From unknown Mon Jun 23 23:53:37 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#38637] (no subject) Resent-From: mpatras Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 16 Dec 2019 15:24:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 38637 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: 38637@debbugs.gnu.org X-Debbugs-Original-To: Received: via spool by submit@debbugs.gnu.org id=B.15765098182040 (code B ref -1); Mon, 16 Dec 2019 15:24:01 +0000 Received: (at submit) by debbugs.gnu.org; 16 Dec 2019 15:23:38 +0000 Received: from localhost ([127.0.0.1]:40217 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1igsDi-0000Wo-CM for submit@debbugs.gnu.org; Mon, 16 Dec 2019 10:23:38 -0500 Received: from lists.gnu.org ([209.51.188.17]:58268) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1igsDh-0000Wg-49 for submit@debbugs.gnu.org; Mon, 16 Dec 2019 10:23:37 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:56549) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1igsDe-0002qA-Jf for guix-patches@gnu.org; Mon, 16 Dec 2019 10:23:36 -0500 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: ** X-Spam-Status: No, score=2.6 required=5.0 tests=BAYES_50,MISSING_SUBJECT, RCVD_IN_DNSWL_NONE,URIBL_BLOCKED autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1igsDd-0002Yz-A0 for guix-patches@gnu.org; Mon, 16 Dec 2019 10:23:34 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:52497) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1igsDc-0002Uh-Qj for guix-patches@gnu.org; Mon, 16 Dec 2019 10:23:33 -0500 Received: from localhost (localhost [127.0.0.1]) by c2062.mx.srv.dfn.de (Postfix) with ESMTP id 9F8C6300070 for ; Mon, 16 Dec 2019 16:23:22 +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=1576509802; x= 1578324203; bh=Hq+Q1OJDYSlu4sQ6uzQAmH+i1saDUMqSIV0+7D4lBOA=; b=T SMdSZ4h+KlJs9f3Yxy+xwA/toa4eOV8odALa6oOVPHS628TidkMKt5ps4umFpvbG hKgRa0ovsP698YMG4o4oz+HQxLCtBvFe3n5b/43jABoJEAycv4FiDd7QlG2EuGGr JL/l28c47V9prCXfWsEwAU9WtEC9lFykrePypQ5Tdw= 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 gAJjmsp8kCfj for ; Mon, 16 Dec 2019 16:23:22 +0100 (CET) Received: from SW-IT-P-CAS1.mdc-berlin.net (mgw10-1.mdc-berlin.de [141.80.113.53]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS for ; Mon, 16 Dec 2019 16:23:22 +0100 (CET) Received: from [141.80.113.108] (141.80.113.108) by SW-IT-P-CAS1.mdc-berlin.net (141.80.113.53) with Microsoft SMTP Server (TLS) id 14.3.468.0; Mon, 16 Dec 2019 16:23:21 +0100 From: mpatras Message-ID: <326bca30-7d18-a02b-9400-2f12bc0e5c21@mdc-berlin.de> Date: Mon, 16 Dec 2019 16:23:21 +0100 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:68.0) Gecko/20100101 Thunderbird/68.2.2 MIME-Version: 1.0 Content-Type: text/plain; charset="utf-8"; format=flowed Content-Language: en-US X-Originating-IP: [141.80.113.108] X-TM-AS-Product-Ver: SMEX-12.5.0.1684-8.5.1010-25108.000 X-TM-AS-Result: No-1.352500-8.000000-10 X-TMASE-MatchedRID: GaP57vPtnWgl08/xxlO+L5PQTDqTymbSL60/awpuq4h7lDzh8Z+Ehs48 74k0JUprIfqPF9C+GOjMdS7HrUtSKJg39Rgsjteo585VzGMOFzAaTOa7uOFmI9AtbEEX0MxBAB5 fZ54AVbsqtq5d3cxkNRqXnrxrKCOX3rRWHXbuL9/rJZzWVJNoZQ8bTDcKz9rGV7MeTQVvw2aCDO m1rnoaWhEfOUfSfVq2msB42YsUbCEeF5LlwpQcnijLmqRM9sY4QwymtxuJ6y0= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-1.352500-8.000000 X-TMASE-Version: SMEX-12.5.0.1684-8.5.1010-25108.000 X-TM-SNTS-SMTP: C301286019538A221E78EA40561AFFDE4341AEACA1D7D811783960CDD66DA6EB2000:9 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] [fuzzy] X-Received-From: 194.95.238.172 X-Spam-Score: 0.6 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -0.4 (/) --=20 M=C4=83d=C4=83lin Ionel Patra=C8=99cu System Administrator Bioinformatics and Omics Data Science The Berlin Institute for Medical Systems Biology (BIMSB) Max Delbr=C3=BCck Center (MDC) Hannoversche Str. 28, 10115 Berlin House 101, room 1.60 From unknown Mon Jun 23 23:53:37 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#38637] [PATCH 1/4] gnu: Add python-iocapture. References: <326bca30-7d18-a02b-9400-2f12bc0e5c21@mdc-berlin.de> In-Reply-To: <326bca30-7d18-a02b-9400-2f12bc0e5c21@mdc-berlin.de> 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: Mon, 16 Dec 2019 15:26:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 38637 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <38637@debbugs.gnu.org> Cc: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Received: via spool by 38637-submit@debbugs.gnu.org id=B38637.15765099432355 (code B ref 38637); Mon, 16 Dec 2019 15:26:02 +0000 Received: (at 38637) by debbugs.gnu.org; 16 Dec 2019 15:25:43 +0000 Received: from localhost ([127.0.0.1]:40225 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1igsFi-0000bu-Vy for submit@debbugs.gnu.org; Mon, 16 Dec 2019 10:25:43 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:55229) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1igsFh-0000bl-Gj for 38637@debbugs.gnu.org; Mon, 16 Dec 2019 10:25:42 -0500 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id 0FD3B160087 for <38637@debbugs.gnu.org>; Mon, 16 Dec 2019 16:25:40 +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=1576509939; x=1578324340; bh=5zU33i8BiD5ycUTmZnBed2ODcJ9T6ysaKfiVDIxXjzI=; b=dLE7G1ifLVKI YZFTQAxGW/Yg32cQ0KUz6dp/k+qe3s0mx+A0j5cIEQ2dCU8i6SGHx29whpgGznK7 fyJh+i6moxHQMUGuYl+GLYBbwXj8+5mYQJon+jgk7QFrDDWE8d5dogntl1l0kKgH 0/DE/kBbMpsZCpkBgfpdzemsSKg7IJk= 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 O-UGlIeq5car for <38637@debbugs.gnu.org>; Mon, 16 Dec 2019 16:25:39 +0100 (CET) Received: from SW-IT-P-CAS4.mdc-berlin.net (mgw10-4.mdc-berlin.de [141.80.113.59]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS for <38637@debbugs.gnu.org>; Mon, 16 Dec 2019 16:25:39 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-CAS4.mdc-berlin.net (141.80.113.59) with Microsoft SMTP Server (TLS) id 14.3.468.0; Mon, 16 Dec 2019 16:25:38 +0100 From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Date: Mon, 16 Dec 2019 16:25:16 +0100 Message-ID: <20191216152519.3595-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.17.1 MIME-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 8bit X-Originating-IP: [141.80.113.106] X-TM-AS-Product-Ver: SMEX-12.5.0.1684-8.5.1010-25108.000 X-TM-AS-Result: No-3.948300-8.000000-10 X-TMASE-MatchedRID: aQJ0g3G0xD+1HHtIgGMIGJzEHTUOuMX3S1zwNuiBtITfUZT83lbkEEzj AvfMcYuiKkq/93/PFXfQGSl+EhfKzolL8gBSDPjtUharQ9sKnjE89zBT8EOluUxmd2Z3Ku/v4/o D+4UDxRLxNTucnkNjDvmh1TGmU0eWI3V3NvDzuZrPmvnL2ai5IBDP6b38u9ZoEd+K6O5Nt53ukJ QjHbvwOZVsRZQI9wGof27yMf+cnuj3uvD+1Bkl7QfBcTvwUB7CGkSehlxL483cmiyPUwQrCp4CI KY/Hg3AcmfM3DjaQLHEQdG7H66TyN+E/XGDLHcMP4pjObwQK01oLHwNwFsHmNUhRVmmH7qX3KP5 1DYPcdkS4JCVpmlWJx51FwtapEXJm1JiyTWAk+CUMIC55vNyrqLpfvQ0IGgtghKt2QgWp647hjZ 1QGEv8FMFhPtEZehbEkAQkfQ24dP1oCdtaxbMdw== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--3.948300-8.000000 X-TMASE-Version: SMEX-12.5.0.1684-8.5.1010-25108.000 X-TM-SNTS-SMTP: 8B4D90F73E7692C0FE61C6C788D34127329351A07CF0E7F1B1C928DC28424AA72000:9 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 (-) * gnu/packages/python-xyz.scm (python-iocapture): New variable. --- gnu/packages/python-xyz.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 03dddcde43..f26bc7719b 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -67,6 +67,7 @@ ;;; Copyright © 2019 Giacomo Leidi ;;; Copyright © 2019 Wiktor Żelazny ;;; Copyright © 2019 Tanguy Le Carrour +;;; Copyright © 2019 Mădălin Ionel Patrașcu ;;; ;;; This file is part of GNU Guix. ;;; @@ -16795,3 +16796,32 @@ services to what you expect in your tests.") (define-public python2-ujson (package-with-python2 python-ujson)) + +(define-public python-iocapture + ;; the latest is more than year newer than the latest realease + (let ((commit "fdc021c431d0840303908dfc3ca8769db383595c") + (revision "1")) + (package + (name "python-iocapture") + (version "0.1.2") + (source + (origin + (method git-fetch) + (uri (git-reference (url "https://github.com/oinume/iocapture.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1mkbhqibxvgwg0p7slr8dfraa3g2s6bsayladhax2jccwj4kcndz")))) + (build-system python-build-system) + (propagated-inputs + `(("python-flexmock" ,python-flexmock) + ("python-pytest" ,python-pytest) + ("python-pytest-cov" ,python-pytest-cov) + ("python-six" ,python-six))) + (home-page "https://github.com/oinume/iocapture") + (synopsis "Phython capuring tool for stdout and stderr") + (description + "python-iocapture helps you to capture the standard out (stdout) and the +standard error channel (stderr) in your program.") + (license license:expat)))) ; MIT license \ No newline at end of file -- 2.17.1 From unknown Mon Jun 23 23:53:37 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#38637] [PATCH 2/4] gnu: Add python-argh. 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: Mon, 16 Dec 2019 15:27:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 38637 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <38637@debbugs.gnu.org> Cc: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Received: via spool by 38637-submit@debbugs.gnu.org id=B38637.15765099712433 (code B ref 38637); Mon, 16 Dec 2019 15:27:02 +0000 Received: (at 38637) by debbugs.gnu.org; 16 Dec 2019 15:26:11 +0000 Received: from localhost ([127.0.0.1]:40230 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1igsGB-0000dB-Bx for submit@debbugs.gnu.org; Mon, 16 Dec 2019 10:26:11 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:46915) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1igsG9-0000d3-2C for 38637@debbugs.gnu.org; Mon, 16 Dec 2019 10:26:09 -0500 Received: from localhost (localhost [127.0.0.1]) by c2062.mx.srv.dfn.de (Postfix) with ESMTP id 5C98230009F for <38637@debbugs.gnu.org>; Mon, 16 Dec 2019 16:26:08 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:references:in-reply-to :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1576509967; x=1578324368; bh=/2keoQ8tg2e0n0ZGOHHV1bwotvXqlnmKYsP5kSBENkI=; b=HgGho7A5zG5L xw3+7MeM2rm7fWcJH3hNMBe2VNl8aDtK4QnEq/+qCTaVlySGsYH3x/JlPzg7hvaA 6PW8yaqQpMviKv0/Ba1Dubi8DAqucCBkdy8Tppg2uh8TUX/oh+49H7G7TK8Avypt k3DBWcElEy3KxOMH/y2HBhdo5JGT+PY= 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 dax7xrIqAm4v for <38637@debbugs.gnu.org>; Mon, 16 Dec 2019 16:26:07 +0100 (CET) Received: from SW-IT-P-CAS4.mdc-berlin.net (mgw10-4.mdc-berlin.de [141.80.113.59]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS for <38637@debbugs.gnu.org>; Mon, 16 Dec 2019 16:26:07 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-CAS4.mdc-berlin.net (141.80.113.59) with Microsoft SMTP Server (TLS) id 14.3.468.0; Mon, 16 Dec 2019 16:26:07 +0100 From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Date: Mon, 16 Dec 2019 16:25:17 +0100 Message-ID: <20191216152519.3595-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.17.1 In-Reply-To: <20191216152519.3595-1-madalinionel.patrascu@mdc-berlin.de> References: <20191216152519.3595-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-TM-AS-Product-Ver: SMEX-12.5.0.1684-8.5.1010-25108.000 X-TM-AS-Result: No-0.600000-8.000000-10 X-TMASE-MatchedRID: cHmOkQj+tbu1HHtIgGMIGJzEHTUOuMX3ljgw/8s6b3cHZBaLwEXlKNnf JrUSEbFDWvdVuCB3RaBf4K3Xpj36sA0dNfaoLdHJB8FxO/BQHsIaRJ6GXEvjzQoRkM1Bz4Qo1GW bKN8y669bpnzCWFVqu/Cjfnyjef0tgtjbI7qady+InASnzB5VfNs4MOUU/wa2NxBxRkrUguDMqE j88z7CrxNvnR3dZuEWNHouaOYdeO/r3ekoeAIzf5ZJ7rgA28k0JMcNgn27HQEi0/kre3GpulcAZ +7BKb2qOWZHzEb+oITBexZ0niPUmJf/BtAg4oG6YuJV6fJ53KPrixWWWJYrHx8TzIzimOwPC24o EZ6SpSk6XEE7Yhw4Flljj5TnBLJ94Ag6QdpnBnf8mKPdapm+f9F1gCp+FnTS9RQdNVjiYG+PTLn BpeQHaG5wxplUyyOW+RSfRoH9AilMiDUVsFKcP6PxvuJPX7GvZjWfMVA8wvMfAjFbCsqQWX7h78 xQkeMv5UQ9TF0JjMw= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--0.600000-8.000000 X-TMASE-Version: SMEX-12.5.0.1684-8.5.1010-25108.000 X-TM-SNTS-SMTP: F75A0BB1D8702B16EF68F235485C93232469A274BAF94D7A5DBF1E04DF2F40732000:9 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 (-) * gnu/packages/python-xyz.scm (python-argh): New variable. --- gnu/packages/python-xyz.scm | 37 ++++++++++++++++++++++++++++++++++++- 1 file changed, 36 insertions(+), 1 deletion(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index f26bc7719b..1f2149c9c4 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -16824,4 +16824,39 @@ services to what you expect in your tests.") (description "python-iocapture helps you to capture the standard out (stdout) and the standard error channel (stderr) in your program.") - (license license:expat)))) ; MIT license \ No newline at end of file + (license license:expat)))) ; MIT license + +(define-public python-argh + ;; there are 21 commits after the latest release + ;; those contains important improvements + (let ((commit "dcd3253f2994400a6a58a700c118c53765bc50a4") + (revision "1")) + (package + (name "python-argh") + (version "0.26.2") + (source + (origin + (method git-fetch) + (uri (git-reference (url "https://github.com/neithere/argh.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1p5h3dnpbsjmqrvil96s71asc6i3gpinmbrabqmwnrsxprz7r3ns")))) + (build-system python-build-system) + (propagated-inputs + `(("python-iocapture" ,python-iocapture) + ("python-mock" ,python-mock) + ("python-pytest" ,python-pytest) + ("python-pytest-cov" ,python-pytest-cov) + ("python-pytest-xdist" ,python-pytest-xdist) + ("python-tox" ,python-tox))) + (home-page "https://github.com/neithere/argh/") + (synopsis "Argparse wrapper with natural syntax") + (description + "python-argh is a small library that provides several layers of +abstraction on top of python-argparse. The layers can be mixed. It is always +possible to declare a command with the highest possible (and least flexible) +layer and then tune the behaviour with any of the lower layers including the +native API of python-argparse.") + (license license:lgpl3)))) -- 2.17.1 From unknown Mon Jun 23 23:53:37 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#38637] [PATCH 3/4] gnu: python-pyfaidx: Update to 0.5.7. 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: Mon, 16 Dec 2019 15:27:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 38637 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <38637@debbugs.gnu.org> Cc: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Received: via spool by 38637-submit@debbugs.gnu.org id=B38637.15765099772451 (code B ref 38637); Mon, 16 Dec 2019 15:27:02 +0000 Received: (at 38637) by debbugs.gnu.org; 16 Dec 2019 15:26:17 +0000 Received: from localhost ([127.0.0.1]:40233 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1igsGG-0000dT-MH for submit@debbugs.gnu.org; Mon, 16 Dec 2019 10:26:16 -0500 Received: from a2062.mx.srv.dfn.de ([194.95.232.172]:33965) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1igsGF-0000dK-27 for 38637@debbugs.gnu.org; Mon, 16 Dec 2019 10:26:15 -0500 Received: from localhost (localhost [127.0.0.1]) by a2062.mx.srv.dfn.de (Postfix) with ESMTP id A766DA0070 for <38637@debbugs.gnu.org>; Mon, 16 Dec 2019 16:26:13 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:references:in-reply-to :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1576509973; x=1578324374; bh=Tbl8puB6TVHvuDG3lkY8mGvVCH6JoCEIdVruoDHQz5A=; b=JanUsK9l30n9 KFIsQFf00qWQZ3IaN1PHk259IDJB9khvtcUPKW6wRUPoWCHKEbnPCGEUfFr1tD3m rQjMpfSBUAI7cRQBp25VA2PFw2FNiW7SGzOgeCjVQ5BpHI9Kv4t7M1fCDRfCM4bJ iMQfNjgQiuvF54Idewjv3qA39Iy93aQ= 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 PfTn0lICufgF for <38637@debbugs.gnu.org>; Mon, 16 Dec 2019 16:26:13 +0100 (CET) Received: from SW-IT-P-CAS4.mdc-berlin.net (mgw10-4.mdc-berlin.de [141.80.113.59]) by a2062.mx.srv.dfn.de (Postfix) with ESMTPS for <38637@debbugs.gnu.org>; Mon, 16 Dec 2019 16:26:13 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-CAS4.mdc-berlin.net (141.80.113.59) with Microsoft SMTP Server (TLS) id 14.3.468.0; Mon, 16 Dec 2019 16:26:12 +0100 From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Date: Mon, 16 Dec 2019 16:25:18 +0100 Message-ID: <20191216152519.3595-3-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.17.1 In-Reply-To: <20191216152519.3595-1-madalinionel.patrascu@mdc-berlin.de> References: <20191216152519.3595-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-TM-AS-Product-Ver: SMEX-12.5.0.1684-8.5.1010-25108.000 X-TM-AS-Result: No-1.708400-8.000000-10 X-TMASE-MatchedRID: kogcqlwISk1eDtEKgt5AZnCO70QAsBdCS1zwNuiBtITfUZT83lbkEEjq KJrwQlkulCvwn7kWok/9E3D6X+2jHW2x/ChgpGE+2pDoO7oaT7PrixWWWJYrHx8TzIzimOwP0C1 sQRfQzEHEQdG7H66TyN+E/XGDLHcMn2AClij7gwobrmSMSpigQPuEm6L5N4z3SXHNEouOt8hWtf hkA2ZJSlrU19DWbn9KFSj8OM7tF8C1Wp2mlHwLqq2UOPu9UOVpghKt2QgWp647hjZ1QGEv8FMFh PtEZehbEkAQkfQ24dP1oCdtaxbMdw== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--1.708400-8.000000 X-TMASE-Version: SMEX-12.5.0.1684-8.5.1010-25108.000 X-TM-SNTS-SMTP: 9E2EEBF194A8351172DF57F4923D3A4A0D4266860C06326FFD9FCAB95496603A2000:9 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 (-) * gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.5.7. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bdb3ff761b..c8396a33dd 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13419,14 +13419,14 @@ bgzipped text file that contains a pair of genomic coordinates per line.") (define-public python-pyfaidx (package (name "python-pyfaidx") - (version "0.5.4.2") + (version "0.5.7") (source (origin (method url-fetch) (uri (pypi-uri "pyfaidx" version)) (sha256 (base32 - "0y5zyjksj1rdglj601xd2bbni5abhdh622y3ck76chyzxz9z4rx8")))) + "02jvdx3ksy6w5gd29i1d0g0zsabbz7c14qg482ff7pza6sdl0b2i")))) (build-system python-build-system) (propagated-inputs `(("python-six" ,python-six))) -- 2.17.1 From unknown Mon Jun 23 23:53:37 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#38637] [PATCH 4/4] gnu: Add python-gffutils. 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: Mon, 16 Dec 2019 15:27:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 38637 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <38637@debbugs.gnu.org> Cc: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Received: via spool by 38637-submit@debbugs.gnu.org id=B38637.15765099812468 (code B ref 38637); Mon, 16 Dec 2019 15:27:03 +0000 Received: (at 38637) by debbugs.gnu.org; 16 Dec 2019 15:26:21 +0000 Received: from localhost ([127.0.0.1]:40236 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1igsGK-0000dk-Vm for submit@debbugs.gnu.org; Mon, 16 Dec 2019 10:26:21 -0500 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:53387) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1igsGI-0000db-Sk for 38637@debbugs.gnu.org; Mon, 16 Dec 2019 10:26:19 -0500 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id 609A6160087 for <38637@debbugs.gnu.org>; Mon, 16 Dec 2019 16:26:18 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:references:in-reply-to :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1576509977; x=1578324378; bh=WdL9SvRpcJJrzI72S/HlsQA2MPbNLi8d3H5jyPRkuOM=; b=FAg2vCvQD56D hL0MhAbXeAo1aBtRgJxJn/yOJXdYCTox3Nj14viyWnzgzcWnBWclH1sTHDi6m5mo uPsLtY/0MYhMh2XIs81kl57PxsFYJmcHWn/kxRA/onVih9uzHQweHRYo40WXbBjU oPFl23AR7Fv+RA0+vh5313pnXg4d/M8= 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 4_CPqCxcpZjV for <38637@debbugs.gnu.org>; Mon, 16 Dec 2019 16:26:17 +0100 (CET) Received: from SW-IT-P-CAS4.mdc-berlin.net (mgw10-4.mdc-berlin.de [141.80.113.59]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS for <38637@debbugs.gnu.org>; Mon, 16 Dec 2019 16:26:17 +0100 (CET) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-CAS4.mdc-berlin.net (141.80.113.59) with Microsoft SMTP Server (TLS) id 14.3.468.0; Mon, 16 Dec 2019 16:26:17 +0100 From: =?UTF-8?Q?M=C4=83d=C4=83lin?= Ionel =?UTF-8?Q?Patra=C8=99cu?= Date: Mon, 16 Dec 2019 16:25:19 +0100 Message-ID: <20191216152519.3595-4-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.17.1 In-Reply-To: <20191216152519.3595-1-madalinionel.patrascu@mdc-berlin.de> References: <20191216152519.3595-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.113.106] X-TM-AS-Product-Ver: SMEX-12.5.0.1684-8.5.1010-25108.000 X-TM-AS-Result: No-9.684700-8.000000-10 X-TMASE-MatchedRID: cDFwyY+CAdryD+EqUBix4ZzEHTUOuMX3S1zwNuiBtITdacCPv0XN4gSm rW+u3NBf8Tx6bfhlbmfqc3eDqWRWoMVVIEyvZyb0N8QmGQ8nUhrIEQTlh1/QMatkcxxU6EVIeyY Rtv+ZW85LVtcjSeah83NERYbQXfHtb52irmhQ5bIHwXE78FAewgRryDXHx6oXOK4yXNWF4bBfPe q3iAoZIjZMBH4YYyYkhbopPwYOhRPnxyk6kt+DQ8sK9y5C/Fiy4k1wcu9E2kRO5bh7WmoyDRaQe ocCrFbE5R08LIISReJChbrzKpI3S3XZkAUtUetntgyUiC29Qd7rixWWWJYrHx8TzIzimOwP8dA3 q/uj/L/EQdG7H66TyF82MXkEdQ77ZpGYo2OTDe+K4HLwdlBk9sFvLeqZLHq5YPD+d6Fcm0TeBYH HPMO4Xw== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--9.684700-8.000000 X-TMASE-Version: SMEX-12.5.0.1684-8.5.1010-25108.000 X-TM-SNTS-SMTP: 1505AEE8AEB2799CBB2C1D5A395228D630B5CCEA83E07A220BFF2974FE49163E2000:9 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 (-) Co-authored-by: Ricardo Wurmus * gnu/packages/bioinformatics.scm (python-gffutils): New variable. --- gnu/packages/bioinformatics.scm | 51 +++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c8396a33dd..14c0b59067 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15370,3 +15370,54 @@ methylation metrics from them. MethylDackel requires an indexed fasta file containing the reference genome as well.") ;; See https://github.com/dpryan79/MethylDackel/issues/85 (license license:expat))) + +(define-public python-gffutils + ;; The latest release is older more than a year than the latest commit + (let ((commit "4034c54600813b1402945e12faa91b3a53162cf1") + (revision "1")) + (package + (name "python-gffutils") + (version (git-version "0.9" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/daler/gffutils.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1rwafjdnbir5wnk0ap06ww4lra3p5frhy7mfs03rlldgfnwxymsn")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda _ + ;; Tests need to access the HOME directory + (setenv "HOME" "/tmp") + (invoke "nosetests" "-a" "!slow"))) + (add-after 'unpack 'make-gz-files-writable + (lambda _ + (for-each make-file-writable + (find-files "." "\\.gz")) + #t))))) + (propagated-inputs + `(("python-argcomplete" ,python-argcomplete) + ("python-argh" ,python-argh) + ("python-biopython" ,python-biopython) + ("python-pybedtools" ,python-pybedtools) + ("python-pyfaidx" ,python-pyfaidx) + ("python-simplejson" ,python-simplejson) + ("python-six" ,python-six))) + (native-inputs + `(("python-nose" , python-nose))) + (home-page "https://github.com/daler/gffutils") + (synopsis "Tool for manipulation of GFF and GTF files") + (description + "python-gffutils is a Python package for working with and manipulating the +GFF and GTF format files typically used for genomic annotations. The files are +loaded into a sqlite3 database, allowing much more complex manipulation of +hierarchical features (e.g., genes, transcripts, and exons) than is possible +with plain-text methods alone.") + (license license:expat)))) ;; MIT license -- 2.17.1 From unknown Mon Jun 23 23:53:37 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#38637] [PATCH 1/4] gnu: Add python-iocapture. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 16 Dec 2019 16:28:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 38637 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: 38637@debbugs.gnu.org Received: via spool by 38637-submit@debbugs.gnu.org id=B38637.157651367916536 (code B ref 38637); Mon, 16 Dec 2019 16:28:01 +0000 Received: (at 38637) by debbugs.gnu.org; 16 Dec 2019 16:27:59 +0000 Received: from localhost ([127.0.0.1]:40314 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1igtDz-0004Ie-Ev for submit@debbugs.gnu.org; Mon, 16 Dec 2019 11:27:59 -0500 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21122) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1igtDx-0004IU-1E for 38637@debbugs.gnu.org; Mon, 16 Dec 2019 11:27:57 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1576513675; cv=none; d=zohomail.com; s=zohoarc; b=m/89skcdwULEUxos6I0r9oRxgZipPcxq658sAXT8MfdgrjUShoeuQjBOGw/vGfHexoBUAJfwIKBLUAkRzwBp9bwEf2e3YCGZID6IP/BVSTMMcqiHMc/AnJefKrWthtNa+b+Pe5O6fRSIxM8t1v2yjyixRAr1lSY2A4RS7pk+MV0= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1576513675; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=rJdGZZrLXw4apLK4KxN6KueTX5jd4aSwkijqkpHzWQw=; b=LlO5FAeFVyocU4eY37b5mdNNTVUsGaDzd9Yv1WpbbZIZds8mZ7AlqDroS0VYbsXZWDiM/mdOoBTFiEkDH5dcSFAwNcrdoaf8a7Y0bcHra958J91SsuMgSNMqz359/suBbLgjH34vk8Ht3KsdFNz2q9q/27OP/YWatWSYVRZz7xI= 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=1576513675; 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=rJdGZZrLXw4apLK4KxN6KueTX5jd4aSwkijqkpHzWQw=; b=BysfK5prt+eI5nbAzD5FseQKxATn5EWxse4cdBVmeLoAsy7XIC+02jR74GN080/Y dFySqugguL+Esg6iUCFSbvviAK3GoPJLS2nG5FZCDUiMBeRi6FwxceSoeRQmtGHwgCb ZHMNMGiA2z8UhJf1gg7sm/XJg6Du7reUEnE7bNaM= Received: from localhost (p54AD4C83.dip0.t-ipconnect.de [84.173.76.131]) by mx.zohomail.com with SMTPS id 1576513674437437.71017388567736; Mon, 16 Dec 2019 08:27:54 -0800 (PST) References: <326bca30-7d18-a02b-9400-2f12bc0e5c21@mdc-berlin.de> <20191216152519.3595-1-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.2.0; emacs 26.3 From: Ricardo Wurmus In-reply-to: <20191216152519.3595-1-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: Mon, 16 Dec 2019 17:27:50 +0100 Message-ID: <87woawb5h5.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/python-xyz.scm (python-iocapture): New variable. thanks for the patch! > +(define-public python-iocapture > + ;; the latest is more than year newer than the latest realease I know what you mean but that=E2=80=99s not what the comment says ;) I changed it. > + (let ((commit "fdc021c431d0840303908dfc3ca8769db383595c") > + (revision "1")) > + (package > + (name "python-iocapture") > + (version "0.1.2") > + (source > + (origin > + (method git-fetch) > + (uri (git-reference (url "https://github.com/oinume/iocapture.git= ") > + (commit commit))) > + (file-name (git-file-name name version)) > + (sha256 > + (base32 > + "1mkbhqibxvgwg0p7slr8dfraa3g2s6bsayladhax2jccwj4kcndz")))) > + (build-system python-build-system) > + (propagated-inputs > + `(("python-flexmock" ,python-flexmock) > + ("python-pytest" ,python-pytest) > + ("python-pytest-cov" ,python-pytest-cov) > + ("python-six" ,python-six))) > + (home-page "https://github.com/oinume/iocapture") > + (synopsis "Phython capuring tool for stdout and stderr") Typos: Phython =E2=80=93> Python; capuring =E2=80=93> capturing > + (description > + "python-iocapture helps you to capture the standard out (stdout) a= nd the > +standard error channel (stderr) in your program.") > + (license license:expat)))) ; MIT license The term =E2=80=9CMIT license=E2=80=9D is ambiguous, so we don=E2=80=99t us= e it, not even in a comment. I noticed that the tests were not actually run, so I overrode the check phase. I pushed this with modifications to the =E2=80=9Cmaster=E2=80=9D branch wit= h commit dbcef44a0b. Thanks again! -- Ricardo From unknown Mon Jun 23 23:53:37 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#38637] [PATCH 2/4] gnu: Add python-argh. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 16 Dec 2019 16:33:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 38637 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: 38637@debbugs.gnu.org Received: via spool by 38637-submit@debbugs.gnu.org id=B38637.157651392817016 (code B ref 38637); Mon, 16 Dec 2019 16:33:01 +0000 Received: (at 38637) by debbugs.gnu.org; 16 Dec 2019 16:32:08 +0000 Received: from localhost ([127.0.0.1]:40323 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1igtHz-0004QO-SD for submit@debbugs.gnu.org; Mon, 16 Dec 2019 11:32:08 -0500 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 1igtHx-0004QF-Mn for 38637@debbugs.gnu.org; Mon, 16 Dec 2019 11:32:06 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1576513924; cv=none; d=zohomail.com; s=zohoarc; b=hVZ3oUmnLkTb4Jr0S0Ax+ynT3f2MuidcwCX7IhSrLfBWsDQ1NXtK4fp98ge+YAUl/YuYmS/opxS2XmKBV2SFgeNI6/FVQfXs2QkxBYhtlbeBH2ak6KdEjjtQG+17lhqaJuYW/RPbqdivp9AlgnnOoqomsyJ6vOZddlDYZ9+n+Jc= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1576513924; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=pgUV/z4OGg2DvUpxpv9enuR+uHj4X+7gAK+KnSCLRNU=; b=NgjUIvcSjtmJKh5RZVdLzDmSAxEQL0+K9UmN6fBE1AbnVf+v6Ezb+icUP0nN6hY+fJqdC4Uq73K3QM9ILAuvuvyFc+zXsSCQBpb/Q/z3BURoQQvkX08aJX/lL1H+OOBihAS1NMOOD/OrggCL+QoPoGpEMAz6lK6Y18TxSBUfPfg= 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=1576513924; 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=pgUV/z4OGg2DvUpxpv9enuR+uHj4X+7gAK+KnSCLRNU=; b=Yxf20UGhMTeftbDdm1pEM0O8h9fwJnDVRp7KgF8pDc3+34+5M96lJrsdGpFtqFOG VmUVz67V9+eFKjJEiML5nEsTdG6/BWt5XtHj50TsgetUk2jVy1TavMmXu2edjPuhOpE 2E75D1aLhyVvMkvc4xCWYmA66OobTt7X80ZvBe7s= Received: from localhost (p54AD4C83.dip0.t-ipconnect.de [84.173.76.131]) by mx.zohomail.com with SMTPS id 1576513922920477.1461315113751; Mon, 16 Dec 2019 08:32:02 -0800 (PST) References: <20191216152519.3595-1-madalinionel.patrascu@mdc-berlin.de> <20191216152519.3595-2-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.2.0; emacs 26.3 From: Ricardo Wurmus In-reply-to: <20191216152519.3595-2-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: Mon, 16 Dec 2019 17:31:59 +0100 Message-ID: <87v9qgb5a8.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 (-) M=C4=83d=C4=83lin Ionel Patra=C8=99cu = writes: > * gnu/packages/python-xyz.scm (python-argh): New variable. Pushed to the =E2=80=9Cmaster=E2=80=9D branch (commit db6bd842aa) with mino= r changes, such as this one: > + (license license:lgpl3)))) It=E2=80=99s actually LGPLv3+. Thank you! -- Ricardo From unknown Mon Jun 23 23:53:37 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#38637] [PATCH 3/4] gnu: python-pyfaidx: Update to 0.5.7. Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 16 Dec 2019 22:27:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 38637 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: 38637@debbugs.gnu.org Received: via spool by 38637-submit@debbugs.gnu.org id=B38637.157653521023675 (code B ref 38637); Mon, 16 Dec 2019 22:27:02 +0000 Received: (at 38637) by debbugs.gnu.org; 16 Dec 2019 22:26:50 +0000 Received: from localhost ([127.0.0.1]:40440 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1igypG-00069n-EG for submit@debbugs.gnu.org; Mon, 16 Dec 2019 17:26:50 -0500 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21124) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1igypE-00069d-NY for 38637@debbugs.gnu.org; Mon, 16 Dec 2019 17:26:49 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1576535207; cv=none; d=zohomail.com; s=zohoarc; b=NTEQEh9ezdNfXdxtig6ZRnIGHP76jZdcX3gFsadPqDhmBk2hanIqSaCB+ANu5JU9wPZmFfdtwMs+b8fULOvJ38klDO/t6hMy/NqgNT6W1FPBpwO9MJ4tq0QV2vEnqlw+9jGN+iffyR9lf9Vuuk/MM2mboP1Eg7SmCpH+J9sd9Wk= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1576535207; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=G/OTr6uciMsNACTRnIikJf4BNeIIukj/zckZevYZjxw=; b=CNEOnK+I18gwpeJrkDRbRYmJIcahRHKqBqdln9AXspE8zglRbZkoe52ydTeICqO/TTF29tZzLluedBVj1cRkAe7QeJkdpqoCqI4ue2BIlsy0DejnP9HjHvy5ySQ8efuqBm8/XbHeUDPf32f3vAh1HkjDiNlRXCzDw7bcNkVU81w= 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=1576535207; 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=G/OTr6uciMsNACTRnIikJf4BNeIIukj/zckZevYZjxw=; b=I9Jn9SUCs/4WQqwXi1imkiTRnbmXaKg3Xo+TLRZ8rJVifVZBDhmk0WxLoYlxIoyI vNknMSRjTXvbiIeDNXB2PwG9N9u5C1cx/lDU2ByVSesuNxKk3oaxftUm6604p7dJmNZ bESkQC/c7+rvUka9y6unVDPxXGjV1ZJD2KZ66nQo= Received: from localhost (p54AD4C83.dip0.t-ipconnect.de [84.173.76.131]) by mx.zohomail.com with SMTPS id 1576535206521817.6905921176365; Mon, 16 Dec 2019 14:26:46 -0800 (PST) References: <20191216152519.3595-1-madalinionel.patrascu@mdc-berlin.de> <20191216152519.3595-3-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.2.0; emacs 26.3 From: Ricardo Wurmus In-reply-to: <20191216152519.3595-3-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: Mon, 16 Dec 2019 23:26:43 +0100 Message-ID: <87lfrbc3fg.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 (-) M=C4=83d=C4=83lin Ionel Patra=C8=99cu = writes: > * gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.5.7. I pushed this after upgrading some other packages to ensure that dependent packages still build. Thank you! --=20 Ricardo From unknown Mon Jun 23 23:53:37 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: mpatras Subject: bug#38637: closed (Re: [bug#38637] [PATCH 4/4] gnu: Add python-gffutils.) Message-ID: References: <87k16vc34g.fsf@elephly.net> <326bca30-7d18-a02b-9400-2f12bc0e5c21@mdc-berlin.de> X-Gnu-PR-Message: they-closed 38637 X-Gnu-PR-Package: guix-patches Reply-To: 38637@debbugs.gnu.org Date: Mon, 16 Dec 2019 22:34:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1576535642-24795-1" This is a multi-part message in MIME format... ------------=_1576535642-24795-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #38637: (no subject) 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 38637@debbugs.gnu.org. --=20 38637: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D38637 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1576535642-24795-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 38637-done) by debbugs.gnu.org; 16 Dec 2019 22:33:29 +0000 Received: from localhost ([127.0.0.1]:40445 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1igyvh-0006R9-50 for submit@debbugs.gnu.org; Mon, 16 Dec 2019 17:33:29 -0500 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21109) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1igyvf-0006R0-6Q for 38637-done@debbugs.gnu.org; Mon, 16 Dec 2019 17:33:27 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1576535604; cv=none; d=zohomail.com; s=zohoarc; b=iONjxFI9t6+ScZbn5pXUtvIAwVUTXjExB6PH0+6fDyocdPj7DX47LAFGZcZZaGjKdjxdYuuSLwX3+72rnYMdpr0WBHdmQ8MyXAci3ax7mreHCGmK1FJhSR7Iw8xgB9dE2AIwHye+rENIwPYRjFpQ+fzWGj/R+vuPHFu29QFNKC8= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1576535604; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=k6TWwX6iLPDJY4mPASdzX2CdhyLPb9D4+Pw1qVa9Shc=; b=XQvCUgddUQDGricbxJhea8emV+0paKlD8upDcGhH7AATlR5oq7/EUQWYpjVqB+Wikguh6u0fz97l8o1MY+jTyJQGk79VvjJ4LZJ2CFXtTh9JbrvTefMWj+8HeQn7Bnhz89/gA6i49tWOUTkxxCo4+IPAqMdcUwiUVc0nhYmv0OY= 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=1576535604; 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=k6TWwX6iLPDJY4mPASdzX2CdhyLPb9D4+Pw1qVa9Shc=; b=OIW8tG4h0vyXLpYrSE5LHJHYHUKkLqvP0R5rHC8ZynxR19SgpyKEoFDRMOSeynrJ WkwaIGZCDDrJe6KB/SY3mVIKg4BBtsPlbI+z67mR0YIAaDxj+BWGmqiU8aArlF0VNay B/vNfn9UkXjNVuFBjdRtN88mw7dZMBSJfEaqHmS4= Received: from localhost (p54AD4C83.dip0.t-ipconnect.de [84.173.76.131]) by mx.zohomail.com with SMTPS id 1576535602403398.50811484335566; Mon, 16 Dec 2019 14:33:22 -0800 (PST) References: <20191216152519.3595-1-madalinionel.patrascu@mdc-berlin.de> <20191216152519.3595-4-madalinionel.patrascu@mdc-berlin.de> User-agent: mu4e 1.2.0; emacs 26.3 From: Ricardo Wurmus To: =?utf-8?B?TcSDZMSDbGlu?= Ionel =?utf-8?Q?Patra=C8=99cu?= Subject: Re: [bug#38637] [PATCH 4/4] gnu: Add python-gffutils. In-reply-to: <20191216152519.3595-4-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: Mon, 16 Dec 2019 23:33:19 +0100 Message-ID: <87k16vc34g.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: 38637-done Cc: 38637-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 (-) M=C4=83d=C4=83lin Ionel Patra=C8=99cu = writes: > Co-authored-by: Ricardo Wurmus > > * gnu/packages/bioinformatics.scm (python-gffutils): New variable. I=E2=80=99ve pushed this to the =E2=80=9Cmaster=E2=80=9D branch with commit= cfd83f3282. Thank you! --=20 Ricardo ------------=_1576535642-24795-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 16 Dec 2019 15:23:38 +0000 Received: from localhost ([127.0.0.1]:40217 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1igsDi-0000Wo-CM for submit@debbugs.gnu.org; Mon, 16 Dec 2019 10:23:38 -0500 Received: from lists.gnu.org ([209.51.188.17]:58268) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1igsDh-0000Wg-49 for submit@debbugs.gnu.org; Mon, 16 Dec 2019 10:23:37 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:56549) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1igsDe-0002qA-Jf for guix-patches@gnu.org; Mon, 16 Dec 2019 10:23:36 -0500 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: ** X-Spam-Status: No, score=2.6 required=5.0 tests=BAYES_50,MISSING_SUBJECT, RCVD_IN_DNSWL_NONE,URIBL_BLOCKED autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1igsDd-0002Yz-A0 for guix-patches@gnu.org; Mon, 16 Dec 2019 10:23:34 -0500 Received: from c2062.mx.srv.dfn.de ([194.95.238.172]:52497) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1igsDc-0002Uh-Qj for guix-patches@gnu.org; Mon, 16 Dec 2019 10:23:33 -0500 Received: from localhost (localhost [127.0.0.1]) by c2062.mx.srv.dfn.de (Postfix) with ESMTP id 9F8C6300070 for ; Mon, 16 Dec 2019 16:23:22 +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=1576509802; x= 1578324203; bh=Hq+Q1OJDYSlu4sQ6uzQAmH+i1saDUMqSIV0+7D4lBOA=; b=T SMdSZ4h+KlJs9f3Yxy+xwA/toa4eOV8odALa6oOVPHS628TidkMKt5ps4umFpvbG hKgRa0ovsP698YMG4o4oz+HQxLCtBvFe3n5b/43jABoJEAycv4FiDd7QlG2EuGGr JL/l28c47V9prCXfWsEwAU9WtEC9lFykrePypQ5Tdw= 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 gAJjmsp8kCfj for ; Mon, 16 Dec 2019 16:23:22 +0100 (CET) Received: from SW-IT-P-CAS1.mdc-berlin.net (mgw10-1.mdc-berlin.de [141.80.113.53]) by c2062.mx.srv.dfn.de (Postfix) with ESMTPS for ; Mon, 16 Dec 2019 16:23:22 +0100 (CET) Received: from [141.80.113.108] (141.80.113.108) by SW-IT-P-CAS1.mdc-berlin.net (141.80.113.53) with Microsoft SMTP Server (TLS) id 14.3.468.0; Mon, 16 Dec 2019 16:23:21 +0100 To: From: mpatras Message-ID: <326bca30-7d18-a02b-9400-2f12bc0e5c21@mdc-berlin.de> Date: Mon, 16 Dec 2019 16:23:21 +0100 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:68.0) Gecko/20100101 Thunderbird/68.2.2 MIME-Version: 1.0 Content-Type: text/plain; charset="utf-8"; format=flowed Content-Language: en-US X-Originating-IP: [141.80.113.108] X-TM-AS-Product-Ver: SMEX-12.5.0.1684-8.5.1010-25108.000 X-TM-AS-Result: No-1.352500-8.000000-10 X-TMASE-MatchedRID: GaP57vPtnWgl08/xxlO+L5PQTDqTymbSL60/awpuq4h7lDzh8Z+Ehs48 74k0JUprIfqPF9C+GOjMdS7HrUtSKJg39Rgsjteo585VzGMOFzAaTOa7uOFmI9AtbEEX0MxBAB5 fZ54AVbsqtq5d3cxkNRqXnrxrKCOX3rRWHXbuL9/rJZzWVJNoZQ8bTDcKz9rGV7MeTQVvw2aCDO m1rnoaWhEfOUfSfVq2msB42YsUbCEeF5LlwpQcnijLmqRM9sY4QwymtxuJ6y0= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10-1.352500-8.000000 X-TMASE-Version: SMEX-12.5.0.1684-8.5.1010-25108.000 X-TM-SNTS-SMTP: C301286019538A221E78EA40561AFFDE4341AEACA1D7D811783960CDD66DA6EB2000:9 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] [fuzzy] X-Received-From: 194.95.238.172 X-Spam-Score: 0.6 (/) 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: -0.4 (/) --=20 M=C4=83d=C4=83lin Ionel Patra=C8=99cu System Administrator Bioinformatics and Omics Data Science The Berlin Institute for Medical Systems Biology (BIMSB) Max Delbr=C3=BCck Center (MDC) Hannoversche Str. 28, 10115 Berlin House 101, room 1.60 ------------=_1576535642-24795-1--