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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 debbugs-submit-bounces@debbugs.gnu.org Fri Mar 05 19:57:40 2021 Received: (at 46955) by debbugs.gnu.org; 6 Mar 2021 00:57:40 +0000 Received: from localhost ([127.0.0.1]:35740 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lILGA-0001Ze-8p for submit@debbugs.gnu.org; Fri, 05 Mar 2021 19:57:40 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:34603) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lILG5-0001ZN-Fv for 46955@debbugs.gnu.org; Fri, 05 Mar 2021 19:57:33 -0500 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id 1488F16012B; Sat, 6 Mar 2021 01:57:23 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1614992242; x=1616806643; bh=tulqpNiVy4P5FQDA4wI7NaUj7QfgFIQVzLR5oYvja6o=; b=h2/lgetSpXLE y8KdVea6t/dbskPKh/L+/oISWNmmyME9etV7aiInNNwjTGSE1cFA45duhdq7Dd1Q 4JtMcPWvx+5VS5l5vlHhXyytScNnUnjZeLp82wLZSJL9km41R/u7MhNuowszrtx1 1UN9lUUsjQX61uEsgqpNl+Pi8bwdAvQ= Received: from b2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-tub.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id RtFq4BUYj4dC; Sat, 6 Mar 2021 01:57:22 +0100 (CET) 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; Sat, 6 Mar 2021 01:57:22 +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; Sat, 6 Mar 2021 01:57:22 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <46955@debbugs.gnu.org> Subject: [PATCH 1/2] gnu: Add python-sparse. Date: Sat, 6 Mar 2021 01:57:02 +0100 Message-ID: <20210306005703.25479-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.30.1 MIME-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit X-Originating-IP: [141.80.113.106] 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-14.0.0.3080-8.6.1012-26012.003 X-TM-AS-Result: No-10--3.042000-8.000000 X-TMASE-MatchedRID: gnUNXwFR0uP/R1NSMc2qCXycvC6I0dJIS1zwNuiBtITfUZT83lbkEJwl bZPQQ0yzb1TGnuLRfUkctkosP3yazCq+GZ9ZHxIhUYXhMajr0x53G1bsm5zfjMZygq/CPmrol8w sFD5lRSvmsKqMEsXxJy2+lyx46iL0+5T6zKmlZhdV1zhVw8duYkPIlAqA4/DEvAe75exuTNFErs sMQdxI5OdccNzwjJTWNx3sWO1UiHFnDmHdcAECAMn9tWHiLD2GW1eClGWYNyjnCThanP/ghGJlH 05V7NzjkysQhBKB3lqXwGaqxb4UjqMOL4ljfmzc9FQh3flUIh4Q5L9qu3flQ5cFdomgH0lngxsf zkNRlfLdB/CxWTRRu3aDLLDbFMGF/tsmPRGXdaiD+EnTB7mS6eikSSNrgo8AgJ8EP/L19sL0xVt oJb5gks/YiEgTarFDgTu0lGnM4Bj+Bp7E1Bftcrvpvs9iIwUk1+xhfuuIbsi45jSrrr4GpqGCNX qyLhLFvoNkWY9hSsutAp7vUZi6bw== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.042000-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-26012.003 X-TM-SNTS-SMTP: 53C155232D36112CF637479049976B7F6D97BD6823FF8BA1EEE9700E04BF6E442000:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 46955 Cc: rekado@elephly.net, =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= 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 (-) * gnu/packages/python-xyz.scm (python-sparse): New variable. --- gnu/packages/python-xyz.scm | 41 ++++++++++++++++++++++++++++++++++++- 1 file changed, 40 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index fbc9ad688d..b5274c39a9 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -67,7 +67,7 @@ ;;; Copyright © 2019, 2020 Giacomo Leidi ;;; Copyright © 2019 Wiktor Żelazny ;;; Copyright © 2019, 2020 Tanguy Le Carrour -;;; Copyright © 2019 Mădălin Ionel Patrașcu +;;; Copyright © 2019, 2021 Mădălin Ionel Patrașcu ;;; Copyright © 2020 Riku Viitanen ;;; Copyright © 2020 Jakub Kądziołka ;;; Copyright © 2020 sirgazil @@ -4719,6 +4719,45 @@ objects.") (define-public python2-colormath (package-with-python2 python-colormath)) +(define-public python-sparse + (package + (name "python-sparse") + (version "0.11.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "sparse" version)) + (sha256 + (base32 + "0kw6ha83gk0dymayrxhh16xxk7aykiyiz3ksxdzj6hhjr3dkap5w")))) + (build-system python-build-system) + (propagated-inputs + `(("python-numba" ,python-numba) + ("python-numpy" ,python-numpy) + ("python-scipy" ,python-scipy))) + (native-inputs + `(("python-dask" ,python-dask) + ("python-pytest" ,python-pytest) + ("python-pytest-black" ,python-pytest-black) + ("python-pytest-cov" ,python-pytest-cov))) + (home-page "https://github.com/pydata/sparse/") + (synopsis "Library for multi-dimensional sparse arrays") + (description + "This package implements sparse arrays of arbitrary dimension on top of +@code{numpy} and @code{scipy.sparse}. Sparse array is a matrix in which most +of the elements are zero. @code{python-sparse} generalizes the +@code{scipy.sparse.coo_matrix} and @code{scipy.sparse.dok_matrix} layouts, but +extends beyond just rows and columns to an arbitrary number of dimensions. +Additionally, this project maintains compatibility with the +@code{numpy.ndarray} interface rather than the @code{numpy.matrix} interface +used in @code{scipy.sparse}. These differences make this project useful in +certain situations where @code{scipy.sparse} matrices are not well suited, but +it should not be considered a full replacement. It lacks layouts that are not +easily generalized like @dfn{compressed sparse row/column}(CSR/CSC) and +depends on @code{scipy.sparse} for some computations.") + ;;https://github.com/pydata/sparse/blob/master/LICENSE + (license license:bsd-3))) + (define-public python-spectra (package (name "python-spectra") -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Fri Mar 05 19:57:40 2021 Received: (at 46955) by debbugs.gnu.org; 6 Mar 2021 00:57:40 +0000 Received: from localhost ([127.0.0.1]:35743 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lILGG-0001Zr-Gi for submit@debbugs.gnu.org; Fri, 05 Mar 2021 19:57:40 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:51133) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lILGE-0001ZX-Cv for 46955@debbugs.gnu.org; Fri, 05 Mar 2021 19:57:39 -0500 Received: from localhost (localhost [127.0.0.1]) by c2062.mx.srv.dfn.de (Postfix) with ESMTP id 0CCD2300119; Sat, 6 Mar 2021 01:57:32 +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= 1614992251; x=1616806652; bh=hDB9R2F95y0mv2J2r96bJzlFd06PhbuiU5P figQ3B70=; b=Ai21/ZrZ7pG361k+9np/7+VeLMait5og+JIDRCEs4Yh7qC5Jh71 bIzEdms+VSx69T+evjR39kBxfM1jFrbAzXJ3GEEEdb81BaiitHA4joLtd5P4iPcv yIEeKwNqu2450Qf9ieRL2O16jXoRU4JOL3SM1AZdy6vPuWatApNbJfYM= 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 nLQ27qW1Vkqr; Sat, 6 Mar 2021 01:57:31 +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; Sat, 6 Mar 2021 01:57:31 +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; Sat, 6 Mar 2021 01:57:31 +0100 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <46955@debbugs.gnu.org> Subject: [PATCH 2/2] gnu: python-cooler: Update to 0.8.10. Date: Sat, 6 Mar 2021 01:57:03 +0100 Message-ID: <20210306005703.25479-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.30.1 In-Reply-To: <20210306005703.25479-1-madalinionel.patrascu@mdc-berlin.de> References: <20210306005703.25479-1-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-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-14.0.0.3080-8.6.1012-26012.003 X-TM-AS-Result: No-10--1.901600-8.000000 X-TMASE-MatchedRID: IajoWEPWtmK6/eEqqZaZmj8Ckw9b/GFeTJDl9FKHbrn7fZJfDdCIXISC l3uvYUiSC6+Zjvylmgt6n3hIvN5dLetbninbl/qrvr7oQh2H9etKhpFNiC3g3hHfiujuTbedu95 6BjcJKyQZDJ72K11ChJNb5HQLbebH7Tqch0zEtNGL6q5RsNhv5PLfqX4QTDm8xaBBt5x+Tc6YDT IhMw3OOX0tCKdnhB589yM15V5aWpj6C0ePs7A07ba607moR85R7if6eFicpJ+/L/l0xOrOcSPbi /Gx1mOfBm/2yD38/KaEQxghebWIdCJm20qIrbV/czCm0bU8FunF7/pJf0EW2mswzhJnyVc0b8fs uEgqM7bRtaXwfRDZE7Qwvjsqb5f0Rg4BBcJumqA+kK598Yf3Mg== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.901600-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-26012.003 X-TM-SNTS-SMTP: 17748E8121FA99A6118D2D72552E4E3E06BF5E29D72A3B461C050DD834DB8A102000:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 46955 Cc: rekado@elephly.net, =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= 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-cooler): Update to 0.8.10/ --- gnu/packages/bioinformatics.scm | 21 ++++++++++++--------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6d21e14360..bc31d50e54 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13636,35 +13636,38 @@ fasta subsequences.") (define-public python-cooler (package (name "python-cooler") - (version "0.8.7") + (version "0.8.10") (source (origin (method url-fetch) (uri (pypi-uri "cooler" version)) (sha256 (base32 - "01g6gqix9ba27sappz6nfyiwabzrlf8i5fn8kwcz8ra356cq9crp")))) + "1hi9anwz8b9p9wigzc5hypnwm6a4ikvlv69ixy3ki8939ngb1sj3")))) (build-system python-build-system) (propagated-inputs `(("python-asciitree" ,python-asciitree) - ("python-biopython" ,python-biopython) ("python-click" ,python-click) ("python-cytoolz" ,python-cytoolz) - ("python-dask" ,python-dask) ("python-h5py" ,python-h5py) ("python-multiprocess" ,python-multiprocess) ("python-numpy" ,python-numpy) ("python-pandas" ,python-pandas) ("python-pyfaidx" ,python-pyfaidx) ("python-pypairix" ,python-pypairix) - ("python-pysam" ,python-pysam) ("python-pyyaml" ,python-pyyaml) ("python-scipy" ,python-scipy) - ("python-simplejson" ,python-simplejson))) + ("python-simplejson" ,python-simplejson) + ("python-six" ,python-six))) (native-inputs - `(("python-mock" ,python-mock) - ("python-pytest" ,python-pytest))) - (home-page "https://github.com/mirnylab/cooler") + `(("python-codecov" ,python-codecov) + ("python-dask" ,python-dask) ;;unittest.runner.TextTestResult + ("python-mock" ,python-mock) + ("python-pytest" ,python-pytest) + ("python-pytest-cov" ,python-pytest-cov) + ("python-pytest-flake8" ,python-pytest-flake8) + ("python-sparse" ,python-sparse))) ;;unittest.runner.TextTestResult + (home-page "https://github.com/open2c/cooler") (synopsis "Sparse binary format for genomic interaction matrices") (description "Cooler is a support library for a sparse, compressed, binary persistent -- 2.30.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 23 23:25:11 2021 Received: (at control) by debbugs.gnu.org; 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Tue, 23 Mar 2021 20:25:02 -0700 (PDT) Date: Wed, 24 Mar 2021 04:15:24 +0100 Message-Id: <867dlxi6nn.fsf@gmail.com> To: control@debbugs.gnu.org From: zimoun Subject: control message for bug #46955 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 46955 Add python-sparse, Update python-cooler quit From debbugs-submit-bounces@debbugs.gnu.org Thu Apr 01 11:08:07 2021 Received: (at 46955) by debbugs.gnu.org; 1 Apr 2021 15:08:07 +0000 Received: from localhost ([127.0.0.1]:58277 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lRyvX-0002kA-64 for submit@debbugs.gnu.org; Thu, 01 Apr 2021 11:08:07 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21146) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lRyvU-0002k1-Mk for 46955@debbugs.gnu.org; Thu, 01 Apr 2021 11:08:05 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1617289681; cv=none; d=zohomail.com; s=zohoarc; b=Whf85bmhhMliqwsGnfl59sU6uBm7jJs12HoDmblcdKKnVehYs0d/1PV9FU61/+oNyfbd/f7MFPoIt+l9Q20OOd01EY6HM3y0j/jNERKIjJiuX20yEDrQm2Fv0sWBCewJHb7nJXeFxEZ4nTsLS1aOwZmVAQiQHkP9Or7qRcSivNE= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1617289681; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=A2Sotdfwn+hO6ZYiEo57QSrX3MMYW7xXaDKxhATESaI=; b=WrGPRk19+PemVe4bEeDR0fMxalM6b6ov77vVSRfN8L9dUq0CzFHO+PN1aET0Gwnjaiu5mPh+08lH/D5L+lRzkA8GwKd2dfAlX4Ka0d3KKfeAUttYIqhcAcfzboZtd7TrFc3f+8L2gp53yIQ3TzlDrCFPmNCTzyGJMh72+hZn570= 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=1617289681; 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=A2Sotdfwn+hO6ZYiEo57QSrX3MMYW7xXaDKxhATESaI=; b=KPNV4ezrA/dLNo3fvFbfdJet1HBF1kvc0V65mUG8MKgSURm3Kfkwc719MCKzfbbM SsetoaylPidRmo0BoMbWVO2MEijVlaAEOmO2SITkEl5caUt8e79+UOqH6WOVsyY8ySZ f0CAd8Lm1Rs9tQPEm0gnyMhbErVAppidZQ7dErPs= Received: from localhost (p54ad4e71.dip0.t-ipconnect.de [84.173.78.113]) by mx.zohomail.com with SMTPS id 1617289677216195.69439609378776; Thu, 1 Apr 2021 08:07:57 -0700 (PDT) References: <20210306005703.25479-1-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.4.15; emacs 27.2 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [PATCH 1/2] gnu: Add python-sparse. In-reply-to: <20210306005703.25479-1-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 17:07:54 +0200 Message-ID: <878s622gc5.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: 46955 Cc: 46955@debbugs.gnu.org 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/python-xyz.scm (python-sparse): New variable. Thanks for the patch! > + (native-inputs > + `(("python-dask" ,python-dask) > + ("python-pytest" ,python-pytest) > + ("python-pytest-black" ,python-pytest-black) > + ("python-pytest-cov" ,python-pytest-cov))) In spite of the addition of all these test inputs the test suite is not run: --8<---------------cut here---------------start------------->8--- starting phase `check' running "python setup.py" with command "test" and parameters () ['numpy', 'scipy>=3D0.19', 'numba>=3D0.49'] ['numpy', 'scipy>=3D0.19', 'numba>=3D0.49'] running test running egg_info writing sparse.egg-info/PKG-INFO writing dependency_links to sparse.egg-info/dependency_links.txt writing entry points to sparse.egg-info/entry_points.txt writing requirements to sparse.egg-info/requires.txt writing top-level names to sparse.egg-info/top_level.txt reading manifest file 'sparse.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.html' under directory 'sparse' no previously-included directories found matching 'docs/_build' writing manifest file 'sparse.egg-info/SOURCES.txt' running build_ext ---------------------------------------------------------------------- Ran 0 tests in 0.000s OK phase `check' succeeded after 1.5 seconds --8<---------------cut here---------------end--------------->8--- Could you please take a look at this? > + ;;https://github.com/pydata/sparse/blob/master/LICENSE > + (license license:bsd-3))) No need to include this comment. --=20 Ricardo From debbugs-submit-bounces@debbugs.gnu.org Thu Apr 01 11:09:11 2021 Received: (at 46955) by debbugs.gnu.org; 1 Apr 2021 15:09:11 +0000 Received: from localhost ([127.0.0.1]:58281 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lRywZ-0002lt-HG for submit@debbugs.gnu.org; Thu, 01 Apr 2021 11:09:11 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21162) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lRywW-0002lk-V8 for 46955@debbugs.gnu.org; Thu, 01 Apr 2021 11:09:10 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1617289747; cv=none; d=zohomail.com; s=zohoarc; b=BqubsKGh2UblY7Gtf9htlvcihPP6C0uiN7IKc4zmCcqUVAYDECa+2C+k3R9inqx1oqWh7qlXFRrQxao6OrlnNnlZUThS1TalzBS+wnGO424qldy+duMVrz9nQ5sEMEztA53XsrwqRzDKNGFcE07pjdj7l3x+TGOwgI7kNZpwr70= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1617289747; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=81hm5cqeXCxEm8OT7awj8DpKWoUQR8JwmBGSqhN7nlo=; b=DzMprsfF0Xi57bj0O530U6ZL7X2SSt+SYny04Gl01nrsl4/ZVULJkFAUjlVpDqPug5PUVX8+UTgbi9+tdWxBdNqcJ8dd1+vw98qX2NwXMreClz0p2CvQi0kck1P0uGBPoa1sJQZ4JCMeplGO7sPuQu+QBQjt4Zx49EjSNxxZkiM= 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=1617289747; 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=81hm5cqeXCxEm8OT7awj8DpKWoUQR8JwmBGSqhN7nlo=; b=iuF/qtTwGvp7HejnC8ZTHOv5+KeR69uwyfBOObu5qpQmRog8Az0Ir1qLKvX57COO /1ildSZIXhqNczqPNp6hQf5kT1nW9mMohlhJOzvYwDUfCwtDeGaaVOOMXosodCM9kt7 6Omj68ujskW1XkrSXJa5RetwC25RI1ZMz4+NrdOs= Received: from localhost (p54ad4e71.dip0.t-ipconnect.de [84.173.78.113]) by mx.zohomail.com with SMTPS id 1617289745185833.4033899770134; Thu, 1 Apr 2021 08:09:05 -0700 (PDT) References: <20210306005703.25479-1-madalinionel.patrascu@mdc-berlin.de> <20210306005703.25479-2-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.4.15; emacs 27.2 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [PATCH 2/2] gnu: python-cooler: Update to 0.8.10. In-reply-to: <20210306005703.25479-2-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 17:09:02 +0200 Message-ID: <875z162ga9.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: 46955 Cc: 46955@debbugs.gnu.org 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 (-) M=C4=83d=C4=83lin Ionel Patra=C8=99cu = writes: > * gnu/packages/bioinformatics.scm (python-cooler): Update to 0.8.10/ There=E2=80=99s a typo (=E2=80=9C/=E2=80=9D instead of =E2=80=9C.=E2=80=9D)= and the changes to the propagated-inputs, native-inputs, and home-page fields are not listed. Could you please add them to the commit message? Thanks! --=20 Ricardo From debbugs-submit-bounces@debbugs.gnu.org Thu Apr 01 11:10:40 2021 Received: (at 46955) by debbugs.gnu.org; 1 Apr 2021 15:10:40 +0000 Received: from localhost ([127.0.0.1]:58285 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lRyxz-0002oE-Sb for submit@debbugs.gnu.org; Thu, 01 Apr 2021 11:10:40 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21188) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lRyxy-0002o6-HC for 46955@debbugs.gnu.org; Thu, 01 Apr 2021 11:10:39 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1617289837; cv=none; d=zohomail.com; s=zohoarc; b=fF54aM4jX9PZMLgclZRBNtoRijJ9zzM0DgNWJOb+dMSZb2ugS8Tlvs6afPx7DfJXmHqzZzvu84+J0DMUOt2v5JbGUhCrtocxchjznSO+1xpb3ylo6xt6eQwUaX8V1YspYuRYbdjiWqEIzThYShqr+1mMkstgKEYVyYpmedzwEX0= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1617289837; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=cIgRnlj9wPl3EQSj6jwu6x+Med+AkL7yFZpGpjaUwIg=; b=gliq0HG1t9/SZ5nAV6cQHKKrz3QEpiYstk02Cf/sF8gLXhWKw387jdcitipcAH5Q6Tnphu2CatPA5rlirgDPE0epwPHRUMhcWtU7Qg/Z3kBrfGA9hZGiCh9OAOgXT18shPBxLC56jcMdAOOBPUO7Pq3y+jjfuqXpF9eSTHAYPmg= 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=1617289837; 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=cIgRnlj9wPl3EQSj6jwu6x+Med+AkL7yFZpGpjaUwIg=; b=D2ZTJi3Vx1KV/QR8/vj+qXFwQVYPhiPVe7HJqy3mtW8DN7SJ04/OPW/EG+eUbeh8 l8qRQQTDCNp85mRCWoEx9DCjoZKrWqMNBphyindnPrcp4j08S1Bi1L6QRRNCUCZZrkV 9nvFAAkLTj4/enPi8I1Uz+CqAmeYHKZSPI1qZ0IA= Received: from localhost (p54ad4e71.dip0.t-ipconnect.de [84.173.78.113]) by mx.zohomail.com with SMTPS id 1617289833597697.3426102786633; Thu, 1 Apr 2021 08:10:33 -0700 (PDT) References: <20210306005703.25479-1-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.4.15; emacs 27.2 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [PATCH 1/2] gnu: Add python-sparse. In-reply-to: <20210306005703.25479-1-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 17:10:30 +0200 Message-ID: <8735wa2g7t.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: 46955 Cc: 46955@debbugs.gnu.org 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 (-) M=C4=83d=C4=83lin Ionel Patra=C8=99cu = writes: > * gnu/packages/python-xyz.scm (python-sparse): New variable. [=E2=80=A6] > +(define-public python-sparse > + (package > + (name "python-sparse") > + (version "0.11.2") =E2=80=9Cguix lint=E2=80=9D tells me: python-sparse@0.11.2: can be upgraded to 0.12.0 Is there a reason why you picked 0.11.2? (Or did I just wait too long to review your patch=E2=80=A6?) --=20 Ricardo From debbugs-submit-bounces@debbugs.gnu.org Thu Jun 03 19:24:06 2021 Received: (at 46955) by debbugs.gnu.org; 3 Jun 2021 23:24:06 +0000 Received: from localhost ([127.0.0.1]:44990 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lowh3-0000Yp-Sq for submit@debbugs.gnu.org; Thu, 03 Jun 2021 19:24:06 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:50901) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lowh1-0000Y5-65 for 46955@debbugs.gnu.org; Thu, 03 Jun 2021 19:24:04 -0400 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id 5DADD1602F8; Fri, 4 Jun 2021 01:23:56 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-language:content-type:content-type:in-reply-to :mime-version:user-agent:date:date:message-id:from:from :references:subject:subject:received:received:received; s=mdc; t=1622762635; x=1624577036; bh=JBgyRVx+sNvciD1UzxSOeXh6GVHf7SHm lUxmSUZzH/k=; b=Ezpo7mRs4KsIdEQi9HCnseXKKEYf+e7GQJ4URMv++dVc3kfu GAlRbVOMUHm30gyBwQ9KSTelBaRGcVPx0kZ6UNbOMDmjzn+c5DcTvJcJ+lvWwD/v zaQ+91ubVydY54dHBqAtTQRal/Y49G0xZwlHYqLR8vHGMcFISw/UedNXAzI= Received: from b2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-tub.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id SrTff1T1n5mT; Fri, 4 Jun 2021 01:23:55 +0200 (CEST) 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; Fri, 4 Jun 2021 01:23:55 +0200 (CEST) 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 15.1.2242.10; Fri, 4 Jun 2021 01:23:55 +0200 Subject: Re: [ext] bug#46955: Acknowledgement ((no subject)) To: <46955@debbugs.gnu.org>, Rekado Wurmus References: <76dfa82e-53e2-c4fc-d002-df71f348cdc8@mdc-berlin.de> From: =?UTF-8?B?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= Message-ID: Date: Fri, 4 Jun 2021 01:23:54 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:78.0) Gecko/20100101 Thunderbird/78.8.1 MIME-Version: 1.0 In-Reply-To: Content-Type: multipart/alternative; boundary="------------E335027B92EEAB329ED52CED" Content-Language: en-US X-Originating-IP: [31.18.50.167] 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-14.0.0.3080-8.6.1012-26198.003 X-TM-AS-Result: No-10--9.162100-8.000000 X-TMASE-MatchedRID: 9vvqFUF7IWlq0U6EhO9EEwCNFKULxGCZK/YFZTiDf+ogcEd8uJSjxHo6 TtPuoiTUA/oe4NwFf2pCoViyuOBM7JilmT/yOYwx3nHtGkYl/VrJ5SXtoJPLyEoMHl9co6FPpgw c/quiinIZyHQ91vYHXtHklQugsTFL/f01C0pM6z9+J3gtIe0gA5GAt645FF0SJvSvlpvK74G95i YVgizGV6bF/OIYMbaagBUyrt61mkZuHV4AXLh2IvZvT2zYoYOwC/ExpXrHizyNnAdfrf4ZXjYKi VeQUM8G+y6mqRPEP2ydPMbNgeHEVNFvbrUsb66CekmbTWzSjHoBqNb4Qv6Vowp+tuYb4NtQUfxY 7Ci+6rel+yVqdiggdOnCdvcnYY1MwJtIpllDubtqG7co9eboC3zIY7d2+Tz9Vxt8iPZNr2w/ziv 0u4cpYZfr3281qUXdImMZ0rsVAm4VnOEgI8O/XFICmG2RRehovO61PPXizynx/es4TBfOp5P1t3 ar8lzT5shPFSKOueTFrscNyk5D6lOse/HBCkRPPNFSp45HGjA4gzHHdVYTMPLIj08N6FsEVIVGp QSjDhtVxdPIPU3eHdtLkQzL45zzlnY09l3qRQwvj6wHfIGxySPx0viUmdeu4WwrKBT2nJ0c3ovV 4KGuUaIXHI3/puiC/76CM4Z/MGbQ3sOMB3Fk1OfOVcxjDhcwawGoUBsEJreuikCL8VXXTHMB3Wa 6sj2dWgRnAzrxzvrl4gfBxJpg2fyhfdNdyqaeDPC/DBHj6Drl8iAVaobfMQBn3JprbCIYU+QJHP wHSQhAVE5Z1y77BQ== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--9.162100-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-26198.003 X-TM-SNTS-SMTP: 85F67B48F6ACAF4F7F40CCA4BB9C63EA37678B281367D5E7C602364C703D53F42000:F X-Spam-Score: -0.9 (/) X-Debbugs-Envelope-To: 46955 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: -1.9 (-) --------------E335027B92EEAB329ED52CED Content-Type: text/plain; charset="utf-8"; format=flowed Content-Transfer-Encoding: 8bit Hi guys, Sorry for the delay! I read all of Ricardo's comments and I made some changes to these patches. I will send a new round of patches after this message because after I tried to run python tests for the cooler package there was a need for a new dependency. Here are some short answers to Ricardo's comments/questions: ---------------------------------------------------------------------- Ran 0 tests in 0.000s OK phase `check' succeeded after 1.5 seconds --8<---------------cut here---------------end--------------->8--- Could you please take a look at this? I fixed that! Please check the new patch! Thanks! “guix lint” tells me: python-sparse 0.11.2: can be upgraded to 0.12.0 Is there a reason why you picked 0.11.2? (Or did I just wait too long to review your patch…?) At that time only version 0.11.2 was available. All the best      Mădălin! On 06.03.2021 01:55, GNU bug Tracking System wrote: > Thank you for filing a new bug report with debbugs.gnu.org. > > This is an automatically generated reply to let you know your message > has been received. > > Your message is being forwarded to the package maintainers and other > interested parties for their attention; they will reply in due course. > > Your message has been sent to the package maintainer(s): > guix-patches@gnu.org > > If you wish to submit further information on this problem, please > send it to 46955@debbugs.gnu.org. > > Please do not send mail to help-debbugs@gnu.org unless you wish > to report a problem with the Bug-tracking system. > -- System Administrator Bioinformatics and Omics Data Science BIMSB - MDC --------------E335027B92EEAB329ED52CED Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: 8bit

Hi guys,


Sorry for the delay!


I read all of Ricardo's comments and I made some changes to these patches.

I will send a new round of patches after this message because after I tried to run python tests for the cooler package there was a need for a new dependency.

Here are some short answers to Ricardo's comments/questions:

----------------------------------------------------------------------
Ran 0 tests in 0.000s

OK
phase `check' succeeded after 1.5 seconds
--8<---------------cut here---------------end--------------->8---

Could you please take a look at this?

I fixed that! Please check the new patch! Thanks!

“guix lint” tells me:

    python-sparse <at> 0.11.2: can be upgraded to 0.12.0

Is there a reason why you picked 0.11.2?  (Or did I just wait too long
to review your patch…?)

At that time only version 0.11.2 was available.


All the best

     Mădălin!


On 06.03.2021 01:55, GNU bug Tracking System wrote:
Thank you for filing a new bug report with debbugs.gnu.org.

This is an automatically generated reply to let you know your message
has been received.

Your message is being forwarded to the package maintainers and other
interested parties for their attention; they will reply in due course.

Your message has been sent to the package maintainer(s):
 guix-patches@gnu.org

If you wish to submit further information on this problem, please
send it to 46955@debbugs.gnu.org.

Please do not send mail to help-debbugs@gnu.org unless you wish
to report a problem with the Bug-tracking system.


-- 
System Administrator
Bioinformatics and Omics Data Science
BIMSB - MDC
--------------E335027B92EEAB329ED52CED-- From debbugs-submit-bounces@debbugs.gnu.org Thu Jun 03 19:25:39 2021 Received: (at 46955) by debbugs.gnu.org; 3 Jun 2021 23:25:39 +0000 Received: from localhost ([127.0.0.1]:44994 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lowiT-0000bD-BZ for submit@debbugs.gnu.org; Thu, 03 Jun 2021 19:25:39 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:52173) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lowiR-0000az-JW for 46955@debbugs.gnu.org; Thu, 03 Jun 2021 19:25:32 -0400 Received: from localhost (localhost [127.0.0.1]) by c2062.mx.srv.dfn.de (Postfix) with ESMTP id 1D4F8300306; Fri, 4 Jun 2021 01:25:25 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1622762724; x=1624577125; bh=UWFJyDehJ1kfpwaXoIjs7U1xylOqymhtwuob30fVkdk=; b=HcJOzh59V2IU Bb9ii9PZQaXSXmmUQCYUxja2tEdfezyZ1rNQT2q87HMITbKhylzPDGB5uP+19UFK 6wLEoI05OSoqGo6+hgPT5AvKMUCGJuH+CATQQIajMGzujwAnyB5XaM75PkP58dYh NMVzxTVKc/zAd/HrwMsv8mk4cpfvJS0= 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 wp-l88jSPyTF; Fri, 4 Jun 2021 01:25:24 +0200 (CEST) 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; Fri, 4 Jun 2021 01:25:24 +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 15.1.2242.10; Fri, 4 Jun 2021 01:25:24 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <46955@debbugs.gnu.org> Subject: [PATCH 1/3] gnu: Add python-sparse. Date: Fri, 4 Jun 2021 01:25:01 +0200 Message-ID: <20210603232503.29253-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.31.1 MIME-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit X-Originating-IP: [141.80.113.106] 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-14.0.0.3080-8.6.1012-26198.003 X-TM-AS-Result: No-10--3.163100-8.000000 X-TMASE-MatchedRID: JsCi/JRnBFH/R1NSMc2qCXycvC6I0dJIS1zwNuiBtITfUZT83lbkEJwl bZPQQ0yzb1TGnuLRfUkctkosP3yazCq+GZ9ZHxIhUYXhMajr0x53G1bsm5zfjMZygq/CPmro6n1 Gl4gVhHhV9cEoYbjAXbc/ZCLk5AauxmNZL79yeAzakOg7uhpPs17OZ6hrwwnz6Mw4RnkAvRKYeA TzrE2lR+awqowSxfEnLb6XLHjqIvT7lPrMqaVmF1XXOFXDx25iF430d3dMHka8B7vl7G5M0USuy wxB3Ejk51xw3PCMlNY3HexY7VSIcWcOYd1wAQIAAD5jSg1rFtBbV4KUZZg3KOcJOFqc/+CEYmUf TlXs3OOTKxCEEoHeWpfAZqrFvhSOow4viWN+bNz0VCHd+VQiHgseQVcTRnF2lwV2iaAfSWeDGx/ OQ1GV8t0H8LFZNFG7doMssNsUwYXo09dPgSR9YSpNcadNZa+YJIT50xoHh8EN9e4Mmup6udS4hm c+rT+o70vMLL1IbJl/vFbd53rshd0wC0yCvbeT4PtO+H6AT5HX7GF+64huyLjmNKuuvgamoYI1e rIuEsW+g2RZj2FKy60Cnu9RmLpv X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.163100-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-26198.003 X-TM-SNTS-SMTP: 6B40151B4D47BCF75A2350635158A5B4D77CEC51A8B6784E622A313B49E33CB62000:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 46955 Cc: rekado@elephly.net, =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= 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 (-) * gnu/packages/python-xyz.scm(python-sparse): New variable. --- gnu/packages/python-xyz.scm | 48 ++++++++++++++++++++++++++++++++++++- 1 file changed, 47 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a5cc04edaf..35ce8d1cbe 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -67,7 +67,7 @@ ;;; Copyright © 2019, 2020 Giacomo Leidi ;;; Copyright © 2019 Wiktor Żelazny ;;; Copyright © 2019, 2020 Tanguy Le Carrour -;;; Copyright © 2019 Mădălin Ionel Patrașcu +;;; Copyright © 2019, 2021 Mădălin Ionel Patrașcu ;;; Copyright © 2020 Riku Viitanen ;;; Copyright © 2020 Jakub Kądziołka ;;; Copyright © 2020 sirgazil @@ -5132,6 +5132,52 @@ objects.") (define-public python2-colormath (package-with-python2 python-colormath)) +(define-public python-sparse + (package + (name "python-sparse") + (version "0.12.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "sparse" version)) + (sha256 + (base32 + "05lmzckv69cvxavhdr36k803bgr5dl04cppglid1l880xswc759c")))) + (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (add-installed-pythonpath inputs outputs) + (invoke "pytest" "-vv") + #t))))) + (propagated-inputs + `(("python-numba" ,python-numba) + ("python-numpy" ,python-numpy) + ("python-scipy" ,python-scipy))) + (native-inputs + `(("python-dask" ,python-dask) + ("python-pytest" ,python-pytest) + ("python-pytest-black" ,python-pytest-black) + ("python-pytest-cov" ,python-pytest-cov))) + (home-page "https://github.com/pydata/sparse/") + (synopsis "Library for multi-dimensional sparse arrays") + (description + "This package implements sparse arrays of arbitrary dimension on top of +@code{numpy} and @code{scipy.sparse}. Sparse array is a matrix in which most +of the elements are zero. @code{python-sparse} generalizes the +@code{scipy.sparse.coo_matrix} and @code{scipy.sparse.dok_matrix} layouts, but +extends beyond just rows and columns to an arbitrary number of dimensions. +Additionally, this project maintains compatibility with the +@code{numpy.ndarray} interface rather than the @code{numpy.matrix} interface +used in @code{scipy.sparse}. These differences make this project useful in +certain situations where @code{scipy.sparse} matrices are not well suited, but +it should not be considered a full replacement. It lacks layouts that are not +easily generalized like @dfn{compressed sparse row/column}(CSR/CSC) and +depends on @code{scipy.sparse} for some computations.") + (license license:bsd-3))) + (define-public python-spectra (package (name "python-spectra") -- 2.31.1 From debbugs-submit-bounces@debbugs.gnu.org Thu Jun 03 19:25:39 2021 Received: (at 46955) by debbugs.gnu.org; 3 Jun 2021 23:25:39 +0000 Received: from localhost ([127.0.0.1]:44997 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lowiZ-0000bS-DY for submit@debbugs.gnu.org; Thu, 03 Jun 2021 19:25:39 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:37589) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lowiX-0000b5-6u for 46955@debbugs.gnu.org; Thu, 03 Jun 2021 19:25:37 -0400 Received: from localhost (localhost [127.0.0.1]) by a2062.mx.srv.dfn.de (Postfix) with ESMTP id 185A0A0297; Fri, 4 Jun 2021 01:25:31 +0200 (CEST) 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= 1622762730; x=1624577131; bh=RG91AJ0nYIl1e7SwwdkAiidN4F38bBWNiD5 QwOMXacw=; b=Ecwc85PQiO48Q3gtWyu6NDl2SXRT7j6dr96E2+fBBJ+7qCU7H3h 78WoUMm3AFwSHvYdbQXlhCDTQ/X38Jaqh9sgBdgOPEN1D1dbAYnS3fjOVWZZs8Df iLmfrw/EMkH1R37YBo8ghffSreufq/KlTO4ozkdLWqqjeagPZzI79jLg= 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 Ii286_C1aw3u; Fri, 4 Jun 2021 01:25:30 +0200 (CEST) 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, 4 Jun 2021 01:25:30 +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 15.1.2242.10; Fri, 4 Jun 2021 01:25:30 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <46955@debbugs.gnu.org> Subject: [PATCH 2/3] gnu: Add python-ipytree. Date: Fri, 4 Jun 2021 01:25:02 +0200 Message-ID: <20210603232503.29253-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.31.1 In-Reply-To: <20210603232503.29253-1-madalinionel.patrascu@mdc-berlin.de> References: <20210603232503.29253-1-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-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-14.0.0.3080-8.6.1012-26198.003 X-TM-AS-Result: No-10--1.443800-8.000000 X-TMASE-MatchedRID: R+JPWGnaB63/R1NSMc2qCT8Ckw9b/GFeTJDl9FKHbrn7fZJfDdCIXISC l3uvYUiSC6+Zjvylmgt6n3hIvN5dLetbninbl/qrTT9ZveSPAxX4qCLIu0mtIPj/xqm3b+MoAsG 1iO+HSl244n+iSEvAXL26V6COZvN4rsq/7BhdGyBkTCSz2kr7Vo5A6wTicMJ0rju6wKzzZAPHwK 23sfEl2YjQSOd69r3fmyiLZetSf8mfop0ytGwvXiq2rl3dzGQ1GpeevGsoI5eWwKqJSwqNM/IJI dnxIpxxbzESoIqU4p+kvztwRuqNxYg1gQ6FVgXjCrJLK5PgSUndPK6/90qLFcnoLQoeCWIeCDWQ DDKs7yDox9rqorLqIj47jot1RqlnCuhB+Hs2Q+XFRuRzIFoKqH7cGd19dSFd X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.443800-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-26198.003 X-TM-SNTS-SMTP: 7CF906DB361AFC2F403392E17F48B0F44BE744F45AE01CF58AA373C3D8721F962000:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 46955 Cc: rekado@elephly.net, =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= 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/python-xyz.scm (python-ipytree): New variable. --- gnu/packages/python-xyz.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 35ce8d1cbe..f416e3a2a8 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -7568,6 +7568,32 @@ away.") (define-public python2-ipython-genutils (package-with-python2 python-ipython-genutils)) +(define-public python-ipytree + (package + (name "python-ipytree") + (version "0.2.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "ipytree" version)) + (sha256 + (base32 + "0ss64kxa4la50irf7vy3474f1p924pn4da5gmb02zvhn2x0pra2j")))) + (build-system python-build-system) + (native-inputs + `(("python-setuptools" ,python-setuptools))) + (propagated-inputs + `(("python-ipywidgets" ,python-ipywidgets) + ("python-jupyter-packaging" ,python-jupyter-packaging))) + (home-page "https://github.com/martinRenou/ipytree") + (synopsis "Tree widget using jsTree and Jupyter-widgets") + (description + "This package provides the possibility to create a tree using +@code{Jupyter-widgets} protocol and @code{jsTree}. @code{Jupyter-widgets} is a +way to create an interactive @dfn{graphical user interface} (GUI) for a Jupyter +notebook. @code{JsTree} is a jquery plugin, that provides interactive trees.") + (license license:expat))) + (define-public python-ipyparallel (package (name "python-ipyparallel") -- 2.31.1 From debbugs-submit-bounces@debbugs.gnu.org Thu Jun 03 19:25:45 2021 Received: (at 46955) by debbugs.gnu.org; 3 Jun 2021 23:25:46 +0000 Received: from localhost ([127.0.0.1]:45000 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lowif-0000bs-L6 for submit@debbugs.gnu.org; Thu, 03 Jun 2021 19:25:45 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:37427) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lowie-0000bY-Pl for 46955@debbugs.gnu.org; Thu, 03 Jun 2021 19:25:45 -0400 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id 656DB1602F8; Fri, 4 Jun 2021 01:25:39 +0200 (CEST) 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= 1622762738; x=1624577139; bh=A4De0ibjdllsAjWcVI7X9bSfi/Zwfp0ls+S xsWWiGRI=; b=ivurtg9Bu8xhL64IsD5lZkDAZFc/WsBbeeaAugNvq99Gvw6SV2V u9QR8kDm8ax4rRbxp7dC/WAuS4za2kivFuLlkFBFAimMp93jyacPSlJaadEBbYSy DsPo7d7ZlENqqZ2p68aP9nWWW/aJbjQ9ak500ucLvNAzeqpFiSwsKLeA= Received: from b2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-tub.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id Jw72f-pvJfb1; Fri, 4 Jun 2021 01:25:38 +0200 (CEST) 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; Fri, 4 Jun 2021 01:25:38 +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 15.1.2242.10; Fri, 4 Jun 2021 01:25:38 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <46955@debbugs.gnu.org> Subject: [PATCH 3/3] gnu: python-cooler: Update to 0.8.11. Date: Fri, 4 Jun 2021 01:25:03 +0200 Message-ID: <20210603232503.29253-3-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.31.1 In-Reply-To: <20210603232503.29253-1-madalinionel.patrascu@mdc-berlin.de> References: <20210603232503.29253-1-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-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-14.0.0.3080-8.6.1012-26198.003 X-TM-AS-Result: No-10--2.378700-8.000000 X-TMASE-MatchedRID: TMejBmzMW4e6/eEqqZaZmj8Ckw9b/GFeTJDl9FKHbrn7fZJfDdCIXISC l3uvYUiSC6+Zjvylmgt6n3hIvN5dLV1nLdLFTV2cB8FxO/BQHsIXivwflisSrPn6214PlHOFxVZ wHGSRvcr7bbB/MBzIMwa+LGYKVz1S64qzaFKxje/p9R8QuoVQfwoXSOLC5a44Mv8YehqjR1W2Ed aacwTXA8A5YhoszcEGg8kdcveGTlnI2RqSAXh33s6KFiylFM8l4k1wcu9E2kRpUUxjTnX0eo/j4 gKDoVqZJhu/MapJ6V4C0+r3OCivMyiFL2ygqPFl3QqJN4m15UHrixWWWJYrHx8TzIzimOwPC24o EZ6SpSk6XEE7Yhw4FjQQWtYtNU6/3IVHw3xPWBkGBazqvYGxYUYUJKPj8nOwe7VnDznzQ45COE5 0dTAZ9S9LkbgYjPPqUedhAKWTm3FiDcew7W+5ZrdKECLo/klXhRFX0MbNzemQ4JrfEHpLweZmgn jb/yyM1RkHasLA4hI= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.378700-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-26198.003 X-TM-SNTS-SMTP: 129F3B016466E13E36D76EC05DF58645FC3D1FA20FD491D7A2B69ACF611DD75F2000:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 46955 Cc: rekado@elephly.net, =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= 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-cooler): Update to 0.8.11. --- gnu/packages/bioinformatics.scm | 39 ++++++++++++++++++++++++++++----- 1 file changed, 33 insertions(+), 6 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 94d15cc4c0..55e25ab486 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11591,15 +11591,35 @@ fasta subsequences.") (define-public python-cooler (package (name "python-cooler") - (version "0.8.7") + (version "0.8.11") (source (origin (method url-fetch) (uri (pypi-uri "cooler" version)) (sha256 (base32 - "01g6gqix9ba27sappz6nfyiwabzrlf8i5fn8kwcz8ra356cq9crp")))) + "1i96fmpsimj4wrx51rxn8lw2gqxf5a2pvrj5rwdd6ivnm3pmhyrn")))) (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-tests + (lambda _ + (substitute* "tests/test_create.py" + (("def test_roundtrip") + (string-append "@pytest.mark.skip(reason=\"requires network " + "access to genome.ucsc.edu\")\n" + "def test_roundtrip"))) + (substitute* "tests/test_util.py" + (("def test_fetch_chromsizes") + (string-append "@pytest.mark.skip(reason=\"requires network " + "access to genome.ucsc.edu\")\n" + "def test_fetch_chromsizes"))) + #t)) + (replace 'check + (lambda _ + (invoke "python" "-m" "pytest" "-v") + #t))))) (propagated-inputs `(("python-asciitree" ,python-asciitree) ("python-biopython" ,python-biopython) @@ -11615,11 +11635,18 @@ fasta subsequences.") ("python-pysam" ,python-pysam) ("python-pyyaml" ,python-pyyaml) ("python-scipy" ,python-scipy) - ("python-simplejson" ,python-simplejson))) + ("python-simplejson" ,python-simplejson) + ("python-six" ,python-six) + ("python-sparse" ,python-sparse))) (native-inputs - `(("python-mock" ,python-mock) - ("python-pytest" ,python-pytest))) - (home-page "https://github.com/mirnylab/cooler") + `(("python-codecov" ,python-codecov) + ("python-ipytree" ,python-ipytree) + ("python-mock" ,python-mock) + ("python-pytest" ,python-pytest) + ("python-pytest-cov" ,python-pytest-cov) + ("python-pytest-flake8" ,python-pytest-flake8))) + ;;almost all the projects of the Mirnylab are moved under Open2C umbrella + (home-page "https://github.com/open2c/cooler") (synopsis "Sparse binary format for genomic interaction matrices") (description "Cooler is a support library for a sparse, compressed, binary persistent -- 2.31.1 From debbugs-submit-bounces@debbugs.gnu.org Sat Jun 05 06:06:10 2021 Received: (at 46955) by debbugs.gnu.org; 5 Jun 2021 10:06:10 +0000 Received: from localhost ([127.0.0.1]:48343 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lpTBy-00056k-CE for submit@debbugs.gnu.org; Sat, 05 Jun 2021 06:06:10 -0400 Received: from baptiste.telenet-ops.be ([195.130.132.51]:50390) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lpTBt-00056X-NR for 46955@debbugs.gnu.org; Sat, 05 Jun 2021 06:06:09 -0400 Received: from ptr-bvsjgyjmffd7q9timvx.18120a2.ip6.access.telenet.be ([IPv6:2a02:1811:8c09:9d00:aaf1:9810:a0b8:a55d]) by baptiste.telenet-ops.be with bizsmtp id DN612500t0mfAB401N62WG; Sat, 05 Jun 2021 12:06:04 +0200 Message-ID: <7c35e0fff0b83ca112cbeda0f6a391536fb2abf8.camel@telenet.be> Subject: Re: [bug#46955] [PATCH 3/3] gnu: python-cooler: Update to 0.8.11. From: Maxime Devos To: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= , 46955@debbugs.gnu.org Date: Sat, 05 Jun 2021 12:06:01 +0200 In-Reply-To: <20210603232503.29253-3-madalinionel.patrascu@mdc-berlin.de> References: <20210603232503.29253-1-madalinionel.patrascu@mdc-berlin.de> <20210603232503.29253-3-madalinionel.patrascu@mdc-berlin.de> Content-Type: multipart/signed; micalg="pgp-sha512"; protocol="application/pgp-signature"; boundary="=-sbu5ucy8Dtd3w8EBUqbY" User-Agent: Evolution 3.34.2 MIME-Version: 1.0 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=telenet.be; s=r21; t=1622887564; bh=CE9sc3Fc8QfSUKK0Lsybm4EWAinmhPb9i4ouoZwhQCk=; h=Subject:From:To:Cc:Date:In-Reply-To:References; b=MH1gQci9FteXaa4y2EWBBETHBOamzlY7WZyywtZNv+dJiEasP4CWCznXOJRtdYQST NqHz61HCSvOMJcdAaNOsfoVLTOPz/YRvauov40fX5cnJ/GmOAo1YDCTMM8wTmjUepQ KLUsHfXcGKpfmRsEJ94UyrG01+B06arK56iL+LPZQc9tUaB6fTXVosyMflahffo2R2 VnBYw86KAGbGOW+FATSNnFqlCfVcZavAPww8KRW+xrBgK9VMrLNBNDTefwFx9npwV9 Dp84Gsqa+LvKEWFkNsf1vG4X8sWy7wL2X6SWD/ZyCP+zT9kAwWEriBuGn83YFLxe3d uDu0jNBlejJng== X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 46955 Cc: rekado@elephly.net 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: -1.7 (-) --=-sbu5ucy8Dtd3w8EBUqbY Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable A comment about a build phase. > [...] > + (replace 'check > + (lambda _ > + (invoke "python" "-m" "pytest" "-v") > + #t))))) This needs to be something like + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python" "-m" "pytest" "-v")))) By respecting 'tests?', the --without-tests build transformation can be use= d. (Try "guix build python-cooler --without-tests=3Dpython-cooler"). This can also be important for cross-compilation (dunno if it applies here though). Trailing #t are not required anymore. The warning that results if it is rem= oved will disappear once core-updates is merged. Greetings, Maxime. --=-sbu5ucy8Dtd3w8EBUqbY Content-Type: application/pgp-signature; name="signature.asc" Content-Description: This is a digitally signed message part Content-Transfer-Encoding: 7bit -----BEGIN PGP SIGNATURE----- iI0EABYKADUWIQTB8z7iDFKP233XAR9J4+4iGRcl7gUCYLtMiRccbWF4aW1lZGV2 b3NAdGVsZW5ldC5iZQAKCRBJ4+4iGRcl7qu1AP9vu8FgJvMl2eMkKjz3nIjdTEY7 J53G6QcOEn+ZYizsvwEA0aRfzmo6PvNgzyCJfZI14/PejpSO8kB/3G4/U3tPIg0= =YCXP -----END PGP SIGNATURE----- --=-sbu5ucy8Dtd3w8EBUqbY-- From debbugs-submit-bounces@debbugs.gnu.org Sat Jun 05 20:03:47 2021 Received: (at 46955) by debbugs.gnu.org; 6 Jun 2021 00:03:47 +0000 Received: from localhost ([127.0.0.1]:50307 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lpgGY-0004iM-WE for submit@debbugs.gnu.org; Sat, 05 Jun 2021 20:03:47 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:51425) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lpgGT-0004i3-EV for 46955@debbugs.gnu.org; Sat, 05 Jun 2021 20:03:45 -0400 Received: from localhost (localhost [127.0.0.1]) by a2062.mx.srv.dfn.de (Postfix) with ESMTP id A299CA00E3; Sun, 6 Jun 2021 02:03:34 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-language:content-transfer-encoding:content-type :content-type:in-reply-to:mime-version:user-agent:date:date :message-id:from:from:references:subject:subject:received :received:received; s=mdc; t=1622937814; x=1624752215; bh=z5ypFw oxSNkQymZVoBHdqYX8UVKfUsrht27RbNW1lls=; b=HKz7RtplgU9tqgsC+nsUvs RpMwUxWy/sf/6vp+IfEJin6DYv7lDcqu+Qe2tdVYyfYYsFjdGzaELGyqjK6rdy6W q80aiTXtuykN3TLXM2zHXw4/S8uHO6meBljGKHOPxum2lYP3C0AqL03Dyt44/GcG 6HNAH9s/4p7MDiU7DOFz8= 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 O7-cww6Q5Er2; Sun, 6 Jun 2021 02:03:34 +0200 (CEST) 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; Sun, 6 Jun 2021 02:03:34 +0200 (CEST) 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 15.1.2242.10; Sun, 6 Jun 2021 02:03:33 +0200 Subject: Re: [ext] Re: [bug#46955] [PATCH 3/3] gnu: python-cooler: Update to 0.8.11. To: <46955@debbugs.gnu.org> References: <20210603232503.29253-1-madalinionel.patrascu@mdc-berlin.de> <20210603232503.29253-3-madalinionel.patrascu@mdc-berlin.de> <7c35e0fff0b83ca112cbeda0f6a391536fb2abf8.camel@telenet.be> From: =?UTF-8?B?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= Message-ID: <5ec8d2b3-811a-013b-28db-6e79b6d2b556@mdc-berlin.de> Date: Sun, 6 Jun 2021 02:03:33 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:78.0) Gecko/20100101 Thunderbird/78.8.1 MIME-Version: 1.0 In-Reply-To: <7c35e0fff0b83ca112cbeda0f6a391536fb2abf8.camel@telenet.be> 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-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-14.0.0.3080-8.6.1012-26202.003 X-TM-AS-Result: No-10--6.726300-8.000000 X-TMASE-MatchedRID: hls5oAVArl8eimh1YYHcKI61Z+HJnvsO52mltlE2n8jLkl8e9W70i9sU UM4+5JDM75eOGXcagECPWx38Q1qIm4ZKkFFIbQIAA9lly13c/gEEa8g1x8eqFwHA0AOzrXiBOXf Z9OHyzWZKvKQkFlo73R+nBl7Pmyp5O5k/PxBAvv7vdQQaH57xxsnlJe2gk8vIF0dfZ5kV9l+yhy zhSQtL0qCQFlbvrjaOLKJOFcgTP0i9sfpYxWNvCx/R5SKe31ARpnx3aOUcbhcLfbSiIF780tnu9 ZdOygfSfS0Ip2eEHny+qryzYw2E8LLn+0Vm71Lcq7rFUcuGp/HCttcwYNipX55Vb9l0vnaPQAX4 7DDRGDB3sESBa5dQK1ebVrmkF91doT7LQSvOTQal216CGmpWVS4DWCC21TAKXroHbJY3f6iSvcC awf/FHHdMG01tVbKNUdNvZjjOj9C63BPMcrcQuXeYWV2RaAfD+kkf6HhPsBc= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--6.726300-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-26202.003 X-TM-SNTS-SMTP: 8CF6AF2E0F7D01EF1D8C5847B04B17CB2C72B02295ADD75F885D7968608163322000:F X-Spam-Score: -2.9 (--) X-Debbugs-Envelope-To: 46955 Cc: rekado@elephly.net, Maxime Devos 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: -3.9 (---) Hi Maxime, Thanks for the explanation, now these things are clear to me! I applied Maxime's advice and I have made some changes on two patches (python-sparse and python-cooler). Because of this reason, I will send again the whole series of patches and I will wait for a full review of them. Thanks, Maxime! On 05.06.2021 12:06, Maxime Devos wrote: > A comment about a build phase. > >> [...] >> + (replace 'check >> + (lambda _ >> + (invoke "python" "-m" "pytest" "-v") >> + #t))))) > This needs to be something like > > + (replace 'check > + (lambda* (#:key tests? #:allow-other-keys) > + (when tests? > + (invoke "python" "-m" "pytest" "-v")))) > > By respecting 'tests?', the --without-tests build transformation can be used. > (Try "guix build python-cooler --without-tests=python-cooler"). > This can also be important for cross-compilation (dunno if it applies here > though). > > Trailing #t are not required anymore. The warning that results if it is removed > will disappear once core-updates is merged. > > Greetings, > Maxime. -- System Administrator Bioinformatics and Omics Data Science BIMSB - MDC From debbugs-submit-bounces@debbugs.gnu.org Sat Jun 05 20:07:21 2021 Received: (at 46955) by debbugs.gnu.org; 6 Jun 2021 00:07:21 +0000 Received: from localhost ([127.0.0.1]:50311 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lpgJv-0004nT-G6 for submit@debbugs.gnu.org; Sat, 05 Jun 2021 20:07:21 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:38309) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lpgJs-0004nD-NA for 46955@debbugs.gnu.org; Sat, 05 Jun 2021 20:07:13 -0400 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id 3C16C1600B8; Sun, 6 Jun 2021 02:07:06 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1622938025; x=1624752426; bh=z09BWfLtSeUg+iUwIuKT8U2XQgaTYM1YTjDc4ZJZTGE=; b=jjQ9AO9qu/qX i1A156klA2G/K4IstZLzjTPeoWAq+8g0dj1bOArEcdQ9FjLBJvSRVNL4loikRpzz jEXRrpHer50gIO7amto/y9xAj//u8GLH9a+H5+TeTVlMUFPnOFcn9BVlvvAHqVm6 VVPamcnVCaMUmmpO1Zdf8dLLXJzjokU= Received: from b2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-tub.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id NSEKTyjYoZMW; Sun, 6 Jun 2021 02:07:05 +0200 (CEST) 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; Sun, 6 Jun 2021 02:07:05 +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 15.1.2242.10; Sun, 6 Jun 2021 02:07:04 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <46955@debbugs.gnu.org> Subject: [PATCH 1/3] gnu: Add python-sparse. Date: Sun, 6 Jun 2021 02:06:49 +0200 Message-ID: <20210606000651.28252-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.31.1 MIME-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit X-Originating-IP: [141.80.113.106] 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-14.0.0.3080-8.6.1012-26202.003 X-TM-AS-Result: No-10--2.213100-8.000000 X-TMASE-MatchedRID: JsCi/JRnBFH/R1NSMc2qCXycvC6I0dJIS1zwNuiBtITfUZT83lbkEJwl bZPQQ0yzb1TGnuLRfUkctkosP3yazCq+GZ9ZHxIhUYXhMajr0x53G1bsm5zfjMZygq/CPmro6n1 Gl4gVhHhV9cEoYbjAXbc/ZCLk5AauxmNZL79yeAxSFqtD2wqeMV7OZ6hrwwnz/gMNehoKqTuXzC wUPmVFK+awqowSxfEnLb6XLHjqIvT7lPrMqaVmF1XXOFXDx25iF430d3dMHka8B7vl7G5M0USuy wxB3Ejk51xw3PCMlNY3HexY7VSIcWcOYd1wAQIAAD5jSg1rFtBbV4KUZZg3KOcJOFqc/+CEYmUf TlXs3OOTKxCEEoHeWpfAZqrFvhSOow4viWN+bNz0VCHd+VQiHgseQVcTRnF2lwV2iaAfSWeDGx/ OQ1GV8t0H8LFZNFG7doMssNsUwYVtH7py2mvPPfIWdF0cpec123hXtA//3sx6dbk5o2QFfNC4vf Hpz8nv70vMLL1IbJl/vFbd53rshd0wC0yCvbeT4PtO+H6AT5HX7GF+64huyLjmNKuuvgamoYI1e rIuEsW+g2RZj2FKy60Cnu9RmLpv X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.213100-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-26202.003 X-TM-SNTS-SMTP: 6FC3FDB4BEA1D5D61810400AA05C087C2A3CFAF259531CB05E39F72620BF9B452000:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 46955 Cc: rekado@elephly.net, =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= 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 (-) * gnu/packages/python-xyz.scm(python-sparse): New variable. --- gnu/packages/python-xyz.scm | 47 ++++++++++++++++++++++++++++++++++++- 1 file changed, 46 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index b63c2852d5..a4fe31a01f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -67,7 +67,7 @@ ;;; Copyright © 2019, 2020 Giacomo Leidi ;;; Copyright © 2019 Wiktor Żelazny ;;; Copyright © 2019, 2020 Tanguy Le Carrour -;;; Copyright © 2019 Mădălin Ionel Patrașcu +;;; Copyright © 2019, 2021 Mădălin Ionel Patrașcu ;;; Copyright © 2020 Riku Viitanen ;;; Copyright © 2020 Jakub Kądziołka ;;; Copyright © 2020 sirgazil @@ -5147,6 +5147,51 @@ objects.") (define-public python2-colormath (package-with-python2 python-colormath)) +(define-public python-sparse + (package + (name "python-sparse") + (version "0.12.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "sparse" version)) + (sha256 + (base32 + "05lmzckv69cvxavhdr36k803bgr5dl04cppglid1l880xswc759c")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python" "-m" "pytest" "-v"))))))) + (propagated-inputs + `(("python-numba" ,python-numba) + ("python-numpy" ,python-numpy) + ("python-scipy" ,python-scipy))) + (native-inputs + `(("python-dask" ,python-dask) + ("python-pytest" ,python-pytest) + ("python-pytest-black" ,python-pytest-black) + ("python-pytest-cov" ,python-pytest-cov))) + (home-page "https://github.com/pydata/sparse/") + (synopsis "Library for multi-dimensional sparse arrays") + (description + "This package implements sparse arrays of arbitrary dimension on top of +@code{numpy} and @code{scipy.sparse}. Sparse array is a matrix in which most +of the elements are zero. @code{python-sparse} generalizes the +@code{scipy.sparse.coo_matrix} and @code{scipy.sparse.dok_matrix} layouts, but +extends beyond just rows and columns to an arbitrary number of dimensions. +Additionally, this project maintains compatibility with the +@code{numpy.ndarray} interface rather than the @code{numpy.matrix} interface +used in @code{scipy.sparse}. These differences make this project useful in +certain situations where @code{scipy.sparse} matrices are not well suited, but +it should not be considered a full replacement. It lacks layouts that are not +easily generalized like @dfn{compressed sparse row/column}(CSR/CSC) and +depends on @code{scipy.sparse} for some computations.") + (license license:bsd-3))) + (define-public python-spectra (package (name "python-spectra") -- 2.31.1 From debbugs-submit-bounces@debbugs.gnu.org Sat Jun 05 20:07:23 2021 Received: (at 46955) by debbugs.gnu.org; 6 Jun 2021 00:07:23 +0000 Received: from localhost ([127.0.0.1]:50314 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lpgK2-0004nq-O8 for submit@debbugs.gnu.org; Sat, 05 Jun 2021 20:07:22 -0400 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:44739) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lpgK0-0004nS-So for 46955@debbugs.gnu.org; Sat, 05 Jun 2021 20:07:21 -0400 Received: from localhost (localhost [127.0.0.1]) by c2062.mx.srv.dfn.de (Postfix) with ESMTP id BB76D3000DD; Sun, 6 Jun 2021 02:07:14 +0200 (CEST) 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= 1622938034; x=1624752435; bh=iotO6oFfUif/RxFJ4CtTN8iprGTNQaF4Kgp xcFFMDLg=; b=haWkUnH9Sq7RDLbdoKbdMbRUOnV8HAf/vNQFNXUwemrI5rFHeA8 hnIgqJjnffFbsUtl/cI2+dLU87mxmVcAH0hHLgJ3qi6uto5YYFDZ/M3MN/4Swt+P GYeUzw6drpd+RBBJFLqCp26+Zerk7mwhlg90Lw3KmBlWntqpVdj+xI5c= 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 r1nnZhU_m21t; Sun, 6 Jun 2021 02:07:14 +0200 (CEST) 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; Sun, 6 Jun 2021 02:07:14 +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 15.1.2242.10; Sun, 6 Jun 2021 02:07:13 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <46955@debbugs.gnu.org> Subject: [PATCH 2/3] gnu: Add python-ipytree. Date: Sun, 6 Jun 2021 02:06:50 +0200 Message-ID: <20210606000651.28252-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.31.1 In-Reply-To: <20210606000651.28252-1-madalinionel.patrascu@mdc-berlin.de> References: <20210606000651.28252-1-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-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-14.0.0.3080-8.6.1012-26202.003 X-TM-AS-Result: No-10--1.443800-8.000000 X-TMASE-MatchedRID: R+JPWGnaB63/R1NSMc2qCT8Ckw9b/GFeTJDl9FKHbrn7fZJfDdCIXISC l3uvYUiSC6+Zjvylmgt6n3hIvN5dLetbninbl/qrTT9ZveSPAxX4qCLIu0mtIPj/xqm3b+MoAsG 1iO+HSl244n+iSEvAXL26V6COZvN4rsq/7BhdGyBkTCSz2kr7Vo5A6wTicMJ0rju6wKzzZAPHwK 23sfEl2YjQSOd69r3fmyiLZetSf8mfop0ytGwvXiq2rl3dzGQ1GpeevGsoI5fs4kKm/I1sQ1MPM Vn7jTEmvWelgXus+6MxI9VXoBbAH4g1gQ6FVgXjCrJLK5PgSUndPK6/90qLFcnoLQoeCWIeCDWQ DDKs7yDox9rqorLqIj47jot1RqlnCuhB+Hs2Q+XFRuRzIFoKqH7cGd19dSFd X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.443800-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-26202.003 X-TM-SNTS-SMTP: CCBD0360B0131F91A16BF35F325F440BBF18BF1B601D36425D27901C6214815F2000:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 46955 Cc: rekado@elephly.net, =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= 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/python-xyz.scm (python-ipytree): New variable. --- gnu/packages/python-xyz.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a4fe31a01f..8ee43b1176 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -7582,6 +7582,32 @@ away.") (define-public python2-ipython-genutils (package-with-python2 python-ipython-genutils)) +(define-public python-ipytree + (package + (name "python-ipytree") + (version "0.2.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "ipytree" version)) + (sha256 + (base32 + "0ss64kxa4la50irf7vy3474f1p924pn4da5gmb02zvhn2x0pra2j")))) + (build-system python-build-system) + (native-inputs + `(("python-setuptools" ,python-setuptools))) + (propagated-inputs + `(("python-ipywidgets" ,python-ipywidgets) + ("python-jupyter-packaging" ,python-jupyter-packaging))) + (home-page "https://github.com/martinRenou/ipytree") + (synopsis "Tree widget using jsTree and Jupyter-widgets") + (description + "This package provides the possibility to create a tree using +@code{Jupyter-widgets} protocol and @code{jsTree}. @code{Jupyter-widgets} is a +way to create an interactive @dfn{graphical user interface} (GUI) for a Jupyter +notebook. @code{JsTree} is a jquery plugin, that provides interactive trees.") + (license license:expat))) + (define-public python-ipyparallel (package (name "python-ipyparallel") -- 2.31.1 From debbugs-submit-bounces@debbugs.gnu.org Sat Jun 05 20:07:28 2021 Received: (at 46955) by debbugs.gnu.org; 6 Jun 2021 00:07:28 +0000 Received: from localhost ([127.0.0.1]:50317 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lpgK8-0004o8-1r for submit@debbugs.gnu.org; Sat, 05 Jun 2021 20:07:28 -0400 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:56081) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lpgK6-0004nj-TT for 46955@debbugs.gnu.org; Sat, 05 Jun 2021 20:07:27 -0400 Received: from localhost (localhost [127.0.0.1]) by a2062.mx.srv.dfn.de (Postfix) with ESMTP id 928D2A00E3; Sun, 6 Jun 2021 02:07:21 +0200 (CEST) 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= 1622938041; x=1624752442; bh=Dk6uvdbfmMUP4XEWvIIrgZsuEE5DpUf1e76 IY/H9yIE=; b=gh4fNZofUfwLo/1189M/nEmrlxXmgeiXzJzOjof8f3MAIQuaUUv WFZQq3zIY29ZaUfFHZn/p7iSdhl5a6mK4Z3OEbTWqk5E9v5Ju3bd1vjg+RSlfLIK Kg83a2VFpIUKpH4exPNSdLOOT67dtp84uvlseh1jxF+EcNhuHiOjSm4g= 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 4IxNbE4hBRqI; Sun, 6 Jun 2021 02:07:21 +0200 (CEST) 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; Sun, 6 Jun 2021 02:07:21 +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 15.1.2242.10; Sun, 6 Jun 2021 02:07:20 +0200 From: =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= To: <46955@debbugs.gnu.org> Subject: [PATCH 3/3] gnu: python-cooler: Update to 0.8.11. Date: Sun, 6 Jun 2021 02:06:51 +0200 Message-ID: <20210606000651.28252-3-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.31.1 In-Reply-To: <20210606000651.28252-1-madalinionel.patrascu@mdc-berlin.de> References: <20210606000651.28252-1-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-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-14.0.0.3080-8.6.1012-26202.003 X-TM-AS-Result: No-10--2.193700-8.000000 X-TMASE-MatchedRID: b81qNyJin326/eEqqZaZmj8Ckw9b/GFeTJDl9FKHbrn7fZJfDdCIXISC l3uvYUiSC6+Zjvylmgt6n3hIvN5dLV1nLdLFTV2cB8FxO/BQHsIXivwflisSrPn6214PlHOFxVZ wHGSRvcr7bbB/MBzIMwa+LGYKVz1S64qzaFKxje/p9R8QuoVQfwoXSOLC5a44Mv8YehqjR1W2Ed aacwTXAwjQkSkt0eZ8xtgTkG+GaOc7mT8/EEC+/tqQ6Du6Gk+zSoaRTYgt4N4R34ro7k23nchyR F2A1zUTGQye9itdQoSTW+R0C23mx+06nIdMxLTR194/5X9VfCzy36l+EEw5vMWgQbecfk3OmA0y ITMNzjl9LQinZ4QefPcjNeVeWlqY+gtHj7OwNO22utO5qEfOUQagFwm5AKiUQc8ZI+qm+CvOWb5 27F6P3e5+ZKC55ULt9iVjwUzsDRMiZttKiK21f3MwptG1PBbpxe/6SX9BFtprMM4SZ8lXNG/H7L hIKjO20bWl8H0Q2RO0ML47Km+X9EYOAQXCbpqgPpCuffGH9zI= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--2.193700-8.000000 X-TMASE-Version: SMEX-14.0.0.3080-8.6.1012-26202.003 X-TM-SNTS-SMTP: 67D3CBE25DC29F6B807DC531479B39371E3A2A267D8CCFAAAD380A15E881181C2000:F X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 46955 Cc: rekado@elephly.net, =?UTF-8?q?M=C4=83d=C4=83lin=20Ionel=20Patra=C8=99cu?= 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-cooler): Update to 0.8.11. --- gnu/packages/bioinformatics.scm | 38 +++++++++++++++++++++++++++------ 1 file changed, 32 insertions(+), 6 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index dab097381a..988f663ceb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11717,15 +11717,34 @@ fasta subsequences.") (define-public python-cooler (package (name "python-cooler") - (version "0.8.7") + (version "0.8.11") (source (origin (method url-fetch) (uri (pypi-uri "cooler" version)) (sha256 (base32 - "01g6gqix9ba27sappz6nfyiwabzrlf8i5fn8kwcz8ra356cq9crp")))) + "1i96fmpsimj4wrx51rxn8lw2gqxf5a2pvrj5rwdd6ivnm3pmhyrn")))) (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-tests + (lambda _ + (substitute* "tests/test_create.py" + (("def test_roundtrip") + (string-append "@pytest.mark.skip(reason=\"requires network " + "access to genome.ucsc.edu\")\n" + "def test_roundtrip"))) + (substitute* "tests/test_util.py" + (("def test_fetch_chromsizes") + (string-append "@pytest.mark.skip(reason=\"requires network " + "access to genome.ucsc.edu\")\n" + "def test_fetch_chromsizes"))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python" "-m" "pytest" "-v"))))))) (propagated-inputs `(("python-asciitree" ,python-asciitree) ("python-biopython" ,python-biopython) @@ -11741,11 +11760,18 @@ fasta subsequences.") ("python-pysam" ,python-pysam) ("python-pyyaml" ,python-pyyaml) ("python-scipy" ,python-scipy) - ("python-simplejson" ,python-simplejson))) + ("python-simplejson" ,python-simplejson) + ("python-six" ,python-six) + ("python-sparse" ,python-sparse))) (native-inputs - `(("python-mock" ,python-mock) - ("python-pytest" ,python-pytest))) - (home-page "https://github.com/mirnylab/cooler") + `(("python-codecov" ,python-codecov) + ("python-ipytree" ,python-ipytree) + ("python-mock" ,python-mock) + ("python-pytest" ,python-pytest) + ("python-pytest-cov" ,python-pytest-cov) + ("python-pytest-flake8" ,python-pytest-flake8))) + ;;almost all the projects of the Mirnylab are moved under Open2C umbrella + (home-page "https://github.com/open2c/cooler") (synopsis "Sparse binary format for genomic interaction matrices") (description "Cooler is a support library for a sparse, compressed, binary persistent -- 2.31.1 From debbugs-submit-bounces@debbugs.gnu.org Sun Jun 06 02:23:34 2021 Received: (at 46955) by debbugs.gnu.org; 6 Jun 2021 06:23:34 +0000 Received: from localhost ([127.0.0.1]:50494 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lpmC6-0007YI-Bg for submit@debbugs.gnu.org; Sun, 06 Jun 2021 02:23:34 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21152) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lpmC1-0007Y7-M0 for 46955@debbugs.gnu.org; Sun, 06 Jun 2021 02:23:32 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1622960606; cv=none; d=zohomail.com; s=zohoarc; b=cXbSdEz2CXi8QxT0gdfpfIHRL+GDLky5tzGUM/chhRhkcR1eX6hV7q4EbgWBkvPSpU22Ct3kVwuxDU5q4KSwNl2UaQR8PHm6ZqRGddQgfEgqaQFtz08YDgcjOMDxLgyAZh7OLVmfeqL1I8ULqg6SYPh/UHMw0w5wV1nefZudLOI= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1622960606; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=H+bqrYZPZbly4ZVcExtIw0pQwC48NUwABsfRcNY8krY=; b=RCPAvCcdpE0Askan7kOYW6WmqPgelwUqXoqgq5sp2yW+SbMCZZub8d45j1QysRmiL8cQ2OVIgXQZYzysElSw/1PR5BzlkrN3aSrXt6mSsEiKU2C42v6V98SelEBjdAObHRvzrsfUmJCYYh9J80JU4kX7eDpUBEu4RhJE5Oq2wKU= 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=1622960606; 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=H+bqrYZPZbly4ZVcExtIw0pQwC48NUwABsfRcNY8krY=; b=R+yCea7rNL6d5V9Y6rxz5/DOqi1GMbPGDnU4tHku968A1zTJVX3yeH5KwfScnqLb XrzlhGhLgadd1L99H8xJk3lkJnbmaw/MbbvOTuhHCQZvyWsbBwGIcxdm0tojs7lYtwg l5OP2/hXElVnWewdyRirTYbcL9Y5/3wxroNQQkZI= Received: from localhost (p54ad4313.dip0.t-ipconnect.de [84.173.67.19]) by mx.zohomail.com with SMTPS id 1622960603461961.8197035867338; Sat, 5 Jun 2021 23:23:23 -0700 (PDT) References: <20210606000651.28252-1-madalinionel.patrascu@mdc-berlin.de> <20210606000651.28252-2-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.4.15; emacs 27.2 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [PATCH 2/3] gnu: Add python-ipytree. In-reply-to: <20210606000651.28252-2-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: Sun, 06 Jun 2021 08:23:20 +0200 Message-ID: <87lf7ntstj.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 46955 Cc: 46955@debbugs.gnu.org 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/python-xyz.scm (python-ipytree): New variable. ipytree contains minified JavaScript that should be built from=20 source instead. We can usually minify JavaScript sources with=20 esbuild. Could you please check if the sources for all minified JavaScript=20 are included and then 1. delete all minified JavaScript in a source snippet 2. add a build phase to minify the JavaScript from readable source=20 code? Thanks! --=20 Ricardo From debbugs-submit-bounces@debbugs.gnu.org Sun Jun 06 02:36:50 2021 Received: (at 46955-done) by debbugs.gnu.org; 6 Jun 2021 06:36:50 +0000 Received: from localhost ([127.0.0.1]:50502 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lpmOv-0007tg-Nn for submit@debbugs.gnu.org; Sun, 06 Jun 2021 02:36:49 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21145) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lpmOn-0007tQ-Dr for 46955-done@debbugs.gnu.org; Sun, 06 Jun 2021 02:36:48 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1622961399; cv=none; d=zohomail.com; s=zohoarc; b=WppD8oHZi6LVPJ64mBdEPGeEMSdFTTf5xHR+dZDwV6aeEGjCa2yajkjuuqwyUqTiEOZxHyUOrgzrMRqQp9n80dppGKennK9h6kIDcjUwvKlLSEl6vUzw+iQpn4hI9DF9/GXOHBMFD9sADp7Yg0HydZlb5mhgXVKU1xsph5HFrSU= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1622961399; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=M0iJw0gDJ24Ryf0k5NcCJswGfUayxSRgjYISp+UtZuw=; b=TtImo5BfaLRmVI0nObdnqTtv+iRMHJTUBVUpj12Phj5hAcyJyxsN0kT17qJ7Kq97j9I2FDWKA2CyIh7MIo2ZhZ/pWCdR242qnlPZ6isNaVd75rYGXl3bIfTK31aOMR9Q4atyv0CJjMDRGdbdWR4x/qGpMoTfY2QgumPP4TXcCBM= 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=1622961399; 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=M0iJw0gDJ24Ryf0k5NcCJswGfUayxSRgjYISp+UtZuw=; b=L1YAa5yjjNc5BpIsF0fAE8NtMDnN1QfLyCSOdWBS6E1sEw6dkTnG7YETeefB0/kf wVfS4zTqpbEwGuVS8VvIfNjrEiUGGgun9f5w4gUb13XzYuaRAj5/bK8etTrrHX3svhJ 5V+qLMTM87tMB2MgCOMn9inJePUhhuVAYohduUec= Received: from localhost (p54ad4313.dip0.t-ipconnect.de [84.173.67.19]) by mx.zohomail.com with SMTPS id 1622961398341787.6157080332341; Sat, 5 Jun 2021 23:36:38 -0700 (PDT) References: <20210606000651.28252-1-madalinionel.patrascu@mdc-berlin.de> <20210606000651.28252-3-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.4.15; emacs 27.2 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [PATCH 3/3] gnu: python-cooler: Update to 0.8.11. In-reply-to: <20210606000651.28252-3-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: Sun, 06 Jun 2021 08:36:35 +0200 Message-ID: <87im2rts7g.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 46955-done Cc: 46955-done@debbugs.gnu.org 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, thanks for the patches! > * gnu/packages/bioinformatics.scm (python-cooler): Update to=20 > 0.8.11. I changed the commit message to mention all changes, including=20 those in arguments, propagated-inputs, and native-inputs. I disabled the one test that needs ipytree and removed ipytree=20 from the inputs. Pushed to the =E2=80=9Cmaster=E2=80=9D branch with commit d1e7b50dbf (excep= t=20 ipytree). (One more thing: please send updated patches with =E2=80=9Cgit=20 format-patch -v2=E2=80=9D (or =E2=80=9Cgit send-email -v2=E2=80=9D), so tha= t we can=20 distinguish different versions of patch series automatically and=20 download them in one batch.) --=20 Ricardo From unknown Thu Jun 19 14:22:20 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Sun, 04 Jul 2021 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