[bug#51207] [PATCH 0/9] More Julia packages toward Flux

[bug#51207] [PATCH 0/9] More Julia packages toward Flux

[zimoun]

Hi,

Since Documenter.jl is now available, let use it and turn on the missing tests
of some packages.

Then, more trivial packages which are dependencies of Flux (machine learning
framework).  The hard part still missing is CUDA.

All the best,
simon


zimoun (9):
  gnu: julia-coordinatetransformations: Enable tests.
  gnu: julia-colortypes: Enable tests.
  gnu: julia-irtools: Enable tests.
  gnu: julia-paddedviews: Enable tests.
  gnu: julia-stackviews: Enable tests.
  gnu: Add julia-functors.
  gnu: Add julia-transcodingstreams.
  gnu: Add julia-codeczlib.
  gnu: Add julia-media.

 gnu/packages/julia-xyz.scm | 139 ++++++++++++++++++++++++++++++++-----
 1 file changed, 122 insertions(+), 17 deletions(-)


base-commit: e2a021a745d5009f2e8386108840146faa33fd86
-- 
2.32.0

[bug#51207] [PATCH 1/9] gnu: julia-coordinatetransformations: Enable tests.

[zimoun]

* gnu/packages/julia-xyz.scm (julia-coordinatetransformations)[arguments]:
Remove.
[native-inputs]: Add julia-documenter, julia-forwarddiff, julia-unitful.
---
 gnu/packages/julia-xyz.scm | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index c1ebc0fba1..62b6e4edfb 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -806,14 +806,12 @@ (define-public julia-coordinatetransformations
         (sha256
          (base32 "15zbkn32v7xlz7559s0r5a0vkwmjwsswxaqpzijly4lky4jnp33d"))))
     (build-system julia-build-system)
-    (arguments
-     `(#:tests? #f))    ; Documenter.jl not packaged yet.
     (propagated-inputs
      `(("julia-staticarrays" ,julia-staticarrays)))
-    ;(native-inputs
-    ; `(("julia-documenter" ,julia-documenter)
-    ;   ("julia-forwarddiff" ,julia-forwarddiff)
-    ;   ("julia-unitful" ,julia-unitful)))
+    (native-inputs
+    `(("julia-documenter" ,julia-documenter)
+      ("julia-forwarddiff" ,julia-forwarddiff)
+      ("julia-unitful" ,julia-unitful)))
     (home-page "https://github.com/JuliaGeometry/CoordinateTransformations.jl")
     (synopsis "Coordinate transformations in Julia")
     (description "@code{CoordinateTransformations} is a Julia package to manage
-- 
2.32.0

[bug#51207] [PATCH 2/9] gnu: julia-colortypes: Enable tests.

[zimoun]

* gnu/packages/julia-xyz (julia-colortypes)[arguments]: Remove.
[native-inputs]: Add julia-documenter.
---
 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 62b6e4edfb..89bb2c0f92 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -624,11 +624,11 @@ (define-public julia-colortypes
        (file-name (git-file-name name version))
        (sha256
         (base32 "0n7h70caqv7yd0khjhn90iax62r73mcif8qzkwj5b4q46li1r8ih"))))
-    (arguments
-     '(#:tests? #f))                    ;require Documenter, not packaged yet
     (build-system julia-build-system)
     (propagated-inputs
      `(("julia-fixedpointnumbers" ,julia-fixedpointnumbers)))
+    (native-inputs
+     `(("julia-documenter" ,julia-documenter)))
     (home-page "https://github.com/JuliaGraphics/ColorTypes.jl")
     (synopsis "Basic color types and constructor")
     (description "This minimalistic package serves as the foundation for
-- 
2.32.0

[bug#51207] [PATCH 3/9] gnu: julia-irtools: Enable tests.

[zimoun]

* gnu/packages/julia-xyz (julia-irtools)[arguements]: Remove.
[native-inputs]: Add julia-documenter.
---
 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 89bb2c0f92..3dd12b60b8 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -2461,11 +2461,11 @@ (define-public julia-irtools
        (file-name (git-file-name name version))
        (sha256
         (base32 "11334fcg2slpwcj0raxf457brhf7pxglgxc6cy8q58ggrpxqfqql"))))
-    (arguments
-     '(#:tests? #f))                    ;require Documenter, not packaged yet
     (build-system julia-build-system)
     (propagated-inputs
      `(("julia-macrotools" ,julia-macrotools)))
+    (native-inputs
+     `(("julia-documenter" ,julia-documenter)))
     (home-page "https://github.com/FluxML/IRTools.jl")
     (synopsis "Simple and flexible IR format")
     (description "This package provides a simple and flexible IR format,
-- 
2.32.0

[bug#51207] [PATCH 4/9] gnu: julia-paddedviews: Enable tests.

[zimoun]

* gnu/packages/julia-xyz (julia-paddedviews)[arguments]: Remove.
[native-inputs]: Add julia-documenter.
---
 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 3dd12b60b8..07b6265473 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -3123,10 +3123,10 @@ (define-public julia-paddedviews
         (sha256
          (base32 "0ran2vj6ahlzib0g77y7g0jhavy3k9s2mqq23ybpgp9z677wf26h"))))
     (build-system julia-build-system)
-    (arguments
-     '(#:tests? #f))                    ;require Documenter, not packaged yet
     (propagated-inputs
      `(("julia-offsetarrays" ,julia-offsetarrays)))
+    (native-inputs
+     `(("julia-documenter" ,julia-documenter)))
     (home-page "https://github.com/JuliaArrays/PaddedViews.jl")
     (synopsis "Add virtual padding to the edges of an array")
     (description "@code{PaddedViews} provides a simple wrapper type,
-- 
2.32.0

[bug#51207] [PATCH 5/9] gnu: julia-stackviews: Enable tests.

[zimoun]

* gnu/packages/julia-xyz (julia-stackviews)[arguments]: Remove #:tests?.
[native-inputs]: Add julia-aqua and julia-documenter.
---
 gnu/packages/julia-xyz.scm | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 07b6265473..9604460600 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -4123,8 +4123,7 @@ (define-public julia-stackviews
          (base32 "1fwiaxdpx1z9dli3jr8kyraych0jbdiny3qklynf0r13px25r6i7"))))
     (build-system julia-build-system)
     (arguments
-     `(#:tests? #f  ; Documenter.jl not packaged yet
-       #:phases
+     `(#:phases
        (modify-phases %standard-phases
          (add-after 'unpack 'skip-doctest
            (lambda _
@@ -4133,9 +4132,9 @@ (define-public julia-stackviews
              #t)))))
     (propagated-inputs
      `(("julia-offsetarrays" ,julia-offsetarrays)))
-    ;(native-inputs
-    ; `(("julia-aqua" ,julia-aqua)
-    ;   ("julia-documenter" ,julia-documenter)))
+    (native-inputs
+    `(("julia-aqua" ,julia-aqua)
+      ("julia-documenter" ,julia-documenter)))
     (home-page "https://github.com/JuliaArrays/StackViews.jl")
     (synopsis "No more catcat")
     (description "StackViews provides only one array type: @code{StackView}.
-- 
2.32.0

[bug#51207] [PATCH 6/9] gnu: Add julia-functors.

[zimoun]

* gnu/packages/julia-xyz.scm (julia-functors): New variable.
---
 gnu/packages/julia-xyz.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 9604460600..86f3446ba3 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -1743,6 +1743,31 @@ (define-public julia-functionwrappers
 arbitrary functions.")
     (license license:expat)))
 
+(define-public julia-functors
+  (package
+    (name "julia-functors")
+    (version "0.2.6")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/FluxML/Functors.jl")
+               (commit (string-append "v" version))))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "0vkyh63v6kj70bqg09z6vsnxm2idz3xwiz7nsr53fgj5c37y2xrj"))))
+    (build-system julia-build-system)
+    (home-page "https://fluxml.ai/Functors")
+    (synopsis "Design pattern for structures as in machine learning")
+    (description "This package provides tools to express a design pattern for
+dealing with large/ nested structures, as in machine learning and
+optimisation.  For large machine learning models it can be cumbersome or
+inefficient to work with parameters as one big, flat vector, and structs help
+in managing complexity; but it is also desirable to easily operate over all
+parameters at once, e.g. for changing precision or applying an optimiser
+update step.")
+    (license license:expat)))
+
 (define-public julia-fuzzycompletions
   (package
     (name "julia-fuzzycompletions")
-- 
2.32.0

[bug#51207] [PATCH 7/9] gnu: Add julia-transcodingstreams.

[zimoun]

* gnu/packages/julia-xyz.scm (julia-transcodingstreams): New variable.
---
 gnu/packages/julia-xyz.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 86f3446ba3..cd865db890 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -4563,6 +4563,31 @@ (define-public julia-tracker
 automatic differentiation for its machine learning platform.")
     (license license:expat)))
 
+(define-public julia-transcodingstreams
+  (package
+    (name "julia-transcodingstreams")
+    (version "0.9.6")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/JuliaIO/TranscodingStreams.jl")
+               (commit (string-append "v" version))))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "1w3klii293caqiclfh28jggv7f53xclm9fr6xmw38brwrn1hjb48"))))
+    (build-system julia-build-system)
+    (arguments
+     `(#:tests? #f))                    ;Circular dependency with CodecZlib
+    (home-page "https://github.com/JuliaIO/TranscodingStreams.jl")
+    (synopsis "Fast I/O transcoding data streams")
+    (description "This package provides tools for transcoding data streams
+which are fast: (small overhead and specialized methods; consistent: basic I/O
+operations work as expected; generic: support any I/O objects like files,
+buffers, pipes, etc.; extensible: easy definition for new codec to transcode
+data.")
+    (license license:expat)))
+
 (define-public julia-typedtables
   (package
     (name "julia-typedtables")
-- 
2.32.0

[bug#51207] [PATCH 8/9] gnu: Add julia-codeczlib.

[zimoun]

* gnu/packages/julia-xyz.scm (julia-codeczlib): New variable.
---
 gnu/packages/julia-xyz.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index cd865db890..da8a3140d5 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -561,6 +561,38 @@ (define-public julia-chainrulestestutils
 dependencies, while keeping @code{ChainRulesCore.jl} as light-weight as possible.")
     (license license:expat)))
 
+(define-public julia-codeczlib
+  (package
+    (name "julia-codeczlib")
+    (version "0.7.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaIO/CodecZlib.jl")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0xm603nylkwk4bzx66zv1g3syzrvn3jh9spdx7kvcvgszzyrrgh4"))))
+    (build-system julia-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before 'reset-gzip-timestamps 'make-files-writable
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out")))
+               (for-each make-file-writable
+                         (find-files out "\\.gz$"))
+               #t))))))
+    (propagated-inputs
+     `(("julia-zlib-jll" ,julia-zlib-jll)
+       ("julia-transcodingstreams" ,julia-transcodingstreams)))
+    (home-page "https://github.com/JuliaIO/CodecZlib.jl")
+    (synopsis "Zlib codecs for @code{TranscodingStreams.jl}")
+    (description "This package provides zlib codecs for
+@code{TranscodingStreams.jl}.")
+    (license license:expat)))
+
 (define-public julia-colors
   (package
     (name "julia-colors")
-- 
2.32.0

[bug#51207] [PATCH 9/9] gnu: Add julia-media.

[zimoun]

* gnu/packages/julia-xyz.scm (julia-media): New variable.
---
 gnu/packages/julia-xyz.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index da8a3140d5..737e8bb733 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -2865,6 +2865,32 @@ (define-public julia-measures
 resolving them into absolute units.")
     (license license:expat)))
 
+(define-public julia-media
+  (package
+    (name "julia-media")
+    (version "0.5.0")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/JunoLab/Media.jl")
+               (commit (string-append "v" version))))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "05jq9j3vs8yfj2lwz3sh1vk5rha06xdcikp9s2q3dn316vryy6di"))))
+    (build-system julia-build-system)
+    ;; Package without Project.toml
+    (arguments
+     '(#:julia-package-name "Media"))
+    (propagated-inputs
+     `(("julia-macrotools" ,julia-macrotools)))
+    (home-page "https://github.com/JunoLab/Media.jl")
+    (synopsis "Unified measure and coordinates types")
+    (description "This package provides a display system which enables the
+user handle multiple input/output devices and decide what media types get
+displayed where.")
+    (license license:expat)))
+
 (define-public julia-missings
   (package
     (name "julia-missings")
-- 
2.32.0

bug#51207: [PATCH 0/9] More Julia packages toward Flux

[Efraim Flashner]

[-- Attachment #1: Type: text/plain, Size: 1361 bytes --]

On Thu, Oct 14, 2021 at 05:56:56PM +0200, zimoun wrote:
> Hi,
> 
> Since Documenter.jl is now available, let use it and turn on the missing tests
> of some packages.
> 
> Then, more trivial packages which are dependencies of Flux (machine learning
> framework).  The hard part still missing is CUDA.

I'm not looking forward to trying to get CUDA working.

I fixed up the home-page in julia-functors and changed
julia-transcodingstreams to use an itemized list for the description.

Patches pushed!

> All the best,
> simon
> 
> 
> zimoun (9):
>   gnu: julia-coordinatetransformations: Enable tests.
>   gnu: julia-colortypes: Enable tests.
>   gnu: julia-irtools: Enable tests.
>   gnu: julia-paddedviews: Enable tests.
>   gnu: julia-stackviews: Enable tests.
>   gnu: Add julia-functors.
>   gnu: Add julia-transcodingstreams.
>   gnu: Add julia-codeczlib.
>   gnu: Add julia-media.
> 
>  gnu/packages/julia-xyz.scm | 139 ++++++++++++++++++++++++++++++++-----
>  1 file changed, 122 insertions(+), 17 deletions(-)
> 
> 
> base-commit: e2a021a745d5009f2e8386108840146faa33fd86
> -- 
> 2.32.0
> 
> 
> 
> 

-- 
Efraim Flashner   <efraim@flashner.co.il>   רנשלפ םירפא
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#51207] [PATCH 0/9] More Julia packages toward Flux

[zimoun]

Hi Efraim,

On Tue, 19 Oct 2021 at 09:24, Efraim Flashner <efraim@flashner.co.il> wrote:

> I'm not looking forward to trying to get CUDA working.

Sadly, I do not have any idea to tackle this.


> I fixed up the home-page in julia-functors and changed
> julia-transcodingstreams to use an itemized list for the description.

Thanks.

Cheers,
simon