Merge remote-tracking branch 'origin/master' into core-updates

1 files changed, 366 insertions, 0 deletions

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index f6de56e858..32288e980b 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -147,6 +147,42 @@ ANSI escape codes to another format.")
 provides functions to run a few automatable checks for Julia packages.")
     (license license:expat)))
 
+(define-public julia-arnoldimethod
+  (package
+    (name "julia-arnoldimethod")
+    (version "0.2.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaLinearAlgebra/ArnoldiMethod.jl")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1gs7pikgdg436srxxfywpnp12ay1mf45f7z80wym92rfrjzakwh2"))))
+    (build-system julia-build-system)
+    (propagated-inputs
+     (list julia-genericschur julia-staticarrays))
+    (home-page "https://github.com/JuliaLinearAlgebra/ArnoldiMethod.jl")
+    (synopsis "Implicitly Restarted Arnoldi Method, natively in Julia")
+    (description
+     "@code{ArnoldiMethod.jl} provides an iterative method to find a few
+approximate solutions to the eigenvalue problem in standard form with main
+goals:
+
+@itemize
+@item Having a native Julia implementation of the @code{eigs} function that
+performs as well as ARPACK.  With native we mean that its implementation should
+be generic and support any number type.  Currently the partialschur function
+does not depend on LAPACK, and removing the last remnants of direct calls to
+BLAS is in the pipeline.
+
+@item Removing the dependency of the Julia language on ARPACK.  This goal was
+already achieved before the package was stable enough, since ARPACK moved to a
+separate repository @code{Arpack.jl}.
+@end itemize")
+    (license license:expat)))
+
 (define-public julia-arrayinterface
   (package
     (name "julia-arrayinterface")
@@ -226,6 +262,36 @@ appropriate BLAS or optimised Julia linear algebra routines.  This supports a
 much wider class of matrix types than Julia's in-built @code{StridedArray}.")
     (license license:expat)))
 
+(define-public julia-astrotime
+  (package
+    (name "julia-astrotime")
+    (version "0.7.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaAstro/AstroTime.jl")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "032hlanan49ypqh4lwlf91pg7052c8h5sgbxqc1771b8j9srbyd2"))))
+    (build-system julia-build-system)
+    (native-inputs
+     (list julia-measurements))
+    (propagated-inputs
+     (list julia-erfa
+           julia-earthorientation
+           julia-itemgraphs
+           julia-macrotools
+           julia-muladdmacro
+           julia-reexport))
+    (home-page "https://github.com/JuliaAstro/AstroTime.jl")
+    (synopsis "Astronomical time keeping in Julia")
+    (description "@code{AstroTime.jl} provides a high-precision, time-scale
+aware, @code{DateTime}-like data type which supports all commonly used
+astronomical time scales.")
+    (license license:expat)))
+
 (define-public julia-automa
   (package
     (name "julia-automa")
@@ -1252,6 +1318,40 @@ both the 256 color and 24 bit true color extensions, and the different text
 styles available to terminals.")
     (license license:expat)))
 
+(define-public julia-cstparser
+  (package
+    (name "julia-cstparser")
+    (version "3.3.4")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/julia-vscode/CSTParser.jl")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "162jpcdph26ybg7rajbvfcbpnngygybpzk5bry4c4ppda3m1dl1i"))))
+    (build-system julia-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'fix-or-ignore-tests
+            (lambda _
+              (substitute* "test/iterate.jl"
+                (("parser.jl")
+                 (string-append #$output "/share/julia/loadpath/CSTParser/test/parser.jl"))
+                (("../src")
+                 (string-append #$output "/share/julia/loadpath/CSTParser/src")))
+              (substitute* "test/check_base.jl"
+                (("testset.*" all)
+                 (string-append all "return\n"))))))))
+    (inputs (list julia-tokenize))
+    (home-page "https://github.com/julia-vscode/CSTParser.jl")
+    (synopsis "Parser for Julia")
+    (description "This package provides a parser for Julia code.")
+    (license license:expat)))
+
 (define-public julia-csv
   (package
     (name "julia-csv")
@@ -1829,6 +1929,31 @@ them.  Conversions and promotions are defined to allow performing operations on
 combinations of dual numbers with predefined Julia numeric types.")
     (license license:expat)))
 
+(define-public julia-earthorientation
+  (package
+    (name "julia-earthorientation")
+    (version "0.7.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaAstro/EarthOrientation.jl")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1fschx4qmfd83q0ymgbzqi1dl0drbh45cd7hlcbqnm9lfmw2d847"))))
+    (build-system julia-build-system)
+    (propagated-inputs
+     (list julia-leapseconds
+           julia-optionaldata
+           julia-remotefiles))
+    (home-page "https://github.com/JuliaAstro/EarthOrientation.jl")
+    (synopsis "Calculate Earth orientation parameters from IERS tables in Julia")
+    (description
+     "This package provides a functionality to calculate Earth orientation parameters
+with data retrieved from @acronym{IERS, International Earth Rotation Service}.")
+    (license license:expat)))
+
 (define-public julia-ellipsisnotation
   (package
     (name "julia-ellipsisnotation")
@@ -3051,6 +3176,33 @@ assigned its own index, which is used to retrieve the value from the
 indexed images, sometimes called \"colormap images\" or \"paletted images.\"")
     (license license:expat)))
 
+(define-public julia-inflate
+  (package
+    (name "julia-inflate")
+    (version "0.1.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/GunnarFarneback/Inflate.jl")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "16nbl40b819yzmfqs860xbcbx8nnxm0pkvzj49qmxibv5jnsj47q"))))
+    (build-system julia-build-system)
+    (arguments
+     ;; FIXME: Tests fail hard with a lot of errors.
+     '(#:tests? #f))
+    (propagated-inputs
+     (list julia-codeczlib))
+    (home-page "https://github.com/GunnarFarneback/Inflate.jl")
+    (synopsis "Julia implementation of zlib decompression")
+    (description "Inflate provides a pure Julia implementation of zlib decompression
+functionality, with both in- memory and streaming interfaces.  This covers
+decompression of the Deflate algorithm and the Zlib and Gzip wrapper formats, as
+specified in RFC 1950, RFC 1951, and RFC 1952.")
+    (license license:expat)))
+
 (define-public julia-infinity
   (package
     (name "julia-infinity")
@@ -3378,6 +3530,31 @@ external IRs.  It can be used with Julia metaprogramming tools such as
 Cassette.")
     (license license:expat)))
 
+(define-public julia-itemgraphs
+  (package
+    (name "julia-itemgraphs")
+    (version "0.4.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/helgee/ItemGraphs.jl")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "16w30y7s922dzp7i64wxdrafv4gy13v3rl4k1z5jkvnmnw68kygg"))))
+    (build-system julia-build-system)
+    (propagated-inputs
+     (list julia-lightgraphs))
+    (home-page "https://github.com/helgee/ItemGraphs.jl")
+    (synopsis "Shortest paths between items")
+    (description
+     "ItemGraphs is a simple wrapper around LightGraphs that enables most
+common use case for graph-like data structures: with collection of items that
+are in relations between each other providing the shortest path between two
+items.")
+    (license license:expat)))
+
 (define-public julia-iteratorinterfaceextensions
   (package
     (name "julia-iteratorinterfaceextensions")
@@ -3576,6 +3753,100 @@ equations in string literals in the Julia language.")
 implementation of matrix-free methods for iterative solvers.")
     (license license:expat)))
 
+(define-public julia-leapseconds
+  (package
+    (name "julia-leapseconds")
+    (version "1.1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaTime/LeapSeconds.jl")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "13xa49dx11n7ii77rw6300h1rfl4qlq05ypsprvfmvyww81angkp"))))
+    (build-system julia-build-system)
+    (native-inputs
+     (list julia-erfa))
+    (home-page "https://github.com/JuliaTime/LeapSeconds.jl")
+    (synopsis "Leap seconds in Julia")
+    (description
+     "@code{LeapSeconds} provides a functionality to return the difference
+between @acronym{TAI, International Atomic Time} and @acronym{UTC, Coordinated
+Universal Time} or vice versa for a given date.  For dates after 1972-01-01, this
+is the number of leap seconds.")
+    (license license:expat)))
+
+(define-public julia-lightgraphs
+  (package
+    (name "julia-lightgraphs")
+    (version "1.3.5")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/sbromberger/LightGraphs.jl")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0ygnbzx32b9ciwgg0rn5i0m33dvrb6dh3an6bnmzac1w67sy2vxq"))))
+    (build-system julia-build-system)
+    (arguments
+     (list
+       #:phases
+       #~(modify-phases %standard-phases
+           ;; FIXME: 8x tests fails adjusting for now.
+           ;; ERROR: LoadError: Some tests did not pass: 29548 passed, 0 failed,
+           ;; 8 errored, 0 broken.
+           (add-after 'unpack 'adjust-tests
+             (lambda _
+               (substitute* "test/runtests.jl"
+                 ;; Got exception outside of a @test BoundsError: attempt to
+                 ;; access 1-element Vector{SubString{String}} at index [2]
+                 ((".*degeneracy.*") "")
+                 ;; Got exception outside of a @test type DataType has no field
+                 ;; mutable
+                 ((".*shortestpaths.*") ""))
+               (substitute* "test/experimental/experimental.jl"
+                 ;; Got exception outside of a @test type DataType has no field mutable
+                 (("\"shortestpaths\",") ""))
+               (substitute* "test/linalg/runtests.jl"
+                 ;; ArgumentError: Illegal buffers for SparseMatrixCSC
+                 ;; construction 5 [1, 3, 5, 7, 9, 10] [1, 2, 1, 3, 2, 4, 3, 5,
+                 ;; 4] [1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
+                 ;;
+                 ;;  ArgumentError: Illegal buffers for SparseMatrixCSC
+                 ;;  construction 5 UInt16[0x0001, 0x0003, 0x0005, 0x0007,
+                 ;;  0x0009, 0x000a] UInt16[0x0001, 0x0002, 0x0001, 0x0003,
+                 ;;  0x0002, 0x0004, 0x0003, 0x0005, 0x0004] [1, 1, 1, 1, 1, 1,
+                 ;;  1, 1, 1, 1]
+                 ;;
+                 ;;  ArgumentError: Illegal buffers for SparseMatrixCSC
+                 ;;  construction 5 Int32[1, 3, 5, 7, 9, 10] Int32[1, 2, 1, 3,
+                 ;;  2, 4, 3, 5, 4] [1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
+                 ((".*spectral.*") ""))
+               (substitute* "test/parallel/runtests.jl"
+                 ;; Got exception outside of a @test type DataType has no field
+                 ;; mutable
+                 ((".*shortestpaths/johnson.*") "")
+                 ;; Got exception outside of a @test TaskFailedException nested
+                 ;; task error: On worker 2: UndefVarError: nv not defined
+                 ((".*utils.*") "")))))))
+    (propagated-inputs
+     (list julia-arnoldimethod
+           julia-datastructures
+           julia-inflate
+           julia-simpletraits))
+    (home-page "https://github.com/sbromberger/LightGraphs.jl")
+    (synopsis "Optimized graphs package for Julia")
+    (description
+     "LightGraphs offers both (a) a set of simple, concrete graph implementations --
+Graph (for undirected graphs) and DiGraph (for directed graphs), and (b) an API
+for the development of more sophisticated graph implementations under the
+AbstractGraph type.")
+    (license license:bsd-2)))
+
 (define-public julia-linesearches
   (package
     (name "julia-linesearches")
@@ -4016,6 +4287,33 @@ aims to provide easy-to-use tools for such tasks.")
 Julia, with type-driven, overloadable packing/unpacking functionality.")
     (license license:expat)))
 
+(define-public julia-muladdmacro
+  (package
+    (name "julia-muladdmacro")
+    (version "0.2.4")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/SciML/MuladdMacro.jl")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0pvmfw7f3igpwx0w8c8i40pls0wfm248b1i662wnlrkqiw56j0yq"))))
+    (build-system julia-build-system)
+    (home-page "https://github.com/SciML/MuladdMacro.jl")
+    (synopsis "Julia macro to convert expressions to use muladd calls and FMA operations")
+    (description
+     "This package provides the @code{@@muladd} macro.  It automatically converts
+expressions with multiplications and additions or subtractions to calls with
+muladd which then fuse via FMA when it would increase the performance of the
+code.  The @code{@@muladd} macro can be placed on code blocks and it will automatically
+find the appropriate expressions and nest muladd expressions when necessary.  In
+mixed expressions summands without multiplication will be grouped together and
+evaluated first but otherwise the order of evaluation of multiplications and
+additions is not changed.")
+    (license license:expat)))
+
 (define-public julia-mutablearithmetics
   (package
     (name "julia-mutablearithmetics")
@@ -4259,6 +4557,29 @@ optimisation rules, and tools for applying them to deeply nested models.")
 JuliaNLSolvers packages.")
     (license license:expat)))
 
+(define-public julia-optionaldata
+  (package
+    (name "julia-optionaldata")
+    (version "1.0.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/helgee/OptionalData.jl")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "11js258j7cz6362ijsi24nih3lx90aalf8k1n3fv6v7iqas8bz5s"))))
+    (build-system julia-build-system)
+    (home-page "https://github.com/helgee/OptionalData.jl")
+    (synopsis "Work with global data that might not be available")
+    (description
+     "This package provides the @code{@@OptionalData} macro and the corresponding
+OptData type which is a thin wrapper around a nullable value (of type @code{Union{T,
+Nothing} where T)}.  It allows you to load and access globally available data at
+runtime in a type-stable way.")
+    (license license:expat)))
+
 (define-public julia-orderedcollections
   (package
     (name "julia-orderedcollections")
@@ -4953,6 +5274,31 @@ recursive arrays like arrays of arrays.")
     (description "This package provides tools to re-export modules and symbols.")
     (license license:expat)))
 
+(define-public julia-remotefiles
+  (package
+    (name "julia-remotefiles")
+    (version "0.5.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/helgee/RemoteFiles.jl")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1zpklzpd4ckp7s4wbf93qmq3dyyrx4pzl41x5i9zbiskadhniqnh"))))
+    (build-system julia-build-system)
+    (arguments
+     '(#:tests? #f)) ; Tests try to download from Internet.
+    (propagated-inputs
+     (list julia-fileio julia-http))
+    (home-page "https://github.com/helgee/RemoteFiles.jl")
+    (synopsis "Download files from the Internet and keep them up-to-date")
+    (description
+     "This package provides a functionality of files download with cURL, wget or
+@code{HTTP.jl} backends.")
+    (license license:expat)))
+
 (define-public julia-referencetests
   (package
     (name "julia-referencetests")
@@ -5928,6 +6274,26 @@ standard named test images and example images for the internal usage in
 package.")
     (license license:expat)))
 
+(define-public julia-tokenize
+  (package
+    (name "julia-tokenize")
+    (version "0.5.24")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaLang/Tokenize.jl")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1l3dy6nad0viavzy26lfnhzpd3gcxgaq7yvm7h1ja280xsh60p3i"))))
+    (build-system julia-build-system)
+    (home-page "https://github.com/JuliaGPU/Tokenize.jl")
+    (synopsis "Tokenize a string or buffer containing Julia code")
+    (description "This package takes a string or buffer containing Julia code,
+performs lexical analysis and returns a stream of tokens.")
+    (license license:expat)))
+
 (define-public julia-tracker
   (package
     (name "julia-tracker")