gn: Upstream julia libraries

1 files changed, 56 insertions, 698 deletions

diff --git a/gn/packages/julia.scm b/gn/packages/julia.scm
index 2a12af6..22c251d 100644
--- a/gn/packages/julia.scm
+++ b/gn/packages/julia.scm
@@ -524,7 +524,7 @@ equations in string literals in the Julia language.")
     (build-system julia-build-system)
     (inputs
      ;; We don't want to propagate the bootstrap version.
-     ;; Cycle with julia-documenter in later versions.
+     ;; Cycle with Documenter.jl in later versions.
      `(("julia-documenter" ,julia-documenter-0.22)))
     (home-page "https://github.com/JuliaDocs/DocumenterMarkdown.jl")
     (synopsis "Documenter's Markdown")
@@ -564,30 +564,6 @@ functions, such as scalar statistics, high-order moment computation, counting,
 ranking, covariances, sampling, and empirical density estimation.")
     (license license:expat)))
 
-;; ready to upstream
-(define-public julia-dataapi
-  (package
-    (name "julia-dataapi")
-    (version "1.6.0")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/JuliaData/DataAPI.jl")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32 "14sfvkz169zcbap3gdwpj16qsap783h86fd07flfxk822abam11w"))))
-    (build-system julia-build-system)
-    (home-page "https://github.com/JuliaData/DataAPI.jl")
-    (synopsis "Data-focused namespace for packages to share functions")
-    (description "This package provides a namespace for data-related generic
-function definitions to solve the optional dependency problem; packages wishing
-to share and/or extend functions can avoid depending directly on each other by
-moving the function definition to DataAPI.jl and each package taking a
-dependency on it.")
-    (license license:expat)))
-
 (define-public julia-optim
   (package
     (name "julia-optim")
@@ -1078,22 +1054,25 @@ structures.")
           "0ab03l9q9vmc176711hp0adc456fphh0d762fv6hcvzvhms4xjkz"))))
     (build-system julia-build-system)
     (arguments
-     `(#:tests? #f
+     `(#:tests? #f  ; not all dependants packaged
        ))
     (propagated-inputs
-     `(
-       ("julia-dataapi" ,julia-dataapi)
+     `(("julia-dataapi" ,julia-dataapi)
        ("julia-invertedindices" ,julia-invertedindices)
        ("julia-missings" ,julia-missings)
        ("julia-pooledarrays" ,julia-pooledarrays)
-       ;("julia-prettytables" ,julia-prettytables)
+       ("julia-prettytables" ,julia-prettytables)
        ("julia-reexport" ,julia-reexport)
        ("julia-sortingalgorithms" ,julia-sortingalgorithms)
-       ("julia-tabletraits" ,julia-tabletraits)
-       ))
+       ("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.")
@@ -1265,230 +1244,6 @@ native to Julia.  Use it with the @code{@@bind} macro in Pluto.")
                  this package is generated by Expronicon, please refer to Expronicon for any issues")
     (license license:expat)))
 
-;; ready to upstream
-(define-public julia-tables
-  (package
-    (name "julia-tables")
-    (version "1.4.3")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/JuliaData/Tables.jl")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32 "0yfjl4v1vglsk9wr7gbqgya4kk3a0q0i6zhi9xdgvnqsqzqrsc7c"))))
-    (build-system julia-build-system)
-    (propagated-inputs
-     `(("julia-dataapi" ,julia-dataapi)
-       ("julia-datavalueinterfaces" ,julia-datavalueinterfaces)
-       ("julia-iteratorinterfaceextensions" ,julia-iteratorinterfaceextensions)
-       ("julia-tabletraits" ,julia-tabletraits)))
-    (native-inputs
-     `(("julia-datavalues" ,julia-datavalues)
-       ("julia-queryoperators" ,julia-queryoperators)))
-    (home-page "https://github.com/JuliaData/Tables.jl")
-    (synopsis "Interface for tables in Julia")
-    (description "The @code{Tables.jl} package provides simple, yet powerful
-interface functions for working with all kinds tabular data.")
-    (license license:expat)))
-
-(define-public julia-datavalueinterfaces
-  (package
-    (name "julia-datavalueinterfaces")
-    (version "1.0.0")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/queryverse/DataValueInterfaces.jl")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32
-          "0g2wj6q7jj956nx6g7dk8x7w1c4l2xcmnr1kq5x8s8fild9kslg8"))))
-    (build-system julia-build-system)
-    (home-page "https://github.com/queryverse/DataValueInterfaces.jl")
-    (synopsis "")
-    (description "This package allows a few \"forward\" definitions for the DataValues.jl package that other packages can utilize for integration without having to take direct dependencies.")
-    (license license:expat)))
-
-(define-public julia-tabletraits
-  (package
-    (name "julia-tabletraits")
-    (version "1.0.1")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/queryverse/TableTraits.jl")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32
-          "08ssb2630wm6j8f2qa985mn2vfibfm5kjcn4ayl2qkhfcyp8daw4"))))
-    (build-system julia-build-system)
-    (propagated-inputs
-     `(("julia-iteratorinterfaceextensions" ,julia-iteratorinterfaceextensions)))
-    (home-page "https://github.com/queryverse/TableTraits.jl")
-    (synopsis "Traits for julia tables")
-    (description "TableTraits defines a generic interface for tabular data.")
-    (license license:expat)))
-
-(define-public julia-iteratorinterfaceextensions
-  (package
-    (name "julia-iteratorinterfaceextensions")
-    (version "1.0.0")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/queryverse/IteratorInterfaceExtensions.jl")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32
-          "1slpay1dhja8f9gy6z7b3psgvgcknn963dvfqqakvg1grk9ppa09"))))
-    (build-system julia-build-system)
-    (home-page "https://github.com/queryverse/IteratorInterfaceExtensions.jl")
-    (synopsis "Traits for julia iterators")
-    (description "IteratorInterfaceExtensions defines a small number of extensions to the iterator interface.")
-    (license license:expat)))
-
-(define-public julia-datavalues
-  (package
-    (name "julia-datavalues")
-    (version "0.4.13")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/queryverse/DataValues.jl")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32
-          "15j3hrqq6nazn533bfsvg32xznacbzsl303j1qs48av59ppnvhhv"))))
-    (build-system julia-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'skip-known-failing-tests
-           (lambda _
-             ;; See upstream report:
-             ;; https://github.com/queryverse/DataValues.jl/issues/83
-             (substitute* "test/array/test_reduce.jl"
-               ((".*DataValue\\(mapreduce.*") "")
-               ((".*DataValue\\(method\\(f.*") ""))
-             #t)))))
-    (propagated-inputs
-     `(("julia-datavalueinterfaces" ,julia-datavalueinterfaces)))
-    (home-page "https://github.com/queryverse/DataValues.jl")
-    (synopsis "Missing values for julia")
-    (description "This package provides the type DataValue that is used to represent missing data.")
-    (license license:expat)))
-
-(define-public julia-queryoperators
-  (package
-    (name "julia-queryoperators")
-    (version "0.9.3")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/queryverse/QueryOperators.jl")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32
-          "06zm4cbn3x49lbpgshhdfvvmgz066qkc8q0d57igm5p8bcp6js22"))))
-    (build-system julia-build-system)
-    (arguments
-     `(;#:tests? #f
-       ))
-    (propagated-inputs
-     `(
-       ("julia-datastructures" ,julia-datastructures)
-       ("julia-iteratorinterfaceextensions" ,julia-iteratorinterfaceextensions)
-       ("julia-tableshowutils" ,julia-tableshowutils)
-       ))
-    (native-inputs
-     `(
-       ;("julia-imagemagick" ,julia-imagemagick)
-       ))
-    (home-page "https://github.com/queryverse/QueryOperators.jl")
-    (synopsis "Query operators for julia")
-    (description "This package contains the underlying query operators that are exposed to users in Query.jl.")
-    (license license:expat)))
-
-(define-public julia-tableshowutils
-  ;; The 0.2.5 release is not fully compatable with newer versions of Julia.
-  (let ((commit "c4e02d8b9bbb31fc81ed6618955e9b1c7cb04460")
-        (revision "1"))
-    (package
-      (name "julia-tableshowutils")
-      (version "0.2.5")
-      (source
-        (origin
-          (method git-fetch)
-          (uri (git-reference
-                 (url "https://github.com/queryverse/TableShowUtils.jl")
-                 (commit commit)))
-          (file-name (git-file-name name version))
-          (sha256
-           (base32
-            "0gp3hpj3jvzfhkp9r345vfic2j2n2s60729wv38hwn75csp74cg5"))))
-      (build-system julia-build-system)
-      (propagated-inputs
-       `(("julia-datavalues" ,julia-datavalues)
-         ("julia-json" ,julia-json)))
-      (home-page "https://github.com/queryverse/TableShowUtils.jl")
-      (synopsis "helpers for implementing show for TableTraits.jl types")
-      (description "This package provides some common helper functions that make it easier to implement various Base.show functions for types that participate in the TableTraits.jl ecosystem.")
-      (license license:expat))))
-
-(define-public julia-missings
-  (package
-    (name "julia-missings")
-    (version "1.0.0")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/JuliaData/Missings.jl")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32
-          "131ma44yvswvj85jdjhm37frzfz46cc60lwj65a9jcmgc77dshsm"))))
-    (build-system julia-build-system)
-    (propagated-inputs
-     `(("julia-dataapi" ,julia-dataapi)))
-    (home-page "https://github.com/JuliaData/Missings.jl")
-    (synopsis "Missing value support for Julia")
-    (description "Part of Julia since 1.0")
-    (license license:expat)))
-
-(define-public julia-statsapi
-  (package
-    (name "julia-statsapi")
-    (version "1.0.0")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com.cnpmjs.org/JuliaStats/StatsAPI.jl")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32 "1k1c3s7i5wzkz4r9fyy4gd7wb97p0qgbc7bmaajm16zqipfmy2bv"))))
-    (build-system julia-build-system)
-    (home-page "https://juliastats.org/")
-    (synopsis "Statistics-focused namespace for packages to share functions")
-    (description "This package provides a namespace for data-related generic function definitions to solve the optional dependency problem; packages wishing to share and/or extend functions can avoid depending directly on each other by moving the function definition to StatsAPI.jl and each package taking a dependency on it.")
-    (license license:expat)))
-
 (define-public julia-statsfuns
   (package
     (name "julia-statsfuns")
@@ -1705,6 +1460,7 @@ interface functions for working with all kinds tabular data.")
     (description "This package provides a wrapper for Rmath.")
     (license license:expat)))
 
+;; ready to upstream
 (define-public julia-bandedmatrices
   (package
     (name "julia-bandedmatrices")
@@ -1717,28 +1473,20 @@ interface functions for working with all kinds tabular data.")
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32
-          "105y5d3208s0byk3p0469sfy79lhjpdblk6karbwj8x7hl26na00"))))
+         (base32 "105y5d3208s0byk3p0469sfy79lhjpdblk6karbwj8x7hl26na00"))))
     (build-system julia-build-system)
-    (arguments
-     `(;#:tests? #f
-       ))
     (propagated-inputs
-     `(
-       ("julia-arraylayouts" ,julia-arraylayouts)
-       ("julia-fillarrays" ,julia-fillarrays)
-       ))
+     `(("julia-arraylayouts" ,julia-arraylayouts)
+       ("julia-fillarrays" ,julia-fillarrays)))
     (native-inputs
-     `(
-       ;("julia-blockbandedmatrices" ,julia-blockbandedmatrices)
-       ("julia-genericlinearalgebra" ,julia-genericlinearalgebra)
-       ))
+     `(("julia-genericlinearalgebra" ,julia-genericlinearalgebra)))
     (home-page "https://github.com/JuliaMatrices/BandedMatrices.jl")
     (synopsis "Julia package for representing banded matrices")
     (description "This package supports representing banded matrices by only
 the entries on the bands.")
     (license license:expat)))
 
+;; ready to upstream
 (define-public julia-blockbandedmatrices
   (package
     (name "julia-blockbandedmatrices")
@@ -1751,17 +1499,14 @@ the entries on the bands.")
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32
-          "0q9ni4pgdkb00jb42fdzlhx745852xx2666vr96k0c4l0cn5mi0y"))))
+         (base32 "0q9ni4pgdkb00jb42fdzlhx745852xx2666vr96k0c4l0cn5mi0y"))))
     (build-system julia-build-system)
     (propagated-inputs
-     `(
-       ("julia-arraylayouts" ,julia-arraylayouts)
+     `(("julia-arraylayouts" ,julia-arraylayouts)
        ("julia-bandedmatrices" ,julia-bandedmatrices)
        ("julia-blockarrays" ,julia-blockarrays)
        ("julia-fillarrays" ,julia-fillarrays)
-       ("julia-matrixfactorizations" ,julia-matrixfactorizations)
-       ))
+       ("julia-matrixfactorizations" ,julia-matrixfactorizations)))
     (home-page "https://github.com/JuliaMatrices/BlockBandedMatrices.jl")
     (synopsis "Block-banded matrices and banded-block-banded matrices")
     (description "This package supports representing block-banded and
@@ -1770,6 +1515,7 @@ A @code{BlockBandedMatrix} is a subtype of @code{BlockMatrix} of BlockArrays.jl
 whose layout of non-zero blocks is banded.")
     (license license:expat)))
 
+;; ready to upstream
 (define-public julia-blockarrays
   (package
     (name "julia-blockarrays")
@@ -1782,8 +1528,7 @@ whose layout of non-zero blocks is banded.")
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32
-          "15nd493bfkx92ihnr8dj8mb155dj44iqw266igv0qr5q0wad2bfr"))))
+         (base32 "15nd493bfkx92ihnr8dj8mb155dj44iqw266igv0qr5q0wad2bfr"))))
     (build-system julia-build-system)
     (propagated-inputs
      `(("julia-arraylayouts" ,julia-arraylayouts)
@@ -1807,31 +1552,7 @@ extraction and insertion of blocks while @code{PseudoBlockArray} supports fast
 access to the full matrix to use in in for example a linear solver.")
     (license license:expat)))
 
-(define-public julia-arraylayouts
-  (package
-    (name "julia-arraylayouts")
-    (version "0.7.0")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/JuliaMatrices/ArrayLayouts.jl")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32
-          "01725v4jp8h8zwn85splw907r206h1hnp205pchmzjin7h4659xz"))))
-    (build-system julia-build-system)
-    (propagated-inputs
-     `(("julia-fillarrays" ,julia-fillarrays)))
-    (home-page "https://github.com/JuliaMatrices/ArrayLayouts.jl")
-    (synopsis "describing array layouts and more general fast linear algebra")
-    (description "This package implements a trait-based framework for describing
-array layouts such as column major, row major, etc. that can be dispatched to
-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)))
-
+;; ready to upstream
 (define-public julia-lazyarrays
   (package
     (name "julia-lazyarrays")
@@ -1844,8 +1565,7 @@ much wider class of matrix types than Julia's in-built @code{StridedArray}.")
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32
-          "0l427zghlpwcr6zcfy28sw3wm3y5zm0ckl008cgf2pwrpjfrahyw"))))
+         (base32 "0l427zghlpwcr6zcfy28sw3wm3y5zm0ckl008cgf2pwrpjfrahyw"))))
     (build-system julia-build-system)
     (propagated-inputs
      `(("julia-arraylayouts" ,julia-arraylayouts)
@@ -1862,42 +1582,6 @@ much wider class of matrix types than Julia's in-built @code{StridedArray}.")
 implementation of matrix-free methods for iterative solvers.")
     (license license:expat)))
 
-(define-public julia-matrixfactorizations
-  (package
-    (name "julia-matrixfactorizations")
-    (version "0.8.3")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/JuliaMatrices/MatrixFactorizations.jl")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32
-          "14c6w1vhyf4pi4454pdp6ryczsxn9pgjg99fg9bkdj03xg5fsxb8"))))
-    (build-system julia-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'skip-failing-test
-           (lambda _
-             ;; Tests with math functions are hard.
-             (substitute* "test/test_ul.jl"
-               (("@test @inferred\\(logdet") "@test @test_nowarn(logdet")
-               ;; Also skip the REPL test.
-               (("test String") "test_nowarn String"))
-             #t)))))
-    (propagated-inputs
-     `(("julia-arraylayouts" ,julia-arraylayouts)))
-    (home-page "https://github.com/JuliaMatrices/MatrixFactorizations.jl")
-    (synopsis "Julia package to contain non-standard matrix factorizations")
-    (description "A Julia package to contain non-standard matrix factorizations.
-At the moment it implements the QL, RQ, and UL factorizations, a combined
-Cholesky factorization with inverse, and polar decompositions.  In the future it
-may include other factorizations such as the LQ factorization.")
-    (license license:expat)))
-
 (define-public julia-tracker
   (package
     (name "julia-tracker")
@@ -1970,22 +1654,22 @@ doesn't provide any other \"high-level\" functionality like layers or AD.")
       (origin
         (method git-fetch)
         (uri (git-reference
-               (url "https://github.com/JuliaLinearAlgebra/GenericLinearAlgebra.jl/")
+               (url "https://github.com/JuliaLinearAlgebra/GenericLinearAlgebra.jl")
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32
-          "0ndwypa397z3pwzdgc3s9plaqlqf63g3d4px5pvym5psgr6lnm3l"))))
+         (base32 "0ndwypa397z3pwzdgc3s9plaqlqf63g3d4px5pvym5psgr6lnm3l"))))
     (build-system julia-build-system)
     (arguments
      `(#:tests? #f))    ; come back to this later
     (native-inputs
      `(("julia-quaternions" ,julia-quaternions)))
-    (home-page "https://github.com/JuliaLinearAlgebra/GenericLinearAlgebra.jl/")
+    (home-page "https://github.com/JuliaLinearAlgebra/GenericLinearAlgebra.jl")
     (synopsis "Generic numerical linear algebra")
     (description "The purpose of this package is partly to extend linear algebra functionality in base to cover generic element types, e.g. @code{BigFloat} and @code{Quaternion}, and partly to be a place to experiment with fast linear algebra routines written in Julia (except for optimized BLAS). It is my hope that it is possible to have implementations that are generic, fast, and readable.")
     (license license:expat)))
 
+;; ready to upstream
 (define-public julia-quaternions
   (package
     (name "julia-quaternions")
@@ -1998,14 +1682,15 @@ doesn't provide any other \"high-level\" functionality like layers or AD.")
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32
-          "1zhynyvchc50hywws2jznpkwydr3njh8cv84d2ylyabhcwwmil9s"))))
+         (base32 "1zhynyvchc50hywws2jznpkwydr3njh8cv84d2ylyabhcwwmil9s"))))
     (build-system julia-build-system)
     (propagated-inputs
      `(("julia-dualnumbers" ,julia-dualnumbers)))
     (home-page "https://github.com/JuliaGeometry/Quaternions.jl")
-    (synopsis "Julia module with quaternion and dual-quaternion functionality")
-    (description "Quaternions are best known for their suitability as representations of 3D rotational orientation. They can also be viewed as an extension of complex numbers.")
+    (synopsis "Quaternion and dual-quaternion functionality")
+    (description "Quaternions are best known for their suitability as
+representations of 3D rotational orientation.  They can also be viewed as an
+extension of complex numbers.")
     (license license:expat)))
 
 (define-public julia-dualnumbers
@@ -2020,8 +1705,7 @@ doesn't provide any other \"high-level\" functionality like layers or AD.")
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32
-          "05vr5wbzqpchnb96b3pmn67x196mbfnkv7r9bdlz3gm56if4awk5"))))
+         (base32 "05vr5wbzqpchnb96b3pmn67x196mbfnkv7r9bdlz3gm56if4awk5"))))
     (build-system julia-build-system)
     (arguments
      `(#:tests? #f))    ; fail hard on test/runtests.jl:4
@@ -2031,29 +1715,7 @@ doesn't provide any other \"high-level\" functionality like layers or AD.")
        ("julia-specialfunctions" ,julia-specialfunctions)))
     (home-page "https://github.com/JuliaDiff/DualNumbers.jl")
     (synopsis "representing dual numbers and for performing dual algebra")
-    (description "The @code{DualNumbers} Julia package defines the @code{Dual} type to represent dual numbers, and supports standard mathematical operations on 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-optimtestproblems
-  (package
-    (name "julia-optimtestproblems")
-    (version "2.0.2")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/JuliaNLSolvers/OptimTestProblems.jl")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32 "10h47x5ws42pkqjccimaz0yxfvz41w0yazq6inamfk4lg5g2g3d9"))))
-    (build-system julia-build-system)
-    (arguments
-     `(#:julia-package-name "OptimTestProblems"))
-    (home-page "https://github.com/JuliaNLSolvers/OptimTestProblems.jl")
-    (synopsis "A collection of test problems for optimization problems")
-    (description "The purpose of this package is to provide test problems for
-JuliaNLSolvers packages.")
+    (description "The @code{DualNumbers} Julia package defines the @code{Dual} type to represent dual numbers, and supports standard mathematical operations on 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-recursivearraytools
@@ -2175,6 +1837,7 @@ recursive arrays like arrays of arrays.")
     (description "DiffEqBase.jl is a component package in the DiffEq ecosystem.  It holds the common types and utility functions which are shared by other component packages in order to reduce the size of dependencies.  This is so that the packages for the common interface do not require one another, allowing users to use the functionality of individual packages if they so please.")
     (license license:expat)))
 
+;; ready to upstream
 (define-public julia-positivefactorizations
   (package
     (name "julia-positivefactorizations")
@@ -2244,7 +1907,7 @@ functions (or any callable object, really).")
       (origin
         (method git-fetch)
         (uri (git-reference
-               (url "https://github.com/yuyichao/FunctionWrappers.jl/")
+               (url "https://github.com/yuyichao/FunctionWrappers.jl")
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
@@ -2252,7 +1915,7 @@ functions (or any callable object, really).")
     (build-system julia-build-system)
     (arguments
      `(#:tests? #f))        ; TODO: Fix test failure
-    (home-page "https://github.com/yuyichao/FunctionWrappers.jl/")
+    (home-page "https://github.com/yuyichao/FunctionWrappers.jl")
     (synopsis "Type stable and efficient wrapper of arbitrary functions")
     (description "This package provides type stable and efficient wrapper of arbitrary functions.")
     (license license:expat)))
@@ -2383,6 +2046,7 @@ polynomials.")
                      AbstractInterval, along with its subtypes Interval and AnchoredInterval, and also Bound.")
     (license license:expat)))
 
+;; ready to upstream
 (define-public julia-infinity
   (package
     (name "julia-infinity")
@@ -2397,22 +2061,17 @@ polynomials.")
         (sha256
          (base32 "1bw7p88l8svb7455srz0jmw8ap17r2wwgz5y02vr9s8cg4lbsps5"))))
     (build-system julia-build-system)
-    ;(arguments
-    ; `(#:tests? #f))
     (propagated-inputs
-     `(
-       ("julia-compat" ,julia-compat)
+     `(("julia-compat" ,julia-compat)
        ("julia-requires" ,julia-requires)
-       ("julia-timezones" ,julia-timezones)
-       ))
+       ("julia-timezones" ,julia-timezones)))
     (native-inputs
-     `(
-       ("julia-compat" ,julia-compat)
-       ("julia-timezones" ,julia-timezones)
-       ))
+     `(("julia-compat" ,julia-compat)
+       ("julia-timezones" ,julia-timezones)))
     (home-page "https://juliahub.com/docs/Infinity/")
     (synopsis "Representation of infinity in Julia")
-    (description "This package provides representations for infinity and negative infinity in Julia.")
+    (description "This package provides representations for infinity and
+negative infinity in Julia.")
     (license license:gpl3)))
 
 ;; TODO: Keep this in sync with tzdata in base.scm
@@ -2475,67 +2134,7 @@ polynomials.")
     (description "IANA time zone database access for the Julia programming language. TimeZones.jl extends the Date/DateTime support for Julia to include a new time zone aware TimeType: ZonedDateTime.")
     (license license:expat)))
 
-(define-public julia-mocking
-  (package
-    (name "julia-mocking")
-    (version "0.7.1")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/invenia/Mocking.jl")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32 "10jz716v6i3gpd403rmcrip6cncjl9lqr12cdl321x1994a5g8ck"))))
-    (build-system julia-build-system)
-    ;(arguments
-    ; `(#:tests? #f))
-    (propagated-inputs
-     `(
-       ("julia-exprtools" ,julia-exprtools)
-       ;("julia-recipesbase" ,julia-recipesbase)
-       ))
-    (native-inputs
-     `(
-       ;("julia-compat" ,julia-compat)
-       ;("julia-timezones" ,julia-timezones)
-       ))
-    (home-page "https://github.com/invenia/Mocking.jl")
-    (synopsis "Julia function calls to be temporarily overloaded for purpose of testing")
-    (description "Allows Julia function calls to be temporarily overloaded for purpose of testing.")
-    (license license:expat)))
-
-(define-public julia-exprtools
-  (package
-    (name "julia-exprtools")
-    (version "0.1.3")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com.cnpmjs.org/invenia/ExprTools.jl")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32 "1lwxi9fx9farf1jdv42gv43xs3f3i3js2xnvr5gf6d0xfx0g6b6a"))))
-    (build-system julia-build-system)
-    ;(arguments
-    ; `(#:tests? #f))
-    (propagated-inputs
-     `(
-       ("julia-recipesbase" ,julia-recipesbase)
-       ))
-    (native-inputs
-     `(
-       ;("julia-compat" ,julia-compat)
-       ;("julia-timezones" ,julia-timezones)
-       ))
-    (home-page "https://github.com.cnpmjs.org/invenia/ExprTools.jl")
-    (synopsis "Light-weight expression manipulation tools")
-    (description "ExprTools provides tooling for working with Julia expressions during metaprogramming. This package aims to provide light-weight performant tooling without requiring additional package dependencies.")
-    (license license:expat)))
-
+;; ready to upstream, if we want
 (define-public julia-lazyartifacts
   (package
     (name "julia-lazyartifacts")
@@ -2550,20 +2149,11 @@ polynomials.")
         (sha256
          (base32 "0qln5pq2zm68wgm104cxyviiql8xkv7rf68hivar2b7x2a8vwnk0"))))
     (build-system julia-build-system)
-    ;(arguments
-    ; `(#:tests? #f))
-    (propagated-inputs
-     `(
-       ;("julia-recipesbase" ,julia-recipesbase)
-       ))
-    (native-inputs
-     `(
-       ;("julia-compat" ,julia-compat)
-       ;("julia-timezones" ,julia-timezones)
-       ))
     (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 LazyArtifacts stdlib as a dependency within packages that still support Julia versions older than 1.6.")
+    (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-mutablearithmetics
@@ -2599,35 +2189,6 @@ polynomials.")
                          ")
     (license license:mpl2.0)))
 
-(define-public julia-quadmath
-  (package
-    (name "julia-quadmath")
-    (version "0.5.5")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/JuliaMath/Quadmath.jl")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32 "051biw4b9zni7cmh2f1yzifp1v8wazlfxrdz4p44lyd1wba6379w"))))
-    (build-system julia-build-system)
-    ;(arguments
-    ; `(#:tests? #f))
-    (propagated-inputs
-     `(
-       ("julia-requires" ,julia-requires)
-       ))
-    (native-inputs
-     `(
-       ("julia-specialfunctions" ,julia-specialfunctions)
-       ))
-    (home-page "https://github.com/JuliaMath/Quadmath.jl")
-    (synopsis "Float128 and libquadmath for the Julia language")
-    (description "This is a Julia interface to libquadmath, providing a Float128 type corresponding to the IEEE754 binary128 floating point format.")
-    (license license:expat)))
-
 (define-public julia-genericschur
   (package
     (name "julia-genericschur")
@@ -2657,35 +2218,6 @@ polynomials.")
     (description "The Schur decomposition is the workhorse for eigensystem analysis of dense matrices. The diagonal eigen-decomposition of normal (especially Hermitian) matrices is an important special case, but for non-normal matrices the Schur form is often more useful.")
     (license license:expat)))
 
-(define-public julia-tensorcore
-  (package
-    (name "julia-tensorcore")
-    (version "0.1.1")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/JuliaMath/TensorCore.jl")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32 "1sy3in4a1rl3l2vk0cm9mzg2nkva7syhr7i35si0kbzhkdwpbqjy"))))
-    (build-system julia-build-system)
-    ;(arguments
-    ; `(#:tests? #f))    ; TODO: Fix later
-    (propagated-inputs
-     `(
-       ;("julia-requires" ,julia-requires)
-       ))
-    (native-inputs
-     `(
-       ;("julia-specialfunctions" ,julia-specialfunctions)
-       ))
-    (home-page "https://github.com/JuliaMath/TensorCore.jl")
-    (synopsis "Lightweight package for sharing tensor-algebra definitions")
-    (description "This package is intended as a lightweight foundation for tensor operations across the Julia ecosystem.  Currently it exports three operations: hadamard, tensor, and boxdot.")
-    (license license:expat)))
-
 (define-public julia-mosaicviews
   (package
     (name "julia-mosaicviews")
@@ -2743,33 +2275,7 @@ polynomials.")
     (description "PaddedViews provides a simple wrapper type, @code{PaddedView}, to add \"virtual\" padding to any array without copying data.  Edge values not specified by the array are assigned a @code{fillvalue}.  Multiple arrays may be \"promoted\" to have common indices using the @code{paddedviews function.")
     (license license:expat)))
 
-(define-public julia-mappedarrays
-  (package
-    (name "julia-mappedarrays")
-    (version "0.4.0")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/JuliaArrays/MappedArrays.jl")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32 "0l5adird8m1cmnsxwhzi5hcr7q9bm1rf7a6018zc7kcn2yxdshy3"))))
-    (build-system julia-build-system)
-    ;(arguments
-    ; `(#:tests? #f))
-    (propagated-inputs
-     `(
-       ("julia-colortypes" ,julia-colortypes)
-       ("julia-fixedpointnumbers" ,julia-fixedpointnumbers)
-       ("julia-offsetarrays" ,julia-offsetarrays)
-       ))
-    (home-page "https://github.com/JuliaArrays/MappedArrays.jl")
-    (synopsis "Lazy in-place transformations of arrays")
-    (description "This package implements \"lazy\" in-place elementwise transformations of arrays for the Julia programming language.  Explicitly, it provides a \"view\" M of an array A so that @code{M[i] = f(A[i])} for a specified (but arbitrary) function f, without ever having to compute M explicitly (in the sense of allocating storage for M).  The name of the package comes from the fact that @code{M == map(f, A)}.")
-    (license license:expat)))
-
+;; ready to upstream
 (define-public julia-stackviews
   (package
     (name "julia-stackviews")
@@ -2799,41 +2305,16 @@ polynomials.")
        ("julia-documenter" ,julia-documenter)))
     (home-page "https://github.com/JuliaArrays/StackViews.jl")
     (synopsis "no more catcat")
-    (description "StackViews provides only one array type: StackView.  There are multiple ways to understand StackView:
+    (description "StackViews provides only one array type: @code{StackView}.
+There are multiple ways to understand @code{StackView}:
 @itemize
-@item inverse of eachslice
-@item cat variant
+@item inverse of @code{eachslice}
+@item @code{cat} variant
 @item view object
-@item lazy version of repeat special case
+@item lazy version of @code{repeat} special case
 @end itemize")
     (license license:expat)))
 
-(define-public julia-graphics
-  (package
-    (name "julia-graphics")
-    (version "1.1.0")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/JuliaGraphics/Graphics.jl")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32 "10h1s09v7qkvrjr6l678zamb1p248n8jv4rrwkf8g7d2bpfz9amn"))))
-    (build-system julia-build-system)
-    ;(arguments
-    ; `(#:tests? #f))
-    (propagated-inputs
-     `(
-       ("julia-colors" ,julia-colors)
-       ("julia-nanmath" ,julia-nanmath)
-       ))
-    (home-page "https://github.com/JuliaGraphics/Graphics.jl")
-    (synopsis "A holding place for Base graphics")
-    (description "Graphics.jl is an abstraction layer for graphical operations in Julia.")
-    (license license:expat)))
-
 (define-public julia-referencetests
   (package
     (name "julia-referencetests")
@@ -2961,25 +2442,6 @@ polynomials.")
     (description "This package for the Julia language provides an array type (the AxisArray) that knows about its dimension names and axis values.  This allows for indexing by name without incurring any runtime overhead.  This permits one to implement algorithms that are oblivious to the storage order of the underlying arrays.  AxisArrays can also be indexed by the values along their axes, allowing column names or interval selections.")
     (license license:expat)))
 
-(define-public julia-rangearrays
-  (package
-    (name "julia-rangearrays")
-    (version "0.3.2")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/JuliaArrays/RangeArrays.jl")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32 "1ihzfyfq1xihkjcvn7xmzfbn6igzidb4fkzdcxwfr5qkvi52gnmg"))))
-    (build-system julia-build-system)
-    (home-page "https://github.com/JuliaArrays/RangeArrays.jl")
-    (synopsis "Efficient and convenient array data structures where the columns of the arrays are generated (on the fly) by Ranges.")
-    (description "The goal of RangeArrays is to provide efficient and convenient array data structures where the columns of the arrays are generated (on the fly) by Ranges.")
-    (license license:expat)))
-
 (define-public julia-intervalsets
   (package
     (name "julia-intervalsets")
@@ -3096,37 +2558,6 @@ polynomials.")
     (description "This package provides a macro-based implementation of traits, using Tim Holy's trait trick.  The main idea behind traits is to group types outside the type-hierarchy and to make dispatch work with that grouping.  The difference to Union-types is that types can be added to a trait after the creation of the trait, whereas Union types are fixed after creation.  The cool thing about Tim's trick is that there is no performance impact compared to using ordinary dispatch.  For a bit of background and a quick introduction to traits watch my 10min JuliaCon 2015 talk.")
     (license license:expat)))
 
-(define-public julia-indirectarrays
-  (package
-    (name "julia-indirectarrays")
-    (version "0.5.1")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/JuliaArrays/IndirectArrays.jl")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32 "0l0jq0jnr9z3k431ni82xycq7mqapgxrbrx4yyk6lycvi41ipm4s"))))
-    (build-system julia-build-system)
-    ;(arguments
-    ; `(#:tests? #f))
-    (propagated-inputs
-     `(
-       ;("julia-macrotools" ,julia-macrotools)
-       ))
-    (native-inputs
-     `(
-       ("julia-colors" ,julia-colors)
-       ("julia-fixedpointnumbers" ,julia-fixedpointnumbers)
-       ("julia-mappedarrays" ,julia-mappedarrays)
-       ))
-    (home-page "https://github.com/JuliaArrays/IndirectArrays.jl")
-    (synopsis "Julia implementation of indexed arrays")
-    (description "An IndirectArray is one that encodes data using a combination of an index and a value table.  Each element is assigned its own index, which is used to retrieve the value from the value table.")
-    (license license:expat)))
-
 (define-public julia-imagetransformations
   (package
     (name "julia-imagetransformations")
@@ -3414,7 +2845,7 @@ polynomials.")
        ;("julia-offsetarrays" ,julia-offsetarrays)
        ;("julia-unitful" ,julia-unitful)
        ))
-    (home-page "https://github.com/timholy/WoodburyMatrices.jl")
+    (home-page "https://github.com/timholy/Ratios.jl")
     (synopsis "Faster Rational-like types for Julia")
     (description "This package provides types similar to Julia's Rational type, which make some sacrifices but have better computational performance.")
     (license license:expat)))
@@ -3621,79 +3052,6 @@ polynomials.")
     (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)))
 
-;; ready to upstream
-(define-public julia-pooledarrays
-  (package
-    (name "julia-pooledarrays")
-    (version "1.2.1")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/JuliaData/PooledArrays.jl")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32 "0ihvhzkxdw4qf0i6sbrickhdcwkmlin9zyixxn9xvgzm8nc0iwqy"))))
-    (build-system julia-build-system)
-    (propagated-inputs
-     `(("julia-dataapi" ,julia-dataapi)))
-    (home-page "https://github.com/JuliaData/PooledArrays.jl")
-    (synopsis "Pooled representation of arrays in Julia")
-    (description "This package provides a pooled representation of arrays for
-purposes of compression when there are few unique elements.")
-    (license license:expat)))
-
-;; ready to upstream
-(define-public julia-weakrefstrings
-  (package
-    (name "julia-weakrefstrings")
-    (version "0.6.2")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/JuliaData/WeakRefStrings.jl")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32 "0129mf1axxycb1ans3idlvw8ch0hmdrl80q98jw63f99zz3ddipr"))))
-    (build-system julia-build-system)
-    (propagated-inputs
-     `(("julia-dataapi" ,julia-dataapi)))
-    (home-page "https://github.com/JuliaData/WeakRefStrings.jl")
-    (synopsis "Efficient string representation and transfer in Julia")
-    (description "This package provides a minimal String type for Julia that
-allows for efficient string representation and transfer")
-    (license license:expat)))
-
-;; ready to upstream
-(define-public julia-typedtables
-  (package
-    (name "julia-typedtables")
-    (version "1.2.4")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/JuliaData/TypedTables.jl")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32 "06k5h7ybsh29b6kiy0p62rp9b2q3xi9jk8p9wf0kq907p5kvfnfy"))))
-    (build-system julia-build-system)
-    (propagated-inputs
-     `(("julia-adapt" ,julia-adapt)
-       ("julia-splitapplycombine" ,julia-splitapplycombine)
-       ("julia-tables" ,julia-tables)))
-    (home-page "https://github.com/JuliaData/TypedTables.jl")
-    (synopsis "Column-based storage for data analysis in Julia")
-    (description "@code{TypedTables.jl} provides two column-based storage
-containers: @code{Table} and @code{FlexTable}, both of which represent an array
-of @code{NamedTuples}.  This package is designed to be lightweight, easy-to-use
-and fast, and presents a very minimal new interface to learn.")
-    (license license:expat)))
-
 (define-public julia-earcut-jll
   ;; Only release tag contains just a license file.
   (let ((commit "b234ae0c064af12eb5482c7474a64af8be0f511e")