From patchwork Mon Dec 16 15:25:16 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 16539 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 94590178BF; Mon, 16 Dec 2019 15:26:20 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,T_DKIM_INVALID, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTP id 459FB17856 for ; Mon, 16 Dec 2019 15:26:20 +0000 (GMT) Received: from localhost ([::1]:55548 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1igsGJ-0004ia-RF for patchwork@mira.cbaines.net; Mon, 16 Dec 2019 10:26:19 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:57211) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1igsG3-0004XE-IN for guix-patches@gnu.org; Mon, 16 Dec 2019 10:26:04 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1igsG2-0005tw-B4 for guix-patches@gnu.org; Mon, 16 Dec 2019 10:26:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:34253) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1igsG2-0005t0-7F for guix-patches@gnu.org; Mon, 16 Dec 2019 10:26:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1igsG2-0000cd-4i for guix-patches@gnu.org; Mon, 16 Dec 2019 10:26:02 -0500 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?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= 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?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= 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?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= 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 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-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 209.51.188.43 X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * 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 From patchwork Mon Dec 16 15:25:17 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 16540 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 6BE6A17856; Mon, 16 Dec 2019 15:27:11 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,T_DKIM_INVALID, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTP id 1B74C17856 for ; Mon, 16 Dec 2019 15:27:11 +0000 (GMT) Received: from localhost ([::1]:55558 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1igsH8-00051b-Hc for patchwork@mira.cbaines.net; Mon, 16 Dec 2019 10:27:10 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:57518) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1igsH1-00051J-QK for guix-patches@gnu.org; Mon, 16 Dec 2019 10:27:04 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1igsH0-0006sb-N6 for guix-patches@gnu.org; Mon, 16 Dec 2019 10:27:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:34263) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1igsH0-0006sK-Jp for guix-patches@gnu.org; Mon, 16 Dec 2019 10:27:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1igsH0-0000eg-GH for guix-patches@gnu.org; Mon, 16 Dec 2019 10:27:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#38637] [PATCH 2/4] gnu: Add python-argh. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= 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?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= 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?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= 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 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-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 209.51.188.43 X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * 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)))) From patchwork Mon Dec 16 15:25:18 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 16541 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 992EE178BF; Mon, 16 Dec 2019 15:27:11 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,T_DKIM_INVALID autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTP id 5F6DD17892 for ; Mon, 16 Dec 2019 15:27:11 +0000 (GMT) Received: from localhost ([::1]:55560 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1igsH8-00051k-Sh for patchwork@mira.cbaines.net; Mon, 16 Dec 2019 10:27:10 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:57523) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1igsH2-00051K-66 for guix-patches@gnu.org; Mon, 16 Dec 2019 10:27:05 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1igsH1-0006sn-5d for guix-patches@gnu.org; Mon, 16 Dec 2019 10:27:04 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:34264) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1igsH1-0006sj-2P for guix-patches@gnu.org; Mon, 16 Dec 2019 10:27:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1igsH0-0000en-WF for guix-patches@gnu.org; Mon, 16 Dec 2019 10:27:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#38637] [PATCH 3/4] gnu: python-pyfaidx: Update to 0.5.7. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= 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?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= 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?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= 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 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-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 209.51.188.43 X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * 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))) From patchwork Mon Dec 16 15:25:19 2019 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 16542 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id DE8A0178BF; Mon, 16 Dec 2019 15:27:16 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,T_DKIM_INVALID, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.0 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTP id 91D2F17856 for ; Mon, 16 Dec 2019 15:27:16 +0000 (GMT) Received: from localhost ([::1]:55566 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1igsHE-0005Bl-5Y for patchwork@mira.cbaines.net; Mon, 16 Dec 2019 10:27:16 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:57536) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1igsH2-00051L-Oj for guix-patches@gnu.org; Mon, 16 Dec 2019 10:27:05 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1igsH1-0006t0-Ia for guix-patches@gnu.org; Mon, 16 Dec 2019 10:27:04 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:34265) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1igsH1-0006su-FG for guix-patches@gnu.org; Mon, 16 Dec 2019 10:27:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1igsH1-0000ev-Cz for guix-patches@gnu.org; Mon, 16 Dec 2019 10:27:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#38637] [PATCH 4/4] gnu: Add python-gffutils. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= 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?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= 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?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= 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 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-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 209.51.188.43 X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches 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