From unknown Tue Aug 19 02:59:36 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#46946] (no subject) Resent-From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 05 Mar 2021 13:51:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 46946 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 46946@debbugs.gnu.org X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.161495223629307 (code B ref -1); Fri, 05 Mar 2021 13:51:01 +0000 Received: (at submit) by debbugs.gnu.org; 5 Mar 2021 13:50:36 +0000 Received: from localhost ([127.0.0.1]:33290 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lIAqi-0007cd-2d for submit@debbugs.gnu.org; Fri, 05 Mar 2021 08:50:36 -0500 Received: from lists.gnu.org ([209.51.188.17]:40520) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lIAqg-0007cW-RU for submit@debbugs.gnu.org; Fri, 05 Mar 2021 08:50:35 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:36836) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lIAqg-0006k6-Iw for guix-patches@gnu.org; Fri, 05 Mar 2021 08:50:34 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:45239) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lIAqe-0004xY-9c for guix-patches@gnu.org; Fri, 05 Mar 2021 08:50:34 -0500 Received: from localhost (localhost [127.0.0.1]) by c2062.mx.srv.dfn.de (Postfix) with ESMTP id 7A0C0300157 for ; Fri, 5 Mar 2021 14:50:28 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-language:content-transfer-encoding:content-type :content-type:mime-version:user-agent:date:date:message-id:from :from:received:received:received; s=mdc; t=1614952228; x= 1616766629; bh=frcCV1k9oG9oKj3dpUqdJg1PxRT2RSN/XKdLCPjaYaY=; b=N oBG+Q5iJmQUMgr2eBbgWIn4Y6KSGddxr/4Zp1DKD5fD33+vQASAZlQheNj7y6l8M fbqLz6inkxvXGYnDSxQtAR7+uDiFky7koY3UEBCaDr4kBPSLiBa3L7dokGQn2Mhc YfdMJWKIyupMlB6MRtC67uXq5ibbcNxHDExNFFz1w8= Received: from c2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-erl.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id jmAz1n-nTRjL for ; Fri, 5 Mar 2021 14:50:28 +0100 (CET) Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS for ; Fri, 5 Mar 2021 14:50:28 +0100 (CET) Received: from [192.168.1.220] (31.18.50.167) 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 15.1.2176.2; Fri, 5 Mar 2021 14:50:27 +0100 From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Message-ID: Date: Fri, 5 Mar 2021 14:50:27 +0100 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:68.0) Gecko/20100101 Thunderbird/68.10.0 MIME-Version: 1.0 Content-Type: text/plain; charset="utf-8"; format=flowed Content-Transfer-Encoding: 7bit Content-Language: en-US X-Originating-IP: [31.18.50.167] 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-14.0.0.3080-8.6.1012-26010.007 X-TM-AS-Result: No-10-2.373600-8.000000 X-TMASE-MatchedRID: zNHEZVbO6+CYN/UYLI7XqOLzNWBegCW2RYvisGWbbS/ITICTZKCMNexJ beH3K4ldgPn1rCdWbriK1w/mwA00Qd0H8LFZNFG73Yq8RVaZivV4OXlDu6jxLpvOJThWZQ3kbSv Uj/BK7J9DE2SiozhChZlMspqOq0CS X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-2.373600-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-26010.007 X-TM-SNTS-SMTP: 16C799DA591B8594B6728BA7D0CBB66FD88536C1527B93CFC41F821FB61AC6B32000:F Received-SPF: pass client-ip=194.95.238.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=c2062.mx.srv.dfn.de X-Spam_score_int: 13 X-Spam_score: 1.3 X-Spam_bar: + X-Spam_report: (1.3 / 5.0 requ) BAYES_00=-1.9, BODY_EMPTY=0.22, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, EMPTY_MESSAGE=2.32, MISSING_SUBJECT=1.799, PYZOR_CHECK=1.392, RCVD_IN_DNSWL_MED=-2.3, RCVD_IN_MSPIKE_H4=0.001, RCVD_IN_MSPIKE_WL=0.001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=no autolearn_force=no X-Spam_action: no action X-Spam-Score: 3.2 (+++) X-Spam-Report: Spam detection software, running on the system "debbugs.gnu.org", has NOT identified this incoming email as spam. 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Content preview: Content analysis details: (2.2 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- -2.3 RCVD_IN_DNSWL_MED RBL: Sender listed at https://www.dnswl.org/, medium trust [209.51.188.17 listed in list.dnswl.org] 0.0 RCVD_IN_MSPIKE_H3 RBL: Good reputation (+3) [209.51.188.17 listed in wl.mailspike.net] -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=madalinionel.patrascu%40mdc-berlin.de;ip=209.51.188.17;r=debbugs.gnu.org] 2.3 EMPTY_MESSAGE Message appears to have no textual parts and no Subject: text 0.0 RCVD_IN_MSPIKE_WL Mailspike good senders 1.8 MISSING_SUBJECT Missing Subject: header 0.2 NO_SUBJECT Extra score for no subject -1.0 MAILING_LIST_MULTI Multiple indicators imply a widely-seen list manager 0.2 BODY_EMPTY No body text in message From unknown Tue Aug 19 02:59:36 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#46946] [PATCH 1/2] gnu: Add python-bioframe. References: In-Reply-To: Resent-From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 05 Mar 2021 14:20:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46946 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <46946@debbugs.gnu.org> Cc: rekado@elephly.net, =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Received: via spool by 46946-submit@debbugs.gnu.org id=B46946.161495399432263 (code B ref 46946); Fri, 05 Mar 2021 14:20:01 +0000 Received: (at 46946) by debbugs.gnu.org; 5 Mar 2021 14:19:54 +0000 Received: from localhost ([127.0.0.1]:33333 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lIBJ3-0008OJ-Ly for submit@debbugs.gnu.org; Fri, 05 Mar 2021 09:19:53 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:38503) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lIBJ1-0008O1-6Q for 46946@debbugs.gnu.org; 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Fri, 5 Mar 2021 15:19:43 +0100 From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Date: Fri, 5 Mar 2021 15:19:29 +0100 Message-ID: <20210305141930.28787-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.30.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] 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-14.0.0.3080-8.6.1012-26010.007 X-TM-AS-Result: No-10-1.195600-8.000000 X-TMASE-MatchedRID: jJK0QAsddvYsaaYlMvaOHAPZZctd3P4BJMLyF26ahp3fc2Xd6VJ+ypz+ ZUWgONn9ONYj3/n/Uxsgy4WsMZaXZD1bnfEEP633a87CDXaKRVIjFTUmyJTlscZygq/CPmro0rC vsVMmyNopTyRGdhl/1t033kdg+s9McznnimP5Cn8fuiiOOXntlUMYrblfIl47+P/Gqbdv4yjuBS 2IhnV8FuQvL5xJoOF9UZJsRgxZser5HING3S/3PVS0U/rncMc4b0NcOFSwefJw9p8oKhdgf0Suy wxB3Ejkk0fkvX74QHq1/ilaMMAcpqVXGK1tVGyudhnFihmbnwUCn5QffvZFlYEp83Hd963HmA0y ITMNzjl9LQinZ4QefPcjNeVeWlqY+gtHj7OwNO34ZhR52Rc1ap0WaS7oZl7kIN+tyZNN2eW568H CLuN/KgIZA7AxGfb+A15KICIMa5Nz2tWWas3a5OWGuQE3ym+9Ys32x4zbCRxICZB0q0w5m2/H7L hIKjO20bWl8H0Q2RO0ML47Km+X9EYOAQXCbpqgJRrsvPnso5c= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-1.195600-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-26010.007 X-TM-SNTS-SMTP: 5B2546B627F6CD4B871E6B0882B039D6EDD436B18E8C330FA55B57284328E2442000:F X-Spam-Score: -2.3 (--) 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: -3.3 (---) * gnu/packages/bioinformatics.scm (python-bioframe): New variable. --- gnu/packages/bioinformatics.scm | 46 +++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d617736e57..fb357b8b6c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -120,6 +120,7 @@ #:use-module (gnu packages popt) #:use-module (gnu packages protobuf) #:use-module (gnu packages python) + #:use-module (gnu packages python-build) #:use-module (gnu packages python-check) #:use-module (gnu packages python-compression) #:use-module (gnu packages python-science) @@ -923,6 +924,51 @@ Python.") `(("python2-pathlib" ,python2-pathlib) ,@(package-native-inputs pybedtools)))))) +(define-public python-bioframe + (package + (name "python-bioframe") + (version "0.2.0") + ;;pypi sources does not contain requirements.txt + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/open2c/bioframe") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0w5xrb93cf3hx3d1lw48a0l1ranghpj260b05b1rpk58wwwcsqfh")))) + (build-system python-build-system) + (propagated-inputs + `(("python-click" ,python-click) + ("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) + ("python-requests" ,python-requests))) + (native-inputs + `(("python-dask" ,python-dask) ;;for unittest.loader + ("python-matplotlib" ,python-matplotlib) ;;for unittest.loader + ("python-numba" ,python-numba) ;;for unittest.loader + ("python-pypairix" ,python-pypairix) ;;for unittest.loader + ("python-pytest" ,python-pytest) + ("python-wheel" ,python-wheel))) + (home-page "https://github.com/open2c/bioframe") + (synopsis + "Framework for genomic data analysis using Pandas dataframes") + (description + "This package is a library to enable flexible and scalable operations on +genomic interval dataframes in python. @code{python-bioframe} enables access +to a rich set of dataframe operations. Working in python enables rapid +visualization (e.g. matplotlib, seaborn) and iteration of genomic analyses. +The philosophy underlying @code{python-bioframe} is to enable flexible +operations: instead of creating a function for every possible use-case, we +instead encourage users to compose functions to achieve their goals. As a +rough rule of thumb, if a function requires three steps and is crucial for +genomic interval arithmetic we have included it; conversely if it can be +performed in a single line by composing two of the core functions, we have not +included it.") + (license license:expat))) + (define-public python-biom-format (package (name "python-biom-format") -- 2.30.1 From unknown Tue Aug 19 02:59:36 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#46946] [PATCH 2/2] gnu: Add python-cooltools. Resent-From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 05 Mar 2021 14:21:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46946 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <46946@debbugs.gnu.org> Cc: rekado@elephly.net, =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Received: via spool by 46946-submit@debbugs.gnu.org id=B46946.161495402232346 (code B ref 46946); Fri, 05 Mar 2021 14:21:02 +0000 Received: (at 46946) by debbugs.gnu.org; 5 Mar 2021 14:20:22 +0000 Received: from localhost ([127.0.0.1]:33337 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lIBJW-0008Pe-0X for submit@debbugs.gnu.org; Fri, 05 Mar 2021 09:20:22 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:51215) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lIBJU-0008PN-0z for 46946@debbugs.gnu.org; Fri, 05 Mar 2021 09:20:20 -0500 Received: from localhost (localhost [127.0.0.1]) by a2062.mx.srv.dfn.de (Postfix) with ESMTP id E049BA00FB; Fri, 5 Mar 2021 15:20:13 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received:received:received; s=mdc; t= 1614954013; x=1616768414; bh=mVzSy73pohHl6zrV+tNB01c8HLLVSVol0uI e+3Gd9uo=; b=TUe51Sel2wRE2sSjLp3+UhrRp/uu+tSL4Fp8CYumZweTZxgsewb jwi8jOIYnQswI7gMIk7C6RJsAKJFyVlNW8gjuBpEqwDm5W/KlECMWFxRnLS2NRFo rmuGGZ7jzQsqlj+Ut6y1ng9Se9StCIEz5HpP1qSRqaq/JmQT1TsWBTPI= Received: from a2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-han.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id 7vE_eJM9p4CL; Fri, 5 Mar 2021 15:20:13 +0100 (CET) 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; Fri, 5 Mar 2021 15:20:13 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) 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 15.1.2176.2; Fri, 5 Mar 2021 15:20:13 +0100 From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Date: Fri, 5 Mar 2021 15:19:30 +0100 Message-ID: <20210305141930.28787-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210305141930.28787-1-madalinionel.patrascu@mdc-berlin.de> References: <20210305141930.28787-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] 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-14.0.0.3080-8.6.1012-26010.007 X-TM-AS-Result: No-10--3.117800-8.000000 X-TMASE-MatchedRID: TYP229Ekev4saaYlMvaOHAPZZctd3P4BRWl9Bl0RPNaH4I6QZJ07keR3 7ySpIkGCOOIn5zbTcyw5gHVxu2yZ5tsJuFUx3wevfOaYwP8dcX7IEQTlh1/QMcgVyTd/p+/Iksg phu0+71BiN1Woi4uYp+pGJSAHQICsyL4SsacYXAO+vuhCHYf16wsE9gx+4jJudroFpVy5w+lFS8 Sy/IDc9G4xLhk/yLgSD7OFUBidaqL4515TanER7FS0U/rncMc4GvHEXpfoEJx6wGV3uXm3apgNM iEzDc45fS0Ip2eEHnz3IzXlXlpamPoLR4+zsDTttrrTuahHzlHbQHDI1WXCIoq800SCYZKNPc8F 00n3OBIJYpLRbF14YQR0T0a3wTZcdLYxms+5aUeJ+qRT860nriFFQEBVOI2U4CC8wZh6tHpvx+y 4SCozttG1pfB9ENkTtDC+Oypvl/RGDgEFwm6aoD6Qrn3xh/cy X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.117800-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-26010.007 X-TM-SNTS-SMTP: 2D7C018D3966EBF7844CF33C1FE6744187A079E7EC07657B08508D608F8D53292000:F X-Spam-Score: -2.3 (--) 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: -3.3 (---) * gnu/packages/bioinformatics.scm (python-cooltools): New variable. --- gnu/packages/bioinformatics.scm | 45 +++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fb357b8b6c..a6ea8f831d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13652,6 +13652,51 @@ storage format, called @code{cool}, used to store genomic interaction data, such as Hi-C contact matrices.") (license license:bsd-3))) +(define-public python-cooltools +;;pypi sources requiere bioframe<0.1 while github latest version requires +;; bioframe>=0.1.0 + (let ((revision "1") + (commit "53ce4fc11d046e84ca36f3591e9e5d548de9f7b2")) + (package + (name "python-cooltools") + (version (git-version "0.3.2" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/open2c/cooltools") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0y1wf7a0by2kih2iy5xrwzdgw1i24cwigfz4352aq5npxrpjvj6q")))) + (build-system python-build-system) + (propagated-inputs + `(("python-bioframe" ,python-bioframe) + ("python-click" ,python-click) + ("python-cooler" ,python-cooler) + ("python-cytoolz" ,python-cytoolz) + ("python-joblib" ,python-joblib) + ("python-matplotlib" ,python-matplotlib) + ("python-multiprocess" ,python-multiprocess) + ("python-numba" ,python-numba) + ("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) + ("python-scikit-learn" ,python-scikit-learn) + ("python-scipy" ,python-scipy) + ("python-tables" ,python-tables))) + (native-inputs + `(("python-cython" ,python-cython))) + (home-page + "https://github.com/open2c/cooltools") + (synopsis + "Analysis tools for genomic interaction data stored in .cool format") + (description + "This package provides necessary tools for the analysis of the genomic +interaction data stored in .cool format. This collection of tools includes +operations like compartment, insulation or peak calling.") + (license license:expat)))) + (define-public python-hicmatrix (package (name "python-hicmatrix") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 23 23:25:14 2021 Received: (at control) by debbugs.gnu.org; 24 Mar 2021 03:25:14 +0000 Received: from localhost ([127.0.0.1]:33648 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lOu8w-0000XW-M1 for submit@debbugs.gnu.org; Tue, 23 Mar 2021 23:25:14 -0400 Received: from mail-wm1-f48.google.com ([209.85.128.48]:37827) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lOu8r-0000Wz-H7 for control@debbugs.gnu.org; Tue, 23 Mar 2021 23:25:10 -0400 Received: by mail-wm1-f48.google.com with SMTP id f22-20020a7bc8d60000b029010c024a1407so369201wml.2 for ; Tue, 23 Mar 2021 20:25:09 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=date:message-id:to:from:subject; bh=Bh6Iz1kdJPBpFEaD4GOalzEvogr1myaOlyUd/sXY3x4=; b=e4qxe4T6VmbBZj+84m6jbH0Lpi52ig/Wbn99yNQuQ8wOD490D6VDRCnFc63FeoNo5U /djtPmVJaovGsXAUpSJEIR9Bl9WzXwf1N7bUyMz9bMBBnrG76xs92jtLRYbivBxbJppr 9l949XWgDuk1z2uuhjgPTDvcW2UydgKBUVFw0J79q5Sc0VU8U/lroTniU1tTXKnH4V9M RsN3v7B0GAl/scIbBodpdJuG1zXmrtyYoJGRWv2d/yKgfkJFJDrs95dhDczNexMWbi3F tsXg+GwEbtCrGa98wssRi7Ypr1KnuUCs8sYqWI1AaOaEEZyLzjKZDE5THK39VtTOXMur BtMA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:date:message-id:to:from:subject; bh=Bh6Iz1kdJPBpFEaD4GOalzEvogr1myaOlyUd/sXY3x4=; b=ooKMOWuKy6tOhHxkU97uvFNdLWdjaAw756ikmbBTm2GCfhbfdpRRQwDlfdtQC4vKJU b0VpuiODU2syijjKv4FUi1enpctXMAj20TnxtktFEoYmd3qjMcCOEt2R918qR4pZITmV ne2JjlZuIQY7SkXD84mVPpkmbgLZa4I2PenxNEXmxE8+RkCuibTVH+NKluK+qdYaeTRo qXodwht3qJTDOlyWxeNI7toKheXBM03/5rSgSiMIUZ8ANIv7tDKSOmnVu9ZDw2aWowPz FKZaScvj67fwR7sJEGmzow5/mW6RpFXyTP9Xb8nZNtLbYr0vFfgRzhfarVpJ4Wz9QaYa Y6fA== X-Gm-Message-State: AOAM533zWjO6JNvweeS8aRNiYm8283gOX1TVqW9kMSBnNQjAViJphfAt rPcsS87M4YdUS5U4xk822CaaFURWhOg= X-Google-Smtp-Source: ABdhPJyZHEZujqnT825YEA9qickl58hlMhsI8YR0hB8dGfx5FPCRNNTapkGenCfKryo8FET6uLx9tA== X-Received: by 2002:a05:600c:4410:: with SMTP id u16mr768899wmn.174.1616556303673; Tue, 23 Mar 2021 20:25:03 -0700 (PDT) Received: from lili ([2a01:e0a:59b:9120:65d2:2476:f637:db1e]) by smtp.gmail.com with ESMTPSA id g16sm1079563wrs.76.2021.03.23.20.25.03 for (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 23 Mar 2021 20:25:03 -0700 (PDT) Date: Wed, 24 Mar 2021 04:16:51 +0100 Message-Id: <865z1hi6l8.fsf@gmail.com> To: control@debbugs.gnu.org From: zimoun Subject: control message for bug #46946 X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: control 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 (-) retitle 46946 Add python-bioframe, python-cooltools quit From unknown Tue Aug 19 02:59:36 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#46946] [PATCH 1/2] gnu: Add python-bioframe. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 01 Apr 2021 15:39:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46946 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Cc: 46946@debbugs.gnu.org Received: via spool by 46946-submit@debbugs.gnu.org id=B46946.161729153613713 (code B ref 46946); Thu, 01 Apr 2021 15:39:02 +0000 Received: (at 46946) by debbugs.gnu.org; 1 Apr 2021 15:38:56 +0000 Received: from localhost ([127.0.0.1]:58347 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lRzPM-0003Z7-EI for submit@debbugs.gnu.org; Thu, 01 Apr 2021 11:38:56 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21166) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lRzPK-0003Yy-Bj for 46946@debbugs.gnu.org; Thu, 01 Apr 2021 11:38:55 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1617291531; cv=none; d=zohomail.com; s=zohoarc; b=WiYeq1VBxQ7YF5gwlOdknGtuAi8Nx6M8VSQNK7LNS7Y4yGhyV0azegk/RTqhaZtMmvMfIq781GHfNhwLxb4MSQtWmP0EGiVePL4ZFVEpti4tM+i6vFj7bwlihnVaBvVM52U+74eeN/xYPeLOWiDI+NEBAJoy8k/yLH8c1Eq21k4= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1617291531; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=8auzYnffugeRchkdEFufK5UrJXXkjXca5w37+f30Gm8=; b=Oa8DjOgUDp6uIym7KIjhtyMtg0iKGHwakIBk/YeDGrD1jf3QvKV2CbZAeNjOHiv6lohMcACVzdFCjH29d+HJSwo5pqW9UwmgPf5e5jJ9GwiK3W1MIvKVVlbrMZ8W6id0ZlY/qk0mvKZZxvYAT8+gWhsjU5NPwRbKLEPVrGy7CWg= 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= header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1617291531; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:To:Cc:Subject:In-reply-to:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding; bh=8auzYnffugeRchkdEFufK5UrJXXkjXca5w37+f30Gm8=; b=cQsOmxX+Ph/WXDyzlnEW6TJhb/2uccr3j16CnItygglZDsNp0DsoMhewfwE+xuIZ 6Afg1o1zi1YAPvPZi9tcUBQ+78EbpMMmj+R/14VGnPtL7DCCM0KmiA30Uo4HuIelJH2 h/Lr41XbzGOjAii3itYpKFTtU7uvAFkWxAYDTUqQ= Received: from localhost (p54ad4e71.dip0.t-ipconnect.de [84.173.78.113]) by mx.zohomail.com with SMTPS id 1617291528542396.7149563884544; Thu, 1 Apr 2021 08:38:48 -0700 (PDT) References: <20210305141930.28787-1-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.4.15; emacs 27.2 From: Ricardo Wurmus In-reply-to: <20210305141930.28787-1-madalinionel.patrascu@mdc-berlin.de> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Thu, 01 Apr 2021 17:38:45 +0200 Message-ID: <87wntm10ca.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-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 (-) Hi M=C4=83d=C4=83lin, > * gnu/packages/bioinformatics.scm (python-bioframe): New variable. Thanks for the patch. Despite all the test inputs the test suite is not actually run: --8<---------------cut here---------------start------------->8--- starting phase `check' running "python setup.py" with command "test" and parameters () running test running egg_info writing bioframe.egg-info/PKG-INFO writing dependency_links to bioframe.egg-info/dependency_links.txt writing requirements to bioframe.egg-info/requires.txt writing top-level names to bioframe.egg-info/top_level.txt reading manifest file 'bioframe.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no previously-included files matching '__pycache__/*' found anywhe= re in distribution warning: no previously-included files matching '*.so' found anywhere in dis= tribution warning: no previously-included files matching '*.pyd' found anywhere in di= stribution warning: no previously-included files matching '*.pyc' found anywhere in di= stribution warning: no previously-included files matching '.git*' found anywhere in di= stribution warning: no previously-included files matching '.deps/*' found anywhere in = distribution warning: no previously-included files matching '.DS_Store' found anywhere i= n distribution writing manifest file 'bioframe.egg-info/SOURCES.txt' running build_ext /tmp/guix-build-python-bioframe-0.2.0.drv-0/source/bioframe/io/dask.py:47: = NumbaWarning:=20 Compilation is falling back to object mode WITH looplifting enabled because= Function "reg2bins" failed type inference due to: No conversion from list(= int64) to int32 for '$262return_value.1', defined at None File "bioframe/io/dask.py", line 79: def reg2bins(rbeg, rend): return lst ^ During: typing of assignment at /tmp/guix-build-python-bioframe-0.2.0.drv-0= /source/bioframe/io/dask.py (79) File "bioframe/io/dask.py", line 79: def reg2bins(rbeg, rend): return lst ^ @numba.jit("int32(int32, int32)") /tmp/guix-build-python-bioframe-0.2.0.drv-0/source/bioframe/io/dask.py:47: = NumbaWarning:=20 Compilation is falling back to object mode WITHOUT looplifting enabled beca= use Function "reg2bins" failed type inference due to: cannot determine Numb= a type of File "bioframe/io/dask.py", line 59: def reg2bins(rbeg, rend): k =3D 9 + (rbeg >> 23) ^ @numba.jit("int32(int32, int32)") /gnu/store/sm6k3ar46q11w77s7cc2q1hv33q8p3v0-python-numba-0.51.2/lib/python3= .8/site-packages/numba/core/object_mode_passes.py:177: NumbaWarning: Functi= on "reg2bins" was compiled in object mode without forceobj=3DTrue, but has = lifted loops. File "bioframe/io/dask.py", line 50: def reg2bins(rbeg, rend): MAX_BIN =3D ((1 << 18) - 1) // 7 ^ warnings.warn(errors.NumbaWarning(warn_msg, /gnu/store/sm6k3ar46q11w77s7cc2q1hv33q8p3v0-python-numba-0.51.2/lib/python3= .8/site-packages/numba/core/object_mode_passes.py:187: NumbaDeprecationWarn= ing:=20 Fall-back from the nopython compilation path to the object mode compilation= path has been detected, this is deprecated behaviour. For more information visit https://numba.pydata.org/numba-doc/latest/refere= nce/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-us= ing-jit File "bioframe/io/dask.py", line 50: def reg2bins(rbeg, rend): MAX_BIN =3D ((1 << 18) - 1) // 7 ^ warnings.warn(errors.NumbaDeprecationWarning(msg, ---------------------------------------------------------------------- Ran 0 tests in 0.000s OK phase `check' succeeded after 3.1 seconds --8<---------------cut here---------------end--------------->8--- I made a couple of cosmestic changes: --8<---------------cut here---------------start------------->8--- (define-public python-bioframe (package (name "python-bioframe") (version "0.2.0") ;; Sources on pypi do not contain requirements.txt (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/open2c/bioframe") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 "0w5xrb93cf3hx3d1lw48a0l1ranghpj260b05b1rpk58wwwcsqfh")))) (build-system python-build-system) (propagated-inputs `(("python-click" ,python-click) ("python-numpy" ,python-numpy) ("python-pandas" ,python-pandas) ("python-requests" ,python-requests))) (native-inputs `(("python-dask" ,python-dask) ; for tests ("python-matplotlib" ,python-matplotlib) ; for tests ("python-numba" ,python-numba) ; for tests ("python-pypairix" ,python-pypairix) ; for tests ("python-pytest" ,python-pytest) ("python-wheel" ,python-wheel))) (home-page "https://github.com/open2c/bioframe") (synopsis "Framework for genomic data analysis using Pandas dataframes") (description "This package is a library to enable flexible and scalable operations = on genomic interval dataframes in Python. @code{python-bioframe} enables acce= ss; to a rich set of dataframe operations. Working in Python enables rapid visualization (e.g. matplotlib, seaborn) and iteration of genomic analyses.= ") (license license:expat))) --8<---------------cut here---------------end--------------->8--- Please note that the lack of requirements.txt on pypi shouldn=E2=80=99t be = an obstacle to use the sources from pypi. It should build just as well. --=20 Ricardo From unknown Tue Aug 19 02:59:36 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#46946] [ext] Re: [PATCH 1/2] gnu: Add python-bioframe. 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References: In-Reply-To: Resent-From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 14 Oct 2022 22:53:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46946 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <46946@debbugs.gnu.org> Received: via spool by 46946-submit@debbugs.gnu.org id=B46946.166578796218946 (code B ref 46946); Fri, 14 Oct 2022 22:53:02 +0000 Received: (at 46946) by debbugs.gnu.org; 14 Oct 2022 22:52:42 +0000 Received: from localhost ([127.0.0.1]:38949 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ojTXm-0004vV-Dc for submit@debbugs.gnu.org; Fri, 14 Oct 2022 18:52:42 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:34745) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ojTXk-0004vE-6Q for 46946@debbugs.gnu.org; Fri, 14 Oct 2022 18:52:40 -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=1665787949; x=1667602350; bh=VNubwo+Xvi9VUxz INocRedig5uaS5+54LZi/cuX+Xjg=; b=oH6hp+xPlvgWshspzwEtQQek3OpovZy Qj/Gx/ztTr+DItg8MRJSePZO817OKvZocw6ktgA5xg+Dzkn80vMxmAtEb/lfiqps uuIpMniVmY+cUtz2uHqc/cb5+QtvyTdavlQ1QxQ6Or0iCU/YpJzmi+vR6MYwjVIz HXSsjootgnpA= 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 98E30160380 for <46946@debbugs.gnu.org>; Sat, 15 Oct 2022 00:52:29 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) 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 15.1.2507.12; Sat, 15 Oct 2022 00:52:28 +0200 From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Date: Sat, 15 Oct 2022 00:52:17 +0200 Message-ID: <20221014225218.13626-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.37.3 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] 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-14.0.0.3092-9.0.1002-27202.003 X-TM-AS-Result: No-10--2.388200-5.000000 X-TMASE-MatchedRID: huMMtcahIlCaVzGETDUtnAgqYHjJNWHeKQNhMboqZlrAuQ0xDMaXkH4q tYI9sRE/jqQ82yy1I7Tbx4dhxASC6J5l5tqvE/eVa87CDXaKRVIxVUWGXs3C8ydEcnIP1FQIOki GGidO7I/ZyfBL0WvJF7edLpfvchkD9bPHgjnnomBIK2DGByysyl7OZ6hrwwnz/gMNehoKqTvtJx 2nLZkrAtTGCputosAbzpa5NzPyAzx9CsAh4VAyKc3WPbtc5QfmBPY4SegK3jwDBQ+XBh4YJfzxf g6IZlFlX/YMDN55TesSU447Pck+mKPFjJEFr+olwXCBO/GKkVr3FLeZXNZS4DXnYt5w4ccjgHXF 9sw5Dnqy84sUa/Axm81gddartF+2hgYnLsv5sqGlRrAhf46dQKRBf4r1DclnVh09B9JWceM9kGB keUdHfKegIxa0HvgjjztWiTRPtkUKGB9MbH1S7rTnVnv1JP77sGTvZJmllrz/PhPL0kApH8kjm+ elEcbI X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.388200-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27202.003 X-TM-SNTS-SMTP: 0D36357AE3EF053C29DC01A66A6BD6BEF018BA011D27D47D322CCBD87A8D6CA42002:F X-Spam-Score: -2.3 (--) 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: -3.3 (---) X-Debbugs-Cc: rekado@elephly.net * gnu/packages/bioinformatics.scm (python-bioframe): New variable. --- gnu/packages/bioinformatics.scm | 46 +++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f2de09aa32..1478ba0c46 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -946,6 +946,52 @@ (define (cythonized? c/c++-file) ;; licensed lgpl2.1+ (license (list license:expat license:lgpl2.1+)))) +(define-public python-bioframe + (package + (name "python-bioframe") + (version "0.3.3") + (source + (origin + (method git-fetch) + ;; pypi version does not contain tests and requirements.txt + (uri (git-reference + (url "https://github.com/open2c/bioframe") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "14lvb18d4npapyi6j2zqh9q94l658dzmka5riiizw1h0zb0kp9xb")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (setenv "MPLCONFIGDIR" "/tmp") + (when tests? + (invoke "pytest" "-v"))))))) + (native-inputs + (list python-biopython + python-pysam + python-pytest + python-wheel)) + (propagated-inputs + (list python-matplotlib + python-numpy + python-pandas + python-requests)) + (home-page "https://github.com/open2c/bioframe") + (synopsis "Pandas utilities for tab-delimited and other genomic files") + (description + "This package is a library to enable flexible and scalable operations on +genomic interval dataframes in @code{python}. @code{python-bioframe} enables +access to a rich set of dataframe operations. Working in @code{python} enables +rapid visualization (e.g. @code{matplotlib}, @code{seaborn}) and iteration of +genomic analyses. The philosophy underlying @code{python-bioframe} is to enable +flexible operations. Instead of creating a function for every possible use-case, +we encourage users to compose functions to achieve their goals.") + (license license:expat))) + (define-public python-biom-format (package (name "python-biom-format") base-commit: 10d429f2fce321d8285684503094694ec3979865 -- 2.37.3 From unknown Tue Aug 19 02:59:36 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#46946] [PATCH 2/2] gnu: Add python-cooltools. Resent-From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 14 Oct 2022 22:53:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 46946 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <46946@debbugs.gnu.org> Received: via spool by 46946-submit@debbugs.gnu.org id=B46946.166578796618960 (code B ref 46946); Fri, 14 Oct 2022 22:53:02 +0000 Received: (at 46946) by debbugs.gnu.org; 14 Oct 2022 22:52:46 +0000 Received: from localhost ([127.0.0.1]:38952 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ojTXp-0004vk-Qv for submit@debbugs.gnu.org; Fri, 14 Oct 2022 18:52:46 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:37813) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ojTXn-0004vL-Sx for 46946@debbugs.gnu.org; Fri, 14 Oct 2022 18:52:44 -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 :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received; s=mdc; t=1665787954; x=1667602355; bh=wX7DPjmBxpmrDG5INvusUAsBUceM5Wb6qoaBMqf07tM=; b=kVib4pJzFKbJ WwVAYMPcWmMgCMhs9/0AIrNPj7Pojcq+PQqH53PhodtSLiQzL0D/13gpIOzFUfGX nlzBH0EF8+KGoy7K9kYVz1fM8kIMmGevU+yX9NDXREHwdDZzeMHuLn+ag1BO0k9n jWrBqon4vIWx2nfa1dx1qvXzgsjdj/c= 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 1036816039C for <46946@debbugs.gnu.org>; Sat, 15 Oct 2022 00:52:34 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) 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 15.1.2507.12; Sat, 15 Oct 2022 00:52:28 +0200 From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Date: Sat, 15 Oct 2022 00:52:18 +0200 Message-ID: <20221014225218.13626-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.37.3 In-Reply-To: <20221014225218.13626-1-madalinionel.patrascu@mdc-berlin.de> References: <20221014225218.13626-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Content-Type: text/plain X-Originating-IP: [141.80.113.106] 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-14.0.0.3092-9.0.1002-27202.003 X-TM-AS-Result: No-10--3.679100-5.000000 X-TMASE-MatchedRID: NGDYxnKYxb2aVzGETDUtnAgqYHjJNWHeKQNhMboqZlrAuQ0xDMaXkH4q tYI9sRE/4K9FmervsqXuNT8xdcEnQwE+dA3RWUSvutvHF25zoU9hXC3lnHCTmdW0pkpPR1DaOXf Z9OHyzWabOWTHQMIg6+Qw/NrlqdZPO5k/PxBAvv6+vuhCHYf16675nIWq13kVQlnkwN3j+RSETM jf6aTOJ8/NOC9mefryF/q6px2NM/mhznSgFQVXH6ubsOtSWY2QgDLqnrRlXrZ8nn9tnqel2MprJ P8FBOIaJIVnHAEf5ZGsT8k1Ey2W3geiuHcJRjyZ+LZxR9gx6EFcZ97q3zV+t4vS025qqeCRs2fA TIQH5n3yLHvZd0qf3Pfo+7Q5y5vLu9e6mwL34S+051Z79ST++7Bk72SZpZa8/z4Ty9JAKR/JI5v npRHGyA== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.679100-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-27202.003 X-TM-SNTS-SMTP: 2881F355960ABEBE15BD112E3518B3697809FD88AD62AF31DF0A0729295FD2642002:F X-Spam-Score: -2.3 (--) 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: -3.3 (---) X-Debbugs-Cc: rekado@elephly.net * gnu/packages/bioinformatics.scm (python-cooltools): New variable. --- gnu/packages/bioinformatics.scm | 45 +++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1478ba0c46..6f228fb907 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12977,6 +12977,51 @@ (define-public python-cooler such as Hi-C contact matrices.") (license license:bsd-3))) +(define-public python-cooltools + (package + (name "python-cooltools") + (version "0.5.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "cooltools" version)) + (sha256 + (base32 + "08hyzd3kazr87nvv6rwp5i1g9rwj7jmrly925lqnvippz4wp7k4g")))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (setenv "MPLCONFIGDIR" "/tmp") + (when tests? + (invoke "pytest" "-v"))))))) + (native-inputs + (list python-cython + python-pytest)) + (propagated-inputs + (list python-bioframe + python-click + python-cooler + python-joblib + python-matplotlib + python-multiprocess + python-numba + python-numpy + python-pandas + python-scikit-image + python-scikit-learn + python-scipy)) + (home-page "https://github.com/open2c/cooltools") + (synopsis + "Analysis tools for genomic interaction data stored in .cool format") + (description + "This package provides necessary tools for the analysis of the genomic +interaction data stored in @code{.cool} format. This collection of tools includes +operations like compartment, insulation or peak calling.") + (license license:expat))) + (define-public python-hicmatrix (package (name "python-hicmatrix") -- 2.37.3 From unknown Tue Aug 19 02:59:36 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Subject: bug#46946: closed (Add python-bioframe, python-cooltools) Message-ID: References: <877d0a6fsz.fsf@elephly.net> X-Gnu-PR-Message: they-closed 46946 X-Gnu-PR-Package: guix-patches Reply-To: 46946@debbugs.gnu.org Date: Fri, 04 Nov 2022 12:55:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1667566502-29926-1" This is a multi-part message in MIME format... ------------=_1667566502-29926-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #46946: Add python-bioframe, python-cooltools which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 46946@debbugs.gnu.org. --=20 46946: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D46946 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1667566502-29926-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 46946-done) by debbugs.gnu.org; 4 Nov 2022 12:54:31 +0000 Received: from localhost ([127.0.0.1]:52039 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oqwDP-0007lq-DP for submit@debbugs.gnu.org; Fri, 04 Nov 2022 08:54:31 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21198) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oqwDL-0007lf-L1 for 46946-done@debbugs.gnu.org; Fri, 04 Nov 2022 08:54:30 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1667566464; cv=none; d=zohomail.com; s=zohoarc; b=Z94TqJY1HOIdieEb4ceJDS4hDGyfeNTxuIJj+d/hO+dUkx2uO6IbX/B1yaw6Rl+luJgmzViypucn288P/8zEH6cHKGpeexWJQLbHcx/xIsQZ2BKc+ZflwI7FfzscJ7YZEE2pws8MEhMHKHv7QEqF1xIb++Y7MFYVO9g/0xDBRfo= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1667566464; h=Content-Type:Date:From:MIME-Version:Message-ID:Subject:To; bh=q27c5/kk2iPwOVW6IGy5+OHmqFmL9q4j9LTan3+IG7A=; b=UVrmztt1iAzHtoV/Km+zrsjsTV+l1RPfKpn3K+oWPkl/k+DFeD0QtWGyAUQygOkg+fLaEPQUn/oQSAuwND490p+drZc5bbbX8Wk16nIqov+LrwHtmGVMq0sBdvK8iA569v0O2vUe98PsL9CbxbPJVp40mSepgdAhB7uowAvd7O0= 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=1667566464; 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=q27c5/kk2iPwOVW6IGy5+OHmqFmL9q4j9LTan3+IG7A=; b=aaZ+g0+BXQXObs1mT03Aw/EzpVP3iqXl8vn/StYd6yy4TXrQQUbbpPv987daqTk8 lIfgk7HiBlL4VuK2/9uNaU2GD6dUZjvdXdrZatdEOhC9mB5unVMigADqMjQ3MXOiKGc fCg972kwyuUaq7xbhuU1Y7xXBedFtuQ/kGMpRu5c= Received: from localhost (34-111-142-46.pool.kielnet.net [46.142.111.34]) by mx.zohomail.com with SMTPS id 1667566463733460.6787565668078; Fri, 4 Nov 2022 05:54:23 -0700 (PDT) User-agent: mu4e 1.8.9; emacs 28.1 From: Ricardo Wurmus To: 46946-done@debbugs.gnu.org Subject: Add python-bioframe, python-cooltools Date: Fri, 04 Nov 2022 13:53:54 +0100 X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <877d0a6fsz.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 46946-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 (-) Applied with indentation changes. Thanks! -- Ricardo ------------=_1667566502-29926-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 5 Mar 2021 13:50:36 +0000 Received: from localhost ([127.0.0.1]:33290 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lIAqi-0007cd-2d for submit@debbugs.gnu.org; Fri, 05 Mar 2021 08:50:36 -0500 Received: from lists.gnu.org ([209.51.188.17]:40520) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lIAqg-0007cW-RU for submit@debbugs.gnu.org; Fri, 05 Mar 2021 08:50:35 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:36836) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lIAqg-0006k6-Iw for guix-patches@gnu.org; Fri, 05 Mar 2021 08:50:34 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:45239) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lIAqe-0004xY-9c for guix-patches@gnu.org; Fri, 05 Mar 2021 08:50:34 -0500 Received: from localhost (localhost [127.0.0.1]) by c2062.mx.srv.dfn.de (Postfix) with ESMTP id 7A0C0300157 for ; Fri, 5 Mar 2021 14:50:28 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-language:content-transfer-encoding:content-type :content-type:mime-version:user-agent:date:date:message-id:from :from:received:received:received; s=mdc; t=1614952228; x= 1616766629; bh=frcCV1k9oG9oKj3dpUqdJg1PxRT2RSN/XKdLCPjaYaY=; b=N oBG+Q5iJmQUMgr2eBbgWIn4Y6KSGddxr/4Zp1DKD5fD33+vQASAZlQheNj7y6l8M fbqLz6inkxvXGYnDSxQtAR7+uDiFky7koY3UEBCaDr4kBPSLiBa3L7dokGQn2Mhc YfdMJWKIyupMlB6MRtC67uXq5ibbcNxHDExNFFz1w8= Received: from c2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-erl.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id jmAz1n-nTRjL for ; Fri, 5 Mar 2021 14:50:28 +0100 (CET) Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS for ; Fri, 5 Mar 2021 14:50:28 +0100 (CET) Received: from [192.168.1.220] (31.18.50.167) 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 15.1.2176.2; Fri, 5 Mar 2021 14:50:27 +0100 To: From: =?UTF-8?B?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= Message-ID: Date: Fri, 5 Mar 2021 14:50:27 +0100 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:68.0) Gecko/20100101 Thunderbird/68.10.0 MIME-Version: 1.0 Content-Type: text/plain; charset="utf-8"; format=flowed Content-Transfer-Encoding: 7bit Content-Language: en-US X-Originating-IP: [31.18.50.167] 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-14.0.0.3080-8.6.1012-26010.007 X-TM-AS-Result: No-10-2.373600-8.000000 X-TMASE-MatchedRID: zNHEZVbO6+CYN/UYLI7XqOLzNWBegCW2RYvisGWbbS/ITICTZKCMNexJ beH3K4ldgPn1rCdWbriK1w/mwA00Qd0H8LFZNFG73Yq8RVaZivV4OXlDu6jxLpvOJThWZQ3kbSv Uj/BK7J9DE2SiozhChZlMspqOq0CS X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-2.373600-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-26010.007 X-TM-SNTS-SMTP: 16C799DA591B8594B6728BA7D0CBB66FD88536C1527B93CFC41F821FB61AC6B32000:F Received-SPF: pass client-ip=194.95.238.172; envelope-from=MadalinIonel.Patrascu@mdc-berlin.de; helo=c2062.mx.srv.dfn.de X-Spam_score_int: 13 X-Spam_score: 1.3 X-Spam_bar: + X-Spam_report: (1.3 / 5.0 requ) BAYES_00=-1.9, BODY_EMPTY=0.22, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, EMPTY_MESSAGE=2.32, MISSING_SUBJECT=1.799, PYZOR_CHECK=1.392, RCVD_IN_DNSWL_MED=-2.3, RCVD_IN_MSPIKE_H4=0.001, RCVD_IN_MSPIKE_WL=0.001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=no autolearn_force=no X-Spam_action: no action X-Spam-Score: 3.2 (+++) X-Spam-Report: Spam detection software, running on the system "debbugs.gnu.org", has NOT identified this incoming email as spam. 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Content preview: Content analysis details: (3.2 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- -2.3 RCVD_IN_DNSWL_MED RBL: Sender listed at https://www.dnswl.org/, medium trust [209.51.188.17 listed in list.dnswl.org] 0.0 RCVD_IN_MSPIKE_H3 RBL: Good reputation (+3) [209.51.188.17 listed in wl.mailspike.net] -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=madalinionel.patrascu%40mdc-berlin.de; ip=209.51.188.17; r=debbugs.gnu.org] 2.3 EMPTY_MESSAGE Message appears to have no textual parts and no Subject: text 0.0 RCVD_IN_MSPIKE_WL Mailspike good senders 1.8 MISSING_SUBJECT Missing Subject: header 0.2 NO_SUBJECT Extra score for no subject 0.2 BODY_EMPTY No body text in message X-Debbugs-Envelope-To: submit 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: 2.2 (++) 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: Content analysis details: (2.2 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- -2.3 RCVD_IN_DNSWL_MED RBL: Sender listed at https://www.dnswl.org/, medium trust [209.51.188.17 listed in list.dnswl.org] 0.0 RCVD_IN_MSPIKE_H3 RBL: Good reputation (+3) [209.51.188.17 listed in wl.mailspike.net] -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=madalinionel.patrascu%40mdc-berlin.de;ip=209.51.188.17;r=debbugs.gnu.org] 2.3 EMPTY_MESSAGE Message appears to have no textual parts and no Subject: text 0.0 RCVD_IN_MSPIKE_WL Mailspike good senders 1.8 MISSING_SUBJECT Missing Subject: header 0.2 NO_SUBJECT Extra score for no subject -1.0 MAILING_LIST_MULTI Multiple indicators imply a widely-seen list manager 0.2 BODY_EMPTY No body text in message ------------=_1667566502-29926-1--