(define-module (gn packages julia)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix gexp)
#:use-module (guix utils)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix build-system gnu)
#:use-module (guix build-system julia)
#:use-module (guix build-system trivial)
#:use-module (gnu packages)
#:use-module (gn packages cran)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages compression)
#:use-module (gnu packages cran)
#:use-module (gnu packages julia-jll)
#:use-module (gnu packages julia-xyz)
#:use-module (gnu packages python)
#:use-module (gnu packages statistics)
#:use-module (gnu packages version-control)
#:use-module (gnu packages video)
#:use-module (ice-9 match))
(define S specification->package)
(define-public julia-visuals
(let ((commit "e8e2b601f40a76c8f20f0ddfe80c56257dd9a294")
(revision "3"))
(package
(name "julia-visuals")
(version (git-version "0.0.0" revision commit))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/sens/visuals")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "0lm9yhk0mq5cvvkcbsgcjc1y7fzhr8qz2nxn38cy1zdxd8vfknsx"))))
(build-system julia-build-system)
(arguments
`(#:tests? #f ; no test suite
#:phases
(modify-phases %standard-phases
(delete 'link-depot) ; Not really needed on this package.
(add-after 'unpack 'patch-source
(lambda* (#:key inputs #:allow-other-keys)
(chmod "runpluto.sh" #o555) ; it starts as #o444
(substitute* "runpluto.sh"
;; The arguments don't pass through the wrapper so we hardcode the port.
(("\\$\\{1\\}") "4343"))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(mkdir-p (string-append out "/bin"))
;; Copied from the Dockerfile.
(for-each
(lambda (file)
(copy-recursively file (string-append out "/" file)))
(list "plutoserver"
"environment.yml"
"setup.py"
"runpluto.sh"
"runsliderserver.sh"
"notebooks"
"Project.toml")))))
(add-after 'install 'wrap-program
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
;; Do we need to wrap this with PYTHONPATH too?
(wrap-script (string-append out "/runpluto.sh")
`("PATH" ":" prefix (,(string-append (assoc-ref inputs "julia") "/bin")
,(string-append (assoc-ref inputs "coreutils") "/bin")))
`("JULIA_LOAD_PATH" ":" prefix (,(getenv "JULIA_LOAD_PATH"))))
(wrap-script (string-append out "/runsliderserver.sh")
`("PATH" ":" prefix (,(string-append (assoc-ref inputs "julia") "/bin")
,(string-append (assoc-ref inputs "coreutils") "/bin")))
`("JULIA_LOAD_PATH" ":" prefix (,(getenv "JULIA_LOAD_PATH")))))))
(add-after 'install 'create-runpluto
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(with-output-to-file (string-append out "/bin/runpluto")
(lambda ()
(format #t "#!~a --no-auto-compile
!#
(setenv \"JULIA_LOAD_PATH\" \"~a\")
(setenv \"PATH\" \"~a\")
(zero? (system*
\"~a\"
\"--project=/home/jovyan\"
\"--optimize=0\"
\"-e\" \"import Pluto;
Pluto.run(
host=\\\"0.0.0.0\\\",
port=4343,
launch_browser=false,
require_secret_for_open_links=false;
require_secret_for_access=false)\"))\n"
(search-input-file inputs "/bin/guile")
(getenv "JULIA_LOAD_PATH")
(dirname (search-input-file inputs "/bin/yes"))
(search-input-file inputs "/bin/julia"))))
(chmod (string-append out "/bin/runpluto") #o555))))
(add-after 'install 'create-runsliderserver
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(with-output-to-file (string-append out "/bin/runsliderserver")
(lambda ()
(format #t "#!~a --no-auto-compile
!#
(setenv \"JULIA_LOAD_PATH\" \"~a\")
(setenv \"PATH\" \"~a\")
;; First initialise or update the julia registry:
(zero? (system* \"~a\"
\"--optimize=0\"
;; Used by L1-penalty.jl:
;; \"-e\" \"import Pkg; Pkg.add(\\\"PlotlyBase\\\")\"
\"-e\" \"import Pkg; Pkg.update()\"))
(zero? (system* \"~a\"
\"--optimize=0\"
\"-e\" \"import PlutoSliderServer;
PlutoSliderServer.run_directory(
\\\"~a/notebooks/\\\",
SliderServer_port=4343,
SliderServer_host=\\\"0.0.0.0\\\")\"))\n"
(search-input-file inputs "/bin/guile")
(getenv "JULIA_LOAD_PATH")
(dirname (search-input-file inputs "/bin/yes"))
(search-input-file inputs "/bin/julia")
(search-input-file inputs "/bin/julia")
out)))
(chmod (string-append out "/bin/runsliderserver") #o555))))
(replace 'precompile
(lambda _
(invoke "julia" "-e" "\"import Pkg; Pkg.instantiate(); Pkg.status(); Pkg.precompile()\""))))))
#;
(propagated-inputs
;; This doesn't seem to actually be used anywhere
`(;; from setup.py
("python-jupyter-server-proxy"
,(@ (gn packages python) python-jupyter-server-proxy-1))))
(inputs
;; Ideally we'd use more of these packages, but we end up downloading
;; most of them anyway when the service starts, so we've commented them
;; out for now.
(list ;julia-cairomakie ; 0.8.13
;julia-distributions ; 0.25.76
;julia-interactiveutils ; stdlib
;julia-latexstrings ; 1.3.0
;julia-markdown ; stdlib
;julia-optim ; 1.7.2
;julia-plots ; 1.35.3
;julia-pluto ; 0.19.11
julia-plutosliderserver ; *
;julia-plutoui ; 0.7.46
;julia-prettytables ; 2.1.0
;julia-quadgk ; 2.5.0
;julia-roots ; 2.0.3
(@ (gnu packages guile) guile-3.0))) ; for wrap-script
(home-page "https://github.com/sens/visuals")
(synopsis "Visualizations using Pluto.jl notebooks")
(description "Visualizations using Pluto.jl notebooks.")
(license #f))))
(define-public julia-liteqtl
(let ((commit "696218524a57a4ab5a933e516850c010915650d5")
(revision "1"))
(package
(name "julia-liteqtl")
;(version (git-version "0.2.1" revision commit))
(version "0.2.1")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/senresearch/LiteQTL.jl")
;(commit commit)))
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0hincjnr56wpcgnd9r1m939gng8ac46zw1fv99ij920w3dpxwhq3"))))
(build-system julia-build-system)
(propagated-inputs
`(;("julia-csv" ,julia-csv)
;("julia-cuda" ,julia-cuda)
("julia-dataframes" ,julia-dataframes)
("julia-distributions" ,julia-distributions)
("julia-docstringextensions" ,julia-docstringextensions)))
(native-inputs
`(("julia-documenter" ,julia-documenter)
("julia-safetestsets" ,julia-safetestsets)
;("r" ,r-minimal)
;("r-data-table" ,r-data-table)
;("r-parallel" ,r-parallel) ; what is this package called?
;("r-qtl" ,r-qtl)
;("r-qtl2" ,r-qtl2)
;("r-tidyverse" ,r-tidyverse)
))
(home-page "https://github.com/senresearch/LiteQTL.jl")
(synopsis "Julia package for eQTL genome scans near real-time")
(description "LiteQTL is a package that runs whole genome QTL scans near
real-time, utilizing the computation power of GPU. LiteQTL uses new algorithms
that enables near-real time whole genome QTL scans for up to 1 million traits.
By using easily parallelizable operations including matrix multiplication,
vectorized operations, and element-wise operations, our method is about 300
times faster than a R/qtl linear model genome scan using 16 threads.")
(license license:expat))))
;; contains bundled libraries?
(define-public julia-packagecompiler
(package
(name "julia-packagecompiler")
(version "1.3.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaLang/PackageCompiler.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1ks7g8cvyc81yj6knkrdcxkkm3rdw61jx1h3nqn2n289p5xxfv26"))))
(build-system julia-build-system)
(arguments
`(#:tests? #f)) ; Test suite needs a copy of the Julia package repository.
(native-inputs
`(("julia-example" ,julia-example)))
(home-page "https://github.com/JuliaLang/PackageCompiler.jl")
(synopsis "Compile your Julia Package")
(description "PackageCompiler is a Julia package with two main purposes:
@itemize
@item Creating custom sysimages for reduced latency when working locally with
packages that has a high startup time.
@item Creating \"apps\" which are a bundle of files including an executable that
can be sent and run on other machines without Julia being installed on that machine.
@end itemize")
(license license:expat)))
(define-public julia-flxqtl
(package
(name "julia-flxqtl")
(version "0.3.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/senresearch/FlxQTL.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "06mzbiv8bp0hgkz2i67ax63xcs5wkbyw80cz3s9snwd1426v2r41"))))
(build-system julia-build-system)
(arguments
`(#:tests? #f
))
(propagated-inputs
`(
("julia-distributions" ,julia-distributions)
;("julia-lossfunctions" ,julia-lossfunctions)
("julia-pyplot" ,julia-pyplot)
;("julia-revise" ,julia-revise)
("julia-staticarrays" ,julia-staticarrays)
("julia-statsbase" ,julia-statsbase)
))
(home-page "https://github.com/senresearch/FlxQTL.jl")
(synopsis "QTL analysis tool by multivariate mixed linear model")
(description "FlxQTL.jl is a a package for a multivariate linear mixed model
based QTL analysis tool that supports incorporating information from trait
covariates such as time or different environments. The package supports
computation of one-dimensional and two-dimensional multivariate genome scans,
visualization of genome scans, support for @acronym{LOCO,
leave-one-chromosome-out}, computation of kinship matrices, and support for
distributed computing.")
(license license:gpl3)))
(define-public julia-conda
(package
(name "julia-conda")
(version "1.5.2")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaPy/Conda.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"01qxrv3xv7b979j760iyn28w3hlls29b2parjginwi81jbzr1vgd"))))
(build-system julia-build-system)
(arguments
`(#:tests? #f ; Tests involve downloading Conda packages.
#:phases
(modify-phases %standard-phases
;(delete 'precompile)
(add-after 'link-depot 'hardcode-conda-path
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "src/Conda.jl"
(("bin_dir\\(ROOTENV\\), \"conda\"") (string-append "\"" (assoc-ref inputs "conda") "/bin/\", \"conda\"")))))
(add-before 'check 'pre-check
(lambda* (#:key inputs #:allow-other-keys)
;(setenv "CONDA_JL_HOME" (string-append (assoc-ref inputs "conda") ))
;(setenv "CONDA_JL_VERSION" "3")
;(setenv "CONDA_JL_USE_MINIFORGE" "false")
;(display (getcwd))
;(setenv "HOME" (getcwd))
;(invoke "conda" "create" "--offline" "--use-local" "-n" "conda_jl" "python" "conda")
;(invoke "ls")
;(invoke "pwd")
;(with-output-to-file "deps/deps.jl"
; (lambda () #t))
;(invoke "touch" "deps/deps.jl")
;(invoke "julia" "-e" "using Pkg; Pkg.add(\"Conda\")")
;(invoke "julia" "-e" "using Pkg; Pkg.build(\"Conda\")")
;; From .travis.yml
;(setenv "CONDA_JL_VERSION" "3")
;(setenv "CONDA_JL_USE_MINIFORGE" "false")
#t)))
))
(native-inputs
`(
("conda" ,(S "conda"))
;("python" ,(S "python-wrapper"))
))
(propagated-inputs
`(
("julia-json" ,julia-json)
("julia-versionparsing" ,julia-versionparsing)
))
(home-page "https://github.com/JuliaPy/Conda.jl")
(synopsis "Conda managing Julia binary dependencies")
(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)))
(define-public julia-distributions
(package
(name "julia-distributions")
(version "0.25.80")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaStats/Distributions.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0nqlnkh8grxfm8d1mivi7dnrvb31bznj9s540a10d2v396ikfggn"))))
(build-system julia-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'adjust-tests
(lambda _
;; Something about logpdf fails in both of these test sets.
(substitute* "test/multivariate/dirichlet.jl"
(("\\@testset \"_logpdf\" begin")
"@testset \"_logpdf\" begin return;"))
(substitute* "test/univariate/discrete/negativebinomial.jl"
;; The negative numbers something something wrong in logpdf.
(("0, 10, 42, -1, -5, -13") "0, 10, 42")))))))
(propagated-inputs
(list julia-chainrulescore ; 1
julia-densityinterface ; 0.4
julia-fillarrays ; 0.9 .. 0.13
julia-pdmats ; 0.10, 0.11
julia-quadgk ; 2
julia-specialfunctions ; 1.2, 2
julia-statsbase ; 0.32, 0.33
julia-statsfuns)) ; 0.9.15, 1
(native-inputs
(list julia-calculus
julia-chainrulestestutils
julia-finitedifferences
julia-forwarddiff
julia-json
julia-offsetarrays
julia-stablerngs
julia-staticarrays))
(home-page "https://github.com/JuliaStats/Distributions.jl")
(synopsis "Probability distributions and associated functions")
(description "Julia package for probability distributions and associated
functions. Particularly, @code{Distributions} implements:
@enumerate
@item Moments (e.g mean, variance, skewness, and kurtosis), entropy, and other
properties
@item Probability density/mass functions (pdf) and their logarithm (logpdf)
@item Moment generating functions and characteristic functions
@item Sampling from population or from a distribution
@item Maximum likelihood estimation
@end enumerate")
(license license:expat)))
(define-public julia-fromfile
(package
(name "julia-fromfile")
(version "0.1.5")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/Roger-luo/FromFile.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0jn394294d4s1fqsfiwpiy6dzlca4ciy54l2xviwyzhvixmlfrwn"))))
(build-system julia-build-system)
(arguments
'(#:tests? #f)) ; Tests require network access
(propagated-inputs
(list julia-requires))
(home-page "https://github.com/Roger-luo/FromFile.jl")
(synopsis "Julia enhancement proposal for implicit per file module in Julia")
(description "This package exports a macro @code{@@from}, which can be used
to import objects from files.")
(license license:expat)))
(define-public julia-git
(package
(name "julia-git")
(version "1.2.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaVersionControl/Git.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0bznzg360cbvbzzpsdkin4dm2v980sb5pv58gy1bp3j9j8bj38h6"))))
(build-system julia-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'disable-network-tests
(lambda _
(substitute* "test/runtests.jl"
(("testset.*Git.jl.*" all)
(string-append all " return\n"))))))))
(propagated-inputs
(list julia-git-jll))
(home-page "https://github.com/JuliaVersionControl/Git.jl")
(synopsis "Use command-line Git in your Julia packages")
(description "Git.jl allows you to use command-line Git in your Julia
packages. You do not need to have Git installed on your computer, and neither
do the users of your packages!")
(license license:expat)))
(define-public julia-git-jll
(package
(name "julia-git-jll")
(version "2.36.1+2")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaBinaryWrappers/Git_jll.jl")
(commit (string-append "Git-v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1n8k363q2mw5qfkagbbqpn4djx181qbn05l7brp3spspvf5aslgm"))))
(build-system julia-build-system)
(arguments
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
(substitute* wrapper
(("generate_wrapper_header.*")
(string-append
"generate_wrapper_header(\"Git\", \""
(assoc-ref inputs "git-minimal") "\")\n"))))
;; There's a Julia file for each platform, override them all
(find-files "src/wrappers/" "\\.jl$")))))))
(inputs
(list git-minimal))
(propagated-inputs
(list julia-jllwrappers
julia-expat-jll
julia-openssl-jll
;julia-libcurl-jll
julia-libiconv-jll
;julia-pcre2-jll
julia-zlib-jll))
(home-page "https://github.com/JuliaBinaryWrappers/Git_jll.jl")
(synopsis "Git library wrappers")
(description "This package provides a wrapper for the git library.")
(license license:expat)))
(define-public julia-glob
(package
(name "julia-glob")
(version "1.3.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/vtjnash/Glob.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "05yp7ba3y3pfibs0hy2sp61phb5b6x7aacsjc93i3lz6wmlpj0jx"))))
(build-system julia-build-system)
(home-page "https://github.com/vtjnash/Glob.jl")
(synopsis "Posix-compliant file name pattern matching")
(description "This implementation of Glob is based on the IEEE Std 1003.1,
2004 Edition (Open Group Base Specifications Issue 6) for fnmatch and glob.")
(license license:expat)))
(define-public julia-terminalloggers
(package
(name "julia-terminalloggers")
(version "0.1.7")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaLogging/TerminalLoggers.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "01l9qsjljwa9pkpvf1pafmbrncjddwdw3737pf44y9q5hrp4hbr7"))))
(build-system julia-build-system)
(propagated-inputs
(list julia-leftchildrightsiblingtrees
julia-progresslogging))
(home-page "https://github.com/JuliaLogging/TerminalLoggers.jl")
(synopsis "Logging sinks and utilites for interactive terminals")
(description "TerminalLoggers provides a logger type @code{TerminalLogger}
which can format your log messages in a richer way than the default
@code{ConsoleLogger} which comes with the julia standard @code{Logging}
library.")
(license license:expat)))
(define-public julia-roots
(package
(name "julia-roots")
(version "2.0.3")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaMath/Roots.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "17d62r8pib3cp73az00iz8nbnd5j0y3dl1mrmcssnj4ln8043056"))))
(build-system julia-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'disable-expensive-tests
(lambda _
(substitute* "test/runtests.jl"
((".*test_composable.*") "")))))))
(propagated-inputs
(list julia-commonsolve
julia-setfield))
(native-inputs
(list julia-benchmarktools
julia-forwarddiff
julia-json
julia-specialfunctions))
(home-page "http://juliamath.github.io/Roots.jl/")
(synopsis "Root finding functions for Julia")
(description "This package contains simple routines for finding roots, or
zeros, of scalar functions of a single real variable using floating-point
math.")
(license license:expat)))
(define-public julia-commonsolve
(package
(name "julia-commonsolve")
(version "0.2.4")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/SciML/CommonSolve.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1w05fp02g5cmqzqp96hcpriwjpqx61sl481rj92gf4y4xpinmdf5"))))
(build-system julia-build-system)
(home-page "https://docs.sciml.ai/CommonSolve/stable")
(synopsis "Common solve function for scientific machine learning")
(description "This holds the common @code{solve}, @code{init},
@code{step!}, and @code{solve!} commands. By using the same definition, solver
libraries from other completely different ecosystems can extend the functions
and thus not clash with SciML if both ecosystems export the @code{solve}
command. The rules are that you must dispatch on one of your own types.")
(license license:expat)))
(define-public julia-setfield
(package
(name "julia-setfield")
(version "1.1.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/jw3126/Setfield.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0vdn9s639f120560599m4lhqkk0nsx7qa87fv2mixs1faaihsf6l"))))
(build-system julia-build-system)
(arguments
`(#:tests? #f)) ; Skip tests, not all dependencies packaged.
(propagated-inputs
(list julia-constructionbase
julia-macrotools
julia-staticarrayscore))
(home-page "https://github.com/jw3126/Setfield.jl")
(synopsis "Update deeply nested immutable structs")
(description "Update deeply nested immutable structs.")
(license license:expat)))
(define-public julia-staticarrayscore
(package
(name "julia-staticarrayscore")
(version "1.4.2")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaArrays/StaticArraysCore.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0m573mxvf0y9h7y8rxrk35haphhqisplx159r77g30qvw7zwpgar"))))
(build-system julia-build-system)
(home-page "https://github.com/JuliaArrays/StaticArraysCore.jl")
(synopsis "Interface package for StaticArrays.jl")
(description
"This package provides an interface package for @code{StaticArrays.jl}.")
(license license:expat)))
(define-public julia-progresslogging
(package
(name "julia-progresslogging")
(version "0.1.4")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaLogging/ProgressLogging.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0ysixnl7wjdykaka892jrhsay2aivpch83h8dnfs43z2xynf9sqn"))))
(build-system julia-build-system)
(native-inputs
(list julia-offsetarrays))
(home-page "https://github.com/JuliaLogging/ProgressLogging.jl")
(synopsis "Define progress logs")
(description "ProgressLogging.jl is a package for defining progress logs.
It can be used to report progress of a loop/loops with time-consuming body.")
(license license:expat)))
(define-public julia-leftchildrightsiblingtrees
(package
(name "julia-leftchildrightsiblingtrees")
(version "0.2.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaCollections/LeftChildRightSiblingTrees.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1rijr0yqmbzhlk668v4rqw5xmxxzqvgziasyqrd6z837376mfyy6"))))
(build-system julia-build-system)
(propagated-inputs
(list julia-abstracttrees))
(home-page "https://github.com/JuliaCollections/LeftChildRightSiblingTrees.jl")
(synopsis "Representation of a tree with arbitrary number of children/node")
(description "A left child, right sibling tree (frequently abbreviated as
\"LCRS\") is a rooted tree data structure that allows a parent node to have
multiple child nodes. Rather than maintain a list of children (which requires
one array per node), instead it is represented as a binary tree, where the
\"left\" branch is the first child, whose \"right\" branch points to its first
sibling.")
(license license:expat)))
;; ready to upstream
(define-public julia-densityinterface
(package
(name "julia-densityinterface")
(version "0.4.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaMath/DensityInterface.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "10yr69lndh4jdyhjnpm421zvbw8v48bimxjawz05lqkd7k4w4lw6"))))
(build-system julia-build-system)
(propagated-inputs
(list julia-inversefunctions))
(native-inputs
(list julia-documenter))
(home-page "https://github.com/JuliaMath/DensityInterface.jl")
(synopsis "Interface for mathematical/statistical densities")
(description "This package defines an interface for mathematical/statistical
densities and objects associated with a density in Julia.")
(license license:expat)))
(define-public julia-plots
(package
(name "julia-plots")
(version "1.35.6")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaPlots/Plots.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "005za8a8al822xr0cz4yi1rm23qj1lzy9iw93vvhwq76x3n8bfpy"))))
(build-system julia-build-system)
(arguments
`(#:tests? #f ; for now
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'adjust-tests
(lambda _
;; Decrease the number of tests we're running.
(substitute* "test/runtests.jl"
((".*VisualRegressionTests.*") "")
((".*pgfplotsx.*") "")
((".*plotlyjs.*") "")
))))
))
(propagated-inputs
(list julia-contour
julia-ffmpeg
julia-fixedpointnumbers
julia-gr
julia-geometrybasics
julia-jlfzf
julia-json
;julia-latexify
julia-measures
julia-nanmath
julia-plotthemes
julia-plotutils
julia-recipesbase
julia-recipespipeline
julia-reexport
julia-relocatablefolders
julia-requires
julia-scratch
julia-showoff
julia-snoopprecompile
julia-statsbase
julia-unicodefun
julia-unzip))
(native-inputs
(list julia-aqua
julia-colors
;julia-conda
julia-distributions
julia-fileio
julia-filepathsbase
;julia-gaston
julia-geometrybasics
;julia-gtk
;julia-hdf5
julia-imagemagick
;julia-images
;julia-inspectdr
julia-offsetarrays
;julia-pgfplotsx
;julia-plotlybase
;julia-plotlyjs
;julia-plotlykaleido
julia-pycall
julia-pyplot
;julia-rdatasets
julia-sentinelarrays
julia-stablerngs
julia-staticarrays
;julia-statsplots
julia-testimages
julia-unicodeplots
julia-unitful
;julia-visualregressiontests
))
(home-page "http://docs.juliaplots.org/")
(synopsis "Powerful convenience for Julia visualizations and data analysis")
(description "Plots is a plotting API and toolset.")
(license license:expat)))
(define-public julia-contour
(package
(name "julia-contour")
(version "0.5.7")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaGeometry/Contour.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0ai6lh5ap9qxhqm2k1pnkfbpm4b95d3v7izhyvrr9cxwbxfjv3vn"))))
(build-system julia-build-system)
(arguments `(#:tests? #f)) ;; FIX ME
(propagated-inputs
(list julia-staticarrays))
(native-inputs
(list julia-offsetarrays
julia-statsbase))
(home-page "https://github.com/JuliaGeometry/Contour.jl")
(synopsis "Calculating contour curves for 2D scalar fields in Julia")
(description "This package provides a generic implementation of the
@url{https://en.wikipedia.org/wiki/Marching_squares, marching squares}
algorithm for tracing contour curves on a scalar 2D field.")
(license license:expat)))
(define-public julia-unicodeplots
(package
(name "julia-unicodeplots")
(version "2.12.4")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaPlots/UnicodePlots.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0plkczznx1297m1lviczkm4873yl29anr5csgyhh9vnvyf1606y2"))))
(build-system julia-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'adjust-tests
(lambda _
;; It is unclear why these tests fail and why some
;; have a suprise dependency on AstroIO (from FileIO)
(substitute* "test/runtests.jl"
((".*tst_world_age.*") "")
((".*tst_io.*") "")
((".*tst_densityplot.*") ""))
(substitute* "test/tst_canvas.jl"
((".*HeatmapCanvas, \"heatmap\".*") ""))
(substitute* "test/tst_histogram.jl"
(("testset.*keyword.*" all)
(string-append all " return;\n"))
(("testset.*vertical\".*" all)
(string-append all " return;\n")))
(substitute* "test/tst_barplot.jl"
(("testset.*maximum.*" all)
(string-append all " return;\n")))
(substitute* "test/tst_spy.jl"
(("testset.*parameters.*" all)
(string-append all " return;\n")))
(substitute* "test/tst_boxplot.jl"
(("testset.*default.*" all)
(string-append all " return;\n"))
(("testset.*scaling.*" all)
(string-append all " return;\n")))
(substitute* "test/tst_volume.jl"
(("testset.*cube.*" all)
(string-append all " return;\n"))))))))
(propagated-inputs
(list julia-colortypes
julia-contour
julia-crayons
julia-fileio
julia-freetypeabstraction
julia-lazymodules
julia-marchingcubes
julia-nanmath
julia-staticarrays
julia-statsbase
julia-unitful))
(native-inputs
(list julia-colortypes
julia-imagemagick
julia-referencetests
julia-stablerngs))
(home-page "https://github.com/JuliaPlots/UnicodePlots.jl")
(synopsis "Unicode-based scientific plotting for working in the terminal")
(description "Advanced Unicode plotting library designed for use in Julia's REPL.")
(license license:expat)))
(define-public julia-lazymodules
(package
(name "julia-lazymodules")
(version "0.3.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/johnnychen94/LazyModules.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "11xz0aw5w338pka9jf3r7mfhgm98fnqzsky5ig9z7b996z0m7lpk"))))
(build-system julia-build-system)
(native-inputs
(list julia-colors
julia-offsetarrays))
(home-page "https://github.com/johnnychen94/LazyModules.jl")
(synopsis "Lazily load Julia modules")
(description "This package provides package developers an alternative
option to delay package loading until used. If some dependency is not used,
then users don't need to pay for its latency.")
(license license:expat)))
(define-public julia-marchingcubes
(package
(name "julia-marchingcubes")
(version "0.1.8")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaGeometry/MarchingCubes.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "14k47lz33j0fiashykf2a8ayiv482k5jkgw0iircw55mdkdrnxc3"))))
(build-system julia-build-system)
(arguments
`(#:tests? #f)) ; Maybe later
(propagated-inputs
(list julia-precompiletools
julia-staticarrays))
#;
(native-inputs
(list julia-benchmarktools
julia-geometrybasics
julia-meshes
julia-plyio))
(home-page "https://github.com/JuliaGeometry/MarchingCubes.jl")
(synopsis "Efficient Implementation of Marching Cubes' Cases with Topological Guarantees")
(description "Julia port of Efficient Implementation of Marching Cubes' Cases with Topological Guarantees.")
(license license:expat)))
(define-public julia-snoopprecompile
(package
(name "julia-snoopprecompile")
(version "1.0.3")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/timholy/SnoopCompile.jl")
(commit "v2.10.0")))
(file-name (git-file-name name version))
(sha256
(base32 "14nnqknswjzlk786x4r7xc7898nmfk7ijfchrc09i81qi2d0mmcn"))))
(build-system julia-build-system)
(arguments
(list
#:tests? #f ; Most tests fail in the build environment.
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _
(chdir "SnoopPrecompile"))))))
(propagated-inputs
(list julia-preferences))
(home-page "https://timholy.github.io/SnoopCompile.jl/dev/")
(synopsis "Effectively precompile code needed by your package")
(description "SnoopPrecompile is a small dependency used to effectively
precompile code needed by your package, particularly on Julia 1.8 and higher.")
(license license:expat)))
(define-public julia-snoopcompile
(package
(name "julia-snoopcompile")
(version "1.7.2")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/timholy/SnoopCompile.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1xy0y5s7q980fl0kygvjbmn74i3sjpzbizsgvis70gd2fibz80h7"))))
(build-system julia-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'adjust-test-suite
(lambda _
;; This module fails to load its dependencies in the 'check phase.
(substitute* "test/runtests.jl"
((".*snoopi\\.jl.*") ""))
(substitute* "test/snoopi.jl"
(("testset \"snoopi\" begin")
"testset \"snoopi\" begin return")))))))
(propagated-inputs
(list julia-snoopcompileanalysis
julia-snoopcompilebot
julia-snoopcompilecore))
(native-inputs
(list
;julia-jld
;julia-matlang
))
(home-page "https://timholy.github.io/SnoopCompile.jl/dev/")
(synopsis "Making packages work faster with more extensive precompilation")
(description "SnoopCompile observes the Julia compiler, causing it to
record the functions and argument types it's compiling. From these lists of
methods, you can generate lists of @code{precompile} directives that may reduce
the latency between loading packages.")
(license license:expat)))
(define-public julia-snoopcompileanalysis
(package/inherit julia-snoopcompile
(name "julia-snoopcompileanalysis")
(arguments
(list
#:tests? #f ; No test folder
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _
(chdir "SnoopCompileAnalysis"))))))
(propagated-inputs
(list julia-cthulhu
julia-orderedcollections))
(native-inputs '())
))
(define-public julia-snoopcompilebot
(package/inherit julia-snoopcompile
(name "julia-snoopcompilebot")
(arguments
(list
#:tests? #f ; Tests to be run in SnoopCompile.jl
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _
(chdir "SnoopCompileBot"))))))
(propagated-inputs
(list julia-filepathsbase
julia-snoopcompileanalysis
julia-snoopcompilecore
julia-yaml))
(native-inputs '())
))
(define-public julia-snoopcompilecore
(package/inherit julia-snoopcompile
(name "julia-snoopcompilecore")
(arguments
(list
#:tests? #f ; No test folder
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _
(chdir "SnoopCompileCore"))))))
(propagated-inputs '())
(native-inputs '())
))
(define-public julia-cthulhu
(package
(name "julia-cthulhu")
(version "1.6.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaDebug/Cthulhu.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1ziax1378kvyzikm4cigg4mq44r085zczqa0mkcbw5g36gcma6qi"))))
(build-system julia-build-system)
(arguments
`(#:tests? #f)) ; Skip for now
(propagated-inputs
(list julia-codetracking
julia-foldingtrees))
(native-inputs
(list julia-staticarrays))
(home-page "https://github.com/JuliaDebug/Cthulhu.jl")
(synopsis "Slow descent into madness")
(description "Cthulhu can help you debug type inference issues by
recursively showing the @code{code_typed} output until you find the exact point
where inference gave up, messed up, or did something unexpected. Using the
Cthulhu interface you can debug type inference problems faster.")
(license license:expat)))
(define-public julia-codetracking
(package
(name "julia-codetracking")
(version "1.3.4")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/timholy/CodeTracking.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0j6mclc7y1vpib5chj3hkabz9zbmdl76jgcr7314f5kbrdqjybbi"))))
(build-system julia-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'adjust-test-suite
(lambda _
(substitute* "test/runtests.jl"
(("test pkgfiles\\(\"Color")
"test_skip pkgfiles\(\"Color")))))))
(home-page "https://github.com/timholy/CodeTracking.jl")
(synopsis "It's editing-time, do you know where your methods are?")
(description "CodeTracking can be thought of as an extension of Julia's
InteractiveUtils library. It provides an interface for obtaining:
@enumerate
@item the strings and expressions of method definitions
@item the method signatures at a specific file & line number
@item location information for \"dynamic\" code that might have moved since it
was first loaded
@item a list of files that comprise a particular package.@end enumerate")
(license license:expat)))
(define-public julia-foldingtrees
(package
(name "julia-foldingtrees")
(version "1.2.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaCollections/FoldingTrees.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1q3w44z1h9j22ykdwwgl8qdm9621m0qqwz4wd2rs2aj0921pdmm4"))))
(build-system julia-build-system)
(propagated-inputs
(list julia-abstracttrees))
(home-page "https://github.com/JuliaCollections/FoldingTrees.jl")
(synopsis "Dynamic tree structure with control over the accessibility of node children")
(description "FoldingTrees implements a dynamic tree structure in which
some nodes may be \"folded,\" i.e., marked to avoid descent among that node's
children. It also supports interactive text menus based on folding trees.")
(license license:expat)))
(define-public julia-jlfzf
(package
(name "julia-jlfzf")
(version "0.1.2")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/Moelf/JLFzf.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0fvcx80lzj0xc4imb9h0iybj8s0cazjc1wn9h8xncih9aln25is4"))))
(build-system julia-build-system)
(arguments
'(#:tests? #f)) ; no tests
(propagated-inputs
(list julia-fzf-jll
julia-pipe))
(home-page "https://github.com/Moelf/JLFzf.jl")
(synopsis "Julia bind to fzf fuzzy finder")
(description "Julia bind to fzf fuzzy finder.")
(license license:expat)))
(define-public julia-pipe
(package
(name "julia-pipe")
(version "1.3.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/oxinabox/Pipe.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "01anm76nfmcajcbr2piji0rknisf5wwhimfndwaadkqkcjv7k4xn"))))
(build-system julia-build-system)
(home-page "https://github.com/oxinabox/Pipe.jl")
(synopsis "Enhancement to Julia piping syntax")
(description "This package provides an enhancement to Julia piping syntax.")
(license license:expat)))
(define-public julia-fzf-jll
(package
(name "julia-fzf-jll")
(version "0.35.1+0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/juliabinarywrappers/fzf_jll.jl")
(commit (string-append "fzf-v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0psl1lsvl6sza69g7qh8ha2ir89fibzid4ka3wzmjgh0r4yjfnw0"))))
(build-system julia-build-system)
(arguments
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
(substitute* wrapper
(("generate_wrapper_header.*")
(string-append
"generate_wrapper_header(\"fzf\", \""
(assoc-ref inputs "fzf") "\")\n"))))
;; There's a Julia file for each platform, override them all
(find-files "src/wrappers/" "\\.jl$")))))))
(inputs
(list (@ (gnu packages terminals) fzf)))
(propagated-inputs
(list julia-jllwrappers))
(home-page "https://github.com/JuliaBinaryWrappers/fzf_jll.jl")
(synopsis "Fzf library wrappers")
(description "This package provides a wrapper for fzf.")
(license license:expat)))
(define-public julia-unicodefun
(package
(name "julia-unicodefun")
(version "0.4.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/SimonDanisch/UnicodeFun.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "11hch4zpi8qby8pcqfvxnx88y45lxan4ind9kj2d0pgw614zkpg0"))))
(build-system julia-build-system)
(home-page "https://github.com/SimonDanisch/UnicodeFun.jl")
(synopsis "Transform text into unicode symbols")
(description "This package offers a unicode transformation library.")
(license license:expat)))
(define-public julia-unzip
(package
(name "julia-unzip")
(version "0.2.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/bramtayl/Unzip.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0i4rkvyd8br024s0sgs3crpi6za2f51m42whkx0jd22wiwg675vb"))))
(build-system julia-build-system)
(native-inputs
(list julia-documenter))
(home-page "https://github.com/bramtayl/Unzip.jl")
(synopsis "")
(description "")
(license license:expat)))
;; Versions after 0.3.11 need a newer version of julia-http
(define-public julia-plutosliderserver
(package
(name "julia-plutosliderserver")
(version "0.3.11")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaPluto/PlutoSliderServer.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1aqc836glwqqs1pd9173sbjwjns3zv197xqdqlkp2xgrkjiw2yzg"))))
(build-system julia-build-system)
(arguments
`(#:tests? #f ; Tests require network access
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'adjust-source
(lambda _
(setenv "GITHUB_ACTIONS" "false")
;; Rip out betterfilewatching, it depends on a rust package.
(substitute* "src/PlutoSliderServer.jl"
((".*watch_folder.*") ""))
;; Remove GitHubActions
(substitute* "src/PlutoSliderServer.jl"
((".*GitHubActions.*") "")))))))
(propagated-inputs
(list julia-abstractplutodingetjes
;julia-betterfilewatching ; should be disabled?
julia-configurations
julia-fromfile
julia-git
;julia-githubactions ; can be disabled
julia-http
julia-json
julia-pluto
julia-terminalloggers))
(home-page "https://github.com/JuliaPluto/PlutoSliderServer.jl")
(synopsis "Web server to run parts of a Pluto.jl notebook")
(description "This package provides a web server to run just the
@code{@@bind} parts of a @code{Pluto.jl} notebook.")
(license license:unlicense)))
;; TODO: unbundle javascript calls to cdn.jsdelivr.net
;; The '-src' commit needs some nodejs packages to build the frontend.
(define-public julia-pluto
(package
(name "julia-pluto")
(version "0.19.9")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/fonsp/Pluto.jl")
;(commit (string-append "v" version "-src"))))
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
;(base32 "0h9sz4mpf3a4k0f5fblbb6j07wdhrnarxajrn0wz6zsq6w30x6yj"))))
(base32 "1qml5id3fi4r6n7hrqvfjwdvp3zp8xfckir3mw7vwswmkc56jzpq"))))
(build-system julia-build-system)
(arguments
`(#:tests? #f ; Test suite tries to download the package registry.
;#:phases
#;(modify-phases %standard-phases
#;(add-before 'check 'pre-check
(lambda _
(setenv "PLUTO_TEST_ONLY_COMPILETIMES" "true")))
(add-after 'link-depot 'dont-check-for-upgrades
(lambda _
(substitute* "frontend/components/welcome/Welcome.js"
((".*new_update_message.*") "")))))))
(propagated-inputs
(list julia-configurations
julia-fuzzycompletions
julia-http
julia-hypertextliteral
julia-mimes
julia-msgpack
julia-precompilesignatures
julia-relocatablefolders
julia-tables
julia-uris))
(native-inputs
(list julia-dataframes
julia-offsetarrays
julia-timeroutputs))
(home-page "https://github.com/fonsp/Pluto.jl")
(synopsis "Simple reactive notebooks for Julia")
(description "A Pluto notebook is made up of small blocks of Julia code
(cells) and together they form a reactive notebook. When you change a variable,
Pluto automatically re-runs the cells that refer to it. Cells can even be
placed in arbitrary order - intelligent syntax analysis figures out the
dependencies between them and takes care of execution.")
(license license:expat)))
(define-public julia-plutoui
(package
(name "julia-plutoui")
(version "0.7.51")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/fonsp/PlutoUI.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0hqaa8wx7mia3krdwhj2yf8aa4a8h4r09j16dxn7nyc0zcz8hgb2"))))
(build-system julia-build-system)
(propagated-inputs
(list julia-abstractplutodingetjes
julia-colortypes
julia-fixedpointnumbers
julia-hyperscript
julia-hypertextliteral
julia-iocapture
julia-json
julia-mimes
julia-reexport
julia-uris))
(home-page "https://github.com/fonsp/PlutoUI.jl")
(synopsis "Helper package for Julia Pluto")
(description "This package helps to make @code{html\"<input>\"} a bit more
native to Julia. Use it with the @code{@@bind} macro in Pluto.")
(license license:unlicense)))
(define-public julia-http-1.5
(package
(inherit julia-http)
(name "julia-http")
(version "1.5.5")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaWeb/HTTP.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0qcfixsq65g8hdimygam7cd8nvcz6w7nzkkjk98mvf65dcby4593"))))
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(add-before 'install 'disable-network-tests
(lambda _
#;(substitute* "test/runtests.jl"
(("\"async.jl") "# \"async.jl")
(("\"client.jl") "# \"client.jl"))
#;(substitute* "test/aws4.jl"
(("@testset.*HTTP.request with AWS authentication.*" all)
(string-append all "return\n")))
#;(substitute* "test/insert_layers.jl"
(("@testset.*Inserted final layer runs handler.*" all)
(string-append all "return\n")))
#;(substitute* "test/multipart.jl"
(("@testset \"Setting of Content-Type.*" all)
(string-append all "return\n"))
(("@testset \"Deprecation of .*" all)
(string-append all "return\n")))
#;(substitute* "test/websockets.jl"
(("@testset.*External Host.*" all)
(string-append all "return\n")))
#;(substitute* "test/messages.jl"
(("@testset.*Read methods.*" all)
(string-append all "return\n"))
(("@testset.*Body - .*" all)
(string-append all "return\n"))
(("@testset.*Write to file.*" all)
(string-append all "return\n")))
#;(substitute* "test/cookies.jl"
(("@testset.*Set-Cookie casing.*" all)
(string-append all "return\n")))
#t)))))
(propagated-inputs
(list julia-codeczlib
julia-inifile
julia-loggingextras
julia-mbedtls
julia-openssl
julia-simplebufferstream
julia-uris))
;; required for tests
(native-inputs
(list julia-bufferedstreams
julia-json))))
(define-public julia-http-1.0
(package
(inherit julia-http)
(name "julia-http")
(version "1.0.5")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaWeb/HTTP.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "15bqf0gv4qz3990cv1s2nj9mjqaka1pkhzymgwc19wxqvacwvwqr"))))
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(add-before 'install 'disable-network-tests
(lambda _
(substitute* "test/runtests.jl"
(("\"async.jl") "# \"async.jl")
(("\"client.jl") "# \"client.jl")
(("\"websockets") "# \"websockets")
(("\"server") "# \"server"))
(substitute* "test/multipart.jl"
(("@testset \"Setting of Content-Type.*" all)
(string-append all "return\n"))
(("@testset \"Deprecation of .*" all)
(string-append all "return\n")))
(substitute* "test/messages.jl"
(("@testset.*Read methods.*" all)
(string-append all "return\n"))
(("@testset.*Body - .*" all)
(string-append all "return\n"))
(("@testset.*Write to file.*" all)
(string-append all "return\n")))
(substitute* "test/cookies.jl"
(("@testset.*Set-Cookie casing.*" all)
(string-append all "return\n")))
)))))
(propagated-inputs
(list julia-codeczlib
julia-inifile
julia-loggingextras
julia-mbedtls
julia-simplebufferstream
julia-uris))
;; required for tests
(native-inputs
(list julia-bufferedstreams
julia-json))))
;; TODO: Unbundle fonts, more?
(define-public julia-makie
(package
(name "julia-makie")
(version "0.17.13")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/MakieOrg/Makie.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0s9rkfmshl3nz82zkgia6fxmfhz4v26ixam6ybqw8swlshdfijrd"))))
(build-system julia-build-system)
(propagated-inputs
(list ;julia-animations
;julia-colorbrewer
julia-colorschemes
julia-colortypes
julia-colors
julia-contour
julia-distributions
julia-docstringextensions
julia-ffmpeg
julia-fileio
julia-fixedpointnumbers
julia-formatting
julia-freetype
julia-freetypeabstraction
julia-geometrybasics
;julia-gridlayout
;julia-imageio
julia-intervalsets
;julia-isoband
;julia-kerneldensity
julia-latexstrings
julia-makiecore
;julia-match
;julia-mathtexengine
julia-observables
julia-offsetarrays
;julia-packing
julia-plotutils
;julia-polygonops
julia-relocatablefolders
julia-showoff
;julia-signeddistancefields
julia-statsbase
julia-statsfuns
julia-structarrays
julia-unicodefun))
(home-page "https://docs.makie.org/stable")
(synopsis "Interactive data visualizations and plotting in Julia")
(description "Makie is a data visualization ecosystem for the Julia
programming language.")
(license license:expat)))
(define-public julia-makiecore
(package/inherit julia-makie
(name "julia-makiecore")
(version "0.4.0") ; Same source, different version
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _
(chdir "MakieCore"))))))
(propagated-inputs
(list julia-observables))
(synopsis "Backend core for Makie")))
(define-public julia-cairomakie
(package/inherit julia-makie
(name "julia-cairomakie")
(version "0.8.13") ; Same source, different version
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _
(chdir "CairoMakie"))))))
(propagated-inputs
(list ;julia-cairo
julia-colors
;julia-fftw
julia-fileio
julia-freetype
julia-geometrybasics
julia-makie))
(synopsis "Cairo Backend for Makie")))
(define-public julia-freetype
(package
(name "julia-freetype")
(version "4.1.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaGraphics/FreeType.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "08kf1x1c7gvllds1ryv6zwy9ai85p50a509ndlcjrkiw31i612m8"))))
(build-system julia-build-system)
(propagated-inputs
(list julia-cenum
julia-freetype2-jll))
(home-page "https://github.com/JuliaGraphics/FreeType.jl")
(synopsis "FreeType 2 bindings for Julia")
(description "This package provides FreeType bindings for Julia.")
(license license:zlib)))
(define-public julia-freetypeabstraction
(package
(name "julia-freetypeabstraction")
(version "0.9.9")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaGraphics/FreeTypeAbstraction.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0zqpwysvxjqh5lmsz7lysgyid7xnis23rr0xzn3fwxlncka7dbyl"))
(snippet
#~(begin
(use-modules (guix build utils))
;; Also find fonts in Guix environments.
(substitute* "src/findfonts.jl"
(("\"/usr/share/fonts\"," all)
(string-append all "\n "
"\"/run/current-system/profile/share/fonts\","
"\n "
"joinpath(get(ENV, \"GUIX_ENVIRONMENT\", homedir()),"
"\"share/fonts\"),"
"\n "
"joinpath(get(ENV, \"GUIX_PROFILE\", homedir()),"
"\"share/fonts\"),") ))))))
(build-system julia-build-system)
(arguments
(list
#:tests? #f ; Can't skip the one test as needed
#:phases
#~(modify-phases %standard-phases
(add-before 'check 'skip-findfont-test
(lambda _
(substitute* "test/runtests.jl"
;; Can't make this find font-dejavu
(("@test findfont\\(font") "@test_skip findfont(font")))))))
(propagated-inputs
(list julia-colorvectorspace
julia-colors
julia-freetype
julia-geometrybasics))
(home-page "https://github.com/JuliaGraphics/FreeTypeAbstraction.jl")
(synopsis "Julian abstraction layer over FreeType.jl")
(description
"This package provides an abstraction layer over the FreeType Julia module.")
(license license:expat)))
;; ready to upstream
(define-public julia-observables
(package
(name "julia-observables")
(version "0.5.4")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaGizmos/Observables.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1l0rk60nrwwgcifqs72x76z9dv1kq6rvcbhy63kp27yqfsx6c20s"))))
(build-system julia-build-system)
(home-page "https://github.com/JuliaGizmos/Observables.jl")
(synopsis "Observable ref")
(description "This package provides the @code{Observable}s type in Julia,
which are like @code{Ref}s but you can listen to changes.")
(license license:expat)))
(define-public julia-simplebufferstream
(package
(name "julia-simplebufferstream")
(version "1.1.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaPackaging/SimpleBufferStream.jl")
;; First commit after 1.1.0 with a license
(commit "80c9854d5d9ea921da6f619624989fa30e83b8be")))
(file-name (git-file-name name version))
(sha256
(base32 "05c4d73ki4cp38g66ljxwbl2d0dni3w05r8xsd6g1v63x2rqqbgn"))))
(build-system julia-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(add-after 'link-depot 'adjust-tests
(lambda _
(substitute* "test/runtests.jl"
;; Tests fail when build machine is too *fast*.
(("0\\.01") "0.001")
;; Don't create circular dependencies with http
(("using HTTP.*") "")
(("@testset.*HTTP.jl.*" all)
(string-append all "return\n"))))))))
(home-page "https://github.com/JuliaPackaging/SimpleBufferStream.jl")
(synopsis "What Base.BufferStream should be")
(description "This is what I wish Base.BufferStream was.")
(license license:expat)))
(define-public julia-openssl
(package
(name "julia-openssl")
(version "1.4.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaWeb/OpenSSL.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1s2h4qh9y3alhkf18p4pjqp77mvsb47qagmk68pq0wsx8r3hzhzx"))))
(build-system julia-build-system)
(arguments
(list
#:phases
#~(modify-phases %standard-phases
(add-before 'install 'disable-network-tests
(lambda _
(substitute* "test/runtests.jl"
;; No /etc/ssl/certs/ca-certificates.crt in the build environment.
(("@testset.*(ReadPEMCert|X509Certificate|X509Store).*" all)
(string-append all "return\n"))
;; No network connection
(("@testset.*(HttpsConnect|ClosedStream|NoCloseStream).*" all)
(string-append all "return\n"))
;; undefined symbol.
;; XXX: THIS BREAKS THE PACKAGE!
(("@testset.*ErrorTaskTLS.*" all)
(string-append all "return\n"))))))))
(propagated-inputs
(list julia-bitflags
julia-openssl-jll))
(home-page "https://github.com/JuliaWeb/OpenSSL.jl")
(synopsis "Openssl Julia bindings")
(description "This package provides Openssl Julia bindings.")
(license license:expat)))
#;(define-public julia-openssl-jll
(package
(name "julia-openssl-jll")
(version "3.0.8+0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaBinaryWrappers/OpenSSL_jll.jl")
(commit (string-append "OpenSSL-v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1d9kcx7a3yv3rgkggq7h436sfjafr66pq8d0lmlcjxdpl46hx3j7"))))
(build-system julia-build-system)
(arguments
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
(substitute* wrapper
(("lib64") "lib")
(("generate_wrapper_header.*")
(string-append
"generate_wrapper_header(\"OpenSSL\", \""
(assoc-ref inputs "openssl") "\")\n"))))
;; There's a Julia file for each platform, override them all
(find-files "src/wrappers/" "\\.jl$")))))))
(inputs
(list (@ (gnu packages tls) openssl)))
(propagated-inputs
(list julia-jllwrappers))
(home-page "https://github.com/JuliaBinaryWrappers/OpenSSL_jll.jl")
(synopsis "Openssl library wrappers")
(description "This package provides a wrapper for openssl.")
(license license:expat)))
#;(define-public julia-openssl-jll-1.1
(package
(name "julia-openssl-jll")
(version "1.1.21+0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaBinaryWrappers/OpenSSL_jll.jl")
(commit (string-append "OpenSSL-v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "05wgsvy0iviffkcq4w1dg8gaafyxknnk26c1gpcgma5yhfia8yfs"))))
(build-system julia-build-system)
(arguments
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
(substitute* wrapper
(("generate_wrapper_header.*")
(string-append
"generate_wrapper_header(\"OpenSSL\", \""
(assoc-ref inputs "openssl") "\")\n"))))
;; There's a Julia file for each platform, override them all
(find-files "src/wrappers/" "\\.jl$")))))))
(inputs
(list (@ (gnu packages tls) openssl-1.1)))
(propagated-inputs
(list julia-jllwrappers))
(home-page "https://github.com/JuliaBinaryWrappers/OpenSSL_jll.jl")
(synopsis "Openssl library wrappers")
(description "This package provides a wrapper for openssl.")
(license license:expat)))
(define-public julia-bitflags
(package
(name "julia-bitflags")
(version "0.1.7")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/jmert/BitFlags.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1wphfpwqm7bsff68d6h9yhhxrh1lq2shyl0afbzp0h5czf6qi2xr"))))
(build-system julia-build-system)
(home-page "https://github.com/jmert/BitFlags.jl")
(synopsis "Enum-like type for bit flag option values")
(description "@code{BitFlag.jl} provides an @code{Enum}-like type for bit
flag option values.")
(license license:expat)))
(define-public julia-relocatablefolders
(package
(name "julia-relocatablefolders")
(version "0.3.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaPackaging/RelocatableFolders.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "116f98y2w5cqkv2fvddmv54422cpby6d7q1dndgqh2rdlkpb44iw"))))
(build-system julia-build-system)
(propagated-inputs
(list julia-scratch))
(home-page "https://github.com/JuliaPackaging/RelocatableFolders.jl")
(synopsis "Reference packages in their project directory")
(description "An alternative to the @code{@@__DIR__} macro. Packages that
wish to reference paths in their project directory run into issues with
relocatability when used in conjunction with @code{PackageCompiler}.")
(license license:expat)))
(define-public julia-scratch
(package
(name "julia-scratch")
(version "1.1.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaPackaging/Scratch.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0s7dmqsskq5vy7sk6pxng5vrznrn6msg7xf8a9kj3a03b617pgap"))))
(build-system julia-build-system)
(arguments
(list #:tests? #f)) ; Tries to download the Julia registry.
(home-page "https://github.com/JuliaPackaging/Scratch.jl")
(synopsis "Scratch spaces for all your persistent mutable data needs")
(description "This repository implements the scratch spaces API for
package-specific mutable containers of data. These spaces can contain
datasets, text, binaries, or any other kind of data that would be convenient to
store in a location specific to your package. As compared to Artifacts, these
containers of data are mutable. Because the scratch space location on disk is
not very user-friendly, scratch spaces should, in general, not be used for a
storing files that the user must interact with through a file browser. In that
event, packages should simply write out to disk at a location given by the
user. Scratch spaces are designed for data caches that are completely managed
by a package and should be removed when the package itself is uninstalled.")
(license license:expat)))
(define-public julia-hypertextliteral
(package
(name "julia-hypertextliteral")
(version "0.9.4")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaPluto/HypertextLiteral.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "06nzgxrl1aac9bqb37l2lak2aicp9h7fd1ijcva9pq80z0d74a8a"))))
(build-system julia-build-system)
(arguments (list #:tests? #f)) ; Disable tests until all inputs are pacakged.
(propagated-inputs
(list julia-tricks))
(native-inputs
(list julia-documenter
;julia-faker
julia-hyperscript
;julia-narrativetest
))
(home-page "https://juliapluto.github.io/HypertextLiteral.jl/stable/")
(synopsis "Julia library for the string interpolation of HTML and SVG")
(description "HypertextLiteral is a Julia package for generating HTML, SVG,
and other SGML tagged content. It works similar to Julia string interpolation,
only that it tracks hypertext escaping needs and provides handy conversions
dependent upon context.")
(license license:expat)))
;; This can be removed with julia-1.10
(define-public julia-tricks
(package
(name "julia-tricks")
(version "0.1.7")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/oxinabox/Tricks.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0870hiqpl14wpr2v16wl6fw89r469yjrchv6gn4pfw2irw3nkjip"))))
(build-system julia-build-system)
(home-page "https://github.com/oxinabox/Tricks.jl")
(synopsis "Cunning tricks though the julia compiler internals")
(description "Tricks.jl is an particularly cunning package that does tricks
with the Julia edge system.")
(license license:expat)))
(define-public julia-registryinstances
(package
(name "julia-registryinstances")
(version "0.1.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/GunnarFarneback/RegistryInstances.jl")
(commit "2796d959014475bc19e2dfa174179cdf02642d28")))
(file-name (git-file-name name version))
(sha256
(base32 "09926dy2s4wcml6s2hrbq1j1r1456d61fvk5fma4sbr9qsvpyyd0"))))
(build-system julia-build-system)
(arguments
(list #:tests? #f)) ; TODO: Got exception outside of a @test
(propagated-inputs
(list julia-lazilyinitializedfields))
(home-page "https://github.com/GunnarFarneback/RegistryInstances.jl")
(synopsis "Access the information in installed Julia registries")
(description "Julia's package manager stores package metadata in registries,
which consist of TOML files in a directory structure.")
(license license:expat)))
(define-public julia-lazilyinitializedfields
(package
(name "julia-lazilyinitializedfields")
(version "1.2.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/KristofferC/LazilyInitializedFields.jl")
(commit "53ed8cbe78b2048105a0e0b355294e7f024e3d14")))
(file-name (git-file-name name version))
(sha256
(base32 "1jwpka27d873cyn0vxrg7h7ns7fmlqlyx5h38cw6zvfbdhkrmi09"))))
(build-system julia-build-system)
(native-inputs
(list julia-documenter))
(home-page "https://github.com/KristofferC/LazilyInitializedFields.jl")
(synopsis "Handle lazily initialized fields")
(description "A package for handling lazily initialized fields.")
(license license:expat)))
(define-public julia-mimes
(package
(name "julia-mimes")
(version "0.1.4")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaWeb/MIMEs.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0vgc2q2mgbrm16px7cbqsrga9l99djlb1ayg5k1djb0mbnprjajk"))))
(build-system julia-build-system)
(home-page "https://github.com/JuliaWeb/MIMEs.jl")
(synopsis "MIME information: filetype, encoding, gzip")
(description "A small package to transform between file extensions and MIME
types, with bonus features.")
(license license:expat)))
(define-public julia-loggingextras
(package
(name "julia-loggingextras")
(version "1.0.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaLogging/LoggingExtras.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0mc0bbr2wsa809q74hg4npdw2xcni4xl40zz50i6djwnxq88yl07"))))
(build-system julia-build-system)
(home-page "https://github.com/JuliaLogging/LoggingExtras.jl")
(synopsis "Composable Loggers for the Julia Logging StdLib")
(description "LoggingExtras is designs around allowing you to build
arbitrarily complicated systems for \"log plumbing\". That is to say basically
routing logged information to different places. It is built around the idea of
simple parts which are composed together, to allow for powerful and flexible
definition of your logging system.")
(license license:expat)))
(define-public julia-precompilesignatures
(package
(name "julia-precompilesignatures")
(version "3.0.3")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/rikhuijzer/PrecompileSignatures.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "11rjdx8n3q10iis7ryzbvlvgdpi6kd2h53qp7lac02yx6rsgsfx1"))))
(build-system julia-build-system)
(arguments
(list #:tests? #f)) ; cycle with Pluto.jl.
;(native-inputs
; (list julia-pluto))
(home-page "https://github.com/rikhuijzer/PrecompileSignatures.jl")
(synopsis "Generate precompile directives by reading method signatures")
(description "This package reads all method signatures in a package and
generates precompile directives for any concrete signature that it can find.")
(license license:expat)))
(define-public julia-precompiletools
(package
(name "julia-precompiletools")
(version "1.1.2")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaLang/PrecompileTools.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "124qzflwnn34d8x8vz3cmj2m4a55mg5qf8i8jdcwyyrnag3si7zr"))))
(build-system julia-build-system)
(arguments
(list #:tests? #f)) ; Tries to download the Julia registry.
(propagated-inputs
(list julia-preferences))
(home-page "https://github.com/JuliaLang/PrecompileTools.jl")
(synopsis "Reduce time-to-first-execution of Julia code")
(description "PrecompileTools allows you to reduce the latency of the first
execution of Julia code. It is applicable for package developers and for
\"ordinary users\" in their personal workflows.")
(license license:expat)))
(define-public julia-timeroutputs
(package
(name "julia-timeroutputs")
(version "0.5.23")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/KristofferC/TimerOutputs.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "031m7d837cw4c7iz4arrm1a1ppqihhj5jsldvm7z1bc72jxgfrcv"))))
(build-system julia-build-system)
(propagated-inputs
(list julia-exprtools))
(home-page "https://github.com/KristofferC/TimerOutputs.jl")
(synopsis "Formatted output of timed sections in Julia")
(description "TimerOutputs is a small Julia package that is used to generate
formatted output from timings made in different sections of a program. It's
main functionality is the @code{@@timeit} macro, similar to the @code{@@time}
macro in Base except one also assigns a label to the code section being timed.
Multiple calls to code sections with the same label (and in the same \"scope\")
will accumulate the data for that label. After the program has executed, it is
possible to print a nicely formatted table presenting how much time,
allocations and number of calls were made in each section. The output can be
customized as to only show the things you are interested in.")
(license license:expat)))
(define-public julia-memoize
(package
(name "julia-memoize")
(version "0.4.4")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaCollections/Memoize.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0mfavihgdmh6zzjx5lzbigmgsa50pa9ik9gk2gq9wam26prkmkba"))))
(build-system julia-build-system)
(propagated-inputs
(list julia-macrotools))
(home-page "https://github.com/JuliaCollections/Memoize.jl")
(synopsis "Memoize macro for Julia")
(description "Easy memoization for Julia.")
(license license:bsd-0)))
(define-public julia-abstractplutodingetjes
(package
(name "julia-abstractplutodingetjes")
(version "1.1.4")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaPluto/AbstractPlutoDingetjes.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "03grnv26n3qdadb2awv3d0rs655l5hhmh7h43v949za9aaaz89j3"))))
(build-system julia-build-system)
(arguments
(list #:tests? #f)) ; No tests for this package.
(home-page "https://docs.juliahub.com/AbstractPlutoDingetjes/UHbnu/")
(synopsis "Abstract package for creating widgets in Pluto.jl")
(description "An abstract package to be implemented by packages/people who
create widgets (or other dingetjes) for Pluto.")
(license license:unlicense)))
(define-public julia-hyperscript
(package
(name "julia-hyperscript")
(version "0.0.4")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaWeb/Hyperscript.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0flap3a9p6fr768kjfk1lkyfgjqcyhzvzl7in7gjszfy04pqj55w"))))
(build-system julia-build-system)
(home-page "https://github.com/JuliaWeb/Hyperscript.jl")
(synopsis "Lightweight DOM representation for Julia")
(description "Hyperscript is a package for working with HTML, SVG, and CSS
in Julia. When using this library you automatically get:
@enumerate
@item A concise DSL for writing HTML, SVG, and CSS.
@item Flexible ways to combine DOM pieces together into larger components.
@item Safe and automatic HTML-escaping.
@item Lightweight and optional support for scoped CSS.
@item Lightweight and optional support for CSS unit arithmetic.
@end enumerate")
(license license:expat)))
;; ready to upstream
(define-public julia-statsfuns
(package
(name "julia-statsfuns")
(version "0.9.18")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaStats/StatsFuns.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1y71gz4skp6hxw8k5vjbjayplxmdfh3m3yjfw4ggi0azav6c9hrk"))))
(build-system julia-build-system)
(propagated-inputs
(list julia-chainrulescore
julia-inversefunctions
julia-irrationalconstants
julia-logexpfunctions
julia-reexport
julia-rmath
julia-specialfunctions))
(native-inputs
(list julia-chainrulestestutils
julia-forwarddiff))
(home-page "https://github.com/JuliaStats/StatsFuns.jl")
(synopsis "Mathematical functions related to statistics")
(description "This package provides a collection of mathematical constants
and numerical functions for statistical computing.")
(license license:expat)))
;; ready to upstream
(define-public julia-inversefunctions
(package
(name "julia-inversefunctions")
(version "0.1.8")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaMath/InverseFunctions.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "05g9f6i735x7syfr56l4yf4fy71kgdisjc6cfxi4jkf46iq86a69"))))
(build-system julia-build-system)
(native-inputs
(list julia-documenter))
(home-page "https://github.com/JuliaMath/InverseFunctions.jl")
(synopsis "Interface for function inversion in Julia")
(description
"This package provides an interface to invert functions in Julia.")
(license license:expat)))
;; ready to upstream
(define-public rmath-for-julia-rmath-jll
;; More recent commits fix various build issues
(let ((commit "5c5dfd6baca358103fbb47cc03dc0ecee04fb1ff")
(revision "1"))
(package
(name "rmath-julia")
(version (git-version "0.3.0" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaStats/Rmath-julia")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "04lf8gfnfcppckk9d7hss0ja91yxaax6qz1gzqya9w0shjr386s5"))))
(build-system julia-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(delete 'precompile) ; No Project.toml.
(delete 'link-depot) ; Not really needed on this package.
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(invoke "julia" "test.jl"))))
(add-before 'install 'build
(lambda _
(invoke "make")))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(install-file "src/libRmath-julia.so" (string-append out "/lib"))))))))
(home-page "https://github.com/JuliaStats/Rmath-julia")
(synopsis "Rmath library from R")
(description "This is a slightly modified version of the standalone Rmath
library from R, built to be used with the @code{Rmath.jl} Julia package.
The main difference is that it is built to allow defining custom random number
generating functions via C function pointers (see @code{include/callback.h}).
When using the library, these should be defined before calling any of the random
functions.")
(properties '((hidden? . #t)))
(license license:gpl2))))
;; ready to upstream
(define-public julia-rmath
(package
(name "julia-rmath")
(version "0.7.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaStats/Rmath.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0cam16ff4v2fl7c9j1wx2ahgjhwba9mk2q6qv3zdknnnqj6w664s"))))
(build-system julia-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'link-depot 'link-to-librmath-directly
(lambda* (#:key inputs #:allow-other-keys)
(let* ((rmath (assoc-ref inputs "rmath"))
(librmath (string-append rmath "/lib/libRmath-julia.so")))
(substitute* "src/Rmath.jl"
(("libRmath\\)") (string-append "\"" librmath "\")")))))))))
(propagated-inputs
`(("julia-rmath-jll" ,julia-rmath-jll)))
(inputs
`(("rmath" ,rmath-for-julia-rmath-jll)))
(native-inputs
`(("rmath" ,rmath-for-julia-rmath-jll)))
(home-page "https://github.com/JuliaStats/Rmath.jl")
(synopsis "Emulate R's d-p-q-r functions for probability distributions")
(description "This package provides an archive of functions that emulate
R's d-p-q-r functions for probability distributions. It is a wrapper around
@code{rmath} for Julia.")
(license license:expat)))
;; ready to upstream
(define-public julia-rmath-jll
(package
(name "julia-rmath-jll")
(version "0.3.0+0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaBinaryWrappers/Rmath_jll.jl")
(commit (string-append "Rmath-v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1idshxhj60bvra4i1xxpyh2prx1lq9nfrvlc47b68jixfpfkxrlg"))))
(build-system julia-build-system)
(arguments
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
(substitute* wrapper
(("generate_wrapper_header.*")
(string-append
"generate_wrapper_header(\"Rmath\", \""
(assoc-ref inputs "rmath") "\")\n"))))
;; There's a Julia file for each platform, override them all
(find-files "src/wrappers/" "\\.jl$")))))))
(inputs
`(("rmath" ,rmath-for-julia-rmath-jll)))
(propagated-inputs
`(("julia-jllwrappers" ,julia-jllwrappers)))
(home-page "https://github.com/JuliaBinaryWrappers/Rmath_jll.jl")
(synopsis "Rmath library wrappers")
(description "This package provides a wrapper for Rmath.")
(license license:expat)))
;; ready to upstream
(define-public julia-doublefloats
(package
(name "julia-doublefloats")
(version "1.1.25")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaMath/DoubleFloats.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0cd3wxa2q77d9cxmi8gp5hpc95bfdf195mw03p6r1z543sfcfg0d"))))
(build-system julia-build-system)
(propagated-inputs
(list julia-genericlinearalgebra
julia-polynomials
julia-quadmath
julia-requires
julia-specialfunctions))
(native-inputs
(list julia-genericlinearalgebra
julia-genericschur
julia-specialfunctions))
(home-page "https://github.com/JuliaMath/DoubleFloats.jl")
(synopsis "Extended precision float and complex types")
(description "This package provides a math library with extended precision
floats and complex types.")
(license license:expat)))
;; ready to upstream
;; This package depends on TimeZones.jl.
(define-public julia-polynomials
(package
(name "julia-polynomials")
(version "2.0.24")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaMath/Polynomials.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1wpnk8m4l3ai7ggiim23xlvaxgbsjhprk614pva2pb4xi2jmclgq"))))
(build-system julia-build-system)
(propagated-inputs
(list julia-intervals
julia-mutablearithmetics
julia-recipesbase))
(native-inputs
(list julia-dualnumbers
julia-offsetarrays
julia-specialfunctions
julia-staticarrays))
(home-page "https://github.com/JuliaMath/Polynomials.jl")
(synopsis "Polynomial manipulations in Julia")
(description "This package provides basic arithmetic, integration,
differentiation, evaluation, and root finding over dense univariate
polynomials.")
(license license:expat)))
;; This package depends on TimeZones.jl.
(define-public julia-intervals
(package
(name "julia-intervals")
(version "1.5.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/invenia/Intervals.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1nj40fjx0q3gszq0r8h6scnzyldp68yv1y2lpmmbxraf47644q0n"))))
(build-system julia-build-system)
(arguments
`(#:tests? #f)) ; TODO: Fix! broken with timezone stuff
(propagated-inputs
(list julia-infinity
julia-recipesbase
julia-timezones))
(native-inputs
(list julia-documenter
julia-imagemagick
julia-infinity
;julia-plots
;julia-visualregressiontests
))
(home-page "https://github.com/invenia/Intervals.jl")
(synopsis "Non-iterable ranges")
(description "This package defines:
AbstractInterval, along with its subtypes Interval and AnchoredInterval, and also Bound.")
(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
(list
#:tests? #f ; TODO: Fix tests!
#:phases
#~(modify-phases %standard-phases
(add-after 'link-depot 'remove-timezones.jl
(lambda _
(substitute* "test/runtests.jl"
(("using TimeZones.*") "")
((".*infextendedtime.*") "")))))))
(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)))
;; TODO: There is talk upstream about separating out the timezone data into a
;; separate package which can allow this to actually be packaged in a sane way.
;; As of 1.7.1 there are 257 items in Artifact.toml
;; https://github.com/JuliaTime/TimeZones.jl/issues/359
;; Versions after 1.5.x introduce a dependency on julia-inlinestrings, which needs help with its test suite.
(define-public julia-timezones
(package
(name "julia-timezones")
(version "1.5.9")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaTime/TimeZones.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1r6vnhfykw4zmpq1nahv9zflsd4gnpdj84admnhd0pnbrfwv8prw"))))
(build-system julia-build-system)
(arguments
(list
;; Tests attempt to download timezone information
;; In its current form this is basically a source-only package.
#:tests? #f))
(propagated-inputs
(list
;julia-inlinestrings
julia-mocking
julia-recipesbase))
(home-page "https://github.com/JuliaTime/TimeZones.jl")
(synopsis "IANA time zone database access for Julia")
(description "IANA time zone database access for the Julia programming
language. @code{TimeZones.jl} extends the Date/DateTime support for Julia to
include a new time zone aware @code{TimeType: ZonedDateTime}.")
(license license:expat)))
(define-public julia-inlinestrings
(package
(name "julia-inlinestrings")
(version "1.1.2")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaStrings/InlineStrings.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1fwbnjrsig0fbi9vjn8apbn186xvzhk7vnw3g661q3g8f2j0snp9"))))
(build-system julia-build-system)
(arguments
(list
#:tests? #f ; TODO: Fix skipping the test in question
;#:phases
;#~(modify-phases %standard-phases
; (add-after 'unpack 'adjust-tests
; (lambda _
; (substitute* "test/runtests.jl"
; ;; Need to skip lines 165, 166?
; ((".*a,\".*") "") ; 165, 167
; ((".*a__\".*") "") ; 166, 168
; ))))
))
(propagated-inputs
(list julia-parsers))
(home-page "https://github.com/JuliaStrings/InlineStrings.jl")
(synopsis "Fixed-width string types for Julia")
(description "This package provides fixed-width string types for
facilitating certain string workflows in Julia.")
(license license:expat)))
;; ready to upstream, if we want
(define-public julia-lazyartifacts
(package
(name "julia-lazyartifacts")
(version "1.3.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaPackaging/LazyArtifacts.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0qln5pq2zm68wgm104cxyviiql8xkv7rf68hivar2b7x2a8vwnk0"))))
(build-system julia-build-system)
(home-page "https://github.com/JuliaPackaging/LazyArtifacts.jl")
(synopsis "LazyArtifacts support for older versions of Julia")
(description "This is a wrapper package meant to bridge the gap for packages
that want to use the @code{LazyArtifacts} stdlib as a dependency within packages
that still support Julia versions older than 1.6.")
(license license:expat)))
(define-public julia-visualregressiontests
(package
(name "julia-visualregressiontests")
(version "1.0.0")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaPlots/VisualRegressionTests.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0fsqm89dqrn9bd466v79544hcd5ljn5ikg6x94hfcashjwa5y0g2"))))
(build-system julia-build-system)
(arguments
`(#:tests? #f)) ; GTK.jl not packaged yet
(propagated-inputs
`(("julia-colortypes" ,julia-colortypes)
("julia-colorvectorspace" ,julia-colorvectorspace)
("julia-fileio" ,julia-fileio)
;("julia-imagefiltering" ,julia-imagefiltering)
("julia-imagemagick" ,julia-imagemagick)
;("julia-quartzimageio" ,julia-quartzimageio) ; for macOS
("julia-requires" ,julia-requires)))
;(native-inputs
; `(;("julia-gtk" ,julia-gtk)
; ("julia-plots" ,julia-plots)
; ("julia-testimages" ,julia-testimages)))
(home-page "https://github.com/JuliaPlots/VisualRegressionTests.jl")
(synopsis "Automated integrated regression tests for graphics libraries")
(description "Easy regression testing for visual packages. Automated tests compare similarity between a newly generated image and a reference image using the Images package. While in interactive mode, the tests can optionally pop up a Gtk GUI window showing a side-by-side comparison of the test and reference image, and then optionally overwrite the reference image with the test image. This allows for straightforward regression testing of image data, even when the \"correct\" images change over time.")
(license license:expat)))
;; https://github.com/JuliaPackaging/Yggdrasil/tree/7e9ec714d786c4c841a80bdf75b84570c5bda7a1/E/EarCut
(define-public julia-earcut-jll
;; The only release tag contains just a license file.
(let ((commit "b234ae0c064af12eb5482c7474a64af8be0f511e")
(revision "1"))
(package
(name "julia-earcut-jll")
(version (git-version "2.1.5+1" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaBinaryWrappers/EarCut_jll.jl")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "0x1zjmsm4kcccwhd1fmnz0w4m0f2na1d2vcc0pj2cf5ccprx7miw"))))
(build-system julia-build-system)
(arguments
`(#:tests? #f ; no runtests.jl
#:phases
(modify-phases %standard-phases
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
(substitute* wrapper
(("generate_wrapper_header.*")
(string-append
"generate_wrapper_header(\"EarCut\", \""
(assoc-ref inputs "earcut") "\")\n"))))
;; There's a Julia file for each platform, override them all.
(find-files "src/wrappers/" "\\.jl$")))))))
(inputs ;required by artifacts
`(("earcut" ,earcut-for-julia-earcut-jll)))
(propagated-inputs
`(("julia-jllwrappers" ,julia-jllwrappers)))
(home-page "https://github.com/JuliaBinaryWrappers/EarCut_jll.jl")
(synopsis "")
(description "")
(license license:expat))))
(define-public earcut-for-julia-earcut-jll
(package
(name "earcut-for-julia-earcut-jll")
(version "2.2.3")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/mapbox/earcut.hpp")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "19qpmpz2sh80lqpvvn08r0k28s3v0vlzb72kg3b56rcwxxknkk5l"))
(modules '((guix build utils)))
(snippet
'(begin
(substitute* "CMakeLists.txt"
((".*add_subdirectory.*") ""))))))
(build-system trivial-build-system)
(arguments
`(#:modules ((guix build utils))
#:builder
(let ((out (assoc-ref %outputs "out"))
(source (assoc-ref %build-inputs "source"))
(cwrapper.cpp (assoc-ref %build-inputs "cwrapper.cpp")))
(begin
(use-modules (guix build utils))
(setenv "PATH"
(string-append
(assoc-ref %build-inputs "gcc-toolchain") "/bin:"
(assoc-ref %build-inputs "xz") "/bin"))
(invoke
(string-append (assoc-ref %build-inputs "tar") "/bin/tar") "xvf" source)
(copy-file
(string-append ,name "-" ,version "-checkout/include/mapbox/earcut.hpp")
"earcut.h")
(copy-file cwrapper.cpp "cwrapper.cpp")
(invoke ,(cxx-for-target)
"-std=c++11"
"-fPIC"
"-shared"
"-o" "libearcut.so"
"cwrapper.cpp")
(install-file "libearcut.so"
(string-append out "/lib"))))))
(inputs
`(("gcc-toolchain" ,(S "gcc-toolchain"))
("cwrapper.cpp"
,(origin
(method url-fetch)
(uri "https://raw.githubusercontent.com/JuliaPackaging/Yggdrasil/7e9ec714d786c4c841a80bdf75b84570c5bda7a1/E/EarCut/bundled/cwrapper.cpp")
(file-name (string-append "cwrapper-for-earcut-for-julia-earcut-jll-" version ".cpp"))
(sha256
(base32 "0yf0r20306qsk1yrls5cz34vpfiazfdqc44f3mqmi76yq1ii0n09"))))))
(native-inputs
`(("tar" ,(S "tar"))
("xz" ,(S "xz"))))
(home-page "https://github.com/mapbox/earcut.hpp")
(synopsis "Header version of EarCut.js")
(description "")
(properties '((hidden? . #t)))
(license license:expat)))
(define-public julia-binaryprovider
(package
(name "julia-binaryprovider")
(version "0.5.10")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaPackaging/BinaryProvider.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "00kin10n3fv5352fx3a4wh8l581702iqqhfz2sng773hkljndi9v"))))
(build-system julia-build-system)
(arguments
'(#:tests? #f ; test suite attempts to download packages
))
(inputs
`(
("busybox" ,(S "busybox"))
))
(home-page "https://github.com/JuliaPackaging/BinaryProvider.jl")
(synopsis "binary provider for Julia")
(description "Packages are installed to a @code{Prefix}; a folder that acts similar to the @code{/usr/local} directory on Unix-like systems, containing a @code{bin} folder for binaries, a @code{lib} folder for libraries, etc... @code{Prefix} objects can have tarballs @code{install()}'ed within them, @code{uninstall()}'ed from them, etc...")
(license license:expat)))
