; Numba needs a writable dir to cache functions. + (add-before 'build 'set-numba-cache-dir + (lambda _ + (setenv "NUMBA_CACHE_DIR" "/tmp")))))) + (propagated-inputs (list python-gseapy + python-kneed + python-matplotlib + python-networkx + python-numpy + python-openpyxl + python-pandas + python-scikit-learn + python-scipy + python-seaborn + python-statsmodels + python-scanpy + python-seaborn + python-tensorly + python-tqdm + python-umap-learn + python-xlrd)) + (native-inputs (list python-pytest)) + (home-page "https://github.com/earmingol/cell2cell") + (synopsis "Python library for cell communication analysis") + (description + "Cell2cell is a Python library for cell communication analysis. +This is a method to calculate, visualize and analyze communication +between cell types. Cell2cell is suitable for single-cell RNA sequencing +(scRNA-seq) data.") + (license license:bsd-3))) + (define-public python-cellbender (package (name "python-cellbender") base-commit: a7d9cd742c3149bb014db95f88d1158d590bc124 -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Fri Jun 02 13:57:44 2023 Received: (at 63849-done) by debbugs.gnu.org; 2 Jun 2023 17:57:44 +0000 Received: from localhost ([127.0.0.1]:40845 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q591z-00007t-RB for submit@debbugs.gnu.org; Fri, 02 Jun 2023 13:57:44 -0400 Received: from sender3-of-o59.zoho.com ([136.143.184.59]:21984) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1q591x-00007h-64 for 63849-done@debbugs.gnu.org; Fri, 02 Jun 2023 13:57:42 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1685728658; cv=none; d=zohomail.com; s=zohoarc; b=lwNAFfMyJnnYlTNyrQx6x/PNHrLsY+yCFNsfBVcVah4ajYW2HXo0MShxRwJ/rhWV/1b0igQCf7pLF2O/oDo3ctL3Lxokgj0lQukzvoSnDvkzQ4YCToalv7JoLFAsjB6lSo/hg2f64cv1XgYdnfPuETI2WmC9OnTVZ7klcK4IKM0= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1685728658; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=BagGsHouZzyT7mo2kzZvSg9iYblQMHxO3pdhQWN3Mpc=; b=Fc9zimbNK4nMhEj0vonkAed64F2EnVOzBU/B43F4RIl4yBhXeIhRvlOgQSz5oNbMCVy/DJJk6YpNjLek9XlwypPqkXvo9FgDeoT48qO8JTkvdQ1/4HhwW0nfo7GHs5VgOhQX3Kw9x9OjaQAYRpOkKk/J69D85OuTfLNNLSW9N7g= 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=1685728658; 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=BagGsHouZzyT7mo2kzZvSg9iYblQMHxO3pdhQWN3Mpc=; b=QGPCN3H/ON6WZWuvizWuPWzYuqntim4l9jRCzQujeiGn3JHXHTtsjcvDpWOEUdKL BsJVK+c1AiYt28MDj4Cw4QhDIodMV5SzJJjCMmviGRClZBAbGKAtfz/MH3rPpVRnmxT NU0Va6szeA5DzAgQ0KihMJrab7qLoQS1yD4z0Rqg= Received: from localhost (78-108-142-46.pool.kielnet.net [46.142.108.78]) by mx.zohomail.com with SMTPS id 1685728656621652.3399857616697; Fri, 2 Jun 2023 10:57:36 -0700 (PDT) User-agent: mu4e 1.10.2; emacs 28.2 From: Ricardo Wurmus To: 63849-done@debbugs.gnu.org Subject: [PATCH] gnu: Add python-cell2cell. Date: Fri, 02 Jun 2023 19:57:01 +0200 Message-ID: <87y1l1rble.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 63849-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 (-) Pushed with a few changes with commit f09944461f97537364231ff213a84faadbfb5fe6. Thank you! -- Ricardo From unknown Sun Jun 22 11:35:27 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Sat, 01 Jul 2023 11:24:09 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator