From debbugs-submit-bounces@debbugs.gnu.org Thu Jan 09 11:10:23 2025 Received: (at submit) by debbugs.gnu.org; 9 Jan 2025 16:10:23 +0000 Received: from localhost ([127.0.0.1]:54008 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tVv70-00008u-HR for submit@debbugs.gnu.org; Thu, 09 Jan 2025 11:10:22 -0500 Received: from lists.gnu.org ([2001:470:142::17]:42170) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tVv6y-00008e-Dx for submit@debbugs.gnu.org; Thu, 09 Jan 2025 11:10:21 -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 1tVv6s-0004lT-Qa for guix-patches@gnu.org; Thu, 09 Jan 2025 11:10:14 -0500 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 1tVv6q-0005aq-Eg for guix-patches@gnu.org; Thu, 09 Jan 2025 11:10:14 -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=1736438993; x=1738253394; bh=IeKM0MTvNn/j9YQ 0AJedolTsDIV9VSdYMKoyMEuCqlY=; b=S2kU0JAwh9q3qhxKnqlj3Frr2J4TPe2 bJ5uz7nF4eGD2zVpDyHGSHq8Ra2jCLuziaBv1pryBrfDqJDm7vZbj/BkVxteMH7/ 1Y+X8BWDkp34fhgVMXM/g/sBt8z0bGHhRlZ44BIxot7PdexGnuTCQEJOqFsr/Zt/ cq23oXiSFxpk= 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 6DDBE160154 for ; Thu, 9 Jan 2025 17:09:53 +0100 (CET) Received: from localhost (141.80.121.117) 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 15.2.1544.14; Thu, 9 Jan 2025 17:09:52 +0100 From: Navid Afkhami To: Subject: [PATCH] gnu: Add python-ngesh. Date: Thu, 9 Jan 2025 16:09:30 +0000 Message-ID: <363c8d863b0105d719b128bbd0176cb5c6dd994d.1736438970.git.navid.afkhami@mdc-berlin.de> X-Mailer: git-send-email 2.43.0 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.121.117] X-ClientProxiedBy: SW-IT-P-EX1.mdc-berlin.net (141.80.113.54) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3223-9.1.2019-28914.000 X-TM-AS-Result: No-10--7.667300-5.000000 X-TMASE-MatchedRID: 2wfub8HDRfNYhP20o6vOMFY9XYa1m8xAJ3y+iqiko29rIVA3IGfCC6DE DQa+uiKUQpP6/vBOuJPABo6AR1sb2oqKGmXzWdcHju2XlcEx9HRR3UkpERYmZE5JZ8kW3GxB1cA AdU8KAUxCBN46V/hNmX+3zY8kY6rX6Kqjemm0j8iwHXnHVkAsxb2XNUZZqZaA4ftEeSASkbK5xE k7XHDs76JYuGaIjh0/7lupSRApbpbocuK7+JBlJKEjYrfdoQAasWZEFZ6FiQBLVQGBtD1N/LJlr Av/CaLAegYAQSDilXQ= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--7.667300-5.000000 X-TMASE-Version: SMEX-14.0.0.3223-9.1.2019-28914.000 X-TM-SNTS-SMTP: 885F4CC3BB40490015C3603A7D0ACF894E05A403EBA2A6198178D222CBA746E62000: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, RCVD_IN_MSPIKE_H2=-0.001, 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-Spam-Score: 0.9 (/) 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: -0.1 (/) * gnu/packages/bioinformatics.scm (python-ngesh): New variable. Change-Id: If51f3075037647e319efa9468331677a845b30cb --- gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 34a39a48f1..f524b53bad 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2880,6 +2880,33 @@ (define-public python-metacells cells).") (license license:expat))) +(define-public python-ngesh + (package + (name "python-ngesh") + (version "1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/tresoldi/ngesh") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "07sj4x95b5hvx57pw24f80sk4ag4hkg1z6wzym3pzi8n5gn85n1z")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-ete3 python-numpy python-six)) + (native-inputs (list python-black python-flake8 python-pytest python-twine + python-wheel)) + (home-page "https://github.com/tresoldi/ngesh") + (synopsis "Library for phylogenetic tree simulation") + (description + "Ngesh is a Python library and CLI tool for simulating phylogenetic trees and data. +It is intended for benchmarking phylogenetic methods, especially in historical +linguistics andstemmatology. The generation of stochastic phylogenetic trees +also goes by the name simulationmethods for phylogenetic trees, synthetic data +generation, or just phylogenetic tree simulation.") + (license license:expat))) + (define-public python-parabam (package (name "python-parabam") base-commit: 66a1a1fe22aff54973ab5c33957a338b33b8274c -- 2.43.0 From debbugs-submit-bounces@debbugs.gnu.org Thu Jan 16 04:48:30 2025 Received: (at 75466-done) by debbugs.gnu.org; 16 Jan 2025 09:48:30 +0000 Received: from localhost ([127.0.0.1]:60060 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tYMUI-0008Pj-6Z for submit@debbugs.gnu.org; Thu, 16 Jan 2025 04:48:30 -0500 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21114) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tYMUE-0008PT-HM for 75466-done@debbugs.gnu.org; Thu, 16 Jan 2025 04:48:28 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1737020900; cv=none; d=zohomail.com; s=zohoarc; b=H5eBkqcP4hglz91siJVVfZ5NxGMnN5CkLttMcWolOXryU5DCR37S3uyJs755ApRnjzIWF2Jdx4nqZLR5mqeho+uEYhmnsSvNH9u4sPY8aKitxGvN042REc+nYCFytKLIL82f4jWHuy2Qe1cUhENlxhvBCQEVC5JWTDeesUutCkI= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1737020900; h=Content-Type:Date:Date:From:From:MIME-Version:Message-ID:Subject:Subject:To:To:Message-Id:Reply-To:Cc; bh=lPBhQcGp9AoUmRmT23sG4S/UVtfy0G4ynmG+9OjzgoE=; b=FWWzP1aimLVD5ACwInYg9NMcotq3tkaf9i+jGF1/lSbH07KnVPcs8BNAvd1P8Y2yF1jOAEhQe8Pz2v6/RwuxEl8EXSrfbjHA9sqizPrT2TaH1BhAG95WqZhUGf4Din551BXd6HysCSxGS10GtQVVQRGL+a7z3nMjUWmA8V5CDRA= 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=1737020900; 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=lPBhQcGp9AoUmRmT23sG4S/UVtfy0G4ynmG+9OjzgoE=; b=gAnlsVKv8UZWQOb5U7oiB1D6Z0OXIF/EHD2r5RFJRm6OZvWRpO0OThG89Y+UR8JQ RS21JcfQ82byLIn0+fDGlAGnXpzj20YhpNE6be+K1WWHbpOfqtLolyKs8TxaVQbVDn8 ss+QuaQKLhyviJ7Vdv+6p9dIXnl7HDblyNmTvqFE= Received: by mx.zohomail.com with SMTPS id 173702089982253.25082145892429; Thu, 16 Jan 2025 01:48:19 -0800 (PST) From: Ricardo Wurmus To: 75466-done@debbugs.gnu.org Subject: [PATCH] gnu: Add python-ngesh. 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