[bug#45972] [PATCH] Add julia-json with dependencies

["Nicolò Balzarotti" <anothersms@gmail.com>]

[-- Attachment #1: Type: text/plain, Size: 144 bytes --]

Hi guix!

This patch series adds julia-json together with its dependencies.

It also enable tests for julia packages.

Thanks, Nicolò


[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: 0001-guix-build-system-julia-Enable-tests.patch --]
[-- Type: text/x-patch, Size: 3140 bytes --]

From a374ec23346cca7ff6f28c8141102f8838db649a Mon Sep 17 00:00:00 2001
From: nixo <nicolo@nixo.xyz>
Date: Mon, 18 Jan 2021 23:56:54 +0100
Subject: [PATCH 1/9] guix: build-system (julia): Enable tests.

* guix/build-system/julia.scm (julia-build): Set tests? default to #t.
* guix/build/julia-build-system.scm (check): Respect tests? and fix julia
  invocation.
  (%standard-phases): Add check phase after install.
---
 guix/build-system/julia.scm       |  2 +-
 guix/build/julia-build-system.scm | 27 +++++++++++++++++----------
 2 files changed, 18 insertions(+), 11 deletions(-)

diff --git a/guix/build-system/julia.scm b/guix/build-system/julia.scm
index 488fe9bb1d..d3cb41c054 100644
--- a/guix/build-system/julia.scm
+++ b/guix/build-system/julia.scm
@@ -75,7 +75,7 @@
 
 (define* (julia-build store name inputs
                       #:key source
-                      (tests? #f)
+                      (tests? #t)
                       (phases '(@ (guix build julia-build-system)
                                   %standard-phases))
                       (outputs '("out"))
diff --git a/guix/build/julia-build-system.scm b/guix/build/julia-build-system.scm
index e8ebcf8ba0..61817e0b47 100644
--- a/guix/build/julia-build-system.scm
+++ b/guix/build/julia-build-system.scm
@@ -69,15 +69,22 @@
      (string-append "pushfirst!(DEPOT_PATH, pop!(DEPOT_PATH)); using " package)))
   #t)
 
-(define* (check #:key source inputs outputs #:allow-other-keys)
-  (let* ((out (assoc-ref outputs "out"))
-         (package (strip-store-file-name source))
-         (builddir (string-append out "/share/julia/")))
-    ;; With a patch, SOURCE_DATE_EPOCH is honored
-    (setenv "SOURCE_DATE_EPOCH" "1")
-    (setenv "JULIA_DEPOT_PATH" builddir)
-    (setenv "JULIA_LOAD_PATH" (string-append builddir "packages/"))
-    (invoke-julia (string-append "using Pkg;Pkg.test(\"" package "\")")))
+(define* (check #:key tests? source inputs outputs #:allow-other-keys)
+  (when tests?
+    (let* ((out (assoc-ref outputs "out"))
+           (package (strip-store-file-name source))
+           (builddir (string-append out "/share/julia/")))
+      ;; With a patch, SOURCE_DATE_EPOCH is honored
+      (setenv "SOURCE_DATE_EPOCH" "1")
+      (setenv "JULIA_DEPOT_PATH" builddir)
+      (setenv "JULIA_LOAD_PATH"
+              (string-append builddir "packages/" ":"
+                             (or (getenv "JULIA_LOAD_PATH")
+                                 "")))
+      (setenv "HOME" "/tmp")
+      (invoke "julia"
+              (string-append builddir "packages/"
+                             package "/test/runtests.jl"))))
   #t)
 
 (define (julia-create-package-toml outputs source
@@ -112,7 +119,7 @@ version = \"" version "\"
     (delete 'check) ; tests must be run after installation
     (replace 'install install)
     (add-after 'install 'precompile precompile)
-    ;; (add-after 'install 'check check)
+    (add-after 'install 'check check)
     ;; TODO: In the future we could add a "system-image-generation" phase
     ;; where we use PackageCompiler.jl to speed up package loading times
     (delete 'configure)
-- 
2.29.2


[-- Attachment #3: 0002-gnu-julia-compat-Update-to-3.25.0.patch --]
[-- Type: text/x-patch, Size: 1428 bytes --]

From 46cc28fe6d532c64006b6fea88604b198acec278 Mon Sep 17 00:00:00 2001
From: nixo <nicolo@nixo.xyz>
Date: Mon, 18 Jan 2021 17:42:50 +0100
Subject: [PATCH 2/9] gnu: julia-compat: Update to 3.25.0.

* gnu/packages/julia-xyz.scm (julia-compat): Update to 3.25.0.
---
 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 f1da66a4be..9a4bf7c678 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz>
+;;; Copyright © 2020, 2021 Nicolò Balzarotti <nicolo@nixo.xyz>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -25,7 +25,7 @@
 (define-public julia-compat
   (package
     (name "julia-compat")
-    (version "3.9.1")
+    (version "3.25.0")
     (source
      (origin
        (method git-fetch)
@@ -34,7 +34,7 @@
              (commit (string-append "v" version))))
        (file-name "Compat")
        (sha256
-        (base32 "01vwjr2134bzgnaxwd67knbibbhnfgnqjw7gxrp29s6y2a6j3882"))))
+        (base32 "1m4r5i8mq29xjp3mllh6047n5a78sdyld57m15anrnsjgaapcgby"))))
     (build-system julia-build-system)
     (home-page "https://github.com/JuliaLang/Compat.jl")
     (synopsis "Compatibility across Julia versions")
-- 
2.29.2


[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #4: 0003-gnu-Add-julia-orderedcollections.patch --]
[-- Type: text/x-patch, Size: 1713 bytes --]

From ac384ede7faccc6ce9ac6c97522c7dbd18200b4a Mon Sep 17 00:00:00 2001
From: nixo <nicolo@nixo.xyz>
Date: Mon, 18 Jan 2021 18:11:42 +0100
Subject: [PATCH 3/9] gnu: Add julia-orderedcollections.

* gnu/packages/julia-xyz.scm (julia-orderedcollections): 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 9a4bf7c678..d3c1f35996 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -43,3 +43,26 @@ between older and newer versions of the Julia language.  The Compat package
 provides a macro that lets you use the latest syntax in a backwards-compatible
 way.")
     (license license:expat)))
+
+(define-public julia-orderedcollections
+  (package
+    (name "julia-orderedcollections")
+    (version "1.3.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaCollections/OrderedCollections.jl")
+             (commit (string-append "v" version))))
+       (file-name "OrderedCollections")
+       (sha256
+        (base32 "0sfip1ixghsz91q2s7d62rgzw3gppg42fg6bccxlplqa3hfmbycf"))))
+    (build-system julia-build-system)
+    (home-page "https://github.com/JuliaCollections/OrderedCollections.jl")
+    (synopsis "Julia implementation of associative containers that preserve
+insertion order")
+    (description "This package implements OrderedDicts and OrderedSets, which
+are similar to containers in base Julia.  However, during iteration the
+Ordered* containers return items in the order in which they were added to the
+collection.")
+    (license license:expat)))
-- 
2.29.2


[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #5: 0004-gnu-Add-julia-datastructures.patch --]
[-- Type: text/x-patch, Size: 1724 bytes --]

From 9736ab882b3348619cf3e74f4282404627dd2b64 Mon Sep 17 00:00:00 2001
From: nixo <nicolo@nixo.xyz>
Date: Mon, 18 Jan 2021 18:17:50 +0100
Subject: [PATCH 4/9] gnu: Add julia-datastructures.

* gnu/packages/julia-xyz.scm (julia-datastructures): New variable.
---
 gnu/packages/julia-xyz.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index d3c1f35996..fee694b1fd 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -44,6 +44,30 @@ provides a macro that lets you use the latest syntax in a backwards-compatible
 way.")
     (license license:expat)))
 
+(define-public julia-datastructures
+  (package
+    (name "julia-datastructures")
+    (version "0.18.8")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaCollections/DataStructures.jl")
+             (commit (string-append "v" version))))
+       (file-name "DataStructures")
+       (sha256
+        (base32 "1r4xswdvnnlbp5rfa7i7k6kzgkwizvqwyz7jscvyqjylcs6wdsnc"))))
+    (propagated-inputs
+     `(("julia-compat" ,julia-compat)
+       ("julia-orderedcollections" ,julia-orderedcollections)))
+    (build-system julia-build-system)
+    (home-page "https://github.com/JuliaCollections/DataStructures.jl")
+    (synopsis "Julia implementation of Data structures")
+    (description "This package implements a variety of data structures,
+including, CircularBuffer, Queue, Stack, Accumulators, Linked Lists, Sorted
+Dicts and many others.")
+    (license license:expat)))
+
 (define-public julia-orderedcollections
   (package
     (name "julia-orderedcollections")
-- 
2.29.2


[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #6: 0005-gnu-Add-julia-fixedpointnumbers.patch --]
[-- Type: text/x-patch, Size: 2363 bytes --]

From 79fa1af823688da6796a12d664352a4f0512d702 Mon Sep 17 00:00:00 2001
From: nixo <nicolo@nixo.xyz>
Date: Mon, 18 Jan 2021 18:25:02 +0100
Subject: [PATCH 5/9] gnu: Add julia-fixedpointnumbers.

* gnu/packages/julia-xyz.scm (julia-fixedpointnumbers): New variable.
---
 gnu/packages/julia-xyz.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index fee694b1fd..f5c9e000db 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -68,6 +68,41 @@ including, CircularBuffer, Queue, Stack, Accumulators, Linked Lists, Sorted
 Dicts and many others.")
     (license license:expat)))
 
+(define-public julia-fixedpointnumbers
+  (package
+    (name "julia-fixedpointnumbers")
+    (version "0.8.4")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaMath/FixedPointNumbers.jl")
+             (commit (string-append "v" version))))
+       (file-name "FixedPointNumbers")
+       (sha256
+        (base32 "0j0n40n04q9sk68wh9jq90m6c67k4ws02k41djjzkrqmpzv4rcdi"))))
+    (build-system julia-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'disable-failing-test
+           (lambda* (#:key outputs #:allow-other-keys)
+             (substitute* "test/fixed.jl"
+               ;; A deprecation warning is not thrown
+               (("@test_logs.*:warn" all) (string-append "# " all)))
+             #t)))))
+    (propagated-inputs `(("julia-compat" ,julia-compat)))
+    (home-page "https://github.com/JuliaMath/FixedPointNumbers.jl")
+    (synopsis "Fixed point types for julia")
+    (description "@code{FixedPointNumbers.jl} implements fixed-point number
+types for Julia.  A fixed-point number represents a fractional, or
+non-integral, number.  In contrast with the more widely known floating-point
+numbers, with fixed-point numbers the decimal point doesn't \"float\":
+fixed-point numbers are effectively integers that are interpreted as being
+scaled by a constant factor.  Consequently, they have a fixed number of
+digits (bits) after the decimal (radix) point.")
+    (license license:expat)))
+
 (define-public julia-orderedcollections
   (package
     (name "julia-orderedcollections")
-- 
2.29.2


[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #7: 0006-gnu-Add-julia-parsers.patch --]
[-- Type: text/x-patch, Size: 1445 bytes --]

From f4ddd59a14cb0fcc259efbf509c2a8073adf62fc Mon Sep 17 00:00:00 2001
From: nixo <nicolo@nixo.xyz>
Date: Mon, 18 Jan 2021 18:27:32 +0100
Subject: [PATCH 6/9] gnu: Add julia-parsers.

* gnu/packages/julia-xyz.scm (julia-parsers): 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 f5c9e000db..b887832df3 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -125,3 +125,23 @@ are similar to containers in base Julia.  However, during iteration the
 Ordered* containers return items in the order in which they were added to the
 collection.")
     (license license:expat)))
+
+(define-public julia-parsers
+  (package
+    (name "julia-parsers")
+    (version "1.0.15")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaData/Parsers.jl")
+             (commit (string-append "v" version))))
+       (file-name "Parsers")
+       (sha256
+        (base32 "16iffl6l28kspgqch48mhi1s8qhspr3cpqcwsph3rqi72lbfqygx"))))
+    (build-system julia-build-system)
+    (home-page "https://github.com/JuliaData/Parsers.jl")
+    (synopsis "Fast parsing machinery for basic types in Julia")
+    (description "@code{Parsers.jl} is a collection of type parsers and
+utilities for Julia.")
+    (license license:expat)))
-- 
2.29.2


[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #8: 0007-gnu-Add-julia-adapt.patch --]
[-- Type: text/x-patch, Size: 1582 bytes --]

From 358d115e218fc433b15474500a221861c9c82abb Mon Sep 17 00:00:00 2001
From: nixo <nicolo@nixo.xyz>
Date: Mon, 18 Jan 2021 23:46:51 +0100
Subject: [PATCH 7/9] gnu: Add julia-adapt.

* gnu/packages/julia-xyz.scm (julia-adapt): 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 b887832df3..3601006976 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -22,6 +22,28 @@
   #:use-module (guix git-download)
   #:use-module (guix build-system julia))
 
+(define-public julia-adapt
+  (package
+    (name "julia-adapt")
+    (version "3.1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaGPU/Adapt.jl")
+             (commit (string-append "v" version))))
+       (file-name "Adapt")
+       (sha256
+        (base32 "1qcj7i75m0wwk0xcdgf89bjymnz2dipv2iwxys8wzpvrashi6wsp"))))
+    (build-system julia-build-system)
+    (home-page "https://github.com/JuliaGPU/Adapt.jl")
+    (synopsis "Package providing the @code{adapt} function, similar to @code{convert}")
+    (description "This julia package provides the @code{adapt(T, x)} function
+acts like @code{convert(T, x)}, but without the restriction of returning a
+T. This allows you to \"convert\" wrapper types like Adjoint to be GPU
+compatible without throwing away the wrapper.")
+    (license license:expat)))
+
 (define-public julia-compat
   (package
     (name "julia-compat")
-- 
2.29.2


[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #9: 0008-gnu-Add-julia-offsetarrays.patch --]
[-- Type: text/x-patch, Size: 1765 bytes --]

From 06f2e7bbbff5b73493c9a0640ec4c9c6c20280c9 Mon Sep 17 00:00:00 2001
From: nixo <nicolo@nixo.xyz>
Date: Tue, 19 Jan 2021 00:01:28 +0100
Subject: [PATCH 8/9] gnu: Add julia-offsetarrays.

* gnu/packages/julia-xyz.scm (julia-offsetarrays): 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 3601006976..429ab0afad 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -148,6 +148,31 @@ Ordered* containers return items in the order in which they were added to the
 collection.")
     (license license:expat)))
 
+(define-public julia-offsetarrays
+  (package
+    (name "julia-offsetarrays")
+    (version "1.5.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaArrays/OffsetArrays.jl")
+             (commit (string-append "v" version))))
+       (file-name "OffsetArrays")
+       (sha256
+        (base32 "0pd42an8kj2mgw3sv00ijfrsvmfjfgf12lfmpan6zkdckqa73jqz"))))
+    (build-system julia-build-system)
+    (propagated-inputs
+     `(("julia-adapt" ,julia-adapt)))
+    ;; CatIndices depends on OffsetArrays, introducing a recursive dependency
+    (arguments '(#:tests? #f))
+    (home-page "https://juliaarrays.github.io/OffsetArrays.jl/stable/")
+    (synopsis "Fortran-like arrays with arbitrary, zero or negative indices")
+    (description "@code{OffsetArrays.jl} provides Julia users with arrays that
+have arbitrary indices, similar to those found in some other programming
+languages like Fortran.")
+    (license license:expat)))
+
 (define-public julia-parsers
   (package
     (name "julia-parsers")
-- 
2.29.2


[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #10: 0009-gnu-Add-julia-json.patch --]
[-- Type: text/x-patch, Size: 1651 bytes --]

From 3ebd72ef6a55ad46522fe2534b775e9b6d20130f Mon Sep 17 00:00:00 2001
From: nixo <nicolo@nixo.xyz>
Date: Tue, 19 Jan 2021 00:06:34 +0100
Subject: [PATCH 9/9] gnu: Add julia-json.

* gnu/packages/julia-xyz.scm (julia-json): New variable.
---
 gnu/packages/julia-xyz.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 429ab0afad..7aba08cdb1 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -125,6 +125,30 @@ scaled by a constant factor.  Consequently, they have a fixed number of
 digits (bits) after the decimal (radix) point.")
     (license license:expat)))
 
+(define-public julia-json
+  (package
+    (name "julia-json")
+    (version "0.21.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/JuliaIO/JSON.jl")
+             (commit (string-append "v" version))))
+       (file-name "JSON")
+       (sha256
+        (base32 "1f9k613kbknmp4fgjxvjaw4d5sfbx8a5hmcszmp1w9rqfqngjx9m"))))
+    (build-system julia-build-system)
+    (propagated-inputs
+     `(("julia-datastructures" ,julia-datastructures)
+       ("julia-fixedpointnumbers" ,julia-fixedpointnumbers)
+       ("julia-parsers" ,julia-parsers)
+       ("julia-offsetarrays" ,julia-offsetarrays)))
+    (home-page "https://github.com/JuliaIO/JSON.jl")
+    (synopsis "JSON parsing and printing")
+    (description "Parsing and printing JSON in pure Julia.")
+    (license license:expat)))
+
 (define-public julia-orderedcollections
   (package
     (name "julia-orderedcollections")
-- 
2.29.2