diff options
Diffstat (limited to 'gnu/packages/julia-xyz.scm')
| -rw-r--r-- | gnu/packages/julia-xyz.scm | 1929 |
1 files changed, 1473 insertions, 456 deletions
diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 492fdd9175..e30cf39dc9 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1,8 +1,9 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2020, 2021 Nicolò Balzarotti <nicolo@nixo.xyz> -;;; Copyright © 2021 Simon Tournier <zimon.toutoune@gmail.com> +;;; Copyright © 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com> ;;; Copyright © 2021 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2021 Vinicius Monego <monego@posteo.net> +;;; Copyright © 2021 jgart <jgart@dismail.de> ;;; ;;; This file is part of GNU Guix. ;;; @@ -47,7 +48,7 @@ (base32 "0083pwdyxjb04i330ir9pc8kmp4bwk59lx1jgc9qi05y8j7xzbp0")))) (build-system julia-build-system) (inputs ;required for tests - `(("julia-unitful" ,julia-unitful))) + (list julia-unitful)) (home-page "https://github.com/JuliaGPU/Adapt.jl") (synopsis "General framework for fast Fourier transforms (FFTs)") (description "This package allows multiple FFT packages to co-exist with @@ -125,7 +126,7 @@ ANSI escape codes to another format.") (define-public julia-aqua (package (name "julia-aqua") - (version "0.5.0") + (version "0.5.1") (source (origin (method git-fetch) @@ -134,8 +135,10 @@ ANSI escape codes to another format.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0zcvrwnyhh2kr4d2xv7ps8dh7byw78dx6yb1m9m4dblgscn5kypb")))) + (base32 "1g0kyzcdykgs247j72jpc2qqall696jwgb3hnn4cxmbi8bkf7wpk")))) (build-system julia-build-system) + (arguments + `(#:parallel-tests? #f)) (home-page "https://github.com/JuliaTesting/Aqua.jl") (synopsis "Automated quality assurance for Julia packages") (description "@acronym{Aqua.jl, Auto QUality Assurance for Julia packages}, @@ -156,17 +159,23 @@ provides functions to run a few automatable checks for Julia packages.") (sha256 (base32 "0cmldnzvdgmfnrnrzgj6v1mfr2rvk5096392rwmhd3iyx7v0pq33")))) (build-system julia-build-system) + (arguments + ;; XXXX: Unexpected failures for i686, e.g., + ;; Expression: @inferred(ArrayInterface.size(Rnr)) === (StaticInt(4),) + ;; Evaluated: (static(2),) === (static(4),) + ;; Disable as stopgap. + `(#:tests? ,(not (target-x86-32?)))) (propagated-inputs - `(("julia-ifelse" ,julia-ifelse) - ("julia-requires" ,julia-requires) - ("julia-static" ,julia-static))) + (list julia-ifelse + julia-requires + julia-static)) (native-inputs - `(("julia-aqua" ,julia-aqua) - ("julia-bandedmatrices" ,julia-bandedmatrices) - ("julia-blockbandedmatrices" ,julia-blockbandedmatrices) - ("julia-ifelse" ,julia-ifelse) - ("julia-offsetarrays" ,julia-offsetarrays) - ("julia-staticarrays" ,julia-staticarrays))) + (list julia-aqua + julia-bandedmatrices + julia-blockbandedmatrices + julia-ifelse + julia-offsetarrays + julia-staticarrays)) (home-page "https://github.com/JuliaArrays/ArrayInterface.jl") (synopsis "Base array interface primitives") (description "The purpose of this library is to solidify extensions to the @@ -181,7 +190,7 @@ no issues with the upgrade.") (define-public julia-arraylayouts (package (name "julia-arraylayouts") - (version "0.7.3") + (version "0.7.6") (source (origin (method git-fetch) @@ -190,10 +199,10 @@ no issues with the upgrade.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0ri05xhfrj2909c6yy09qm6zi8v8s5fvmbbwbg8qgjq0yxnviw32")))) + (base32 "05q62pks8j23pgbrfny072rrwzrz6q19l68srnjxxv39ncmdmrvg")))) (build-system julia-build-system) (propagated-inputs - `(("julia-fillarrays" ,julia-fillarrays))) + (list julia-fillarrays)) (home-page "https://github.com/JuliaMatrices/ArrayLayouts.jl") (synopsis "Array layouts and general fast linear algebra") (description "This package implements a trait-based framework for describing @@ -202,6 +211,34 @@ appropriate BLAS or optimised Julia linear algebra routines. This supports a 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") @@ -217,7 +254,7 @@ much wider class of matrix types than Julia's in-built @code{StridedArray}.") (base32 "00x85lnfln7xkfnirpplzyi8r6q92nfqwya8il156bf7b1pa20gk")))) (build-system julia-build-system) (propagated-inputs - `(("julia-woodburymatrices" ,julia-woodburymatrices))) + (list julia-woodburymatrices)) (home-page "https://github.com/timholy/AxisAlgorithms.jl") (synopsis "Filtering and linear algebra routines for multidimensional arrays") (description "@code{AxisAlgorithms} is a collection of filtering and linear @@ -241,12 +278,12 @@ axis (dimension).") (base32 "03kzan1lm4fxfhzv1xjg3ysf6y7nagcc61vfz15kvdrp1dqxlynk")))) (build-system julia-build-system) (propagated-inputs - `(("julia-rangearrays" ,julia-rangearrays) - ("julia-intervalsets" ,julia-intervalsets) - ("julia-itertools" ,julia-itertools))) + (list julia-rangearrays + julia-intervalsets + julia-itertools)) (native-inputs - `(("julia-offsetarrays" ,julia-offsetarrays) - ("julia-unitful" ,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 @@ -272,10 +309,10 @@ axes, allowing column names or interval selections.") (base32 "0rlfj9gr9ss621v5kw5b06206yaak21s2vq9vk7r8a7p2ylncism")))) (build-system julia-build-system) (propagated-inputs - `(("julia-arraylayouts" ,julia-arraylayouts) - ("julia-fillarrays" ,julia-fillarrays))) + (list julia-arraylayouts + julia-fillarrays)) (native-inputs - `(("julia-genericlinearalgebra" ,julia-genericlinearalgebra))) + (list julia-genericlinearalgebra)) (home-page "https://github.com/JuliaMatrices/BandedMatrices.jl") (synopsis "Julia package for representing banded matrices") (description "This package supports representing banded matrices by only @@ -296,7 +333,27 @@ the entries on the bands.") (sha256 (base32 "1xz3kdrphp4b158pg7dwkiry49phs2fjjpdvk1hjpww5ykxacks8")))) (build-system julia-build-system) - (propagated-inputs `(("julia-json" ,julia-json))) + (arguments + `(#:phases + ,@(if (target-x86-32?) + '((modify-phases %standard-phases + (add-after 'unpack 'remove-failing-tests-i686 + (lambda _ + (substitute* "test/GroupsTests.jl" + (("@test sprint\\(show, g1\\)") + "@test_broken sprint(show, g1)") + (("@test sprint\\(show, g1; context = :boundto => 1\\)") + "@test_broken sprint(show, g1; context = :boundto => 1)") + (("@test sprint\\(show, g1; context = :limit => false\\)") + "@test_broken sprint(show, g1; context = :limit => false)") + (("@test @test_deprecated") "@test_broken")) + (substitute* "test/ExecutionTests.jl" + ;; Evaluated: 12 == 8 + (("@test @ballocated\\(Ref\\(1\\)\\)") + "@test_broken @ballocated(Ref(1))")))))) + '(%standard-phases)))) + (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 @@ -304,10 +361,133 @@ code easy by supplying a framework for writing and running groups of 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 alignment algorithm and data structures") + (description "This package provides alignment 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") + (revision "1")) + (package + (name "julia-biogenerics") + (version (git-version "0.0.0" 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-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") + ;; Older release for compatibility with julia-biosequences. + (version "4.0.4") + (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 + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'adjust-tests + (lambda _ + (substitute* "test/runtests.jl" + (("\\@testset \\\"Range.*" all) + (string-append all " return\n")))))))) + (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") - (version "0.16.3") + (version "0.16.8") (source (origin (method git-fetch) @@ -316,15 +496,24 @@ benchmarks as well as comparing benchmark results.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1f9pnnfv97vww2dxklpx8pa2k85fw2l3pzsj7n28nws1xlwnj96c")))) + (base32 "1by26036fk9mawmcgqxpwizgbs398v9p6vrbsgg7h6llqn3q9iw1")))) (build-system julia-build-system) + (arguments + `(#:phases + ,@(if (target-64bit?) + '(%standard-phases) + '((modify-phases %standard-phases + (add-after 'unpack 'fix-tests-int32-i686 + (lambda _ + (substitute* "test/test_blockarrays.jl" + (("Int64") "Int32"))))))))) (propagated-inputs - `(("julia-arraylayouts" ,julia-arraylayouts) - ("julia-fillarrays" ,julia-fillarrays))) + (list julia-arraylayouts + julia-fillarrays)) (native-inputs - `(("julia-lazyarrays" ,julia-lazyarrays) - ("julia-offsetarrays" ,julia-offsetarrays) - ("julia-staticarrays" ,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 @@ -355,11 +544,11 @@ access to the full matrix to use in in for example a linear solver.") (base32 "10n1r6kmmv2wa307jfg9y2m6p16j8hngjp3fjavpbdy1r5haasm9")))) (build-system julia-build-system) (propagated-inputs - `(("julia-arraylayouts" ,julia-arraylayouts) - ("julia-bandedmatrices" ,julia-bandedmatrices) - ("julia-blockarrays" ,julia-blockarrays) - ("julia-fillarrays" ,julia-fillarrays) - ("julia-matrixfactorizations" ,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 @@ -368,6 +557,29 @@ A @code{BlockBandedMatrix} is a subtype of @code{BlockMatrix} of @code{BlockArrays.jl} whose layout of non-zero blocks is banded.") (license license:expat))) +(define-public julia-bson + (package + (name "julia-bson") + (version "0.3.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaIO/BSON.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1l5608ma2ys7v2gpcqbiv9mwfc6yrlqkihrfx1pf7fgv5llhd4fn")))) + (build-system julia-build-system) + (native-inputs + (list julia-dataframes)) + (home-page "https://github.com/JuliaIO/BSON.jl") + (synopsis "Binary JSON serialisation format") + (description "@code{BSON.jl} is a Julia package for working with the Binary +JSON serialisation format. It can be used as a general store for Julia data +structures.") + (license license:expat))) + (define-public julia-bufferedstreams (package (name "julia-bufferedstreams") @@ -387,8 +599,10 @@ A @code{BlockBandedMatrix} is a subtype of @code{BlockMatrix} of ;; https://travis-ci.org/BioJulia/BufferedStreams.jl/jobs/491050182 (arguments '(#:tests? #f - #:julia-package-name "BufferedStreams")) - (propagated-inputs `(("julia-compat" ,julia-compat))) + #:julia-package-name "BufferedStreams" + #:julia-package-uuid "e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d")) + (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 @@ -435,14 +649,14 @@ methods.") (base32 "1bcfylxdaizgasnmlkjjkf4dgfvy2y9ycnphw2d0z6mm9vx3n04x")))) (build-system julia-build-system) (native-inputs - `(("julia-pooledarrays" ,julia-pooledarrays))) + (list julia-pooledarrays)) (propagated-inputs - `(("julia-dataapi" ,julia-dataapi) - ("julia-json" ,julia-json) - ("julia-json3" ,julia-json3) - ("julia-missings" ,julia-missings) - ("julia-recipesbase" ,julia-recipesbase) - ("julia-structtypes" ,julia-structtypes))) + (list julia-dataapi + julia-json + julia-json3 + julia-missings + julia-recipesbase + julia-structtypes)) (home-page "https://github.com/JuliaData/CategoricalArrays.jl") (synopsis "Arrays for working with categorical data") (description "This package provides tools for working with categorical @@ -465,15 +679,15 @@ variables, both with unordered (nominal variables) and ordered categories (base32 "0if93pd3b3scg2x3gmk1cbwjk0ax1n792vy8c38y3xl7jpd5cb70")))) (build-system julia-build-system) (inputs ;required for test - `(("julia-chainrulestestutils" ,julia-chainrulestestutils) - ("julia-finitedifferences" ,julia-finitedifferences) - ("julia-nanmath" ,julia-nanmath) - ("julia-specialfunctions" ,julia-specialfunctions))) + (list julia-chainrulestestutils + julia-finitedifferences + julia-nanmath + julia-specialfunctions)) (propagated-inputs - `(("julia-chainrulescore" ,julia-chainrulescore) - ("julia-compat" ,julia-compat) - ("julia-reexport" ,julia-reexport) - ("julia-requires" ,julia-requires))) + (list julia-chainrulescore + julia-compat + julia-reexport + julia-requires)) (home-page "https://github.com/JuliaDiff/ChainRules.jl") (synopsis "Common utilities for automatic differentiation") (description "The is package provides a variety of common utilities that @@ -496,10 +710,10 @@ execute forward-, reverse-, and mixed-mode primitives.") (base32 "1866xv30h1bi7f2m993nljzf58wwmv8zlgn6ffn9j3wckch1nfpb")))) (build-system julia-build-system) (inputs ;required for tests - `(("julia-benchmarktools" ,julia-benchmarktools) - ("julia-staticarrays" ,julia-staticarrays))) + (list julia-benchmarktools + julia-staticarrays)) (propagated-inputs - `(("julia-compat" ,julia-compat))) + (list julia-compat)) (home-page "https://github.com/JuliaDiff/ChainRulesCore.jl") (synopsis "Common utilities used by downstream automatic differentiation tools") (description "The package provides a light-weight dependency for defining @@ -509,7 +723,7 @@ sensitivities for functions without the need to depend on ChainRules itself.") (define-public julia-chainrulestestutils (package (name "julia-chainrulestestutils") - (version "1.0.0") + (version "1.2.3") (source (origin (method git-fetch) @@ -518,12 +732,12 @@ sensitivities for functions without the need to depend on ChainRules itself.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "07l4sjc7avmmp4v1dsym1jyb46q4jsvv7i0yzszf72gj8d9k6lwa")))) + (base32 "1vlkyp72d514gyb4k3yhjl1g7f24ncmz61j56p4sdi9f76rk9fx9")))) (build-system julia-build-system) (propagated-inputs - `(("julia-chainrulescore" ,julia-chainrulescore) - ("julia-compat" ,julia-compat) - ("julia-finitedifference" ,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 @@ -538,6 +752,38 @@ can be a test-only dependency, allowing it to have potentially heavy dependencies, while keeping @code{ChainRulesCore.jl} as light-weight as possible.") (license license:expat))) +(define-public julia-codeczlib + (package + (name "julia-codeczlib") + (version "0.7.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaIO/CodecZlib.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0xm603nylkwk4bzx66zv1g3syzrvn3jh9spdx7kvcvgszzyrrgh4")))) + (build-system julia-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'reset-gzip-timestamps 'make-files-writable + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (for-each make-file-writable + (find-files out "\\.gz$")) + #t)))))) + (propagated-inputs + (list julia-transcodingstreams + julia-zlib-jll)) + (home-page "https://github.com/JuliaIO/CodecZlib.jl") + (synopsis "Zlib codecs for @code{TranscodingStreams.jl}") + (description "This package provides zlib codecs for +@code{TranscodingStreams.jl}.") + (license license:expat))) + (define-public julia-colors (package (name "julia-colors") @@ -553,9 +799,9 @@ dependencies, while keeping @code{ChainRulesCore.jl} as light-weight as possible (base32 "0kx3hq7rf8p5zx6ly9k5j90zijmc7yrwmy96cgkl2ibdfbnhmya3")))) (build-system julia-build-system) (propagated-inputs - `(("julia-colortypes" ,julia-colortypes) - ("julia-fixedpointnumbers" ,julia-fixedpointnumbers) - ("julia-reexport" ,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 @@ -567,7 +813,7 @@ color scales for graphics.") (define-public julia-colorschemes (package (name "julia-colorschemes") - (version "3.13.0") + (version "3.15.0") (source (origin (method git-fetch) @@ -576,13 +822,13 @@ color scales for graphics.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "13gy1njxlkfnxmpj2z6aj1bzbzn7jipaxr9fgkv41yiy0xjhqiyh")))) + (base32 "0kpjhmqd5cj8dh8bmh9b5g6bscyp7h23hzpr2s93pnrp57q1wvhq")))) (build-system julia-build-system) (propagated-inputs - `(("julia-colors" ,julia-colors) - ("julia-colortypes" ,julia-colortypes) - ("julia-fixedpointnumbers" ,julia-fixedpointnumbers) - ("julia-staticarrays" ,julia-staticarrays))) + (list julia-colors + julia-colortypes + julia-fixedpointnumbers + julia-staticarrays)) (home-page "https://github.com/JuliaGraphics/ColorSchemes.jl") (synopsis "Colorschemes, colormaps, gradients, and palettes") (description "This package provides a collection of colorschemes.") @@ -601,11 +847,11 @@ color scales for graphics.") (file-name (git-file-name name version)) (sha256 (base32 "0n7h70caqv7yd0khjhn90iax62r73mcif8qzkwj5b4q46li1r8ih")))) - (arguments - '(#:tests? #f)) ;require Documenter, not packaged yet (build-system julia-build-system) (propagated-inputs - `(("julia-fixedpointnumbers" ,julia-fixedpointnumbers))) + (list julia-fixedpointnumbers)) + (native-inputs + (list julia-documenter)) (home-page "https://github.com/JuliaGraphics/ColorTypes.jl") (synopsis "Basic color types and constructor") (description "This minimalistic package serves as the foundation for @@ -617,7 +863,7 @@ with.") (define-public julia-colorvectorspace (package (name "julia-colorvectorspace") - (version "0.9.5") + (version "0.9.7") (source (origin (method git-fetch) @@ -626,14 +872,14 @@ with.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1gx4k1bvf6lkzxphnvpkw857ihrkifhb68yvsj889k9pf1vda3fq")))) + (base32 "02gk7f5g5wjxdasbjf8bvv1m7clksh7mw1xmygjdirjz1q0d6dwi")))) (build-system julia-build-system) (propagated-inputs - `(("julia-colortypes" ,julia-colortypes) - ("julia-specialfunctions" ,julia-specialfunctions) - ("julia-tensorcore" ,julia-tensorcore))) + (list julia-colortypes + julia-specialfunctions + julia-tensorcore)) (native-inputs - `(("julia-colors" ,julia-colors))) + (list julia-colors)) (home-page "https://github.com/JuliaGraphics/ColorVectorSpace.jl") (synopsis "Treat colors as n-vectors for the purposes of arithmetic") (description "This package is an add-on to @code{ColorTypes.jl} and provides @@ -677,7 +923,7 @@ focusing mostly (as of now) on enumerative combinatorics and permutations.") (base32 "0mgy90kk8ksv3l720kkk04gnhn4aqhh2dj4sp3x8yy3limngfjay")))) (build-system julia-build-system) (propagated-inputs - `(("julia-macrotools" ,julia-macrotools))) + (list julia-macrotools)) (home-page "https://github.com/rdeits/CommonSubexpressions.jl") (synopsis "@code{@@cse} macro for Julia") (description "This package provides the @code{@@cse} macro, which performs @@ -687,7 +933,7 @@ common subexpression elimination.") (define-public julia-compat (package (name "julia-compat") - (version "3.32.0") + (version "3.39.0") (source (origin (method git-fetch) @@ -696,7 +942,7 @@ common subexpression elimination.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1zif3dj0a85w7xqbg0chrdhw8dk410zxcqbnkf764xmylwbps498")))) + (base32 "0qzvaqi5gqgc747fnajbvvf5vqbh6cwykwky00c7glvmvdsgk3z0")))) (build-system julia-build-system) (home-page "https://github.com/JuliaLang/Compat.jl") (synopsis "Compatibility across Julia versions") @@ -706,6 +952,53 @@ provides a macro that lets you use the latest syntax in a backwards-compatible way.") (license license:expat))) +(define-public julia-configurations + (package + (name "julia-configurations") + (version "0.16.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Roger-luo/Configurations.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1b23p0zk8dx2sf01cnw177mqci7qd81b9s32ixz9clsh0r0icl1b")))) + (build-system julia-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'link-depot 'fix-tests + (lambda _ + (substitute* "test/runtests.jl" + (("option.toml") "test/option.toml")))) + (add-after 'link-depot 'dont-use-exproniconlite + (lambda _ + (substitute* '("Project.toml" + "src/Configurations.jl" + "test/runtests.jl") + (("ExproniconLite") "Expronicon")) + (substitute* "Project.toml" + (("55351af7-c7e9-48d6-89ff-24e801d99491") + "6b7a57c9-7cc1-4fdf-b7f5-e857abae3636")))) + ,@(if (target-64bit?) + '() + '((add-after 'unpack 'fix-tests-int32-i686 + (lambda _ + (substitute* "test/runtests.jl" + (("Int64") "Int32"))))))))) + (propagated-inputs + (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 +let you define @code{structs} to represent options/configurations, and serialize +between different option/configuration file formats such as @code{TOML}.") + (license license:expat))) + (define-public julia-constructionbase (package (name "julia-constructionbase") @@ -740,14 +1033,12 @@ for construction of objects.") (sha256 (base32 "15zbkn32v7xlz7559s0r5a0vkwmjwsswxaqpzijly4lky4jnp33d")))) (build-system julia-build-system) - (arguments - `(#:tests? #f)) ; Documenter.jl not packaged yet. (propagated-inputs - `(("julia-staticarrays" ,julia-staticarrays))) - ;(native-inputs - ; `(("julia-documenter" ,julia-documenter) - ; ("julia-forwarddiff" ,julia-forwarddiff) - ; ("julia-unitful" ,julia-unitful))) + (list julia-staticarrays)) + (native-inputs + (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 @@ -806,6 +1097,63 @@ moving the function definition to DataAPI.jl and each package taking a dependency on it.") (license license:expat))) +(define-public julia-dataframes + (package + (name "julia-dataframes") + (version "1.2.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaData/DataFrames.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1bk0amrghgjrkyn1mm4ac23swwbgszl1d0qyl9137qj5zvv9dasp")))) + (build-system julia-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'link-depot 'skip-failing-test + (lambda _ + ;; Tests with non-standard colors. + (substitute* "test/show.jl" + (("test (sprint\\(show, df, context=:color=>true)" _ test) + (string-append "test_nowarn " test))) + (substitute* "test/io.jl" + (("testset \\\"improved.*" all) + (string-append all "return\n"))) + (substitute* "test/join.jl" + (("test (levels\\(outerjoin\\(B)" _ test) + (string-append "test_nowarn " test))) + #t))))) + (propagated-inputs + (list julia-dataapi + julia-invertedindices + julia-iteratorinterfaceextensions + julia-missings + julia-pooledarrays + julia-prettytables + julia-reexport + julia-sortingalgorithms + julia-tables + julia-tabletraits)) + (native-inputs + (list julia-categoricalarrays + julia-combinatorics + julia-datastructures + julia-datavalues + julia-offsetarrays + julia-unitful)) + (home-page "https://dataframes.juliadata.org/stable/") + (synopsis "In-memory tabular data") + (description "This package provides a set of tools for working with tabular +data in Julia. Its design and functionality are similar to those of Pandas from +Python or @code{data.frame}, @code{data.table} and @code{dplyr} from R, making +it a great general purpose data science tool, especially for those coming to +Julia from R or Python.") + (license license:expat))) + (define-public julia-datastructures (package (name "julia-datastructures") @@ -820,9 +1168,22 @@ dependency on it.") (sha256 (base32 "0hdqp8ipsqdw5bqqkdvz4j6n67x80sj5azr9vzyxwjfsgkfbnk2l")))) (propagated-inputs - `(("julia-compat" ,julia-compat) - ("julia-orderedcollections" ,julia-orderedcollections))) + (list julia-compat + julia-orderedcollections)) (build-system julia-build-system) + (arguments + `(#:phases + ,@(if (target-x86-32?) + '((modify-phases %standard-phases + (add-after 'unpack 'remove-failing-test-i686 + (lambda _ + ;; The evaluation returns the correct value, + ;; Evaluated: "Accumulator(1 => 3, 3 => 4)" + ;; but, for some reasons, is considered as failed. + (substitute* "test/test_accumulator.jl" + (("@test sprint\\(show,Accumulator\\(1 => 3, 3 => 4\\)\\)") + "@test_broken sprint(show, Accumulator(1 => 3, 3 => 4))")))))) + '(%standard-phases)))) (home-page "https://github.com/JuliaCollections/DataStructures.jl") (synopsis "Julia module providing different data structures") (description "This package implements a variety of data structures, @@ -869,7 +1230,7 @@ without having to take direct dependencies.") `(#:tests? #f ; Tests need upgrading with newer Julia version. #:phases (modify-phases %standard-phases - (add-after 'unpack 'skip-known-failing-tests + (add-after 'link-depot 'skip-known-failing-tests (lambda _ ;; See upstream report: ;; https://github.com/queryverse/DataValues.jl/issues/83 @@ -878,7 +1239,7 @@ without having to take direct dependencies.") ((".*DataValue\\(method\\(f.*") "")) #t))))) (propagated-inputs - `(("julia-datavalueinterfaces" ,julia-datavalueinterfaces))) + (list julia-datavalueinterfaces)) (home-page "https://github.com/queryverse/DataValues.jl") (synopsis "Missing values for Julia") (description "This package provides the type @code{DataValue} that is used @@ -923,7 +1284,7 @@ dictionaries where values associated with a particular key may change, (base32 "1mm43hm8hd6sgmkkpqhbqhvap7mpkjwzmz5algxi6manp580gkr5")))) (build-system julia-build-system) (propagated-inputs - `(("julia-indexing" ,julia-indexing))) + (list julia-indexing)) (home-page "https://github.com/andyferris/Dictionaries.jl") (synopsis "Alternative interface for dictionaries in Julia") (description "This package provides an alternative interface for @@ -947,7 +1308,7 @@ dictionaries in Julia, for improved productivity and performance.") (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'skip-flakey-tests + (add-after 'link-depot 'skip-flakey-tests (lambda _ ;; Some combination of these tests fail nondeterministically ;; each of the times this package is built. @@ -957,10 +1318,10 @@ dictionaries in Julia, for improved productivity and performance.") (("test dist\\(z, x") "test_nowarn dist(z, x") (("test dist\\(z, y") "test_nowarn dist(z, y"))))))) (propagated-inputs - `(("julia-statsapi" ,julia-statsapi))) + (list julia-statsapi)) (native-inputs - `(("julia-offsetarrays" ,julia-offsetarrays) - ("julia-unitful" ,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 @@ -1013,33 +1374,31 @@ valuable enough at this time.") (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'patch-source + (add-after 'link-depot 'patch-source (lambda* (#:key inputs #:allow-other-keys) (substitute* "src/Deps.jl" (("pip install") - (string-append (assoc-ref inputs "python") - "/bin/pip install"))) - #t)) - (add-after 'unpack 'remove-javascript-downloads + (string-append (search-input-file inputs "bin/pip") + " install"))))) + (add-after 'link-depot 'remove-javascript-downloads (lambda _ (substitute* "src/Writers/HTMLWriter.jl" (("cdnjs.cloudflare.com") "example.com")) ;; 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 - `(("julia-ansicoloredprinters" ,julia-ansicoloredprinters) - ("julia-docstringextensions" ,julia-docstringextensions) - ("julia-iocapture" ,julia-iocapture) - ("julia-json" ,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.") @@ -1076,7 +1435,7 @@ valuable enough at this time.") (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)) (home-page "https://github.com/JuliaDocs/DocumenterMarkdown.jl") (synopsis "Documenter's Markdown") (description "This package enables the Markdown / MkDocs backend of @@ -1102,13 +1461,13 @@ valuable enough at this time.") (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 - `(("julia-docstringextensions" ,julia-docstringextensions) - ("julia-gumbo" ,julia-gumbo) - ("julia-sass" ,julia-sass))) + (list julia-docstringextensions + julia-gumbo + julia-sass)) (native-inputs - `(("julia-example" ,julia-example))) + (list julia-example)) (home-page "https://github.com/JuliaDocs/DocumenterTools.jl") (synopsis "Extra tools for setting up Documenter.jl") (description "This package contains utilities for setting up documentation @@ -1128,9 +1487,9 @@ generation with @code{Documenter.jl}.") (file-name (git-file-name name version)) (sha256 (base32 "1w6p3yxajvclax5b9g7cr2jmbc7lvr5nk4gq0aljxdycdq1d2y3v")))) - (propagated-inputs - `(("julia-staticarrays" ,julia-staticarrays))) (build-system julia-build-system) + (propagated-inputs + (list julia-staticarrays)) (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 @@ -1150,10 +1509,10 @@ be passed to in-place differentiation methods instead of an output buffer.") (file-name (git-file-name name version)) (sha256 (base32 "0cwjvj4gma7924fm3yas0nf0jlnwwx4v7fi79ii3s290lkdldzfl")))) - (propagated-inputs - `(("julia-nanmath" ,julia-nanmath) - ("julia-specialfunctions" ,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 @@ -1199,15 +1558,15 @@ stressing the robustness of differentiation tools.") (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'adjust-test-suite + (add-after 'link-depot 'adjust-test-suite (lambda _ (substitute* "test/runtests.jl" ;; Seems to not play nicely with SpecialFunctions ((".*isempty.*") ""))))))) (propagated-inputs - `(("julia-calculus" ,julia-calculus) - ("julia-nanmath" ,julia-nanmath) - ("julia-specialfunctions" ,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} @@ -1233,13 +1592,13 @@ combinations of dual numbers with predefined Julia numeric types.") (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'adjust-test-suite + (add-after 'link-depot 'adjust-test-suite (lambda _ (substitute* "test/runtests.jl" ;; Seems to not play nicely with Julia-1.6. ((".*basic.jl.*") ""))))))) (propagated-inputs - `(("julia-arrayinterface" ,julia-arrayinterface))) + (list julia-arrayinterface)) (home-page "https://github.com/ChrisRackauckas/EllipsisNotation.jl") (synopsis "Elipsis notation implementation") (description "This implements the notation @code{..} for indexing arrays. @@ -1267,6 +1626,40 @@ before (or after)\".") (description "This package provides various examples.") (license license:expat)))) +;; ExproniconLite.jl is autogenerated from this package. +(define-public julia-expronicon + (package + (name "julia-expronicon") + (version "0.6.10") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Roger-luo/Expronicon.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0h8aaynqlxrkn8575k5vqmhzil4vvxchhf0bcxa6zwawp558gj2y")))) + (build-system julia-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'link-depot 'skip-network-tests + (lambda _ + (substitute* "test/runtests.jl" + ;; This test tries to access the Julia package registry. + ((".*expand\\.jl.*") ""))))))) + (propagated-inputs + (list julia-mlstyle)) + (native-inputs + (list julia-documenter)) + (home-page "https://expronicon.rogerluo.dev/dev/") + (synopsis "Collective tools for metaprogramming on Julia Expr") + (description "This package provides a collection of tools for +metaprogramming on Julia Expr, the meta programming standard library for +@code{MLStyle}.") + (license license:expat))) + (define-public julia-exprtools (package (name "julia-exprtools") @@ -1303,8 +1696,8 @@ performant tooling without requiring additional package dependencies.") (base32 "1ldxbp0kq3ip67x7sp82dz56aq4p5i0chspbgx2zgskr6jcbjj1b")))) (build-system julia-build-system) (propagated-inputs - `(("julia-ffmpeg-jll" ,julia-ffmpeg-jll) - ("julia-x264-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 @@ -1330,7 +1723,7 @@ need the ffmpeg binaries + executables, and don't want the overhead of `(#:phases (modify-phases %standard-phases (delete 'reset-gzip-timestamps) - (add-after 'unpack 'skip-network-tests + (add-after 'link-depot 'skip-network-tests (lambda _ ;; These tests try to download audio/video files. (substitute* "test/query.jl" @@ -1348,11 +1741,11 @@ need the ffmpeg binaries + executables, and don't want the overhead of (substitute* "test/runtests.jl" ((".*test_mimesave.*") ""))))))) (propagated-inputs - `(("julia-requires" ,julia-requires))) + (list julia-requires)) (native-inputs - `(("julia-colortypes" ,julia-colortypes) - ("julia-filepathsbase" ,julia-filepathsbase) - ("julia-http" ,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 @@ -1387,7 +1780,7 @@ working with filesystem paths in Julia.") (define-public julia-fillarrays (package (name "julia-fillarrays") - (version "0.12.1") + (version "0.12.6") (source (origin (method git-fetch) @@ -1396,10 +1789,10 @@ working with filesystem paths in Julia.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1va8vvcxbxcy5xp487hdqfp0ps3m8q0819xrxygsf5135azp3qrh")))) + (base32 "1sx96pzrgyh8k7x2w8vmyi6cazlmp7rg1n7wbl47qfzqjggka6kz")))) (build-system julia-build-system) (inputs ;required by tests - `(("julia-staticarrays" ,julia-staticarrays))) + (list julia-staticarrays)) (home-page "https://github.com/JuliaArrays/FillArrays.jl") (synopsis "Lazy matrix representation") (description "This package lazily represents matrices filled with @@ -1432,13 +1825,13 @@ following types: @code{Eye}, @code{Fill}, @code{Ones}, @code{Zeros}, (setenv "GROUP" "Core") #t))))) (propagated-inputs - `(("julia-arrayinterface" ,julia-arrayinterface) - ("julia-requires" ,julia-requires) - ("julia-staticarrays" ,julia-staticarrays))) + (list julia-arrayinterface + julia-requires + julia-staticarrays)) (native-inputs - `(("julia-bandedmatrices" ,julia-bandedmatrices) - ("julia-blockbandedmatrices" ,julia-blockbandedmatrices) - ("julia-safetestsets" ,julia-safetestsets))) + (list julia-bandedmatrices + julia-blockbandedmatrices + julia-safetestsets)) (home-page "https://github.com/JuliaDiff/FiniteDiff.jl") (synopsis "Calculations of gradients, Jacobians, and Hessians") (description "This package is for calculating derivatives, gradients, @@ -1461,12 +1854,23 @@ types and sparsity.") (sha256 (base32 "09nsf9cgk49yrvprflnhd9h5rrgs280rgj8sad3csghxdx6jqk5c")))) (build-system julia-build-system) + (arguments + `(#:phases + ,@(if (target-x86-32?) + '((modify-phases %standard-phases + (add-after 'unpack 'remove-failing-test-i686 + (lambda _ + ;; Machine Precision incorrectly handled + (substitute* "test/methods.jl" + (("@test central_fdm\\(15, 5, adapt=2\\)\\(exp, 1.0\\)") + "@test_broken central_fdm(15, 5, adapt=2)(exp, 1.0)")))))) + '(%standard-phases)))) (inputs - `(("julia-benchmarktools" ,julia-benchmarktools))) + (list julia-benchmarktools)) (propagated-inputs - `(("julia-chainrulescore" ,julia-chainrulescore) - ("julia-richardson" ,julia-richardson) - ("julia-staticarrays" ,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 @@ -1490,13 +1894,14 @@ using finite difference.") (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'disable-failing-test + (add-after 'link-depot 'disable-failing-test (lambda* (#:key outputs #:allow-other-keys) (substitute* "test/fixed.jl" ;; A deprecation warning is not thrown (("@test_logs.*:warn" all) (string-append "# " all))) #t))))) - (propagated-inputs `(("julia-compat" ,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 @@ -1542,16 +1947,22 @@ c-style numerical formatting.") (sha256 (base32 "1vb46x8mcn61g1l14qrk22c043khg2ml4q1ci7h4k2v34f2ak5fs")))) (build-system julia-build-system) + (arguments + ;; XXXX: Unexpected and non-deterministic failures for i686, e.g., + ;; Expression: dual_isapprox(FDNUM ^ PRIMAL, exp(PRIMAL * log(FDNUM))) + ;; ERROR: LoadError: LoadError: There was an error during testing + ;; Disable as stopgap. + `(#:tests? ,(not (target-x86-32?)))) (inputs ;required for tests - `(("julia-calculus" ,julia-calculus) - ("julia-difftests" ,julia-difftests))) + (list julia-calculus + julia-difftests)) (propagated-inputs - `(("julia-commonsubexpressions" ,julia-commonsubexpressions) - ("julia-diffresults" ,julia-diffresults) - ("julia-diffrules" ,julia-diffrules) - ("julia-nanmath" ,julia-nanmath) - ("julia-specialfunctions" ,julia-specialfunctions) - ("julia-staticarrays" ,julia-staticarrays))) + (list julia-commonsubexpressions + julia-diffresults + julia-diffrules + julia-nanmath + julia-specialfunctions + julia-staticarrays)) (home-page "https://github.com/JuliaDiff/ForwardDiff.jl") (synopsis "Methods to take multidimensional derivatives") (description "This package implements methods to take derivatives, @@ -1577,7 +1988,7 @@ differentiation (AD).") (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'adjust-tests + (add-after 'link-depot 'adjust-tests (lambda _ (substitute* "test/runtests.jl" (("testset \\\"Abstract.*" all) @@ -1588,6 +1999,31 @@ differentiation (AD).") arbitrary functions.") (license license:expat))) +(define-public julia-functors + (package + (name "julia-functors") + (version "0.2.7") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/FluxML/Functors.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "03ry1wn1y2jssq65l29bi6q4ki041aa6gl1nd2w6cgl00k2mrxf3")))) + (build-system julia-build-system) + (home-page "https://fluxml.ai/Functors.jl/stable/") + (synopsis "Design pattern for structures as in machine learning") + (description "This package provides tools to express a design pattern for +dealing with large/ nested structures, as in machine learning and +optimisation. For large machine learning models it can be cumbersome or +inefficient to work with parameters as one big, flat vector, and structs help +in managing complexity; but it is also desirable to easily operate over all +parameters at once, e.g. for changing precision or applying an optimiser +update step.") + (license license:expat))) + (define-public julia-fuzzycompletions (package (name "julia-fuzzycompletions") @@ -1605,7 +2041,7 @@ arbitrary functions.") (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'skip-failing-test + (add-after 'link-depot 'skip-failing-test (lambda _ (substitute* "test/runtests.jl" ((".*RPLE.*") ""))))))) @@ -1632,12 +2068,12 @@ arbitrary functions.") (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'adjust-test-suite + (add-after 'link-depot 'adjust-test-suite (lambda _ (substitute* "test/runtests.jl" ((".*lapack.*") ""))))))) (native-inputs - `(("julia-quaternions" ,julia-quaternions))) + (list julia-quaternions)) (home-page "https://github.com/JuliaLinearAlgebra/GenericLinearAlgebra.jl") (synopsis "Generic numerical linear algebra") (description "The purpose of this package is partly to extend linear algebra @@ -1663,7 +2099,7 @@ algebra routines written in Julia (except for optimized BLAS).") (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'adjust-test-suite + (add-after 'link-depot 'adjust-test-suite (lambda _ (substitute* "test/complex.jl" ;; expected Array{Int32,1}, got a value of type Array{Int64,1} @@ -1683,6 +2119,77 @@ analysis of dense matrices. The diagonal eigen-decomposition of normal matrices the Schur form is often more useful.") (license license:expat))) +(define-public julia-geometrybasics + (package + (name "julia-geometrybasics") + (version "0.4.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaGeometry/GeometryBasics.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "057j3hjpli3q5b98cqkpi4p10x2k9pyksrz62hjmv1kb5qzdvhsj")))) + (build-system julia-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'link-depot 'remove-earcut + (lambda _ + (substitute* '("Project.toml" + "src/GeometryBasics.jl") + ((".*EarCut.*") "")))) + (add-after 'link-depot 'skip-incompatible-test + (lambda _ + (substitute* "test/runtests.jl" + (("@testset.*MetaT and heterogeneous data.*" all) + (string-append all "return\n"))))) + ,@(if (target-64bit?) + '() + '((add-after 'unpack 'fix-tests-int32-i686 + (lambda _ + (substitute* "test/runtests.jl" + (("Int64") "Int32"))))))))) + (propagated-inputs + (list julia-itertools + julia-staticarrays + julia-structarrays + julia-tables)) + (native-inputs + (list julia-offsetarrays)) + (home-page "https://github.com/JuliaGeometry/GeometryBasics.jl") + (synopsis "Basic Geometry Types") + (description "This package aims to offer a standard set of Geometry types, +which easily work with metadata, query frameworks on geometries and different +memory layouts. The aim is to create a solid basis for Graphics/Plotting, +finite elements analysis, Geo applications, and general geometry manipulations +- while offering a Julian API, that still allows performant C-interop.") + (license license:expat))) + +(define-public julia-gr + (package + (name "julia-gr") + (version "0.58.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/jheinen/GR.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "18zxa1w2wmrf44c5l10qbh99zjdp7h94gxlymh47cf5kj5fc4xmx")))) + (build-system julia-build-system) + (propagated-inputs + (list julia-gr-jll)) + (home-page "https://github.com/jheinen/GR.jl") + (synopsis "Plotting for Julia based on GR") + (description "This module provides a Julia interface to GR, a framework for +visualisation applications.") + (license license:expat))) + (define-public julia-graphics (package (name "julia-graphics") @@ -1698,8 +2205,8 @@ matrices the Schur form is often more useful.") (base32 "10h1s09v7qkvrjr6l678zamb1p248n8jv4rrwkf8g7d2bpfz9amn")))) (build-system julia-build-system) (propagated-inputs - `(("julia-colors" ,julia-colors) - ("julia-nanmath" ,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 @@ -1721,8 +2228,8 @@ operations in Julia.") (base32 "1g22dv3v7caakspv3pdahnqn937fzzsg9y87rj72hid9g8lxl1gm")))) (build-system julia-build-system) (propagated-inputs - `(("julia-abstracttrees" ,julia-abstracttrees) - ("julia-gumbo-jll" ,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 @@ -1774,13 +2281,13 @@ library for parsing HTML.") (string-append all "return\n"))) #t))))) (propagated-inputs - `(("julia-inifile" ,julia-inifile) - ("julia-mbedtls" ,julia-mbedtls) - ("julia-uris" ,julia-uris))) + (list julia-inifile + julia-mbedtls + julia-uris)) ;; required for tests (inputs - `(("julia-json" ,julia-json) - ("julia-bufferedstreams" ,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, @@ -1802,7 +2309,7 @@ implementing both a client and a server.") (base32 "0jvl4xn8f8k70sn473li5q62wbiycl5qi25b5k456h3a0j1lbiml")))) (build-system julia-build-system) (propagated-inputs - `(("julia-offsetarrays" ,julia-offsetarrays))) + (list julia-offsetarrays)) (home-page "https://github.com/JuliaArrays/IdentityRanges.jl") (synopsis "Ranges that preserve indices of views") (description "@code{IdentityRanges} are Julia-language a helper type for @@ -1848,12 +2355,12 @@ conditional ifelse. It is similar to @code{Core.ifelse} but it is extendable.") (base32 "15zqxani1jjh8849s7rdps6b6prqdwv8yxx893y536vkpk7i07qd")))) (build-system julia-build-system) (propagated-inputs - `(("julia-axisarrays" ,julia-axisarrays) - ("julia-imagecore" ,julia-imagecore) - ("julia-reexport" ,julia-reexport) - ("julia-simpletraits" ,julia-simpletraits))) + (list julia-axisarrays + julia-imagecore + julia-reexport + julia-simpletraits)) (native-inputs - `(("julia-unitful" ,julia-unitful))) + (list julia-unitful)) (home-page "https://github.com/JuliaImages/ImageAxes.jl") (synopsis "Julia package for giving \"meaning\" to the axes of an image") (description "This small package supports the representation of images as @@ -1878,8 +2385,8 @@ such arrays easy via traits.") (arguments `(#:tests? #f)) ; Cycle with ImageMagick.jl. (propagated-inputs - `(("julia-imagecore" ,julia-imagecore) - ("julia-reexport" ,julia-reexport))) + (list julia-imagecore + julia-reexport)) ;(native-inputs ; `(("julia-imagemagick" ,julia-imagemagick) ; ("julia-offsetarrays" ,julia-offsetarrays) @@ -1909,16 +2416,16 @@ dependencies.") (arguments `(#:tests? #f)) ; Cycle with ImageMagick.jl. (propagated-inputs - `(("julia-abstractffts" ,julia-abstractffts) - ("julia-colors" ,julia-colors) - ("julia-colorvectorspace" ,julia-colorvectorspace) - ("julia-fixedpointnumbers" ,julia-fixedpointnumbers) - ("julia-graphics" ,julia-graphics) - ("julia-mappedarrays" ,julia-mappedarrays) - ("julia-mosaicviews" ,julia-mosaicviews) - ("julia-offsetarrays" ,julia-offsetarrays) - ("julia-paddedviews" ,julia-paddedviews) - ("julia-reexport" ,julia-reexport))) + (list julia-abstractffts + julia-colors + julia-colorvectorspace + julia-fixedpointnumbers + julia-graphics + julia-mappedarrays + julia-mosaicviews + julia-offsetarrays + julia-paddedviews + julia-reexport)) ;(native-inputs ; `(("julia-aqua" ,julia-aqua) ; ("julia-colorvectorspace" ,julia-colorvectorspace) @@ -1951,10 +2458,10 @@ of packages designed to support image processing and computer vision.") (arguments `(#:tests? #f)) ; Cycle with ReferenceTests.jl. (propagated-inputs - `(("julia-crayons" ,julia-crayons) - ("julia-imagebase" ,julia-imagebase) - ("julia-imagecore" ,julia-imagecore) - ("julia-requires" ,julia-requires))) + (list julia-crayons + julia-imagebase + julia-imagecore + julia-requires)) ;(native-inputs ; `(("julia-coordinatetransformations" ,julia-coordinatetransformations) ; ("julia-imagemagick" ,julia-imagemagick) @@ -1989,7 +2496,7 @@ be downscaled to fit into the size of your active terminal session.") (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'skip-failing-test + (add-after 'link-depot 'skip-failing-test (lambda _ ;; These tests try to download from the imagemagick.org (substitute* "test/runtests.jl" @@ -2000,18 +2507,18 @@ be downscaled to fit into the size of your active terminal session.") (("test (B == map)" _ test) (string-append "test_nowarn " test))) #t))))) (propagated-inputs - `(("julia-fileio" ,julia-fileio) - ("julia-imagecore" ,julia-imagecore) - ("julia-imagemagick-jll" ,julia-imagemagick-jll))) + (list julia-fileio + julia-imagecore + julia-imagemagick-jll)) (native-inputs - `(("julia-colors" ,julia-colors) - ("julia-colorvectorspace" ,julia-colorvectorspace) - ("julia-imagemetadata" ,julia-imagemetadata) - ("julia-imageshow" ,julia-imageshow) - ("julia-imagetransformations" ,julia-imagetransformations) - ("julia-indirectarrays" ,julia-indirectarrays) - ("julia-offsetarrays" ,julia-offsetarrays) - ("julia-zipfile" ,julia-zipfile))) + (list julia-colors + julia-colorvectorspace + julia-imagemetadata + julia-imageshow + julia-imagetransformations + julia-indirectarrays + julia-offsetarrays + julia-zipfile)) (home-page "https://github.com/JuliaIO/ImageMagick.jl") (synopsis "Thin wrapper for ImageMagick") (description "This package provides a wrapper around ImageMagick version 6. @@ -2033,14 +2540,14 @@ It was split off from @code{Images.jl} to make image I/O more modular.") (base32 "0iv154ms370xgcr56bwsjl13iwmy671cbxjl9ld5yfj85pclcwi1")))) (build-system julia-build-system) (propagated-inputs - `(("julia-axisarrays" ,julia-axisarrays) - ("julia-imageaxes" ,julia-imageaxes) - ("julia-imagecore" ,julia-imagecore) - ("julia-indirectarrays" ,julia-indirectarrays))) + (list julia-axisarrays + julia-imageaxes + julia-imagecore + julia-indirectarrays)) (native-inputs - `(("julia-offsetarrays" ,julia-offsetarrays) - ("julia-simpletraits" ,julia-simpletraits) - ("julia-unitful" ,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 @@ -2067,11 +2574,11 @@ information about the detector used to acquire the image.") (arguments `(#:tests? #f)) ; cycle with ImageMagick.jl. (propagated-inputs - `(("julia-fileio" ,julia-fileio) - ("julia-imagebase" ,julia-imagebase) - ("julia-imagecore" ,julia-imagecore) - ("julia-offsetarrays" ,julia-offsetarrays) - ("julia-stackviews" ,julia-stackviews))) + (list julia-fileio + julia-imagebase + julia-imagecore + julia-offsetarrays + julia-stackviews)) ;(native-inputs ; `(("julia-imagedistances" ,julia-imagedistances) ; ("julia-imagemagick" ,julia-imagemagick) @@ -2102,15 +2609,15 @@ inline presentation of greyscale or color images.") (arguments `(#:tests? #f)) ; Cycle with ImageMagick.jl. (propagated-inputs - `(("julia-axisalgorithms" ,julia-axisalgorithms) - ("julia-colorvectorspace" ,julia-colorvectorspace) - ("julia-coordinatetransformations" ,julia-coordinatetransformations) - ("julia-identityranges" ,julia-identityranges) - ("julia-imagecore" ,julia-imagecore) - ("julia-interpolations" ,julia-interpolations) - ("julia-offsetarrays" ,julia-offsetarrays) - ("julia-rotations" ,julia-rotations) - ("julia-staticarrays" ,julia-staticarrays))) + (list julia-axisalgorithms + julia-colorvectorspace + julia-coordinatetransformations + julia-identityranges + julia-imagecore + julia-interpolations + julia-offsetarrays + julia-rotations + julia-staticarrays)) ;(native-inputs ; `(("julia-imagemagick" ,julia-imagemagick) ; ("julia-referencetests" ,julia-referencetests) @@ -2121,6 +2628,39 @@ inline presentation of greyscale or color images.") 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") @@ -2157,9 +2697,9 @@ out of dictionaries, tuples, etc, extending this ability beyond (base32 "0l0jq0jnr9z3k431ni82xycq7mqapgxrbrx4yyk6lycvi41ipm4s")))) (build-system julia-build-system) (native-inputs - `(("julia-colors" ,julia-colors) - ("julia-fixedpointnumbers" ,julia-fixedpointnumbers) - ("julia-mappedarrays" ,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 @@ -2169,6 +2709,39 @@ assigned its own index, which is used to retrieve the value from the indexed images, sometimes called \"colormap images\" or \"paletted images.\"") (license license:expat))) +(define-public julia-infinity + (package + (name "julia-infinity") + (version "0.2.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/cjdoris/Infinity.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1941lwvrdjnrynigzixxin3chpg1ba6xplvcwc89x0f6z658hwmm")))) + (build-system julia-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'link-depot 'remove-timezones.jl + (lambda _ + (substitute* "test/runtests.jl" + (("using TimeZones.*") "") + ((".*infextendedtime.*") "")) + #t))))) + (propagated-inputs + (list julia-requires)) + (native-inputs + (list julia-compat)) + (home-page "https://docs.juliahub.com/Infinity/") + (synopsis "Representation of infinity in Julia") + (description "This package provides representations for infinity and +negative infinity in Julia.") + (license license:expat))) + (define-public julia-inifile (package (name "julia-inifile") @@ -2203,19 +2776,25 @@ interfaces with @file{.ini} files.") (sha256 (base32 "1236c20k388qlh7k74mhf7hkbn0vf7ss8b1rgh1a6aj0234ayfnc")))) (build-system julia-build-system) + (arguments + `(#:parallel-tests? #f + ;; XXXX: Unexpected failures for i686, e.g., + ;; Got exception outside of a @test + ;; OverflowError: 96908232 * 106943408 overflowed for type Int32 + ;; Disable as stopgap. + #:tests? ,(not (target-x86-32?)))) (propagated-inputs - `(("julia-axisalgorithms" ,julia-axisalgorithms) - ("julia-offsetarrays" ,julia-offsetarrays) - ("julia-ratios" ,julia-ratios) - ("julia-requires" ,julia-requires) - ("julia-staticarrays" ,julia-staticarrays) - ("julia-woodburymatrices" ,julia-woodburymatrices))) + (list julia-axisalgorithms + julia-offsetarrays + julia-ratios + julia-requires + julia-staticarrays + julia-woodburymatrices)) (native-inputs - `(("julia-dualnumbers" ,julia-dualnumbers) - ("julia-forwarddiff" ,julia-forwarddiff) - ("julia-offsetarrays" ,julia-offsetarrays) - ("julia-unitful" ,julia-unitful) - ("julia-zygote" ,julia-zygote))) + (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") (description "This package implements a variety of interpolation schemes for @@ -2237,10 +2816,24 @@ and exceptional performance.") (sha256 (base32 "0gsz89cd3iygbl5qr389k9vwpg7w1nk0s90g25nsmk34y9hifxag")))) (build-system julia-build-system) + (arguments + `(#:phases + ,@(if (target-x86-32?) + '((modify-phases %standard-phases + (add-after 'unpack 'remove-failing-test-i686 + (lambda _ + (substitute* "test/runtests.jl" + ;; For some reason, the output is correct but the test + ;; is considered as failed: + ;; Expression: duration(ClosedInterval(A, B)) ≡ 60 + ;; Evaluated: 60 ≡ 60 + (("@test duration\\(ClosedInterval") + "@test_broken duration(ClosedInterval")))))) + '(%standard-phases)))) (propagated-inputs - `(("julia-ellipsisnotation" ,julia-ellipsisnotation))) + (list julia-ellipsisnotation)) (native-inputs - `(("julia-offsetarrays" ,julia-offsetarrays))) + (list julia-offsetarrays)) (home-page "https://github.com/JuliaMath/IntervalSets.jl") (synopsis "Interval Sets for Julia") (description "This package is intended to implement a \"minimal\" foundation @@ -2249,6 +2842,31 @@ encourage type-piracy for the reason that only one interval package can 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") + (revision "1")) + (package + (name "julia-intervaltrees") + (version (git-version "1.0.0" revision 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") @@ -2264,7 +2882,7 @@ unambiguously define the @code{..} and @code{±} operators.") (base32 "1179z20yxnkyziip7gn26wr1g3k3ssl1ci7pig3khc900f62di46")))) (build-system julia-build-system) (native-inputs - `(("julia-offsetarrays" ,julia-offsetarrays))) + (list julia-offsetarrays)) (home-page "https://github.com/mbauman/InvertedIndices.jl") (synopsis "Index type that allows for inverted selections") (description "This package just exports one type: the @code{InvertedIndex}, @@ -2306,11 +2924,11 @@ as a string together with the return value.") (file-name (git-file-name name version)) (sha256 (base32 "11334fcg2slpwcj0raxf457brhf7pxglgxc6cy8q58ggrpxqfqql")))) - (arguments - '(#:tests? #f)) ;require Documenter, not packaged yet (build-system julia-build-system) (propagated-inputs - `(("julia-macrotools" ,julia-macrotools))) + (list julia-macrotools)) + (native-inputs + (list julia-documenter)) (home-page "https://github.com/FluxML/IRTools.jl") (synopsis "Simple and flexible IR format") (description "This package provides a simple and flexible IR format, @@ -2359,6 +2977,25 @@ extensions to the iterator interface.") "Common functional iterator patterns (formerly @code{Iterators.jl}).") (license license:expat))) +(define-public julia-jive + (package + (name "julia-jive") + (version "0.2.20") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/wookay/Jive.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0khwsdh8472jxcfi9lqw14l49sqlbsixql1jb4irnyajxkdjrcsf")))) + (build-system julia-build-system) + (home-page "https://github.com/wookay/Jive.jl") + (synopsis "Julia package to help with writing tests") + (description "@code{Jive.jl} is a Julia package to help with writing tests.") + (license license:expat))) + (define-public julia-json (package (name "julia-json") @@ -2374,10 +3011,10 @@ extensions to the iterator interface.") (base32 "1f9k613kbknmp4fgjxvjaw4d5sfbx8a5hmcszmp1w9rqfqngjx9m")))) (build-system julia-build-system) (propagated-inputs - `(("julia-datastructures" ,julia-datastructures) - ("julia-fixedpointnumbers" ,julia-fixedpointnumbers) - ("julia-parsers" ,julia-parsers) - ("julia-offsetarrays" ,julia-offsetarrays))) + (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") (description "@code{JSON.jl} is a pure Julia module which supports parsing @@ -2399,18 +3036,40 @@ and printing JSON documents.") (base32 "11z5maz7v50wd99id8z7838higza0cllh2amkdkrlskbri3v2f17")))) (build-system julia-build-system) (propagated-inputs - `(("julia-parsers" ,julia-parsers) - ("julia-structtypes" ,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 focus on speed and slick struct mapping.") (license license:expat))) +(define-public julia-latexstrings + (package + (name "julia-latexstrings") + (version "1.2.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/stevengj/LaTeXStrings.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "117z27krcf8fydgp6mb0pgn75r4gng9qs7v90qb4bqzsry3faadp")))) + (build-system julia-build-system) + (native-inputs + (list julia-documenter)) + (home-page "https://github.com/stevengj/LaTeXStrings.jl") + (synopsis "Input and display of LaTeX equation strings") + (description "This is a small package to make it easier to type LaTeX +equations in string literals in the Julia language.") + (license license:expat))) + (define-public julia-lazyarrays (package (name "julia-lazyarrays") - (version "0.21.14") + (version "0.22.2") (source (origin (method git-fetch) @@ -2419,16 +3078,25 @@ focus on speed and slick struct mapping.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "130kqyfk0h17s9dr9r1p9n1dgvzzlb1jwn6pj14lwr83s36glpv1")))) + (base32 "17rhlrmgfvdw8w62pg32ikr9j4xy2ylr7mx7ar0hnpzryv929rp5")))) (build-system julia-build-system) + (arguments + `(#:phases + ,@(if (target-64bit?) + '(%standard-phases) + '((modify-phases %standard-phases + (add-after 'unpack 'fix-tests-int32-i686 + (lambda _ + (substitute* "test/multests.jl" + (("Int64") "Int32"))))))))) (propagated-inputs - `(("julia-arraylayouts" ,julia-arraylayouts) - ("julia-fillarrays" ,julia-fillarrays) - ("julia-macrotools" ,julia-macrotools) - ("julia-matrixfactorizations" ,julia-matrixfactorizations) - ("julia-staticarrays" ,julia-staticarrays))) + (list julia-arraylayouts + julia-fillarrays + julia-macrotools + julia-matrixfactorizations + julia-staticarrays)) (native-inputs - `(("julia-tracker" ,julia-tracker))) + (list julia-tracker)) (home-page "https://github.com/JuliaArrays/LazyArrays.jl") (synopsis "Lazy arrays and linear algebra") (description "This package supports lazy analogues of array operations like @@ -2451,9 +3119,9 @@ implementation of matrix-free methods for iterative solvers.") (base32 "0rvms3mmq8a1viqlyzdgs2ccddcy6j0c677dlb8m5nk6hkiwr16n")))) (build-system julia-build-system) (propagated-inputs - `(("julia-docstringextensions" ,julia-docstringextensions))) + (list julia-docstringextensions)) (native-inputs - `(("julia-offsetarrays" ,julia-offsetarrays))) + (list julia-offsetarrays)) (home-page "https://github.com/JuliaStats/LogExpFunctions.jl") (synopsis "Special functions based on @code{log} and @code{exp}") (description "Various special functions based on log and exp moved from @@ -2497,12 +3165,21 @@ that let you do deep transformations of code.") (sha256 (base32 "0l5adird8m1cmnsxwhzi5hcr7q9bm1rf7a6018zc7kcn2yxdshy3")))) (build-system julia-build-system) + (arguments + `(#:phases + ,@(if (target-64bit?) + '(%standard-phases) + '((modify-phases %standard-phases + (add-after 'unpack 'fix-tests-int32-i686 + (lambda _ + (substitute* "test/runtests.jl" + (("Int64") "Int32"))))))))) (propagated-inputs - `(("julia-fixedpointnumbers" ,julia-fixedpointnumbers))) + (list julia-fixedpointnumbers)) (native-inputs - `(("julia-colortypes" ,julia-colortypes) - ("julia-fixedpointnumbers" ,julia-fixedpointnumbers) - ("julia-offsetarrays" ,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 @@ -2530,7 +3207,7 @@ comes from the fact that @code{M == map(f, A)}.") (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'skip-failing-test + (add-after 'link-depot 'skip-failing-test (lambda _ ;; Tests with math functions are hard. (substitute* "test/test_ul.jl" @@ -2539,7 +3216,7 @@ comes from the fact that @code{M == map(f, A)}.") (("test String") "test_nowarn String")) #t))))) (propagated-inputs - `(("julia-arraylayouts" ,julia-arraylayouts))) + (list julia-arraylayouts)) (home-page "https://github.com/JuliaMatrices/MatrixFactorizations.jl") (synopsis "Julia package to contain non-standard matrix factorizations") (description "A Julia package to contain non-standard matrix factorizations. @@ -2571,7 +3248,8 @@ may include other factorizations such as the LQ factorization.") (substitute* "test/runtests.jl" (("testhost =") "return #")) #t))))) - (propagated-inputs `(("julia-mbedtls-jll" ,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 @@ -2593,13 +3271,13 @@ TLS} and cryptography C library for Julia.") (base32 "05p3f0gr4sv4maq8cix5fi8ldq0zagswqsd43xn6fhy046f936mz")))) (build-system julia-build-system) (propagated-inputs - `(("julia-calculus" ,julia-calculus) - ("julia-recipesbase" ,julia-recipesbase) - ("julia-requires" ,julia-requires))) + (list julia-calculus + julia-recipesbase + julia-requires)) (native-inputs - `(("julia-quadgk" ,julia-quadgk) - ("julia-specialfunctions" ,julia-specialfunctions) - ("julia-unitful" ,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 @@ -2631,10 +3309,60 @@ expressions involving differing types of units that are then evaluated, resolving them into absolute units.") (license license:expat))) +(define-public julia-media + (package + (name "julia-media") + (version "0.5.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JunoLab/Media.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "05jq9j3vs8yfj2lwz3sh1vk5rha06xdcikp9s2q3dn316vryy6di")))) + (build-system julia-build-system) + ;; Package without Project.toml + (arguments + '(#:julia-package-name "Media" + #:julia-package-uuid "e89f7d12-3494-54d1-8411-f7d8b9ae1f27")) + (propagated-inputs + (list julia-macrotools)) + (home-page "https://github.com/JunoLab/Media.jl") + (synopsis "Unified measure and coordinates types") + (description "This package provides a display system which enables the +user handle multiple input/output devices and decide what media types get +displayed where.") + (license license:expat))) + +(define-public julia-millboard + (package + (name "julia-millboard") + (version "0.2.5") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/wookay/Millboard.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0k9jqgp285qhckldvvsmfk6s69dcr8s74m2fijgm2vxjj2gqjs1n")))) + (build-system julia-build-system) + (native-inputs + (list julia-jive)) + (home-page "https://github.com/wookay/Millboard.jl") + (synopsis "Displaying data in tables for Julia") + (description + "@code{Millboard.jl} provides a library for getting data in a tablized +format to arrange into rows and columns of cells.") + (license license:expat))) + (define-public julia-missings (package (name "julia-missings") - (version "1.0.0") + (version "1.0.2") (source (origin (method git-fetch) @@ -2643,10 +3371,10 @@ resolving them into absolute units.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "131ma44yvswvj85jdjhm37frzfz46cc60lwj65a9jcmgc77dshsm")))) + (base32 "1k481rm5lahmjyh34j177d4n10svgr0wm7ps5m3ar3xx6nr26ad5")))) (build-system julia-build-system) (propagated-inputs - `(("julia-dataapi" ,julia-dataapi))) + (list julia-dataapi)) (home-page "https://github.com/JuliaData/Missings.jl") (synopsis "Additional missing value support for Julia") (description "This package provides additional functionality for working @@ -2668,7 +3396,7 @@ with @code{missing} values in Julia.") (base32 "0h1cd7cr4c4cnpqyj3180113gdbvcc047lqphp8a8gq5smp3c059")))) (build-system julia-build-system) (native-inputs - `(("julia-datastructures" ,julia-datastructures))) + (list julia-datastructures)) (home-page "https://thautwarm.github.io/MLStyle.jl/latest/") (synopsis "Julia functional programming infrastructures") (description "This package provides consistent and extensible functional @@ -2678,7 +3406,7 @@ programming infrastructures, and metaprogramming facilities.") (define-public julia-mocking (package (name "julia-mocking") - (version "0.7.1") + (version "0.7.3") (source (origin (method git-fetch) @@ -2687,10 +3415,11 @@ programming infrastructures, and metaprogramming facilities.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "10jz716v6i3gpd403rmcrip6cncjl9lqr12cdl321x1994a5g8ck")))) + (base32 "1cg2is83bjmrchmmxcgx57k8c9b9vlamrw38v4fdhbb6d4six5cg")))) (build-system julia-build-system) (propagated-inputs - `(("julia-exprtools" ,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 @@ -2714,9 +3443,9 @@ to be temporarily overloaded for the purpose of testing.") (arguments `(#:tests? #f)) ; Cycle with ImageCore.jl (propagated-inputs - `(("julia-mappedarrays" ,julia-mappedarrays) - ("julia-paddedviews" ,julia-paddedviews) - ("julia-stackviews" ,julia-stackviews))) + (list julia-mappedarrays + julia-paddedviews + julia-stackviews)) ;(native-inputs ; `(("julia-colorvectorspace" ,julia-colorvectorspace) ; ("julia-imagecore" ,julia-imagecore))) @@ -2763,8 +3492,24 @@ Julia, with type-driven, overloadable packing/unpacking functionality.") (sha256 (base32 "1isyj8h4nx96cr6892d154v8pw1nhr7mjyz5bd6ffr2mkzb2bq4f")))) (build-system julia-build-system) + (arguments + `(#:phases + ,@(if (target-x86-32?) + '((modify-phases %standard-phases + (add-after 'unpack 'remove-failing-test-i686 + (lambda _ + (substitute* "test/utilities.jl" + ;; Non-deterministic returned value, e.g., + ;; Expression: n == @allocated(f()) + ;; Evaluated: 240 == 120 + ;; and for some other values: + ;; Got correct result, please change to @test + ;; so @test_broken is not enough. + (("@test n == @allocated f\\(\\)") + " ")))))) + '(%standard-phases)))) (propagated-inputs - `(("julia-offsetarrays" ,julia-offsetarrays))) + (list julia-offsetarrays)) (home-page "https://github.com/jump-dev/MutableArithmetics.jl") (synopsis "Interface for arithmetics on mutable types in Julia") (description "MutableArithmetics is a Julia package which allows: @@ -2810,12 +3555,12 @@ still being completely generic (base32 "0n8qh5a2ghjx1j70zxn0hmh8gzpa46kmjg8di879y9974bfk0f98")))) (build-system julia-build-system) (propagated-inputs - `(("julia-diffresults" ,julia-diffresults) - ("julia-finitediff" ,julia-finitediff) - ("julia-forwarddiff" ,julia-forwarddiff))) + (list julia-diffresults + julia-finitediff + julia-forwarddiff)) (native-inputs - `(("julia-optimtestproblems" ,julia-optimtestproblems) - ("julia-recursivearraytools" ,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, @@ -2827,7 +3572,7 @@ interface to interact with these types.") (define-public julia-nnlib (package (name "julia-nnlib") - (version "0.7.25") + (version "0.7.29") (source (origin (method git-fetch) @@ -2836,25 +3581,25 @@ interface to interact with these types.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0vp4kcn9ivkhmqgkyvnabcdqi6pv7ghbmjc1llkwv1kzhylyf86p")))) + (base32 "16vn5w5274kcywh1xp0zqjk5q10xrk125aznz5av6wifwrvghk8s")))) (build-system julia-build-system) (arguments - `(#:tests? #f ; Test suite not updated for ChainRulesTestUtils-1.0. - #:phases + `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'drop-cuda-support + (add-after 'link-depot 'skip-cuda-tests (lambda _ (substitute* "test/runtests.jl" - (("using CUDA") "")) + (("using CUDA") "") + (("&& CUDA\\.functional\\(\\)") "")) (setenv "NNLIB_TEST_CUDA" "false")))))) (propagated-inputs - `(("julia-adapt" ,julia-adapt) - ("julia-chainrulescore" ,julia-chainrulescore) - ("julia-requires" ,julia-requires))) + (list julia-adapt + julia-chainrulescore + julia-requires)) (native-inputs - `(("julia-chainrulestestutils" ,julia-chainrulestestutils) - ("julia-stablerngs" ,julia-stablerngs) - ("julia-zygote" ,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 @@ -2877,7 +3622,8 @@ doesn't provide any other \"high-level\" functionality like layers or AD.") (base32 "10h47x5ws42pkqjccimaz0yxfvz41w0yazq6inamfk4lg5g2g3d9")))) (build-system julia-build-system) (arguments - `(#:julia-package-name "OptimTestProblems")) + `(#:julia-package-name "OptimTestProblems" + #:julia-package-uuid "cec144fc-5a64-5bc6-99fb-dde8f63e154c")) (home-page "https://github.com/JuliaNLSolvers/OptimTestProblems.jl") (synopsis "Collection of optimization test problems") (description "The purpose of this package is to provide test problems for @@ -2921,7 +3667,7 @@ which they were added to the collection.") (base32 "0j5a8ar8yc0j9h87gwfyrcqm23wpyv5yv5gn8vzilpg4vr0fiasc")))) (build-system julia-build-system) (propagated-inputs - `(("julia-adapt" ,julia-adapt))) + (list julia-adapt)) ;; CatIndices depends on OffsetArrays, introducing a recursive dependency (arguments '(#:tests? #f)) (home-page "https://juliaarrays.github.io/OffsetArrays.jl/stable/") @@ -2945,10 +3691,10 @@ languages like Fortran.") (sha256 (base32 "0ran2vj6ahlzib0g77y7g0jhavy3k9s2mqq23ybpgp9z677wf26h")))) (build-system julia-build-system) - (arguments - '(#:tests? #f)) ;require Documenter, not packaged yet (propagated-inputs - `(("julia-offsetarrays" ,julia-offsetarrays))) + (list julia-offsetarrays)) + (native-inputs + (list julia-documenter)) (home-page "https://github.com/JuliaArrays/PaddedViews.jl") (synopsis "Add virtual padding to the edges of an array") (description "@code{PaddedViews} provides a simple wrapper type, @@ -2973,8 +3719,8 @@ Multiple arrays may be \"promoted\" to have common indices using the (base32 "0b8lawi7kcws4axfsdf023gyxca15irl648ciyi1kw3wghz3pfi2")))) (build-system julia-build-system) (propagated-inputs - `(("julia-orderedcollections" ,julia-orderedcollections) - ("julia-unpack" ,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 @@ -3042,8 +3788,8 @@ actual computation.") (base32 "1fd27w9z1vhz0d1bzrs5vcavpb5r5jviyh27d9c4ka37phz4xvmh")))) (build-system julia-build-system) (propagated-inputs - `(("julia-plotutils" ,julia-plotutils) - ("julia-requires" ,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 @@ -3053,7 +3799,7 @@ actual computation.") (define-public julia-plotutils (package (name "julia-plotutils") - (version "1.0.11") + (version "1.0.15") (source (origin (method git-fetch) @@ -3062,14 +3808,14 @@ actual computation.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0pqd3yvs3w48sr50c8rcqk5pzvpdy9nf4kimcvyz9dvwc3jgh6rd")))) + (base32 "12aw5gkkcfhpczv2w510k65w1j0hjnh825ihimi223v8plsi5105")))) (build-system julia-build-system) (propagated-inputs - `(("julia-colors" ,julia-colors) - ("julia-colorschemes" ,julia-colorschemes) - ("julia-reexport" ,julia-reexport))) + (list julia-colors + julia-colorschemes + julia-reexport)) (native-inputs - `(("julia-stablerngs" ,julia-stablerngs))) + (list julia-stablerngs)) (home-page "https://github.com/JuliaPlots/PlotUtils.jl") (synopsis "Helper algorithms for building plotting components") (description "This package contains generic helper algorithms for building @@ -3079,7 +3825,7 @@ plotting components.") (define-public julia-pooledarrays (package (name "julia-pooledarrays") - (version "1.2.1") + (version "1.3.0") (source (origin (method git-fetch) @@ -3088,10 +3834,10 @@ plotting components.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0ihvhzkxdw4qf0i6sbrickhdcwkmlin9zyixxn9xvgzm8nc0iwqy")))) + (base32 "0qdwvf1p5z6z0q4s4hn85ysd8wq47zy6hlzddc5ijvhk86ccqlrr")))) (build-system julia-build-system) (propagated-inputs - `(("julia-dataapi" ,julia-dataapi))) + (list julia-dataapi)) (home-page "https://github.com/JuliaData/PooledArrays.jl") (synopsis "Pooled representation of arrays in Julia") (description "This package provides a pooled representation of arrays for @@ -3113,8 +3859,8 @@ purposes of compression when there are few unique elements.") (base32 "1wxy6ak7f3hvibcgc8q88cgkf9zvi649mmjy1zlkx1qk80hgvz23")))) (build-system julia-build-system) (native-inputs - `(("julia-forwarddiff" ,julia-forwarddiff) - ("julia-reversediff" ,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 @@ -3167,16 +3913,16 @@ everything from run time algorithm choice to code generation at compile time.") (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'skip-color-tests + (add-after 'link-depot 'skip-color-tests (lambda _ (substitute* "test/text_backend.jl" ((".*colors\\.jl.*") "")) #t))))) (propagated-inputs - `(("julia-crayons" ,julia-crayons) - ("julia-formatting" ,julia-formatting) - ("julia-reexport" ,julia-reexport) - ("julia-tables" ,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 @@ -3186,7 +3932,7 @@ human-readable format.") (define-public julia-pycall (package (name "julia-pycall") - (version "1.92.3") + (version "1.92.5") (source (origin (method git-fetch) @@ -3196,7 +3942,7 @@ human-readable format.") (file-name (git-file-name name version)) (sha256 (base32 - "07r99ni6nkxpyrp3wsb5qg4jxz7i2r08dyqbiffy2zm3g0bn88jq")))) + "1fj5d1ihnhnm0pl4hbx6hcd2bpdyhm8jiaqah2axsbd069j70saf")))) (build-system julia-build-system) (arguments `(#:imported-modules ((guix build python-build-system) @@ -3206,7 +3952,7 @@ human-readable format.") ((guix build python-build-system) #:prefix python:)) #:phases (modify-phases %standard-phases - (add-after 'unpack 'remove-conda + (add-after 'link-depot 'remove-conda (lambda _ (substitute* "Project.toml" ((".*Conda.*") "")) @@ -3216,7 +3962,7 @@ human-readable format.") (substitute* "deps/depsutils.jl" (("Conda.PYTHONDIR") "\"/\"")) #t)) - (add-after 'unpack 'set-python + (add-after 'link-depot 'set-python (lambda* (#:key inputs outputs #:allow-other-keys) (let ((python (assoc-ref inputs "python"))) (setenv "PYCALL_JL_RUNTIME_PYTHON" @@ -3243,12 +3989,12 @@ human-readable format.") (setenv "JULIA_PKGEVAL" "true") #t))))) (propagated-inputs - `(("julia-macrotools" ,julia-macrotools) - ("julia-versionparsing" ,julia-versionparsing))) + (list julia-macrotools + julia-versionparsing)) (inputs - `(("python" ,python))) + (list python)) (native-inputs - `(("python-numpy" ,python-numpy))) + (list python-numpy)) (home-page "https://github.com/JuliaPy/PyCall.jl") (synopsis "Call Python functions from the Julia language") (description "This package provides the ability to directly call and fully @@ -3258,6 +4004,35 @@ types between Julia and Python), define Python classes from Julia methods, and share large data structures between Julia and Python without copying them.") (license license:expat))) +(define-public julia-pyplot + (package + (name "julia-pyplot") + (version "2.10.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaPy/PyPlot.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "007zs0imfgs69f30pp2a3rc93kl0qiq7qjx6ig35z4wzkmps4skd")))) + (build-system julia-build-system) + (propagated-inputs + (list julia-colors + julia-latexstrings + julia-pycall + julia-versionparsing + ;; python-matplotlib is expected to be available at runtime. + python-matplotlib)) + (home-page "https://github.com/JuliaPy/PyPlot.jl") + (synopsis "Plotting for Julia based on matplotlib.pyplot") + (description "This package provides a Julia interface to the Matplotlib +plotting library from Python, and specifically to the @code{matplotlib.pyplot} +module. PyPlot uses the Julia PyCall package to call Matplotlib directly from +Julia with little or no overhead (arrays are passed without making a copy).") + (license license:expat))) + (define-public julia-quadgk (package (name "julia-quadgk") @@ -3273,7 +4048,7 @@ share large data structures between Julia and Python without copying them.") (base32 "1hy0629yai6xflgxaflk9764lzr1lzhlghimxk1aqi212q9c6n33")))) (build-system julia-build-system) (propagated-inputs - `(("julia-datastructures" ,julia-datastructures))) + (list julia-datastructures)) (home-page "https://github.com/JuliaMath/QuadGK.jl") (synopsis "Adaptive 1d numerical Gauss–Kronrod integration") (description "This package provides support for one-dimensional numerical @@ -3300,7 +4075,7 @@ arbitrary normed vector spaces (e.g. matrix-valued integrands).") (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'hardcode-libmath-location + (add-after 'link-depot 'hardcode-libmath-location (lambda* (#:key inputs #:allow-other-keys) (let ((gcclib (assoc-ref inputs "gcc:lib"))) (substitute* "src/Quadmath.jl" @@ -3308,11 +4083,11 @@ arbitrary normed vector spaces (e.g. matrix-valued integrands).") (("libquadmath.so.0" lib) (string-append gcclib "/lib/" lib))) #t)))))) (propagated-inputs - `(("julia-requires" ,julia-requires))) + (list julia-requires)) (inputs `(("gcc:lib" ,gcc "lib"))) (native-inputs - `(("julia-specialfunctions" ,julia-specialfunctions))) + (list julia-specialfunctions)) (home-page "https://github.com/JuliaMath/Quadmath.jl") (synopsis "Float128 and libquadmath for the Julia language") (description "This is a Julia interface to @code{libquadmath}, providing a @@ -3335,7 +4110,7 @@ format.") (base32 "1zhynyvchc50hywws2jznpkwydr3njh8cv84d2ylyabhcwwmil9s")))) (build-system julia-build-system) (propagated-inputs - `(("julia-dualnumbers" ,julia-dualnumbers))) + (list julia-dualnumbers)) (home-page "https://github.com/JuliaGeometry/Quaternions.jl") (synopsis "Quaternion and dual-quaternion functionality") (description "Quaternions are best known for their suitability as @@ -3358,9 +4133,9 @@ extension of complex numbers.") (base32 "06zm4cbn3x49lbpgshhdfvvmgz066qkc8q0d57igm5p8bcp6js22")))) (build-system julia-build-system) (propagated-inputs - `(("julia-datastructures" ,julia-datastructures) - ("julia-iteratorinterfaceextensions" ,julia-iteratorinterfaceextensions) - ("julia-tableshowutils" ,julia-tableshowutils))) + (list julia-datastructures + julia-iteratorinterfaceextensions + julia-tableshowutils)) (home-page "https://github.com/queryverse/QueryOperators.jl") (synopsis "Query operators for Julia") (description "This package contains the underlying query operators that are @@ -3449,9 +4224,9 @@ more complex visualizations.") (arguments `(#:tests? #f)) ; Cycle with Plots.jl. (propagated-inputs - `(("julia-nanmath" ,julia-nanmath) - ("julia-plotutils" ,julia-plotutils) - ("julia-recipesbase" ,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 @@ -3479,13 +4254,13 @@ recipes to full specifications for a plot.") (arguments `(#:tests? #f)) ; Cycle with OrdinaryDiffEq.jl. (propagated-inputs - `(("julia-arrayinterface" ,julia-arrayinterface) - ("julia-chainrulescore" ,julia-chainrulescore) - ("julia-docstringextensions" ,julia-docstringextensions) - ("julia-recipesbase" ,julia-recipesbase) - ("julia-requires" ,julia-requires) - ("julia-staticarrays" ,julia-staticarrays) - ("julia-zygoterules" ,julia-zygoterules))) + (list julia-arrayinterface + julia-chainrulescore + julia-docstringextensions + julia-recipesbase + julia-requires + julia-staticarrays + julia-zygoterules)) ;(native-inputs ; `(("julia-forwarddiff" ,julia-forwarddiff) ; ("julia-nlsolve" ,julia-nlsolve) @@ -3501,7 +4276,7 @@ recursive arrays like arrays of arrays.") (define-public julia-reexport (package (name "julia-reexport") - (version "1.1.0") + (version "1.2.2") (source (origin (method git-fetch) @@ -3510,7 +4285,7 @@ recursive arrays like arrays of arrays.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1wj4vnxxmnblm6ajkkdvwb7v4835qrrc406q5is74qv1n68xql7l")))) + (base32 "0inf5q6f01ncd5c5wm8mwzv2hs627ng6xlh8dhrlflp321hbamwf")))) (build-system julia-build-system) (home-page "https://github.com/simonster/Reexport.jl") (synopsis "Re-export modules and symbols") @@ -3534,11 +4309,11 @@ recursive arrays like arrays of arrays.") (arguments `(#:tests? #f)) ; Cycle with ImageCore.jl through ImageMagick.jl. (propagated-inputs - `(("julia-deepdiffs" ,julia-deepdiffs) - ("julia-distances" ,julia-distances) - ("julia-fileio" ,julia-fileio) - ("julia-imagecore" ,julia-imagecore) - ("julia-imageinterminal" ,julia-imageinterminal))) + (list julia-deepdiffs + julia-distances + julia-fileio + julia-imagecore + julia-imageinterminal)) ;(native-inputs ; `(("julia-csvfiles" ,julia-csvfiles) ; ("julia-dataframes" ,julia-dataframes) @@ -3569,10 +4344,12 @@ package can help create and update if need be.") (sha256 (base32 "03hyfy7c0ma45b0y756j76awi3az2ii4bz4s8cxm3xw9yy1z7b01")))) (build-system julia-build-system) + (arguments + `(#:parallel-tests? #f)) (inputs ;required for test - `(("julia-example" ,julia-example))) + (list julia-example)) (propagated-inputs - `(("julia-colors" ,julia-colors))) + (list julia-colors)) (home-page "https://github.com/JuliaPackaging/Requires.jl/") (synopsis "Faster package loader") (description "This package make loading packages faster, maybe. It @@ -3595,18 +4372,24 @@ can be avoided.") (sha256 (base32 "1wrr6sqj2xl9grkvdp88rw3manxy9vbx28zq2wssya5ns1xabsnl")))) (build-system julia-build-system) + (arguments + ;; XXXX: Test suite failing for i686, e.g., + ;; Expression: hash(tr_float, hash(1)) === hash(v_float, hash(1)) + ;; MethodError: no method matching decompose(::ReverseDiff.TrackedReal{Float64, Float64, Nothing}) + ;; Disable as stopgap. + `(#:tests? ,(not (target-x86-32?)))) (propagated-inputs - `(("julia-diffresults" ,julia-diffresults) - ("julia-diffrules" ,julia-diffrules) - ("julia-forwarddiff" ,julia-forwarddiff) - ("julia-functionwrappers" ,julia-functionwrappers) - ("julia-macrotools" ,julia-macrotools) - ("julia-nanmath" ,julia-nanmath) - ("julia-specialfunctions" ,julia-specialfunctions) - ("julia-staticarrays" ,julia-staticarrays))) + (list julia-diffresults + julia-diffrules + julia-forwarddiff + julia-functionwrappers + julia-macrotools + julia-nanmath + julia-specialfunctions + julia-staticarrays)) (native-inputs - `(("julia-difftests" ,julia-difftests) - ("julia-fillarrays" ,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 @@ -3660,11 +4443,11 @@ other power series in @code{h}.") (base32 "01wwqbdmj61yiz7rkmams4xg7gb9hbmg325173846ky4b9x1wb19")))) (build-system julia-build-system) (propagated-inputs - `(("julia-staticarrays" ,julia-staticarrays))) + (list julia-staticarrays)) (native-inputs - `(("julia-benchmarktools" ,julia-benchmarktools) - ("julia-forwarddiff" ,julia-forwarddiff) - ("julia-unitful" ,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 @@ -3692,9 +4475,10 @@ through matrix-vector multiplication.") (base32 "1fb1dfdmiw2ggx60hf70954xlps0r48fcb3k3dvxynlz7ylphp96")))) (build-system julia-build-system) (arguments - `(#:julia-package-name "SafeTestsets")) + `(#:julia-package-name "SafeTestsets" + #:julia-package-uuid "1bc83da4-3b8d-516f-aca4-4fe02f6d838f")) (native-inputs - `(("julia-staticarrays" ,julia-staticarrays))) + (list julia-staticarrays)) (home-page "https://github.com/YingboMa/SafeTestsets.jl") (synopsis "Julia's testset in a module") (description "This package contains the testset from Julia, packaged into @@ -3716,13 +4500,36 @@ a loadable module.") (base32 "0y7kkkj717h5cj659ssry89i5r64symr6pvhr6vv4qmaxrnjxj92")))) (build-system julia-build-system) (propagated-inputs - `(("julia-libsass-jll" ,julia-libsass-jll))) + (list julia-libsass-jll)) (home-page "https://github.com/piever/Sass.jl") (synopsis "Compile scss and sass file to css") (description "This package provides a simple Julian API to use the @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/jakobnissen/ScanByte.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") @@ -3772,6 +4579,31 @@ formatting an array of n things, e.g. numbers, dates, unitful values. It's used 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 "3.4.0") + (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 "0z7m5fykc6r4bxz4hfm6d3v1h7gg0c322l4zv8r3vrb8hrd6h263")))) + (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") @@ -3787,7 +4619,7 @@ in @code{Gadfly}, @code{Plots} and @code{Makie} to label axes and keys.") (base32 "1qvmkqcvhc2nilvkk36szccxdlcv9ls2i0ksxgl2yfjr3b3qlr05")))) (build-system julia-build-system) (propagated-inputs - `(("julia-macrotools" ,julia-macrotools))) + (list julia-macrotools)) (home-page "https://github.com/mauro3/SimpleTraits.jl") (synopsis "Simple Traits for Julia") (description "This package provides a macro-based implementation of traits. @@ -3797,6 +4629,29 @@ types can be added to a trait after the creation of the trait, whereas Union types are fixed after creation.") (license license:expat))) +(define-public julia-softglobalscope + (package + (name "julia-softglobalscope") + (version "1.1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/stevengj/SoftGlobalScope.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1n3l0al1vw5jpb4k9a29a71666cdb617nmiqg34wcmyfzrxpvv39")))) + (build-system julia-build-system) + (home-page "https://github.com/stevengj/SoftGlobalScope.jl") + (synopsis "Utilities for soft global scope in interactive Julia environments") + (description + "SoftGlobalScope is a package for the Julia language that simplifies the +variable scoping rules for code in global scope. It is intended for interactive +shells to make it easier to work interactively with Julia, especially for +beginners.") + (license license:expat))) + (define-public julia-sortingalgorithms (package (name "julia-sortingalgorithms") @@ -3814,7 +4669,7 @@ types are fixed after creation.") (arguments `(#:tests? #f)) ; cycle with StatsBase.jl (propagated-inputs - `(("julia-datastructures" ,julia-datastructures))) + (list julia-datastructures)) ;(native-inputs ; `(("julia-statsbase" ,julia-statsbase))) (home-page "https://github.com/JuliaCollections/SortingAlgorithms.jl") @@ -3839,11 +4694,11 @@ timsort and radixsort.") (base32 "0nfpnglx7zl9g20w2mgfkg17hcw9ri0shaq2rwplj0ij5pwz8yf0")))) (build-system julia-build-system) (inputs - `(("julia-chainrulestestutils" ,julia-chainrulestestutils))) + (list julia-chainrulestestutils)) (propagated-inputs - `(("julia-chainrulescore" ,julia-chainrulescore) - ("julia-logexpfunctions" ,julia-logexpfunctions) - ("julia-openspecfun-jll" ,julia-openspecfun-jll))) + (list julia-chainrulescore + julia-logexpfunctions + julia-openspecfun-jll)) (home-page "https://github.com/JuliaMath/SpecialFunctions.jl") (synopsis "Special mathematical functions") (description "This package provides special mathematical functions, @@ -3867,8 +4722,8 @@ polygamma functions.") (base32 "1qzaqvk57b0s5krzn8bxkzmr5kz6hi9dm3jbf2sl7z4vznsgbn9x")))) (build-system julia-build-system) (propagated-inputs - `(("julia-dictionaries" ,julia-dictionaries) - ("julia-indexing" ,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 @@ -3916,19 +4771,18 @@ some performance improvements).") (base32 "1fwiaxdpx1z9dli3jr8kyraych0jbdiny3qklynf0r13px25r6i7")))) (build-system julia-build-system) (arguments - `(#:tests? #f ; Documenter.jl not packaged yet - #:phases + `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'skip-doctest + (add-after 'link-depot 'skip-doctest (lambda _ (substitute* "test/runtests.jl" ((".*doctest.*") "")) #t))))) (propagated-inputs - `(("julia-offsetarrays" ,julia-offsetarrays))) - ;(native-inputs - ; `(("julia-aqua" ,julia-aqua) - ; ("julia-documenter" ,julia-documenter))) + (list julia-offsetarrays)) + (native-inputs + (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}. @@ -3956,9 +4810,9 @@ There are multiple ways to understand @code{StackView}: (base32 "19k7h47zhz3zz28i0l4b3cc0r07pzp8kf35z0yammpy361b644l2")))) (build-system julia-build-system) (propagated-inputs - `(("julia-ifelse" ,julia-ifelse))) + (list julia-ifelse)) (native-inputs - `(("julia-aqua" ,julia-aqua))) + (list julia-aqua)) (home-page "https://github.com/SciML/Static.jl") (synopsis "Static types useful for dispatch and generated functions") (description "Static.jl defines a limited set of statically parameterized @@ -3968,7 +4822,7 @@ types and a common interface that is shared between them.") (define-public julia-staticarrays (package (name "julia-staticarrays") - (version "1.2.9") + (version "1.2.13") (source (origin (method git-fetch) @@ -3977,10 +4831,10 @@ types and a common interface that is shared between them.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1902bl9p96mfq7d1rbilwp98wz2g82ml9svcgx7sczglyjbs4nsk")))) + (base32 "041mijzgzm8r61a3gwspr2wcxjikqksvj2rbnl4gmcy41alqmx79")))) (build-system julia-build-system) (inputs - `(("julia-benchmarktools" ,julia-benchmarktools))) + (list julia-benchmarktools)) (home-page "https://github.com/JuliaArrays/StaticArrays.jl") (synopsis "Statically sized arrays") (description "This package provides a framework for implementing @@ -4028,13 +4882,13 @@ dependency on it.") (base32 "02y4pm5yvg713a2pn970bbcfkrn2h133rxbxk1da18svhqw3czhi")))) (build-system julia-build-system) (propagated-inputs - `(("julia-dataapi" ,julia-dataapi) - ("julia-datastructures" ,julia-datastructures) - ("julia-missings" ,julia-missings) - ("julia-sortingalgorithms" ,julia-sortingalgorithms) - ("julia-statsapi" ,julia-statsapi))) + (list julia-dataapi + julia-datastructures + julia-missings + julia-sortingalgorithms + julia-statsapi)) (native-inputs - `(("julia-stablerngs" ,julia-stablerngs))) + (list julia-stablerngs)) (home-page "https://github.com/JuliaStats/StatsBase.jl") (synopsis "Basic statistics for Julia") (description "StatsBase.jl is a Julia package that provides basic support @@ -4058,7 +4912,7 @@ ranking, covariances, sampling, and empirical density estimation.") (base32 "0n5707wplbibzhhv1xmshvc025d7xk6mnikclc3hvq5cdc0gy9f7")))) (build-system julia-build-system) (propagated-inputs - `(("julia-distances" ,julia-distances))) + (list julia-distances)) (home-page "https://github.com/matthieugomez/StringDistances.jl") (synopsis "String Distances in Julia") (description "This package provides string distances in Julia. Distances @@ -4067,6 +4921,82 @@ are defined for @code{AbstractStrings}, and any iterator that define 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") + (version "0.6.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaArrays/StructArrays.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0rjcpyjwzg70n87q5r9c5i1qzigavncslxssm3rk5a3y549py56v")))) + (build-system julia-build-system) + (arguments + `(#:phases + ,@(if (target-64bit?) + '(%standard-phases) + '((modify-phases %standard-phases + (add-after 'unpack 'fix-tests-int32-i686 + (lambda _ + (substitute* '("src/utils.jl" + "test/runtests.jl") + (("Int64") "Int32"))))))))) + (propagated-inputs + (list julia-dataapi + julia-staticarrays + julia-tables)) + (native-inputs + (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 +an @code{AbstractArray} whose elements are @code{struct} (for example +@code{NamedTuples}, or @code{ComplexF64}, or a custom user defined +@code{struct}). While a @code{StructArray} iterates @code{structs}, the layout +is column based (meaning each field of the @code{struct} is stored in a separate +@code{Array}).") + (license license:expat))) + (define-public julia-structtypes (package (name "julia-structtypes") @@ -4145,13 +5075,13 @@ the @code{Pluto.jl} tabular data import functionality.") (base32 "1sqqagzqvav8b1rv5ywwbgy9ixvlmipq95fkwfwn0m8769i8jwzb")))) (build-system julia-build-system) (propagated-inputs - `(("julia-dataapi" ,julia-dataapi) - ("julia-datavalueinterfaces" ,julia-datavalueinterfaces) - ("julia-iteratorinterfaceextensions" ,julia-iteratorinterfaceextensions) - ("julia-tabletraits" ,julia-tabletraits))) + (list julia-dataapi + julia-datavalueinterfaces + julia-iteratorinterfaceextensions + julia-tabletraits)) (native-inputs - `(("julia-datavalues" ,julia-datavalues) - ("julia-queryoperators" ,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 @@ -4176,8 +5106,8 @@ interface functions for working with all kinds tabular data.") (base32 "0gp3hpj3jvzfhkp9r345vfic2j2n2s60729wv38hwn75csp74cg5")))) (build-system julia-build-system) (propagated-inputs - `(("julia-datavalues" ,julia-datavalues) - ("julia-json" ,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 @@ -4200,7 +5130,7 @@ participate in the @code{TableTraits.jl} ecosystem.") (base32 "08ssb2630wm6j8f2qa985mn2vfibfm5kjcn4ayl2qkhfcyp8daw4")))) (build-system julia-build-system) (propagated-inputs - `(("julia-iteratorinterfaceextensions" ,julia-iteratorinterfaceextensions))) + (list julia-iteratorinterfaceextensions)) (home-page "https://github.com/queryverse/TableTraits.jl") (synopsis "Traits for Julia tables") (description "TableTraits defines a generic interface for tabular data.") @@ -4246,11 +5176,11 @@ dimensions}.") (arguments `(#:tests? #f)) ; cycle with ImageMagick.jl (propagated-inputs - `(("julia-axisarrays" ,julia-axisarrays) - ("julia-colortypes" ,julia-colortypes) - ("julia-fileio" ,julia-fileio) - ("julia-offsetarrays" ,julia-offsetarrays) - ("julia-stringdistances" ,julia-stringdistances))) + (list julia-axisarrays + julia-colortypes + julia-fileio + julia-offsetarrays + julia-stringdistances)) ;(native-inputs ; `(("julia-colors" ,julia-colors) ; ("julia-fixedpointnumbers" ,julia-fixedpointnumbers) @@ -4282,22 +5212,71 @@ package.") (patches (search-patches "julia-tracker-16-compat.patch")))) (build-system julia-build-system) (propagated-inputs - `(("julia-adapt" ,julia-adapt) - ("julia-diffrules" ,julia-diffrules) - ("julia-forwarddiff" ,julia-forwarddiff) - ("julia-macrotools" ,julia-macrotools) - ("julia-nanmath" ,julia-nanmath) - ("julia-nnlib" ,julia-nnlib) - ("julia-requires" ,julia-requires) - ("julia-specialfunctions" ,julia-specialfunctions))) + (list julia-adapt + julia-diffrules + julia-forwarddiff + julia-macrotools + julia-nanmath + julia-nnlib + julia-requires + julia-specialfunctions)) (native-inputs - `(("julia-pdmats" ,julia-pdmats))) + (list julia-pdmats)) (home-page "https://github.com/FluxML/Tracker.jl") (synopsis "Operator overloading reverse-mode automatic differentiator") (description "@code{Tracker.jl} previously provided @code{Flux.jl} with automatic differentiation for its machine learning platform.") (license license:expat))) +(define-public julia-transcodingstreams + (package + (name "julia-transcodingstreams") + (version "0.9.6") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaIO/TranscodingStreams.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1w3klii293caqiclfh28jggv7f53xclm9fr6xmw38brwrn1hjb48")))) + (build-system julia-build-system) + (arguments + `(#:tests? #f)) ; Circular dependency with various codecs. + (home-page "https://github.com/JuliaIO/TranscodingStreams.jl") + (synopsis "Fast I/O transcoding data streams") + (description "This package provides tools for transcoding data streams +which are: +@itemize +@item fast: small overhead and specialized methods +@item consistent: basic I/O operations work as expected +@item generic: support any I/O objects like files, buffers, pipes, etc. +@item extensible: easy definition for new codec to transcode data +@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/SabrinaJaye/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") @@ -4313,9 +5292,9 @@ automatic differentiation for its machine learning platform.") (base32 "0nk6zhqvl2r8yhjdhb59kxq0srd3vy4ysg4d8rszj9a43dnn3w3i")))) (build-system julia-build-system) (propagated-inputs - `(("julia-adapt" ,julia-adapt) - ("julia-splitapplycombine" ,julia-splitapplycombine) - ("julia-tables" ,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 @@ -4360,6 +5339,7 @@ types, modules, and dictionaries.") (build-system julia-build-system) (arguments '(#:julia-package-name "URIs" ;required to run tests + #:julia-package-uuid "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" #:phases (modify-phases %standard-phases (add-before 'check 'change-dir @@ -4367,10 +5347,10 @@ types, modules, and dictionaries.") (lambda* (#:key source outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) (chdir - (string-append out "/share/julia/packages/URIs/test"))) + (string-append out "/share/julia/loadpath/URIs/test"))) #t))))) ;; required for tests - (inputs `(("julia-json" ,julia-json))) + (inputs (list julia-json)) (home-page "https://github.com/JuliaWeb/URIs.jl") (synopsis "URI parsing in Julia") (description "@code{URIs.jl} is a Julia package that allows parsing and @@ -4392,8 +5372,10 @@ working with @acronym{URIs,Uniform Resource Identifiers}, as defined in RFC (sha256 (base32 "10qwscd15dnmvx116dwvg99m7kmwgmj5ahdkq7psiq48lcc554gq")))) (build-system julia-build-system) + (arguments + `(#:parallel-tests? #f)) (propagated-inputs - `(("julia-constructionbase" ,julia-constructionbase))) + (list julia-constructionbase)) (home-page "https://painterqubits.github.io/Unitful.jl/stable/") (synopsis "Physical units in Julia") (description "This package supports SI units and also many other unit @@ -4440,8 +5422,8 @@ useful in order to support @code{VersionNumber} comparisons applied to (base32 "14h1vdnc3rx87w6v2rr59lgb4kai2hd1wzqpxhmzsi8karg2z219")))) (build-system julia-build-system) (propagated-inputs - `(("julia-dataapi" ,julia-dataapi) - ("julia-parsers" ,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 @@ -4462,6 +5444,16 @@ allows for efficient string representation and transfer") (sha256 (base32 "04yykivi8zrbryxlmb0p5xa6lma8iq22r5s863117dnnqj5gaffd")))) (build-system julia-build-system) + (arguments + `(#:phases + ,@(if (target-x86-32?) + '((modify-phases %standard-phases + (add-after 'unpack 'remove-failing-test-i686 + (lambda _ + (substitute* "test/woodbury.jl" + (("@test logdet\\(W\\)") + "@test_broken logdet(W)")))))) + '(%standard-phases)))) (home-page "https://github.com/timholy/WoodburyMatrices.jl") (synopsis "Support for the Woodbury matrix identity for Julia") (description "This package provides support for the Woodbury matrix identity @@ -4471,6 +5463,31 @@ for floating-point roundoff errors, so be prepared for a certain amount of 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") @@ -4487,7 +5504,7 @@ inaccuracy in the result.") "15bm3ki5mb9nvqs2byznrryq0bilnjcvsfy3k05hxhk9vapilw7k")))) (build-system julia-build-system) (propagated-inputs - `(("julia-zlib-jll" ,julia-zlib-jll))) + (list julia-zlib-jll)) (home-page "https://github.com/fhs/ZipFile.jl") (synopsis "Read/Write ZIP archives in Julia") (description "This module provides support for reading and writing ZIP @@ -4509,7 +5526,7 @@ archives in Julia.") (base32 "07i2mf6rr5b8i6l82qgwl5arsb5pwyyzyfasgnszhdqllk9501bs")))) (build-system julia-build-system) (propagated-inputs - `(("julia-macrotools" ,julia-macrotools))) + (list julia-macrotools)) (home-page "https://github.com/FluxML/ZygoteRules.jl") (synopsis "Add minimal custom gradients to Zygote") (description "Minimal package which enables to add custom gradients to @@ -4533,17 +5550,17 @@ Zygote, without depending on Zygote itself.") (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 |