From unknown Sat Jun 21 10:38:45 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#69011 <69011@debbugs.gnu.org> To: bug#69011 <69011@debbugs.gnu.org> Subject: Status: [PATCH] gnu: Add python-pdbfixer. Reply-To: bug#69011 <69011@debbugs.gnu.org> Date: Sat, 21 Jun 2025 17:38:45 +0000 retitle 69011 [PATCH] gnu: Add python-pdbfixer. reassign 69011 guix-patches submitter 69011 nafkhamdc severity 69011 normal tag 69011 patch thanks From debbugs-submit-bounces@debbugs.gnu.org Sat Feb 10 05:15:44 2024 Received: (at submit) by debbugs.gnu.org; 10 Feb 2024 10:15:45 +0000 Received: from localhost ([127.0.0.1]:57975 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rYkOe-0002k0-Ed for submit@debbugs.gnu.org; Sat, 10 Feb 2024 05:15:44 -0500 Received: from lists.gnu.org ([2001:470:142::17]:57014) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rYkOb-0002jd-K0 for submit@debbugs.gnu.org; Sat, 10 Feb 2024 05:15:42 -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 1rYkOE-0005rs-R9 for guix-patches@gnu.org; Sat, 10 Feb 2024 05:15:19 -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 1rYkO5-0000mg-Di for guix-patches@gnu.org; Sat, 10 Feb 2024 05:15:18 -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=1707560091; x=1709374492; bh=tqoCecpfnV2Texf D/VLYp8jaqOL/H7safLWmL7q+9ME=; b=ghVvwzkMtUWpoRZimmEVrvr3qJmyaFp /zZgBOgURGpgbLVBHFvM366W5T3u97Iwyu4uR/OgAhCg0D/qUQ8UySC7BO8OK05w Y1YMFb5JZeH7zDP3aYNlGBR5kdi0itcNIWWTdCKM9AVOFG63NFsNMJkXcIMdUwfV J6120/m2OrzU= 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 4C9F5160187 for ; Sat, 10 Feb 2024 11:14:51 +0100 (CET) Received: from localhost (89.247.175.55) 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 15.2.1258.28; Sat, 10 Feb 2024 11:14:50 +0100 From: nafkhamdc To: Subject: [PATCH] gnu: Add python-pdbfixer. Date: Sat, 10 Feb 2024 10:14:48 +0000 Message-ID: <6b3d0b29311e02f801f0990ccb88033763f00e56.1707560088.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: [89.247.175.55] 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-14.0.0.3152-9.1.1006-28182.006 X-TM-AS-Result: No-10--7.035200-5.000000 X-TMASE-MatchedRID: DIEPoA0d9jx6fjezFKxXHArcxrzwsv5ucV3n4J/0zUPAuQ0xDMaXkH4q tYI9sRE/4K9FmervsqXuNT8xdcEnQwE+dA3RWUSvnVTWWiNp+v/BDDo09qAAYhe1yJq6HIhHuJE UmdYPGSWEMtiLBwts/TsEKoanhl9fFffDzUcDqzDAtiT41LFzmkAqB87qNpwZpjlkbDvDJ4dG1z aoYFqfLuiD0RMD6CFs75CiMHOaU2WzYcCczGhD2+OnF2j8nBWblKW//2SWQOICGfvnVpx+25gNM iEzDc45fS0Ip2eEHnwj/1Rbkzl1EymDnI5x2hWC9xS3mVzWUuA152LecOHHI4B1xfbMOQ56yFCb A2tr4+ouxMpbaIihQ13hma03GgBJplZ359y7qKT+JdxhuKiGQw== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--7.035200-5.000000 X-TMASE-Version: SMEX-14.0.0.3152-9.1.1006-28182.006 X-TM-SNTS-SMTP: AB2E87958299B1FE83D50A2AACCDEB64F717843DA9F7DC13EFF95A02069AEC8F2000: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: 4.5 (++++) X-Spam-Report: Spam detection software, running on the system "debbugs.gnu.org", has NOT identified this incoming email as spam. The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: * gnu/packages/bioinformatics.scm (python-pdbfixer): New variable. Change-Id: I2894a08ab3eed463f052b9df6372d4016b718d1a --- gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) Content analysis details: (4.5 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- 3.6 RCVD_IN_SBL_CSS RBL: Received via a relay in Spamhaus SBL-CSS [89.247.175.55 listed in zen.spamhaus.org] -0.0 SPF_HELO_PASS SPF: HELO matches SPF record 0.9 SPF_FAIL SPF: sender does not match SPF record (fail) [SPF failed: Please see http://www.openspf.org/Why?s=mfrom; id=navid.afkhami%40mdc-berlin.de; ip=2001%3A470%3A142%3A%3A17; r=debbugs.gnu.org] -0.0 T_SCC_BODY_TEXT_LINE No description available. 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: 3.5 (+++) X-Spam-Report: Spam detection software, running on the system "debbugs.gnu.org", has NOT identified this incoming email as spam. The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: * gnu/packages/bioinformatics.scm (python-pdbfixer): New variable. Change-Id: I2894a08ab3eed463f052b9df6372d4016b718d1a --- gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) Content analysis details: (3.5 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- 3.6 RCVD_IN_SBL_CSS RBL: Received via a relay in Spamhaus SBL-CSS [89.247.175.55 listed in zen.spamhaus.org] -0.0 SPF_HELO_PASS SPF: HELO matches SPF record 0.9 SPF_FAIL SPF: sender does not match SPF record (fail) [SPF failed: Please see http://www.openspf.org/Why?s=mfrom;id=navid.afkhami%40mdc-berlin.de;ip=2001%3A470%3A142%3A%3A17;r=debbugs.gnu.org] -0.0 T_SCC_BODY_TEXT_LINE No description available. -1.0 MAILING_LIST_MULTI Multiple indicators imply a widely-seen list manager * gnu/packages/bioinformatics.scm (python-pdbfixer): New variable. Change-Id: I2894a08ab3eed463f052b9df6372d4016b718d1a --- gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 56709c0332..2c1917be95 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2244,6 +2244,37 @@ (define-public python-parabam defined rule on an input file.") (license license:gpl3))) +(define-public python-pdbfixer + (package + (name "python-pdbfixer") + (version "1.9") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/openmm/pdbfixer") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1zjhb19q5dclkwvzh8n29p31n1vzkhlmmzwqllimi89jsis1cx35")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags '(list "-k" + ;; These tests fail because they require internet access. + (string-append "not test_build_and_simulate.py" + " and not test_cli.py" + " and not test_mutate.py")))) + (propagated-inputs (list python-numpy openmm)) + (native-inputs (list python-pytest)) + (home-page "https://github.com/openmm/pdbfixer") + (synopsis "Application for fixing problems in Protein Data Bank") + (description + "PDBFixer is designed to rectify issues in Protein Data Bank files. +Its intuitive interface simplifies the process of resolving problems +encountered in PDB files prior to simulation tasks.") + (license license:expat))) + (define-public python-peaks2utr (package (name "python-peaks2utr") base-commit: 10dba10fd6551ab480a38d00301e6f102def674d prerequisite-patch-id: 3a59afadab83198b19921e19197e26925523b4a3 prerequisite-patch-id: 116b12264d1713957eef349460a71f04b0757a9e -- 2.34.1 From debbugs-submit-bounces@debbugs.gnu.org Sat Feb 10 05:22:46 2024 Received: (at 69011-done) by debbugs.gnu.org; 10 Feb 2024 10:22:46 +0000 Received: from localhost ([127.0.0.1]:58258 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rYkVS-00030E-6A for submit@debbugs.gnu.org; Sat, 10 Feb 2024 05:22:46 -0500 Received: from sender4-of-o50.zoho.com ([136.143.188.50]:21021) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1rYkVQ-000303-0I for 69011-done@debbugs.gnu.org; Sat, 10 Feb 2024 05:22:44 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1707560544; cv=none; d=zohomail.com; s=zohoarc; b=b4cOx7f6B4UHXjVYckKaNsdxj+SqJyjq5uF9QcFaAEWQa198QNM4fG726dC48/aPw0LdDjJdB7qAea6tPwnRat5QyaTCcz+3LVw0qNIY0wbiYPXuofupnd4IF6Te2Fgwz18G6JR3/fAs09g01F5CJJafv1iSRKFmO/BrwousLrk= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1707560544; h=Content-Type:Content-Transfer-Encoding:Cc:Cc:Date:Date:From:From:MIME-Version:Message-ID:Subject:Subject:To:To:Message-Id:Reply-To; bh=vyMA5SRMbc+wc98/SohBW20rcZuTtKVO/3yIFzVwLBs=; b=BExI/QFWi3plDWpuiy5wQ4Fn/ynk/R0cbvPzPoxq/JnC8q9HnpJmPLuF2JywS2TRomhciqKXhywq2jXoaGVpCqyIks9RzJPYA4FNbspSEcNDz45DRdW6rNem9NyXCyCIZ5ARNK56oL8/vt+RJwny6Q4w0Mkmr5FPrR0rQ3XzYpg= 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=1707560544; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Cc:Cc:Subject:Subject:Date:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding:Message-Id:Reply-To; bh=vyMA5SRMbc+wc98/SohBW20rcZuTtKVO/3yIFzVwLBs=; b=fE7ZiujKq5ky0UVCJ7qCNwzt4RPSbbLAZE9KwetZ5sAGVerdg88155ZlcvkJQzLx K5+1C50tR8MaZ3bX/2uGW4LcwnakY84d/uCGq5a2fKm+nag2L7N9HaOCVB7SoyKzpCV c7H/dFCSSmiF3SRn8175UFJVfIPzT5/9V3xUhxjg= Received: from localhost (100-108-142-46.pool.kielnet.net [46.142.108.100]) by mx.zohomail.com with SMTPS id 170756054016145.337366550957995; Sat, 10 Feb 2024 02:22:20 -0800 (PST) User-agent: mu4e 1.10.8; emacs 29.1 From: Ricardo Wurmus To: 69011-done@debbugs.gnu.org Subject: [PATCH] gnu: Add python-pdbfixer. Date: Sat, 10 Feb 2024 11:21:39 +0100 Message-ID: <87ttmgsjom.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 69011-done Cc: navid.afkhami@mdc-berlin.de 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=E2=80=99ve applied it and pushed with commit ca4c9062c4a04a3550fdcf67cb2b41daa13627d8. --=20 Ricardo From unknown Sat Jun 21 10:38:45 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, 09 Mar 2024 12:24:06 +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