From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp0 ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms11 with LMTPS id EFVKI4JV7l4RagAA0tVLHw (envelope-from ) for ; Sat, 20 Jun 2020 18:29:22 +0000 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp0 with LMTPS id MLZKH4JV7l45LAAA1q6Kng (envelope-from ) for ; Sat, 20 Jun 2020 18:29:22 +0000 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id B1B55940220 for ; Sat, 20 Jun 2020 18:29:21 +0000 (UTC) Received: from localhost ([::1]:35556 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1jmiEy-0003WI-3Y for larch@yhetil.org; Sat, 20 Jun 2020 14:29:20 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:60602) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1jmiEg-0003VQ-HE for guix-patches@gnu.org; Sat, 20 Jun 2020 14:29:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:47181) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1jmiEg-0004yW-7R for guix-patches@gnu.org; Sat, 20 Jun 2020 14:29:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1jmiEg-0000ZD-2t for guix-patches@gnu.org; Sat, 20 Jun 2020 14:29:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#41968] [PATCH 1/5] gnu: deeptools: Deprecate in favor of python-deeptools. Resent-From: Pierre Langlois Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 20 Jun 2020 18:29:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 41968 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 41968@debbugs.gnu.org Cc: Pierre Langlois Received: via spool by 41968-submit@debbugs.gnu.org id=B41968.15926777262156 (code B ref 41968); Sat, 20 Jun 2020 18:29:02 +0000 Received: (at 41968) by debbugs.gnu.org; 20 Jun 2020 18:28:46 +0000 Received: from localhost ([127.0.0.1]:58727 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jmiEM-0000Yd-BM for submit@debbugs.gnu.org; Sat, 20 Jun 2020 14:28:46 -0400 Received: from mout.gmx.net ([212.227.17.20]:38667) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jmiEK-0000YK-3j for 41968@debbugs.gnu.org; Sat, 20 Jun 2020 14:28:41 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=gmx.net; s=badeba3b8450; t=1592677713; bh=y7/hKzLXhyX6eKm5JxDfqR6E9IIBoi1fbQ7TepGUnF8=; h=X-UI-Sender-Class:References:From:To:Cc:Subject:In-reply-to:Date; b=SuhOD3o3zLJaO2Ir1JXFeNfqPqWIz5q7MA1zMzgBjYZaZcgO5cDwCmpf0YRgPG/qi 8hVP8KYK9djbx3fW42H39RLj9KvM46MEAC5HS7C69uk1cCM4nJWrbjSbyNXjiA5Tn2 YuoIcHolypuxxh+8IUKbDT7rqqq97xIkzB7oU+7Q= X-UI-Sender-Class: 01bb95c1-4bf8-414a-932a-4f6e2808ef9c Received: from e119807-lin ([93.22.246.159]) by mail.gmx.com (mrgmx105 [212.227.17.174]) with ESMTPSA (Nemesis) id 1Mwfac-1ixd0d0Up8-00y6AO; Sat, 20 Jun 2020 20:28:33 +0200 References: <87r1u9ha11.fsf@gmx.com> User-agent: mu4e 1.4.10; emacs 26.3 From: Pierre Langlois In-reply-to: <87r1u9ha11.fsf@gmx.com> Date: Sat, 20 Jun 2020 20:28:31 +0200 Message-ID: <87k101h9rk.fsf@gmx.com> MIME-Version: 1.0 Content-Type: text/x-patch; charset=utf-8 Content-Disposition: inline; filename=0001-gnu-deeptools-Deprecate-in-favor-of-python-deeptools.patch Content-Transfer-Encoding: quoted-printable X-Provags-ID: V03:K1:orrsvJcMyYzc6zbz4BZSalueURDKsbxXXXwsPwVGfl9SAjZrj6y WnQ3E5tTG+C3EMHPOqHHETN+6Naa7dbRtNExPZvYIr0gSJXHATayd7yVONmtkd2gio7xIcG cMBtEj60CCGUadSvT5Advch6rkySiy7jEYFn373/dc76RW343ci8lR7p0KanMiF2Ctl7wMf 1Q2fOc2TDVjacBcGckYeg== X-UI-Out-Filterresults: notjunk:1;V03:K0:05HqM9/16lY=:7DjlK+hnofcxItxKgfWO6K mQUUTE8Xm1jvYdmM7b3qBYoBSDkP7lvKHavYJMJA7hl+cf+sqXya6IFXI1PpDnitg+DsdcoEN HouJsIv9qtTd59R6Ym+bEMtKuT+X4j7fmp26XwM3LKPDK/vcPaN4jv5SDtA7mWxml8MRT0H+T FjlS93LmjgiyCAuTV9soyDcOnVYg7UNWiVTkF8s0b4ZY7s5tTrTudtUj43MZA0JPjYmpSotmS 6zgW5IOXYHZLcPaT2oMSmJBxJVoRA/CYqBTJLOrEp03ZdPPkhgiXvER6fvJ+LiCYtoNFaz+wQ 8rY/rbUD9ppnj0Br+VYfdEHe4DVANZ8eltU+0/UxreygPhJ0MoRfhn3ZxPYiEyg6ugzsU9wmG 5luZ/BaCAR2GbgTSGpypCHIqJPm49TB/fjbfh2b4yc54425UpbWkXMKqzcr6QTBkO0oVrHZVW tO6VYgLGc4xfuA0kEA2OU4pTd9w28ueI356SgyCOWdvp6bp2TTCOTFdgI9kpHMTT6urB5Ktad e5VJqv6HdiE/09BNDAJXxM/T8ifT7Gymp89kgan5pJiSKrXsUrSMm841dqAPq3PUTjSQZ5PHP qnGtcayn/1WD+eTgdqUu52PTSGD9pse9Jne9n4YOMiAgAVdNheW+O7q//hm+mnxzz25X91mWD DcY2ePcDR3dJO87xQIxmqwqksdOKOf4OZNN5ikVWJeZC8aQrSFt0LFs6Ed8riqR6aTt60C7ew QgzpFfYI1jnhdgt89vIuja3SiAMDLllvqb2hU1GFtHb86UdamegxHLnWwxb25mHqLOoNGoEJw pBHqMyPiVNrAHimuwILAlXQbL8eBJoIbwgplgBd3JYDln+/K2fIkm/bhK52Gog6ZaAOve0fKH 72EkfLY4YAhSPG8klekBBB9A3v4SBoKWdkNyX/6w/Spf26E8QVetRnE2EToaDv1bt86AYbZ2G xdNBjXNpv0TI7aBILuaXN/rmIdZOSZaRnT1JC2/3pO6xkBbAP/m+NhPGVzl+RwD2/PPwb45Ex 9K/sXDSrTg/hm7Ig+eWCg5UCvANHy836ak5W0UUSY25GxRflKIiO1g5XxsQdbPv2gBukE3Fyk EDdvEAM3DFzadqHtOeFCMvlXYiVXemxLVkqYBgq33S0iUw5TrmsRmJbo+EgsxEp2JIVqdC88O s2JprSHPQrdUxSgas3UnuV5ztoMs0wFn5wgNtPt9xJ8f4i/mkwgks8ZtTdVvtzjlqJB4GwLW2 T4HR6QdJ+NbBLkzYu X-Spam-Score: -0.7 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-Spam-Score: -1.7 (-) X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Scanner: scn0 Authentication-Results: aspmx1.migadu.com; dkim=fail (rsa verify failed) header.d=gmx.net header.s=badeba3b8450 header.b=SuhOD3o3; dmarc=none; spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Spam-Score: -0.01 X-TUID: lglUD8GUV9uw >From b46bef2216620ac085bea41762904b16f2c6aec5 Mon Sep 17 00:00:00 2001 From: Pierre Langlois Date: Sat, 20 Jun 2020 18:42:04 +0200 Subject: [PATCH 1/5] gnu: deeptools: Deprecate in favor of python-deeptools. And make sure python-deeptools's tests are running. * gnu/packages/bioinformatics.scm (python-deeptools): Fetch source using gi= t. [native-inputs]: Add python-mock and python-nose. (deeptools): Mark as deprecated. --- gnu/packages/bioinformatics.scm | 61 +++++++-------------------------- 1 file changed, 13 insertions(+), 48 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.= scm index 95f8b16db3..580488fc49 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -17,6 +17,7 @@ ;;; Copyright =C2=A9 2019 Brett Gilio ;;; Copyright =C2=A9 2020 Bj=C3=B6rn H=C3=B6fling ;;; Copyright =C2=A9 2020 Jakub K=C4=85dzio=C5=82ka +;;; Copyright =C2=A9 2020 Pierre Langlois ;;; ;;; This file is part of GNU Guix. ;;; @@ -53,6 +54,7 @@ #:use-module (guix build-system ruby) #:use-module (guix build-system scons) #:use-module (guix build-system trivial) + #:use-module (guix deprecation) #:use-module (gnu packages) #:use-module (gnu packages autotools) #:use-module (gnu packages algebra) @@ -2406,12 +2408,18 @@ interval trees with associated meta-data. It is pr= imarily used by the (name "python-deeptools") (version "3.4.3") (source (origin - (method url-fetch) - (uri (pypi-uri "deepTools" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/deeptools/deepTools.git") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "1azgjniss5ff6a90nicdjkxyjwqmi3gzfn09gra42hwlz19hipxb")))) + "0l09vyynz6s6w7fnyd94rpys4a6aja6kp4gli64pngdxdz3md1nl")))) (build-system python-build-system) + (native-inputs + `(("python-mock" ,python-mock) + ("python-nose" ,python-nose))) (propagated-inputs `(("python-matplotlib" ,python-matplotlib) ("python-numpy" ,python-numpy) @@ -2436,6 +2444,8 @@ annotations of the genome.") ;; remainder of the code is licensed under the MIT license. (license (list license:bsd-3 license:expat)))) =20 +(define-deprecated deeptools python-deeptools) + (define-public cutadapt (package (name "cutadapt") @@ -2599,51 +2609,6 @@ trees (phylogenies) and characters.") with Python.") (license license:expat))) =20 -(define-public deeptools - (package - (name "deeptools") - (version "3.1.3") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/deeptools/deepTools.git") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1vggnf52g6q2vifdl4cyi7s2fnfqq0ky2zrkj5zv2qfzsc3p3siw")))) - (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - ;; This phase fails, but it's not needed. - (delete 'reset-gzip-timestamps)))) - (inputs - `(("python-plotly" ,python-plotly) - ("python-scipy" ,python-scipy) - ("python-numpy" ,python-numpy) - ("python-numpydoc" ,python-numpydoc) - ("python-matplotlib" ,python-matplotlib) - ("python-pysam" ,python-pysam) - ("python-py2bit" ,python-py2bit) - ("python-pybigwig" ,python-pybigwig))) - (native-inputs - `(("python-mock" ,python-mock) ;for tests - ("python-nose" ,python-nose) ;for tests - ("python-pytz" ,python-pytz))) ;for tests - (home-page "https://github.com/deeptools/deepTools") - (synopsis "Tools for normalizing and visualizing deep-sequencing data") - (description - "DeepTools addresses the challenge of handling the large amounts of d= ata -that are now routinely generated from DNA sequencing centers. To do so, -deepTools contains useful modules to process the mapped reads data to crea= te -coverage files in standard bedGraph and bigWig file formats. By doing so, -deepTools allows the creation of normalized coverage files or the comparis= on -between two files (for example, treatment and control). Finally, using su= ch -normalized and standardized files, multiple visualizations can be created = to -identify enrichments with functional annotations of the genome.") - (license license:gpl3+))) - (define-public delly (package (name "delly") --=20 2.26.2