From unknown Tue Jun 24 20:52:03 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#70731 <70731@debbugs.gnu.org> To: bug#70731 <70731@debbugs.gnu.org> Subject: Status: [PATCH] gnu: Add python-pyrodigal. Reply-To: bug#70731 <70731@debbugs.gnu.org> Date: Wed, 25 Jun 2025 03:52:03 +0000 retitle 70731 [PATCH] gnu: Add python-pyrodigal. reassign 70731 guix-patches submitter 70731 nafkhamdc severity 70731 normal tag 70731 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Fri May 03 05:55:51 2024 Received: (at submit) by debbugs.gnu.org; 3 May 2024 09:55:51 +0000 Received: from localhost ([127.0.0.1]:46303 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1s2pdu-0004T6-RY for submit@debbugs.gnu.org; Fri, 03 May 2024 05:55:51 -0400 Received: from lists.gnu.org ([2001:470:142::17]:37460) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1s2pdq-0004T0-P4 for submit@debbugs.gnu.org; Fri, 03 May 2024 05:55:49 -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 1s2pdO-0004d6-T4 for guix-patches@gnu.org; Fri, 03 May 2024 05:55:19 -0400 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 1s2pdM-0001Bl-KV for guix-patches@gnu.org; Fri, 03 May 2024 05:55:18 -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=1714730111; x=1716544512; bh=pJzENwxiBdXinaG 0ty0/psO940HUZVu/fqVny/HG4dA=; b=FO83Ro7MfqztxsO2OXIHW4yOR9OWTYk L1m0hkq71MYl0UnD5XJVUnCmobbTTwyCaUREWfR6E0kcacBCkhG51xzpKmN9pzgt Uq+3EKTkowTF8+PYhjgy1u8CtBaz1a2f89OHnjhDQhy7hoSKATDzVFU5jav1dIQB JA+HW5T9FgOo= 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 AD98BA015C for ; Fri, 3 May 2024 11:55:11 +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 15.2.1544.11; Fri, 3 May 2024 11:55:10 +0200 From: nafkhamdc To: Subject: [PATCH] gnu: Add python-pyrodigal. Date: Fri, 3 May 2024 09:53:12 +0000 Message-ID: <076e35e70f743849d45c10197865b1d74d3f9978.1714729992.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-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3152-9.1.2019-28358.006 X-TM-AS-Result: No-10--3.643800-5.000000 X-TMASE-MatchedRID: cSoPLjBYd51YhP20o6vOMFY9XYa1m8xAJ3y+iqiko29rIVA3IGfCC6DE DQa+uiKUQpP6/vBOuJPABo6AR1sb2oqKGmXzWdcHju2XlcEx9HRR3UkpERYmZIOFKfeCA1CKg0h EuCUZp7MNa6SgEPEhvSjuayktjkEIHVBkDs6L3kWdFMmljtUAp69JSkXsXWchAtvBVlY5IRceCI eEUj1PHWF+VLwkTNcJoGC5cBpjyvuhNw8qOqBP17AdecdWQCzFvZc1RlmploDh+0R5IBKRsr/a0 nd+hIFC0KBwVrJVSIiys4MQjA230K4m343mzLBO5F3tD07DLDPr4psifESNrsV2iZWpOZYMbjVZ wgDETAfadgsTWP/xTt24GWw5WxwlSryYC0D3INFI2mlYBfyh6dfsYX7riG7IuOY0q66+BqahgjV 6si4Sxb6DZFmPYUrLrQKe71GYum8= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.643800-5.000000 X-TMASE-Version: SMEX-14.0.0.3152-9.1.2019-28358.006 X-TM-SNTS-SMTP: 5577D1DD7BD0D3ED72851CD1F2DB95C73B0038A502D0B9ED315F8F86D6FB262B2000: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: 0.9 (/) X-Debbugs-Envelope-To: submit Cc: nafkhamdc 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-pyrodigal): New variable. Change-Id: Iaa0bdb4b918d93f990d5b904f1df3a3f910726b0 --- gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b90a1c7824..bc10123a8f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -17710,6 +17710,37 @@ (define-public python-pypairix bgzipped text file that contains a pair of genomic coordinates per line.") (license license:expat))) +(define-public python-pyrodigal + (package + (name "python-pyrodigal") + (version "3.3.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/althonos/pyrodigal") + (commit (string-append "v" version)) + (recursive? #t))) + (file-name (git-file-name name version)) + (sha256 + (base32 "10vxbm9i33wari0ifsr78xnfn7d0yqwzqpc5pchirjflf1mmnr6w")))) + (build-system pyproject-build-system) + (arguments + `(#:phases (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (with-directory-excursion "/tmp" + (invoke "python3" "-m" "unittest" "discover" "-vv")))))))) + (propagated-inputs (list python-archspec python-importlib-resources)) + (native-inputs (list python-cython-3 python-mock python-unittest2)) + (home-page "https://github.com/althonos/pyrodigal") + (synopsis "Cython bindings and Python interface for Prodigal") + (description + "This package offers Cython bindings and a Python interface for Prodigal. + Prodigal is an ORF finder designed for both genomes and metagenomes.") + (license license:gpl3))) + (define-public python-pyfaidx (package (name "python-pyfaidx") base-commit: aa9ac252206615713ab988d7068da9e14a9bccc0 prerequisite-patch-id: 68498b47732fb0359e4db6d2f1c86f44d8c700ab prerequisite-patch-id: 8cad86329867720ca9938e551ece489b056b37ad -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Mon May 06 07:03:54 2024 Received: (at 70731-done) by debbugs.gnu.org; 6 May 2024 11:03:54 +0000 Received: from localhost ([127.0.0.1]:37290 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1s3w8Q-0008Cz-AE for submit@debbugs.gnu.org; Mon, 06 May 2024 07:03:54 -0400 Received: from sender3-of-o57.zoho.com ([136.143.184.57]:21761) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1s3w8O-0008Cs-JM for 70731-done@debbugs.gnu.org; Mon, 06 May 2024 07:03:53 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1714993405; cv=none; d=zohomail.com; s=zohoarc; b=oCo/Dyn9jYlEPwqN4R9qrZlwdFgAr93mhoutBhjHJt5gwAGXI5bpMhV+BQMWSmQKXMP5+mj+f5xpIjRKunkz82BDWTMk/zxsWmksXcRdb44RchR1tm+ARjCw04FBAmEf5KOTkQE6ijIDPm7DxDPTRGSVmEQtGi7wXrcWc6DKmfw= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1714993405; h=Content-Type:Date:Date:From:From:MIME-Version:Message-ID:Subject:Subject:To:To:Message-Id:Reply-To:Cc; bh=k1LwwMLC3I/SsakTdL2VRTiQttH2Tm1l9rCPzxxO6vY=; b=Y6ceL3X9RZAlwzpsSjWfATc0pJSYgNLcNeoISCGFaQB+bG44HrmM1TCGltIyjRSaqUX03aLiv2BEQK/PN31LN4FBOKRMCuFl14o77UQ72IYrgzu2MUdEa7u8s9XmFgUzGRGHvxrgUE2b/DrRd4bcg2ABaMJZTYiueFmXat8Q+oo= 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=1714993405; 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=k1LwwMLC3I/SsakTdL2VRTiQttH2Tm1l9rCPzxxO6vY=; b=brNtOoiW9fTot6sdN+PZ8te0q4JdwEwPzAfLBsWCy8ZFbPeGZen9fwOjxQ5sRmk4 PEHTXMYpq5k52020Wi5HfPRHfywIj+saugHJUL81WvKAgefBiQvpXkWTQJMxPU5SZ8i Re0FImk1LhBxuVP048q9h4ceYS9IEwGk9Y67O6Qs= Received: by mx.zohomail.com with SMTPS id 1714993404505145.41724184582836; Mon, 6 May 2024 04:03:24 -0700 (PDT) From: Ricardo Wurmus To: 70731-done@debbugs.gnu.org Subject: [PATCH] gnu: Add python-pyrodigal. User-Agent: mu4e 1.12.4; emacs 29.3 Date: Mon, 06 May 2024 13:03:21 +0200 Message-ID: <87ttjbjj7q.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 70731-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 it to actually run the tests and pushed it to the "master" branch. -- Ricardo From unknown Tue Jun 24 20:52:03 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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