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gn: Update julia packages

wip-tensorflow
Efraim Flashner 3 months ago
parent
commit
0fc3b080e8
Signed by: efraim GPG Key ID: 41AAE7DCCA3D8351
  1. 274
      gn/packages/julia.scm

274
gn/packages/julia.scm

@ -386,7 +386,7 @@ equations in string literals in the Julia language.")
(define-public julia-distributions
(package
(name "julia-distributions")
(version "0.25.1")
(version "0.25.6")
(source
(origin
(method git-fetch)
@ -395,18 +395,17 @@ equations in string literals in the Julia language.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0p3998sh667f1bskd011z9hfdkbdw5kgh9n1771jx4madxscy7dq"))))
(base32 "07n7g5zxp1b82k6yvqa5kh51jww2cy1f5pyvh60k3fp6rdp8sy1j"))))
(build-system julia-build-system)
(arguments
`(;#:tests? #f
))
(propagated-inputs
`(
;("julia-fillarrays" ,julia-fillarrays)
;("julia-distributed" ,julia-distributed)
("julia-fillarrays" ,julia-fillarrays)
("julia-pdmats" ,julia-pdmats)
;("julia-quadgk" ,julia-quadgk)
;("julia-specialfunctions" ,julia-specialfunctions)
("julia-specialfunctions" ,julia-specialfunctions)
("julia-statsbase" ,julia-statsbase)
("julia-statsfuns" ,julia-statsfuns) ; fix Rmath.jl
))
@ -429,7 +428,7 @@ equations in string literals in the Julia language.")
(define-public julia-documenter
(package
(name "julia-documenter")
(version "0.26.3")
(version "0.27.2")
(source
(origin
(method git-fetch)
@ -439,12 +438,11 @@ equations in string literals in the Julia language.")
(file-name (git-file-name name version))
(sha256
(base32
"1d4mdjc56w0hrc50qia361zfp8zapq163cqgagkbbjn0k83zp21x"))))
"0x99ns9fvnpm5jrqgfssfxdspxlx82qx7w5g0jy1x530yknk8ijq"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-docstringextensions" ,julia-docstringextensions)
;; TODO: Switch to julia-iocapture after 0.27.
("julia-iocapture" ,julia-iocapture-0.1)
("julia-iocapture" ,julia-iocapture)
("julia-json" ,julia-json)))
(native-inputs
`(("git" ,(S "git-minimal"))
@ -454,22 +452,6 @@ equations in string literals in the Julia language.")
(description "This package provides a documentation generator for Julia.")
(license license:expat)))
;; Upstream with julia-documenter
(define-public julia-iocapture-0.1
(package
(inherit julia-iocapture)
(name "julia-iocapture")
(version "0.1.1")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaDocs/IOCapture.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0wm8pag5mk46064h3qpvgz8m63138104rq0smx1za7lh7j32925h"))))))
;; ready to upstream with julia-documenter
(define-public julia-documenter-0.22
(package
@ -509,7 +491,7 @@ equations in string literals in the Julia language.")
(define-public julia-documentermarkdown
(package
(name "julia-documentermarkdown")
(version "0.2.1")
(version "0.2.2")
(source
(origin
(method git-fetch)
@ -518,8 +500,7 @@ equations in string literals in the Julia language.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"11l7yrifg8pdr4q6h75zydfw5i8vww07p5bci5mi8gwwcpi3jksb"))))
(base32 "0sx89hi5p2f8zi2rp5qrv06m270d90pxj5d2y5cxls1spax7wqx8"))))
(build-system julia-build-system)
(inputs
;; We don't want to propagate the bootstrap version.
@ -527,10 +508,40 @@ equations in string literals in the Julia language.")
`(("julia-documenter" ,julia-documenter-0.22)))
(home-page "https://github.com/JuliaDocs/DocumenterMarkdown.jl")
(synopsis "Documenter's Markdown")
(description "his package enables the Markdown / MkDocs backend of
(description "This package enables the Markdown / MkDocs backend of
@code{Documenter.jl}.")
(license license:expat)))
(define-public julia-documentertools
(package
(name "julia-documentertools")
(version "0.1.13")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaDocs/DocumenterTools.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "05p57p8xlkn42m1lv9gq4hl96vp7hpj19d51p828ai1rbpcpi3a6"))))
(build-system julia-build-system)
(inputs
;; We don't want to propagate the bootstrap version.
;; Cycle with Documenter.jl in later versions.
`(("julia-documenter" ,julia-documenter-0.22)))
(propagated-inputs
`(
("julia-docstringextensions" ,julia-docstringextensions)
("julia-gumbo" ,julia-gumbo)
;("julia-sass" ,julia-sass)
))
(home-page "https://github.com/JuliaDocs/DocumenterTools.jl")
(synopsis "Extra tools for setting up Documenter")
(description "This package contains utilities for setting up documentation
generation with @code{Documenter.jl}.")
(license license:expat)))
(define-public julia-optim
(package
(name "julia-optim")
@ -571,7 +582,7 @@ optimization of functions.")
(define-public julia-plots
(package
(name "julia-plots")
(version "1.15.1")
(version "1.16.6")
(source
(origin
(method git-fetch)
@ -580,8 +591,7 @@ optimization of functions.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1bw76zzrq4zlwglhr7nkr1h0w0wl1i49rp35nnbbdqkdj46bz52y"))))
(base32 "0ipv9408r4czsx1j01sv2f7ww52b329jc0v79npn4x2mf827nsik"))))
(build-system julia-build-system)
(arguments
`(#:tests? #f ; for now
@ -610,19 +620,19 @@ optimization of functions.")
(native-inputs
`(
;("julia-distributions" ,julia-distributions)
;("julia-fileio" ,julia-fileio)
("julia-fileio" ,julia-fileio)
;("julia-gtk" ,julia-gtk)
;("julia-hdf5" ,julia-hdf5)
("julia-imagemagick" ,julia-imagemagick)
;("julia-images" ,julia-images)
;("julia-offsetarrays" ,julia-offsetarrays)
("julia-offsetarrays" ,julia-offsetarrays)
;("julia-pgfplotsx" ,julia-pgfplotsx)
;("julia-plotlyjs" ,julia-plotlyjs)
;("julia-rdatasets" ,julia-rdatasets)
;("julia-stablerngs" ,julia-stablerngs)
;("julia-staticarrays" ,julia-staticarrays)
("julia-stablerngs" ,julia-stablerngs)
("julia-staticarrays" ,julia-staticarrays)
;("julia-statsplots" ,julia-statsplots)
;("julia-testimages" ,julia-testimages)
("julia-testimages" ,julia-testimages)
;("julia-unicodeplots" ,julia-unicodeplots)
;("julia-visualregressiontests" ,julia-visualregressiontests)
))
@ -743,7 +753,7 @@ variables, both with unordered (nominal variables) and ordered categories
(define-public julia-pluto
(package
(name "julia-pluto")
(version "0.14.7")
(version "0.14.8")
(source
(origin
(method git-fetch)
@ -752,8 +762,7 @@ variables, both with unordered (nominal variables) and ordered categories
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0b2g3j78kpkayhrm3am855cc5kjb3w73ygcvjbvhz2p5i1ivji7b"))))
(base32 "0kzl70fgb6q23yxifkadxrxp7nhc26pqnklna83bqdczk0543q3w"))))
(build-system julia-build-system)
(arguments
`(#:tests? #f ; Many tests need network connectivity or a browser.
@ -805,10 +814,11 @@ 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 "0.15.4")
(version "0.16.0")
(source
(origin
(method git-fetch)
@ -817,19 +827,36 @@ native to Julia. Use it with the @code{@@bind} macro in Pluto.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"1dz1h64nqgcv6ai70pfv2dv4mqx9rqmh08196k7j73bqlc6r00w1"))))
(base32 "033wc6bqslvv6fkknlc725432j2vc2wcji2167klnx3qwlac2965"))))
(build-system julia-build-system)
(arguments
`(#:tests? #f)) ; cannot find test/option.toml
`(#: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-exproniconlite" ,julia-exproniconlite)
("julia-expronicon" ,julia-expronicon)
("julia-orderedcollections" ,julia-orderedcollections)
("julia-toml" ,julia-toml)))
(home-page "https://configurations.rogerluo.dev/stable")
(synopsis "Options & Configurations made easy")
(description "Configurations is a Julia Language package.")
(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)))
;; XXX: Part of base Julia as of 1.6+
@ -853,6 +880,8 @@ native to Julia. Use it with the @code{@@bind} macro in Pluto.")
(description "TOML v1.0.0 parser for Julia.")
(license license:expat)))
;; ready to upstream
;; ExproniconLite.jl is autogenerated from this package.
(define-public julia-expronicon
(package
(name "julia-expronicon")
@ -865,44 +894,41 @@ native to Julia. Use it with the @code{@@bind} macro in Pluto.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0lbzfn1li2ph02z6hl5286bj6bf17g63vfp6qn4cz40d760fcw8a"))))
(base32 "0lbzfn1li2ph02z6hl5286bj6bf17g63vfp6qn4cz40d760fcw8a"))))
(build-system julia-build-system)
(arguments
`(;#:tests? #f
))
(propagated-inputs
`(
;("julia-mlstyle" ,julia-mlstyle)
))
(home-page "https://expronicon.rogerluo.dev/")
`(("julia-mlstyle" ,julia-mlstyle)
("julia-toml" ,julia-toml)))
(native-inputs
`(("julia-documenter" ,julia-documenter)))
(home-page "https://expronicon.rogerluo.dev/dev/")
(synopsis "Collective tools for metaprogramming on Julia Expr")
(description "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)))
;; autogenerated package?
(define-public julia-exproniconlite
;; ready to upstream
(define-public julia-mlstyle
(package
(name "julia-exproniconlite")
(version "0.6.8")
(name "julia-mlstyle")
(version "0.4.10")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/Roger-luo/ExproniconLite.jl")
(url "https://github.com/thautwarm/MLStyle.jl")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"02zm5r3fi7zx4fnr2ikxpapb9rvmnqvklrfyd4j9418q1mryh04l"))))
(base32 "0h1cd7cr4c4cnpqyj3180113gdbvcc047lqphp8a8gq5smp3c059"))))
(build-system julia-build-system)
(native-inputs
`(("julia-documenter" ,julia-documenter)))
(home-page "https://expronicon.rogerluo.dev/")
(synopsis "Collective tools for metaprogramming on Julia Expr")
(description "no fancy pattern matching, no dependencies, Light-weight Expronicon for low latency.
this package is generated by Expronicon, please refer to Expronicon for any issues")
`(("julia-datastructures" ,julia-datastructures)))
(home-page "https://thautwarm.github.io/MLStyle.jl/latest/")
(synopsis "Julia functional programming infrastructures")
(description "This package provides consistent and extensible functional
programming infrastructures, and metaprogramming facilities.")
(license license:expat)))
(define-public julia-statsfuns
@ -943,13 +969,15 @@ native to Julia. Use it with the @code{@@bind} macro in Pluto.")
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaStats/Rmath-julia")
(commit (string-append "v" version))))
;(commit (string-append "v" version))))
(commit "5c5dfd6baca358103fbb47cc03dc0ecee04fb1ff")))
(file-name (git-file-name name version))
(sha256
(base32 "11a6h3wwmpnb2d55pkm6av111b3pxlvxfnbz8b0n77afpllgb8j2"))))
;(base32 "11a6h3wwmpnb2d55pkm6av111b3pxlvxfnbz8b0n77afpllgb8j2"))))
(base32 "04lf8gfnfcppckk9d7hss0ja91yxaax6qz1gzqya9w0shjr386s5"))))
(build-system julia-build-system)
(arguments
`(#:tests? #f ; Test not defined, tests not often run upstream.
`(;#:tests? #f ; Test not defined, tests not often run upstream.
#:phases
(modify-phases %standard-phases
(delete 'precompile)
@ -978,7 +1006,6 @@ native to Julia. Use it with the @code{@@bind} macro in Pluto.")
(package
(name "julia-rmath")
(version "0.7.0")
;(version "0.6.1")
(source
(origin
(method git-fetch)
@ -988,30 +1015,27 @@ native to Julia. Use it with the @code{@@bind} macro in Pluto.")
(file-name (git-file-name name version))
(sha256
(base32 "0cam16ff4v2fl7c9j1wx2ahgjhwba9mk2q6qv3zdknnnqj6w664s"))))
;(base32 "1745xajy5c8hdcy1hgi2rr9lrapr55hp0jm2dcb1ksyskvm5drsr"))))
(build-system julia-build-system)
(arguments
`(;#:tests? #f ; Test not defined
#:phases
`(#:phases
(modify-phases %standard-phases
;(add-after 'unpack 'patch-source
; (lambda _
; ;; see upstream julia bug
; ;; ERROR: LoadError: InitError: UndefVarError: libRmath_path not defined
; (substitute* "src/Rmath.jl"
; (("libRmath\\)") "libRmath_path)"))
; #t))
)
))
(add-after 'unpack 'link-to-librmath-directly
(lambda* (#:key inputs #:allow-other-keys)
(let* ((rmath (assoc-ref inputs "rmath"))
(librmath (string-append rmath "/lib/libRmath-julia.so")))
;; see upstream julia bug
;; ERROR: LoadError: InitError: UndefVarError: libRmath_path not defined
(substitute* "src/Rmath.jl"
(("libRmath\\)") (string-append "\"" librmath "\")")))
;(substitute* "test/runtests.jl"
; (("Rmath\\.libRmath\\)") (string-append "\"" librmath "\")")))
#t))))))
(propagated-inputs
`(
("julia-rmath-jll" ,julia-rmath-jll)
;("julia-rmath-jll" ,julia-rmath-jll-0.2)
))
`(("julia-rmath-jll" ,julia-rmath-jll)))
(inputs
`(("rmath" ,rmath-julia)))
(native-inputs
`(
;("julia-offsetarrays" ,julia-offsetarrays)
))
`(("rmath" ,rmath-julia)))
(home-page "https://github.com/JuliaStats/Rmath.jl")
(synopsis "functions that emulate R's d-p-q-r functions for probability distributions")
(description "
@ -1019,6 +1043,7 @@ native to Julia. Use it with the @code{@@bind} macro in Pluto.")
Archive of functions that emulate R's d-p-q-r functions for probability distributions.")
(license license:expat)))
;; This package seems to be bugged, doesn't load libRmath-julia.so correctly.
(define-public julia-rmath-jll
(package
(name "julia-rmath-jll")
@ -1050,8 +1075,7 @@ native to Julia. Use it with the @code{@@bind} macro in Pluto.")
;; There's a Julia file for each platform, override them all
(find-files "src/wrappers/" "\\.jl$")))))))
(inputs
`(
;; It wants the custom rmath.
`(;; It wants the custom rmath.
("rmath" ,rmath-julia)
;("rmath" ,(S "rmath-standalone"))
))
@ -1062,42 +1086,6 @@ native to Julia. Use it with the @code{@@bind} macro in Pluto.")
(description "This package provides a wrapper for Rmath.")
(license license:expat)))
(define-public julia-rmath-jll-0.2
(package
(name "julia-rmath-jll")
(version "0.2.2+2")
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/JuliaBinaryWrappers/Rmath_jll.jl")
(commit (string-append "Rmath-v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "13wvx4n0ai7bsda3rvlw8xbqwdbdwhjijbgjgl0k2yzq5l8x5dmh"))))
(build-system julia-build-system)
(arguments
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
(substitute* wrapper
(("artifact\"Rmath\"")
(string-append "\"" (assoc-ref inputs "rmath") "\""))))
;; There's a Julia file for each platform, override them all
(find-files "src/wrappers/" "\\.jl$")))))))
(inputs
`(("rmath" ,rmath-julia)))
(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-linesearches
(package
@ -1170,7 +1158,7 @@ floats and complex types.")
(define-public julia-polynomials
(package
(name "julia-polynomials")
(version "2.0.10")
(version "2.0.12")
(source
(origin
(method git-fetch)
@ -1179,7 +1167,7 @@ floats and complex types.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0mz7ls281d6166w9808lwgn007dsk8pqi4qmdf0jiiipy5a0a4ji"))))
(base32 "1ydxw1ich5gkd6mlrr6x4clyjkr0xkmlf0l054g4k73symw2bc7x"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-intervals" ,julia-intervals)
@ -1378,7 +1366,7 @@ that still support Julia versions older than 1.6.")
(define-public julia-geometrybasics
(package
(name "julia-geometrybasics")
(version "0.3.12")
(version "0.3.13")
(source
(origin
(method git-fetch)
@ -1387,7 +1375,7 @@ that still support Julia versions older than 1.6.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1wsx287i1hlzkw7ljfc929ssla6b4qn647nsa3j32v2f8gzd86ag"))))
(base32 "05wq41s6c69zay2awgdhjld8gsycdb5jbvf6a785i3f12av6ndk0"))))
(build-system julia-build-system)
(arguments
`(;#:tests? #f
@ -1421,7 +1409,7 @@ that still support Julia versions older than 1.6.")
(define-public julia-structarrays
(package
(name "julia-structarrays")
(version "0.5.1")
(version "0.6.0")
(source
(origin
(method git-fetch)
@ -1430,10 +1418,11 @@ that still support Julia versions older than 1.6.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "0i1h3pbjp04dwic786yjnx81ifppgcbdysvgjs00cd9zmpn3xnqw"))))
(base32 "05yxsmzi82fp9f0bg5kihpcls4xjxdy4chnnflmg8h4i457pbr5v"))))
(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)
@ -1551,7 +1540,7 @@ is column based (meaning each field of the @code{struct} is stored in a separate
(define-public julia-gr
(package
(name "julia-gr")
(version "0.57.4")
(version "0.57.5")
(source
(origin
(method git-fetch)
@ -1560,8 +1549,7 @@ is column based (meaning each field of the @code{struct} is stored in a separate
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
"0hwzxwnak3sixm8jlm2zz6578gn713sbbznq49s11h38n0aczjx2"))))
(base32 "14nra7fx2g8y2ll3saxgccanzbcl5s58qzgd2jlha3r0ngfhrvxg"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-gr-jll" ,julia-gr-jll)))
@ -1625,7 +1613,7 @@ in Julia).")
(define-public julia-gr-jll
(package
(name "julia-gr-jll")
(version "0.57.2+0")
(version "0.57.3+0")
(source
(origin
(method git-fetch)
@ -1634,7 +1622,7 @@ in Julia).")
(commit (string-append "GR-v" version))))
(file-name (git-file-name name version))
(sha256
(base32 "1fqm531s5pm8q2rqz0gmrbj2qsivmc6x04sgn8gzfpz9jrmglbzq"))))
(base32 "0a568qxxdrfi951s0lhy5081yw8pw6sv39vfkzxw5cxic92w6rbs"))))
(build-system julia-build-system)
(arguments
'(#:tests? #f ; no runtests

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