[bug#60075] [PATCH 00/58] New julia patches

[bug#60075] [PATCH 00/58] New julia patches

[Efraim Flashner]

This should take care of nearly all the julia packages. I believe the
only one that is still failing to build is julia-deepdiffs and the
package which depends on it, julia-referencetests.

julia-colors@0.12.9 still hasn't been tagged in the git repo, but it has
been sent off to the registry. It looks like something is acting up with
the tagbot.

I haven't tried building all the packages on i686-linux or aarch64-linux
yet.

Efraim Flashner (58):
  gnu: julia-fillarrays: Update to 0.13.6.
  gnu: julia-arraylayouts: Update to 0.8.16.
  gnu: julia-coordinatetransformations: Update to 0.6.2-1.78f5a5c.
  gnu: julia-mappedarrays: Update to 0.4.1.
  gnu: julia-imagecore: Update to 0.9.4.
  gnu: julia-imagebase: Update to 0.1.5.
  gnu: julia-imagetransformations: Update to 0.9.5.
  gnu: Remove julia-identityranges.
  gnu: Add julia-irrationalconstants.
  gnu: Add julia-inversefunctions.
  gnu: Add julia-changesofvariables.
  gnu: julia-logexpfunctions: Update to 0.3.17.
  gnu: julia-nanmath: Update to 0.3.7.
  gnu: julia-diffrules: Update to 1.12.2.
  gnu: julia-forwarddiff: Update to 0.10.34.
  gnu: julia-safetestsets: Fix build.
  gnu: Add julia-shiftedarrays.
  gnu: julia-invertedindices: Update to 1.1.0.
  gnu: julia-categoricalarrays: Update to 0.10.7.
  gnu: julia-pooledarrays: Update to 1.4.2.
  gnu: julia-dataapi: Update to 1.13.0.
  gnu: julia-offsetarrays: Update to 1.12.8.
  gnu: julia-dataframes: Update to 1.3.6.
  gnu: julia-reversediff: Update to 1.14.4.
  gnu: julia-functors: Update to 0.4.1.
  gnu: julia-zygoterules: Update to 0.2.2.
  gnu: julia-zygote: Update to 0.6.41.
  gnu: julia-nnlib: Update to 0.7.34.
  gnu: julia-chainrulescore: Update to 1.12.2.
  gnu: julia-chainrulestestutils: Update to 1.5.1.
  gnu: Add julia-realdot.
  gnu: julia-chainrules: Update to 1.35.0.
  gnu: Add julia-optimisers.
  gnu: julia-tracker: Update to 0.2.22.
  gnu: julia-specialfunctions: Update to 1.8.7.
  gnu: julia-lazyarrays: Update to 0.22.16.
  gnu: julia-bson: Update to 0.3.6.
  gnu: julia-interpolations: Update to 0.13.6.
  gnu: julia-requires: Update to 1.3.0.
  gnu: julia-colors: Update to 0.12.9.
  gnu: julia-colorvectorspace: Update to 0.9.9.
  gnu: julia-plotutils: Update to 1.2.0.
  gnu: Remove julia-infinity.
  gnu: julia-indexablebitvectors: Limit to 64-bit systems.
  gnu: julia-blockarrays: Update to 0.16.23.
  gnu: julia-scanbyte: Update to 0.3.2.
  gnu: julia-scanbyte: Limit to x86_64-linux.
  gnu: julia-matrixfactorizations: Update to 0.9.3.
  gnu: Add julia-static-0.6.
  gnu: julia-arrayinterface: Update to 5.0.8.
  gnu: julia-bandedmatrices: Update to 0.17.9.
  gnu: julia-blockbandedmatrices: Update to 0.11.9.
  gnu: julia-ellipsisnotation: Update to 1.6.0.
  gnu: julia-axisarrays: Update to 0.4.6.
  gnu: julia-graphics: Update to 1.1.2.
  gnu: julia-imageaxes: Update to 0.6.10.
  gnu: julia-paddedviews: Update to 0.5.11.
  gnu: julia-imagemetadata: Update to 0.9.8.

 gnu/local.mk                                  |   1 -
 gnu/packages/julia-xyz.scm                    | 743 ++++++++++++------
 .../patches/julia-tracker-16-compat.patch     |  40 -
 3 files changed, 496 insertions(+), 288 deletions(-)
 delete mode 100644 gnu/packages/patches/julia-tracker-16-compat.patch


base-commit: 8125c22ea2b61b1bbe7acb8741f8895b4d1f6f9f
-- 
2.38.1

[bug#60075] [PATCH 01/58] gnu: julia-fillarrays: Update to 0.13.6.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-fillarrays): Update to 0.13.6.
[propagated-inputs]: Add julia-aqua.
---
 gnu/packages/julia-xyz.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index d2fae6a465..72bc595c7a 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -1915,7 +1915,7 @@ (define-public julia-filepathsbase
 (define-public julia-fillarrays
   (package
     (name "julia-fillarrays")
-    (version "0.12.6")
+    (version "0.13.6")
     (source
      (origin
        (method git-fetch)
@@ -1924,8 +1924,10 @@ (define-public julia-fillarrays
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1sx96pzrgyh8k7x2w8vmyi6cazlmp7rg1n7wbl47qfzqjggka6kz"))))
+        (base32 "1c4i8awmw9qq8dqfhxwjh76mc1nlmzrl5j754fpnbajv8p49gdv5"))))
     (build-system julia-build-system)
+    (propagated-inputs
+     (list julia-aqua))
     (inputs                             ;required by tests
      (list julia-staticarrays))
     (home-page "https://github.com/JuliaArrays/FillArrays.jl")
-- 
2.38.1

[bug#60075] [PATCH 02/58] gnu: julia-arraylayouts: Update to 0.8.16.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-arraylayouts): Update to 0.8.16.
[arguments]: Add a phase to mark a test broken.
[native-inputs]: Add julia-stablerngs.
---
 gnu/packages/julia-xyz.scm | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 72bc595c7a..441821e80a 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -192,7 +192,7 @@ (define-public julia-arrayinterface
 (define-public julia-arraylayouts
   (package
     (name "julia-arraylayouts")
-    (version "0.7.6")
+    (version "0.8.16")
     (source
       (origin
         (method git-fetch)
@@ -201,10 +201,20 @@ (define-public julia-arraylayouts
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "05q62pks8j23pgbrfny072rrwzrz6q19l68srnjxxv39ncmdmrvg"))))
+         (base32 "1j11jid4scw9icrbr8g6myp17nabjzmf4f40cichb20lzf1agz8l"))))
     (build-system julia-build-system)
+    (arguments
+     (list
+       #:phases
+       #~(modify-phases %standard-phases
+           (add-after 'unpack 'adjust-tests
+             (lambda _
+               (substitute* "test/test_layoutarray.jl"
+                 (("@test all\\(B") "@test_broken all(B")))))))
     (propagated-inputs
      (list julia-fillarrays))
+    (native-inputs
+     (list julia-stablerngs))
     (home-page "https://github.com/JuliaMatrices/ArrayLayouts.jl")
     (synopsis "Array layouts and general fast linear algebra")
     (description "This package implements a trait-based framework for describing
-- 
2.38.1

[bug#60075] [PATCH 03/58] gnu: julia-coordinatetransformations: Update to 0.6.2-1.78f5a5c.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-coordinatetransformations): Update
to 0.6.2-1.78f5a5c.
---
 gnu/packages/julia-xyz.scm | 49 ++++++++++++++++++++------------------
 1 file changed, 26 insertions(+), 23 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 441821e80a..b31ef2faac 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -1099,28 +1099,31 @@ (define-public julia-constructionbase
     (license license:expat)))
 
 (define-public julia-coordinatetransformations
-  (package
-    (name "julia-coordinatetransformations")
-    (version "0.6.1")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/JuliaGeometry/CoordinateTransformations.jl")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32 "15zbkn32v7xlz7559s0r5a0vkwmjwsswxaqpzijly4lky4jnp33d"))))
-    (build-system julia-build-system)
-    (propagated-inputs
-     (list julia-staticarrays))
-    (native-inputs
-    (list julia-documenter
-          julia-forwarddiff
-          julia-unitful))
-    (home-page "https://github.com/JuliaGeometry/CoordinateTransformations.jl")
-    (synopsis "Coordinate transformations in Julia")
-    (description "@code{CoordinateTransformations} is a Julia package to manage
+  ;; Test suite fixed after the last release.
+  (let ((commit "78f5a5cc8cf77f21407b4f175673fa4f6bf86633")
+        (revision "1"))
+    (package
+      (name "julia-coordinatetransformations")
+      (version (git-version "0.6.2" revision commit))
+      (source
+        (origin
+          (method git-fetch)
+          (uri (git-reference
+                 (url "https://github.com/JuliaGeometry/CoordinateTransformations.jl")
+                 (commit commit)))
+          (file-name (git-file-name name version))
+          (sha256
+           (base32 "026g3b2m2z509jdlqvd46yhnhg8y6m00plr3k7cjlbzrfi2yjjn8"))))
+      (build-system julia-build-system)
+      (propagated-inputs
+       (list julia-staticarrays))
+      (native-inputs
+      (list julia-documenter
+            julia-forwarddiff
+            julia-unitful))
+      (home-page "https://github.com/JuliaGeometry/CoordinateTransformations.jl")
+      (synopsis "Coordinate transformations in Julia")
+      (description "@code{CoordinateTransformations} is a Julia package to manage
 simple or complex networks of coordinate system transformations.
 Transformations can be easily applied, inverted, composed, and differentiated
 (both with respect to the input coordinates and with respect to transformation
@@ -1129,7 +1132,7 @@ (define-public julia-coordinatetransformations
 while support for both explicit and automatic differentiation makes it easy to
 perform optimization and therefore ideal for computer vision applications such
 as SLAM (simultaneous localization and mapping).")
-    (license license:expat)))
+      (license license:expat))))
 
 (define-public julia-crayons
   (package
-- 
2.38.1

[bug#60075] [PATCH 04/58] gnu: julia-mappedarrays: Update to 0.4.1.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-mappedarrays): Update to 0.4.1.
[source]: Add snippet to fix deprecation warning and to fix the
testsuite.
[arguments]: Add 'adjust-tests phase to skip a test and absorb the
i686-linux specific phase 'fix-tests-int32-i686.
[native-inputs]: Remove julia-colortypes. Add julia-colors.
---
 gnu/packages/julia-xyz.scm | 34 ++++++++++++++++++++++++----------
 1 file changed, 24 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index b31ef2faac..01a3569e8d 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -3438,7 +3438,7 @@ (define-public julia-macrotools
 (define-public julia-mappedarrays
   (package
     (name "julia-mappedarrays")
-    (version "0.4.0")
+    (version "0.4.1")
     (source
       (origin
         (method git-fetch)
@@ -3447,22 +3447,36 @@ (define-public julia-mappedarrays
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "0l5adird8m1cmnsxwhzi5hcr7q9bm1rf7a6018zc7kcn2yxdshy3"))))
+         (base32 "08kb28dv1zzqbbxblhyllgs4sjxyp76dgjqhdizcq4zg4i1kls6p"))
+        (snippet
+         #~(begin
+             (use-modules (guix build utils))
+             ;; Fix deprecation warning
+             ;; https://github.com/JuliaArrays/MappedArrays.jl/pull/51
+             (substitute* "src/MappedArrays.jl"
+               (("Vararg\\{<:AbstractArray") "Vararg{AbstractArray"))
+             ;; Fix test failures
+             ;; https://github.com/JuliaArrays/MappedArrays.jl/pull/50
+             (substitute* "test/runtests.jl"
+               (("_zero\\(x\\) = x > 0 \\? x : 0")
+                "_zero(x) = ismissing(x) ? x : (x > 0 ? x : 0)"))))))
     (build-system julia-build-system)
     (arguments
      (list
       #:phases
-      (if (target-64bit?)
-          #~%standard-phases
-          #~(modify-phases %standard-phases
-              (add-after 'unpack 'fix-tests-int32-i686
-                (lambda _
-                  (substitute* "test/runtests.jl"
-                    (("Int64") "Int32"))))))))
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'adjust-tests
+            (lambda _
+              (substitute* "test/runtests.jl"
+                ((".*@test_throws ErrorException b.*") ""))
+
+              (when #$(not (target-64bit?))
+                (substitute* "test/runtests.jl"
+                  (("Int64") "Int32"))))))))
     (propagated-inputs
      (list julia-fixedpointnumbers))
     (native-inputs
-     (list julia-colortypes
+     (list julia-colors
            julia-fixedpointnumbers
            julia-offsetarrays))
     (home-page "https://github.com/JuliaArrays/MappedArrays.jl")
-- 
2.38.1

[bug#60075] [PATCH 05/58] gnu: julia-imagecore: Update to 0.9.4.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-imagecore): Update to 0.9.4.
---
 gnu/packages/julia-xyz.scm | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 01a3569e8d..130df81ae2 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -2583,7 +2583,7 @@ (define-public julia-imagebase
 (define-public julia-imagecore
   (package
     (name "julia-imagecore")
-    (version "0.9.1")
+    (version "0.9.4")
     (source
       (origin
         (method git-fetch)
@@ -2592,7 +2592,7 @@ (define-public julia-imagecore
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "0h9m3pl3wic1jrgaqkdifz24cya5vxd3m6qdmm37pxg2y2ii2vcq"))))
+         (base32 "0a6m3cszgh2bfsgs08i64f1h1pwh6by4267rvwyvdk470z0ayc8q"))))
     (build-system julia-build-system)
     (arguments
      (list #:tests? #f))    ; Cycle with ImageMagick.jl.
@@ -2608,14 +2608,14 @@ (define-public julia-imagecore
            julia-paddedviews
            julia-reexport))
     ;(native-inputs
-    ; `(("julia-aqua" ,julia-aqua)
-    ;   ("julia-colorvectorspace" ,julia-colorvectorspace)
-    ;   ("julia-documenter" ,julia-documenter)
-    ;   ("julia-fftw" ,julia-fftw)
-    ;   ("julia-imageinterminal" ,julia-imageinterminal)
-    ;   ("julia-imagemagick" ,julia-imagemagick)
-    ;   ("julia-referencetests" ,julia-referencetests)
-    ;   ("julia-statistics" ,julia-statistics)))
+    ; (list julia-aqua
+    ;       julia-blockarrays
+    ;       julia-documenter
+    ;       julia-fftw
+    ;       julia-imageinterminal
+    ;       julia-imagemagick
+    ;       julia-referencetests
+    ;       julia-statistics))
     (home-page "https://github.com/JuliaImages/ImageCore.jl")
     (synopsis "Julia types for representing images")
     (description "@code{ImageCore} is the lowest-level component of the system
-- 
2.38.1

[bug#60075] [PATCH 05/58] gnu: julia-imagecore: Update to 0.9.4.

[zimoun]

Hi,

On Wed, 14 Dec 2022 at 22:35, Efraim Flashner <efraim@flashner.co.il> wrote:
> * gnu/packages/julia-xyz.scm (julia-imagecore): Update to 0.9.4.

>      ;(native-inputs
> -    ; `(("julia-aqua" ,julia-aqua)
> -    ;   ("julia-colorvectorspace" ,julia-colorvectorspace)
> -    ;   ("julia-documenter" ,julia-documenter)
> -    ;   ("julia-fftw" ,julia-fftw)
> -    ;   ("julia-imageinterminal" ,julia-imageinterminal)
> -    ;   ("julia-imagemagick" ,julia-imagemagick)
> -    ;   ("julia-referencetests" ,julia-referencetests)
> -    ;   ("julia-statistics" ,julia-statistics)))
> +    ; (list julia-aqua
> +    ;       julia-blockarrays
> +    ;       julia-documenter
> +    ;       julia-fftw
> +    ;       julia-imageinterminal
> +    ;       julia-imagemagick
> +    ;       julia-referencetests
> +    ;       julia-statistics))

Is this change useful?


Cheers,
simon

[bug#60075] [PATCH 05/58] gnu: julia-imagecore: Update to 0.9.4.

[Efraim Flashner]

[-- Attachment #1: Type: text/plain, Size: 1244 bytes --]

On Mon, Dec 19, 2022 at 07:30:19PM +0100, zimoun wrote:
> Hi,
> 
> On Wed, 14 Dec 2022 at 22:35, Efraim Flashner <efraim@flashner.co.il> wrote:
> > * gnu/packages/julia-xyz.scm (julia-imagecore): Update to 0.9.4.
> 
> >      ;(native-inputs
> > -    ; `(("julia-aqua" ,julia-aqua)
> > -    ;   ("julia-colorvectorspace" ,julia-colorvectorspace)
> > -    ;   ("julia-documenter" ,julia-documenter)
> > -    ;   ("julia-fftw" ,julia-fftw)
> > -    ;   ("julia-imageinterminal" ,julia-imageinterminal)
> > -    ;   ("julia-imagemagick" ,julia-imagemagick)
> > -    ;   ("julia-referencetests" ,julia-referencetests)
> > -    ;   ("julia-statistics" ,julia-statistics)))
> > +    ; (list julia-aqua
> > +    ;       julia-blockarrays
> > +    ;       julia-documenter
> > +    ;       julia-fftw
> > +    ;       julia-imageinterminal
> > +    ;       julia-imagemagick
> > +    ;       julia-referencetests
> > +    ;       julia-statistics))
> 
> Is this change useful?

Not really. I've switched it back.

-- 
Efraim Flashner   <efraim@flashner.co.il>   אפרים פלשנר
GPG key = A28B F40C 3E55 1372 662D  14F7 41AA E7DC CA3D 8351
Confidentiality cannot be guaranteed on emails sent or received unencrypted

[-- Attachment #2: signature.asc --]
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[bug#60075] [PATCH 06/58] gnu: julia-imagebase: Update to 0.1.5.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-imagebase): Update to 0.1.5.
---
 gnu/packages/julia-xyz.scm | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 130df81ae2..599940f0c7 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -2552,7 +2552,7 @@ (define-public julia-imageaxes
 (define-public julia-imagebase
   (package
     (name "julia-imagebase")
-    (version "0.1.1")
+    (version "0.1.5")
     (source
       (origin
         (method git-fetch)
@@ -2561,7 +2561,7 @@ (define-public julia-imagebase
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "1n63f2zs6ail9pcl7rzgv3l0z8v1idjsaza3zgvgy7iacxsdpcj2"))))
+         (base32 "00gi268jsyhlkadkkbyiffph6c8yb7zw34px76n6hs7dkfzp6jm3"))))
     (build-system julia-build-system)
     (arguments
      (list #:tests? #f))    ; Cycle with ImageMagick.jl.
@@ -2569,9 +2569,14 @@ (define-public julia-imagebase
      (list julia-imagecore
            julia-reexport))
     ;(native-inputs
-    ; `(("julia-imagemagick" ,julia-imagemagick)
-    ;   ("julia-offsetarrays" ,julia-offsetarrays)
-    ;   ("julia-testimages" ,julia-testimages)))
+    ; (list julia-aqua
+    ;       julia-documenter
+    ;       julia-imagefiltering
+    ;       julia-imageio
+    ;       julia-imagemagick
+    ;       julia-offsetarrays
+    ;       jula-statistics
+    ;       julia-testimages))
     (home-page "https://github.com/JuliaImages/ImageBase.jl")
     (synopsis "Wrapper package around ImageCore")
     (description "This is a twin package to @code{ImageCore} with functions that
-- 
2.38.1

[bug#60075] [PATCH 06/58] gnu: julia-imagebase: Update to 0.1.5.

[zimoun]

Hi,

On Wed, 14 Dec 2022 at 22:35, Efraim Flashner <efraim@flashner.co.il> wrote:
> * gnu/packages/julia-xyz.scm (julia-imagebase): Update to 0.1.5.

>      (arguments
>       (list #:tests? #f))    ; Cycle with ImageMagick.jl.

[...]

>      ;(native-inputs
> -    ; `(("julia-imagemagick" ,julia-imagemagick)
> -    ;   ("julia-offsetarrays" ,julia-offsetarrays)
> -    ;   ("julia-testimages" ,julia-testimages)))
> +    ; (list julia-aqua
> +    ;       julia-documenter
> +    ;       julia-imagefiltering
> +    ;       julia-imageio
> +    ;       julia-imagemagick
> +    ;       julia-offsetarrays
> +    ;       jula-statistics
> +    ;       julia-testimages))

Is this change useful?  Is it for maintaining an accurate list for
passing tests if we cut the cycle?


Cheers,
simon

[bug#60075] [PATCH 06/58] gnu: julia-imagebase: Update to 0.1.5.

[Efraim Flashner]

[-- Attachment #1: Type: text/plain, Size: 1458 bytes --]

On Mon, Dec 19, 2022 at 07:32:00PM +0100, zimoun wrote:
> Hi,
> 
> On Wed, 14 Dec 2022 at 22:35, Efraim Flashner <efraim@flashner.co.il> wrote:
> > * gnu/packages/julia-xyz.scm (julia-imagebase): Update to 0.1.5.
> 
> >      (arguments
> >       (list #:tests? #f))    ; Cycle with ImageMagick.jl.
> 
> [...]
> 
> >      ;(native-inputs
> > -    ; `(("julia-imagemagick" ,julia-imagemagick)
> > -    ;   ("julia-offsetarrays" ,julia-offsetarrays)
> > -    ;   ("julia-testimages" ,julia-testimages)))
> > +    ; (list julia-aqua
> > +    ;       julia-documenter
> > +    ;       julia-imagefiltering
> > +    ;       julia-imageio
> > +    ;       julia-imagemagick
> > +    ;       julia-offsetarrays
> > +    ;       jula-statistics
> > +    ;       julia-testimages))
> 
> Is this change useful?  Is it for maintaining an accurate list for
> passing tests if we cut the cycle?

Its an updated list of the packages we would need for the tests to run.
I'd rather have them listed (and up to date) than missing and have to
start searching before finding out how much effort it'll be to cut the
cycle. On its own it's not a useful change, but with the actual package
upgrade it seemed like a good change to make.

-- 
Efraim Flashner   <efraim@flashner.co.il>   אפרים פלשנר
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[bug#60075] [PATCH 07/58] gnu: julia-imagetransformations: Update to 0.9.5.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-imagetransformations): Update to 0.9.5.
[propagated-inputs]: Remove julia-identityranges. Add julia-imagebase.
---
 gnu/packages/julia-xyz.scm | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 599940f0c7..6ec4df3486 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -2781,7 +2781,7 @@ (define-public julia-imageshow
 (define-public julia-imagetransformations
   (package
     (name "julia-imagetransformations")
-    (version "0.8.12")
+    (version "0.9.5")
     (source
       (origin
         (method git-fetch)
@@ -2790,7 +2790,7 @@ (define-public julia-imagetransformations
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "0i8gw68hljshsy9wdl5mrpbb31irhmayqyglsxi7jwm88iy9pxhm"))))
+         (base32 "1wavfs5chq8s9ma0k8fxfaqam4560w4l2j3lhbd9aqsjlgvi3swc"))))
     (build-system julia-build-system)
     (arguments
      (list #:tests? #f))    ; Cycle with ImageMagick.jl.
@@ -2798,16 +2798,19 @@ (define-public julia-imagetransformations
      (list julia-axisalgorithms
            julia-colorvectorspace
            julia-coordinatetransformations
-           julia-identityranges
+           julia-imagebase
            julia-imagecore
            julia-interpolations
            julia-offsetarrays
            julia-rotations
            julia-staticarrays))
     ;(native-inputs
-    ; `(("julia-imagemagick" ,julia-imagemagick)
-    ;   ("julia-referencetests" ,julia-referencetests)
-    ;   ("julia-testimages" ,julia-testimages)))
+    ; (list julia-endpointranges
+    ;       julia-imageio
+    ;       julia-imagemagick
+    ;       julia-referencetests
+    ;       julia-tau
+    ;       julia-testimages))
     (home-page "https://github.com/JuliaImages/ImageTransformations.jl")
     (synopsis "Geometric transformations on images for Julia")
     (description "This package provides support for image resizing, image
-- 
2.38.1

[bug#60075] [PATCH 08/58] gnu: Remove julia-identityranges.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-identityranges): Delete variable.
---
 gnu/packages/julia-xyz.scm | 26 --------------------------
 1 file changed, 26 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 6ec4df3486..845e71f0f2 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -2475,32 +2475,6 @@ (define-public julia-http
 implementing both a client and a server.")
     (license license:expat)))
 
-(define-public julia-identityranges
-  (package
-    (name "julia-identityranges")
-    (version "0.3.1")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/JuliaArrays/IdentityRanges.jl")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32 "0jvl4xn8f8k70sn473li5q62wbiycl5qi25b5k456h3a0j1lbiml"))))
-    (build-system julia-build-system)
-    (propagated-inputs
-     (list julia-offsetarrays))
-    (home-page "https://github.com/JuliaArrays/IdentityRanges.jl")
-    (synopsis "Ranges that preserve indices of views")
-    (description "@code{IdentityRanges} are Julia-language a helper type for
-creating \"views\" of arrays.  They are a custom type of AbstractUnitRange that
-makes it easy to preserve the indices of array views.  The key property of an
-@code{IdentityRange r} is that @code{r[i] == i} (hence the name of the
-type/package), and that they support arbitrary start/stop indices (i.e., not
-just starting at 1).")
-    (license license:expat)))
-
 (define-public julia-ifelse
   (package
     (name "julia-ifelse")
-- 
2.38.1

[bug#60075] [PATCH 08/58] gnu: Remove julia-identityranges.

[zimoun]

Hi,

On Wed, 14 Dec 2022 at 22:35, Efraim Flashner <efraim@flashner.co.il> wrote:
> * gnu/packages/julia-xyz.scm (julia-identityranges): Delete variable.

Is it an issue to keep it?


Cheers,
simon

[bug#60075] [PATCH 08/58] gnu: Remove julia-identityranges.

[Efraim Flashner]

[-- Attachment #1: Type: text/plain, Size: 612 bytes --]

On Mon, Dec 19, 2022 at 07:32:51PM +0100, zimoun wrote:
> Hi,
> 
> On Wed, 14 Dec 2022 at 22:35, Efraim Flashner <efraim@flashner.co.il> wrote:
> > * gnu/packages/julia-xyz.scm (julia-identityranges): Delete variable.
> 
> Is it an issue to keep it?

It doesn't build with the upgrade to julia. There's also an open bug
report with them to deprecate it in favor of Base.IdentityUnitRange.

-- 
Efraim Flashner   <efraim@flashner.co.il>   אפרים פלשנר
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[bug#60075] [PATCH 09/58] gnu: Add julia-irrationalconstants.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-irrationalconstants): New variable.
---
 gnu/packages/julia-xyz.scm | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 845e71f0f2..33856fcf32 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -3104,6 +3104,25 @@ (define-public julia-iocapture
 as a string together with the return value.")
     (license license:expat)))
 
+(define-public julia-irrationalconstants
+  (package
+    (name "julia-irrationalconstants")
+    (version "0.1.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaMath/IrrationalConstants.jl")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1a007iyh26x67a1bj6fcz7pfxa43kn2v7jpmnz727jkk3xgppg2s"))))
+    (build-system julia-build-system)
+    (home-page "https://github.com/JuliaMath/IrrationalConstants.jl")
+    (synopsis "Additional irrationals for Julia")
+    (description "This package defines the following irrational constants in Julia.")
+    (license license:expat)))
+
 (define-public julia-irtools
   (package
     (name "julia-irtools")
-- 
2.38.1

[bug#60075] [PATCH 09/58] gnu: Add julia-irrationalconstants.

[zimoun]

Hi,

On Wed, 14 Dec 2022 at 22:35, Efraim Flashner <efraim@flashner.co.il> wrote:
> * gnu/packages/julia-xyz.scm (julia-irrationalconstants): New variable.

[...]

> +    (description "This package defines the following irrational constants in Julia.")

This description looks incomplete.  I suggest to replace by:

--8<---------------cut here---------------start------------->8---
This package defines more irrational constants in Julia.
--8<---------------cut here---------------end--------------->8---

or by:

--8<---------------cut here---------------start------------->8---
+      (description "This package provides these irrational constants:
+@itemize
+@item
+@item twoπ       = 2π
+@item fourπ      = 4π
+@item halfπ      = π / 2
+@item quartπ     = π / 4
+@item invπ       = 1 / π
+@item twoinvπ    = 2 / π
+@item fourinvπ   = 4 / π
+@item inv2π      = 1 / (2π)
+@item inv4π      = 1 / (4π)
+@item sqrt2      = √2
+@item sqrt3      = √3
+@item sqrtπ      = √π
+@item sqrt2π     = √2π
+@item sqrt4π     = √4π
+@item sqrthalfπ  = √(π / 2)
+@item invsqrt2   = 1 / √2
+@item invsqrtπ   = 1 / √π
+@item invsqrt2π  = 1 / √2π
+@item loghalf    = log(1 / 2)
+@item logtwo     = log(2)
+@item logten     = log(10)
+@item logπ       = log(π)
+@item log2π      = log(2π)
+@item log4π      = log(4π)
+@end itemize")
--8<---------------cut here---------------end--------------->8---

With a preference for the latter.

Cheers,
simon

[bug#60075] [PATCH 09/58] gnu: Add julia-irrationalconstants.

[Efraim Flashner]

[-- Attachment #1: Type: text/plain, Size: 2002 bytes --]

On Mon, Dec 19, 2022 at 07:11:32PM +0100, zimoun wrote:
> Hi,
> 
> On Wed, 14 Dec 2022 at 22:35, Efraim Flashner <efraim@flashner.co.il> wrote:
> > * gnu/packages/julia-xyz.scm (julia-irrationalconstants): New variable.
> 
> [...]
> 
> > +    (description "This package defines the following irrational constants in Julia.")
> 
> This description looks incomplete.  I suggest to replace by:
> 
> --8<---------------cut here---------------start------------->8---
> This package defines more irrational constants in Julia.
> --8<---------------cut here---------------end--------------->8---
> 
> or by:
> 
> --8<---------------cut here---------------start------------->8---
> +      (description "This package provides these irrational constants:
> +@itemize
> +@item
> +@item twoπ       = 2π
> +@item fourπ      = 4π
> +@item halfπ      = π / 2
> +@item quartπ     = π / 4
> +@item invπ       = 1 / π
> +@item twoinvπ    = 2 / π
> +@item fourinvπ   = 4 / π
> +@item inv2π      = 1 / (2π)
> +@item inv4π      = 1 / (4π)
> +@item sqrt2      = √2
> +@item sqrt3      = √3
> +@item sqrtπ      = √π
> +@item sqrt2π     = √2π
> +@item sqrt4π     = √4π
> +@item sqrthalfπ  = √(π / 2)
> +@item invsqrt2   = 1 / √2
> +@item invsqrtπ   = 1 / √π
> +@item invsqrt2π  = 1 / √2π
> +@item loghalf    = log(1 / 2)
> +@item logtwo     = log(2)
> +@item logten     = log(10)
> +@item logπ       = log(π)
> +@item log2π      = log(2π)
> +@item log4π      = log(4π)
> +@end itemize")
> --8<---------------cut here---------------end--------------->8---
> 
> With a preference for the latter.

I'd argue that the original doesn't just look incomplete, it's not a
full sentence. I've gone with the second.

-- 
Efraim Flashner   <efraim@flashner.co.il>   אפרים פלשנר
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[bug#60075] [PATCH 10/58] gnu: Add julia-inversefunctions.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-inversefunctions): New variable.
---
 gnu/packages/julia-xyz.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 33856fcf32..90b2678815 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -3060,6 +3060,28 @@ (define-public julia-intervaltrees
 The type @code{K} may be any ordered type.")
       (license license:expat))))
 
+(define-public julia-inversefunctions
+  (package
+    (name "julia-inversefunctions")
+    (version "0.1.8")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/JuliaMath/InverseFunctions.jl")
+               (commit (string-append "v" version))))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "05g9f6i735x7syfr56l4yf4fy71kgdisjc6cfxi4jkf46iq86a69"))))
+    (build-system julia-build-system)
+    (native-inputs
+     (list julia-documenter))
+    (home-page "https://github.com/JuliaMath/InverseFunctions.jl")
+    (synopsis "Interface for function inversion in Julia")
+    (description
+     "@code{InverseFunctions.jl} defines an interface to invert functions.")
+    (license license:expat)))
+
 (define-public julia-invertedindices
   (package
     (name "julia-invertedindices")
-- 
2.38.1

[bug#60075] [PATCH 10/58] gnu: Add julia-inversefunctions.

[zimoun]

Hi,

On Wed, 14 Dec 2022 at 22:35, Efraim Flashner <efraim@flashner.co.il> wrote:
> * gnu/packages/julia-xyz.scm (julia-inversefunctions): New variable.

[...]

> +    (synopsis "Interface for function inversion in Julia")

I would remove « in Julia ».

> +    (description
> +     "@code{InverseFunctions.jl} defines an interface to invert functions.")
> +    (license license:expat)))

I think this description:

--8<---------------cut here---------------start------------->8---
+    (description "This package provides an interface to invert functions.  It
+is a lightweight package.")
--8<---------------cut here---------------end--------------->8---


Cheers,
simon

[bug#60075] [PATCH 10/58] gnu: Add julia-inversefunctions.

[Efraim Flashner]

[-- Attachment #1: Type: text/plain, Size: 1105 bytes --]

On Mon, Dec 19, 2022 at 07:13:55PM +0100, zimoun wrote:
> Hi,
> 
> On Wed, 14 Dec 2022 at 22:35, Efraim Flashner <efraim@flashner.co.il> wrote:
> > * gnu/packages/julia-xyz.scm (julia-inversefunctions): New variable.
> 
> [...]
> 
> > +    (synopsis "Interface for function inversion in Julia")
> 
> I would remove « in Julia ».

done

> > +    (description
> > +     "@code{InverseFunctions.jl} defines an interface to invert functions.")
> > +    (license license:expat)))
> 
> I think this description:
> 
> --8<---------------cut here---------------start------------->8---
> +    (description "This package provides an interface to invert functions.  It
> +is a lightweight package.")
> --8<---------------cut here---------------end--------------->8---

I used the first sentence. It may be a lightweight package but it is a
little too like marketing for me.

-- 
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[bug#60075] [PATCH 11/58] gnu: Add julia-changesofvariables.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-changesofvariables): New variable.
---
 gnu/packages/julia-xyz.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 90b2678815..c3b12ee90c 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -822,6 +822,33 @@ (define-public julia-chainrulestestutils
 dependencies, while keeping @code{ChainRulesCore.jl} as light-weight as possible.")
     (license license:expat)))
 
+(define-public julia-changesofvariables
+  (package
+    (name "julia-changesofvariables")
+    (version "0.1.4")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaMath/ChangesOfVariables.jl")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1migyhiqr1rq496302wlkb0s5l8zwqs97ajfkip0jzpvrk2s2xxy"))))
+    (build-system julia-build-system)
+    (arguments
+     ;; Pulls in ForwardDiff, would have a cyclical
+     ;; dependency with LogExpFunctions.
+     (list #:tests? #f))
+    (propagated-inputs
+     (list julia-chainrulescore))
+    (home-page "https://github.com/JuliaMath/ChangesOfVariables.jl")
+    (synopsis "Interface for transformation functions in Julia")
+    (description "ChangesOfVariables.jl defines functionality to calculate
+volume element changes for functions that perform a change of variables (like
+coordinate transformations).")
+    (license license:expat)))
+
 (define-public julia-codeczlib
   (package
     (name "julia-codeczlib")
-- 
2.38.1

[bug#60075] [PATCH 11/58] gnu: Add julia-changesofvariables.

[zimoun]

Hi,

On Wed, 14 Dec 2022 at 22:35, Efraim Flashner <efraim@flashner.co.il> wrote:
> * gnu/packages/julia-xyz.scm (julia-changesofvariables): New variable.

> +    (description "ChangesOfVariables.jl defines functionality to calculate
> +volume element changes for functions that perform a change of variables (like
> +coordinate transformations).")
> +    (license license:expat)))

Well, to keep consistency with the rest, I suggest to apply @code or to
start with «This package defines…».


Cheers,
simon

[bug#60075] [PATCH 11/58] gnu: Add julia-changesofvariables.

[Efraim Flashner]

[-- Attachment #1: Type: text/plain, Size: 845 bytes --]

On Mon, Dec 19, 2022 at 07:34:37PM +0100, zimoun wrote:
> Hi,
> 
> On Wed, 14 Dec 2022 at 22:35, Efraim Flashner <efraim@flashner.co.il> wrote:
> > * gnu/packages/julia-xyz.scm (julia-changesofvariables): New variable.
> 
> > +    (description "ChangesOfVariables.jl defines functionality to calculate
> > +volume element changes for functions that perform a change of variables (like
> > +coordinate transformations).")
> > +    (license license:expat)))
> 
> Well, to keep consistency with the rest, I suggest to apply @code or to
> start with «This package defines…».

Changed it to "This package defines ..."

-- 
Efraim Flashner   <efraim@flashner.co.il>   אפרים פלשנר
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[bug#60075] [PATCH 12/58] gnu: julia-logexpfunctions: Update to 0.3.17.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-logexpfunctions): Update to 0.3.17.
[propagated-inputs]: Add julia-chainrulescore, julia-changesofvariables,
julia-inversefunctions and julia-irrationalcontants.
[native-inputs]: Add julia-chainrulestestutils.
---
 gnu/packages/julia-xyz.scm | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index c3b12ee90c..2fc1786c71 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -3441,7 +3441,7 @@ (define-public julia-linesearches
 (define-public julia-logexpfunctions
   (package
     (name "julia-logexpfunctions")
-    (version "0.2.4")
+    (version "0.3.17")
     (source
       (origin
         (method git-fetch)
@@ -3450,12 +3450,17 @@ (define-public julia-logexpfunctions
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "0rvms3mmq8a1viqlyzdgs2ccddcy6j0c677dlb8m5nk6hkiwr16n"))))
+         (base32 "0272c1256r42y6g4wsjmgpwcl5s7z98b8sfmyycckqf0zp5dzxg4"))))
     (build-system julia-build-system)
     (propagated-inputs
-     (list julia-docstringextensions))
+     (list julia-chainrulescore
+           julia-changesofvariables
+           julia-docstringextensions
+           julia-inversefunctions
+           julia-irrationalconstants))
     (native-inputs
-     (list julia-offsetarrays))
+     (list julia-chainrulestestutils
+           julia-offsetarrays))
     (home-page "https://github.com/JuliaStats/LogExpFunctions.jl")
     (synopsis "Special functions based on @code{log} and @code{exp}")
     (description "Various special functions based on log and exp moved from
-- 
2.38.1

[bug#60075] [PATCH 13/58] gnu: julia-nanmath: Update to 0.3.7.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-nanmath): Update to 0.3.7.
---
 gnu/packages/julia-xyz.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 2fc1786c71..019f3e3196 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -3881,7 +3881,7 @@ (define-public julia-mutablearithmetics
 (define-public julia-nanmath
   (package
     (name "julia-nanmath")
-    (version "0.3.5")
+    (version "0.3.7")
     (source
      (origin
        (method git-fetch)
@@ -3890,7 +3890,7 @@ (define-public julia-nanmath
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1hczhz00qj99w63vp627kwk02l2sr2qmzc2rkwwkdwvzy670p25q"))))
+        (base32 "1fwqa2fzl84a86ppjb2xaqh93b5gg42zyrclbjfdm5l0044hwii6"))))
     (build-system julia-build-system)
     (home-page "https://github.com/mlubin/NaNMath.jl")
     (synopsis "Implementations of basic math functions")
-- 
2.38.1

[bug#60075] [PATCH 14/58] gnu: julia-diffrules: Update to 1.12.2.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-diffrules): Update to 1.12.2.
[propagated-inputs]: Add julia-irriationalconstants,
julia-logexpfunctions.
[native-inputs]: Add julia-finitedifferences.
---
 gnu/packages/julia-xyz.scm | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 019f3e3196..11b27c82f2 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -1670,7 +1670,7 @@ (define-public julia-diffresults
 (define-public julia-diffrules
   (package
     (name "julia-diffrules")
-    (version "1.0.2")
+    (version "1.12.2")
     (source
      (origin
        (method git-fetch)
@@ -1679,11 +1679,15 @@ (define-public julia-diffrules
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0cwjvj4gma7924fm3yas0nf0jlnwwx4v7fi79ii3s290lkdldzfl"))))
+        (base32 "0l983kzy01y7qqw42pi0ihpvx3yzfnwrhcmk38avw7y513qlm7vf"))))
     (build-system julia-build-system)
     (propagated-inputs
-     (list julia-nanmath
+     (list julia-irrationalconstants
+           julia-logexpfunctions
+           julia-nanmath
            julia-specialfunctions))
+    (native-inputs
+     (list julia-finitedifferences))
     (home-page "https://github.com/JuliaDiff/DiffRules.jl")
     (synopsis "Primitive differentiation rules")
     (description "This package provides primitive differentiation rules that
-- 
2.38.1

[bug#60075] [PATCH 15/58] gnu: julia-forwarddiff: Update to 0.10.34.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-forwarddiff): Update to 0.10.34.
[propagated-inputs]: Add julia-calculus, julia-difftests.
---
 gnu/packages/julia-xyz.scm | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 11b27c82f2..c01ba44c19 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -2113,7 +2113,7 @@ (define-public julia-formatting
 (define-public julia-forwarddiff
   (package
     (name "julia-forwarddiff")
-    (version "0.10.18")
+    (version "0.10.34")
     (source
      (origin
        (method git-fetch)
@@ -2122,7 +2122,7 @@ (define-public julia-forwarddiff
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1vb46x8mcn61g1l14qrk22c043khg2ml4q1ci7h4k2v34f2ak5fs"))))
+        (base32 "1lwjw2jzkffwk06hfc30vxhv36ng3gf12qjc43swmqiakkd3m5jx"))))
     (build-system julia-build-system)
     (arguments
      ;; XXXX: Unexpected and non-deterministic failures for i686, e.g.,
@@ -2135,9 +2135,11 @@ (define-public julia-forwarddiff
      (list julia-calculus
            julia-difftests))
     (propagated-inputs
-     (list julia-commonsubexpressions
+     (list julia-calculus
+           julia-commonsubexpressions
            julia-diffresults
            julia-diffrules
+           julia-difftests
            julia-nanmath
            julia-specialfunctions
            julia-staticarrays))
-- 
2.38.1

[bug#60075] [PATCH 16/58] gnu: julia-safetestsets: Fix build.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-safetestsets)[arguments]: Add phase
to fix the version string in the generated Project.toml.
---
 gnu/packages/julia-xyz.scm | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index c01ba44c19..a73d3e90d0 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -4893,7 +4893,13 @@ (define-public julia-safetestsets
       (arguments
        (list
         #:julia-package-name "SafeTestsets"
-        #:julia-package-uuid "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"))
+        #:julia-package-uuid "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
+        #:phases
+        #~(modify-phases %standard-phases
+            (add-after 'link-depot 'fix-package-toml
+              (lambda _
+                (substitute* "Project.toml"
+                  (("version = .*") "version = \"0.0.1\"\n")))))))
       (native-inputs
        (list julia-staticarrays))
       (home-page "https://github.com/YingboMa/SafeTestsets.jl")
-- 
2.38.1

[bug#60075] [PATCH 17/58] gnu: Add julia-shiftedarrays.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-shiftedarrays): New variable.
---
 gnu/packages/julia-xyz.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index a73d3e90d0..5c3c944c94 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -5002,6 +5002,26 @@ (define-public julia-sentinelarrays
 argument.")
     (license license:expat)))
 
+(define-public julia-shiftedarrays
+  (package
+    (name "julia-shiftedarrays")
+    (version "1.0.0")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/JuliaArrays/ShiftedArrays.jl")
+               (commit (string-append "v" version))))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "0wy7k29qx2lvj587kiz31fzdc60808mjsgpp41h6b682ypz8rw0c"))))
+    (build-system julia-build-system)
+    (home-page "https://github.com/JuliaArrays/ShiftedArrays.jl")
+    (synopsis "Lazy shifted arrays for data analysis in Julia")
+    (description
+     "This package provides an Implementation of shifted arrays for Julia.")
+    (license license:expat)))
+
 (define-public julia-showoff
   (package
     (name "julia-showoff")
-- 
2.38.1

[bug#60075] [PATCH 17/58] gnu: Add julia-shiftedarrays.

[zimoun]

Hi,

On Wed, 14 Dec 2022 at 22:35, Efraim Flashner <efraim@flashner.co.il> wrote:
> * gnu/packages/julia-xyz.scm (julia-shiftedarrays): New variable.

> +     "This package provides an Implementation of shifted arrays for Julia.")
                                --^
                            Why?

Why this Capital letter?


Cheers,
simon

[bug#60075] [PATCH 17/58] gnu: Add julia-shiftedarrays.

[Efraim Flashner]

[-- Attachment #1: Type: text/plain, Size: 671 bytes --]

On Mon, Dec 19, 2022 at 07:35:52PM +0100, zimoun wrote:
> Hi,
> 
> On Wed, 14 Dec 2022 at 22:35, Efraim Flashner <efraim@flashner.co.il> wrote:
> > * gnu/packages/julia-xyz.scm (julia-shiftedarrays): New variable.
> 
> > +     "This package provides an Implementation of shifted arrays for Julia.")
>                                 --^
>                             Why?
> 
> Why this Capital letter?

Its A Very Important Letter.

...fixed.

-- 
Efraim Flashner   <efraim@flashner.co.il>   אפרים פלשנר
GPG key = A28B F40C 3E55 1372 662D  14F7 41AA E7DC CA3D 8351
Confidentiality cannot be guaranteed on emails sent or received unencrypted

[-- Attachment #2: signature.asc --]
[-- Type: application/pgp-signature, Size: 833 bytes --]

[bug#60075] [PATCH 18/58] gnu: julia-invertedindices: Update to 1.1.0.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-invertedindices): Update to 1.1.0.
---
 gnu/packages/julia-xyz.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 5c3c944c94..b579df01ce 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -3118,7 +3118,7 @@ (define-public julia-inversefunctions
 (define-public julia-invertedindices
   (package
     (name "julia-invertedindices")
-    (version "1.0.0")
+    (version "1.1.0")
     (source
       (origin
         (method git-fetch)
@@ -3127,7 +3127,7 @@ (define-public julia-invertedindices
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "1179z20yxnkyziip7gn26wr1g3k3ssl1ci7pig3khc900f62di46"))))
+         (base32 "15ym4dzyi4fkz0dznni032w3c84zmfa6mrzj2ljqvlqx1i6agqis"))))
     (build-system julia-build-system)
     (native-inputs
      (list julia-offsetarrays))
-- 
2.38.1

[bug#60075] [PATCH 19/58] gnu: julia-categoricalarrays: Update to 0.10.7.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-categoricalarrays): Update to 0.10.7.
[arguments]: Add phase to skip tests depending on julia-plots.
[native-inputs]: Add julia-json, julia-json3, julia-recipesbase,
julia-sentinelarrays, julia-structtypes.
[propagated-inputs]: Add julia-requires, julia-sentinelarrays.
---
 gnu/packages/julia-xyz.scm | 23 ++++++++++++++++++++---
 1 file changed, 20 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index b579df01ce..3948102a6b 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -679,7 +679,7 @@ (define-public julia-calculus
 (define-public julia-categoricalarrays
   (package
     (name "julia-categoricalarrays")
-    (version "0.9.7")
+    (version "0.10.7")
     (source
      (origin
        (method git-fetch)
@@ -688,16 +688,33 @@ (define-public julia-categoricalarrays
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1bcfylxdaizgasnmlkjjkf4dgfvy2y9ycnphw2d0z6mm9vx3n04x"))))
+        (base32 "17fix7wlwqbif5jbcrbi0a0ghdl3429km3l6lqa962p7jf1gjd2d"))))
     (build-system julia-build-system)
+    (arguments
+     (list
+       #:phases
+       #~(modify-phases %standard-phases
+           (add-after 'unpack 'adjust-tests
+             (lambda _
+               ;; Plots.jl isn't packaged yet.
+               (substitute* "test/runtests.jl"
+                 ((".*13_arraycommon\\.jl.*") "")))))))
     (native-inputs
-     (list julia-pooledarrays))
+     (list julia-json
+           julia-json3
+           ;julia-plots
+           julia-pooledarrays
+           julia-recipesbase
+           julia-sentinelarrays
+           julia-structtypes))
     (propagated-inputs
      (list julia-dataapi
            julia-json
            julia-json3
            julia-missings
            julia-recipesbase
+           julia-requires
+           julia-sentinelarrays
            julia-structtypes))
     (home-page "https://github.com/JuliaData/CategoricalArrays.jl")
     (synopsis "Arrays for working with categorical data")
-- 
2.38.1

[bug#60075] [PATCH 20/58] gnu: julia-pooledarrays: Update to 1.4.2.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-pooledarrays): Update to 1.4.2.
[native-inputs]: Add julia-offsetarrays.
---
 gnu/packages/julia-xyz.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 3948102a6b..2e12f57c1a 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -4259,7 +4259,7 @@ (define-public julia-plotutils
 (define-public julia-pooledarrays
   (package
     (name "julia-pooledarrays")
-    (version "1.3.0")
+    (version "1.4.2")
     (source
       (origin
         (method git-fetch)
@@ -4268,10 +4268,12 @@ (define-public julia-pooledarrays
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "0qdwvf1p5z6z0q4s4hn85ysd8wq47zy6hlzddc5ijvhk86ccqlrr"))))
+         (base32 "0g30d46n8cc8vr9icjhfkqz2il2185ijh7xhfy9vhcnmllzpd0yg"))))
     (build-system julia-build-system)
     (propagated-inputs
      (list julia-dataapi))
+    (native-inputs
+     (list julia-offsetarrays))
     (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
-- 
2.38.1

[bug#60075] [PATCH 21/58] gnu: julia-dataapi: Update to 1.13.0.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-dataapi): Update to 1.13.0.
---
 gnu/packages/julia-xyz.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 2e12f57c1a..3da94b74d7 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -1246,7 +1246,7 @@ (define-public julia-csv
 (define-public julia-dataapi
   (package
     (name "julia-dataapi")
-    (version "1.7.0")
+    (version "1.13.0")
     (source
       (origin
         (method git-fetch)
@@ -1255,7 +1255,7 @@ (define-public julia-dataapi
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "0swk31p83fycz5cdj4fg6b0wfqj473lnx94q2fl7ybxkkc6afba7"))))
+         (base32 "1x5pdpjlbk29766ark7rmzjbl0rhxmsb1cp04lc891aknh30rn3i"))))
     (build-system julia-build-system)
     (home-page "https://github.com/JuliaData/DataAPI.jl")
     (synopsis "Data-focused namespace for packages to share functions")
-- 
2.38.1

[bug#60075] [PATCH 22/58] gnu: julia-offsetarrays: Update to 1.12.8.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-offsetarrays): Update to 1.12.8.
---
 gnu/packages/julia-xyz.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 3da94b74d7..648a2a4210 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -4089,7 +4089,7 @@ (define-public julia-orderedcollections
 (define-public julia-offsetarrays
   (package
     (name "julia-offsetarrays")
-    (version "1.10.3")
+    (version "1.12.8")
     (source
      (origin
        (method git-fetch)
@@ -4098,7 +4098,7 @@ (define-public julia-offsetarrays
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0j5a8ar8yc0j9h87gwfyrcqm23wpyv5yv5gn8vzilpg4vr0fiasc"))))
+        (base32 "09cidr42q0xwp6wwyaw09hl580vqi85wb5f78pxrxcfm75yg3xki"))))
     (build-system julia-build-system)
     (propagated-inputs
      (list julia-adapt))
-- 
2.38.1

[bug#60075] [PATCH 23/58] gnu: julia-dataframes: Update to 1.3.6.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-dataframes): Update to 1.3.6.
[arguments]: Adjust 'skip-failing-test phase to adjust a test to pass
with julia-1.8.
[propagated-inputs]: Add julia-categoricalarrays, julia-compat,
julia-shiftedarrays, julia-unitful.
[native-inputs]: Add julia-shiftedarrays.
---
 gnu/packages/julia-xyz.scm | 19 ++++++++++++++-----
 1 file changed, 14 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 648a2a4210..0e4b2546e2 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -1269,7 +1269,7 @@ (define-public julia-dataapi
 (define-public julia-dataframes
   (package
     (name "julia-dataframes")
-    (version "1.2.2")
+    (version "1.3.6")
     (source
       (origin
         (method git-fetch)
@@ -1278,7 +1278,7 @@ (define-public julia-dataframes
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "1bk0amrghgjrkyn1mm4ac23swwbgszl1d0qyl9137qj5zvv9dasp"))))
+         (base32 "01ybc1ckn5wi7kwp29g5ms4m3g650856z4xv71racbdr8475pmg5"))))
     (build-system julia-build-system)
     (arguments
      (list
@@ -1295,24 +1295,33 @@ (define-public julia-dataframes
                  (string-append all "return\n")))
               (substitute* "test/join.jl"
                 (("test (levels\\(outerjoin\\(B)" _ test)
-                 (string-append "test_nowarn " test))))))))
+                 (string-append "test_nowarn " test)))
+              ;; Compat with julia-1.8, remove with next package update.
+              (substitute* "test/indexing_offset.jl"
+                (("@test_throws ErrorException")
+                 "@test_throws Base.CanonicalIndexError")))))))
     (propagated-inputs
-     (list julia-dataapi
+     (list julia-categoricalarrays
+           julia-compat
+           julia-dataapi
            julia-invertedindices
            julia-iteratorinterfaceextensions
            julia-missings
            julia-pooledarrays
            julia-prettytables
            julia-reexport
+           julia-shiftedarrays
            julia-sortingalgorithms
            julia-tables
-           julia-tabletraits))
+           julia-tabletraits
+           julia-unitful))
     (native-inputs
      (list julia-categoricalarrays
            julia-combinatorics
            julia-datastructures
            julia-datavalues
            julia-offsetarrays
+           julia-shiftedarrays
            julia-unitful))
     (home-page "https://dataframes.juliadata.org/stable/")
     (synopsis "In-memory tabular data")
-- 
2.38.1

[bug#60075] [PATCH 24/58] gnu: julia-reversediff: Update to 1.14.4.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-reversediff): Update to 1.14.4.
[propagated-inputs]: Add julia-chainrulescore, julia-difftests,
julia-logexpfunctions.
---
 gnu/packages/julia-xyz.scm | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 0e4b2546e2..de13a4f967 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -4804,7 +4804,7 @@ (define-public julia-requires
 (define-public julia-reversediff
   (package
     (name "julia-reversediff")
-    (version "1.9.0")
+    (version "1.14.4")
     (source
       (origin
         (method git-fetch)
@@ -4813,7 +4813,7 @@ (define-public julia-reversediff
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "1wrr6sqj2xl9grkvdp88rw3manxy9vbx28zq2wssya5ns1xabsnl"))))
+         (base32 "0hwsjmr4wiscqa5kaj4mw0i4agyyzdcmq4r1gp2i563nc1ziaylg"))))
     (build-system julia-build-system)
     (arguments
      ;; XXXX: Test suite failing for i686, e.g.,
@@ -4823,10 +4823,13 @@ (define-public julia-reversediff
      (list #:tests? (not (or (%current-target-system)
                              (target-x86-32?)))))
     (propagated-inputs
-     (list julia-diffresults
+     (list julia-chainrulescore
+           julia-diffresults
            julia-diffrules
+           julia-difftests
            julia-forwarddiff
            julia-functionwrappers
+           julia-logexpfunctions
            julia-macrotools
            julia-nanmath
            julia-specialfunctions
-- 
2.38.1

[bug#60075] [PATCH 25/58] gnu: julia-functors: Update to 0.4.1.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-functors): Update to 0.4.1.
[propagated-inputs]: Add julia-documenter, julia-staticarrays,
julia-zygote.
---
 gnu/packages/julia-xyz.scm | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index de13a4f967..b87b09f54c 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -2209,7 +2209,7 @@ (define-public julia-functionwrappers
 (define-public julia-functors
   (package
     (name "julia-functors")
-    (version "0.2.7")
+    (version "0.4.1")
     (source
       (origin
         (method git-fetch)
@@ -2218,8 +2218,12 @@ (define-public julia-functors
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "03ry1wn1y2jssq65l29bi6q4ki041aa6gl1nd2w6cgl00k2mrxf3"))))
+         (base32 "00rzbj2rs2lq91wz8qyxq14bg7p9i49dq7y44fvxn6jaikha2ymw"))))
     (build-system julia-build-system)
+    (native-inputs
+     (list julia-documenter
+           julia-staticarrays
+           julia-zygote))
     (home-page "https://fluxml.ai/Functors.jl/stable/")
     (synopsis "Design pattern for structures as in machine learning")
     (description "This package provides tools to express a design pattern for
-- 
2.38.1

[bug#60075] [PATCH 26/58] gnu: julia-zygoterules: Update to 0.2.2.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-zygoterules): Update to 0.2.2.
---
 gnu/packages/julia-xyz.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index b87b09f54c..2dffb9a74c 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -6006,7 +6006,7 @@ (define-public julia-zipfile
 (define-public julia-zygoterules
   (package
     (name "julia-zygoterules")
-    (version "0.2.1")
+    (version "0.2.2")
     (source
      (origin
        (method git-fetch)
@@ -6015,7 +6015,7 @@ (define-public julia-zygoterules
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "07i2mf6rr5b8i6l82qgwl5arsb5pwyyzyfasgnszhdqllk9501bs"))))
+        (base32 "0h9m9ibxfcw9cqa7p0aylpvibvlxsn5nlfzkz1pk68jy58vkzhca"))))
     (build-system julia-build-system)
     (propagated-inputs
      (list julia-macrotools))
-- 
2.38.1

[bug#60075] [PATCH 27/58] gnu: julia-zygote: Update to 0.6.41.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-zygote): Update to 0.6.41.
[propagated-inputs]: Add julia-chainrulescore, julia-logexpfuntions.
---
 gnu/packages/julia-xyz.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 2dffb9a74c..07eaab01e0 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -6028,7 +6028,7 @@ (define-public julia-zygoterules
 (define-public julia-zygote
   (package
     (name "julia-zygote")
-    (version "0.6.17")
+    (version "0.6.41")
     (source
      (origin
        (method git-fetch)
@@ -6037,17 +6037,19 @@ (define-public julia-zygote
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1cx66sp30s34ln6p0fpqk1ggjxfxg2gp8791zz3cl85dmk4dl14b"))))
+        (base32 "02bgj6m1j25sm3pa5sgmds706qpxk1qsbm0s2j3rjlrz9xn7glgk"))))
     (build-system julia-build-system)
     (arguments
      (list #:tests? #f))                    ;require CUDA, not packaged yet
     (propagated-inputs
      (list julia-abstractffts
            julia-chainrules
+           julia-chainrulescore
            julia-diffrules
            julia-fillarrays
            julia-forwarddiff
            julia-irtools
+           julia-logexpfunctions
            julia-macrotools
            julia-nanmath
            julia-requires
-- 
2.38.1

[bug#60075] [PATCH 28/58] gnu: julia-nnlib: Update to 0.7.34.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-nnlib): Update to 0.7.34.
[arguments]: Rename 'skip-cuda-tests to 'skip-some-tests. Adjust to skip
doctests.
[propagated-inputs]: Add julia-compat.
---
 gnu/packages/julia-xyz.scm | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 07eaab01e0..50201aa383 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -3966,7 +3966,7 @@ (define-public julia-nlsolversbase
 (define-public julia-nnlib
   (package
     (name "julia-nnlib")
-    (version "0.7.29")
+    (version "0.7.34")
     (source
       (origin
         (method git-fetch)
@@ -3975,21 +3975,26 @@ (define-public julia-nnlib
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "16vn5w5274kcywh1xp0zqjk5q10xrk125aznz5av6wifwrvghk8s"))))
+         (base32 "1xzlh7pj6aqmbkrskqgwvifprg9a6xkkdh00ls6f6xnzqfrnhwna"))))
     (build-system julia-build-system)
     (arguments
      (list
       #:phases
       #~(modify-phases %standard-phases
-          (add-after 'link-depot 'skip-cuda-tests
+          (add-after 'link-depot 'skip-some-tests
             (lambda _
               (substitute* "test/runtests.jl"
+                ;; Skip the CUDA tests
                 (("using CUDA") "")
-                (("&& CUDA\\.functional\\(\\)") ""))
+                (("&& CUDA\\.functional\\(\\)") "")
+
+                ;; UnicodePlots is only used for the doctests
+                (("if VERSION <.*") "if true\n"))
               (setenv "NNLIB_TEST_CUDA" "false"))))))
     (propagated-inputs
      (list julia-adapt
            julia-chainrulescore
+           julia-compat
            julia-requires))
     (native-inputs
      (list julia-chainrulestestutils
-- 
2.38.1

[bug#60075] [PATCH 29/58] gnu: julia-chainrulescore: Update to 1.12.2.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-chainrulescore): Update to 1.12.2.
[arguments]: Adjust 'adjust-tests phase for changes in the source.
---
 gnu/packages/julia-xyz.scm | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 50201aa383..064dda6de7 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -776,7 +776,7 @@ (define-public julia-chainrules
 (define-public julia-chainrulescore
   (package
     (name "julia-chainrulescore")
-    (version "1.0.2")
+    (version "1.12.2")
     (source
      (origin
        (method git-fetch)
@@ -785,7 +785,7 @@ (define-public julia-chainrulescore
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1866xv30h1bi7f2m993nljzf58wwmv8zlgn6ffn9j3wckch1nfpb"))))
+        (base32 "0lgfcsb7f6c7knhiz5dbqh8x47d370pn71y9ys2y6763g0b4pm61"))))
     (build-system julia-build-system)
     (arguments
      (list
@@ -793,7 +793,9 @@ (define-public julia-chainrulescore
        #~(modify-phases %standard-phases
            (add-after 'unpack 'adjust-tests
              (lambda _
-               (substitute* "test/differentials/composite.jl"
+               (substitute* "test/tangent_types/tangent.jl"
+                 ;; This test is disabled after the release.
+                 (("@test haskey.*Float.*") "")
                  (("@test (.*construct)" _ test)
                   (string-append "@test_broken " test))))))))
     (inputs                             ;required for tests
-- 
2.38.1

[bug#60075] [PATCH 30/58] gnu: julia-chainrulestestutils: Update to 1.5.1.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-chainrulestestutils): Update to 1.5.1.
---
 gnu/packages/julia-xyz.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 064dda6de7..80dfe37996 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -812,7 +812,7 @@ (define-public julia-chainrulescore
 (define-public julia-chainrulestestutils
   (package
     (name "julia-chainrulestestutils")
-    (version "1.2.3")
+    (version "1.5.1")
     (source
      (origin
        (method git-fetch)
@@ -821,7 +821,7 @@ (define-public julia-chainrulestestutils
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1vlkyp72d514gyb4k3yhjl1g7f24ncmz61j56p4sdi9f76rk9fx9"))))
+        (base32 "0vk7cpp049pjj7g5zqxr7djp5v0swhvhq3wvkxyw8m8xvqlnfncc"))))
     (build-system julia-build-system)
     (propagated-inputs
      (list julia-chainrulescore
-- 
2.38.1

[bug#60075] [PATCH 31/58] gnu: Add julia-realdot.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-realdot): New variable.
---
 gnu/packages/julia-xyz.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 80dfe37996..3bf1060e4f 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -4637,6 +4637,29 @@ (define-public julia-ratios
 type, which make some sacrifices but have better computational performance.")
     (license license:expat)))
 
+(define-public julia-realdot
+  (package
+    (name "julia-realdot")
+    (version "0.1.0")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/JuliaMath/RealDot.jl")
+               (commit (string-append "v" version))))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "1jr8dq110j8axjfz936b1lqqcnqg3979rfg11w76rq1iz7zgi691"))))
+    (build-system julia-build-system)
+    (home-page "https://github.com/JuliaMath/RealDot.jl")
+    (synopsis "Compute realdot efficiently")
+    (description "This package only contains and exports a single function
+@code{realdot(x, y)}.  It computes @code{real(LinearAlgebra.dot(x, y))} while
+avoiding computing the imaginary part of @code{LinearAlgebra.dot(x, y)} if
+possible.  The real dot product is useful when one treats complex numbers as
+embedded in a real vector space.")
+    (license license:expat)))
+
 (define-public julia-recipesbase
   (package
     (name "julia-recipesbase")
-- 
2.38.1

[bug#60075] [PATCH 32/58] gnu: julia-chainrules: Update to 1.35.0.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-chainrules): Update to 1.35.0.
[arguments]: Skip tests.
[inputs]: Comment out inputs.
[propagated-inputs]: Remove julia-reexport, julia-requires. Add
julia-irrationalconstants, julia-realdot.
---
 gnu/packages/julia-xyz.scm | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 3bf1060e4f..126c82bf5a 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -745,7 +745,7 @@ (define-public julia-cenum
 (define-public julia-chainrules
   (package
     (name "julia-chainrules")
-    (version "1.1.0")
+    (version "1.35.0")
     (source
      (origin
        (method git-fetch)
@@ -754,18 +754,19 @@ (define-public julia-chainrules
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0if93pd3b3scg2x3gmk1cbwjk0ax1n792vy8c38y3xl7jpd5cb70"))))
+        (base32 "17irgz3gamyrmzsjhq4s1n1sblvhkj10yg5y5y53yr631cl2fr6a"))))
     (build-system julia-build-system)
-    (inputs                             ;required for test
-     (list julia-chainrulestestutils
-           julia-finitedifferences
-           julia-nanmath
-           julia-specialfunctions))
+    (arguments
+     (list #:tests? #f))        ; JuliaInterpreter.jl not packaged yet.
+    ;(inputs                             ;required for test
+    ; (list julia-chainrulestestutils
+    ;       julia-finitedifferences
+    ;       julia-juliainterpreter))
     (propagated-inputs
      (list julia-chainrulescore
            julia-compat
-           julia-reexport
-           julia-requires))
+           julia-irrationalconstants
+           julia-realdot))
     (home-page "https://github.com/JuliaDiff/ChainRules.jl")
     (synopsis "Common utilities for automatic differentiation")
     (description "The is package provides a variety of common utilities that
-- 
2.38.1

[bug#60075] [PATCH 33/58] gnu: Add julia-optimisers.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-optimisers): New variable.
---
 gnu/packages/julia-xyz.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 126c82bf5a..b844070f56 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -4057,6 +4057,33 @@ (define-public julia-optim
 optimization of functions.")
     (license license:expat)))
 
+(define-public julia-optimisers
+  (package
+    (name "julia-optimisers")
+    (version "0.2.13")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/FluxML/Optimisers.jl")
+               (commit (string-append "v" version))))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "1xs51r365l6r56rpm08kba00nfcl5jlglwy8494w06vbi22ysbq7"))))
+    (build-system julia-build-system)
+    (propagated-inputs
+     (list julia-chainrulescore
+           julia-functors
+           julia-zygote))
+    (native-inputs
+     (list julia-staticarrays
+           julia-zygote))
+    (home-page "https://github.com/FluxML/Optimisers.jl")
+    (synopsis "Optimisers and utilities for learning loops")
+    (description "@code{Optimisers.jl} defines many standard gradient-based
+optimisation rules, and tools for applying them to deeply nested models.")
+    (license license:expat)))
+
 (define-public julia-optimtestproblems
   (package
     (name "julia-optimtestproblems")
-- 
2.38.1

[bug#60075] [PATCH 34/58] gnu: julia-tracker: Update to 0.2.22.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-tracker): Update to 0.2.22.
[source]: Remove patch.
[propagated-inputs]: Add julia-functors, julia-logexpfunctions,
julia-optimisers.
* gnu/packages/patches/julia-tracker-16-compat.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
---
 gnu/local.mk                                  |  1 -
 gnu/packages/julia-xyz.scm                    |  8 ++--
 .../patches/julia-tracker-16-compat.patch     | 40 -------------------
 3 files changed, 5 insertions(+), 44 deletions(-)
 delete mode 100644 gnu/packages/patches/julia-tracker-16-compat.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 60a422fd7e..ae6cc38abb 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1376,7 +1376,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/json-c-0.12-CVE-2020-12762.patch	\
   %D%/packages/patches/jsoncpp-pkg-config-version.patch		\
   %D%/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch	\
-  %D%/packages/patches/julia-tracker-16-compat.patch		\
   %D%/packages/patches/libffi-3.3-powerpc-fixes.patch		\
   %D%/packages/patches/libffi-float128-powerpc64le.patch	\
   %D%/packages/patches/libobjc2-unbundle-robin-map.patch	\
diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index b844070f56..55e96e53ea 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -5758,7 +5758,7 @@ (define-public julia-testimages
 (define-public julia-tracker
   (package
     (name "julia-tracker")
-    (version "0.2.12")
+    (version "0.2.22")
     (source
       (origin
         (method git-fetch)
@@ -5767,16 +5767,18 @@ (define-public julia-tracker
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "1s4mdywbp7nli7z985fqaj1rs4i6d92b1jx3lhg0qhk1s5wc0v8j"))
-        (patches (search-patches "julia-tracker-16-compat.patch"))))
+         (base32 "0sxncn999dc5j15y0h3cw28x41pv5qjaw64drhy1y4rn3na48504"))))
     (build-system julia-build-system)
     (propagated-inputs
      (list julia-adapt
            julia-diffrules
            julia-forwarddiff
+           julia-functors
+           julia-logexpfunctions
            julia-macrotools
            julia-nanmath
            julia-nnlib
+           julia-optimisers
            julia-requires
            julia-specialfunctions))
     (native-inputs
diff --git a/gnu/packages/patches/julia-tracker-16-compat.patch b/gnu/packages/patches/julia-tracker-16-compat.patch
deleted file mode 100644
index 4fff423e44..0000000000
--- a/gnu/packages/patches/julia-tracker-16-compat.patch
+++ /dev/null
@@ -1,40 +0,0 @@
-https://github.com/FluxML/Tracker.jl/commit/f6550ba38a9ea5802e2de4fa9c939929ba711f0d.patch
-from an upstream pull request
-https://github.com/FluxML/Tracker.jl/pull/94
-
-
-From f6550ba38a9ea5802e2de4fa9c939929ba711f0d Mon Sep 17 00:00:00 2001
-From: Michael Abbott <me@escbook>
-Date: Wed, 3 Feb 2021 22:58:33 +0100
-Subject: [PATCH] two fixes for 1.6
-
----
- src/lib/array.jl | 2 +-
- src/lib/real.jl  | 1 +
- 2 files changed, 2 insertions(+), 1 deletion(-)
-
-diff --git a/src/lib/array.jl b/src/lib/array.jl
-index 92f2b39..f8cbbac 100644
---- a/src/lib/array.jl
-+++ b/src/lib/array.jl
-@@ -298,7 +298,7 @@ Base.reverse(xs::TrackedArray; dims) = track(reverse, xs, dims = dims)
- @grad reverse(xs; dims) = reverse(data(xs), dims = dims), Δ -> (reverse(Δ, dims = dims), nothing)
- Base.reverse(xs::TrackedVector) = track(reverse, xs)
- @grad reverse(xs::TrackedVector) = reverse(data(xs)), Δ -> (reverse(Δ),)
--Base.reverse(xs::TrackedVector, start, stop) = track(reverse, xs, start, stop)
-+Base.reverse(xs::TrackedVector, start::Integer, stop::Integer) = track(reverse, xs, start, stop)
- @grad reverse(xs, start, stop) = reverse(data(xs), start, stop), Δ -> (reverse(Δ, start, stop), nothing, nothing)
- 
- function _kron(mat1::AbstractMatrix,mat2::AbstractMatrix)
-diff --git a/src/lib/real.jl b/src/lib/real.jl
-index 737afd8..e1975ac 100644
---- a/src/lib/real.jl
-+++ b/src/lib/real.jl
-@@ -55,6 +55,7 @@ for f in :[isinf, isnan, isfinite].args
- end
- 
- Printf.fix_dec(x::TrackedReal, n::Int, a...) = Printf.fix_dec(data(x), n, a...)
-+Printf.tofloat(x::TrackedReal) = Printf.tofloat(data(x))
- 
- Base.float(x::TrackedReal) = x
- 
-- 
2.38.1

[bug#60075] [PATCH 35/58] gnu: julia-specialfunctions: Update to 1.8.7.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-specialfunctions): Update to 1.8.7.
[propagated-inputs]: Add julia-irrationalconstants.
---
 gnu/packages/julia-xyz.scm | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 55e96e53ea..afae3ed1fc 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -5239,7 +5239,7 @@ (define-public julia-sortingalgorithms
 (define-public julia-specialfunctions
   (package
     (name "julia-specialfunctions")
-    (version "1.6.0")
+    (version "1.8.7")
     (source
      (origin
        (method git-fetch)
@@ -5248,12 +5248,13 @@ (define-public julia-specialfunctions
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0nfpnglx7zl9g20w2mgfkg17hcw9ri0shaq2rwplj0ij5pwz8yf0"))))
+        (base32 "0shlgx9lkbjb1awdf5lrbkq06bmkyahc92qay2a049b4lvqrhj7a"))))
     (build-system julia-build-system)
     (inputs
      (list julia-chainrulestestutils))
     (propagated-inputs
      (list julia-chainrulescore
+           julia-irrationalconstants
            julia-logexpfunctions
            julia-openspecfun-jll))
     (home-page "https://github.com/JuliaMath/SpecialFunctions.jl")
-- 
2.38.1

[bug#60075] [PATCH 36/58] gnu: julia-lazyarrays: Update to 0.22.16.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-lazyarrays): Update to 0.22.16.
[propagated-inputs]: Add julia-aqua.
[native-inputs]: Add julia-aqua.
---
 gnu/packages/julia-xyz.scm | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index afae3ed1fc..066d76ec95 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -3397,7 +3397,7 @@ (define-public julia-latexstrings
 (define-public julia-lazyarrays
   (package
     (name "julia-lazyarrays")
-    (version "0.22.2")
+    (version "0.22.16")
     (source
       (origin
         (method git-fetch)
@@ -3406,7 +3406,7 @@ (define-public julia-lazyarrays
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "17rhlrmgfvdw8w62pg32ikr9j4xy2ylr7mx7ar0hnpzryv929rp5"))))
+         (base32 "127yld4f26lchw5jwp30g2jkjbm7narfsxwcbggy7dfp43s531c5"))))
     (build-system julia-build-system)
     (arguments
      (list
@@ -3419,13 +3419,15 @@ (define-public julia-lazyarrays
                   (substitute* "test/multests.jl"
                     (("Int64") "Int32"))))))))
     (propagated-inputs
-     (list julia-arraylayouts
+     (list julia-aqua
+           julia-arraylayouts
            julia-fillarrays
            julia-macrotools
            julia-matrixfactorizations
            julia-staticarrays))
     (native-inputs
-     (list julia-tracker))
+     (list julia-aqua
+           julia-tracker))
     (home-page "https://github.com/JuliaArrays/LazyArrays.jl")
     (synopsis "Lazy arrays and linear algebra")
     (description "This package supports lazy analogues of array operations like
-- 
2.38.1

[bug#60075] [PATCH 37/58] gnu: julia-bson: Update to 0.3.6.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-bson): Update to 0.3.6.
---
 gnu/packages/julia-xyz.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 066d76ec95..6929fcf915 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -601,7 +601,7 @@ (define-public julia-blockbandedmatrices
 (define-public julia-bson
   (package
     (name "julia-bson")
-    (version "0.3.3")
+    (version "0.3.6")
     (source
       (origin
         (method git-fetch)
@@ -610,7 +610,7 @@ (define-public julia-bson
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "1l5608ma2ys7v2gpcqbiv9mwfc6yrlqkihrfx1pf7fgv5llhd4fn"))))
+         (base32 "1accra3casg66fhn5r07hz3rgs7qf9ld9ajnz8f80aid85zyp891"))))
     (build-system julia-build-system)
     (native-inputs
      (list julia-dataframes))
-- 
2.38.1

[bug#60075] [PATCH 38/58] gnu: julia-interpolations: Update to 0.13.6.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-interpolations): Update to 0.13.6.
[propagated-inputs]: Add julia-chainrulescore.
[native-inputs]: Add julia-colorvectorspace.
---
 gnu/packages/julia-xyz.scm | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 6929fcf915..fb83bb6171 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -3021,7 +3021,7 @@ (define-public julia-inlinestrings
 (define-public julia-interpolations
   (package
     (name "julia-interpolations")
-    (version "0.13.3")
+    (version "0.13.6")
     (source
       (origin
         (method git-fetch)
@@ -3030,7 +3030,7 @@ (define-public julia-interpolations
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "1236c20k388qlh7k74mhf7hkbn0vf7ss8b1rgh1a6aj0234ayfnc"))))
+         (base32 "1skzvgd63rhj1zpn45gi3974rbrir9p2y17zyfmkz6c6nird7bkj"))))
     (build-system julia-build-system)
     (arguments
      (list
@@ -3043,16 +3043,19 @@ (define-public julia-interpolations
                         (target-x86-32?)))))
     (propagated-inputs
      (list julia-axisalgorithms
+           julia-chainrulescore
            julia-offsetarrays
            julia-ratios
            julia-requires
            julia-staticarrays
            julia-woodburymatrices))
     (native-inputs
-     (list julia-dualnumbers
+     (list julia-colorvectorspace
+           julia-dualnumbers
            julia-forwarddiff
            julia-offsetarrays
-           julia-unitful julia-zygote))
+           julia-unitful
+           julia-zygote))
     (home-page "https://github.com/JuliaMath/Interpolations.jl")
     (synopsis "Continuous interpolation of discrete datasets")
     (description "This package implements a variety of interpolation schemes for
-- 
2.38.1

[bug#60075] [PATCH 39/58] gnu: julia-requires: Update to 1.3.0.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-requires): Update to 1.3.0.
[propagated-inputs, inputs]: Move packages ...
[native-inputs]: ... to here.
---
 gnu/packages/julia-xyz.scm | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index fb83bb6171..a89ef60459 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -4843,7 +4843,7 @@ (define-public julia-referencetests
 (define-public julia-requires
   (package
     (name "julia-requires")
-    (version "1.1.3")
+    (version "1.3.0")
     (source
      (origin
        (method git-fetch)
@@ -4852,14 +4852,13 @@ (define-public julia-requires
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "03hyfy7c0ma45b0y756j76awi3az2ii4bz4s8cxm3xw9yy1z7b01"))))
+        (base32 "0gmqs7f17aq500lbdff4ibws00f8m0pnzskvf4b3ig520xv3n3nm"))))
     (build-system julia-build-system)
     (arguments
-     (list #:parallel-tests? #f))
-    (inputs                             ;required for test
-     (list julia-example))
-    (propagated-inputs
-     (list julia-colors))
+     (list #:parallel-tests? #f))       ; Test suite has race conditions.
+    (native-inputs
+     (list julia-colors
+           julia-example))
     (home-page "https://github.com/JuliaPackaging/Requires.jl/")
     (synopsis "Faster package loader")
     (description "This package make loading packages faster, maybe.  It
-- 
2.38.1

[bug#60075] [PATCH 40/58] gnu: julia-colors: Update to 0.12.9.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-colors): Update to 0.12.9.
[arguments]: Add phase to skip ambiguities tests.
[native-inputs]: Add julia-abstracttrees.
---
 gnu/packages/julia-xyz.scm | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index a89ef60459..3ffbd54684 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -895,21 +895,32 @@ (define-public julia-codeczlib
 (define-public julia-colors
   (package
     (name "julia-colors")
-    (version "0.12.8")
+    (version "0.12.9")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/JuliaGraphics/Colors.jl")
-             (commit (string-append "v" version))))
+             ;; The commit is registered but isn't tagged yet.
+             (commit "df7cc128e92d9ee5ef3696ba49ffbe3714539eb4")))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0kx3hq7rf8p5zx6ly9k5j90zijmc7yrwmy96cgkl2ibdfbnhmya3"))))
+        (base32 "1g0fvvz09pfk6jxqrdplwkw1yywcqvwjd3ga24hblq71mah367n6"))))
     (build-system julia-build-system)
+    (arguments
+     (list
+       #:phases
+       #~(modify-phases %standard-phases
+           (add-after 'unpack 'adjust-tests
+             (lambda _
+               (substitute* "test/runtests.jl"
+                 ((".*detect_ambiguities.*") "")))))))
     (propagated-inputs
      (list julia-colortypes
            julia-fixedpointnumbers
            julia-reexport))
+    (native-inputs
+     (list julia-abstracttrees))
     (home-page "https://github.com/JuliaGraphics/Colors.jl")
     (synopsis "Tools for dealing with color")
     (description "This package provides a wide array of functions for dealing
-- 
2.38.1

[bug#60075] [PATCH 41/58] gnu: julia-colorvectorspace: Update to 0.9.9.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-colorvectorspace): Update to 0.9.9.
[arguments]: Skip tests. Add phase to skip ambiguities tests.
[propagated-inputs]: Add julia-fixedpointnumbers.
---
 gnu/packages/julia-xyz.scm | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 3ffbd54684..c3d6d642c1 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -991,7 +991,7 @@ (define-public julia-colortypes
 (define-public julia-colorvectorspace
   (package
     (name "julia-colorvectorspace")
-    (version "0.9.7")
+    (version "0.9.9")
     (source
       (origin
         (method git-fetch)
@@ -1000,10 +1000,20 @@ (define-public julia-colorvectorspace
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "02gk7f5g5wjxdasbjf8bvv1m7clksh7mw1xmygjdirjz1q0d6dwi"))))
+         (base32 "07scws2bn2z3f2crhnx1zxk3zk3vzfv9iz6lv3i9785nplmsgdx9"))))
     (build-system julia-build-system)
+    (arguments
+     (list
+       #:tests? #f      ; TODO: Reenable the test suite.
+       #:phases
+       #~(modify-phases %standard-phases
+           (add-after 'unpack 'adjust-tests
+             (lambda _
+               (substitute* "test/runtests.jl"
+                 ((".*detect_ambiguities.*") "")))))))
     (propagated-inputs
      (list julia-colortypes
+           julia-fixedpointnumbers
            julia-specialfunctions
            julia-tensorcore))
     (native-inputs
-- 
2.38.1

[bug#60075] [PATCH 41/58] gnu: julia-colorvectorspace: Update to 0.9.9.

[zimoun]

Hi,

On Wed, 14 Dec 2022 at 22:35, Efraim Flashner <efraim@flashner.co.il> wrote:
> * gnu/packages/julia-xyz.scm (julia-colorvectorspace): Update to 0.9.9.
> [arguments]: Skip tests. Add phase to skip ambiguities tests.
> [propagated-inputs]: Add julia-fixedpointnumbers.

[...]

> +    (arguments
> +     (list
> +       #:tests? #f      ; TODO: Reenable the test suite.

Why skip the tests?

> +       #:phases
> +       #~(modify-phases %standard-phases
> +           (add-after 'unpack 'adjust-tests
> +             (lambda _
> +               (substitute* "test/runtests.jl"
> +                 ((".*detect_ambiguities.*") "")))))))

And add a phases modifying the test suite?


Cheers,
simon

[bug#60075] [PATCH 42/58] gnu: julia-plotutils: Update to 1.2.0.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-plotutils): Update to 1.2.0.
[arguments]: Add a phase to adjust the test suite.
---
 gnu/packages/julia-xyz.scm | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index c3d6d642c1..4ef88ad850 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -4307,7 +4307,7 @@ (define-public julia-plotthemes
 (define-public julia-plotutils
   (package
     (name "julia-plotutils")
-    (version "1.0.15")
+    (version "1.2.0")
     (source
       (origin
         (method git-fetch)
@@ -4316,8 +4316,17 @@ (define-public julia-plotutils
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "12aw5gkkcfhpczv2w510k65w1j0hjnh825ihimi223v8plsi5105"))))
+         (base32 "1yml9ayaniqnzx5r8sfjckifcm99ck7qhc19cd8fs0bwzkh7nza7"))))
     (build-system julia-build-system)
+    (arguments
+     (list
+       #:phases
+       #~(modify-phases %standard-phases
+           (add-after 'unpack 'adjust-test-suite
+             (lambda _
+               (substitute* "test/runtests.jl"
+                 (("(@test_throws) ErrorException (.*notacolor)" _ @test notacolor)
+                  (string-append @test " ArgumentError " notacolor))))))))
     (propagated-inputs
      (list julia-colors
            julia-colorschemes
-- 
2.38.1

[bug#60075] [PATCH 43/58] gnu: Remove julia-infinity.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-infinity): Delete variable.
---
 gnu/packages/julia-xyz.scm | 33 ---------------------------------
 1 file changed, 33 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 4ef88ad850..2b4e8e2579 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -2960,39 +2960,6 @@ (define-public julia-indirectarrays
 indexed images, sometimes called \"colormap images\" or \"paletted images.\"")
     (license license:expat)))
 
-(define-public julia-infinity
-  (package
-    (name "julia-infinity")
-    (version "0.2.4")
-    (source
-      (origin
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/cjdoris/Infinity.jl")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32 "1941lwvrdjnrynigzixxin3chpg1ba6xplvcwc89x0f6z658hwmm"))))
-    (build-system julia-build-system)
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'link-depot 'remove-timezones.jl
-            (lambda _
-              (substitute* "test/runtests.jl"
-                (("using TimeZones.*") "")
-                ((".*infextendedtime.*") "")))))))
-    (propagated-inputs
-     (list julia-requires))
-    (native-inputs
-     (list julia-compat))
-    (home-page "https://docs.juliahub.com/Infinity/")
-    (synopsis "Representation of infinity in Julia")
-    (description "This package provides representations for infinity and
-negative infinity in Julia.")
-    (license license:expat)))
-
 (define-public julia-inifile
   (package
     (name "julia-inifile")
-- 
2.38.1

[bug#60075] [PATCH 43/58] gnu: Remove julia-infinity.

[zimoun]

Hi,

On Wed, 14 Dec 2022 at 22:35, Efraim Flashner <efraim@flashner.co.il> wrote:
> * gnu/packages/julia-xyz.scm (julia-infinity): Delete variable.

I think it costs nothing to keep it.  WDYT?


Cheers,
simon

[bug#60075] [PATCH 43/58] gnu: Remove julia-infinity.

[Efraim Flashner]

[-- Attachment #1: Type: text/plain, Size: 497 bytes --]

On Mon, Dec 19, 2022 at 07:40:35PM +0100, zimoun wrote:
> Hi,
> 
> On Wed, 14 Dec 2022 at 22:35, Efraim Flashner <efraim@flashner.co.il> wrote:
> > * gnu/packages/julia-xyz.scm (julia-infinity): Delete variable.
> 
> I think it costs nothing to keep it.  WDYT?

Works for me

-- 
Efraim Flashner   <efraim@flashner.co.il>   אפרים פלשנר
GPG key = A28B F40C 3E55 1372 662D  14F7 41AA E7DC CA3D 8351
Confidentiality cannot be guaranteed on emails sent or received unencrypted

[-- Attachment #2: signature.asc --]
[-- Type: application/pgp-signature, Size: 833 bytes --]

[bug#60075] [PATCH 44/58] gnu: julia-indexablebitvectors: Limit to 64-bit systems.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-indexablebitvectors)
[supported-systems]: New field.
---
 gnu/packages/julia-xyz.scm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 2b4e8e2579..ed7c62c0be 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -2910,6 +2910,7 @@ (define-public julia-indexablebitvectors
 index of i-th occurrence of @code{b} in @code{bv}.
 @end itemize
 and other shortcuts or types.")
+    (supported-systems %64bit-supported-systems)
     (license license:expat)))
 
 (define-public julia-indexing
-- 
2.38.1

[bug#60075] [PATCH 44/58] gnu: julia-indexablebitvectors: Limit to 64-bit systems.

[zimoun]

Hi,

On Wed, 14 Dec 2022 at 22:35, Efraim Flashner <efraim@flashner.co.il> wrote:
> * gnu/packages/julia-xyz.scm (julia-indexablebitvectors)
> [supported-systems]: New field.

> +    (supported-systems %64bit-supported-systems)

It means that julia-bioalignments will not build for non-64bit system.

Well, is it because upstream does not support other than 64bits?


Cheers,
simon

[bug#60075] [PATCH 44/58] gnu: julia-indexablebitvectors: Limit to 64-bit systems.

[Efraim Flashner]

[-- Attachment #1: Type: text/plain, Size: 806 bytes --]

On Mon, Dec 19, 2022 at 07:43:06PM +0100, zimoun wrote:
> Hi,
> 
> On Wed, 14 Dec 2022 at 22:35, Efraim Flashner <efraim@flashner.co.il> wrote:
> > * gnu/packages/julia-xyz.scm (julia-indexablebitvectors)
> > [supported-systems]: New field.
> 
> > +    (supported-systems %64bit-supported-systems)
> 
> It means that julia-bioalignments will not build for non-64bit system.
> 
> Well, is it because upstream does not support other than 64bits?

There's a bunch of bitwise math that expects 64-bit ints and things like
that. I'll add a comment above the supported-systems field.

-- 
Efraim Flashner   <efraim@flashner.co.il>   אפרים פלשנר
GPG key = A28B F40C 3E55 1372 662D  14F7 41AA E7DC CA3D 8351
Confidentiality cannot be guaranteed on emails sent or received unencrypted

[-- Attachment #2: signature.asc --]
[-- Type: application/pgp-signature, Size: 833 bytes --]

[bug#60075] [PATCH 45/58] gnu: julia-blockarrays: Update to 0.16.23.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-blockarrays): Update to 0.16.23.
[native-inputs]: Remove julia-lazyarrays; add julia-aqua.
---
 gnu/packages/julia-xyz.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index ed7c62c0be..7c6a83475b 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -527,7 +527,7 @@ (define-public julia-biosymbols
 (define-public julia-blockarrays
   (package
     (name "julia-blockarrays")
-    (version "0.16.8")
+    (version "0.16.23")
     (source
       (origin
         (method git-fetch)
@@ -536,7 +536,7 @@ (define-public julia-blockarrays
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "1by26036fk9mawmcgqxpwizgbs398v9p6vrbsgg7h6llqn3q9iw1"))))
+         (base32 "14gby25ixbp9ha0y2aj4gnjkzha4c7v4y3sicicgbkysnq921qd0"))))
     (build-system julia-build-system)
     (arguments
      (list
@@ -552,7 +552,7 @@ (define-public julia-blockarrays
      (list julia-arraylayouts
            julia-fillarrays))
     (native-inputs
-     (list julia-lazyarrays
+     (list julia-aqua
            julia-offsetarrays
            julia-staticarrays))
     (home-page "https://github.com/JuliaArrays/BlockArrays.jl")
-- 
2.38.1

[bug#60075] [PATCH 46/58] gnu: julia-scanbyte: Update to 0.3.2.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-scanbyte): Update to 0.3.2.
---
 gnu/packages/julia-xyz.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 7c6a83475b..82f71b298b 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -5028,7 +5028,7 @@ (define-public julia-sass
 (define-public julia-scanbyte
   (package
     (name "julia-scanbyte")
-    (version "0.3")
+    (version "0.3.2")
     (source
       (origin
         (method git-fetch)
@@ -5037,7 +5037,7 @@ (define-public julia-scanbyte
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "0dqqa3d7c87358144pji6ik8xlki2hj0hkvjs72j5aypfms8rwn3"))))
+         (base32 "1c18hkcb0h6l437v2s02kijjkyly91mqark84czvh8yzxm19hr7k"))))
     (build-system julia-build-system)
     (propagated-inputs
      (list julia-simd))
-- 
2.38.1

[bug#60075] [PATCH 47/58] gnu: julia-scanbyte: Limit to x86_64-linux.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-scanbyte)[supported-systems]: New
field.
---
 gnu/packages/julia-xyz.scm | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 82f71b298b..0dd075a959 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -5046,6 +5046,8 @@ (define-public julia-scanbyte
     (description "This package finds the first occurrence of a byte or set of
 bytes in a chunk of memory.  Think of it like a much faster version of
 @code{findfirst} that only iterates over bytes in memory.")
+    ;; https://github.com/jakobnissen/ScanByte.jl/issues/2
+    (supported-systems '("x86_64-linux"))
     (license license:expat)))
 
 (define-public julia-scratch
-- 
2.38.1

[bug#60075] [PATCH 47/58] gnu: julia-scanbyte: Limit to x86_64-linux.

[zimoun]

Hi,

On Wed, 14 Dec 2022 at 22:35, Efraim Flashner <efraim@flashner.co.il> wrote:
> * gnu/packages/julia-xyz.scm (julia-scanbyte)[supported-systems]: New
> field.

> +    ;; https://github.com/jakobnissen/ScanByte.jl/issues/2
> +    (supported-systems '("x86_64-linux"))

In patch [1]:

    [PATCH 44/58] gnu: julia-indexablebitvectors: Limit to 64-bit systems.

is introduced, instead, the change:

--8<---------------cut here---------------start------------->8---
+    (supported-systems %64bit-supported-systems)
--8<---------------cut here---------------end--------------->8---

Well, I think it would better to keep consistency.

1: https://issues.guix.gnu.org/msgid/ce3eb363cbd85c064a8a8aebac5e99e1c40edec4.1671049574.git.efraim@flashner.co.il


Cheers,
simon

[bug#60075] [PATCH 47/58] gnu: julia-scanbyte: Limit to x86_64-linux.

[Efraim Flashner]

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On Mon, Dec 19, 2022 at 07:47:23PM +0100, zimoun wrote:
> Hi,
> 
> On Wed, 14 Dec 2022 at 22:35, Efraim Flashner <efraim@flashner.co.il> wrote:
> > * gnu/packages/julia-xyz.scm (julia-scanbyte)[supported-systems]: New
> > field.
> 
> > +    ;; https://github.com/jakobnissen/ScanByte.jl/issues/2
> > +    (supported-systems '("x86_64-linux"))
> 
> In patch [1]:
> 
>     [PATCH 44/58] gnu: julia-indexablebitvectors: Limit to 64-bit systems.
> 
> is introduced, instead, the change:
> 
> --8<---------------cut here---------------start------------->8---
> +    (supported-systems %64bit-supported-systems)
> --8<---------------cut here---------------end--------------->8---
> 
> Well, I think it would better to keep consistency.
> 
> 1: https://issues.guix.gnu.org/msgid/ce3eb363cbd85c064a8a8aebac5e99e1c40edec4.1671049574.git.efraim@flashner.co.il

scanbyte relies on architecture specific implementations of functions
and hasn't been ported to other architectures yet. I actually started
looking into it before I realized it was something I could save for
later.

-- 
Efraim Flashner   <efraim@flashner.co.il>   אפרים פלשנר
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[bug#60075] [PATCH 48/58] gnu: julia-matrixfactorizations: Update to 0.9.3.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-matrixfactorizations): Update to
0.9.3.
[arguments]: Re-enable one of the skipped tests.
---
 gnu/packages/julia-xyz.scm | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 0dd075a959..2b05a722d2 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -3580,7 +3580,7 @@ (define-public julia-mappedarrays
 (define-public julia-matrixfactorizations
   (package
     (name "julia-matrixfactorizations")
-    (version "0.8.4")
+    (version "0.9.3")
     (source
       (origin
         (method git-fetch)
@@ -3589,7 +3589,7 @@ (define-public julia-matrixfactorizations
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "15zvcv2l4iqmjpnqjyx2kry7a85p652nbjy9pj3wq0piksqcz4jb"))))
+         (base32 "0sqmig01irmvh617h2rsw44hl39qwv2913nlqjsdz9si5vli2hsl"))))
     (build-system julia-build-system)
     (arguments
      (list
@@ -3597,10 +3597,8 @@ (define-public julia-matrixfactorizations
       #~(modify-phases %standard-phases
           (add-after 'link-depot '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.
+                ;; Don't warn on the REPL test.
                 (("test String") "test_nowarn String")))))))
     (propagated-inputs
      (list julia-arraylayouts))
-- 
2.38.1

[bug#60075] [PATCH 49/58] gnu: Add julia-static-0.6.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-static-0.6): New variable.
---
 gnu/packages/julia-xyz.scm | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 2b05a722d2..ad26209404 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -5379,6 +5379,21 @@ (define-public julia-static
 types and a common interface that is shared between them.")
     (license license:expat)))
 
+(define-public julia-static-0.6
+  (package
+    (inherit julia-static)
+    (name "julia-static")
+    (version "0.6.6")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/SciML/Static.jl")
+               (commit (string-append "v" version))))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "03ri8nl046cz7l433p0nlr84yywxvjykyymqparm8lxxwkv0rxqd"))))))
+
 (define-public julia-staticarrays
   (package
     (name "julia-staticarrays")
-- 
2.38.1

[bug#60075] [PATCH 50/58] gnu: julia-arrayinterface: Update to 5.0.8.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-arrayinterface): Update to 5.0.8.
[propagated-inputs]: Remove julia-static; add julia-compat and julia-static-0.6.
[native-inputs]: Add julia-static-0.6.
---
 gnu/packages/julia-xyz.scm | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index ad26209404..b8b07aab91 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -149,7 +149,7 @@ (define-public julia-aqua
 (define-public julia-arrayinterface
   (package
     (name "julia-arrayinterface")
-    (version "3.1.19")
+    (version "5.0.8")
     (source
       (origin
         (method git-fetch)
@@ -158,7 +158,7 @@ (define-public julia-arrayinterface
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "0cmldnzvdgmfnrnrzgj6v1mfr2rvk5096392rwmhd3iyx7v0pq33"))))
+         (base32 "0b0h4ihc8sykd96rn16vpk5kfk0p1si5iim61cixk9x12ma8ia3h"))))
     (build-system julia-build-system)
     (arguments
      ;; XXXX: Unexpected failures for i686, e.g.,
@@ -168,15 +168,17 @@ (define-public julia-arrayinterface
      (list #:tests? (not (or (%current-target-system)
                              (target-x86-32?)))))
     (propagated-inputs
-     (list julia-ifelse
+     (list julia-compat
+           julia-ifelse
            julia-requires
-           julia-static))
+           julia-static-0.6))
     (native-inputs
      (list julia-aqua
            julia-bandedmatrices
            julia-blockbandedmatrices
            julia-ifelse
            julia-offsetarrays
+           julia-static-0.6
            julia-staticarrays))
     (home-page "https://github.com/JuliaArrays/ArrayInterface.jl")
     (synopsis "Base array interface primitives")
-- 
2.38.1

[bug#60075] [PATCH 51/58] gnu: julia-bandedmatrices: Update to 0.17.9.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-bandedmatrices): Update to 0.17.9.
[propagated-inputs]: Add julia-aqua.
[native-inputs]: Add julia-aqua.
---
 gnu/packages/julia-xyz.scm | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index b8b07aab91..9e0c96733b 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -311,7 +311,7 @@ (define-public julia-axisarrays
 (define-public julia-bandedmatrices
   (package
     (name "julia-bandedmatrices")
-    (version "0.16.10")
+    (version "0.17.9")
     (source
       (origin
         (method git-fetch)
@@ -320,13 +320,15 @@ (define-public julia-bandedmatrices
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "0rlfj9gr9ss621v5kw5b06206yaak21s2vq9vk7r8a7p2ylncism"))))
+         (base32 "0nrcasjdpwf15z7l2lzyhxjqxlnqk5if78s15sh4gdgxf9kzj3a6"))))
     (build-system julia-build-system)
     (propagated-inputs
-     (list julia-arraylayouts
+     (list julia-aqua
+           julia-arraylayouts
            julia-fillarrays))
     (native-inputs
-     (list julia-genericlinearalgebra))
+     (list julia-aqua
+           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
-- 
2.38.1

[bug#60075] [PATCH 52/58] gnu: julia-blockbandedmatrices: Update to 0.11.9.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-blockbandedmatrices): Update to 0.11.9.
---
 gnu/packages/julia-xyz.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 9e0c96733b..8bbd8f89d2 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -577,7 +577,7 @@ (define-public julia-blockarrays
 (define-public julia-blockbandedmatrices
   (package
     (name "julia-blockbandedmatrices")
-    (version "0.10.7")
+    (version "0.11.9")
     (source
       (origin
         (method git-fetch)
@@ -586,7 +586,7 @@ (define-public julia-blockbandedmatrices
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "10n1r6kmmv2wa307jfg9y2m6p16j8hngjp3fjavpbdy1r5haasm9"))))
+         (base32 "1qag5awl8cmsyhpajv6llhpqbzxfii1bacppbjvmb1fqs9s0lifd"))))
     (build-system julia-build-system)
     (propagated-inputs
      (list julia-arraylayouts
-- 
2.38.1

[bug#60075] [PATCH 53/58] gnu: julia-ellipsisnotation: Update to 1.6.0.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-ellipsisnotation): Update to 1.6.0.
[arguments]: Remove phase adjusting the test suite.
---
 gnu/packages/julia-xyz.scm | 13 ++-----------
 1 file changed, 2 insertions(+), 11 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 8bbd8f89d2..8699ec1aa6 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -1808,7 +1808,7 @@ (define-public julia-dualnumbers
 (define-public julia-ellipsisnotation
   (package
     (name "julia-ellipsisnotation")
-    (version "1.1.0")
+    (version "1.6.0")
     (source
       (origin
         (method git-fetch)
@@ -1817,17 +1817,8 @@ (define-public julia-ellipsisnotation
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "0py46kxl702r8pw3v7x4cqllf7yc91b0dr7vb60xh2qi7d6y3jc7"))))
+         (base32 "0l4fc180chhxlq9d67122c0lgq2hfsxsmcgml2bfl2rnh13gya2b"))))
     (build-system julia-build-system)
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'link-depot 'adjust-test-suite
-            (lambda _
-              (substitute* "test/runtests.jl"
-                ;; Seems to not play nicely with Julia-1.6.
-                ((".*basic.jl.*") "")))))))
     (propagated-inputs
      (list julia-arrayinterface))
     (home-page "https://github.com/ChrisRackauckas/EllipsisNotation.jl")
-- 
2.38.1

[bug#60075] [PATCH 54/58] gnu: julia-axisarrays: Update to 0.4.6.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-axisarrays): Update to 0.4.6.
---
 gnu/packages/julia-xyz.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 8699ec1aa6..e4bbf1464d 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -280,7 +280,7 @@ (define-public julia-axisalgorithms
 (define-public julia-axisarrays
   (package
     (name "julia-axisarrays")
-    (version "0.4.4")
+    (version "0.4.6")
     (source
       (origin
         (method git-fetch)
@@ -289,7 +289,7 @@ (define-public julia-axisarrays
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "03kzan1lm4fxfhzv1xjg3ysf6y7nagcc61vfz15kvdrp1dqxlynk"))))
+         (base32 "1bsd6y866ldfb4072hfm8fvc2k0vy72z2blcwfy2mpj8dlyskx3n"))))
     (build-system julia-build-system)
     (propagated-inputs
      (list julia-rangearrays
-- 
2.38.1

[bug#60075] [PATCH 55/58] gnu: julia-graphics: Update to 1.1.2.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-graphics): Update to 1.1.2.
---
 gnu/packages/julia-xyz.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index e4bbf1464d..7c27adc1b8 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -2453,7 +2453,7 @@ (define-public julia-gr
 (define-public julia-graphics
   (package
     (name "julia-graphics")
-    (version "1.1.0")
+    (version "1.1.2")
     (source
       (origin
         (method git-fetch)
@@ -2462,7 +2462,7 @@ (define-public julia-graphics
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "10h1s09v7qkvrjr6l678zamb1p248n8jv4rrwkf8g7d2bpfz9amn"))))
+         (base32 "083fppcbmchgnqp4xqdsd4asavq51jq31w8ak35ns701534hr82p"))))
     (build-system julia-build-system)
     (propagated-inputs
      (list julia-colors
-- 
2.38.1

[bug#60075] [PATCH 56/58] gnu: julia-imageaxes: Update to 0.6.10.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-imageaxes): Update to 0.6.10.
[arguments]: Add a phase to skip a greyscale test.
[propagated-inputs]: Add julia-imagebase.
[native-inputs]: Add julia-aqua and julia-documenter.
---
 gnu/packages/julia-xyz.scm | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 7c27adc1b8..f3a61a3de6 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -2580,7 +2580,7 @@ (define-public julia-ifelse
 (define-public julia-imageaxes
   (package
     (name "julia-imageaxes")
-    (version "0.6.9")
+    (version "0.6.10")
     (source
       (origin
         (method git-fetch)
@@ -2589,15 +2589,27 @@ (define-public julia-imageaxes
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "15zqxani1jjh8849s7rdps6b6prqdwv8yxx893y536vkpk7i07qd"))))
+         (base32 "15f3y46vcr88fplr7rlibrm3k852p8rzwid5dgmbhc03a8xqd50s"))))
     (build-system julia-build-system)
+    (arguments
+     (list
+       #:phases
+       #~(modify-phases %standard-phases
+           (add-after 'unpack 'adjust-tests
+             (lambda _
+               (substitute* "test/runtests.jl"
+                 ;; Skip the constantly failing grayscale test.
+                 (("@test summary") "@test_broken summary")))))))
     (propagated-inputs
      (list julia-axisarrays
+           julia-imagebase
            julia-imagecore
            julia-reexport
            julia-simpletraits))
     (native-inputs
-     (list julia-unitful))
+     (list julia-aqua
+           julia-documenter
+           julia-unitful))
     (home-page "https://github.com/JuliaImages/ImageAxes.jl")
     (synopsis "Julia package for giving \"meaning\" to the axes of an image")
     (description "This small package supports the representation of images as
-- 
2.38.1

[bug#60075] [PATCH 57/58] gnu: julia-paddedviews: Update to 0.5.11.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-paddedviews): Update to 0.5.11.
---
 gnu/packages/julia-xyz.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index f3a61a3de6..954b610d97 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -4161,7 +4161,7 @@ (define-public julia-offsetarrays
 (define-public julia-paddedviews
   (package
     (name "julia-paddedviews")
-    (version "0.5.8")
+    (version "0.5.11")
     (source
       (origin
         (method git-fetch)
@@ -4170,7 +4170,7 @@ (define-public julia-paddedviews
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "0ran2vj6ahlzib0g77y7g0jhavy3k9s2mqq23ybpgp9z677wf26h"))))
+         (base32 "1835q06g6ymqh1k7625ssahwm46j08370v2inb61y1lw8vd99f3x"))))
     (build-system julia-build-system)
     (propagated-inputs
      (list julia-offsetarrays))
-- 
2.38.1

[bug#60075] [PATCH 58/58] gnu: julia-imagemetadata: Update to 0.9.8.

[Efraim Flashner]

* gnu/packages/julia-xyz.scm (julia-imagemetadata): Update to 0.9.8.
[arguments]: Add phase to skip greyscale test.
[propagated-inputs]: Remove julia-indirectarrays; add julia-imagebase.
[native-inputs]: Add julia-indirectarrays.
---
 gnu/packages/julia-xyz.scm | 21 ++++++++++++++++-----
 1 file changed, 16 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 954b610d97..3b2d2516ce 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -2782,7 +2782,7 @@ (define-public julia-imagemagick
 (define-public julia-imagemetadata
   (package
     (name "julia-imagemetadata")
-    (version "0.9.6")
+    (version "0.9.8")
     (source
       (origin
         (method git-fetch)
@@ -2791,15 +2791,26 @@ (define-public julia-imagemetadata
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "0iv154ms370xgcr56bwsjl13iwmy671cbxjl9ld5yfj85pclcwi1"))))
+         (base32 "0rdzvya5szlkg5ds3fw7lpk47hn16655i6265czwf8fxs3hb1gvf"))))
     (build-system julia-build-system)
+    (arguments
+     (list
+       #:phases
+       #~(modify-phases %standard-phases
+           (add-after 'unpack 'adjust-tests
+             (lambda _
+               (substitute* "test/operations.jl"
+                 ;; Skip the constantly failing greyscale test.
+                 (("\\@testset \\\"operations.*" all)
+                  (string-append all " return\n"))))))))
     (propagated-inputs
      (list julia-axisarrays
            julia-imageaxes
-           julia-imagecore
-           julia-indirectarrays))
+           julia-imagebase
+           julia-imagecore))
     (native-inputs
-     (list julia-offsetarrays
+     (list julia-indirectarrays
+           julia-offsetarrays
            julia-simpletraits
            julia-unitful))
     (home-page "https://github.com/JuliaImages/ImageMetadata.jl")
-- 
2.38.1

[bug#60075] [PATCH 00/58] New julia patches

[zimoun]

Hi Efraim,

On Wed, 14 Dec 2022 at 22:32, Efraim Flashner <efraim@flashner.co.il> wrote:

> Efraim Flashner (58):

>  gnu/packages/julia-xyz.scm                    | 743 ++++++++++++------

All LGTM, except the ones with minor comments here or there.

Thanks for this update.

Cheers,
simon

[bug#60075] [PATCH 00/58] New julia patches

[Efraim Flashner]

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On Mon, Dec 19, 2022 at 07:50:09PM +0100, zimoun wrote:
> Hi Efraim,
> 
> On Wed, 14 Dec 2022 at 22:32, Efraim Flashner <efraim@flashner.co.il> wrote:
> 
> > Efraim Flashner (58):
> 
> >  gnu/packages/julia-xyz.scm                    | 743 ++++++++++++------
> 
> All LGTM, except the ones with minor comments here or there.
> 
> Thanks for this update.

julia-colors 0.12.9 finally got tagged, and then it looks like 0.12.10
got tagged the same day. I'm going to see what that's about before
pushing the series.

-- 
Efraim Flashner   <efraim@flashner.co.il>   אפרים פלשנר
GPG key = A28B F40C 3E55 1372 662D  14F7 41AA E7DC CA3D 8351
Confidentiality cannot be guaranteed on emails sent or received unencrypted

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bug#60075: [PATCH 00/58] New julia patches

[Efraim Flashner]

[-- Attachment #1: Type: text/plain, Size: 691 bytes --]

On Mon, Dec 19, 2022 at 07:50:09PM +0100, zimoun wrote:
> Hi Efraim,
> 
> On Wed, 14 Dec 2022 at 22:32, Efraim Flashner <efraim@flashner.co.il> wrote:
> 
> > Efraim Flashner (58):
> 
> >  gnu/packages/julia-xyz.scm                    | 743 ++++++++++++------
> 
> All LGTM, except the ones with minor comments here or there.
> 
> Thanks for this update.

Turns out the update came with a few more broken tests. Pushing these 57
patches.

Thanks for the review!

-- 
Efraim Flashner   <efraim@flashner.co.il>   אפרים פלשנר
GPG key = A28B F40C 3E55 1372 662D  14F7 41AA E7DC CA3D 8351
Confidentiality cannot be guaranteed on emails sent or received unencrypted

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