From patchwork Sat Jun 20 18:31:07 2020 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Pierre Langlois X-Patchwork-Id: 22802 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 9F43227BBE3; Sat, 20 Jun 2020 19:32:33 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=BAYES_00,DKIM_SIGNED, FREEMAIL_FROM,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H4,RCVD_IN_MSPIKE_WL, T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTP id 7355F27BBE1 for ; Sat, 20 Jun 2020 19:32:32 +0100 (BST) Received: from localhost ([::1]:37252 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1jmiI3-0004z4-Rv for patchwork@mira.cbaines.net; Sat, 20 Jun 2020 14:32:32 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:32974) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1jmiHa-0004yl-Ai for guix-patches@gnu.org; Sat, 20 Jun 2020 14:32:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:47198) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1jmiHa-0005YR-1R for guix-patches@gnu.org; Sat, 20 Jun 2020 14:32:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1jmiHZ-0000ft-V9 for guix-patches@gnu.org; Sat, 20 Jun 2020 14:32:01 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#41968] [PATCH 5/5] gnu: python-plotly: Update to 4.8.1. Resent-From: Pierre Langlois Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 20 Jun 2020 18:32:01 +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=B41968.15926778842549 (code B ref 41968); Sat, 20 Jun 2020 18:32:01 +0000 Received: (at 41968) by debbugs.gnu.org; 20 Jun 2020 18:31:24 +0000 Received: from localhost ([127.0.0.1]:58744 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jmiGt-0000ex-7w for submit@debbugs.gnu.org; Sat, 20 Jun 2020 14:31:24 -0400 Received: from mout.gmx.net ([212.227.15.19]:51753) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jmiGq-0000ej-TH for 41968@debbugs.gnu.org; Sat, 20 Jun 2020 14:31:17 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=gmx.net; s=badeba3b8450; t=1592677871; bh=s6abgJ4FwdJ473XqVcnel83gL70EMUB0jSughrW+1KA=; h=X-UI-Sender-Class:References:From:To:Cc:Subject:In-reply-to:Date; b=QGNhVoNu+YMh2C/252LBiU1DNi39QXKKkPhTVeyzAb9Hsakwf8Ka3wOeaRcR6/roy mVDCp2Bh7oR3aClvbBL8kU1EQRxxRXwk05Ir45CWheptaDVIEfh45rhJhQKwtG6mZ2 6fKlpznQbbMKWM79ey6TzbmBAphj7sOJi2OvIsvU= X-UI-Sender-Class: 01bb95c1-4bf8-414a-932a-4f6e2808ef9c Received: from e119807-lin ([93.22.246.159]) by mail.gmx.com (mrgmx005 [212.227.17.184]) with ESMTPSA (Nemesis) id 1MA7Ka-1jbD080fZC-00Bax7; Sat, 20 Jun 2020 20:31:11 +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 20:31:07 +0200 Message-ID: <87366ph9n8.fsf@gmx.com> MIME-Version: 1.0 Content-Disposition: inline; filename=0005-gnu-python-plotly-Update-to-4.8.1.patch X-Provags-ID: V03:K1:lrKaMbkYzxBKF5I/n7XqMGN4JaUEC5qd/7HstomiIPhbyZP+C5K W8gb1m+A7u8dJ3Bc5v41cKC351f3v8qVFE8gthN5m6a2wz0JXgfjlfVj8otHqeb2zoESZcm +BAhpQ2u6LQg01y6kBNYIdKmMfg1GZkdK5eEOyDVJmmkLhIYitmBc3hQrv6VbvLHtgqxin1 TYntqlurZ3TiXyioYsuYQ== X-UI-Out-Filterresults: notjunk:1;V03:K0:6VKg+INA1Fw=:Lj4CmruktHk6Llu+k2KAYv Pd+UDfvnTUBmmDU8+4ZgNckjcAMvW2aWvqV8SCqx1rpRUxS1kXxBa91FajGIidlfd8VhbV7FB 4trJ2587cjBwGgKWBAt7gh6ihstoacELU4xiiuPuD+QvT46W/PR1tCIDP2jm+2jyHAWnt7XKw 64/yBh483e0KlvZqx0gctC1N7/pd9VDZaXlJIwc81hcZHUVSV5T09DjNvD1Euaz1gm95aIBqJ D6h+IahVr79t3dTjjW+raxRr/ReMVnB2UAt29lpAYLA6xKneZ+zB0JPIWjoVSKh2mF3y9xt+u vH+sVwCe4uY1GDzZT88COn/QdDKKzUaMU4PkB1w5xigbfyZI/9RAs2jI6qyLx7dE8eXHK/3+L 1Fghcgr3l5mlFesFmS466usZQWptG8YCavePUUkAqCswlmcd0p4CxMQ1TH6fGX1ITHIZ4C8wV NpY5tCLsG8VuXYjdUszCMpoX32vu6DagFn2UFaJ7riXtagGbYTzJKT0+vwU5P/ayCiM9V1Kuk wBjEahE1yNgXRwn3taq6mS/ZFJWlyYnUUJKOzCSkgtf2jrA1yTq+8IAtnxokZRKjs4AdcqWVM CL7Yrnf0RXfbh9NLvYQefggkyT0wsr/FTrnHTkKKUs7VLbnYwUlzk+utMY16yjC/zuHTmGg6J MHlskZsxVycaWOeFbJPHuiG3dJ0c0+PJ8zpfF/RTRa/xzF2uk+IWBiyCmHHDKoj+oijHA/4bG uA54MzSvkMXRNoLlSAI6YpIZ4hyxneTFy9D5luxz3DzY0wfTQMvHKYk+IUnAfWP08eaxCXFzp FZEQY4bndnmmnC8mi6Bzpn/apFOqCEd7hu0f6/n3e9czTEXdyGJN2TAialV6/sohWuP5xPI0m BYWBMy61znF7W1lb6cVbUxe9Q4hzOiij+N2F5giSr5jb34cXE9uszEzYvDxUaa2Er88Qj9502 Hniwe8qIqbbDLkn+yhjmUteR7Dzt94AmPlSMl3jaLDPMZbBVVLB3+YGsOoxgxABfh8csT7y5L FTTpOFsDxLTKWX99b0R1Sbm873T/nOTlDwiych9E7xdswmpyPMLd9q9C4ihnbI2SIEipR9p9l ZcxQ9MyLQ4717hhWYCxe9Ga2r3BeCXEiePZFL8R1Oq/kjBEl6rR4qutCMRF9HtG0PGwgnPUny oriFW+uTB7m7vb+Eu4dG1dAaoHYLufUeAuZgBExkHQrFpBW+sj7azf+okbbEx0/Z4nsE7cmdV om+/Jpr1f8fxsd1kb X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list 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 From a1526919f28d8ea4a958ef3b672b3187c8c3bd82 Mon Sep 17 00:00:00 2001 From: Pierre Langlois Date: Thu, 18 Jun 2020 00:59:09 +0200 Subject: [PATCH 5/5] gnu: python-plotly: Update to 4.8.1. But keep version 2.4.1 around for packages that still need it and for python2 support. * gnu/packages/graph.scm (python-plotly): Update to 4.8.1. [source]: Use git-fetch so that tests are also included. [arguments]: Enable tests. [home-page]: Follow redirect. (python-plotly-2.4.1): New variable. (python2-plotly): Inherit from python-plotly-2.4.1. * gnu/packages/bioinformatics.scm (python-deeptools)[native-inputs]: Depend on python-plotly-2.4.1. --- gnu/packages/bioinformatics.scm | 2 +- gnu/packages/graph.scm | 74 ++++++++++++++++++++++++++------- 2 files changed, 61 insertions(+), 15 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3ee134db77..ce54c613b0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2431,7 +2431,7 @@ interval trees with associated meta-data. It is primarily used by the ("python-pysam" ,python-pysam) ("python-scipy" ,python-scipy) ("python-deeptoolsintervals" ,python-deeptoolsintervals) - ("python-plotly" ,python-plotly))) + ("python-plotly" ,python-plotly-2.4.1))) (home-page "https://pypi.org/project/deepTools/") (synopsis "Useful tools for exploring deep sequencing data") (description "This package addresses the challenge of handling large amounts diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm index dc8f2c64a2..762ee30632 100644 --- a/gnu/packages/graph.scm +++ b/gnu/packages/graph.scm @@ -5,6 +5,7 @@ ;;; Copyright © 2019 Efraim Flashner ;;; Copyright © 2019 Andreas Enge ;;; Copyright © 2020 Alexander Krotov +;;; Copyright © 2020 Pierre Langlois ;;; ;;; This file is part of GNU Guix. ;;; @@ -235,25 +236,49 @@ lines.") (define-public python-plotly (package (name "python-plotly") - (version "2.4.1") - (source - (origin - (method url-fetch) - (uri (pypi-uri "plotly" version)) - (sha256 - (base32 - "0s9gk2fl53x8wwncs3fwii1vzfngr0sskv15v3mpshqmrqfrk27m")))) + (version "4.8.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/plotly/plotly.py.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "08ab677gr85m10zhixr6dnmlfws8q6sra7nhyb8nf3r8dx1ffqhz")))) (build-system python-build-system) (arguments - '(#:tests? #f)) ; The tests are not distributed in the release + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ + (chdir "packages/python/plotly") + #t)) + (replace 'check + (lambda _ + (invoke "pytest" "-x" "plotly/tests/test_core") + (invoke "pytest" "-x" "plotly/tests/test_io") + ;; FIXME: Add optional dependencies and enable their tests. + ;; (invoke "pytest" "-x" "plotly/tests/test_optional") + (invoke "pytest" "_plotly_utils/tests"))) + (add-before 'reset-gzip-timestamps 'make-files-writable + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (for-each (lambda (file) (chmod file #o644)) + (find-files out "\\.gz")) + #t)))))) + (native-inputs + `(("python-pytest" ,python-pytest))) (propagated-inputs `(("python-decorator" ,python-decorator) - ("python-nbformat" ,python-nbformat) + ("python-ipywidgets" ,python-ipywidgets) ("python-pandas" ,python-pandas) - ("python-pytz" ,python-pytz) ("python-requests" ,python-requests) - ("python-six" ,python-six))) - (home-page "https://plot.ly/python/") + ("python-retrying" ,python-retrying) + ("python-six" ,python-six) + ("python-statsmodels" ,python-statsmodels) + ("python-xarray" ,python-xarray))) + (home-page "https://plotly.com/python/") (synopsis "Interactive plotting library for Python") (description "Plotly's Python graphing library makes interactive, publication-quality graphs online. Examples of how to make line plots, scatter @@ -261,8 +286,29 @@ plots, area charts, bar charts, error bars, box plots, histograms, heatmaps, subplots, multiple-axes, polar charts, and bubble charts. ") (license license:expat))) +(define-public python-plotly-2.4.1 + (package (inherit python-plotly) + (version "2.4.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "plotly" version)) + (sha256 + (base32 + "0s9gk2fl53x8wwncs3fwii1vzfngr0sskv15v3mpshqmrqfrk27m")))) + (native-inputs '()) + (propagated-inputs + `(("python-decorator" ,python-decorator) + ("python-nbformat" ,python-nbformat) + ("python-pandas" ,python-pandas) + ("python-pytz" ,python-pytz) + ("python-requests" ,python-requests) + ("python-six" ,python-six))) + (arguments + '(#:tests? #f)))) ; The tests are not distributed in the release + (define-public python2-plotly - (package-with-python2 python-plotly)) + (package-with-python2 python-plotly-2.4.1)) (define-public python-louvain (package -- 2.26.2