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[95.244.15.108]) by smtp.gmail.com with ESMTPSA id m18sm33258712wrw.43.2021.01.18.15.47.56 for (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 18 Jan 2021 15:47:56 -0800 (PST) From: =?UTF-8?Q?Nicol=C3=B2?= Balzarotti Date: Tue, 19 Jan 2021 00:47:55 +0100 Message-ID: <87ft2xzu1g.fsf@guixSD.i-did-not-set--mail-host-address--so-tickle-me> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" Received-SPF: pass client-ip=2a00:1450:4864:20::333; envelope-from=anothersms@gmail.com; helo=mail-wm1-x333.google.com X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Migadu-Flow: FLOW_IN X-Migadu-Spam-Score: -1.25 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20161025 header.b=MxxN8I3K; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Migadu-Queue-Id: 62820940274 X-Spam-Score: -1.25 X-Migadu-Scanner: scn0.migadu.com X-TUID: oDwTUK2RYFwf --=-=-= Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hi guix! This patch series adds julia-json together with its dependencies. It also enable tests for julia packages. Thanks, Nicol=C3=B2 --=-=-= Content-Type: text/x-patch Content-Disposition: attachment; filename=0001-guix-build-system-julia-Enable-tests.patch >From a374ec23346cca7ff6f28c8141102f8838db649a Mon Sep 17 00:00:00 2001 From: nixo 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 --=-=-= Content-Type: text/x-patch; charset=utf-8 Content-Disposition: attachment; filename=0002-gnu-julia-compat-Update-to-3.25.0.patch Content-Transfer-Encoding: quoted-printable >From 46cc28fe6d532c64006b6fea88604b198acec278 Mon Sep 17 00:00:00 2001 From: nixo 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 =C2=A9 2020 Nicol=C3=B2 Balzarotti +;;; Copyright =C2=A9 2020, 2021 Nicol=C3=B2 Balzarotti ;;; ;;; 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") --=20 2.29.2 --=-=-= Content-Type: text/x-patch Content-Disposition: attachment; filename=0003-gnu-Add-julia-orderedcollections.patch >From ac384ede7faccc6ce9ac6c97522c7dbd18200b4a Mon Sep 17 00:00:00 2001 From: nixo 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 --=-=-= Content-Type: text/x-patch Content-Disposition: attachment; filename=0004-gnu-Add-julia-datastructures.patch >From 9736ab882b3348619cf3e74f4282404627dd2b64 Mon Sep 17 00:00:00 2001 From: nixo 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 --=-=-= Content-Type: text/x-patch Content-Disposition: attachment; filename=0005-gnu-Add-julia-fixedpointnumbers.patch >From 79fa1af823688da6796a12d664352a4f0512d702 Mon Sep 17 00:00:00 2001 From: nixo 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 --=-=-= Content-Type: text/x-patch Content-Disposition: attachment; filename=0006-gnu-Add-julia-parsers.patch >From f4ddd59a14cb0fcc259efbf509c2a8073adf62fc Mon Sep 17 00:00:00 2001 From: nixo 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 --=-=-= Content-Type: text/x-patch Content-Disposition: attachment; filename=0007-gnu-Add-julia-adapt.patch >From 358d115e218fc433b15474500a221861c9c82abb Mon Sep 17 00:00:00 2001 From: nixo 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 --=-=-= Content-Type: text/x-patch Content-Disposition: attachment; filename=0008-gnu-Add-julia-offsetarrays.patch >From 06f2e7bbbff5b73493c9a0640ec4c9c6c20280c9 Mon Sep 17 00:00:00 2001 From: nixo 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 --=-=-= Content-Type: text/x-patch Content-Disposition: attachment; filename=0009-gnu-Add-julia-json.patch >From 3ebd72ef6a55ad46522fe2534b775e9b6d20130f Mon Sep 17 00:00:00 2001 From: nixo 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 --=-=-=--