(address . guix-patches@gnu.org)
Hi guix!
This patch series adds julia-json together with its dependencies.
It also enable tests for julia packages.
Thanks, Nicolò
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(-)
Toggle diff (60 lines)
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
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(-)
Toggle diff (31 lines)
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
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(+)
Toggle diff (33 lines)
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
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(+)
Toggle diff (37 lines)
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
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(+)
Toggle diff (48 lines)
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
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(+)
Toggle diff (30 lines)
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
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(+)
Toggle diff (35 lines)
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
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(+)
Toggle diff (38 lines)
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
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(+)
Toggle diff (37 lines)
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