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gn: Upstream julia packages

wip-kaleido
Efraim Flashner 2 months ago
parent
commit
6b7e7e6299
Signed by: efraim GPG Key ID: 41AAE7DCCA3D8351
  1. 2
      VERSION
  2. 245
      gn/packages/julia.scm

2
VERSION

@ -1 +1 @@
7b59508ca711d1fe299de3f8d9710da36aeb6829
03f6a44cfc46cd49886d7a7ec6429cc22dd97c9c

245
gn/packages/julia.scm

@ -202,36 +202,6 @@ leave-one-chromosome-out}, computation of kinship matrices, and support for
distributed computing.")
(license license:gpl3)))
;; ready to upstream
(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
`(("julia-colors" ,julia-colors)
("julia-latexstrings" ,julia-latexstrings)
("julia-pycall" ,julia-pycall)
("julia-versionparsing" ,julia-versionparsing)
;; python-matplotlib is expected to be available at runtime.
("python-matplotlib" ,(S "python-matplotlib"))))
(home-page "https://github.com/JuliaPy/PyPlot.jl")
(synopsis "Plotting for Julia based on matplotlib.pyplot")
(description "This module 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-conda
(package
(name "julia-conda")
@ -292,29 +262,6 @@ Julia with little or no overhead (arrays are passed without making a copy).")
(description "This package allows one to use @code{conda} as a cross-platform binary provider for Julia for other Julia packages, especially to install binaries that have complicated dependencies like Python.")
(license license:expat)))
;; ready to upstream
(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
`(("julia-documenter" ,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-distributions
(package
(name "julia-distributions")
@ -458,84 +405,6 @@ optimization of functions.")
(description "Plots is a plotting API and toolset.")
(license license:expat)))
;; ready to upstream
(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
`(("julia-dataframes" ,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)))
;; ready to upstream
(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 'unpack '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
`(("julia-dataapi" ,julia-dataapi)
("julia-invertedindices" ,julia-invertedindices)
("julia-iteratorinterfaceextensions" ,julia-iteratorinterfaceextensions)
("julia-missings" ,julia-missings)
("julia-pooledarrays" ,julia-pooledarrays)
("julia-prettytables" ,julia-prettytables)
("julia-reexport" ,julia-reexport)
("julia-sortingalgorithms" ,julia-sortingalgorithms)
("julia-tables" ,julia-tables)
("julia-tabletraits" ,julia-tabletraits)))
(native-inputs
`(("julia-categoricalarrays" ,julia-categoricalarrays)
("julia-combinatorics" ,julia-combinatorics)
("julia-datastructures" ,julia-datastructures)
("julia-datavalues" ,julia-datavalues)
("julia-offsetarrays" ,julia-offsetarrays)
("julia-unitful" ,julia-unitful)))
(home-page "https://dataframes.juliadata.org/stable/")
(synopsis "In-memory tabular data")
(description "Tools for working with tabular data in Julia.")
(license license:expat)))
;; TODO: unbundle javascript calls to cdn.jsdelivr.net
(define-public julia-pluto
(package
@ -611,85 +480,6 @@ dependencies between them and takes care of execution.")
native to Julia. Use it with the @code{@@bind} macro in Pluto.")
(license license:expat)))
;; ready to upstream
(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 'unpack 'fix-tests
(lambda _
(substitute* "test/runtests.jl"
(("option.toml") "test/option.toml"))
#t))
(add-after 'unpack '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"))
#t)))))
(propagated-inputs
`(("julia-crayons" ,julia-crayons)
("julia-expronicon" ,julia-expronicon)
("julia-orderedcollections" ,julia-orderedcollections)))
(home-page "https://configurations.rogerluo.dev/stable/")
(synopsis "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)))
;; ready to upstream
;; 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 'unpack 'skip-network-tests
(lambda _
(substitute* "test/runtests.jl"
;; This test tries to access the Julia package registry.
((".*expand\\.jl.*") "")))))))
(propagated-inputs
`(("julia-mlstyle" ,julia-mlstyle)))
(native-inputs
`(("julia-documenter" ,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)))
;; ready to upstream
(define-public julia-statsfuns
(package
@ -1169,41 +959,6 @@ that still support Julia versions older than 1.6.")
(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)))
;; ready to upstream
(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)
(propagated-inputs
`(("julia-dataapi" ,julia-dataapi)
("julia-staticarrays" ,julia-staticarrays)
("julia-tables" ,julia-tables)))
(native-inputs
`(("julia-documenter" ,julia-documenter)
("julia-offsetarrays" ,julia-offsetarrays)
("julia-pooledarrays" ,julia-pooledarrays)
("julia-typedtables" ,julia-typedtables)
("julia-weakrefstrings" ,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-earcut-jll
;; Only release tag contains just a license file.
(let ((commit "b234ae0c064af12eb5482c7474a64af8be0f511e")

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