diff options
Diffstat (limited to 'gnu/packages/julia-xyz.scm')
| -rw-r--r-- | gnu/packages/julia-xyz.scm | 700 |
1 files changed, 586 insertions, 114 deletions
diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 2ad1c4cd5d..e30cf39dc9 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2020, 2021 Nicolò Balzarotti <[email protected]> -;;; Copyright © 2021 Simon Tournier <[email protected]> +;;; Copyright © 2021, 2022 Simon Tournier <[email protected]> ;;; Copyright © 2021 Efraim Flashner <[email protected]> ;;; Copyright © 2021 Vinicius Monego <[email protected]> ;;; Copyright © 2021 jgart <[email protected]> @@ -166,7 +166,9 @@ provides functions to run a few automatable checks for Julia packages.") ;; Disable as stopgap. `(#:tests? ,(not (target-x86-32?)))) (propagated-inputs - (list julia-ifelse julia-requires julia-static)) + (list julia-ifelse + julia-requires + julia-static)) (native-inputs (list julia-aqua julia-bandedmatrices @@ -209,6 +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") @@ -248,9 +278,12 @@ axis (dimension).") (base32 "03kzan1lm4fxfhzv1xjg3ysf6y7nagcc61vfz15kvdrp1dqxlynk")))) (build-system julia-build-system) (propagated-inputs - (list julia-rangearrays julia-intervalsets julia-itertools)) + (list julia-rangearrays + julia-intervalsets + julia-itertools)) (native-inputs - (list julia-offsetarrays julia-unitful)) + (list julia-offsetarrays + julia-unitful)) (home-page "http://juliaarrays.github.io/AxisArrays.jl/latest/") (synopsis "Arrays where each dimension can have a named axis with values") (description "This package for the Julia language provides an array type @@ -276,7 +309,8 @@ axes, allowing column names or interval selections.") (base32 "0rlfj9gr9ss621v5kw5b06206yaak21s2vq9vk7r8a7p2ylncism")))) (build-system julia-build-system) (propagated-inputs - (list julia-arraylayouts julia-fillarrays)) + (list julia-arraylayouts + julia-fillarrays)) (native-inputs (list julia-genericlinearalgebra)) (home-page "https://github.com/JuliaMatrices/BandedMatrices.jl") @@ -318,7 +352,8 @@ the entries on the bands.") (("@test @ballocated\\(Ref\\(1\\)\\)") "@test_broken @ballocated(Ref(1))")))))) '(%standard-phases)))) - (propagated-inputs (list julia-json)) + (propagated-inputs + (list julia-json)) (home-page "https://github.com/JuliaCI/BenchmarkTools.jl") (synopsis "Benchmarking framework for the Julia language") (description "@code{BenchmarkTools.jl} makes performance tracking of Julia @@ -326,6 +361,129 @@ 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") @@ -350,9 +508,12 @@ benchmarks as well as comparing benchmark results.") (substitute* "test/test_blockarrays.jl" (("Int64") "Int32"))))))))) (propagated-inputs - (list julia-arraylayouts julia-fillarrays)) + (list julia-arraylayouts + julia-fillarrays)) (native-inputs - (list julia-lazyarrays julia-offsetarrays julia-staticarrays)) + (list julia-lazyarrays + julia-offsetarrays + julia-staticarrays)) (home-page "https://github.com/JuliaArrays/BlockArrays.jl") (synopsis "BlockArrays for Julia") (description "A block array is a partition of an array into blocks or @@ -383,8 +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 - (list julia-arraylayouts julia-bandedmatrices julia-blockarrays - julia-fillarrays julia-matrixfactorizations)) + (list julia-arraylayouts + julia-bandedmatrices + julia-blockarrays + julia-fillarrays + julia-matrixfactorizations)) (home-page "https://github.com/JuliaMatrices/BlockBandedMatrices.jl") (synopsis "Block-banded matrices and banded-block-banded matrices") (description "This package supports representing block-banded and @@ -437,7 +601,8 @@ structures.") '(#:tests? #f #:julia-package-name "BufferedStreams" #:julia-package-uuid "e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d")) - (propagated-inputs (list julia-compat)) + (propagated-inputs + (list julia-compat)) (home-page "https://github.com/BioJulia/BufferedStreams.jl") (synopsis "Fast composable IO streams") (description "@code{BufferedStreams.jl} provides buffering for IO @@ -514,10 +679,14 @@ variables, both with unordered (nominal variables) and ordered categories (base32 "0if93pd3b3scg2x3gmk1cbwjk0ax1n792vy8c38y3xl7jpd5cb70")))) (build-system julia-build-system) (inputs ;required for test - (list julia-chainrulestestutils julia-finitedifferences julia-nanmath + (list julia-chainrulestestutils + julia-finitedifferences + julia-nanmath julia-specialfunctions)) (propagated-inputs - (list julia-chainrulescore julia-compat julia-reexport + (list julia-chainrulescore + julia-compat + julia-reexport julia-requires)) (home-page "https://github.com/JuliaDiff/ChainRules.jl") (synopsis "Common utilities for automatic differentiation") @@ -541,7 +710,8 @@ execute forward-, reverse-, and mixed-mode primitives.") (base32 "1866xv30h1bi7f2m993nljzf58wwmv8zlgn6ffn9j3wckch1nfpb")))) (build-system julia-build-system) (inputs ;required for tests - (list julia-benchmarktools julia-staticarrays)) + (list julia-benchmarktools + julia-staticarrays)) (propagated-inputs (list julia-compat)) (home-page "https://github.com/JuliaDiff/ChainRulesCore.jl") @@ -565,7 +735,9 @@ sensitivities for functions without the need to depend on ChainRules itself.") (base32 "1vlkyp72d514gyb4k3yhjl1g7f24ncmz61j56p4sdi9f76rk9fx9")))) (build-system julia-build-system) (propagated-inputs - (list julia-chainrulescore julia-compat julia-finitedifferences)) + (list julia-chainrulescore + julia-compat + julia-finitedifferences)) (home-page "https://github.com/JuliaDiff/ChainRulesTestUtils.jl") (synopsis "Common utilities used by downstream automatic differentiation tools") (description "This package is designed to help in testing @@ -604,7 +776,8 @@ dependencies, while keeping @code{ChainRulesCore.jl} as light-weight as possible (find-files out "\\.gz$")) #t)))))) (propagated-inputs - (list julia-zlib-jll julia-transcodingstreams)) + (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 @@ -626,7 +799,9 @@ dependencies, while keeping @code{ChainRulesCore.jl} as light-weight as possible (base32 "0kx3hq7rf8p5zx6ly9k5j90zijmc7yrwmy96cgkl2ibdfbnhmya3")))) (build-system julia-build-system) (propagated-inputs - (list julia-colortypes julia-fixedpointnumbers julia-reexport)) + (list julia-colortypes + julia-fixedpointnumbers + julia-reexport)) (home-page "https://github.com/JuliaGraphics/Colors.jl") (synopsis "Tools for dealing with color") (description "This package provides a wide array of functions for dealing @@ -650,7 +825,9 @@ color scales for graphics.") (base32 "0kpjhmqd5cj8dh8bmh9b5g6bscyp7h23hzpr2s93pnrp57q1wvhq")))) (build-system julia-build-system) (propagated-inputs - (list julia-colors julia-colortypes julia-fixedpointnumbers + (list julia-colors + julia-colortypes + julia-fixedpointnumbers julia-staticarrays)) (home-page "https://github.com/JuliaGraphics/ColorSchemes.jl") (synopsis "Colorschemes, colormaps, gradients, and palettes") @@ -698,7 +875,9 @@ with.") (base32 "02gk7f5g5wjxdasbjf8bvv1m7clksh7mw1xmygjdirjz1q0d6dwi")))) (build-system julia-build-system) (propagated-inputs - (list julia-colortypes julia-specialfunctions julia-tensorcore)) + (list julia-colortypes + julia-specialfunctions + julia-tensorcore)) (native-inputs (list julia-colors)) (home-page "https://github.com/JuliaGraphics/ColorVectorSpace.jl") @@ -810,7 +989,9 @@ way.") (substitute* "test/runtests.jl" (("Int64") "Int32"))))))))) (propagated-inputs - (list julia-crayons julia-expronicon julia-orderedcollections)) + (list julia-crayons + julia-expronicon + julia-orderedcollections)) (home-page "https://configurations.rogerluo.dev/stable/") (synopsis "Tools for options and configurations in Julia") (description "@code{Configurations.jl} provides a macro @code{@@option} to @@ -855,7 +1036,9 @@ for construction of objects.") (propagated-inputs (list julia-staticarrays)) (native-inputs - (list julia-documenter julia-forwarddiff julia-unitful)) + (list julia-documenter + julia-forwarddiff + julia-unitful)) (home-page "https://github.com/JuliaGeometry/CoordinateTransformations.jl") (synopsis "Coordinate transformations in Julia") (description "@code{CoordinateTransformations} is a Julia package to manage @@ -985,7 +1168,8 @@ Julia from R or Python.") (sha256 (base32 "0hdqp8ipsqdw5bqqkdvz4j6n67x80sj5azr9vzyxwjfsgkfbnk2l")))) (propagated-inputs - (list julia-compat julia-orderedcollections)) + (list julia-compat + julia-orderedcollections)) (build-system julia-build-system) (arguments `(#:phases @@ -1136,7 +1320,8 @@ dictionaries in Julia, for improved productivity and performance.") (propagated-inputs (list julia-statsapi)) (native-inputs - (list julia-offsetarrays julia-unitful)) + (list julia-offsetarrays + julia-unitful)) (home-page "https://github.com/JuliaStats/Distances.jl") (synopsis "Julia package for evaluating distances (metrics) between vectors") (description "A Julia package for evaluating distances(metrics) between @@ -1193,9 +1378,8 @@ valuable enough at this time.") (lambda* (#:key inputs #:allow-other-keys) (substitute* "src/Deps.jl" (("pip install") - (string-append (assoc-ref inputs "python") - "/bin/pip install"))) - #t)) + (string-append (search-input-file inputs "bin/pip") + " install"))))) (add-after 'link-depot 'remove-javascript-downloads (lambda _ (substitute* "src/Writers/HTMLWriter.jl" @@ -1203,17 +1387,18 @@ valuable enough at this time.") ;; Removing the javascript downloads causes these tests fail. (substitute* "test/examples/tests.jl" ((".*Main\\.examples_html_doc.*") "") - ((".*Main\\.examples_html_mathjax3_doc.*") "")) - #t))))) + ((".*Main\\.examples_html_mathjax3_doc.*") ""))))))) (propagated-inputs - (list julia-ansicoloredprinters julia-docstringextensions - julia-iocapture julia-json)) + (list julia-ansicoloredprinters + julia-docstringextensions + julia-iocapture + julia-json)) (inputs - `(("python" ,python-wrapper))) + (list python-wrapper)) (native-inputs - `(("git" ,git-minimal) - ("julia-documentermarkdown" ,julia-documentermarkdown) - ("julia-documentertools" ,julia-documentertools))) + (list git-minimal + julia-documentermarkdown + julia-documentertools)) (home-page "https://juliadocs.github.io/Documenter.jl") (synopsis "Documentation generator for Julia") (description "This package provides a documentation generator for Julia.") @@ -1276,9 +1461,11 @@ 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 - (list julia-docstringextensions julia-gumbo julia-sass)) + (list julia-docstringextensions + julia-gumbo + julia-sass)) (native-inputs (list julia-example)) (home-page "https://github.com/JuliaDocs/DocumenterTools.jl") @@ -1300,9 +1487,9 @@ generation with @code{Documenter.jl}.") (file-name (git-file-name name version)) (sha256 (base32 "1w6p3yxajvclax5b9g7cr2jmbc7lvr5nk4gq0aljxdycdq1d2y3v")))) + (build-system julia-build-system) (propagated-inputs (list julia-staticarrays)) - (build-system julia-build-system) (home-page "https://github.com/JuliaDiff/DiffResults.jl") (synopsis "In-place differentiation methods of primal values at multi-order") (description "This package provides the @code{DiffResult} type, which can @@ -1322,9 +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 - (list julia-nanmath julia-specialfunctions)) (build-system julia-build-system) + (propagated-inputs + (list julia-nanmath + julia-specialfunctions)) (home-page "https://github.com/JuliaDiff/DiffRules.jl") (synopsis "Primitive differentiation rules") (description "This package provides primitive differentiation rules that @@ -1376,7 +1564,9 @@ stressing the robustness of differentiation tools.") ;; Seems to not play nicely with SpecialFunctions ((".*isempty.*") ""))))))) (propagated-inputs - (list julia-calculus julia-nanmath julia-specialfunctions)) + (list julia-calculus + julia-nanmath + julia-specialfunctions)) (home-page "https://github.com/JuliaDiff/DualNumbers.jl") (synopsis "Represent dual numbers and for perform dual algebra") (description "The @code{DualNumbers} Julia package defines the @code{Dual} @@ -1506,7 +1696,8 @@ performant tooling without requiring additional package dependencies.") (base32 "1ldxbp0kq3ip67x7sp82dz56aq4p5i0chspbgx2zgskr6jcbjj1b")))) (build-system julia-build-system) (propagated-inputs - (list julia-ffmpeg-jll julia-x264-jll)) + (list julia-ffmpeg-jll + julia-x264-jll)) (home-page "https://github.com/JuliaIO/FFMPEG.jl") (synopsis "Julia Package for ffmpeg") (description "This package is made to be included into packages that just @@ -1552,7 +1743,9 @@ need the ffmpeg binaries + executables, and don't want the overhead of (propagated-inputs (list julia-requires)) (native-inputs - (list julia-colortypes julia-filepathsbase julia-http)) + (list julia-colortypes + julia-filepathsbase + julia-http)) (home-page "https://github.com/JuliaIO/FileIO.jl") (synopsis "Main Package for IO, loading all different kind of files") (description "@code{FileIO} aims to provide a common framework for detecting @@ -1632,9 +1825,12 @@ following types: @code{Eye}, @code{Fill}, @code{Ones}, @code{Zeros}, (setenv "GROUP" "Core") #t))))) (propagated-inputs - (list julia-arrayinterface julia-requires julia-staticarrays)) + (list julia-arrayinterface + julia-requires + julia-staticarrays)) (native-inputs - (list julia-bandedmatrices julia-blockbandedmatrices + (list julia-bandedmatrices + julia-blockbandedmatrices julia-safetestsets)) (home-page "https://github.com/JuliaDiff/FiniteDiff.jl") (synopsis "Calculations of gradients, Jacobians, and Hessians") @@ -1672,7 +1868,9 @@ types and sparsity.") (inputs (list julia-benchmarktools)) (propagated-inputs - (list julia-chainrulescore julia-richardson julia-staticarrays)) + (list julia-chainrulescore + julia-richardson + julia-staticarrays)) (home-page "https://github.com/JuliaDiff/FiniteDifferences.jl") (synopsis "Estimates derivatives with finite differences") (description "This package calculates approximate derivatives numerically @@ -1702,7 +1900,8 @@ using finite difference.") ;; A deprecation warning is not thrown (("@test_logs.*:warn" all) (string-append "# " all))) #t))))) - (propagated-inputs (list julia-compat)) + (propagated-inputs + (list julia-compat)) (home-page "https://github.com/JuliaMath/FixedPointNumbers.jl") (synopsis "Fixed point types for Julia") (description "@code{FixedPointNumbers.jl} implements fixed-point number @@ -1755,7 +1954,8 @@ c-style numerical formatting.") ;; Disable as stopgap. `(#:tests? ,(not (target-x86-32?)))) (inputs ;required for tests - (list julia-calculus julia-difftests)) + (list julia-calculus + julia-difftests)) (propagated-inputs (list julia-commonsubexpressions julia-diffresults @@ -1953,7 +2153,9 @@ matrices the Schur form is often more useful.") (substitute* "test/runtests.jl" (("Int64") "Int32"))))))))) (propagated-inputs - (list julia-itertools julia-staticarrays julia-structarrays + (list julia-itertools + julia-staticarrays + julia-structarrays julia-tables)) (native-inputs (list julia-offsetarrays)) @@ -2003,7 +2205,8 @@ visualisation applications.") (base32 "10h1s09v7qkvrjr6l678zamb1p248n8jv4rrwkf8g7d2bpfz9amn")))) (build-system julia-build-system) (propagated-inputs - (list julia-colors julia-nanmath)) + (list julia-colors + julia-nanmath)) (home-page "https://github.com/JuliaGraphics/Graphics.jl") (synopsis "Base graphics in Julia") (description "@code{Graphics.jl} is an abstraction layer for graphical @@ -2025,7 +2228,8 @@ operations in Julia.") (base32 "1g22dv3v7caakspv3pdahnqn937fzzsg9y87rj72hid9g8lxl1gm")))) (build-system julia-build-system) (propagated-inputs - (list julia-abstracttrees julia-gumbo-jll)) + (list julia-abstracttrees + julia-gumbo-jll)) (home-page "https://github.com/JuliaWeb/Gumbo.jl") (synopsis "Julia wrapper around Google's gumbo C library for parsing HTML") (description "@code{Gumbo.jl} is a Julia wrapper around Google's gumbo @@ -2077,10 +2281,13 @@ library for parsing HTML.") (string-append all "return\n"))) #t))))) (propagated-inputs - (list julia-inifile julia-mbedtls julia-uris)) + (list julia-inifile + julia-mbedtls + julia-uris)) ;; required for tests (inputs - (list julia-json julia-bufferedstreams)) + (list julia-json + julia-bufferedstreams)) (home-page "https://juliaweb.github.io/HTTP.jl/") (synopsis "HTTP support for Julia") (description "@code{HTTP.jl} is a Julia library for HTTP Messages, @@ -2148,7 +2355,9 @@ conditional ifelse. It is similar to @code{Core.ifelse} but it is extendable.") (base32 "15zqxani1jjh8849s7rdps6b6prqdwv8yxx893y536vkpk7i07qd")))) (build-system julia-build-system) (propagated-inputs - (list julia-axisarrays julia-imagecore julia-reexport + (list julia-axisarrays + julia-imagecore + julia-reexport julia-simpletraits)) (native-inputs (list julia-unitful)) @@ -2176,7 +2385,8 @@ such arrays easy via traits.") (arguments `(#:tests? #f)) ; Cycle with ImageMagick.jl. (propagated-inputs - (list julia-imagecore julia-reexport)) + (list julia-imagecore + julia-reexport)) ;(native-inputs ; `(("julia-imagemagick" ,julia-imagemagick) ; ("julia-offsetarrays" ,julia-offsetarrays) @@ -2248,7 +2458,10 @@ of packages designed to support image processing and computer vision.") (arguments `(#:tests? #f)) ; Cycle with ReferenceTests.jl. (propagated-inputs - (list julia-crayons julia-imagebase julia-imagecore julia-requires)) + (list julia-crayons + julia-imagebase + julia-imagecore + julia-requires)) ;(native-inputs ; `(("julia-coordinatetransformations" ,julia-coordinatetransformations) ; ("julia-imagemagick" ,julia-imagemagick) @@ -2294,7 +2507,9 @@ be downscaled to fit into the size of your active terminal session.") (("test (B == map)" _ test) (string-append "test_nowarn " test))) #t))))) (propagated-inputs - (list julia-fileio julia-imagecore julia-imagemagick-jll)) + (list julia-fileio + julia-imagecore + julia-imagemagick-jll)) (native-inputs (list julia-colors julia-colorvectorspace @@ -2325,10 +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 - (list julia-axisarrays julia-imageaxes julia-imagecore + (list julia-axisarrays + julia-imageaxes + julia-imagecore julia-indirectarrays)) (native-inputs - (list julia-offsetarrays julia-simpletraits julia-unitful)) + (list julia-offsetarrays + julia-simpletraits + julia-unitful)) (home-page "https://github.com/JuliaImages/ImageMetadata.jl") (synopsis "Julia package for images having metadata") (description "@code{ImageMetadata} is a simple package providing utilities @@ -2355,8 +2574,11 @@ information about the detector used to acquire the image.") (arguments `(#:tests? #f)) ; cycle with ImageMagick.jl. (propagated-inputs - (list julia-fileio julia-imagebase julia-imagecore - julia-offsetarrays julia-stackviews)) + (list julia-fileio + julia-imagebase + julia-imagecore + julia-offsetarrays + julia-stackviews)) ;(native-inputs ; `(("julia-imagedistances" ,julia-imagedistances) ; ("julia-imagemagick" ,julia-imagemagick) @@ -2406,6 +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") @@ -2442,7 +2697,9 @@ out of dictionaries, tuples, etc, extending this ability beyond (base32 "0l0jq0jnr9z3k431ni82xycq7mqapgxrbrx4yyk6lycvi41ipm4s")))) (build-system julia-build-system) (native-inputs - (list julia-colors julia-fixedpointnumbers julia-mappedarrays)) + (list julia-colors + julia-fixedpointnumbers + julia-mappedarrays)) (home-page "https://github.com/JuliaArrays/IndirectArrays.jl") (synopsis "Julia implementation of indexed arrays") (description "An @code{IndirectArray} is one that encodes data using a @@ -2534,7 +2791,9 @@ interfaces with @file{.ini} files.") julia-staticarrays julia-woodburymatrices)) (native-inputs - (list julia-dualnumbers julia-forwarddiff julia-offsetarrays + (list julia-dualnumbers + julia-forwarddiff + julia-offsetarrays julia-unitful julia-zygote)) (home-page "https://github.com/JuliaMath/Interpolations.jl") (synopsis "Continuous interpolation of discrete datasets") @@ -2583,6 +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") @@ -2727,7 +3011,9 @@ extensions to the iterator interface.") (base32 "1f9k613kbknmp4fgjxvjaw4d5sfbx8a5hmcszmp1w9rqfqngjx9m")))) (build-system julia-build-system) (propagated-inputs - (list julia-datastructures julia-fixedpointnumbers julia-parsers + (list julia-datastructures + julia-fixedpointnumbers + julia-parsers julia-offsetarrays)) (home-page "https://github.com/JuliaIO/JSON.jl") (synopsis "JSON parsing and printing library for Julia") @@ -2750,7 +3036,8 @@ and printing JSON documents.") (base32 "11z5maz7v50wd99id8z7838higza0cllh2amkdkrlskbri3v2f17")))) (build-system julia-build-system) (propagated-inputs - (list julia-parsers julia-structtypes)) + (list julia-parsers + julia-structtypes)) (home-page "https://github.com/quinnj/JSON3.jl") (synopsis "JSON package for Julia") (description "This package provides another JSON package for Julia, with a @@ -2803,8 +3090,11 @@ equations in string literals in the Julia language.") (substitute* "test/multests.jl" (("Int64") "Int32"))))))))) (propagated-inputs - (list julia-arraylayouts julia-fillarrays julia-macrotools - julia-matrixfactorizations julia-staticarrays)) + (list julia-arraylayouts + julia-fillarrays + julia-macrotools + julia-matrixfactorizations + julia-staticarrays)) (native-inputs (list julia-tracker)) (home-page "https://github.com/JuliaArrays/LazyArrays.jl") @@ -2887,7 +3177,9 @@ that let you do deep transformations of code.") (propagated-inputs (list julia-fixedpointnumbers)) (native-inputs - (list julia-colortypes julia-fixedpointnumbers julia-offsetarrays)) + (list julia-colortypes + julia-fixedpointnumbers + julia-offsetarrays)) (home-page "https://github.com/JuliaArrays/MappedArrays.jl") (synopsis "Lazy in-place transformations of arrays") (description "This package implements \"lazy\" in-place elementwise @@ -2956,7 +3248,8 @@ may include other factorizations such as the LQ factorization.") (substitute* "test/runtests.jl" (("testhost =") "return #")) #t))))) - (propagated-inputs (list julia-mbedtls-jll)) + (propagated-inputs + (list julia-mbedtls-jll)) (home-page "https://github.com/JuliaLang/MbedTLS.jl") (synopsis "Apache's mbed TLS library wrapper") (description "@code{MbedTLS.jl} provides a wrapper around the @code{mbed @@ -2978,9 +3271,13 @@ TLS} and cryptography C library for Julia.") (base32 "05p3f0gr4sv4maq8cix5fi8ldq0zagswqsd43xn6fhy046f936mz")))) (build-system julia-build-system) (propagated-inputs - (list julia-calculus julia-recipesbase julia-requires)) + (list julia-calculus + julia-recipesbase + julia-requires)) (native-inputs - (list julia-quadgk julia-specialfunctions julia-unitful)) + (list julia-quadgk + julia-specialfunctions + julia-unitful)) (home-page "https://juliaphysics.github.io/Measurements.jl/stable/") (synopsis "Error propagation calculator and library") (description "@code{Measurements.jl} is an error propagation calculator and @@ -3121,7 +3418,8 @@ programming infrastructures, and metaprogramming facilities.") (base32 "1cg2is83bjmrchmmxcgx57k8c9b9vlamrw38v4fdhbb6d4six5cg")))) (build-system julia-build-system) (propagated-inputs - (list julia-compat julia-exprtools)) + (list julia-compat + julia-exprtools)) (home-page "https://github.com/invenia/Mocking.jl") (synopsis "Overload Julia function calls") (description "The purpose of this package is to allow Julia function calls @@ -3145,7 +3443,9 @@ to be temporarily overloaded for the purpose of testing.") (arguments `(#:tests? #f)) ; Cycle with ImageCore.jl (propagated-inputs - (list julia-mappedarrays julia-paddedviews julia-stackviews)) + (list julia-mappedarrays + julia-paddedviews + julia-stackviews)) ;(native-inputs ; `(("julia-colorvectorspace" ,julia-colorvectorspace) ; ("julia-imagecore" ,julia-imagecore))) @@ -3255,9 +3555,12 @@ still being completely generic (base32 "0n8qh5a2ghjx1j70zxn0hmh8gzpa46kmjg8di879y9974bfk0f98")))) (build-system julia-build-system) (propagated-inputs - (list julia-diffresults julia-finitediff julia-forwarddiff)) + (list julia-diffresults + julia-finitediff + julia-forwarddiff)) (native-inputs - (list julia-optimtestproblems julia-recursivearraytools)) + (list julia-optimtestproblems + julia-recursivearraytools)) (home-page "https://github.com/JuliaNLSolvers/NLSolversBase.jl") (synopsis "Optimization and equation solver software in JuliaNLSolvers") (description "This package aims at establishing common ground for Optim.jl, @@ -3290,9 +3593,13 @@ interface to interact with these types.") (("&& CUDA\\.functional\\(\\)") "")) (setenv "NNLIB_TEST_CUDA" "false")))))) (propagated-inputs - (list julia-adapt julia-chainrulescore julia-requires)) + (list julia-adapt + julia-chainrulescore + julia-requires)) (native-inputs - (list julia-chainrulestestutils julia-stablerngs julia-zygote)) + (list julia-chainrulestestutils + julia-stablerngs + julia-zygote)) (home-page "https://github.com/FluxML/NNlib.jl") (synopsis "Neural Network primitives with multiple backends") (description "This package will provide a library of functions useful for @@ -3412,7 +3719,8 @@ Multiple arrays may be \"promoted\" to have common indices using the (base32 "0b8lawi7kcws4axfsdf023gyxca15irl648ciyi1kw3wghz3pfi2")))) (build-system julia-build-system) (propagated-inputs - (list julia-orderedcollections julia-unpack)) + (list julia-orderedcollections + julia-unpack)) (home-page "https://github.com/mauro3/Parameters.jl") (synopsis "Numerical-model parameter helpers") (description "This package contains types with default field values, keyword @@ -3480,7 +3788,8 @@ actual computation.") (base32 "1fd27w9z1vhz0d1bzrs5vcavpb5r5jviyh27d9c4ka37phz4xvmh")))) (build-system julia-build-system) (propagated-inputs - (list julia-plotutils julia-requires)) + (list julia-plotutils + julia-requires)) (home-page "https://github.com/JuliaPlots/PlotThemes.jl") (synopsis "Themes for the Julia plotting package Plots.jl") (description @@ -3502,7 +3811,9 @@ actual computation.") (base32 "12aw5gkkcfhpczv2w510k65w1j0hjnh825ihimi223v8plsi5105")))) (build-system julia-build-system) (propagated-inputs - (list julia-colors julia-colorschemes julia-reexport)) + (list julia-colors + julia-colorschemes + julia-reexport)) (native-inputs (list julia-stablerngs)) (home-page "https://github.com/JuliaPlots/PlotUtils.jl") @@ -3548,7 +3859,8 @@ purposes of compression when there are few unique elements.") (base32 "1wxy6ak7f3hvibcgc8q88cgkf9zvi649mmjy1zlkx1qk80hgvz23")))) (build-system julia-build-system) (native-inputs - (list julia-forwarddiff julia-reversediff)) + (list julia-forwarddiff + julia-reversediff)) (home-page "https://github.com/timholy/PositiveFactorizations.jl") (synopsis "Positive-definite \"approximations\" to matrices") (description "@code{PositiveFactorizations} is a package for computing a @@ -3607,7 +3919,10 @@ everything from run time algorithm choice to code generation at compile time.") ((".*colors\\.jl.*") "")) #t))))) (propagated-inputs - (list julia-crayons julia-formatting julia-reexport julia-tables)) + (list julia-crayons + julia-formatting + julia-reexport + julia-tables)) (home-page "https://github.com/ronisbr/PrettyTables.jl") (synopsis "Print data in formatted tables") (description "This package has the purpose to print data in matrices in a @@ -3674,7 +3989,8 @@ human-readable format.") (setenv "JULIA_PKGEVAL" "true") #t))))) (propagated-inputs - (list julia-macrotools julia-versionparsing)) + (list julia-macrotools + julia-versionparsing)) (inputs (list python)) (native-inputs @@ -3817,7 +4133,8 @@ extension of complex numbers.") (base32 "06zm4cbn3x49lbpgshhdfvvmgz066qkc8q0d57igm5p8bcp6js22")))) (build-system julia-build-system) (propagated-inputs - (list julia-datastructures julia-iteratorinterfaceextensions + (list julia-datastructures + julia-iteratorinterfaceextensions julia-tableshowutils)) (home-page "https://github.com/queryverse/QueryOperators.jl") (synopsis "Query operators for Julia") @@ -3907,7 +4224,9 @@ more complex visualizations.") (arguments `(#:tests? #f)) ; Cycle with Plots.jl. (propagated-inputs - (list julia-nanmath julia-plotutils julia-recipesbase)) + (list julia-nanmath + julia-plotutils + julia-recipesbase)) (home-page "http://juliaplots.org/RecipesPipeline.jl/dev/") (synopsis "Utilities for processing recipes") (description "This package was factored out of @code{Plots.jl} to allow any @@ -3990,7 +4309,10 @@ recursive arrays like arrays of arrays.") (arguments `(#:tests? #f)) ; Cycle with ImageCore.jl through ImageMagick.jl. (propagated-inputs - (list julia-deepdiffs julia-distances julia-fileio julia-imagecore + (list julia-deepdiffs + julia-distances + julia-fileio + julia-imagecore julia-imageinterminal)) ;(native-inputs ; `(("julia-csvfiles" ,julia-csvfiles) @@ -4066,7 +4388,8 @@ can be avoided.") julia-specialfunctions julia-staticarrays)) (native-inputs - (list julia-difftests julia-fillarrays)) + (list julia-difftests + julia-fillarrays)) (home-page "https://github.com/JuliaDiff/ReverseDiff.jl") (synopsis "Reverse Mode Automatic Differentiation for Julia") (description "@code{ReverseDiff.jl} is a fast and compile-able tape-based @@ -4122,7 +4445,9 @@ other power series in @code{h}.") (propagated-inputs (list julia-staticarrays)) (native-inputs - (list julia-benchmarktools julia-forwarddiff julia-unitful)) + (list julia-benchmarktools + julia-forwarddiff + julia-unitful)) (home-page "https://github.com/JuliaGeometry/Rotations.jl") (synopsis "Julia implementations for different rotation parameterisations") (description "This package implements various 3D rotation parameterizations @@ -4182,6 +4507,29 @@ a loadable module.") @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") @@ -4231,6 +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") @@ -4323,7 +4696,8 @@ timsort and radixsort.") (inputs (list julia-chainrulestestutils)) (propagated-inputs - (list julia-chainrulescore julia-logexpfunctions + (list julia-chainrulescore + julia-logexpfunctions julia-openspecfun-jll)) (home-page "https://github.com/JuliaMath/SpecialFunctions.jl") (synopsis "Special mathematical functions") @@ -4348,7 +4722,8 @@ polygamma functions.") (base32 "1qzaqvk57b0s5krzn8bxkzmr5kz6hi9dm3jbf2sl7z4vznsgbn9x")))) (build-system julia-build-system) (propagated-inputs - (list julia-dictionaries julia-indexing)) + (list julia-dictionaries + julia-indexing)) (home-page "https://github.com/JuliaData/SplitApplyCombine.jl") (synopsis "Split-apply-combine strategies for Julia") (description "@code{SplitApplyCombine.jl} provides high-level, generic tools @@ -4406,7 +4781,8 @@ some performance improvements).") (propagated-inputs (list julia-offsetarrays)) (native-inputs - (list julia-aqua julia-documenter)) + (list julia-aqua + julia-documenter)) (home-page "https://github.com/JuliaArrays/StackViews.jl") (synopsis "No more catcat") (description "StackViews provides only one array type: @code{StackView}. @@ -4506,8 +4882,11 @@ dependency on it.") (base32 "02y4pm5yvg713a2pn970bbcfkrn2h133rxbxk1da18svhqw3czhi")))) (build-system julia-build-system) (propagated-inputs - (list julia-dataapi julia-datastructures julia-missings - julia-sortingalgorithms julia-statsapi)) + (list julia-dataapi + julia-datastructures + julia-missings + julia-sortingalgorithms + julia-statsapi)) (native-inputs (list julia-stablerngs)) (home-page "https://github.com/JuliaStats/StatsBase.jl") @@ -4542,6 +4921,38 @@ 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") @@ -4567,10 +4978,15 @@ applied to any distance.") "test/runtests.jl") (("Int64") "Int32"))))))))) (propagated-inputs - (list julia-dataapi julia-staticarrays julia-tables)) + (list julia-dataapi + julia-staticarrays + julia-tables)) (native-inputs - (list julia-documenter julia-offsetarrays julia-pooledarrays - julia-typedtables julia-weakrefstrings)) + (list julia-documenter + julia-offsetarrays + julia-pooledarrays + julia-typedtables + julia-weakrefstrings)) (home-page "https://github.com/JuliaArrays/StructArrays.jl") (synopsis "Efficient implementation of struct arrays in Julia") (description "This package introduces the type @code{StructArray} which is @@ -4659,10 +5075,13 @@ the @code{Pluto.jl} tabular data import functionality.") (base32 "1sqqagzqvav8b1rv5ywwbgy9ixvlmipq95fkwfwn0m8769i8jwzb")))) (build-system julia-build-system) (propagated-inputs - (list julia-dataapi julia-datavalueinterfaces - julia-iteratorinterfaceextensions julia-tabletraits)) + (list julia-dataapi + julia-datavalueinterfaces + julia-iteratorinterfaceextensions + julia-tabletraits)) (native-inputs - (list julia-datavalues julia-queryoperators)) + (list julia-datavalues + julia-queryoperators)) (home-page "https://github.com/JuliaData/Tables.jl") (synopsis "Interface for tables in Julia") (description "The @code{Tables.jl} package provides simple, yet powerful @@ -4687,7 +5106,8 @@ interface functions for working with all kinds tabular data.") (base32 "0gp3hpj3jvzfhkp9r345vfic2j2n2s60729wv38hwn75csp74cg5")))) (build-system julia-build-system) (propagated-inputs - (list julia-datavalues julia-json)) + (list julia-datavalues + julia-json)) (home-page "https://github.com/queryverse/TableShowUtils.jl") (synopsis "Implement show for TableTraits.jl types") (description "This package provides some common helper functions that make @@ -4756,8 +5176,11 @@ dimensions}.") (arguments `(#:tests? #f)) ; cycle with ImageMagick.jl (propagated-inputs - (list julia-axisarrays julia-colortypes julia-fileio - julia-offsetarrays julia-stringdistances)) + (list julia-axisarrays + julia-colortypes + julia-fileio + julia-offsetarrays + julia-stringdistances)) ;(native-inputs ; `(("julia-colors" ,julia-colors) ; ("julia-fixedpointnumbers" ,julia-fixedpointnumbers) @@ -4833,6 +5256,27 @@ which are: @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") @@ -4848,7 +5292,9 @@ which are: (base32 "0nk6zhqvl2r8yhjdhb59kxq0srd3vy4ysg4d8rszj9a43dnn3w3i")))) (build-system julia-build-system) (propagated-inputs - (list julia-adapt julia-splitapplycombine julia-tables)) + (list julia-adapt + julia-splitapplycombine + julia-tables)) (home-page "https://github.com/JuliaData/TypedTables.jl") (synopsis "Column-based storage for data analysis in Julia") (description "@code{TypedTables.jl} provides two column-based storage @@ -4976,7 +5422,8 @@ useful in order to support @code{VersionNumber} comparisons applied to (base32 "14h1vdnc3rx87w6v2rr59lgb4kai2hd1wzqpxhmzsi8karg2z219")))) (build-system julia-build-system) (propagated-inputs - (list julia-dataapi julia-parsers)) + (list julia-dataapi + julia-parsers)) (home-page "https://github.com/JuliaData/WeakRefStrings.jl") (synopsis "Efficient string representation and transfer in Julia") (description "This package provides a minimal String type for Julia that @@ -5016,6 +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") @@ -5078,17 +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 |