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authorEfraim Flashner2021-06-13 21:55:30 +0300
committerEfraim Flashner2021-06-13 21:55:30 +0300
commit22956c03a2a10f21ea4c9aa912f0a5836403d353 (patch)
treebaf06801debb38e088a0b605c76a291e5b8b52fb /gn/packages
parent4644e440af5c81beb30b5b768079e85bed3c115e (diff)
downloadguix-bioinformatics-22956c03a2a10f21ea4c9aa912f0a5836403d353.tar.gz
gn: Julia packaging
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/julia.scm211
1 files changed, 150 insertions, 61 deletions
diff --git a/gn/packages/julia.scm b/gn/packages/julia.scm
index 285c1d9..2aefdaa 100644
--- a/gn/packages/julia.scm
+++ b/gn/packages/julia.scm
@@ -832,7 +832,7 @@ of packages designed to support image processing and computer vision.")
(define-public julia-fileio
(package
(name "julia-fileio")
- (version "1.9.0")
+ (version "1.9.1")
(source
(origin
(method git-fetch)
@@ -841,7 +841,7 @@ of packages designed to support image processing and computer vision.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "15q4bmya5bn17pxfq1nbs1y05y723zb711ps0q8164c086yrj6d9"))))
+ (base32 "1b18x43i737g5q41n9818xbnc2pgd98q1m6yw3h29yri0clg4gfx"))))
(build-system julia-build-system)
(arguments
`(#:tests? #f ; skip for now
@@ -853,13 +853,17 @@ of packages designed to support image processing and computer vision.")
`(("julia-requires" ,julia-requires)))
(native-inputs
`(
- ;("julia-filepathsbase" ,julia-filepathsbase)
+ ;("julia-csvfiles" ,julia-csvfiles)
+ ;("julia-colortypes" ,julia-colortypes)
+ ("julia-filepathsbase" ,julia-filepathsbase)
+ ;("julia-http" ,julia-http)
))
(home-page "https://github.com/JuliaIO/FileIO.jl")
(synopsis "Main Package for IO, loading all different kind of files")
(description "FileIO aims to provide a common framework for detecting file formats and dispatching to appropriate readers/writers. The two core functions in this package are called load and save, and offer high-level support for formatted files (in contrast with julia's low-level read and write). To avoid name conflicts, packages that provide support for standard file formats through functions named load and save are encouraged to register with FileIO.")
(license license:expat)))
+;; ready to upstream
(define-public julia-filepathsbase
(package
(name "julia-filepathsbase")
@@ -872,36 +876,21 @@ of packages designed to support image processing and computer vision.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32
- "136wm4ik6isrdanmpi4gdr1qw0qhr15i925qzjxbawk5hnyzwng9"))))
+ (base32 "136wm4ik6isrdanmpi4gdr1qw0qhr15i925qzjxbawk5hnyzwng9"))))
(build-system julia-build-system)
(arguments
- `(;#:tests? #f
- ))
- (propagated-inputs
- `(
- ;("julia-requires" ,julia-requires)
- ;("julia-fillarrays" ,julia-fillarrays)
- ;("julia-linesearches" ,julia-linesearches)
- ;("julia-nlsolversbase" ,julia-nlsolversbase)
- ;("julia-nanmath" ,julia-nanmath)
- ;("julia-parameters" ,julia-parameters)
- ;("julia-positivefactorizations" ,julia-positivefactorizations)
- ;("julia-statsbase" ,julia-statsbase)
- ))
- (native-inputs
- `(
- ("julia-jlso" ,julia-jlso)
- ))
+ `(#:tests? #f)) ; Cycle with JLSO.jl
(home-page "https://github.com/rofinn/FilePathsBase.jl")
(synopsis "Filesystem path types in Julia")
- (description "FilePathsBase.jl provides a type based approach to working with filesystem paths in julia.")
+ (description "@code{FilePathsBase.jl} provides a type based approach to
+working with filesystem paths in Julia.")
(license license:expat)))
+;; unneeded
(define-public julia-jlso
(package
(name "julia-jlso")
- (version "2.5.0")
+ (version "2.6.0")
(source
(origin
(method git-fetch)
@@ -910,8 +899,7 @@ of packages designed to support image processing and computer vision.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32
- "1x00mrn4njvkhjns4g8bzjj40g4n6slaxlpsbbccalyabs9sz6id"))))
+ (base32 "0wmwpf6nh4sfcm6daq7hfrvas7ian0kdh501lfv4r0js1d2fxszf"))))
(build-system julia-build-system)
(arguments
`(;#:tests? #f
@@ -919,23 +907,29 @@ of packages designed to support image processing and computer vision.")
(propagated-inputs
`(
("julia-bson" ,julia-bson)
- ;("julia-fillarrays" ,julia-fillarrays)
- ;("julia-linesearches" ,julia-linesearches)
- ;("julia-nlsolversbase" ,julia-nlsolversbase)
- ;("julia-nanmath" ,julia-nanmath)
- ;("julia-parameters" ,julia-parameters)
- ;("julia-positivefactorizations" ,julia-positivefactorizations)
- ;("julia-statsbase" ,julia-statsbase)
+ ;("julia-codeczlib" ,julia-codeczlib)
+ ("julia-filepathsbase" ,julia-filepathsbase)
+ ;("julia-memento" ,julia-memento)
+ ;("julia-timezones" ,julia-timezones)
))
(native-inputs
`(
- ;("julia-jlso" ,julia-jlso)
+ ;("julia-axisarrays" ,julia-axisarrays)
+ ;("julia-dataframes" ,julia-dataframes)
+ ;("julia-dates" ,julia-dates)
+ ;("julia-distributed" ,julia-distributed)
+ ;("julia-distributions" ,julia-distributions)
+ ;("julia-documenter" ,julia-documenter)
+ ;("julia-interactiveutils" ,julia-interactiveutils)
+ ;("julia-suppressor" ,julia-suppressor)
+ ;("julia-timezones" ,julia-timezones)
))
(home-page "https://github.com/invenia/JLSO.jl")
(synopsis "Julia Serialized Object (JLSO) file format for storing checkpoint data")
- (description "JLSO is a storage container for serialized Julia objects. Think of it less as a serialization format but as a container, that employs a serializer, and a compressor, handles all the other concerns including metadata and saving. Such that the serializer just needs to determine how to turn a julia object into a streamVector{UInt8}, and the compressor just needs to determine how to turn one stream of UInt8s into a smaller one (and the reverse).")
+ (description "@code{JLSO} is a storage container for serialized Julia objects. Think of it less as a serialization format but as a container, that employs a serializer, and a compressor, handles all the other concerns including metadata and saving. Such that the serializer just needs to determine how to turn a Julia object into a streamVector{UInt8}, and the compressor just needs to determine how to turn one stream of UInt8s into a smaller one (and the reverse).")
(license license:expat)))
+;; ready to upstream
(define-public julia-bson
(package
(name "julia-bson")
@@ -948,27 +942,10 @@ of packages designed to support image processing and computer vision.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32
- "1l5608ma2ys7v2gpcqbiv9mwfc6yrlqkihrfx1pf7fgv5llhd4fn"))))
+ (base32 "1l5608ma2ys7v2gpcqbiv9mwfc6yrlqkihrfx1pf7fgv5llhd4fn"))))
(build-system julia-build-system)
- (arguments
- `(;#:tests? #f
- ))
- (propagated-inputs
- `(
- ;("julia-bson" ,julia-bson)
- ;("julia-fillarrays" ,julia-fillarrays)
- ;("julia-linesearches" ,julia-linesearches)
- ;("julia-nlsolversbase" ,julia-nlsolversbase)
- ;("julia-nanmath" ,julia-nanmath)
- ;("julia-parameters" ,julia-parameters)
- ;("julia-positivefactorizations" ,julia-positivefactorizations)
- ;("julia-statsbase" ,julia-statsbase)
- ))
(native-inputs
- `(
- ("julia-dataframes" ,julia-dataframes)
- ))
+ `(("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
@@ -976,6 +953,7 @@ 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")
@@ -988,12 +966,24 @@ structures.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32
- "0ab03l9q9vmc176711hp0adc456fphh0d762fv6hcvzvhms4xjkz"))))
+ (base32 "0ab03l9q9vmc176711hp0adc456fphh0d762fv6hcvzvhms4xjkz"))))
(build-system julia-build-system)
(arguments
- `(#:tests? #f ; not all dependants packaged
- ))
+ `(#: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)
@@ -1004,9 +994,8 @@ structures.")
("julia-sortingalgorithms" ,julia-sortingalgorithms)
("julia-tabletraits" ,julia-tabletraits)))
(native-inputs
- `(
- ;("julia-categoricalarrays" ,julia-categoricalarrays)
- ;("julia-combinatorics" ,julia-combinatorics)
+ `(("julia-categoricalarrays" ,julia-categoricalarrays)
+ ("julia-combinatorics" ,julia-combinatorics)
("julia-datastructures" ,julia-datastructures)
("julia-datavalues" ,julia-datavalues)
("julia-offsetarrays" ,julia-offsetarrays)
@@ -1016,6 +1005,106 @@ structures.")
(description "Tools for working with tabular data in Julia.")
(license license:expat)))
+;; ready to upstream
+(define-public julia-combinatorics
+ (package
+ (name "julia-combinatorics")
+ (version "1.0.2")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/JuliaMath/Combinatorics.jl")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0gafqkqi874zfm9h99akw9q95lk3ih5gip2h8p12fj9h7rvyf4j5"))))
+ (build-system julia-build-system)
+ (home-page "https://github.com/JuliaMath/Combinatorics.jl")
+ (synopsis "Combinatorics library for Julia")
+ (description "This package provides a combinatorics library for Julia,
+focusing mostly (as of now) on enumerative combinatorics and permutations.")
+ (license license:expat)))
+
+;; ready to upstream
+(define-public julia-categoricalarrays
+ (package
+ (name "julia-categoricalarrays")
+ (version "0.10.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/JuliaData/CategoricalArrays.jl")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "09ddkl5cspcihwrld8g1nf31i66hf20d8hsilj1swfcnshmns0vx"))))
+ (build-system julia-build-system)
+ (propagated-inputs
+ `(("julia-dataapi" ,julia-dataapi)
+ ("julia-json" ,julia-json)
+ ("julia-missings" ,julia-missings)
+ ("julia-recipesbase" ,julia-recipesbase)
+ ("julia-structtypes" ,julia-structtypes)))
+ (native-inputs
+ `(("julia-json3" ,julia-json3)
+ ("julia-plots" ,julia-plots)
+ ("julia-pooledarrays" ,julia-pooledarrays)))
+ (home-page "https://github.com/JuliaData/CategoricalArrays.jl")
+ (synopsis "Arrays for working with categorical data")
+ (description "This package provides tools for working with categorical
+variables, both with unordered (nominal variables) and ordered categories
+(ordinal variables), optionally with missing values.")
+ (license license:expat)))
+
+;; ready to upstream
+(define-public julia-structtypes
+ (package
+ (name "julia-structtypes")
+ (version "1.7.2")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/JuliaData/StructTypes.jl")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "02mn4kkhn3927dk7945c9bjwlldihydxgn5ilmqqvs8dknvbw8p1"))))
+ (build-system julia-build-system)
+ (home-page "https://juliadata.github.io/StructTypes.jl/stable/")
+ (synopsis "Abstract definitions and convenience methods for Julia objects")
+ (description "This package provides the @code{StructTypes.StructType} trait
+for Julia types to declare the kind of \"struct\" they are, providing
+serialization/deserialization packages patterns and strategies to automatically
+construct objects.")
+ (license license:expat)))
+
+;; ready to upstream
+(define-public julia-json3
+ (package
+ (name "julia-json3")
+ (version "1.8.2")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/quinnj/JSON3.jl")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1mc3byqm6ygg4mjpdrx6grkr4gn06p25nr7050jgq1k2cf06iqba"))))
+ (build-system julia-build-system)
+ (propagated-inputs
+ `(("julia-parsers" ,julia-parsers)
+ ("julia-structtypes" ,julia-structtypes)))
+ (home-page "https://github.com/quinnj/JSON3.jl")
+ (synopsis "JSON package for Julia")
+ (description "This package provides another JSON package for Julia, with a
+focus on speed and slick struct mapping.")
+ (license license:expat)))
+
;; TODO: unbundle javascript calls to cdn.jsdelivr.net
(define-public julia-pluto
(package