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-rw-r--r--VERSION2
-rw-r--r--gn/packages/julia.scm245
2 files changed, 1 insertions, 246 deletions
diff --git a/VERSION b/VERSION
index 78cb503..ccd904d 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-7b59508ca711d1fe299de3f8d9710da36aeb6829
+03f6a44cfc46cd49886d7a7ec6429cc22dd97c9c
diff --git a/gn/packages/julia.scm b/gn/packages/julia.scm
index f53431a..491db13 100644
--- a/gn/packages/julia.scm
+++ b/gn/packages/julia.scm
@@ -202,36 +202,6 @@ leave-one-chromosome-out}, computation of kinship matrices, and support for
distributed computing.")
(license license:gpl3)))
-;; ready to upstream
-(define-public julia-pyplot
- (package
- (name "julia-pyplot")
- (version "2.10.0")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/JuliaPy/PyPlot.jl")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32 "007zs0imfgs69f30pp2a3rc93kl0qiq7qjx6ig35z4wzkmps4skd"))))
- (build-system julia-build-system)
- (propagated-inputs
- `(("julia-colors" ,julia-colors)
- ("julia-latexstrings" ,julia-latexstrings)
- ("julia-pycall" ,julia-pycall)
- ("julia-versionparsing" ,julia-versionparsing)
- ;; python-matplotlib is expected to be available at runtime.
- ("python-matplotlib" ,(S "python-matplotlib"))))
- (home-page "https://github.com/JuliaPy/PyPlot.jl")
- (synopsis "Plotting for Julia based on matplotlib.pyplot")
- (description "This module provides a Julia interface to the Matplotlib
-plotting library from Python, and specifically to the @code{matplotlib.pyplot}
-module. PyPlot uses the Julia PyCall package to call Matplotlib directly from
-Julia with little or no overhead (arrays are passed without making a copy).")
- (license license:expat)))
-
(define-public julia-conda
(package
(name "julia-conda")
@@ -292,29 +262,6 @@ Julia with little or no overhead (arrays are passed without making a copy).")
(description "This package allows one to use @code{conda} as a cross-platform binary provider for Julia for other Julia packages, especially to install binaries that have complicated dependencies like Python.")
(license license:expat)))
-;; ready to upstream
-(define-public julia-latexstrings
- (package
- (name "julia-latexstrings")
- (version "1.2.1")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/stevengj/LaTeXStrings.jl")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32 "117z27krcf8fydgp6mb0pgn75r4gng9qs7v90qb4bqzsry3faadp"))))
- (build-system julia-build-system)
- (native-inputs
- `(("julia-documenter" ,julia-documenter)))
- (home-page "https://github.com/stevengj/LaTeXStrings.jl")
- (synopsis "Input and display of LaTeX equation strings")
- (description "This is a small package to make it easier to type LaTeX
-equations in string literals in the Julia language.")
- (license license:expat)))
-
(define-public julia-distributions
(package
(name "julia-distributions")
@@ -458,84 +405,6 @@ optimization of functions.")
(description "Plots is a plotting API and toolset.")
(license license:expat)))
-;; ready to upstream
-(define-public julia-bson
- (package
- (name "julia-bson")
- (version "0.3.3")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/JuliaIO/BSON.jl")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32 "1l5608ma2ys7v2gpcqbiv9mwfc6yrlqkihrfx1pf7fgv5llhd4fn"))))
- (build-system julia-build-system)
- (native-inputs
- `(("julia-dataframes" ,julia-dataframes)))
- (home-page "https://github.com/JuliaIO/BSON.jl")
- (synopsis "Binary JSON serialisation format")
- (description "@code{BSON.jl} is a Julia package for working with the Binary
-JSON serialisation format. It can be used as a general store for Julia data
-structures.")
- (license license:expat)))
-
-;; ready to upstream
-(define-public julia-dataframes
- (package
- (name "julia-dataframes")
- (version "1.2.2")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/JuliaData/DataFrames.jl")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32 "1bk0amrghgjrkyn1mm4ac23swwbgszl1d0qyl9137qj5zvv9dasp"))))
- (build-system julia-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'skip-failing-test
- (lambda _
- ;; Tests with non-standard colors.
- (substitute* "test/show.jl"
- (("test (sprint\\(show, df, context=:color=>true)" _ test)
- (string-append "test_nowarn " test)))
- (substitute* "test/io.jl"
- (("testset \\\"improved.*" all)
- (string-append all "return\n")))
- (substitute* "test/join.jl"
- (("test (levels\\(outerjoin\\(B)" _ test)
- (string-append "test_nowarn " test)))
- #t)))))
- (propagated-inputs
- `(("julia-dataapi" ,julia-dataapi)
- ("julia-invertedindices" ,julia-invertedindices)
- ("julia-iteratorinterfaceextensions" ,julia-iteratorinterfaceextensions)
- ("julia-missings" ,julia-missings)
- ("julia-pooledarrays" ,julia-pooledarrays)
- ("julia-prettytables" ,julia-prettytables)
- ("julia-reexport" ,julia-reexport)
- ("julia-sortingalgorithms" ,julia-sortingalgorithms)
- ("julia-tables" ,julia-tables)
- ("julia-tabletraits" ,julia-tabletraits)))
- (native-inputs
- `(("julia-categoricalarrays" ,julia-categoricalarrays)
- ("julia-combinatorics" ,julia-combinatorics)
- ("julia-datastructures" ,julia-datastructures)
- ("julia-datavalues" ,julia-datavalues)
- ("julia-offsetarrays" ,julia-offsetarrays)
- ("julia-unitful" ,julia-unitful)))
- (home-page "https://dataframes.juliadata.org/stable/")
- (synopsis "In-memory tabular data")
- (description "Tools for working with tabular data in Julia.")
- (license license:expat)))
-
;; TODO: unbundle javascript calls to cdn.jsdelivr.net
(define-public julia-pluto
(package
@@ -612,85 +481,6 @@ native to Julia. Use it with the @code{@@bind} macro in Pluto.")
(license license:expat)))
;; ready to upstream
-(define-public julia-configurations
- (package
- (name "julia-configurations")
- (version "0.16.4")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/Roger-luo/Configurations.jl")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32 "1b23p0zk8dx2sf01cnw177mqci7qd81b9s32ixz9clsh0r0icl1b"))))
- (build-system julia-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'fix-tests
- (lambda _
- (substitute* "test/runtests.jl"
- (("option.toml") "test/option.toml"))
- #t))
- (add-after 'unpack 'dont-use-exproniconlite
- (lambda _
- (substitute* '("Project.toml"
- "src/Configurations.jl"
- "test/runtests.jl")
- (("ExproniconLite") "Expronicon"))
- (substitute* "Project.toml"
- (("55351af7-c7e9-48d6-89ff-24e801d99491")
- "6b7a57c9-7cc1-4fdf-b7f5-e857abae3636"))
- #t)))))
- (propagated-inputs
- `(("julia-crayons" ,julia-crayons)
- ("julia-expronicon" ,julia-expronicon)
- ("julia-orderedcollections" ,julia-orderedcollections)))
- (home-page "https://configurations.rogerluo.dev/stable/")
- (synopsis "Options and configurations in Julia")
- (description "@code{Configurations.jl} provides a macro @code{@@option} to
-let you define @code{structs} to represent options/configurations, and serialize
-between different option/configuration file formats such as @code{TOML}.")
- (license license:expat)))
-
-;; ready to upstream
-;; ExproniconLite.jl is autogenerated from this package.
-(define-public julia-expronicon
- (package
- (name "julia-expronicon")
- (version "0.6.10")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/Roger-luo/Expronicon.jl")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32 "0h8aaynqlxrkn8575k5vqmhzil4vvxchhf0bcxa6zwawp558gj2y"))))
- (build-system julia-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'skip-network-tests
- (lambda _
- (substitute* "test/runtests.jl"
- ;; This test tries to access the Julia package registry.
- ((".*expand\\.jl.*") "")))))))
- (propagated-inputs
- `(("julia-mlstyle" ,julia-mlstyle)))
- (native-inputs
- `(("julia-documenter" ,julia-documenter)))
- (home-page "https://expronicon.rogerluo.dev/dev/")
- (synopsis "Collective tools for metaprogramming on Julia Expr")
- (description "This package provides a collection of tools for
-metaprogramming on Julia Expr, the meta programming standard library for
-@code{MLStyle}.")
- (license license:expat)))
-
-;; ready to upstream
(define-public julia-statsfuns
(package
(name "julia-statsfuns")
@@ -1169,41 +959,6 @@ that still support Julia versions older than 1.6.")
(description "This package aims to offer a standard set of Geometry types, which easily work with metadata, query frameworks on geometries and different memory layouts. The aim is to create a solid basis for Graphics/Plotting, finite elements analysis, Geo applications, and general geometry manipulations - while offering a julian API, that still allows performant C-interop.")
(license license:expat)))
-;; ready to upstream
-(define-public julia-structarrays
- (package
- (name "julia-structarrays")
- (version "0.6.3")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/JuliaArrays/StructArrays.jl")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32 "0rjcpyjwzg70n87q5r9c5i1qzigavncslxssm3rk5a3y549py56v"))))
- (build-system julia-build-system)
- (propagated-inputs
- `(("julia-dataapi" ,julia-dataapi)
- ("julia-staticarrays" ,julia-staticarrays)
- ("julia-tables" ,julia-tables)))
- (native-inputs
- `(("julia-documenter" ,julia-documenter)
- ("julia-offsetarrays" ,julia-offsetarrays)
- ("julia-pooledarrays" ,julia-pooledarrays)
- ("julia-typedtables" ,julia-typedtables)
- ("julia-weakrefstrings" ,julia-weakrefstrings)))
- (home-page "https://github.com/JuliaArrays/StructArrays.jl")
- (synopsis "Efficient implementation of struct arrays in Julia")
- (description "This package introduces the type @code{StructArray} which is
-an @code{AbstractArray} whose elements are @code{struct} (for example
-@code{NamedTuples}, or @code{ComplexF64}, or a custom user defined
-@code{struct}). While a @code{StructArray} iterates @code{structs}, the layout
-is column based (meaning each field of the @code{struct} is stored in a separate
-@code{Array}).")
- (license license:expat)))
-
(define-public julia-earcut-jll
;; Only release tag contains just a license file.
(let ((commit "b234ae0c064af12eb5482c7474a64af8be0f511e")