From patchwork Tue Jan 4 22:47:39 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 35963 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 BF13927BBEA; Tue, 4 Jan 2022 22:49:46 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_INVALID,DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI, RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 760E327BBE9 for ; Tue, 4 Jan 2022 22:49:44 +0000 (GMT) Received: from localhost ([::1]:43768 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1n4sch-0000KM-J4 for patchwork@mira.cbaines.net; Tue, 04 Jan 2022 17:49:43 -0500 Received: from eggs.gnu.org ([209.51.188.92]:43454) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1n4sc3-0007bZ-GI for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:55744) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1n4sc3-0006yq-6X for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1n4sc3-0003qJ-5b for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#53017] [PATCH 01/17] gnu: julia-xyz: Adjust style. References: <20220104224502.1142878-1-zimon.toutoune@gmail.com> In-Reply-To: <20220104224502.1142878-1-zimon.toutoune@gmail.com> Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 04 Jan 2022 22:49:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 53017 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 53017@debbugs.gnu.org Cc: efraim@flashner.co.il, zimoun Received: via spool by 53017-submit@debbugs.gnu.org id=B53017.164133649814607 (code B ref 53017); Tue, 04 Jan 2022 22:49:03 +0000 Received: (at 53017) by debbugs.gnu.org; 4 Jan 2022 22:48:18 +0000 Received: from localhost ([127.0.0.1]:39026 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbH-0003n3-6u for submit@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:17 -0500 Received: from mail-wm1-f42.google.com ([209.85.128.42]:54137) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbA-0003l8-Qk for 53017@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:10 -0500 Received: by mail-wm1-f42.google.com with SMTP id l4so24198826wmq.3 for <53017@debbugs.gnu.org>; Tue, 04 Jan 2022 14:48:08 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=Nb0wEBVhafZBKYzEkjKVq7vOlxP7jXzjn0ZGQK+VhU4=; b=G1I9sUhuB3zG+ArOLiDx+/OgkGWHy/xZD/0Fj2ufvYG3BYssr4mFT/oVd0NHKdXqs/ YZpjOUz5/FgpvSrULd9/jgpwvt1KxWodyx/n23xrb5a4oUaqkM5bD/QPdTw22ifztIdA QUerIP0DrNchmLLQYs5S7LdpPuR99cjmimMtedmq5qVf/JD6/GEupZs3ASgb5GlqghO1 3Tf37FEhYlguFq19slMpZCJ9C6CPThN17hDhFgQQLTiF7tCtMOpYljFKrc0g4fXEleol JfkPIVx5A5CUnnRH4xbxtNblhKiQFkouwt6sd/h9uV4Z0Tz+S1OW+5XW109jC7Nguf/H YGrQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=Nb0wEBVhafZBKYzEkjKVq7vOlxP7jXzjn0ZGQK+VhU4=; b=bg1kGMbfKH7vgKzgIlRXR88dhy3Bn3aie4nIGSGDoY5vJQfVLX7+mWCdT3hQjSlGiI 2iQdjsLksz7a/mHOJLy9Iz2yu4TfRpjl9FVkUWEkKv0h/azw7DATkbeBxaBkZlkSHddz jAf57e2otVmG11UBpKCkrngUpVr9riSrTsRIWHzSGVXMGROSuNI/2FzUeLhGntp4FCrM l2fyMckBP6F1g5U5vWG6sFbHf2YhXMG3SYLfTkivh6Us1USOY3PfitAAjoEJF39kKuSD YKA9BvC0jyVJRxmx6mPC/nMF9QTNvUXBvkeKRW1SxTYabwnXnj3iygkOTDoVWTW7KQIA i0Iw== X-Gm-Message-State: AOAM5323TCCRwrhSXvpMqtkvkgoOG1sYJUzrVnJ7ZdejwinXP7NdqoZY vMlv1wITJ87EpxyUI7cntjotfv3Kmdo= X-Google-Smtp-Source: ABdhPJxmjy74uFa4dEO4uIbR6gOE2t7SqB7efmh+MpUJ2RzShndzJb4yWmnGiQsjKwy7/jVcmpIAgA== X-Received: by 2002:a05:600c:2188:: with SMTP id e8mr401944wme.55.1641336482853; Tue, 04 Jan 2022 14:48:02 -0800 (PST) Received: from localhost.localdomain ([193.48.40.117]) by smtp.gmail.com with ESMTPSA id c9sm732842wml.12.2022.01.04.14.48.02 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 04 Jan 2022 14:48:02 -0800 (PST) From: zimoun Date: Tue, 4 Jan 2022 23:47:39 +0100 Message-Id: <20220104224755.1142897-1-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.33.1 MIME-Version: 1.0 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 * gnu/packages/julia-xyz: Align all inputs. --- gnu/packages/julia-xyz.scm | 313 ++++++++++++++++++++++++++----------- 1 file changed, 224 insertions(+), 89 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 2ad1c4cd5d..3701bf3996 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -166,7 +166,9 @@ (define-public julia-arrayinterface ;; Disable as stopgap. `(#:tests? ,(not (target-x86-32?)))) (propagated-inputs - (list julia-ifelse julia-requires julia-static)) + (list julia-ifelse + julia-requires + julia-static)) (native-inputs (list julia-aqua julia-bandedmatrices @@ -248,9 +250,12 @@ (define-public julia-axisarrays (base32 "03kzan1lm4fxfhzv1xjg3ysf6y7nagcc61vfz15kvdrp1dqxlynk")))) (build-system julia-build-system) (propagated-inputs - (list julia-rangearrays julia-intervalsets julia-itertools)) + (list julia-rangearrays + julia-intervalsets + julia-itertools)) (native-inputs - (list julia-offsetarrays julia-unitful)) + (list julia-offsetarrays + julia-unitful)) (home-page "http://juliaarrays.github.io/AxisArrays.jl/latest/") (synopsis "Arrays where each dimension can have a named axis with values") (description "This package for the Julia language provides an array type @@ -276,7 +281,8 @@ (define-public julia-bandedmatrices (base32 "0rlfj9gr9ss621v5kw5b06206yaak21s2vq9vk7r8a7p2ylncism")))) (build-system julia-build-system) (propagated-inputs - (list julia-arraylayouts julia-fillarrays)) + (list julia-arraylayouts + julia-fillarrays)) (native-inputs (list julia-genericlinearalgebra)) (home-page "https://github.com/JuliaMatrices/BandedMatrices.jl") @@ -318,7 +324,8 @@ (define-public julia-benchmarktools (("@test @ballocated\\(Ref\\(1\\)\\)") "@test_broken @ballocated(Ref(1))")))))) '(%standard-phases)))) - (propagated-inputs (list julia-json)) + (propagated-inputs + (list julia-json)) (home-page "https://github.com/JuliaCI/BenchmarkTools.jl") (synopsis "Benchmarking framework for the Julia language") (description "@code{BenchmarkTools.jl} makes performance tracking of Julia @@ -350,9 +357,12 @@ (define-public julia-blockarrays (substitute* "test/test_blockarrays.jl" (("Int64") "Int32"))))))))) (propagated-inputs - (list julia-arraylayouts julia-fillarrays)) + (list julia-arraylayouts + julia-fillarrays)) (native-inputs - (list julia-lazyarrays julia-offsetarrays julia-staticarrays)) + (list julia-lazyarrays + julia-offsetarrays + julia-staticarrays)) (home-page "https://github.com/JuliaArrays/BlockArrays.jl") (synopsis "BlockArrays for Julia") (description "A block array is a partition of an array into blocks or @@ -383,8 +393,11 @@ (define-public julia-blockbandedmatrices (base32 "10n1r6kmmv2wa307jfg9y2m6p16j8hngjp3fjavpbdy1r5haasm9")))) (build-system julia-build-system) (propagated-inputs - (list julia-arraylayouts julia-bandedmatrices julia-blockarrays - julia-fillarrays julia-matrixfactorizations)) + (list julia-arraylayouts + julia-bandedmatrices + julia-blockarrays + julia-fillarrays + julia-matrixfactorizations)) (home-page "https://github.com/JuliaMatrices/BlockBandedMatrices.jl") (synopsis "Block-banded matrices and banded-block-banded matrices") (description "This package supports representing block-banded and @@ -437,7 +450,8 @@ (define-public julia-bufferedstreams '(#:tests? #f #:julia-package-name "BufferedStreams" #:julia-package-uuid "e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d")) - (propagated-inputs (list julia-compat)) + (propagated-inputs + (list julia-compat)) (home-page "https://github.com/BioJulia/BufferedStreams.jl") (synopsis "Fast composable IO streams") (description "@code{BufferedStreams.jl} provides buffering for IO @@ -514,10 +528,14 @@ (define-public julia-chainrules (base32 "0if93pd3b3scg2x3gmk1cbwjk0ax1n792vy8c38y3xl7jpd5cb70")))) (build-system julia-build-system) (inputs ;required for test - (list julia-chainrulestestutils julia-finitedifferences julia-nanmath + (list julia-chainrulestestutils + julia-finitedifferences + julia-nanmath julia-specialfunctions)) (propagated-inputs - (list julia-chainrulescore julia-compat julia-reexport + (list julia-chainrulescore + julia-compat + julia-reexport julia-requires)) (home-page "https://github.com/JuliaDiff/ChainRules.jl") (synopsis "Common utilities for automatic differentiation") @@ -541,7 +559,8 @@ (define-public julia-chainrulescore (base32 "1866xv30h1bi7f2m993nljzf58wwmv8zlgn6ffn9j3wckch1nfpb")))) (build-system julia-build-system) (inputs ;required for tests - (list julia-benchmarktools julia-staticarrays)) + (list julia-benchmarktools + julia-staticarrays)) (propagated-inputs (list julia-compat)) (home-page "https://github.com/JuliaDiff/ChainRulesCore.jl") @@ -565,7 +584,9 @@ (define-public julia-chainrulestestutils (base32 "1vlkyp72d514gyb4k3yhjl1g7f24ncmz61j56p4sdi9f76rk9fx9")))) (build-system julia-build-system) (propagated-inputs - (list julia-chainrulescore julia-compat julia-finitedifferences)) + (list julia-chainrulescore + julia-compat + julia-finitedifferences)) (home-page "https://github.com/JuliaDiff/ChainRulesTestUtils.jl") (synopsis "Common utilities used by downstream automatic differentiation tools") (description "This package is designed to help in testing @@ -604,7 +625,8 @@ (define-public julia-codeczlib (find-files out "\\.gz$")) #t)))))) (propagated-inputs - (list julia-zlib-jll julia-transcodingstreams)) + (list julia-zlib-jll + julia-transcodingstreams)) (home-page "https://github.com/JuliaIO/CodecZlib.jl") (synopsis "Zlib codecs for @code{TranscodingStreams.jl}") (description "This package provides zlib codecs for @@ -626,7 +648,9 @@ (define-public julia-colors (base32 "0kx3hq7rf8p5zx6ly9k5j90zijmc7yrwmy96cgkl2ibdfbnhmya3")))) (build-system julia-build-system) (propagated-inputs - (list julia-colortypes julia-fixedpointnumbers julia-reexport)) + (list julia-colortypes + julia-fixedpointnumbers + julia-reexport)) (home-page "https://github.com/JuliaGraphics/Colors.jl") (synopsis "Tools for dealing with color") (description "This package provides a wide array of functions for dealing @@ -650,7 +674,9 @@ (define-public julia-colorschemes (base32 "0kpjhmqd5cj8dh8bmh9b5g6bscyp7h23hzpr2s93pnrp57q1wvhq")))) (build-system julia-build-system) (propagated-inputs - (list julia-colors julia-colortypes julia-fixedpointnumbers + (list julia-colors + julia-colortypes + julia-fixedpointnumbers julia-staticarrays)) (home-page "https://github.com/JuliaGraphics/ColorSchemes.jl") (synopsis "Colorschemes, colormaps, gradients, and palettes") @@ -698,7 +724,9 @@ (define-public julia-colorvectorspace (base32 "02gk7f5g5wjxdasbjf8bvv1m7clksh7mw1xmygjdirjz1q0d6dwi")))) (build-system julia-build-system) (propagated-inputs - (list julia-colortypes julia-specialfunctions julia-tensorcore)) + (list julia-colortypes + julia-specialfunctions + julia-tensorcore)) (native-inputs (list julia-colors)) (home-page "https://github.com/JuliaGraphics/ColorVectorSpace.jl") @@ -810,7 +838,9 @@ (define-public julia-configurations (substitute* "test/runtests.jl" (("Int64") "Int32"))))))))) (propagated-inputs - (list julia-crayons julia-expronicon julia-orderedcollections)) + (list julia-crayons + julia-expronicon + julia-orderedcollections)) (home-page "https://configurations.rogerluo.dev/stable/") (synopsis "Tools for options and configurations in Julia") (description "@code{Configurations.jl} provides a macro @code{@@option} to @@ -855,7 +885,9 @@ (define-public julia-coordinatetransformations (propagated-inputs (list julia-staticarrays)) (native-inputs - (list julia-documenter julia-forwarddiff julia-unitful)) + (list julia-documenter + julia-forwarddiff + julia-unitful)) (home-page "https://github.com/JuliaGeometry/CoordinateTransformations.jl") (synopsis "Coordinate transformations in Julia") (description "@code{CoordinateTransformations} is a Julia package to manage @@ -985,7 +1017,8 @@ (define-public julia-datastructures (sha256 (base32 "0hdqp8ipsqdw5bqqkdvz4j6n67x80sj5azr9vzyxwjfsgkfbnk2l")))) (propagated-inputs - (list julia-compat julia-orderedcollections)) + (list julia-compat + julia-orderedcollections)) (build-system julia-build-system) (arguments `(#:phases @@ -1136,7 +1169,8 @@ (define-public julia-distances (propagated-inputs (list julia-statsapi)) (native-inputs - (list julia-offsetarrays julia-unitful)) + (list julia-offsetarrays + julia-unitful)) (home-page "https://github.com/JuliaStats/Distances.jl") (synopsis "Julia package for evaluating distances (metrics) between vectors") (description "A Julia package for evaluating distances(metrics) between @@ -1300,9 +1334,9 @@ (define-public julia-diffresults (file-name (git-file-name name version)) (sha256 (base32 "1w6p3yxajvclax5b9g7cr2jmbc7lvr5nk4gq0aljxdycdq1d2y3v")))) + (build-system julia-build-system) (propagated-inputs (list julia-staticarrays)) - (build-system julia-build-system) (home-page "https://github.com/JuliaDiff/DiffResults.jl") (synopsis "In-place differentiation methods of primal values at multi-order") (description "This package provides the @code{DiffResult} type, which can @@ -1322,9 +1356,10 @@ (define-public julia-diffrules (file-name (git-file-name name version)) (sha256 (base32 "0cwjvj4gma7924fm3yas0nf0jlnwwx4v7fi79ii3s290lkdldzfl")))) - (propagated-inputs - (list julia-nanmath julia-specialfunctions)) (build-system julia-build-system) + (propagated-inputs + (list julia-nanmath + julia-specialfunctions)) (home-page "https://github.com/JuliaDiff/DiffRules.jl") (synopsis "Primitive differentiation rules") (description "This package provides primitive differentiation rules that @@ -1376,7 +1411,9 @@ (define-public julia-dualnumbers ;; Seems to not play nicely with SpecialFunctions ((".*isempty.*") ""))))))) (propagated-inputs - (list julia-calculus julia-nanmath julia-specialfunctions)) + (list julia-calculus + julia-nanmath + julia-specialfunctions)) (home-page "https://github.com/JuliaDiff/DualNumbers.jl") (synopsis "Represent dual numbers and for perform dual algebra") (description "The @code{DualNumbers} Julia package defines the @code{Dual} @@ -1506,7 +1543,8 @@ (define-public julia-ffmpeg (base32 "1ldxbp0kq3ip67x7sp82dz56aq4p5i0chspbgx2zgskr6jcbjj1b")))) (build-system julia-build-system) (propagated-inputs - (list julia-ffmpeg-jll julia-x264-jll)) + (list julia-ffmpeg-jll + julia-x264-jll)) (home-page "https://github.com/JuliaIO/FFMPEG.jl") (synopsis "Julia Package for ffmpeg") (description "This package is made to be included into packages that just @@ -1552,7 +1590,9 @@ (define-public julia-fileio (propagated-inputs (list julia-requires)) (native-inputs - (list julia-colortypes julia-filepathsbase julia-http)) + (list julia-colortypes + julia-filepathsbase + julia-http)) (home-page "https://github.com/JuliaIO/FileIO.jl") (synopsis "Main Package for IO, loading all different kind of files") (description "@code{FileIO} aims to provide a common framework for detecting @@ -1632,9 +1672,12 @@ (define-public julia-finitediff (setenv "GROUP" "Core") #t))))) (propagated-inputs - (list julia-arrayinterface julia-requires julia-staticarrays)) + (list julia-arrayinterface + julia-requires + julia-staticarrays)) (native-inputs - (list julia-bandedmatrices julia-blockbandedmatrices + (list julia-bandedmatrices + julia-blockbandedmatrices julia-safetestsets)) (home-page "https://github.com/JuliaDiff/FiniteDiff.jl") (synopsis "Calculations of gradients, Jacobians, and Hessians") @@ -1672,7 +1715,9 @@ (define-public julia-finitedifferences (inputs (list julia-benchmarktools)) (propagated-inputs - (list julia-chainrulescore julia-richardson julia-staticarrays)) + (list julia-chainrulescore + julia-richardson + julia-staticarrays)) (home-page "https://github.com/JuliaDiff/FiniteDifferences.jl") (synopsis "Estimates derivatives with finite differences") (description "This package calculates approximate derivatives numerically @@ -1702,7 +1747,8 @@ (define-public julia-fixedpointnumbers ;; A deprecation warning is not thrown (("@test_logs.*:warn" all) (string-append "# " all))) #t))))) - (propagated-inputs (list julia-compat)) + (propagated-inputs + (list julia-compat)) (home-page "https://github.com/JuliaMath/FixedPointNumbers.jl") (synopsis "Fixed point types for Julia") (description "@code{FixedPointNumbers.jl} implements fixed-point number @@ -1755,7 +1801,8 @@ (define-public julia-forwarddiff ;; Disable as stopgap. `(#:tests? ,(not (target-x86-32?)))) (inputs ;required for tests - (list julia-calculus julia-difftests)) + (list julia-calculus + julia-difftests)) (propagated-inputs (list julia-commonsubexpressions julia-diffresults @@ -1953,7 +2000,9 @@ (define-public julia-geometrybasics (substitute* "test/runtests.jl" (("Int64") "Int32"))))))))) (propagated-inputs - (list julia-itertools julia-staticarrays julia-structarrays + (list julia-itertools + julia-staticarrays + julia-structarrays julia-tables)) (native-inputs (list julia-offsetarrays)) @@ -2003,7 +2052,8 @@ (define-public julia-graphics (base32 "10h1s09v7qkvrjr6l678zamb1p248n8jv4rrwkf8g7d2bpfz9amn")))) (build-system julia-build-system) (propagated-inputs - (list julia-colors julia-nanmath)) + (list julia-colors + julia-nanmath)) (home-page "https://github.com/JuliaGraphics/Graphics.jl") (synopsis "Base graphics in Julia") (description "@code{Graphics.jl} is an abstraction layer for graphical @@ -2025,7 +2075,8 @@ (define-public julia-gumbo (base32 "1g22dv3v7caakspv3pdahnqn937fzzsg9y87rj72hid9g8lxl1gm")))) (build-system julia-build-system) (propagated-inputs - (list julia-abstracttrees julia-gumbo-jll)) + (list julia-abstracttrees + julia-gumbo-jll)) (home-page "https://github.com/JuliaWeb/Gumbo.jl") (synopsis "Julia wrapper around Google's gumbo C library for parsing HTML") (description "@code{Gumbo.jl} is a Julia wrapper around Google's gumbo @@ -2077,10 +2128,13 @@ (define-public julia-http (string-append all "return\n"))) #t))))) (propagated-inputs - (list julia-inifile julia-mbedtls julia-uris)) + (list julia-inifile + julia-mbedtls + julia-uris)) ;; required for tests (inputs - (list julia-json julia-bufferedstreams)) + (list julia-json + julia-bufferedstreams)) (home-page "https://juliaweb.github.io/HTTP.jl/") (synopsis "HTTP support for Julia") (description "@code{HTTP.jl} is a Julia library for HTTP Messages, @@ -2148,7 +2202,9 @@ (define-public julia-imageaxes (base32 "15zqxani1jjh8849s7rdps6b6prqdwv8yxx893y536vkpk7i07qd")))) (build-system julia-build-system) (propagated-inputs - (list julia-axisarrays julia-imagecore julia-reexport + (list julia-axisarrays + julia-imagecore + julia-reexport julia-simpletraits)) (native-inputs (list julia-unitful)) @@ -2176,7 +2232,8 @@ (define-public julia-imagebase (arguments `(#:tests? #f)) ; Cycle with ImageMagick.jl. (propagated-inputs - (list julia-imagecore julia-reexport)) + (list julia-imagecore + julia-reexport)) ;(native-inputs ; `(("julia-imagemagick" ,julia-imagemagick) ; ("julia-offsetarrays" ,julia-offsetarrays) @@ -2248,7 +2305,10 @@ (define-public julia-imageinterminal (arguments `(#:tests? #f)) ; Cycle with ReferenceTests.jl. (propagated-inputs - (list julia-crayons julia-imagebase julia-imagecore julia-requires)) + (list julia-crayons + julia-imagebase + julia-imagecore + julia-requires)) ;(native-inputs ; `(("julia-coordinatetransformations" ,julia-coordinatetransformations) ; ("julia-imagemagick" ,julia-imagemagick) @@ -2294,7 +2354,9 @@ (define-public julia-imagemagick (("test (B == map)" _ test) (string-append "test_nowarn " test))) #t))))) (propagated-inputs - (list julia-fileio julia-imagecore julia-imagemagick-jll)) + (list julia-fileio + julia-imagecore + julia-imagemagick-jll)) (native-inputs (list julia-colors julia-colorvectorspace @@ -2325,10 +2387,14 @@ (define-public julia-imagemetadata (base32 "0iv154ms370xgcr56bwsjl13iwmy671cbxjl9ld5yfj85pclcwi1")))) (build-system julia-build-system) (propagated-inputs - (list julia-axisarrays julia-imageaxes julia-imagecore + (list julia-axisarrays + julia-imageaxes + julia-imagecore julia-indirectarrays)) (native-inputs - (list julia-offsetarrays julia-simpletraits julia-unitful)) + (list julia-offsetarrays + julia-simpletraits + julia-unitful)) (home-page "https://github.com/JuliaImages/ImageMetadata.jl") (synopsis "Julia package for images having metadata") (description "@code{ImageMetadata} is a simple package providing utilities @@ -2355,8 +2421,11 @@ (define-public julia-imageshow (arguments `(#:tests? #f)) ; cycle with ImageMagick.jl. (propagated-inputs - (list julia-fileio julia-imagebase julia-imagecore - julia-offsetarrays julia-stackviews)) + (list julia-fileio + julia-imagebase + julia-imagecore + julia-offsetarrays + julia-stackviews)) ;(native-inputs ; `(("julia-imagedistances" ,julia-imagedistances) ; ("julia-imagemagick" ,julia-imagemagick) @@ -2442,7 +2511,9 @@ (define-public julia-indirectarrays (base32 "0l0jq0jnr9z3k431ni82xycq7mqapgxrbrx4yyk6lycvi41ipm4s")))) (build-system julia-build-system) (native-inputs - (list julia-colors julia-fixedpointnumbers julia-mappedarrays)) + (list julia-colors + julia-fixedpointnumbers + julia-mappedarrays)) (home-page "https://github.com/JuliaArrays/IndirectArrays.jl") (synopsis "Julia implementation of indexed arrays") (description "An @code{IndirectArray} is one that encodes data using a @@ -2534,7 +2605,9 @@ (define-public julia-interpolations julia-staticarrays julia-woodburymatrices)) (native-inputs - (list julia-dualnumbers julia-forwarddiff julia-offsetarrays + (list julia-dualnumbers + julia-forwarddiff + julia-offsetarrays julia-unitful julia-zygote)) (home-page "https://github.com/JuliaMath/Interpolations.jl") (synopsis "Continuous interpolation of discrete datasets") @@ -2727,7 +2800,9 @@ (define-public julia-json (base32 "1f9k613kbknmp4fgjxvjaw4d5sfbx8a5hmcszmp1w9rqfqngjx9m")))) (build-system julia-build-system) (propagated-inputs - (list julia-datastructures julia-fixedpointnumbers julia-parsers + (list julia-datastructures + julia-fixedpointnumbers + julia-parsers julia-offsetarrays)) (home-page "https://github.com/JuliaIO/JSON.jl") (synopsis "JSON parsing and printing library for Julia") @@ -2750,7 +2825,8 @@ (define-public julia-json3 (base32 "11z5maz7v50wd99id8z7838higza0cllh2amkdkrlskbri3v2f17")))) (build-system julia-build-system) (propagated-inputs - (list julia-parsers julia-structtypes)) + (list julia-parsers + julia-structtypes)) (home-page "https://github.com/quinnj/JSON3.jl") (synopsis "JSON package for Julia") (description "This package provides another JSON package for Julia, with a @@ -2803,8 +2879,11 @@ (define-public julia-lazyarrays (substitute* "test/multests.jl" (("Int64") "Int32"))))))))) (propagated-inputs - (list julia-arraylayouts julia-fillarrays julia-macrotools - julia-matrixfactorizations julia-staticarrays)) + (list julia-arraylayouts + julia-fillarrays + julia-macrotools + julia-matrixfactorizations + julia-staticarrays)) (native-inputs (list julia-tracker)) (home-page "https://github.com/JuliaArrays/LazyArrays.jl") @@ -2887,7 +2966,9 @@ (define-public julia-mappedarrays (propagated-inputs (list julia-fixedpointnumbers)) (native-inputs - (list julia-colortypes julia-fixedpointnumbers julia-offsetarrays)) + (list julia-colortypes + julia-fixedpointnumbers + julia-offsetarrays)) (home-page "https://github.com/JuliaArrays/MappedArrays.jl") (synopsis "Lazy in-place transformations of arrays") (description "This package implements \"lazy\" in-place elementwise @@ -2956,7 +3037,8 @@ (define-public julia-mbedtls (substitute* "test/runtests.jl" (("testhost =") "return #")) #t))))) - (propagated-inputs (list julia-mbedtls-jll)) + (propagated-inputs + (list julia-mbedtls-jll)) (home-page "https://github.com/JuliaLang/MbedTLS.jl") (synopsis "Apache's mbed TLS library wrapper") (description "@code{MbedTLS.jl} provides a wrapper around the @code{mbed @@ -2978,9 +3060,13 @@ (define-public julia-measurements (base32 "05p3f0gr4sv4maq8cix5fi8ldq0zagswqsd43xn6fhy046f936mz")))) (build-system julia-build-system) (propagated-inputs - (list julia-calculus julia-recipesbase julia-requires)) + (list julia-calculus + julia-recipesbase + julia-requires)) (native-inputs - (list julia-quadgk julia-specialfunctions julia-unitful)) + (list julia-quadgk + julia-specialfunctions + julia-unitful)) (home-page "https://juliaphysics.github.io/Measurements.jl/stable/") (synopsis "Error propagation calculator and library") (description "@code{Measurements.jl} is an error propagation calculator and @@ -3121,7 +3207,8 @@ (define-public julia-mocking (base32 "1cg2is83bjmrchmmxcgx57k8c9b9vlamrw38v4fdhbb6d4six5cg")))) (build-system julia-build-system) (propagated-inputs - (list julia-compat julia-exprtools)) + (list julia-compat + julia-exprtools)) (home-page "https://github.com/invenia/Mocking.jl") (synopsis "Overload Julia function calls") (description "The purpose of this package is to allow Julia function calls @@ -3145,7 +3232,9 @@ (define-public julia-mosaicviews (arguments `(#:tests? #f)) ; Cycle with ImageCore.jl (propagated-inputs - (list julia-mappedarrays julia-paddedviews julia-stackviews)) + (list julia-mappedarrays + julia-paddedviews + julia-stackviews)) ;(native-inputs ; `(("julia-colorvectorspace" ,julia-colorvectorspace) ; ("julia-imagecore" ,julia-imagecore))) @@ -3255,9 +3344,12 @@ (define-public julia-nlsolversbase (base32 "0n8qh5a2ghjx1j70zxn0hmh8gzpa46kmjg8di879y9974bfk0f98")))) (build-system julia-build-system) (propagated-inputs - (list julia-diffresults julia-finitediff julia-forwarddiff)) + (list julia-diffresults + julia-finitediff + julia-forwarddiff)) (native-inputs - (list julia-optimtestproblems julia-recursivearraytools)) + (list julia-optimtestproblems + julia-recursivearraytools)) (home-page "https://github.com/JuliaNLSolvers/NLSolversBase.jl") (synopsis "Optimization and equation solver software in JuliaNLSolvers") (description "This package aims at establishing common ground for Optim.jl, @@ -3290,9 +3382,13 @@ (define-public julia-nnlib (("&& CUDA\\.functional\\(\\)") "")) (setenv "NNLIB_TEST_CUDA" "false")))))) (propagated-inputs - (list julia-adapt julia-chainrulescore julia-requires)) + (list julia-adapt + julia-chainrulescore + julia-requires)) (native-inputs - (list julia-chainrulestestutils julia-stablerngs julia-zygote)) + (list julia-chainrulestestutils + julia-stablerngs + julia-zygote)) (home-page "https://github.com/FluxML/NNlib.jl") (synopsis "Neural Network primitives with multiple backends") (description "This package will provide a library of functions useful for @@ -3412,7 +3508,8 @@ (define-public julia-parameters (base32 "0b8lawi7kcws4axfsdf023gyxca15irl648ciyi1kw3wghz3pfi2")))) (build-system julia-build-system) (propagated-inputs - (list julia-orderedcollections julia-unpack)) + (list julia-orderedcollections + julia-unpack)) (home-page "https://github.com/mauro3/Parameters.jl") (synopsis "Numerical-model parameter helpers") (description "This package contains types with default field values, keyword @@ -3480,7 +3577,8 @@ (define-public julia-plotthemes (base32 "1fd27w9z1vhz0d1bzrs5vcavpb5r5jviyh27d9c4ka37phz4xvmh")))) (build-system julia-build-system) (propagated-inputs - (list julia-plotutils julia-requires)) + (list julia-plotutils + julia-requires)) (home-page "https://github.com/JuliaPlots/PlotThemes.jl") (synopsis "Themes for the Julia plotting package Plots.jl") (description @@ -3502,7 +3600,9 @@ (define-public julia-plotutils (base32 "12aw5gkkcfhpczv2w510k65w1j0hjnh825ihimi223v8plsi5105")))) (build-system julia-build-system) (propagated-inputs - (list julia-colors julia-colorschemes julia-reexport)) + (list julia-colors + julia-colorschemes + julia-reexport)) (native-inputs (list julia-stablerngs)) (home-page "https://github.com/JuliaPlots/PlotUtils.jl") @@ -3548,7 +3648,8 @@ (define-public julia-positivefactorizations (base32 "1wxy6ak7f3hvibcgc8q88cgkf9zvi649mmjy1zlkx1qk80hgvz23")))) (build-system julia-build-system) (native-inputs - (list julia-forwarddiff julia-reversediff)) + (list julia-forwarddiff + julia-reversediff)) (home-page "https://github.com/timholy/PositiveFactorizations.jl") (synopsis "Positive-definite \"approximations\" to matrices") (description "@code{PositiveFactorizations} is a package for computing a @@ -3607,7 +3708,10 @@ (define-public julia-prettytables ((".*colors\\.jl.*") "")) #t))))) (propagated-inputs - (list julia-crayons julia-formatting julia-reexport julia-tables)) + (list julia-crayons + julia-formatting + julia-reexport + julia-tables)) (home-page "https://github.com/ronisbr/PrettyTables.jl") (synopsis "Print data in formatted tables") (description "This package has the purpose to print data in matrices in a @@ -3674,7 +3778,8 @@ (define-public julia-pycall (setenv "JULIA_PKGEVAL" "true") #t))))) (propagated-inputs - (list julia-macrotools julia-versionparsing)) + (list julia-macrotools + julia-versionparsing)) (inputs (list python)) (native-inputs @@ -3817,7 +3922,8 @@ (define-public julia-queryoperators (base32 "06zm4cbn3x49lbpgshhdfvvmgz066qkc8q0d57igm5p8bcp6js22")))) (build-system julia-build-system) (propagated-inputs - (list julia-datastructures julia-iteratorinterfaceextensions + (list julia-datastructures + julia-iteratorinterfaceextensions julia-tableshowutils)) (home-page "https://github.com/queryverse/QueryOperators.jl") (synopsis "Query operators for Julia") @@ -3907,7 +4013,9 @@ (define-public julia-recipespipeline (arguments `(#:tests? #f)) ; Cycle with Plots.jl. (propagated-inputs - (list julia-nanmath julia-plotutils julia-recipesbase)) + (list julia-nanmath + julia-plotutils + julia-recipesbase)) (home-page "http://juliaplots.org/RecipesPipeline.jl/dev/") (synopsis "Utilities for processing recipes") (description "This package was factored out of @code{Plots.jl} to allow any @@ -3990,7 +4098,10 @@ (define-public julia-referencetests (arguments `(#:tests? #f)) ; Cycle with ImageCore.jl through ImageMagick.jl. (propagated-inputs - (list julia-deepdiffs julia-distances julia-fileio julia-imagecore + (list julia-deepdiffs + julia-distances + julia-fileio + julia-imagecore julia-imageinterminal)) ;(native-inputs ; `(("julia-csvfiles" ,julia-csvfiles) @@ -4066,7 +4177,8 @@ (define-public julia-reversediff julia-specialfunctions julia-staticarrays)) (native-inputs - (list julia-difftests julia-fillarrays)) + (list julia-difftests + julia-fillarrays)) (home-page "https://github.com/JuliaDiff/ReverseDiff.jl") (synopsis "Reverse Mode Automatic Differentiation for Julia") (description "@code{ReverseDiff.jl} is a fast and compile-able tape-based @@ -4122,7 +4234,9 @@ (define-public julia-rotations (propagated-inputs (list julia-staticarrays)) (native-inputs - (list julia-benchmarktools julia-forwarddiff julia-unitful)) + (list julia-benchmarktools + julia-forwarddiff + julia-unitful)) (home-page "https://github.com/JuliaGeometry/Rotations.jl") (synopsis "Julia implementations for different rotation parameterisations") (description "This package implements various 3D rotation parameterizations @@ -4323,7 +4437,8 @@ (define-public julia-specialfunctions (inputs (list julia-chainrulestestutils)) (propagated-inputs - (list julia-chainrulescore julia-logexpfunctions + (list julia-chainrulescore + julia-logexpfunctions julia-openspecfun-jll)) (home-page "https://github.com/JuliaMath/SpecialFunctions.jl") (synopsis "Special mathematical functions") @@ -4348,7 +4463,8 @@ (define-public julia-splitapplycombine (base32 "1qzaqvk57b0s5krzn8bxkzmr5kz6hi9dm3jbf2sl7z4vznsgbn9x")))) (build-system julia-build-system) (propagated-inputs - (list julia-dictionaries julia-indexing)) + (list julia-dictionaries + julia-indexing)) (home-page "https://github.com/JuliaData/SplitApplyCombine.jl") (synopsis "Split-apply-combine strategies for Julia") (description "@code{SplitApplyCombine.jl} provides high-level, generic tools @@ -4406,7 +4522,8 @@ (define-public julia-stackviews (propagated-inputs (list julia-offsetarrays)) (native-inputs - (list julia-aqua julia-documenter)) + (list julia-aqua + julia-documenter)) (home-page "https://github.com/JuliaArrays/StackViews.jl") (synopsis "No more catcat") (description "StackViews provides only one array type: @code{StackView}. @@ -4506,8 +4623,11 @@ (define-public julia-statsbase (base32 "02y4pm5yvg713a2pn970bbcfkrn2h133rxbxk1da18svhqw3czhi")))) (build-system julia-build-system) (propagated-inputs - (list julia-dataapi julia-datastructures julia-missings - julia-sortingalgorithms julia-statsapi)) + (list julia-dataapi + julia-datastructures + julia-missings + julia-sortingalgorithms + julia-statsapi)) (native-inputs (list julia-stablerngs)) (home-page "https://github.com/JuliaStats/StatsBase.jl") @@ -4567,10 +4687,15 @@ (define-public julia-structarrays "test/runtests.jl") (("Int64") "Int32"))))))))) (propagated-inputs - (list julia-dataapi julia-staticarrays julia-tables)) + (list julia-dataapi + julia-staticarrays + julia-tables)) (native-inputs - (list julia-documenter julia-offsetarrays julia-pooledarrays - julia-typedtables julia-weakrefstrings)) + (list julia-documenter + julia-offsetarrays + julia-pooledarrays + julia-typedtables + julia-weakrefstrings)) (home-page "https://github.com/JuliaArrays/StructArrays.jl") (synopsis "Efficient implementation of struct arrays in Julia") (description "This package introduces the type @code{StructArray} which is @@ -4659,10 +4784,13 @@ (define-public julia-tables (base32 "1sqqagzqvav8b1rv5ywwbgy9ixvlmipq95fkwfwn0m8769i8jwzb")))) (build-system julia-build-system) (propagated-inputs - (list julia-dataapi julia-datavalueinterfaces - julia-iteratorinterfaceextensions julia-tabletraits)) + (list julia-dataapi + julia-datavalueinterfaces + julia-iteratorinterfaceextensions + julia-tabletraits)) (native-inputs - (list julia-datavalues julia-queryoperators)) + (list julia-datavalues + julia-queryoperators)) (home-page "https://github.com/JuliaData/Tables.jl") (synopsis "Interface for tables in Julia") (description "The @code{Tables.jl} package provides simple, yet powerful @@ -4687,7 +4815,8 @@ (define-public julia-tableshowutils (base32 "0gp3hpj3jvzfhkp9r345vfic2j2n2s60729wv38hwn75csp74cg5")))) (build-system julia-build-system) (propagated-inputs - (list julia-datavalues julia-json)) + (list julia-datavalues + julia-json)) (home-page "https://github.com/queryverse/TableShowUtils.jl") (synopsis "Implement show for TableTraits.jl types") (description "This package provides some common helper functions that make @@ -4756,8 +4885,11 @@ (define-public julia-testimages (arguments `(#:tests? #f)) ; cycle with ImageMagick.jl (propagated-inputs - (list julia-axisarrays julia-colortypes julia-fileio - julia-offsetarrays julia-stringdistances)) + (list julia-axisarrays + julia-colortypes + julia-fileio + julia-offsetarrays + julia-stringdistances)) ;(native-inputs ; `(("julia-colors" ,julia-colors) ; ("julia-fixedpointnumbers" ,julia-fixedpointnumbers) @@ -4848,7 +4980,9 @@ (define-public julia-typedtables (base32 "0nk6zhqvl2r8yhjdhb59kxq0srd3vy4ysg4d8rszj9a43dnn3w3i")))) (build-system julia-build-system) (propagated-inputs - (list julia-adapt julia-splitapplycombine julia-tables)) + (list julia-adapt + julia-splitapplycombine + julia-tables)) (home-page "https://github.com/JuliaData/TypedTables.jl") (synopsis "Column-based storage for data analysis in Julia") (description "@code{TypedTables.jl} provides two column-based storage @@ -4976,7 +5110,8 @@ (define-public julia-weakrefstrings (base32 "14h1vdnc3rx87w6v2rr59lgb4kai2hd1wzqpxhmzsi8karg2z219")))) (build-system julia-build-system) (propagated-inputs - (list julia-dataapi julia-parsers)) + (list julia-dataapi + julia-parsers)) (home-page "https://github.com/JuliaData/WeakRefStrings.jl") (synopsis "Efficient string representation and transfer in Julia") (description "This package provides a minimal String type for Julia that From patchwork Tue Jan 4 22:47:40 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 35968 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 5375227BBEA; Tue, 4 Jan 2022 22:50:46 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_INVALID,DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI, RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id B5AB627BBE9 for ; Tue, 4 Jan 2022 22:50:45 +0000 (GMT) Received: from localhost ([::1]:46152 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1n4sdg-0001xO-V4 for patchwork@mira.cbaines.net; Tue, 04 Jan 2022 17:50:44 -0500 Received: from eggs.gnu.org ([209.51.188.92]:43444) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1n4sc1-0007Xr-Vm for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:01 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:55740) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1n4sc1-0006yL-KW for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:01 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1n4sc1-0003pp-Iq for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:01 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#53017] [PATCH 02/17] build: julia-build-system: Create 'Project.toml' file when missing. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 04 Jan 2022 22:49:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 53017 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 53017@debbugs.gnu.org Cc: efraim@flashner.co.il, zimoun Received: via spool by 53017-submit@debbugs.gnu.org id=B53017.164133649214510 (code B ref 53017); Tue, 04 Jan 2022 22:49:01 +0000 Received: (at 53017) by debbugs.gnu.org; 4 Jan 2022 22:48:12 +0000 Received: from localhost ([127.0.0.1]:39010 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbD-0003lw-6C for submit@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:11 -0500 Received: from mail-wm1-f49.google.com ([209.85.128.49]:40775) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbA-0003l9-Vx for 53017@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:09 -0500 Received: by mail-wm1-f49.google.com with SMTP id j140-20020a1c2392000000b003399ae48f58so606320wmj.5 for <53017@debbugs.gnu.org>; Tue, 04 Jan 2022 14:48:08 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=J8w7M+1Ix+Uc1q5NPheaYn+7vXV2B0vv2DXCTEMnOSo=; b=AN2S2q2EYASgbohoS6t3u8bwTHvIcPPD1XMlew8mVQWcInkWQI/TnHu2SVBYWAVNAf n5+7q7ev270xBwBwHO1T2dgsGVOvoWlg3QA89DFOWymsUib82fJsfiMO1cXwduAMPn2E Ez3KAFZFVlRsmzL5SO/pS+WaGZhDxJ4Xot9MF8jrq9EUb0VB5iuoqTS0Yp7ZtK/KtN9X 2jojG25qkDF+5NV7biPHGCgg90nUMHhwgfgv1gWnN5RidY+Yi+xf2Lq3GBdCu12KXXyy X4yXGRZecOqtVtl4OaIhpSseYYYf+nPQ3AonqaKIsGJedDqrondSeqD/+Vs2vJy7SmNw pQ2A== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=J8w7M+1Ix+Uc1q5NPheaYn+7vXV2B0vv2DXCTEMnOSo=; b=vPCs0Oe97zozoevJAETckMCG4u7D20FcJNLd07EzpIOx+xigRdSyUHVK533ptKpolL d+n/auJ/FZwZB0WFEIfhOroLvAkbXyOxseOy7oy5IB2P2qw64b7qOtRka+eURWdSWSFW ZIy2Ik3gIR2cys+HxQphqHhCWHdcU9PafIQYfyf/nGgISriKJ02IcuXUan4HEGj+2YaK ukNQon/jZbXbUXkg6p0mH44yAqxWFSSJSpY0WdLRhEyHa3gDc8x4m58JzM96iyKMqrzw 6jFw7KggzM/t6j+VfdN4A1xpvNnJwP+Co2bZ0p6w6nCi4ij278iTQu5T6RYJVrRIDIhh pm0A== X-Gm-Message-State: AOAM531pd+b527G/NF89EsdtsaQj3IgHE+1uU5R/rF7VScE0cu71Wqc4 SG9RgqcC/XP+FmXEvL34TDO8WhkeF6Y= X-Google-Smtp-Source: ABdhPJyoSSCYc/D2BJLq9mAEq4XTS9HE4T3O4y9TlMvOzz/DU0nHUEx0f21slwy+GGBaUbPwHJGbIA== X-Received: by 2002:a1c:f70d:: with SMTP id v13mr396948wmh.133.1641336483319; Tue, 04 Jan 2022 14:48:03 -0800 (PST) Received: from localhost.localdomain ([193.48.40.117]) by smtp.gmail.com with ESMTPSA id c9sm732842wml.12.2022.01.04.14.48.02 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 04 Jan 2022 14:48:03 -0800 (PST) From: zimoun Date: Tue, 4 Jan 2022 23:47:40 +0100 Message-Id: <20220104224755.1142897-2-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.33.1 In-Reply-To: <20220104224755.1142897-1-zimon.toutoune@gmail.com> References: <20220104224755.1142897-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 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 * guix/build/julia-build-system.scm (link-depot): Create 'Project.toml' file when missing using data provided by the user. (julia-create-package-toml): Remove from export. * doc/guix.texi (Build Systems): Update julia-build-system section. --- doc/guix.texi | 19 +++++++++--------- guix/build/julia-build-system.scm | 33 ++++++++++++++++++++----------- 2 files changed, 30 insertions(+), 22 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index dfb94be74e..603f8dcca3 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -71,7 +71,7 @@ Copyright @copyright{} 2019 Kyle Andrews@* Copyright @copyright{} 2019 Alex Griffin@* Copyright @copyright{} 2019, 2020, 2021 Guillaume Le Vaillant@* Copyright @copyright{} 2020 Liliana Marie Prikler@* -Copyright @copyright{} 2019, 2020, 2021 Simon Tournier@* +Copyright @copyright{} 2019, 2020, 2021, 2022 Simon Tournier@* Copyright @copyright{} 2020 Wiktor Żelazny@* Copyright @copyright{} 2020 Damien Cassou@* Copyright @copyright{} 2020 Jakub Kądziołka@* @@ -8363,9 +8363,10 @@ julia} packages, which essentially is similar to running @samp{julia -e @env{JULIA_LOAD_PATH} contains the paths to all Julia package inputs. Tests are run by calling @code{/test/runtests.jl}. -The Julia package name is read from the file @file{Project.toml}. This -value can be overridden by passing the argument @code{#:julia-package-name} -(which must be correctly capitalized). +The Julia package name and uuid is read from the file +@file{Project.toml}. These values can be overridden by passing the +argument @code{#:julia-package-name} (which must be correctly +capitalized) or @code{#:julia-package-uuid}. Julia packages usually manage their binary dependencies via @code{JLLWrappers.jl}, a Julia package that creates a module (named @@ -8393,12 +8394,10 @@ MbedTLS package: (find-files "src/wrappers/" "\\.jl$")))) @end lisp -Some older packages that aren't using @file{Package.toml} yet, will require -this file to be created, too. The function @code{julia-create-package-toml} -helps creating the file. You need to pass the outputs and the source of the -package, its name (the same as the @code{file-name} parameter), the package -uuid, the package version, and a list of dependencies specified by their name -and their uuid. +Some older packages that aren't using @file{Project.toml} yet, will +require this file to be created, too. It is internally done if the +arguments @code{#:julia-package-name} and @code{#:julia-package-uuid} +are provided. @end defvr @defvr {Scheme Variable} maven-build-system diff --git a/guix/build/julia-build-system.scm b/guix/build/julia-build-system.scm index b4e0044567..03d669be64 100644 --- a/guix/build/julia-build-system.scm +++ b/guix/build/julia-build-system.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2019, 2020 Nicolò Balzarotti ;;; Copyright © 2021 Jean-Baptiste Volatier -;;; Copyright © 2021 Simon Tournier +;;; Copyright © 2021, 2022 Simon Tournier ;;; ;;; This file is part of GNU Guix. ;;; @@ -27,8 +27,8 @@ (define-module (guix build julia-build-system) #:use-module (ice-9 regex) #:use-module (ice-9 rdelim) #:use-module (ice-9 popen) + #:use-module (srfi srfi-1) #:export (%standard-phases - julia-create-package-toml julia-build)) ;; Commentary: @@ -138,6 +138,8 @@ (define* (check #:key tests? source inputs outputs julia-package-name (define* (link-depot #:key source inputs outputs julia-package-name julia-package-uuid #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) + (name+version (strip-store-file-name out)) + (version (last (string-split name+version #\-))) (package-name (or julia-package-name (project.toml->name "Project.toml"))) @@ -148,6 +150,14 @@ (define* (link-depot #:key source inputs outputs println(Base.version_slug(Base.UUID(\"~a\"), Base.SHA1(Pkg.GitTools.tree_hash(\".\"))))" uuid))) (slug (string-trim-right (get-string-all pipe)))) + ;; Few packages do not have the regular Project.toml file, then when they + ;; are propagated, dependencies do not find them and an raise error. + (unless (file-exists? "Project.toml") + (julia-create-package-toml (getcwd) + julia-package-name julia-package-uuid + version + #:file "Project.toml")) + ;; When installing a package, julia looks first at in the JULIA_DEPOT_PATH ;; for a path like packages/PACKAGE/XXXX ;; Where XXXX is a slug encoding the package UUID and SHA1 of the files @@ -157,17 +167,16 @@ (define* (link-depot #:key source inputs outputs (symlink package-dir (string-append out "/share/julia/packages/" package-name "/" slug)))) -(define (julia-create-package-toml outputs source - name uuid version - deps) - "Some packages are not using the new Package.toml dependency specifications. -Write this file manually, so that Julia can find its dependencies." +(define* (julia-create-package-toml location + name uuid version + #:optional + (deps '()) + #:key + (file "Project.toml")) + "Some packages are not using the new Project.toml dependency specifications. +Write this FILE manually, so that Julia can find its dependencies." (let ((f (open-file - (string-append - (assoc-ref outputs "out") - %package-path - (string-append - name "/Project.toml")) + (string-append location "/" file) "w"))) (display (string-append " From patchwork Tue Jan 4 22:47:41 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 35958 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 5DDFA27BBEA; Tue, 4 Jan 2022 22:49:20 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_INVALID,DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI, RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 259D127BBE9 for ; Tue, 4 Jan 2022 22:49:20 +0000 (GMT) Received: from localhost ([::1]:42132 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1n4scJ-0007cB-9v for patchwork@mira.cbaines.net; Tue, 04 Jan 2022 17:49:19 -0500 Received: from eggs.gnu.org ([209.51.188.92]:43446) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1n4sc2-0007Yo-9u for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:02 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:55741) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1n4sc2-0006yR-0V for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1n4sc1-0003px-VZ for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:01 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#53017] [PATCH 03/17] gnu: julia-zygote: Adjust style. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 04 Jan 2022 22:49:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 53017 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 53017@debbugs.gnu.org Cc: efraim@flashner.co.il, zimoun Received: via spool by 53017-submit@debbugs.gnu.org id=B53017.164133649214528 (code B ref 53017); Tue, 04 Jan 2022 22:49:01 +0000 Received: (at 53017) by debbugs.gnu.org; 4 Jan 2022 22:48:12 +0000 Received: from localhost ([127.0.0.1]:39013 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbD-0003lz-Ni for submit@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:12 -0500 Received: from mail-wm1-f47.google.com ([209.85.128.47]:40774) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbB-0003lB-KP for 53017@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:10 -0500 Received: by mail-wm1-f47.google.com with SMTP id j140-20020a1c2392000000b003399ae48f58so606337wmj.5 for <53017@debbugs.gnu.org>; Tue, 04 Jan 2022 14:48:09 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=wZS459oqUTC/rNACQwDP5ZOzoiDpOklFDaQcjQkDXBo=; b=E56anDlPX0taSA1I6mHhLMTxp6Bhv+g0bZGAhCWAGOIUqO6sLkR3qjR1An8wPZJYxq k3Rh65x4VT42Fy0Gr32XVZKHPl1UB2OLSO5RK6GBEctcdyXiij7KOYX/vXFDPyRknx40 OUklcg44KADsXPSLGJ0v+Wy77gPWEln26DikYQ5qkyFsq/ba54MqQVHN+zRnE6ZNYs6W DqAjk87YvfQf4O6oSIkrtAi453NMA2W4cLyvj+0yRj4WObQljze5LTQk9yWZeolkUHLi UKyHck3+8MWUi5ubK/EM7D/E/C/wWuA05zJtLdmpj1slqrXrovsuH+Iy7nJsEmFtAjzk p48g== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=wZS459oqUTC/rNACQwDP5ZOzoiDpOklFDaQcjQkDXBo=; b=yPiJQygkTT4n7GvF+nGrqE6JPprsm40URPDxE9rVyJ2jO98ia98gT2FlZ0q6SSEi+3 wtcDVJ+6608X+2vCcXpwpx5yRY8vHkrENQ8N5SBO7c196rJedL96NsSLWjhq5cr8241h 1DmDUhmuRIABcJM4vwg22fgmoDJLF8Y84+0qspG7V2aD6iIIT+OIzYwzKcUyrH+6f9Lr glUIMpR/tVeD6KPZY7D4hLnb18M0zXCYOtaYDzYPRJh6/jLb/MRpw6dOX5X+aXu26uI8 bWpdLbg+8VAv/gtc0/SdaCYKvtJ99dUbclcRQSfI8RM46KOJJ5RkACAZXd9fLhgx8xIz gGvw== X-Gm-Message-State: AOAM532+OqcweE7+DDQgmehJ9OGKnUHjWLZNAcq9j+0JeTXzW1vle2qj kmy0bFleEtN5fTmw5rkpUdRoaX8o6Bg= X-Google-Smtp-Source: ABdhPJyHN1cdG1Lo+kAhZDvsUjnVpPRqsB+s3HoN3sN912y6gotYlXnJDrjmxTQYOUlKSch7z9D3lQ== X-Received: by 2002:a7b:c243:: with SMTP id b3mr401693wmj.61.1641336483895; Tue, 04 Jan 2022 14:48:03 -0800 (PST) Received: from localhost.localdomain ([193.48.40.117]) by smtp.gmail.com with ESMTPSA id c9sm732842wml.12.2022.01.04.14.48.03 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 04 Jan 2022 14:48:03 -0800 (PST) From: zimoun Date: Tue, 4 Jan 2022 23:47:41 +0100 Message-Id: <20220104224755.1142897-3-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.33.1 In-Reply-To: <20220104224755.1142897-1-zimon.toutoune@gmail.com> References: <20220104224755.1142897-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 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 * gnu/packages/julia-xyz.scm (julia-zygote)[propagated-inputs]: Remove labels. --- gnu/packages/julia-xyz.scm | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 3701bf3996..e6733fce92 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -5213,17 +5213,17 @@ (define-public julia-zygote (arguments `(#:tests? #f)) ;require CUDA, not packaged yet (propagated-inputs - `(("julia-abstractffs" ,julia-abstractffts) - ("julia-chainrules" ,julia-chainrules) - ("julia-diffrules" ,julia-diffrules) - ("julia-fillarrays" ,julia-fillarrays) - ("julia-forwarddiff" ,julia-forwarddiff) - ("julia-irtools" ,julia-irtools) - ("julia-macrotools" ,julia-macrotools) - ("julia-nanmath" ,julia-nanmath) - ("julia-requires" ,julia-requires) - ("julia-specialfunctions" ,julia-specialfunctions) - ("julia-zygote-rules" ,julia-zygoterules))) + (list julia-abstractffts + julia-chainrules + julia-diffrules + julia-fillarrays + julia-forwarddiff + julia-irtools + julia-macrotools + julia-nanmath + julia-requires + julia-specialfunctions + julia-zygoterules)) (home-page "https://fluxml.ai/Zygote.jl") (synopsis "Automatic differentiation in Julia") (description "Zygote provides source-to-source automatic From patchwork Tue Jan 4 22:47:42 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 35960 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 517F127BBEA; Tue, 4 Jan 2022 22:49:34 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_INVALID,DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI, RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 1EFB027BBE9 for ; Tue, 4 Jan 2022 22:49:34 +0000 (GMT) Received: from localhost ([::1]:42926 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1n4scW-0008EP-WF for patchwork@mira.cbaines.net; Tue, 04 Jan 2022 17:49:33 -0500 Received: from eggs.gnu.org ([209.51.188.92]:43450) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1n4sc2-0007Zz-NU for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:55742) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1n4sc2-0006ye-E7 for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1n4sc2-0003q4-DH for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#53017] [PATCH 04/17] gnu: julia-documentertools: Adjust style. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 04 Jan 2022 22:49:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 53017 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 53017@debbugs.gnu.org Cc: efraim@flashner.co.il, zimoun Received: via spool by 53017-submit@debbugs.gnu.org id=B53017.164133649214535 (code B ref 53017); Tue, 04 Jan 2022 22:49:02 +0000 Received: (at 53017) by debbugs.gnu.org; 4 Jan 2022 22:48:12 +0000 Received: from localhost ([127.0.0.1]:39016 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbE-0003mH-BZ for submit@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:12 -0500 Received: from mail-wm1-f51.google.com ([209.85.128.51]:54146) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbB-0003lC-VE for 53017@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:10 -0500 Received: by mail-wm1-f51.google.com with SMTP id l4so24198846wmq.3 for <53017@debbugs.gnu.org>; Tue, 04 Jan 2022 14:48:09 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=wb19Av6ug9mtrVdFXk1R25VsCI/D8z49omhvQv97kf0=; b=khGDTPwFtdcy6Zyetx/hMco1ZCzQ9KQ2tYX/X2VsVmMb4apQJQpGRt2g7hJw72CbpP nzkyShYsiySDa/0y/USAvnyGtAdLVKk8XDgBXPvok53lcxUIeg/wsxO5rgJWMKZqVDDy sO2XTYsXCaNYYtSFGJAl+b5/fnlMXmMrnP4/Jv/rSvZPtfG3p7A3Z4G3PGrWQeCbu+zl c3FgP6qsdC5jLCaNf01SmtKvkP+5FB2K5FKp5OJVl/NdXK025bya65iHPiQxQeCj7juA wtejQaWceRCeNmy1/ZTOos8vykXsGqmR8s7hZMTOmFCY6H6qcn/xP1HXsWjqIB9hhT9e zlOg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=wb19Av6ug9mtrVdFXk1R25VsCI/D8z49omhvQv97kf0=; b=GShuqr1OQklXpfjObRoezicOxyiDHI6u6o1UL9bRwJ458IeTclP6ep5KwSjwjocr5X vkRIpCr6LJHh7VZd+GsxGzNwyMsKl5KULWWvYC9u5XoMgbS5CqoB+jQZvryo5Onzo6Zc Nff/q5g6p6wrnRGU01E2x/yIkDX6kKv8I+QomVYQiQ+UC1R6tsqpoXMAgm9DiNcQwqzf 5iprJIcv4v3+NRwwDVCFTes3ExLX6YnLwiBsq5DJNZB8IXk/sJ+PBSBG1VeBNn/NwAdr YySiRYQCsZ8ofR8wTATi4UMxkhIV14k7xK6dQGB7TDdhXzOpQFDf1pcE/eUDeVBYaPNc pxqg== X-Gm-Message-State: AOAM531zBhvi6mr5fefoweEvKTY2K+mmAt8FYr6LWzpKcWEbMiSgkg9o ZpjCdYsrGPCzsgsf+d/oH35iVloDECk= X-Google-Smtp-Source: ABdhPJyzaKmONeIebo8pelHHFwemRlxQqWW204jmIEqATBVd/E6JPL4pl7FdxhCGZwNehDPpFtlO/g== X-Received: by 2002:a1c:f616:: with SMTP id w22mr394247wmc.75.1641336484407; Tue, 04 Jan 2022 14:48:04 -0800 (PST) Received: from localhost.localdomain ([193.48.40.117]) by smtp.gmail.com with ESMTPSA id c9sm732842wml.12.2022.01.04.14.48.03 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 04 Jan 2022 14:48:04 -0800 (PST) From: zimoun Date: Tue, 4 Jan 2022 23:47:42 +0100 Message-Id: <20220104224755.1142897-4-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.33.1 In-Reply-To: <20220104224755.1142897-1-zimon.toutoune@gmail.com> References: <20220104224755.1142897-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 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 * gnu/packages/julia-xyz.scm (julia-documentertools)[inputs]: Remove label. [propagated-inputs]: Adjust. --- gnu/packages/julia-xyz.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index e6733fce92..928fd39c37 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1310,9 +1310,11 @@ (define-public julia-documentertools (inputs ;; We don't want to propagate the bootstrap version. ;; Cycle with Documenter.jl in later versions. - `(("julia-documenter" ,julia-documenter-bootstrap))) + (list julia-documenter-bootstrap)) (propagated-inputs - (list julia-docstringextensions julia-gumbo julia-sass)) + (list julia-docstringextensions + julia-gumbo + julia-sass)) (native-inputs (list julia-example)) (home-page "https://github.com/JuliaDocs/DocumenterTools.jl") From patchwork Tue Jan 4 22:47:43 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 35969 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 A527627BBEA; Tue, 4 Jan 2022 22:51:00 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_INVALID,DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI, RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 6CC0C27BBE9 for ; Tue, 4 Jan 2022 22:51:00 +0000 (GMT) Received: from localhost ([::1]:46372 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1n4sdu-00026R-6d for patchwork@mira.cbaines.net; Tue, 04 Jan 2022 17:50:58 -0500 Received: from eggs.gnu.org ([209.51.188.92]:43452) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1n4sc3-0007aW-6U for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:55743) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1n4sc2-0006yk-QT for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1n4sc2-0003qC-Pg for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:02 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#53017] [PATCH 05/17] gnu: julia-documenter: Adjust style. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 04 Jan 2022 22:49:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 53017 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 53017@debbugs.gnu.org Cc: efraim@flashner.co.il, zimoun Received: via spool by 53017-submit@debbugs.gnu.org id=B53017.164133649514576 (code B ref 53017); Tue, 04 Jan 2022 22:49:02 +0000 Received: (at 53017) by debbugs.gnu.org; 4 Jan 2022 22:48:15 +0000 Received: from localhost ([127.0.0.1]:39023 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbG-0003mu-N7 for submit@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:15 -0500 Received: from mail-wm1-f42.google.com ([209.85.128.42]:51803) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbC-0003lE-Bu for 53017@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:10 -0500 Received: by mail-wm1-f42.google.com with SMTP id e5so23799642wmq.1 for <53017@debbugs.gnu.org>; Tue, 04 Jan 2022 14:48:10 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=lVDx4AwWb1dLuTnWV0NB1wGMnQWCtJVRYqEvGAsAfkw=; b=b3N5bSFVn3F3Ef/r+EoxfNMNooWWo9OzT5vgFpaBeA+7GG0OE4BM+cEhjCBbNu4rMU WmvWnZ5HrWkJW13HSYPgv4ihdFs0+AhX8Un4QduT1veSeehzA8YxCbMHvDGPdLbyvJ7R 3+QBPtYwB4sFy3tb+zx/4fza3MDmQvZQQRYVVMLHZR2kwe5atQ7cG3d/zh1Y1/QYxfLY HkXQrFLd1hpXM4LQ85rwwWdD8vGPo3DQFEUGDT6rK6tMordZ7Md+yI+s/P6qLFkMQT7h DH4gXT9g3+ysGxNoHScZDFYaJXn9I+c3A1A872MhrltagaP8shnVBfQCYLhWlEy8tR9w 654A== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=lVDx4AwWb1dLuTnWV0NB1wGMnQWCtJVRYqEvGAsAfkw=; b=b+8i4cq6PyGXBWmR4dr2TxfHa5l7PZormQgNkHDv8ks1AJZWblvgA26zcjFhUeehbh x9lri1HPUtpF/lkKy2zeX+zGpzBJDmbF6zEf020IKd8JxJzHgDCYGXV7E6Dh2hwcsBo1 cNShirNMayBHNqPQaY4C3IbkXinbZ//s/SHX6N3eZaEv1bqabYxiUknieHU+rfXdJoFS 4QY9QIjUzcSz1GXr0SoND+VRXyKRFcF9s9VXo5Q6QdWlIzDJB8gwezyltoqrNDfX5tW3 5D0kbcO3nCpYzU+9uL+olhL0mgnbwCVD9siOKxedBmz6cRCuAj6ZENbg3K6HV0Dk6SGt Zq+A== X-Gm-Message-State: AOAM530ay1hVMNiiD1A76RtC5P4S6vFfpRywfyeEkvlvU52Vcz/QRtnG cpj2bfg0nKRkAsf5GyOpbTA/tg2HakU= X-Google-Smtp-Source: ABdhPJxa0A8YjbEAA8lUkvyoZw4lEexacknoP36KAlKD99hpqQn+0w99hx4zznhKtn15JGjAwKIaRQ== X-Received: by 2002:a05:600c:4142:: with SMTP id h2mr397851wmm.141.1641336484865; Tue, 04 Jan 2022 14:48:04 -0800 (PST) Received: from localhost.localdomain ([193.48.40.117]) by smtp.gmail.com with ESMTPSA id c9sm732842wml.12.2022.01.04.14.48.04 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 04 Jan 2022 14:48:04 -0800 (PST) From: zimoun Date: Tue, 4 Jan 2022 23:47:43 +0100 Message-Id: <20220104224755.1142897-5-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.33.1 In-Reply-To: <20220104224755.1142897-1-zimon.toutoune@gmail.com> References: <20220104224755.1142897-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 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 * gnu/packages/julia-xyz.scm (julia-documenter)[propagated-inputs] Remove labels. [inputs, native-inputs]: Remove labels. [arguments]: Remove unnecessary return '#t'. --- gnu/packages/julia-xyz.scm | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 928fd39c37..26a1f31c25 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1228,8 +1228,7 @@ (define-public julia-documenter (substitute* "src/Deps.jl" (("pip install") (string-append (assoc-ref inputs "python") - "/bin/pip install"))) - #t)) + "/bin/pip install"))))) (add-after 'link-depot 'remove-javascript-downloads (lambda _ (substitute* "src/Writers/HTMLWriter.jl" @@ -1237,17 +1236,18 @@ (define-public julia-documenter ;; Removing the javascript downloads causes these tests fail. (substitute* "test/examples/tests.jl" ((".*Main\\.examples_html_doc.*") "") - ((".*Main\\.examples_html_mathjax3_doc.*") "")) - #t))))) + ((".*Main\\.examples_html_mathjax3_doc.*") ""))))))) (propagated-inputs - (list julia-ansicoloredprinters julia-docstringextensions - julia-iocapture julia-json)) + (list julia-ansicoloredprinters + julia-docstringextensions + julia-iocapture + julia-json)) (inputs - `(("python" ,python-wrapper))) + (list python-wrapper)) (native-inputs - `(("git" ,git-minimal) - ("julia-documentermarkdown" ,julia-documentermarkdown) - ("julia-documentertools" ,julia-documentertools))) + (list git-minimal + julia-documentermarkdown + julia-documentertools)) (home-page "https://juliadocs.github.io/Documenter.jl") (synopsis "Documentation generator for Julia") (description "This package provides a documentation generator for Julia.") From patchwork Tue Jan 4 22:47:44 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 35965 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 A806727BBEA; Tue, 4 Jan 2022 22:49:53 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_INVALID,DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI, RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 781FB27BBE9 for ; Tue, 4 Jan 2022 22:49:53 +0000 (GMT) Received: from localhost ([::1]:44610 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1n4scq-0000tI-MQ for patchwork@mira.cbaines.net; Tue, 04 Jan 2022 17:49:52 -0500 Received: from eggs.gnu.org ([209.51.188.92]:43458) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1n4sc4-0007eR-8W for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:04 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:55746) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1n4sc3-0006z2-VH for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1n4sc3-0003qY-U5 for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#53017] [PATCH 06/17] gnu: Add julia-biogenerics. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 04 Jan 2022 22:49:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 53017 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 53017@debbugs.gnu.org Cc: efraim@flashner.co.il, zimoun Received: via spool by 53017-submit@debbugs.gnu.org id=B53017.164133649814623 (code B ref 53017); Tue, 04 Jan 2022 22:49:03 +0000 Received: (at 53017) by debbugs.gnu.org; 4 Jan 2022 22:48:18 +0000 Received: from localhost ([127.0.0.1]:39033 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbK-0003nf-7a for submit@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:18 -0500 Received: from mail-wm1-f53.google.com ([209.85.128.53]:41710) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbC-0003lF-SV for 53017@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:11 -0500 Received: by mail-wm1-f53.google.com with SMTP id b186-20020a1c1bc3000000b00345734afe78so2259947wmb.0 for <53017@debbugs.gnu.org>; Tue, 04 Jan 2022 14:48:10 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=2EE1GqFYCW0p5kfCuiUTituC9ty8YHnctX1kquzW+qU=; b=bG0X+x4d9Oo2nYFbsC0/0Po5mFDcPaDvT5cxHqznVlBpKl31Kajd9H1BpiIxgkz5RZ wtUIBVH3hV96R8/O4NPiCWlTtfYlVD/1vcPzYuQf1ju85fAk+v3iJFuikWUA0YQysPh/ CYi6sAWavrOCTtlmXqgPB711pFM6Jakz44N1UUbiL/pU1s4hzxeFoo7XLBzNopf9zNPB qAOdGeg3bzo2LLno5htzbEWKPm+fWwsmUmEkrKsp0cGOen+CIgTl1fVOO+8qiJZTRbXE SobTLtjTsDKbvY55Msxvr2oCqQaYQglbcCu5lmZ2sPJrCTLpSjchMuBjI+ugXMkZiTvJ acUw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=2EE1GqFYCW0p5kfCuiUTituC9ty8YHnctX1kquzW+qU=; b=qzSRzieNZyi5EwstGUFHg8tZMLJE4k3AoDzx4aDhNnZY3pkJQJNTla1M5t90ZeU+/8 RVT+21ePdQKhy0Wz5oAhsayRnLDzb6Pzlh+Smu9TR+udaeutYEBjd+xd3OGa5quLN/0M /sfRbGKbNfA2+L5R3OoeYNMYIUi9D9ow+EhWuZYXcjQ4Uhn6TIZ/DSB+NpqLDvncyxjT qxrgs+edVkd67uLJjn3wkHsjPie98fvOEozytwrxIr4wNnYNxsBqZO6Aye2OLiIf+KGP U971mUx3VSGAGbZh3NXzqBzpdQ+qQBss8oNdyqm0MCdVW0RNPGQ8CM5wY6nSq2xqFSYz anLA== X-Gm-Message-State: AOAM532hvhTyhQMv5RZ7wni0YEn5jmC+qr19sabA7MXCpZq4EEmlxc5K 0ACPpQL6JXAp7dTVgNXfqs9d5rd7KTs= X-Google-Smtp-Source: ABdhPJyUt08y+A8ckKwN82DEPifSlDZz5NZ7Fd4x1yD0S9r4lp1/AJBtkDhbAUQjl3pAvT+2cr7TvA== X-Received: by 2002:a05:600c:231a:: with SMTP id 26mr436221wmo.12.1641336485329; Tue, 04 Jan 2022 14:48:05 -0800 (PST) Received: from localhost.localdomain ([193.48.40.117]) by smtp.gmail.com with ESMTPSA id c9sm732842wml.12.2022.01.04.14.48.04 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 04 Jan 2022 14:48:05 -0800 (PST) From: zimoun Date: Tue, 4 Jan 2022 23:47:44 +0100 Message-Id: <20220104224755.1142897-6-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.33.1 In-Reply-To: <20220104224755.1142897-1-zimon.toutoune@gmail.com> References: <20220104224755.1142897-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 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 * gnu/packages/julia-xyz.scm (julia-biogenerics): New variable. --- gnu/packages/julia-xyz.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 26a1f31c25..49bf6ae26f 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -333,6 +333,32 @@ (define-public julia-benchmarktools benchmarks as well as comparing benchmark results.") (license license:expat))) +(define-public julia-biogenerics + ;; No upstream release + (let ((commit "a75abaf459250e2b5e22b4d9adf25fd36d2acab6") + (revision "0")) + (package + (name "julia-biogenerics") + (version (git-version "0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/BioJulia/BioGenerics.jl") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "17d222vi9nssjwr5l349fss7jnglnjimp1z62kmfmxa4fsn8lk8l")))) + (build-system julia-build-system) + (inputs + (list julia-transcodingstreams)) + (home-page "https://github.com/BioJulia/BioGenerics.jl") + (synopsis "Generic methods used by BioJulia packages") + (description "This package provides generic methods and modules used in +many of the other BioJulia packages. This package defines IO, exceptions, and +other types or methods used by other BioJulia packages.") + (license license:expat)))) + (define-public julia-blockarrays (package (name "julia-blockarrays") From patchwork Tue Jan 4 22:47:45 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 35970 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 4A9D227BBEA; Tue, 4 Jan 2022 22:51:10 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_INVALID,DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI, RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 1578A27BBE9 for ; Tue, 4 Jan 2022 22:51:10 +0000 (GMT) Received: from localhost ([::1]:46598 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1n4se5-0002Me-8o for patchwork@mira.cbaines.net; Tue, 04 Jan 2022 17:51:09 -0500 Received: from eggs.gnu.org ([209.51.188.92]:43456) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1n4sc3-0007ci-Sw for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:55745) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1n4sc3-0006yx-Im for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:03 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1n4sc3-0003qQ-Hq for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:03 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#53017] [PATCH 07/17] gnu: Add julia-indexablebitvectors. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 04 Jan 2022 22:49:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 53017 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 53017@debbugs.gnu.org Cc: efraim@flashner.co.il, zimoun Received: via spool by 53017-submit@debbugs.gnu.org id=B53017.164133649814614 (code B ref 53017); Tue, 04 Jan 2022 22:49:03 +0000 Received: (at 53017) by debbugs.gnu.org; 4 Jan 2022 22:48:18 +0000 Received: from localhost ([127.0.0.1]:39031 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbJ-0003nY-UA for submit@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:18 -0500 Received: from mail-wm1-f48.google.com ([209.85.128.48]:36697) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbD-0003lH-C1 for 53017@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:11 -0500 Received: by mail-wm1-f48.google.com with SMTP id n19-20020a7bc5d3000000b003466ef16375so624496wmk.1 for <53017@debbugs.gnu.org>; Tue, 04 Jan 2022 14:48:11 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=eWsRtHsKGu12w2yvqOp/zIQaRnq1mSSpB9CeM2i3j24=; b=aaLL2qxCRvo1lI8IgqMARS85RnDwS8wTOEs/zpoaTwp40716eSeKygBRmKZYycPVr0 T0PEzVFn0DVH8pGWo4BMCLGnwpH1LljzD0RlCjKTcGJTH7+tsdyrvq2GD6bFEOXDOejF 6brJtO8d3Nsb3sPiHOvdOpUUuOkQIICgvzGoOp0DyA09M5g/FSphcdy6ryGV+21N6kJc Lue09FJR1ovotD7vgpiXuNg/whFaj2tHOh5kea7PZVju/u5eKd9bdfY3+AArPAJM+F/G vuRSwc2k+EkVtUKwec4KuI/h/zts97iNsLoLFmWjC1wrSGVnhzq1lmty1mOV/laZ987X vjIQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=eWsRtHsKGu12w2yvqOp/zIQaRnq1mSSpB9CeM2i3j24=; b=s18xIX4hrzThU2jK0c3ErdZUlLeW+GlLEc6pP5Xk3jvNqVeA/3r87PUcvsnQfa4pDC EfNI2WBwtANJaA9Qy5oQRLFv8Yq5iMBAvhfnEM5d0g1anlCzI97l9AiqBCsdW59PDrWI a2pRbESLkaYro+TU19iROHq0vrJghxO8gP0a88lJa267JqdmIpkM/OgeggHW5tGN1CMM 20by6fOdojG9XL5t93BFeC6S8nW4rzWeXualTdXKwA9NYxQJiurhe6Hexd3PKHoHh0Jd mAuxR212Vhw4R7MpIH7lLS2QOvOhHLIGartoG7hjes7+0HBMu3XKhwajkjtcWODAG5zy zpbg== X-Gm-Message-State: AOAM530ZvhnoNJNyug1uszMa9M1l7Kgsd5PLXmYD0fjiv+kC94UzPBEE 9JabWfU6pHLudPwFjsPTMncc2hTW82o= X-Google-Smtp-Source: ABdhPJwGSEUoVna5VXJa4OnhuyCVkTFIHvH+XYkf7NGIrchh8zb+U+HS29qwELeBq57kCSqjAt27rQ== X-Received: by 2002:a1c:ed17:: with SMTP id l23mr406562wmh.118.1641336485800; Tue, 04 Jan 2022 14:48:05 -0800 (PST) Received: from localhost.localdomain ([193.48.40.117]) by smtp.gmail.com with ESMTPSA id c9sm732842wml.12.2022.01.04.14.48.05 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 04 Jan 2022 14:48:05 -0800 (PST) From: zimoun Date: Tue, 4 Jan 2022 23:47:45 +0100 Message-Id: <20220104224755.1142897-7-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.33.1 In-Reply-To: <20220104224755.1142897-1-zimon.toutoune@gmail.com> References: <20220104224755.1142897-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 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 * gnu/packages/julia-xyz.scm (julia-indexablebitvectors): New variable. --- gnu/packages/julia-xyz.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 49bf6ae26f..1508a86dd1 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -2503,6 +2503,39 @@ (define-public julia-imagetransformations rotation, and other spatial transformations of arrays.") (license license:expat))) +(define-public julia-indexablebitvectors + (package + (name "julia-indexablebitvectors") + (version "1.0.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/BioJulia/IndexableBitVectors.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1khaycydwa31sxwvrrvvlylpzdb77kkxfmb8cax3i22ix0c2nmlc")))) + (build-system julia-build-system) + ;; Package without Project.toml + (arguments + '(#:julia-package-name "IndexableBitVectors" + #:julia-package-uuid "1cb3b9ac-1ffd-5777-9e6b-a3d42300664d")) + (home-page "https://github.com/BioJulia/IndexableBitVectors.jl") + (synopsis "Bit vectors operations with extremely fast speed") + (description "This package exports following operations over bit vectors +with extremely fast speed while keeping extra memory usage small: +@itemize +@item @code{getindex(bv::IndexableBitVectors, i::Integer)}: @code{i}-th +element of @code{bv} +@item @code{rank(b::Bool, bv::AbstractIndexableBitVector, i::Integer)}: the +number of occurrences of bit @code{b} in @code{bv[1:i]} +@item @code{select(b::Bool, bv::AbstractIndexableBitVector, i::Integer)}: the +index of i-th occurrence of @code{b} in @code{bv}. +@end itemize +and other shortcuts or types.") + (license license:expat))) + (define-public julia-indexing (package (name "julia-indexing") From patchwork Tue Jan 4 22:47:46 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 35971 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 CE2C927BBEA; Tue, 4 Jan 2022 22:51:16 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_INVALID,DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI, RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 957E627BBE9 for ; Tue, 4 Jan 2022 22:51:16 +0000 (GMT) Received: from localhost ([::1]:46824 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1n4seB-0002Vs-QO for patchwork@mira.cbaines.net; Tue, 04 Jan 2022 17:51:15 -0500 Received: from eggs.gnu.org ([209.51.188.92]:43462) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1n4sc4-0007gG-Nl for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:04 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:55747) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1n4sc4-0006zC-B0 for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:04 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1n4sc4-0003qf-A7 for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:04 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#53017] [PATCH 08/17] gnu: Add julia-twiddle. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 04 Jan 2022 22:49:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 53017 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 53017@debbugs.gnu.org Cc: efraim@flashner.co.il, zimoun Received: via spool by 53017-submit@debbugs.gnu.org id=B53017.164133649914630 (code B ref 53017); Tue, 04 Jan 2022 22:49:04 +0000 Received: (at 53017) by debbugs.gnu.org; 4 Jan 2022 22:48:19 +0000 Received: from localhost ([127.0.0.1]:39035 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbK-0003no-G9 for submit@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:19 -0500 Received: from mail-wm1-f43.google.com ([209.85.128.43]:44574) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbD-0003lI-Sf for 53017@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:12 -0500 Received: by mail-wm1-f43.google.com with SMTP id f134-20020a1c1f8c000000b00345c05bc12dso2245278wmf.3 for <53017@debbugs.gnu.org>; Tue, 04 Jan 2022 14:48:11 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=xljBjVD7etUsCEr5BGPRHlgwPkR9crzcCPvkpEtaPjM=; b=aYfjN37rW/G4Eri6FLFUeQutPcf56dJfjlezGfavXevJBlzo23DC1ERXyCRMS02u14 uPRI901jacCTzW16C5988ukR6jMMOFdybW51gA0xxCIA0WQVOF7YnHqoO14woyVjCmsE 6O3xLCKT3K3/6j3U+R2nYLAdCaY9VwAFjb66wZmueAmjw+ZRI0UgOKiaym/Bg7rDOYfB 818aUVF6lxUGm3z76vhxmSHNTLr3H8a5prQwm/30fw99oSiUU2rLWRo3WMOVbbOMa11n 4hT0XwyLJ8RrJi6s/GjULrkIiMVqG8F+iBxfbMOw6HTb2IQpTPqeXdiB2+f6YgzQ2WkM iUHw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=xljBjVD7etUsCEr5BGPRHlgwPkR9crzcCPvkpEtaPjM=; b=1YPstHpf3nK+XLtuPWjlKWwxBD2iIA17KLtra34fKUO+pNLSsv2WSTGI6iuAzWNAC9 FrBxFGDL+A1J8x6oUoVX6nH3UXsuzrW/HtNgR6rkkd/IAnFCcUyxvginQvf9lO4dkp0u mT0taMzZVYNYzJRvopUSaMEM5TmdbZBku0o0TeWFJBr/CdbBa7BcuyHxhWQzNHDm44Ux 9ssrDHN6yHrGajWVaPurOXHrkv0m6beyEj0vCbh29E5kwm7bB5hJKBtjUwLKd+ysLssf MM0n6qIHTBIItPJcLMtmYndeGuh4v5SbvcN50JNYawQogdnRC1qY0AjjYZ74lc5xakr6 vh9g== X-Gm-Message-State: AOAM530ru0YaLakaW/w+yFq71G4nE8xX3CGJBQjVAUUIfw+VIsCUPXKQ Tf0FsPqH8VSsyVBevnrSJlMiwj19Pag= X-Google-Smtp-Source: ABdhPJw+Kwc+OSdCuYFQtBp49P/fJis7btK0cYqin2/e0Z02jGjemjsmjFPn+14hhnpu7Hg1S14uVA== X-Received: by 2002:a1c:7317:: with SMTP id d23mr436679wmb.30.1641336486262; Tue, 04 Jan 2022 14:48:06 -0800 (PST) Received: from localhost.localdomain ([193.48.40.117]) by smtp.gmail.com with ESMTPSA id c9sm732842wml.12.2022.01.04.14.48.05 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 04 Jan 2022 14:48:06 -0800 (PST) From: zimoun Date: Tue, 4 Jan 2022 23:47:46 +0100 Message-Id: <20220104224755.1142897-8-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.33.1 In-Reply-To: <20220104224755.1142897-1-zimon.toutoune@gmail.com> References: <20220104224755.1142897-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 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 * gnu/packages/julia-xyz.scm (julia-twiddle): New variable. --- gnu/packages/julia-xyz.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 1508a86dd1..e407b1aec5 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -5026,6 +5026,27 @@ (define-public julia-transcodingstreams @end itemize") (license license:expat))) +(define-public julia-twiddle + (package + (name "julia-twiddle") + (version "1.1.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/BenJWard/Twiddle.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1c2gdv7sy4n1d8687w2q0yzwmwmanf4p6mvzvkz5gm4baxyzmbh2")))) + (build-system julia-build-system) + (home-page "https://ben-ward.science/Twiddle.jl/stable") + (synopsis "Ready to use bit-twiddling tricks") + (description "This package provides a collection of useful bit-twiddling +tricks, ready to use as functions, with detailed documentation and example +real-world use cases.") + (license license:expat))) + (define-public julia-typedtables (package (name "julia-typedtables") From patchwork Tue Jan 4 22:47:47 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 35966 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 4024A27BBEA; Tue, 4 Jan 2022 22:50:02 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_INVALID,DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI, RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id E8D2727BBE9 for ; Tue, 4 Jan 2022 22:50:01 +0000 (GMT) Received: from localhost ([::1]:45118 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1n4scz-0001EY-4i for patchwork@mira.cbaines.net; Tue, 04 Jan 2022 17:50:01 -0500 Received: from eggs.gnu.org ([209.51.188.92]:43464) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1n4sc5-0007hI-1E for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:05 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:55748) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1n4sc4-0006zL-Nc for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:04 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1n4sc4-0003qm-Mr for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:04 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#53017] [PATCH 09/17] gnu: Add julia-simd. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 04 Jan 2022 22:49:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 53017 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 53017@debbugs.gnu.org Cc: efraim@flashner.co.il, zimoun Received: via spool by 53017-submit@debbugs.gnu.org id=B53017.164133649914637 (code B ref 53017); Tue, 04 Jan 2022 22:49:04 +0000 Received: (at 53017) by debbugs.gnu.org; 4 Jan 2022 22:48:19 +0000 Received: from localhost ([127.0.0.1]:39037 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbL-0003nv-1W for submit@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:19 -0500 Received: from mail-wm1-f53.google.com ([209.85.128.53]:40782) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbE-0003lJ-Ar for 53017@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:13 -0500 Received: by mail-wm1-f53.google.com with SMTP id j140-20020a1c2392000000b003399ae48f58so606414wmj.5 for <53017@debbugs.gnu.org>; Tue, 04 Jan 2022 14:48:12 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=zxclmE4iUjzXp7kO1vPb4J+aMYwofceYBr5aKmnfPAU=; b=et4jIHh3O+Ni+xphALmzaVsY0JihmxfwCM9c0pMadQJq/jB/uzhTq8oCCKZhmGlHBA pGLtYmqVb7Z4t9Pfc8tj7fm2bqz9Q9WmXCUjjaUN8uUfP/JPAeObute8gQSJIqSfS+Sn Yfs2DcxT9HZrMHb1sAKMCkHyWox2TQ1FJmf5Ih9Faog/w7yyeNU/3OqGVzQRvaybh2DD 9mzRhRPDdLPAV2HOE2kYRrrIgU1MYjQQottEVZof8yy5wRS+mnhQgqZCdTmFIRVhYyNQ Htm5k9Ek73X6lh1C+mtm5C6A+883RXDCR8VVNy/L2v0TMDlIfMZHpxNzm2o1sN5sUm2M mRpw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=zxclmE4iUjzXp7kO1vPb4J+aMYwofceYBr5aKmnfPAU=; b=IzaQuKmMXhqhl7vK/5PBG+9vllVfspU2OHMADr0TVfCEiLk3dJz4jhVv52gyhV7DiK /UT5tqHg+oTzS4IN+hQLzVqemfntps8HEsb8cd5Hz4FLTONivLfhMy7yh56sVUCINKjs SWGMQpzrlaIPz0BDseRU1sEhX+TVNuE689XeebfiWx5FYkaio5fYzt7YllFtT7hB2CrE 1bBAFVzccHTa3EO0mLSeTlgLZl1rSYlGEtnpVxpqtroIloPgjZ5LkqnYIoaELkRn3NYj VVBJXTCH5P88qL2hk8DSjoAlajng9FDi1+CWcARmPPBz9LVA+piym5Vrf3esTtM0dPAS 8jxA== X-Gm-Message-State: AOAM530RwgyVJYx+2eP6V2Gtfp3J1E03kJFzjh+Z1OQg+A9D1IakhiDm o/SjqeFa4a+0MqA5004+0DvMlVzRbfA= X-Google-Smtp-Source: ABdhPJySd7++d8ucYb3vnIU+Ihxe0f7Vt7pocBbayknx2LrdRFBbz2TCjyMEysuFvm0o1TAE+aZgwQ== X-Received: by 2002:a1c:23cb:: with SMTP id j194mr404076wmj.13.1641336486812; Tue, 04 Jan 2022 14:48:06 -0800 (PST) Received: from localhost.localdomain ([193.48.40.117]) by smtp.gmail.com with ESMTPSA id c9sm732842wml.12.2022.01.04.14.48.06 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 04 Jan 2022 14:48:06 -0800 (PST) From: zimoun Date: Tue, 4 Jan 2022 23:47:47 +0100 Message-Id: <20220104224755.1142897-9-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.33.1 In-Reply-To: <20220104224755.1142897-1-zimon.toutoune@gmail.com> References: <20220104224755.1142897-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 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 * gnu/packages/julia-xyz.scm (julia-simd): New variable. --- gnu/packages/julia-xyz.scm | 27 ++++++++++++++++++++++++++- 1 file changed, 26 insertions(+), 1 deletion(-) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index e407b1aec5..4a3ca18666 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2020, 2021 Nicolò Balzarotti -;;; Copyright © 2021 Simon Tournier +;;; Copyright © 2021, 2022 Simon Tournier ;;; Copyright © 2021 Efraim Flashner ;;; Copyright © 2021 Vinicius Monego ;;; Copyright © 2021 jgart @@ -4406,6 +4406,31 @@ (define-public julia-showoff in @code{Gadfly}, @code{Plots} and @code{Makie} to label axes and keys.") (license license:expat))) +(define-public julia-simd + (package + (name "julia-simd") + (version "3.3.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/eschnett/SIMD.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1jiic2hcl9l6zh6jgqzbd3ik2girmgvni4bq65kdci5l12k9la68")))) + (build-system julia-build-system) + (home-page "https://github.com/eschnett/SIMD.jl") + (synopsis "Explicit SIMD vectorization") + (description "This package allows programmers to explicitly SIMD-vectorize +their Julia code. By exposing SIMD vector types and corresponding operations, +the programmer can explicitly vectorize their code. While this does not +guarantee that the generated machine code is efficient, it relieves the +compiler from determining whether it is legal to vectorize the code, deciding +whether it is beneficial to do so, and rearranging the code to synthesize +vector instructions.") + (license license:expat))) + (define-public julia-simpletraits (package (name "julia-simpletraits") From patchwork Tue Jan 4 22:47:48 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 35972 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 8A89627BBEA; Tue, 4 Jan 2022 22:51:26 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_INVALID,DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI, RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 5174327BBE9 for ; Tue, 4 Jan 2022 22:51:26 +0000 (GMT) Received: from localhost ([::1]:47132 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1n4seL-0002iZ-HE for patchwork@mira.cbaines.net; Tue, 04 Jan 2022 17:51:25 -0500 Received: from eggs.gnu.org ([209.51.188.92]:43466) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1n4sc5-0007it-E4 for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:05 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:55749) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1n4sc5-0006zT-4Z for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:05 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1n4sc5-0003qu-32 for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:05 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#53017] [PATCH 10/17] gnu: Add julia-scanbyte. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 04 Jan 2022 22:49:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 53017 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 53017@debbugs.gnu.org Cc: efraim@flashner.co.il, zimoun Received: via spool by 53017-submit@debbugs.gnu.org id=B53017.164133649914644 (code B ref 53017); Tue, 04 Jan 2022 22:49:05 +0000 Received: (at 53017) by debbugs.gnu.org; 4 Jan 2022 22:48:19 +0000 Received: from localhost ([127.0.0.1]:39039 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbL-0003o2-Fl for submit@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:19 -0500 Received: from mail-wm1-f53.google.com ([209.85.128.53]:38813) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbE-0003lL-Sy for 53017@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:13 -0500 Received: by mail-wm1-f53.google.com with SMTP id p1-20020a1c7401000000b00345c2d068bdso612815wmc.3 for <53017@debbugs.gnu.org>; Tue, 04 Jan 2022 14:48:12 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=QECjlt8vdXluBlcfscUchGx037cnHRTPDozvatYh+lw=; b=MaVrbBJ7dHGm6LgUaeBKhgstknuAn9YcPoZIRRumImNyytYA1qOSMHvfJtV2tHhGCA YIdSr80qK2D1i0cCrJd5ny47NPD+skXRbYOKD2ZbbH0jiTt9O746U7K6sef12LxDYSTg Yw2xNXo7w86ppmThUc9icueC/l3rOYSlf8lfvOorqhw0DlWcDc3SZzoZN5CVG1W1Vyw+ PuEKkubca8FQ/EcxzTIeSBU36SiMXt5ji3z41164GltF1gFHboJuOJKHmbZxUKgJVCGR eHYCoiowlQNJArThrC6A664f4PqrDHlMXYBEKpOKmTLcw8VdLX0omWSaxj3x8GLm1C9F tk4Q== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=QECjlt8vdXluBlcfscUchGx037cnHRTPDozvatYh+lw=; b=C9HUm6yqTxFKjuwqjBwLjNG4eHvilXhp9D+G3XtRUZzms2qr424gd+kl9rdT5Ldhnd LHFV38A/x3XiaUubYmTigyn9PNZL08mxBWQ458LvegJxtLBRrAcNW8siHJTozetXzFWC hqkvSVAsyyqTK9vfnOk+rs4HuabnOeEe7mrtJxAn+V54XCj63M6rGxLHg6OVuddZS1dt g/GucyT6yMpE6OXAVIWTwqc2P9JnJb0QBx6gZ+xnScjbY0gjCzAXooI6eMap6VWBfJj9 +oTOuiiHY52WOFagg9spW3b7KXeTkqD7698n06t0SxqjMXIEJMlaM7i9BVI7Ni2CY79X sQwQ== X-Gm-Message-State: AOAM531rkKZAbt3HAHrpu/059lVsF79qzpCLmRSIdeat97jc/1zacduY /BBmYS9BJRJGBlD7mV86V56fzmb1kXw= X-Google-Smtp-Source: ABdhPJyBgYahMGgpD8N7g/P2sAu/YDgQjY8dfUS+ESZ8kFVwYpOL75Rbnqgzb3W38oD+R66kOeyfIw== X-Received: by 2002:a7b:c3c5:: with SMTP id t5mr408724wmj.168.1641336487369; Tue, 04 Jan 2022 14:48:07 -0800 (PST) Received: from localhost.localdomain ([193.48.40.117]) by smtp.gmail.com with ESMTPSA id c9sm732842wml.12.2022.01.04.14.48.06 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 04 Jan 2022 14:48:07 -0800 (PST) From: zimoun Date: Tue, 4 Jan 2022 23:47:48 +0100 Message-Id: <20220104224755.1142897-10-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.33.1 In-Reply-To: <20220104224755.1142897-1-zimon.toutoune@gmail.com> References: <20220104224755.1142897-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 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 * gnu/packages/julia-xyz.scm (julia-scanbyte): New variable. --- gnu/packages/julia-xyz.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 4a3ca18666..524e5c3fb4 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -4357,6 +4357,29 @@ (define-public julia-sass @code{libsass} library to compile scss and sass files to css.") (license license:expat))) +(define-public julia-scanbyte + (package + (name "julia-scanbyte") + (version "0.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/jakobnissen/ScanByte.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0dqqa3d7c87358144pji6ik8xlki2hj0hkvjs72j5aypfms8rwn3")))) + (build-system julia-build-system) + (propagated-inputs + (list julia-simd)) + (home-page "https://github.com/JuliaPackaging/Scratch.jl") + (synopsis "Find the first occurrence of set of bytes in a chunk of memory") + (description "This package finds the first occurrence of a byte or set of +bytes in a chunk of memory. Think of it like a much faster version of +@code{findfirst} that only iterates over bytes in memory.") + (license license:expat))) + (define-public julia-scratch (package (name "julia-scratch") From patchwork Tue Jan 4 22:47:49 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 35962 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 9875D27BBEA; Tue, 4 Jan 2022 22:49:39 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_INVALID,DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI, RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id AB1A927BBEB for ; Tue, 4 Jan 2022 22:49:38 +0000 (GMT) Received: from localhost ([::1]:43172 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1n4scb-0008O0-Se for patchwork@mira.cbaines.net; Tue, 04 Jan 2022 17:49:37 -0500 Received: from eggs.gnu.org ([209.51.188.92]:43468) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1n4sc5-0007jx-RG for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:05 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:55750) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1n4sc5-0006zZ-GM for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:05 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1n4sc5-0003r1-FG for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:05 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#53017] [PATCH 11/17] gnu: Add julia-automa. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 04 Jan 2022 22:49:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 53017 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 53017@debbugs.gnu.org Cc: efraim@flashner.co.il, zimoun Received: via spool by 53017-submit@debbugs.gnu.org id=B53017.164133650014651 (code B ref 53017); Tue, 04 Jan 2022 22:49:05 +0000 Received: (at 53017) by debbugs.gnu.org; 4 Jan 2022 22:48:20 +0000 Received: from localhost ([127.0.0.1]:39041 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbL-0003o9-Pl for submit@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:20 -0500 Received: from mail-wm1-f50.google.com ([209.85.128.50]:43804) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbF-0003lM-EJ for 53017@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:13 -0500 Received: by mail-wm1-f50.google.com with SMTP id k66-20020a1ca145000000b00345fa984108so2239813wme.2 for <53017@debbugs.gnu.org>; Tue, 04 Jan 2022 14:48:13 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=GW94n+d6G2gxq8MqhnOJL8Sa7U6lZI9kOmMVfczvB7o=; b=JXU+1h4SVHrcXBlwYmxAmX9hAarSE3sEBQMDeOZKQO/izq1e59QGOSwLOynaCHdbcm 9kg363g7H3ClNbhFZBvL2EbWYRhSJXeQtf2EEcWcqg+erBdtJmEdJmhDZOif9ROkCsF+ RJ05jIcyk3aAZPYRXV5nb3o7yAyTbo1ZW7Z+XMKKgESft2N51GOdd6CaQkShm5EURC7o Lh3K6Jn+dDnFSLPz55NGUTpMESpXtcVPjmgjmky4Km19dRCkwCsA84N0WzIYU69hMWGy Dyj7PY9qcbVMXV7fzgc1ldYXxuj9PUqKL+VIVVGgoX6wTb9gpavvJ7Gudfq8pNuNGXvm k3Ww== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=GW94n+d6G2gxq8MqhnOJL8Sa7U6lZI9kOmMVfczvB7o=; b=uVKbvlPvE6zP3Zy9FmBYuo8mZOdIghIPyHvexwKAMBYhVOyOpbqrd4++cAJ2NFAarM ACm3t2XSCwUEWGMtCkLBXyvH0PaA9X2TJlY9yXp+bBe8ipQ0wXWHffkoiw1gRLfvC+0j 6wlr9/hfxfBl5mhz0cACcgXNCA4DybPw4q1x3Z1LvCSCR6wiHl+qyddIjn/ieLP2ftVA XMvIy2KewWg3/lxI5G24yXJpDHTZJCMDu5aIfH1e+5T2pIOVtjpSqh7eFRXxKJdjTckz aMB+fdBFz5NJJqKXeScxLf0TSkMDomQrofgHr4YbHtryD/UzJtoOg06eqJ09IW6CLrmt MbFA== X-Gm-Message-State: AOAM533kVf294X7SfNPm98x11A88Y6ZNr8PPb63iGqxVSUol0VuBb+1B rIptfM46e188aPseipcSnabWGdIN3uY= X-Google-Smtp-Source: ABdhPJzG6A2TE9ZYwNDfmgckNroXqyft4b/VR+SuB5+yOWGm0wGyZ3GU9CyLLlXIzL1K1PL1Kz1+hA== X-Received: by 2002:a05:600c:190b:: with SMTP id j11mr398993wmq.182.1641336487896; Tue, 04 Jan 2022 14:48:07 -0800 (PST) Received: from localhost.localdomain ([193.48.40.117]) by smtp.gmail.com with ESMTPSA id c9sm732842wml.12.2022.01.04.14.48.07 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 04 Jan 2022 14:48:07 -0800 (PST) From: zimoun Date: Tue, 4 Jan 2022 23:47:49 +0100 Message-Id: <20220104224755.1142897-11-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.33.1 In-Reply-To: <20220104224755.1142897-1-zimon.toutoune@gmail.com> References: <20220104224755.1142897-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 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 * gnu/packages/julia-xyz.scm (julia-automa): New variable. --- gnu/packages/julia-xyz.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 524e5c3fb4..757030301d 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -211,6 +211,34 @@ (define-public julia-arraylayouts much wider class of matrix types than Julia's in-built @code{StridedArray}.") (license license:expat))) +(define-public julia-automa + (package + (name "julia-automa") + (version "0.8.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/BioJulia/Automa.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0hmwvk3qw54p7f63a2dnzlmvkynfs62x9n8x952bcmczp35csgq0")))) + (build-system julia-build-system) + (propagated-inputs + (list julia-scanbyte + julia-transcodingstreams)) + (home-page "https://github.com/BioJulia/Automa.jl") + (synopsis "Validation, parsing, and tokenizing based on state machine compiler.") + (description "This package compiles regular expressions into Julia code, +which is then compiled into low-level machine code by the Julia compiler. The +package is designed to generate very efficient code to scan large text data, +which is often much faster than handcrafted code. @code{Automa.jl} can insert +arbitrary Julia code that will be executed in state transitions. This makes +it possible, for example, to extract substrings that match a part of a regular +expression.") + (license license:expat))) + (define-public julia-axisalgorithms (package (name "julia-axisalgorithms") From patchwork Tue Jan 4 22:47:50 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 35973 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 0037427BBEA; Tue, 4 Jan 2022 22:51:51 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_INVALID,DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI, RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id C240B27BBE9 for ; Tue, 4 Jan 2022 22:51:51 +0000 (GMT) Received: from localhost ([::1]:47550 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1n4sel-0002zW-0I for patchwork@mira.cbaines.net; Tue, 04 Jan 2022 17:51:51 -0500 Received: from eggs.gnu.org ([209.51.188.92]:43472) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1n4sc6-0007lM-5d for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:06 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:55751) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1n4sc5-0006zk-Se for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:05 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1n4sc5-0003r8-RR for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:05 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#53017] [PATCH 12/17] gnu: Add julia-stringencodings. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 04 Jan 2022 22:49:05 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 53017 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 53017@debbugs.gnu.org Cc: efraim@flashner.co.il, zimoun Received: via spool by 53017-submit@debbugs.gnu.org id=B53017.164133650014658 (code B ref 53017); Tue, 04 Jan 2022 22:49:05 +0000 Received: (at 53017) by debbugs.gnu.org; 4 Jan 2022 22:48:20 +0000 Received: from localhost ([127.0.0.1]:39043 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbM-0003oG-2r for submit@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:20 -0500 Received: from mail-wm1-f45.google.com ([209.85.128.45]:38806) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbF-0003lO-Uz for 53017@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:14 -0500 Received: by mail-wm1-f45.google.com with SMTP id p1-20020a1c7401000000b00345c2d068bdso612832wmc.3 for <53017@debbugs.gnu.org>; Tue, 04 Jan 2022 14:48:13 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=7DujSLRnGnTMrtzD0lbv+cyV93UNZvuaYtTRnEfzRFk=; b=JkJimGM4wC6lRXngrWSebOBnpMb/tzaD3xCBVqiBNQsnU71mh2ND+SVBtrfxFYPO7G VvUjO9oAPHNhvMgSH6oWpXCztujlN1diZauIxbAw2lXAyIsRTdHwn+HGNt/LWm5eD4uR qOziU5iYQutKcmCQidnN86s6Iioh2zDYNrxhU8gOrv1gVe9WfDOEtwt5O18BndcjWuTQ ooOlOC0DbHVr9BLEPyl9rEZWctThtOmnk9DfoQ/mE3D7rLmfZnJcIeYqP9PI5Iwp1qYj PiTTaNz5I0G6woyJjwl/I8P6dUBtQ17sCQix377kcs2XgtQ1PuYyaJ2J4qXeQ5T/2l6+ O9RQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=7DujSLRnGnTMrtzD0lbv+cyV93UNZvuaYtTRnEfzRFk=; b=QzSJOoSVbhhZ2UzVYRcNolYa3D2kbCq0N0hopWdQp8i4G+6ZvFKAC0yNWhCp+u3HxL Bj3SWjT14XQpnpE8x4f1dAJYePNlo+lz49Fc9FSBdblLSSfS1hG7M5N9MrF/aF4GDISQ Y+GmYFBTM5Ut/A9uwWIfpW1Jc7ezviKrLK+ijFT0DEZbJZ2k2dYAkhVFJidD+xYP4e8p 74/CrahLDDzEUbp6Xcc8km3dN8FE/UcH+hx5c4OHosFVWg3tXUdFhwKVjErd2MynNDAI H6kt26UkG4TJ6wLMdlXMt8LVn6+R++uUwE+ubKDgPZRbYDNM92jl5SD276l7FSL6vNx4 g5Kg== X-Gm-Message-State: AOAM531UEqGcj+DQu8YjwfcnpgTu2DIr7Ugnn56VCd/MipoPxqAUt11v HT1frzxmRt2c80/PnwhiXlCwW76FsYU= X-Google-Smtp-Source: ABdhPJxDA9Qr9pbpmBxz2D+5nhXcs+pR8U0lM8p6vrck3ctny3XnnhcoNqjkMLpEkqIqbDlYyfhoMw== X-Received: by 2002:a7b:cc8d:: with SMTP id p13mr135140wma.6.1641336488348; Tue, 04 Jan 2022 14:48:08 -0800 (PST) Received: from localhost.localdomain ([193.48.40.117]) by smtp.gmail.com with ESMTPSA id c9sm732842wml.12.2022.01.04.14.48.07 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 04 Jan 2022 14:48:08 -0800 (PST) From: zimoun Date: Tue, 4 Jan 2022 23:47:50 +0100 Message-Id: <20220104224755.1142897-12-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.33.1 In-Reply-To: <20220104224755.1142897-1-zimon.toutoune@gmail.com> References: <20220104224755.1142897-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 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 * gnu/packages/julia-xyz.scm (julia-stringencodings): New variable. --- gnu/packages/julia-xyz.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 757030301d..84a6fef3a6 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -4799,6 +4799,38 @@ (define-public julia-stringdistances applied to any distance.") (license license:expat))) +(define-public julia-stringencodings + (package + (name "julia-stringencodings") + (version "0.3.5") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaStrings/StringEncodings.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1qwc5ll68ng80b5921ww6fvifxbsmiylakfgsbsjbzg7lzyb5i67")))) + (build-system julia-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'skip-failing-test + (lambda _ + ;; https://github.com/JuliaStrings/StringEncodings.jl/issues/49 + (substitute* "test/runtests.jl" + (("\"SHIFT_JIS\", \"SHIFT_JISX0213\"") + " "))))))) + (propagated-inputs + (list julia-libiconv-jll)) + (home-page "https://github.com/JuliaStrings/StringEncodings.jl") + (synopsis "Support for decoding and encoding texts ") + (description "This package provides support for decoding and encoding +texts between multiple character encodings. It is currently based on the +@code{iconv} interface, and supports all major platforms using GNU libiconv.") + (license license:expat))) + (define-public julia-structarrays (package (name "julia-structarrays") From patchwork Tue Jan 4 22:47:51 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 35959 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 96DAD27BBEA; Tue, 4 Jan 2022 22:49:26 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_INVALID,DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI, RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 600E327BBE9 for ; Tue, 4 Jan 2022 22:49:26 +0000 (GMT) Received: from localhost ([::1]:42394 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1n4scP-0007pe-HP for patchwork@mira.cbaines.net; Tue, 04 Jan 2022 17:49:25 -0500 Received: from eggs.gnu.org ([209.51.188.92]:43476) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1n4sc6-0007li-I4 for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:06 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:55752) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1n4sc6-0006zu-9F for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:06 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1n4sc6-0003rG-7h for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:06 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#53017] [PATCH 13/17] gnu: Add julia-yaml. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 04 Jan 2022 22:49:06 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 53017 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 53017@debbugs.gnu.org Cc: efraim@flashner.co.il, zimoun Received: via spool by 53017-submit@debbugs.gnu.org id=B53017.164133650014664 (code B ref 53017); Tue, 04 Jan 2022 22:49:06 +0000 Received: (at 53017) by debbugs.gnu.org; 4 Jan 2022 22:48:20 +0000 Received: from localhost ([127.0.0.1]:39045 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbM-0003oO-Dj for submit@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:20 -0500 Received: from mail-wm1-f41.google.com ([209.85.128.41]:40773) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbG-0003lP-D8 for 53017@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:14 -0500 Received: by mail-wm1-f41.google.com with SMTP id j140-20020a1c2392000000b003399ae48f58so606453wmj.5 for <53017@debbugs.gnu.org>; Tue, 04 Jan 2022 14:48:14 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=9BeE5lLx7XhxckutVz1Cyt8OzQhXgBt3TFVXmc42r6k=; b=KT+MTwiYbYwZnQE57+FT4bzGKfHbhf1jEcQ20JcdMbEf8d/0baaH44JYe8CK3+AKwU fetP/qxHTg8rNI1iwhy1DAv+BWp6XzCmmbe4ALU7X5hfa7ofhASbPbCgcOhIGoSSU/WE NCDA0K3vpPDc+JD38k6msllzBG88B0HUMctz5h19QHHDjhgwhJw0O7GtbT155cd5/LLc P3BHtF5Z6MxVhiYr3CW4lhWET3q3nxxO6Hw2naRfhQxCfzsiXKgmmVprL28B4MU8o6Bz b7lnb0GZ23NwaH4V0hDfa0XjcyrHRn+vcVzQtMpiHXj7uY0uXJwFQOK27v0cWK0ikqsA UTxA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=9BeE5lLx7XhxckutVz1Cyt8OzQhXgBt3TFVXmc42r6k=; b=Nwy4rh6uMZDMSg7vWOziLwV6cG4Lf7zWYnyTRXMw5BnFzhQ6eRzxZte4no+/2nSvj/ h7SGQYFD+0a0mxuLPtZjPwAMECgfJbxE8abkvf7by7Y5iQMpasnmgu77rb5LzsCOU4bK RL7zDg7uDDC7FojYIjRoU9sGII1xLH3G69c6N4Ul45ECvuGF0T3qiza6HltQm0vq9zvt Nn3S8Y8IJREam1A3PG2rSW/3OaNP7BnU9wTJO1whnI6TaF+Vjf/x6g60IOe8CevkNffO qupq5g7DM5OH0yXgZeHUnBZsHMfIbnMS9cPkxGPuavnOPaht9qHTa/lhEOCKuOD0n2Wj aveA== X-Gm-Message-State: AOAM5322gvNPMvk53Jeow6l5IiVuyWgi8NgBjlw4ncCgJ2z+P2WOl45V 5VRhEQp5GUWnAE4qFqtQgGF7RZBCDCY= X-Google-Smtp-Source: ABdhPJxeLkeOluzCybZqPrM7bj3/fpaDUBLjROFk6czFI7T8mcctUkzdmlH8SanRMRb8P7Zyxybr2Q== X-Received: by 2002:a05:600c:286:: with SMTP id 6mr417586wmk.194.1641336488857; Tue, 04 Jan 2022 14:48:08 -0800 (PST) Received: from localhost.localdomain ([193.48.40.117]) by smtp.gmail.com with ESMTPSA id c9sm732842wml.12.2022.01.04.14.48.08 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 04 Jan 2022 14:48:08 -0800 (PST) From: zimoun Date: Tue, 4 Jan 2022 23:47:51 +0100 Message-Id: <20220104224755.1142897-13-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.33.1 In-Reply-To: <20220104224755.1142897-1-zimon.toutoune@gmail.com> References: <20220104224755.1142897-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 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 * gnu/packages/julia-xyz.scm (julia-yaml): New variable. --- gnu/packages/julia-xyz.scm | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 84a6fef3a6..404c35627c 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -5341,6 +5341,31 @@ (define-public julia-woodburymatrices inaccuracy in the result.") (license license:expat))) +(define-public julia-yaml + (package + (name "julia-yaml") + (version "0.4.7") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaData/YAML.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "00k8456ffldbf75k2q5yxim7cgz3p0pbshsvmpm1331g8qy6liin")))) + (build-system julia-build-system) + (propagated-inputs + (list julia-stringencodings)) + (native-inputs + (list julia-datastructures + julia-orderedcollections)) + (home-page "https://github.com/JuliaData/YAML.jl") + (synopsis "Parses YAML documents into native Julia types") + (description "This package parses YAML documents into native Julia types +and dumps them back into YAML documents.") + (license license:expat))) + (define-public julia-zipfile (package (name "julia-zipfile") From patchwork Tue Jan 4 22:47:52 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 35974 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 9DC5427BBEA; Tue, 4 Jan 2022 22:52:10 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_INVALID,DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI, RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 633D327BBE9 for ; Tue, 4 Jan 2022 22:52:10 +0000 (GMT) Received: from localhost ([::1]:47940 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1n4sf2-0003GM-Js for patchwork@mira.cbaines.net; Tue, 04 Jan 2022 17:52:09 -0500 Received: from eggs.gnu.org ([209.51.188.92]:43482) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1n4sc6-0007my-VJ for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:07 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:55753) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1n4sc6-000705-LM for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:06 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1n4sc6-0003rN-KD for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:06 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#53017] [PATCH 14/17] gnu: Add julia-biosymbols. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 04 Jan 2022 22:49:06 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 53017 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 53017@debbugs.gnu.org Cc: efraim@flashner.co.il, zimoun Received: via spool by 53017-submit@debbugs.gnu.org id=B53017.164133650314674 (code B ref 53017); Tue, 04 Jan 2022 22:49:06 +0000 Received: (at 53017) by debbugs.gnu.org; 4 Jan 2022 22:48:23 +0000 Received: from localhost ([127.0.0.1]:39047 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbO-0003oa-MU for submit@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:22 -0500 Received: from mail-wm1-f46.google.com ([209.85.128.46]:43801) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbG-0003lR-Tn for 53017@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:15 -0500 Received: by mail-wm1-f46.google.com with SMTP id k66-20020a1ca145000000b00345fa984108so2239828wme.2 for <53017@debbugs.gnu.org>; Tue, 04 Jan 2022 14:48:14 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=sna8O4NT2s2FeSYOFeL54rv3MfFT1CT9p1llM/HWkAs=; b=MuUoYzqXPEDxk+npucW6Wg3JxI9KnMa7qHmvNHqiybtTGoVUMtu4wHry4ZfM7JKwKt lFqLnog//IAFSdJn50AZY3nHF38g3PWaHM1eKNMK7IkKlrQexiyerdC3Aun5s5CUnY2M ouE5v/FKJICj+dmR2XPzRSkMqJaX90dAdLfB6Ko/TVz6rMaDTZk4xRPDesvkBe3G+wq0 GfUBQGYAFMz52aUq35oCH4b5uBFdz8yOdksgb0F8lNEIBOoGqOUltRxvnmtExGm+ahqT UaejGf7162tcdC4o0qlfvkjcycohWCkluA24uN4qGXzZz/XN50dBY6nZsydLRdk3fmv8 hcEQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=sna8O4NT2s2FeSYOFeL54rv3MfFT1CT9p1llM/HWkAs=; b=NuCUDFoP98chs3Xunktehee/BO5taemli5ZQPb+ogsvvP+V2eAvLpqpDxGVuR/ZbEr bZROFWbvDY6cF/Tfij1zr1po9M5I2/UwgR5cZ3e2MksFzR5FYrU3wWuXQi5CSEXzJ0+J +tJmn/wBszsFMeK/h23eWPgSHgFhQGPpN+6Hm0ioiD816dtbfDOPKHRMxJSuvw7+pF/Q 1BNKZV19i+3/g55P7KL5zZyUrCfWERbWNbZTFOM9AAeXMJddRyGpFo8HFXSj9PNriekM WnRIsJ+Y26P/6GCci3tV51EIDI2hqsDy64YNk4no2KJnOFNcmEGMgzv0q0rSpA0VBNBA su8A== X-Gm-Message-State: AOAM530t+E1dR4j4rUbIe5iw8QSTPXfba4MHKSVteTOCk/qY0Irp2LDc y8zV/YrweTYPU+83qM1E7lGrEyHNKJs= X-Google-Smtp-Source: ABdhPJzyZrdHvkEGLW/T8E8Mz/PcoNkTp0+YUKe+UBLALosLuCx0qnzsRHnBc0flB6YWYTUNy4jnCA== X-Received: by 2002:a05:600c:3b24:: with SMTP id m36mr419464wms.4.1641336489358; Tue, 04 Jan 2022 14:48:09 -0800 (PST) Received: from localhost.localdomain ([193.48.40.117]) by smtp.gmail.com with ESMTPSA id c9sm732842wml.12.2022.01.04.14.48.08 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 04 Jan 2022 14:48:09 -0800 (PST) From: zimoun Date: Tue, 4 Jan 2022 23:47:52 +0100 Message-Id: <20220104224755.1142897-14-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.33.1 In-Reply-To: <20220104224755.1142897-1-zimon.toutoune@gmail.com> References: <20220104224755.1142897-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 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 * gnu/packages/julia-xyz.scm (julia-biosymbols): New variable. --- gnu/packages/julia-xyz.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 404c35627c..04d0beeb96 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -387,6 +387,30 @@ (define-public julia-biogenerics other types or methods used by other BioJulia packages.") (license license:expat)))) +(define-public julia-biosymbols + (package + (name "julia-biosymbols") + (version "4.0.4") ;Older release for compatibility with julia-biosequence + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/BioJulia/BioSymbols.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1222rwdndi777lai8a6dwrh35i5rgmj75kcrhn8si72sxgz0syjm")))) + (build-system julia-build-system) + (arguments + `(#:tests? #f)) + (propagated-inputs + (list julia-automa)) + (home-page "https://github.com/BioJulia/BioSymbols.jl") + (synopsis "Primitive types for nucleic acids and amino acids") + (description "This package defines the primitive types for nucleic acids +and amino acids that are used ny otherBioJulia packages.") + (license license:expat))) + (define-public julia-blockarrays (package (name "julia-blockarrays") From patchwork Tue Jan 4 22:47:53 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 35967 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 C1A2527BBEA; Tue, 4 Jan 2022 22:50:31 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_INVALID,DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI, RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 8CCE027BBE9 for ; Tue, 4 Jan 2022 22:50:31 +0000 (GMT) Received: from localhost ([::1]:45570 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1n4sdS-0001Z9-O2 for patchwork@mira.cbaines.net; Tue, 04 Jan 2022 17:50:30 -0500 Received: from eggs.gnu.org ([209.51.188.92]:43486) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1n4sc7-0007nT-B2 for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:07 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:55754) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1n4sc7-00070M-1u for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:07 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1n4sc7-0003rU-0d for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:07 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#53017] [PATCH 15/17] gnu: Add julia-biosequences. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 04 Jan 2022 22:49:06 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 53017 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 53017@debbugs.gnu.org Cc: efraim@flashner.co.il, zimoun Received: via spool by 53017-submit@debbugs.gnu.org id=B53017.164133651514694 (code B ref 53017); Tue, 04 Jan 2022 22:49:06 +0000 Received: (at 53017) by debbugs.gnu.org; 4 Jan 2022 22:48:35 +0000 Received: from localhost ([127.0.0.1]:39049 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbO-0003od-Ut for submit@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:35 -0500 Received: from mail-wm1-f53.google.com ([209.85.128.53]:36705) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbH-0003lY-9r for 53017@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:16 -0500 Received: by mail-wm1-f53.google.com with SMTP id n19-20020a7bc5d3000000b003466ef16375so624571wmk.1 for <53017@debbugs.gnu.org>; Tue, 04 Jan 2022 14:48:15 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=utPyNMNQajSzrgkKE7hyQ0cKtCJqHDpRhRQXOIh2DRI=; b=aa5VG7lfUnQOTjOL0367C5l80jdK8owh2rCO9Z2l4I4DKhXC9eltSSHYR4AKaZz1UZ FUJKveT3/p6qeeFEw6rk3xk+gwdS/+YmzAqOV8tW/B1D6jMv42Ul6ebvw30FWXv3UPcF m+XtGLOXJ3rEGOSQTk4m5wUhni91FHvhAK3r+rh4bUwVHT2sE9edt0uUi0xw6oTmF9ci dFbrFKTqxrzGGEGin68fb01f6sLhA7hYUHYczk11HRAsyzlCo3ewKyob/cPycQnZUkNl EYGWzw0VggKgLc6vC4Cd8O8rVupbKXcy1zDBw8yPm3zLCWOc2krig1D+Qt5U6XzP0Evn x5KQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=utPyNMNQajSzrgkKE7hyQ0cKtCJqHDpRhRQXOIh2DRI=; b=R/UbNrL5jqrayjQ4fIYGaTFx0K1TeS/67CdnmsOvJaw/n8alG4C/HpCHSPuP2BzkNl yTKP5FabEyZBSh04gXtmtqiHANB+5uuAh0iwHkZRWJQ3JvAerbo8TRoJ+SvHeRhJ2OrP fGvHR5P94uLy30MhjALee4zG5j/JVIPy6HVso+aC6gnUlDy20kRdrC3e6USuWY6eAQat jaGanaTKKn0Tt+s5Bk3SohlzJEXzxQiCxBuyAiwJe2oq3leUUNMRITHmSkSxGi7+LPqK A4CxTH+9VeTyaBstiIWUbmtH3q/o53/Um38B63rXC4ROm5eSmim/cUVgdicQF+iui0cq PZog== X-Gm-Message-State: AOAM532w/Y487wqWLmSDBtKauWA57Cz7qDbdidAVwDib7p3yNJXYyKlg F39cJsg3b2JG1BPxwIqqDgPINFtP1oM= X-Google-Smtp-Source: ABdhPJyxCeGse4z+aNG9pijnjQ//K2YJeVrQZqiUYSVukC8zd1VOEmXnwzW8ohsZjlAjfCtz69QBUg== X-Received: by 2002:a05:600c:3797:: with SMTP id o23mr411264wmr.178.1641336489822; Tue, 04 Jan 2022 14:48:09 -0800 (PST) Received: from localhost.localdomain ([193.48.40.117]) by smtp.gmail.com with ESMTPSA id c9sm732842wml.12.2022.01.04.14.48.09 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 04 Jan 2022 14:48:09 -0800 (PST) From: zimoun Date: Tue, 4 Jan 2022 23:47:53 +0100 Message-Id: <20220104224755.1142897-15-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.33.1 In-Reply-To: <20220104224755.1142897-1-zimon.toutoune@gmail.com> References: <20220104224755.1142897-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 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 * gnu/packages/julia-xyz.scm (julia-biosequences): New variable. --- gnu/packages/julia-xyz.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 04d0beeb96..e028f37a28 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -387,6 +387,37 @@ (define-public julia-biogenerics other types or methods used by other BioJulia packages.") (license license:expat)))) +(define-public julia-biosequences + (package + (name "julia-biosequences") + (version "2.0.5") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/BioJulia/BioSequences.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0ns6zk0zvnsf4hlsys9ck2xrn20qck0b0aghh484vc6n458zq2gw")))) + (build-system julia-build-system) + (propagated-inputs + (list julia-biogenerics + julia-biosymbols + julia-combinatorics + julia-indexablebitvectors + julia-stablerngs + julia-twiddle)) + (native-inputs + (list julia-statsbase + julia-yaml)) + (home-page "https://biojulia.net/BioSequences.jl/stable/") + (synopsis "Data types and methods for common operations with biological sequences") + (description "This package provides Data types and methods for common +operations with biological sequences, including DNA, RNA, and amino acid +sequences.") + (license license:expat))) + (define-public julia-biosymbols (package (name "julia-biosymbols") From patchwork Tue Jan 4 22:47:54 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 35961 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 1B6D427BBEC; Tue, 4 Jan 2022 22:49:39 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_INVALID,DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI, RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id AA5FA27BBEA for ; Tue, 4 Jan 2022 22:49:38 +0000 (GMT) Received: from localhost ([::1]:43298 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1n4scb-0008Sm-SH for patchwork@mira.cbaines.net; Tue, 04 Jan 2022 17:49:37 -0500 Received: from eggs.gnu.org ([209.51.188.92]:43488) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1n4sc7-0007nU-O3 for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:07 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:55755) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1n4sc7-00070U-Eu for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:07 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1n4sc7-0003rd-DS for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:07 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#53017] [PATCH 16/17] gnu: Add julia-intervaltrees. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 04 Jan 2022 22:49:07 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 53017 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 53017@debbugs.gnu.org Cc: efraim@flashner.co.il, zimoun Received: via spool by 53017-submit@debbugs.gnu.org id=B53017.164133651514701 (code B ref 53017); Tue, 04 Jan 2022 22:49:07 +0000 Received: (at 53017) by debbugs.gnu.org; 4 Jan 2022 22:48:35 +0000 Received: from localhost ([127.0.0.1]:39051 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbb-0003ox-37 for submit@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:35 -0500 Received: from mail-wr1-f43.google.com ([209.85.221.43]:42616) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbH-0003lk-UI for 53017@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:16 -0500 Received: by mail-wr1-f43.google.com with SMTP id w20so70057820wra.9 for <53017@debbugs.gnu.org>; Tue, 04 Jan 2022 14:48:15 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=ghGcouP/lbjPeLez2Fl1GxD7NrMJ6q/vdpWdJoJ5xXg=; b=Qa+dIY+7CB6kLUuxngUjvpwF7RJhbCeKoDqJH7x+Y3IqSYKr3rQnNo1vfEk2ylK3Ul isr3MqCNhkaYSzU1Wb9jgHEpOpMiZmhVuyiP/K2DntGqVLD1mVbvopMGZqphiT4TswDg qaBDRpy+zSuCuzO2RxyM6kMiXKeSJb/znMXdWiUFOCgKMKetvvygksc1csdfeXvQQ1JM 0uT14NdZ8UpKR64b3L/PTS/X09ZmlGf8E2+Bf1G3qkWRIQJGp+Pjw/saPdaqtMozjWXR mlCeAn1v2x7IeiTXkmYx1LuUIc9iSlnSKj+mzT/teDgfolVb4pS/i5xRDBb2GkWR22Ok WGFw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=ghGcouP/lbjPeLez2Fl1GxD7NrMJ6q/vdpWdJoJ5xXg=; b=tBYkIaJEaj8Ds+t4HsUNqBjiqQT4yuWjmZe20WzNMKBKivMpDUZ7HTBhTYHt/dvPKK t+X4BRruXYr9Rl7QhfSSNDr/FOfF+FclLuTkszrtc7ceDT+WK9P54io6+Yyv18Ue8N5Z UoLatxEWosb+PNgcExLiuWwlaLOg7/jSZWBXB6P7WPLzlly1IMwh4GPOj7qjBrcQe8xv iVRGmObmjQJeBeNRmv21kNA9Ltm/HHJE6eCBOlXwLkfyDTSH94ek/97jC4uk24jkajD0 NuvGbGQiyB7HD6uGk+dm3Kg2GS5FALFp30WviqiYbXriJoom9mSxwcCX730Jj4tTofxR Sgvg== X-Gm-Message-State: AOAM531JwSsqxRD/FzGs2vvxgiVzqwdiOcP+UD5kcgudoWWMHAogdlf3 4RlQ4H9lPqKm21R0dnHsZsQ0wbB9Iwc= X-Google-Smtp-Source: ABdhPJzbfnOKFE//rCwTJOVLSAoe4P8LMzd/MbnLWSYuNU6ZRdJn27eEzf2t0BLwI62iJc0rbi9DLw== X-Received: by 2002:a05:6000:1687:: with SMTP id y7mr43208884wrd.636.1641336490297; Tue, 04 Jan 2022 14:48:10 -0800 (PST) Received: from localhost.localdomain ([193.48.40.117]) by smtp.gmail.com with ESMTPSA id c9sm732842wml.12.2022.01.04.14.48.09 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 04 Jan 2022 14:48:10 -0800 (PST) From: zimoun Date: Tue, 4 Jan 2022 23:47:54 +0100 Message-Id: <20220104224755.1142897-16-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.33.1 In-Reply-To: <20220104224755.1142897-1-zimon.toutoune@gmail.com> References: <20220104224755.1142897-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 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 * gnu/packages/julia-xyz.scm (julia-intervaltrees): New variable. --- gnu/packages/julia-xyz.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index e028f37a28..2e726aed23 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -2800,6 +2800,30 @@ (define-public julia-intervalsets unambiguously define the @code{..} and @code{±} operators.") (license license:expat))) +(define-public julia-intervaltrees + ;; Last upstream release on May 2020 and this last release does not contain + ;; the file Project.toml. + (let ((commit "e37edab61568d08141a3e9c25ec55caac21e5aa5")) + (package + (name "julia-intervaltrees") + (version (git-version "1.0.0" "0" commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/BioJulia/IntervalTrees.jl") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "01x48a5zrx0833s1kjhf0ml4x9xz8xja4ymran770akmf6968yl9")))) + (build-system julia-build-system) + (home-page "https://github.com/BioJulia/IntervalTrees.jl") + (synopsis "Interval Trees for Julia") + (description "This package provides an implementation of an associative +container mapping @code{(K,V)} pairs via the type @code{IntervalTree{K, V}}. +The type @code{K} may be any ordered type.") + (license license:expat)))) + (define-public julia-invertedindices (package (name "julia-invertedindices") From patchwork Tue Jan 4 22:47:55 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Simon Tournier X-Patchwork-Id: 35964 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 6531F27BBEA; Tue, 4 Jan 2022 22:49:47 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_ADSP_CUSTOM_MED, DKIM_INVALID,DKIM_SIGNED,FREEMAIL_FROM,MAILING_LIST_MULTI, RCVD_IN_MSPIKE_H3,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 31DED27BBE9 for ; Tue, 4 Jan 2022 22:49:47 +0000 (GMT) Received: from localhost ([::1]:44132 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1n4sck-0000Zi-Aj for patchwork@mira.cbaines.net; Tue, 04 Jan 2022 17:49:46 -0500 Received: from eggs.gnu.org ([209.51.188.92]:43490) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1n4sc8-0007oj-4J for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:08 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:55756) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1n4sc7-00070Z-Rj for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:07 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1n4sc7-0003rl-Qp for guix-patches@gnu.org; Tue, 04 Jan 2022 17:49:07 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#53017] [PATCH 17/17] gnu: Add julia-bioalignments. Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 04 Jan 2022 22:49:07 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 53017 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 53017@debbugs.gnu.org Cc: efraim@flashner.co.il, zimoun Received: via spool by 53017-submit@debbugs.gnu.org id=B53017.164133651514707 (code B ref 53017); Tue, 04 Jan 2022 22:49:07 +0000 Received: (at 53017) by debbugs.gnu.org; 4 Jan 2022 22:48:35 +0000 Received: from localhost ([127.0.0.1]:39053 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbb-0003p4-BQ for submit@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:35 -0500 Received: from mail-wr1-f44.google.com ([209.85.221.44]:34577) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n4sbI-0003lv-C6 for 53017@debbugs.gnu.org; Tue, 04 Jan 2022 17:48:16 -0500 Received: by mail-wr1-f44.google.com with SMTP id s1so79182390wrg.1 for <53017@debbugs.gnu.org>; Tue, 04 Jan 2022 14:48:16 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=insOHsRBUEpQTmnQ5M+u8d8rFiGOpa9UU9H+yIAAUYM=; b=BlA6Xh2+GUoBwmM4Rql8JyjyfFoqhTnthUpYAzq4cPzhjWMJiA7HczprwQFKnu3yHJ hNPFZbIZmD+kWwOltAPqY5erzpJCTMxpYvd44YsbjJBFoPO+9nsP0RW2LyNm8tH3wy6p oYnDa3GlcrZ9XAVdyauo9SfK3aolpNaIsccOFAlU493byqIcY1kfrXZIPsdkbX3JqDNV DqIazuepH4IsCZB3DEfQ+PHYNxMGbHLB1Gge7dVZw/vPT54RiTiD6vgI1hE1gqY8x4B0 giGwffAELHRi5NDb/OBWd8K6yVq/xhmUTOo9o3TSz6DrSBwJBvMyo6jE4v+nmNJ2lvTi i/Xg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=insOHsRBUEpQTmnQ5M+u8d8rFiGOpa9UU9H+yIAAUYM=; b=CqcqtmlUhDPvky1tlj5KYCWb1k8wByDli69okDvPvO0QmFG3JG3aSd9Ia7VUo/k6Q2 41P+XR+yVQrJUZzfBQnyPazm26QNV15/VXh6HbTLissYAfgnEXOum1vPvqqywAYNWlG1 G28TF3BUe8EcLWRsXrH57PBvdO90Xt3GiNw+mmwSgwpnEFHizekAD4xvtb6FqusxesgZ 84pPT7vwu5sIaNTT5gJnCY2gd147uIq0YmZNktvyDqfnsNDnhNgCDthA0OE9VCdFV8eW FIT7K+smQXKekrwiYyxbrhzVmT1qmpvvHmnoJvGfDqvoA6IgfBXxLRqfHgHkKFP0Tahi agww== X-Gm-Message-State: AOAM531JAciiuaXCYhuBWu8ZY0SOKS8WOEN1HGUbn2ASBeuhn6cgpCVr tHPFT4sYHSBBAovd5z1aRR0x+ccooUU= X-Google-Smtp-Source: ABdhPJwD+J4ib8nta/X/QifdW79FHhLwCqukWF7VOEc9PAQc7+PlUx3Jnd/0seZ2hUO5xaiVTOTNPA== X-Received: by 2002:adf:d1e2:: with SMTP id g2mr45470112wrd.179.1641336490765; Tue, 04 Jan 2022 14:48:10 -0800 (PST) Received: from localhost.localdomain ([193.48.40.117]) by smtp.gmail.com with ESMTPSA id c9sm732842wml.12.2022.01.04.14.48.10 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 04 Jan 2022 14:48:10 -0800 (PST) From: zimoun Date: Tue, 4 Jan 2022 23:47:55 +0100 Message-Id: <20220104224755.1142897-17-zimon.toutoune@gmail.com> X-Mailer: git-send-email 2.33.1 In-Reply-To: <20220104224755.1142897-1-zimon.toutoune@gmail.com> References: <20220104224755.1142897-1-zimon.toutoune@gmail.com> MIME-Version: 1.0 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 * gnu/packages/julia-xyz.scm (julia-bioalignments): New variable. --- gnu/packages/julia-xyz.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 2e726aed23..b7a4224694 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -361,6 +361,41 @@ (define-public julia-benchmarktools benchmarks as well as comparing benchmark results.") (license license:expat))) +(define-public julia-bioalignments + (package + (name "julia-bioalignments") + (version "2.0.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/BioJulia/BioAlignments.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1wf6qgsada59r2fykxfj9hcr635wl8maqxbd3w8qpa01k9glxa0k")))) + (build-system julia-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'skip-test + (lambda _ + ;; Test fails because an unexpected type representation from + ;; BioSequences. The aligned value is correct though. + (substitute* "test/runtests.jl" + (("@test sprint\\(show, aln\\)") + "@test_broken sprint(show, aln)"))))))) + (propagated-inputs + (list julia-biogenerics + julia-biosequences + julia-biosymbols + julia-intervaltrees)) + (home-page "https://github.com/BioJulia/BioAlignments.jl") + (synopsis "Sequence alignement algorithm and data structures") + (description "This package provides alignement algorithms and data +structures for sequence of DNA, RNA, and amino acid sequences.") + (license license:expat))) + (define-public julia-biogenerics ;; No upstream release (let ((commit "a75abaf459250e2b5e22b4d9adf25fd36d2acab6")