diff options
Diffstat (limited to 'gnu/packages/julia-xyz.scm')
| -rw-r--r-- | gnu/packages/julia-xyz.scm | 1240 |
1 files changed, 728 insertions, 512 deletions
diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index e30cf39dc9..5d45c07115 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1,7 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2020, 2021 Nicolò Balzarotti <nicolo@nixo.xyz> ;;; Copyright © 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com> -;;; Copyright © 2021 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2021, 2022 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2021 Vinicius Monego <monego@posteo.net> ;;; Copyright © 2021 jgart <jgart@dismail.de> ;;; @@ -23,6 +23,7 @@ (define-module (gnu packages julia-xyz) #:use-module ((guix licenses) #:prefix license:) #:use-module (gnu packages) + #:use-module (guix gexp) #:use-module (guix utils) #:use-module (guix packages) #:use-module (guix git-download) @@ -138,7 +139,7 @@ ANSI escape codes to another format.") (base32 "1g0kyzcdykgs247j72jpc2qqall696jwgb3hnn4cxmbi8bkf7wpk")))) (build-system julia-build-system) (arguments - `(#:parallel-tests? #f)) + (list #:parallel-tests? #f)) (home-page "https://github.com/JuliaTesting/Aqua.jl") (synopsis "Automated quality assurance for Julia packages") (description "@acronym{Aqua.jl, Auto QUality Assurance for Julia packages}, @@ -164,7 +165,7 @@ provides functions to run a few automatable checks for Julia packages.") ;; Expression: @inferred(ArrayInterface.size(Rnr)) === (StaticInt(4),) ;; Evaluated: (static(2),) === (static(4),) ;; Disable as stopgap. - `(#:tests? ,(not (target-x86-32?)))) + (list #:tests? (not (target-x86-32?)))) (propagated-inputs (list julia-ifelse julia-requires @@ -334,24 +335,25 @@ the entries on the bands.") (base32 "1xz3kdrphp4b158pg7dwkiry49phs2fjjpdvk1hjpww5ykxacks8")))) (build-system julia-build-system) (arguments - `(#:phases - ,@(if (target-x86-32?) - '((modify-phases %standard-phases - (add-after 'unpack 'remove-failing-tests-i686 - (lambda _ - (substitute* "test/GroupsTests.jl" - (("@test sprint\\(show, g1\\)") - "@test_broken sprint(show, g1)") - (("@test sprint\\(show, g1; context = :boundto => 1\\)") - "@test_broken sprint(show, g1; context = :boundto => 1)") - (("@test sprint\\(show, g1; context = :limit => false\\)") - "@test_broken sprint(show, g1; context = :limit => false)") - (("@test @test_deprecated") "@test_broken")) - (substitute* "test/ExecutionTests.jl" - ;; Evaluated: 12 == 8 - (("@test @ballocated\\(Ref\\(1\\)\\)") - "@test_broken @ballocated(Ref(1))")))))) - '(%standard-phases)))) + (list + #:phases + (if (target-x86-32?) + #~(modify-phases %standard-phases + (add-after 'unpack 'remove-failing-tests-i686 + (lambda _ + (substitute* "test/GroupsTests.jl" + (("@test sprint\\(show, g1\\)") + "@test_broken sprint(show, g1)") + (("@test sprint\\(show, g1; context = :boundto => 1\\)") + "@test_broken sprint(show, g1; context = :boundto => 1)") + (("@test sprint\\(show, g1; context = :limit => false\\)") + "@test_broken sprint(show, g1; context = :limit => false)") + (("@test @test_deprecated") "@test_broken")) + (substitute* "test/ExecutionTests.jl" + ;; Evaluated: 12 == 8 + (("@test @ballocated\\(Ref\\(1\\)\\)") + "@test_broken @ballocated(Ref(1))"))))) + #~%standard-phases))) (propagated-inputs (list julia-json)) (home-page "https://github.com/JuliaCI/BenchmarkTools.jl") @@ -361,6 +363,34 @@ code easy by supplying a framework for writing and running groups of benchmarks as well as comparing benchmark results.") (license license:expat))) +(define-public julia-bfloat16s + ;; Not tagged upstream + (let ((commit "ef6051e4308ed0c02f10168b99d226237e0ae33c") + (version "0.2.0")) + (package + (name "julia-bfloat16s") + (version version) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaMath/BFloat16s.jl") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "16sr578k4i47lhziri47nvspdrsni2wc1qjhs6hzffh9si6a7jfq")))) + (build-system julia-build-system) + (home-page "https://github.com/JuliaMath/BFloat16s.jl") + (synopsis "Define BFloat16 data type") + (description "This package defines the @code{BFloat16} data type. The +only currently available hardware implementation of this datatype are Google's +Cloud TPUs. As such, this package is suitable to evaluate whether using TPUs +would cause precision problems for any particular algorithm, even without +access to TPU hardware. Note that this package is designed for functionality, +not performance, so this package should be used for precision experiments +only, not performance experiments.") + (license license:expat)))) + (define-public julia-bioalignments (package (name "julia-bioalignments") @@ -376,15 +406,16 @@ benchmarks as well as comparing benchmark results.") (base32 "1wf6qgsada59r2fykxfj9hcr635wl8maqxbd3w8qpa01k9glxa0k")))) (build-system julia-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'skip-test - (lambda _ - ;; Test fails because an unexpected type representation from - ;; BioSequences. The aligned value is correct though. - (substitute* "test/runtests.jl" - (("@test sprint\\(show, aln\\)") - "@test_broken sprint(show, aln)"))))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'skip-test + (lambda _ + ;; Test fails because an unexpected type representation from + ;; BioSequences. The aligned value is correct though. + (substitute* "test/runtests.jl" + (("@test sprint\\(show, aln\\)") + "@test_broken sprint(show, aln)"))))))) (propagated-inputs (list julia-biogenerics julia-biosequences @@ -469,13 +500,14 @@ sequences.") (base32 "1222rwdndi777lai8a6dwrh35i5rgmj75kcrhn8si72sxgz0syjm")))) (build-system julia-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'adjust-tests - (lambda _ - (substitute* "test/runtests.jl" - (("\\@testset \\\"Range.*" all) - (string-append all " return\n")))))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'adjust-tests + (lambda _ + (substitute* "test/runtests.jl" + (("\\@testset \\\"Range.*" all) + (string-append all " return\n")))))))) (propagated-inputs (list julia-automa)) (home-page "https://github.com/BioJulia/BioSymbols.jl") @@ -499,14 +531,15 @@ and amino acids that are used ny otherBioJulia packages.") (base32 "1by26036fk9mawmcgqxpwizgbs398v9p6vrbsgg7h6llqn3q9iw1")))) (build-system julia-build-system) (arguments - `(#:phases - ,@(if (target-64bit?) - '(%standard-phases) - '((modify-phases %standard-phases - (add-after 'unpack 'fix-tests-int32-i686 - (lambda _ - (substitute* "test/test_blockarrays.jl" - (("Int64") "Int32"))))))))) + (list + #:phases + (if (target-64bit?) + #~%standard-phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-tests-int32-i686 + (lambda _ + (substitute* "test/test_blockarrays.jl" + (("Int64") "Int32")))))))) (propagated-inputs (list julia-arraylayouts julia-fillarrays)) @@ -598,9 +631,10 @@ structures.") ;; freeze, see ;; https://travis-ci.org/BioJulia/BufferedStreams.jl/jobs/491050182 (arguments - '(#:tests? #f - #:julia-package-name "BufferedStreams" - #:julia-package-uuid "e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d")) + (list + #:tests? #f + #:julia-package-name "BufferedStreams" + #:julia-package-uuid "e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d")) (propagated-inputs (list julia-compat)) (home-page "https://github.com/BioJulia/BufferedStreams.jl") @@ -664,6 +698,25 @@ variables, both with unordered (nominal variables) and ordered categories (ordinal variables), optionally with missing values.") (license license:expat))) +(define-public julia-cenum + (package + (name "julia-cenum") + (version "0.4.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaInterop/CEnum.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0h079mggvv420bw87j8s3hsgk7vavjgm4j1cvk0pnzrrh8ib1381")))) + (build-system julia-build-system) + (home-page "https://github.com/JuliaInterop/CEnum.jl") + (synopsis "C-compatible enum for Julia") + (description "This package provides a C-compatible enum for Julia.") + (license license:expat))) + (define-public julia-chainrules (package (name "julia-chainrules") @@ -766,15 +819,6 @@ dependencies, while keeping @code{ChainRulesCore.jl} as light-weight as possible (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$")) - #t)))))) (propagated-inputs (list julia-transcodingstreams julia-zlib-jll)) @@ -967,27 +1011,28 @@ way.") (base32 "1b23p0zk8dx2sf01cnw177mqci7qd81b9s32ixz9clsh0r0icl1b")))) (build-system julia-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'link-depot 'fix-tests - (lambda _ - (substitute* "test/runtests.jl" - (("option.toml") "test/option.toml")))) - (add-after 'link-depot 'dont-use-exproniconlite - (lambda _ - (substitute* '("Project.toml" - "src/Configurations.jl" - "test/runtests.jl") - (("ExproniconLite") "Expronicon")) - (substitute* "Project.toml" - (("55351af7-c7e9-48d6-89ff-24e801d99491") - "6b7a57c9-7cc1-4fdf-b7f5-e857abae3636")))) - ,@(if (target-64bit?) - '() - '((add-after 'unpack 'fix-tests-int32-i686 - (lambda _ - (substitute* "test/runtests.jl" - (("Int64") "Int32"))))))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'link-depot 'fix-tests + (lambda _ + (substitute* "test/runtests.jl" + (("option.toml") "test/option.toml")))) + (add-after 'link-depot 'dont-use-exproniconlite + (lambda _ + (substitute* '("Project.toml" + "src/Configurations.jl" + "test/runtests.jl") + (("ExproniconLite") "Expronicon")) + (substitute* "Project.toml" + (("55351af7-c7e9-48d6-89ff-24e801d99491") + "6b7a57c9-7cc1-4fdf-b7f5-e857abae3636")))) + #$@(if (target-64bit?) + '() + '((add-after 'unpack 'fix-tests-int32-i686 + (lambda _ + (substitute* "test/runtests.jl" + (("Int64") "Int32"))))))))) (propagated-inputs (list julia-crayons julia-expronicon @@ -1112,21 +1157,21 @@ dependency on it.") (base32 "1bk0amrghgjrkyn1mm4ac23swwbgszl1d0qyl9137qj5zvv9dasp")))) (build-system julia-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'link-depot 'skip-failing-test - (lambda _ - ;; Tests with non-standard colors. - (substitute* "test/show.jl" - (("test (sprint\\(show, df, context=:color=>true)" _ test) - (string-append "test_nowarn " test))) - (substitute* "test/io.jl" - (("testset \\\"improved.*" all) - (string-append all "return\n"))) - (substitute* "test/join.jl" - (("test (levels\\(outerjoin\\(B)" _ test) - (string-append "test_nowarn " test))) - #t))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'link-depot 'skip-failing-test + (lambda _ + ;; Tests with non-standard colors. + (substitute* "test/show.jl" + (("test (sprint\\(show, df, context=:color=>true)" _ test) + (string-append "test_nowarn " test))) + (substitute* "test/io.jl" + (("testset \\\"improved.*" all) + (string-append all "return\n"))) + (substitute* "test/join.jl" + (("test (levels\\(outerjoin\\(B)" _ test) + (string-append "test_nowarn " test)))))))) (propagated-inputs (list julia-dataapi julia-invertedindices @@ -1172,18 +1217,19 @@ Julia from R or Python.") julia-orderedcollections)) (build-system julia-build-system) (arguments - `(#:phases - ,@(if (target-x86-32?) - '((modify-phases %standard-phases - (add-after 'unpack 'remove-failing-test-i686 - (lambda _ - ;; The evaluation returns the correct value, - ;; Evaluated: "Accumulator(1 => 3, 3 => 4)" - ;; but, for some reasons, is considered as failed. - (substitute* "test/test_accumulator.jl" - (("@test sprint\\(show,Accumulator\\(1 => 3, 3 => 4\\)\\)") - "@test_broken sprint(show, Accumulator(1 => 3, 3 => 4))")))))) - '(%standard-phases)))) + (list + #:phases + (if (target-x86-32?) + #~(modify-phases %standard-phases + (add-after 'unpack 'remove-failing-test-i686 + (lambda _ + ;; The evaluation returns the correct value, + ;; Evaluated: "Accumulator(1 => 3, 3 => 4)" + ;; but, for some reasons, is considered as failed. + (substitute* "test/test_accumulator.jl" + (("@test sprint\\(show,Accumulator\\(1 => 3, 3 => 4\\)\\)") + "@test_broken sprint(show, Accumulator(1 => 3, 3 => 4))"))))) + #~%standard-phases))) (home-page "https://github.com/JuliaCollections/DataStructures.jl") (synopsis "Julia module providing different data structures") (description "This package implements a variety of data structures, @@ -1227,17 +1273,17 @@ without having to take direct dependencies.") (base32 "15j3hrqq6nazn533bfsvg32xznacbzsl303j1qs48av59ppnvhhv")))) (build-system julia-build-system) (arguments - `(#:tests? #f ; Tests need upgrading with newer Julia version. - #:phases - (modify-phases %standard-phases - (add-after 'link-depot 'skip-known-failing-tests - (lambda _ - ;; See upstream report: - ;; https://github.com/queryverse/DataValues.jl/issues/83 - (substitute* "test/array/test_reduce.jl" - ((".*DataValue\\(mapreduce.*") "") - ((".*DataValue\\(method\\(f.*") "")) - #t))))) + (list + #:tests? #f ; Tests need upgrading with newer Julia version. + #:phases + #~(modify-phases %standard-phases + (add-after 'link-depot 'skip-known-failing-tests + (lambda _ + ;; See upstream report: + ;; https://github.com/queryverse/DataValues.jl/issues/83 + (substitute* "test/array/test_reduce.jl" + ((".*DataValue\\(mapreduce.*") "") + ((".*DataValue\\(method\\(f.*") ""))))))) (propagated-inputs (list julia-datavalueinterfaces)) (home-page "https://github.com/queryverse/DataValues.jl") @@ -1306,17 +1352,18 @@ dictionaries in Julia, for improved productivity and performance.") (base32 "1yqd9wg4z15k42mrp4y14j2x0sq7yrjhm5zpqklrw6w6j1c367ig")))) (build-system julia-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'link-depot 'skip-flakey-tests - (lambda _ - ;; Some combination of these tests fail nondeterministically - ;; each of the times this package is built. - (substitute* "test/test_dists.jl" - (("test dyz ≥") "test_nowarn dyz ≥") - (("test dist\\(y, x") "test_nowarn dist(y, x") - (("test dist\\(z, x") "test_nowarn dist(z, x") - (("test dist\\(z, y") "test_nowarn dist(z, y"))))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'link-depot 'skip-flakey-tests + (lambda _ + ;; Some combination of these tests fail nondeterministically + ;; each of the times this package is built. + (substitute* "test/test_dists.jl" + (("test dyz ≥") "test_nowarn dyz ≥") + (("test dist\\(y, x") "test_nowarn dist(y, x") + (("test dist\\(z, x") "test_nowarn dist(z, x") + (("test dist\\(z, y") "test_nowarn dist(z, y"))))))) (propagated-inputs (list julia-statsapi)) (native-inputs @@ -1345,7 +1392,7 @@ straightforward loop implementation.") (base32 "0fy4kfnfacyfmlly6nqxn77dk2gqw80b69zb4m1i0i39zv3cpqfb")))) (build-system julia-build-system) (arguments - `(#:tests? #f)) ; Tests try to read SSL certificates. + (list #:tests? #f)) ; Tests try to read SSL certificates. (home-page "https://juliadocs.github.io/DocStringExtensions.jl/latest/") (synopsis "Extensions for Julia's docsystem") (description "This package provides a collection of useful extensions for @@ -1372,22 +1419,23 @@ valuable enough at this time.") (base32 "00ai3c24i3fkn5plmavampcxm0ijhwk0v5cn9xwm7rvbjnnvaaam")))) (build-system julia-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'link-depot 'patch-source - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "src/Deps.jl" - (("pip install") - (string-append (search-input-file inputs "bin/pip") - " install"))))) - (add-after 'link-depot 'remove-javascript-downloads - (lambda _ - (substitute* "src/Writers/HTMLWriter.jl" - (("cdnjs.cloudflare.com") "example.com")) - ;; Removing the javascript downloads causes these tests fail. - (substitute* "test/examples/tests.jl" - ((".*Main\\.examples_html_doc.*") "") - ((".*Main\\.examples_html_mathjax3_doc.*") ""))))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'link-depot 'patch-source + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "src/Deps.jl" + (("pip install") + (string-append (search-input-file inputs "bin/pip") + " install"))))) + (add-after 'link-depot 'remove-javascript-downloads + (lambda _ + (substitute* "src/Writers/HTMLWriter.jl" + (("cdnjs.cloudflare.com") "example.com")) + ;; Removing the javascript downloads causes these tests fail. + (substitute* "test/examples/tests.jl" + ((".*Main\\.examples_html_doc.*") "") + ((".*Main\\.examples_html_mathjax3_doc.*") ""))))))) (propagated-inputs (list julia-ansicoloredprinters julia-docstringextensions @@ -1457,7 +1505,7 @@ valuable enough at this time.") (base32 "05p57p8xlkn42m1lv9gq4hl96vp7hpj19d51p828ai1rbpcpi3a6")))) (build-system julia-build-system) (arguments - `(#:tests? #f)) ; Tests require network. + (list #:tests? #f)) ; Tests require network. (inputs ;; We don't want to propagate the bootstrap version. ;; Cycle with Documenter.jl in later versions. @@ -1556,13 +1604,14 @@ stressing the robustness of differentiation tools.") (base32 "05vr5wbzqpchnb96b3pmn67x196mbfnkv7r9bdlz3gm56if4awk5")))) (build-system julia-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'link-depot 'adjust-test-suite - (lambda _ - (substitute* "test/runtests.jl" - ;; Seems to not play nicely with SpecialFunctions - ((".*isempty.*") ""))))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'link-depot 'adjust-test-suite + (lambda _ + (substitute* "test/runtests.jl" + ;; Seems to not play nicely with SpecialFunctions + ((".*isempty.*") ""))))))) (propagated-inputs (list julia-calculus julia-nanmath @@ -1590,13 +1639,14 @@ combinations of dual numbers with predefined Julia numeric types.") (base32 "0py46kxl702r8pw3v7x4cqllf7yc91b0dr7vb60xh2qi7d6y3jc7")))) (build-system julia-build-system) (arguments - `(#: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.*") ""))))))) + (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") @@ -1642,13 +1692,14 @@ before (or after)\".") (base32 "0h8aaynqlxrkn8575k5vqmhzil4vvxchhf0bcxa6zwawp558gj2y")))) (build-system julia-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'link-depot 'skip-network-tests - (lambda _ - (substitute* "test/runtests.jl" - ;; This test tries to access the Julia package registry. - ((".*expand\\.jl.*") ""))))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'link-depot 'skip-network-tests + (lambda _ + (substitute* "test/runtests.jl" + ;; This test tries to access the Julia package registry. + ((".*expand\\.jl.*") ""))))))) (propagated-inputs (list julia-mlstyle)) (native-inputs @@ -1720,26 +1771,27 @@ need the ffmpeg binaries + executables, and don't want the overhead of (base32 "1b18x43i737g5q41n9818xbnc2pgd98q1m6yw3h29yri0clg4gfx")))) (build-system julia-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (delete 'reset-gzip-timestamps) - (add-after 'link-depot 'skip-network-tests - (lambda _ - ;; These tests try to download audio/video files. - (substitute* "test/query.jl" - (("testset.*(MP4|OGG|MATROSKA).*" all) - (string-append all "return\n"))) - (substitute* "test/loadsave.jl" - (("testset.*CSVFiles.*" all) - (string-append all "return\n"))) - ;; This test tries to download a Julia package. - (substitute* "test/error_handling.jl" - (("testset.*Not installed.*" all) - (string-append all "return\n"))) - ;; This test tries to write to the store. - ;; (Error says can't find User 0) - (substitute* "test/runtests.jl" - ((".*test_mimesave.*") ""))))))) + (list + #:phases + #~(modify-phases %standard-phases + (delete 'reset-gzip-timestamps) + (add-after 'link-depot 'skip-network-tests + (lambda _ + ;; These tests try to download audio/video files. + (substitute* "test/query.jl" + (("testset.*(MP4|OGG|MATROSKA).*" all) + (string-append all "return\n"))) + (substitute* "test/loadsave.jl" + (("testset.*CSVFiles.*" all) + (string-append all "return\n"))) + ;; This test tries to download a Julia package. + (substitute* "test/error_handling.jl" + (("testset.*Not installed.*" all) + (string-append all "return\n"))) + ;; This test tries to write to the store. + ;; (Error says can't find User 0) + (substitute* "test/runtests.jl" + ((".*test_mimesave.*") ""))))))) (propagated-inputs (list julia-requires)) (native-inputs @@ -1770,7 +1822,7 @@ high-level support for formatted files (in contrast with Julia's low-level (base32 "136wm4ik6isrdanmpi4gdr1qw0qhr15i925qzjxbawk5hnyzwng9")))) (build-system julia-build-system) (arguments - `(#:tests? #f)) ; Cycle with JLSO.jl + (list #:tests? #f)) ; Cycle with JLSO.jl (home-page "https://github.com/rofinn/FilePathsBase.jl") (synopsis "Filesystem path types in Julia") (description "@code{FilePathsBase.jl} provides a type based approach to @@ -1816,14 +1868,14 @@ following types: @code{Eye}, @code{Fill}, @code{Ones}, @code{Zeros}, (base32 "105f6r0hq97n9mxf1nacmz94dpca66vzqj5p3zh4h0brshmggqnq")))) (build-system julia-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-before 'check 'pre-check - (lambda _ - ;; We don't want to run all the tests; the Downstream tests - ;; try to download the package registry. - (setenv "GROUP" "Core") - #t))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'check 'pre-check + (lambda _ + ;; We don't want to run all the tests; the Downstream tests + ;; try to download the package registry. + (setenv "GROUP" "Core")))))) (propagated-inputs (list julia-arrayinterface julia-requires @@ -1855,16 +1907,17 @@ types and sparsity.") (base32 "09nsf9cgk49yrvprflnhd9h5rrgs280rgj8sad3csghxdx6jqk5c")))) (build-system julia-build-system) (arguments - `(#:phases - ,@(if (target-x86-32?) - '((modify-phases %standard-phases - (add-after 'unpack 'remove-failing-test-i686 - (lambda _ - ;; Machine Precision incorrectly handled - (substitute* "test/methods.jl" - (("@test central_fdm\\(15, 5, adapt=2\\)\\(exp, 1.0\\)") - "@test_broken central_fdm(15, 5, adapt=2)(exp, 1.0)")))))) - '(%standard-phases)))) + (list + #:phases + (if (target-x86-32?) + #~(modify-phases %standard-phases + (add-after 'unpack 'remove-failing-test-i686 + (lambda _ + ;; Machine Precision incorrectly handled + (substitute* "test/methods.jl" + (("@test central_fdm\\(15, 5, adapt=2\\)\\(exp, 1.0\\)") + "@test_broken central_fdm(15, 5, adapt=2)(exp, 1.0)"))))) + #~%standard-phases))) (inputs (list julia-benchmarktools)) (propagated-inputs @@ -1892,14 +1945,14 @@ using finite difference.") (base32 "0j0n40n04q9sk68wh9jq90m6c67k4ws02k41djjzkrqmpzv4rcdi")))) (build-system julia-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'link-depot '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))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'link-depot '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)))))))) (propagated-inputs (list julia-compat)) (home-page "https://github.com/JuliaMath/FixedPointNumbers.jl") @@ -1952,7 +2005,7 @@ c-style numerical formatting.") ;; Expression: dual_isapprox(FDNUM ^ PRIMAL, exp(PRIMAL * log(FDNUM))) ;; ERROR: LoadError: LoadError: There was an error during testing ;; Disable as stopgap. - `(#:tests? ,(not (target-x86-32?)))) + (list #:tests? (not (target-x86-32?)))) (inputs ;required for tests (list julia-calculus julia-difftests)) @@ -1986,13 +2039,14 @@ differentiation (AD).") (base32 "02jilpjr7px6138dx2w7ixricvfgsxqdk84d9dgviranibhnjcxa")))) (build-system julia-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'link-depot 'adjust-tests - (lambda _ - (substitute* "test/runtests.jl" - (("testset \\\"Abstract.*" all) - (string-append all "return\n")))))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'link-depot 'adjust-tests + (lambda _ + (substitute* "test/runtests.jl" + (("testset \\\"Abstract.*" all) + (string-append all "return\n")))))))) (home-page "https://github.com/yuyichao/FunctionWrappers.jl") (synopsis "Type stable and efficient wrapper of arbitrary functions") (description "This package provides a type stable and efficient wrapper of @@ -2039,12 +2093,13 @@ update step.") (base32 "07sv88c472n6w4x7diy952igbcfm1s104ysnnvprld83312siw06")))) (build-system julia-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'link-depot 'skip-failing-test - (lambda _ - (substitute* "test/runtests.jl" - ((".*RPLE.*") ""))))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'link-depot 'skip-failing-test + (lambda _ + (substitute* "test/runtests.jl" + ((".*RPLE.*") ""))))))) (home-page "https://github.com/JunoLab/FuzzyCompletions.jl") (synopsis "Fuzzy completion provider for Julia") (description @@ -2066,12 +2121,13 @@ update step.") (base32 "0ndwypa397z3pwzdgc3s9plaqlqf63g3d4px5pvym5psgr6lnm3l")))) (build-system julia-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'link-depot 'adjust-test-suite - (lambda _ - (substitute* "test/runtests.jl" - ((".*lapack.*") ""))))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'link-depot 'adjust-test-suite + (lambda _ + (substitute* "test/runtests.jl" + ((".*lapack.*") ""))))))) (native-inputs (list julia-quaternions)) (home-page "https://github.com/JuliaLinearAlgebra/GenericLinearAlgebra.jl") @@ -2097,20 +2153,21 @@ algebra routines written in Julia (except for optimized BLAS).") (base32 "12x6lxzxm91y3k6s9dam46dq5hrby5sr0gy0fdfnp0xhjzdy2j0d")))) (build-system julia-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'link-depot 'adjust-test-suite - (lambda _ - (substitute* "test/complex.jl" - ;; expected Array{Int32,1}, got a value of type Array{Int64,1} - (("A = _example") "#A = _example") - (("schurtest\\(A,20\\)") "")) - (substitute* "test/runtests.jl" - ;; Test errors relating to liblapack.so - ((".*complex\\.jl.*") "") - ((".*real\\.jl.*") "") - ;; GenericSVD is deprecated upstream - ((".*gordschur\\.jl.*") ""))))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'link-depot 'adjust-test-suite + (lambda _ + (substitute* "test/complex.jl" + ;; expected Array{Int32,1}, got a value of type Array{Int64,1} + (("A = _example") "#A = _example") + (("schurtest\\(A,20\\)") "")) + (substitute* "test/runtests.jl" + ;; Test errors relating to liblapack.so + ((".*complex\\.jl.*") "") + ((".*real\\.jl.*") "") + ;; GenericSVD is deprecated upstream + ((".*gordschur\\.jl.*") ""))))))) (home-page "https://github.com/RalphAS/GenericSchur.jl") (synopsis "Schur decomposition of matrices with generic element types") (description "The Schur decomposition is the workhorse for eigensystem @@ -2134,24 +2191,25 @@ matrices the Schur form is often more useful.") (base32 "057j3hjpli3q5b98cqkpi4p10x2k9pyksrz62hjmv1kb5qzdvhsj")))) (build-system julia-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'link-depot 'remove-earcut - (lambda _ - (substitute* '("Project.toml" - "src/GeometryBasics.jl") - ((".*EarCut.*") "")))) - (add-after 'link-depot 'skip-incompatible-test - (lambda _ - (substitute* "test/runtests.jl" - (("@testset.*MetaT and heterogeneous data.*" all) - (string-append all "return\n"))))) - ,@(if (target-64bit?) - '() - '((add-after 'unpack 'fix-tests-int32-i686 - (lambda _ - (substitute* "test/runtests.jl" - (("Int64") "Int32"))))))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'link-depot 'remove-earcut + (lambda _ + (substitute* '("Project.toml" + "src/GeometryBasics.jl") + ((".*EarCut.*") "")))) + (add-after 'link-depot 'skip-incompatible-test + (lambda _ + (substitute* "test/runtests.jl" + (("@testset.*MetaT and heterogeneous data.*" all) + (string-append all "return\n"))))) + #$@(if (target-64bit?) + '() + '((add-after 'unpack 'fix-tests-int32-i686 + (lambda _ + (substitute* "test/runtests.jl" + (("Int64") "Int32"))))))))) (propagated-inputs (list julia-itertools julia-staticarrays @@ -2168,6 +2226,32 @@ finite elements analysis, Geo applications, and general geometry manipulations - while offering a Julian API, that still allows performant C-interop.") (license license:expat))) +(define-public julia-gpuarrays + (package + (name "julia-gpuarrays") + (version "8.1.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaGPU/GPUArrays.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "129q8m94b2xq3vij28pkb7dry3r7qbiqrz72a26ma9kilcr35gk4")))) + (build-system julia-build-system) + (inputs + (list julia-adapt)) + (home-page "https://github.com/JuliaGPU/GPUArrays.jl") + (synopsis "Reusable GPU array functionality for various GPU backends") + (description "This package is the counterpart of AbstractArray interface, +but for GPU array types. It provides functionality and tooling to speed-up +development of new GPU array types. This package is not intended for end +users; instead, you should use one of the packages that builds on +@code{GPUArrays.jl}, such as @code{CUDA.jl}, @code{oneAPI.jl} or +@code{AMDGPU.jl}.") + (license license:expat))) + (define-public julia-gr (package (name "julia-gr") @@ -2251,35 +2335,35 @@ library for parsing HTML.") (base32 "1jsyk3mhnwj4h19cxclx26igdqdrw51fd3k1hgav0nm67dy4cxyk")))) (build-system julia-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-before 'install 'disable-network-tests - (lambda _ - (substitute* "test/runtests.jl" - (("\"async.jl") "# \"async.jl") - (("\"client.jl") "# \"client.jl")) - (substitute* "test/aws4.jl" - (("@testset.*HTTP.request with AWS authentication.*" all) - (string-append all "return\n"))) - (substitute* "test/insert_layers.jl" - (("@testset.*Inserted final layer runs handler.*" all) - (string-append all "return\n"))) - (substitute* "test/multipart.jl" - (("@testset \"Setting of Content-Type.*" all) - (string-append all "return\n")) - (("@testset \"Deprecation of .*" all) - (string-append all "return\n"))) - (substitute* "test/websockets.jl" - (("@testset.*External Host.*" all) - (string-append all "return\n"))) - (substitute* "test/messages.jl" - (("@testset.*Read methods.*" all) - (string-append all "return\n")) - (("@testset.*Body - .*" all) - (string-append all "return\n")) - (("@testset.*Write to file.*" all) - (string-append all "return\n"))) - #t))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'install 'disable-network-tests + (lambda _ + (substitute* "test/runtests.jl" + (("\"async.jl") "# \"async.jl") + (("\"client.jl") "# \"client.jl")) + (substitute* "test/aws4.jl" + (("@testset.*HTTP.request with AWS authentication.*" all) + (string-append all "return\n"))) + (substitute* "test/insert_layers.jl" + (("@testset.*Inserted final layer runs handler.*" all) + (string-append all "return\n"))) + (substitute* "test/multipart.jl" + (("@testset \"Setting of Content-Type.*" all) + (string-append all "return\n")) + (("@testset \"Deprecation of .*" all) + (string-append all "return\n"))) + (substitute* "test/websockets.jl" + (("@testset.*External Host.*" all) + (string-append all "return\n"))) + (substitute* "test/messages.jl" + (("@testset.*Read methods.*" all) + (string-append all "return\n")) + (("@testset.*Body - .*" all) + (string-append all "return\n")) + (("@testset.*Write to file.*" all) + (string-append all "return\n")))))))) (propagated-inputs (list julia-inifile julia-mbedtls @@ -2383,7 +2467,7 @@ such arrays easy via traits.") (base32 "1n63f2zs6ail9pcl7rzgv3l0z8v1idjsaza3zgvgy7iacxsdpcj2")))) (build-system julia-build-system) (arguments - `(#:tests? #f)) ; Cycle with ImageMagick.jl. + (list #:tests? #f)) ; Cycle with ImageMagick.jl. (propagated-inputs (list julia-imagecore julia-reexport)) @@ -2414,7 +2498,7 @@ dependencies.") (base32 "0h9m3pl3wic1jrgaqkdifz24cya5vxd3m6qdmm37pxg2y2ii2vcq")))) (build-system julia-build-system) (arguments - `(#:tests? #f)) ; Cycle with ImageMagick.jl. + (list #:tests? #f)) ; Cycle with ImageMagick.jl. (propagated-inputs (list julia-abstractffts julia-colors @@ -2456,7 +2540,7 @@ of packages designed to support image processing and computer vision.") (base32 "0bbpzi7bv8jdiggq1wmcn67vnf96qagvwg0fk95s125wy5980xsl")))) (build-system julia-build-system) (arguments - `(#:tests? #f)) ; Cycle with ReferenceTests.jl. + (list #:tests? #f)) ; Cycle with ReferenceTests.jl. (propagated-inputs (list julia-crayons julia-imagebase @@ -2494,18 +2578,18 @@ be downscaled to fit into the size of your active terminal session.") (base32 "05vzv4jsj3l9pv6yrix28hlw7wnag0mqdfjwv8shn4x71hcfxl1p")))) (build-system julia-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'link-depot 'skip-failing-test - (lambda _ - ;; These tests try to download from the imagemagick.org - (substitute* "test/runtests.jl" - ((".*readremote\\.jl.*") "")) - ;; Tests with the color gray are hard. - (substitute* "test/constructed_images.jl" - (("test (b == aa)" _ test) (string-append "test_nowarn " test)) - (("test (B == map)" _ test) (string-append "test_nowarn " test))) - #t))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'link-depot 'skip-failing-test + (lambda _ + ;; These tests try to download from the imagemagick.org + (substitute* "test/runtests.jl" + ((".*readremote\\.jl.*") "")) + ;; Tests with the color gray are hard. + (substitute* "test/constructed_images.jl" + (("test (b == aa)" _ test) (string-append "test_nowarn " test)) + (("test (B == map)" _ test) (string-append "test_nowarn " test)))))))) (propagated-inputs (list julia-fileio julia-imagecore @@ -2572,7 +2656,7 @@ information about the detector used to acquire the image.") (base32 "00wq3ab8y6nyhxwc5lpz9dnslsmcr1vg3cjdkh7wb7k6a8bw98mh")))) (build-system julia-build-system) (arguments - `(#:tests? #f)) ; cycle with ImageMagick.jl. + (list #:tests? #f)) ; cycle with ImageMagick.jl. (propagated-inputs (list julia-fileio julia-imagebase @@ -2607,7 +2691,7 @@ inline presentation of greyscale or color images.") (base32 "0i8gw68hljshsy9wdl5mrpbb31irhmayqyglsxi7jwm88iy9pxhm")))) (build-system julia-build-system) (arguments - `(#:tests? #f)) ; Cycle with ImageMagick.jl. + (list #:tests? #f)) ; Cycle with ImageMagick.jl. (propagated-inputs (list julia-axisalgorithms julia-colorvectorspace @@ -2644,8 +2728,9 @@ rotation, and other spatial transformations of arrays.") (build-system julia-build-system) ;; Package without Project.toml (arguments - '(#:julia-package-name "IndexableBitVectors" - #:julia-package-uuid "1cb3b9ac-1ffd-5777-9e6b-a3d42300664d")) + (list + #:julia-package-name "IndexableBitVectors" + #:julia-package-uuid "1cb3b9ac-1ffd-5777-9e6b-a3d42300664d")) (home-page "https://github.com/BioJulia/IndexableBitVectors.jl") (synopsis "Bit vectors operations with extremely fast speed") (description "This package exports following operations over bit vectors @@ -2724,14 +2809,14 @@ indexed images, sometimes called \"colormap images\" or \"paletted images.\"") (base32 "1941lwvrdjnrynigzixxin3chpg1ba6xplvcwc89x0f6z658hwmm")))) (build-system julia-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'link-depot 'remove-timezones.jl - (lambda _ - (substitute* "test/runtests.jl" - (("using TimeZones.*") "") - ((".*infextendedtime.*") "")) - #t))))) + (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 @@ -2777,12 +2862,13 @@ interfaces with @file{.ini} files.") (base32 "1236c20k388qlh7k74mhf7hkbn0vf7ss8b1rgh1a6aj0234ayfnc")))) (build-system julia-build-system) (arguments - `(#:parallel-tests? #f - ;; XXXX: Unexpected failures for i686, e.g., - ;; Got exception outside of a @test - ;; OverflowError: 96908232 * 106943408 overflowed for type Int32 - ;; Disable as stopgap. - #:tests? ,(not (target-x86-32?)))) + (list + #:parallel-tests? #f + ;; XXXX: Unexpected failures for i686, e.g., + ;; Got exception outside of a @test + ;; OverflowError: 96908232 * 106943408 overflowed for type Int32 + ;; Disable as stopgap. + #:tests? (not (target-x86-32?)))) (propagated-inputs (list julia-axisalgorithms julia-offsetarrays @@ -2817,19 +2903,20 @@ and exceptional performance.") (base32 "0gsz89cd3iygbl5qr389k9vwpg7w1nk0s90g25nsmk34y9hifxag")))) (build-system julia-build-system) (arguments - `(#:phases - ,@(if (target-x86-32?) - '((modify-phases %standard-phases - (add-after 'unpack 'remove-failing-test-i686 - (lambda _ - (substitute* "test/runtests.jl" - ;; For some reason, the output is correct but the test - ;; is considered as failed: - ;; Expression: duration(ClosedInterval(A, B)) ≡ 60 - ;; Evaluated: 60 ≡ 60 - (("@test duration\\(ClosedInterval") - "@test_broken duration(ClosedInterval")))))) - '(%standard-phases)))) + (list + #:phases + (if (target-x86-32?) + #~(modify-phases %standard-phases + (add-after 'unpack 'remove-failing-test-i686 + (lambda _ + (substitute* "test/runtests.jl" + ;; For some reason, the output is correct but the test + ;; is considered as failed: + ;; Expression: duration(ClosedInterval(A, B)) ≡ 60 + ;; Evaluated: 60 ≡ 60 + (("@test duration\\(ClosedInterval") + "@test_broken duration(ClosedInterval"))))) + #~%standard-phases))) (propagated-inputs (list julia-ellipsisnotation)) (native-inputs @@ -3044,6 +3131,34 @@ and printing JSON documents.") focus on speed and slick struct mapping.") (license license:expat))) +(define-public julia-juno + (package + (name "julia-juno") + (version "0.8.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JunoLab/Juno.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "02ryj5blnrmck3jisrpwn1x563i7rsg65d7zms52njsvv499gygk")))) + (build-system julia-build-system) + (inputs + (list julia-media)) + (home-page "https://github.com/JunoLab/Juno.jl") + (synopsis "Integrated Development Environment (IDE) for Julia") + (description "This package provides tools to help you develop code. Juno +is built on the Atom text editor. Juno consists of both Julia and Atom +packages in order to add Julia-specific enhancements, such as syntax +highlighting, a plot pane, integration with Julia's debugger, a console for +running code, and much more. + +Consider that the package is “maintenance-only mode” and only receives bug +fixes. The Julia IDE effort is pointed to extension for VSCode.") + (license license:expat))) + (define-public julia-latexstrings (package (name "julia-latexstrings") @@ -3081,14 +3196,15 @@ equations in string literals in the Julia language.") (base32 "17rhlrmgfvdw8w62pg32ikr9j4xy2ylr7mx7ar0hnpzryv929rp5")))) (build-system julia-build-system) (arguments - `(#:phases - ,@(if (target-64bit?) - '(%standard-phases) - '((modify-phases %standard-phases - (add-after 'unpack 'fix-tests-int32-i686 - (lambda _ - (substitute* "test/multests.jl" - (("Int64") "Int32"))))))))) + (list + #:phases + (if (target-64bit?) + #~%standard-phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-tests-int32-i686 + (lambda _ + (substitute* "test/multests.jl" + (("Int64") "Int32")))))))) (propagated-inputs (list julia-arraylayouts julia-fillarrays @@ -3104,6 +3220,50 @@ equations in string literals in the Julia language.") implementation of matrix-free methods for iterative solvers.") (license license:expat))) +(define-public julia-linesearches + (package + (name "julia-linesearches") + (version "7.1.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaNLSolvers/LineSearches.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1qc4la07w6s1xhcyd0hvbnpr31zc1a2ssgyybc8biv5m00g0dnr0")))) + (build-system julia-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'link-depot 'skip-optim-tests + (lambda _ + (substitute* "test/examples.jl" + ;; Prevent a cycle with Optim.jl. + (("^ SKIPFILE.*") "") + (("^ #SKIPFILE") " SKIPFILE")))) + (add-after 'link-depot 'skip-doublefloats-tests + (lambda _ + (substitute* "test/runtests.jl" + (("using DoubleFloats.*") "") + ((".*arbitrary_precision\\.jl.*") ""))))))) + (propagated-inputs + (list julia-nlsolversbase + julia-nanmath + julia-parameters)) + (native-inputs + ;; DoubleFloats.jl transitively depends on TimeZones.jl, which is currently + ;; unpackageable due to its oversized Artifacts.toml. + (list ;julia-doublefloats + julia-optimtestproblems)) + (home-page "https://github.com/JuliaNLSolvers/LineSearches.jl") + (synopsis "Line search methods for optimization and root-finding") + (description "This package provides an interface to line search algorithms +implemented in Julia.") + (license license:expat))) + (define-public julia-logexpfunctions (package (name "julia-logexpfunctions") @@ -3166,14 +3326,15 @@ that let you do deep transformations of code.") (base32 "0l5adird8m1cmnsxwhzi5hcr7q9bm1rf7a6018zc7kcn2yxdshy3")))) (build-system julia-build-system) (arguments - `(#:phases - ,@(if (target-64bit?) - '(%standard-phases) - '((modify-phases %standard-phases - (add-after 'unpack 'fix-tests-int32-i686 - (lambda _ - (substitute* "test/runtests.jl" - (("Int64") "Int32"))))))))) + (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")))))))) (propagated-inputs (list julia-fixedpointnumbers)) (native-inputs @@ -3205,16 +3366,16 @@ comes from the fact that @code{M == map(f, A)}.") (base32 "15zvcv2l4iqmjpnqjyx2kry7a85p652nbjy9pj3wq0piksqcz4jb")))) (build-system julia-build-system) (arguments - `(#:phases - (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. - (("test String") "test_nowarn String")) - #t))))) + (list + #:phases + #~(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. + (("test String") "test_nowarn String"))))))) (propagated-inputs (list julia-arraylayouts)) (home-page "https://github.com/JuliaMatrices/MatrixFactorizations.jl") @@ -3240,14 +3401,14 @@ may include other factorizations such as the LQ factorization.") (base32 "0zjzf2r57l24n3k0gcqkvx3izwn5827iv9ak0lqix0aa5967wvfb")))) (build-system julia-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-before 'install 'disable-network-tests - ;; Tries to connect to httpbin.org - (lambda _ - (substitute* "test/runtests.jl" - (("testhost =") "return #")) - #t))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'install 'disable-network-tests + ;; Tries to connect to httpbin.org + (lambda _ + (substitute* "test/runtests.jl" + (("testhost =") "return #"))))))) (propagated-inputs (list julia-mbedtls-jll)) (home-page "https://github.com/JuliaLang/MbedTLS.jl") @@ -3325,8 +3486,11 @@ resolving them into absolute units.") (build-system julia-build-system) ;; Package without Project.toml (arguments - '(#:julia-package-name "Media" - #:julia-package-uuid "e89f7d12-3494-54d1-8411-f7d8b9ae1f27")) + (list + #:julia-package-name "Media" + #:julia-package-uuid "e89f7d12-3494-54d1-8411-f7d8b9ae1f27" + #:julia-package-dependencies + #~(list '("MacroTools" . "1914dd2f-81c6-5fcd-8719-6d5c9610ff09")))) (propagated-inputs (list julia-macrotools)) (home-page "https://github.com/JunoLab/Media.jl") @@ -3441,7 +3605,7 @@ to be temporarily overloaded for the purpose of testing.") (base32 "04fgxghyb7n2ji76xkb1r1fjhzsdbgmp5wsfyyn3yjcsdqbyp8pz")))) (build-system julia-build-system) (arguments - `(#:tests? #f)) ; Cycle with ImageCore.jl + (list #:tests? #f)) ; Cycle with ImageCore.jl (propagated-inputs (list julia-mappedarrays julia-paddedviews @@ -3493,21 +3657,22 @@ Julia, with type-driven, overloadable packing/unpacking functionality.") (base32 "1isyj8h4nx96cr6892d154v8pw1nhr7mjyz5bd6ffr2mkzb2bq4f")))) (build-system julia-build-system) (arguments - `(#:phases - ,@(if (target-x86-32?) - '((modify-phases %standard-phases - (add-after 'unpack 'remove-failing-test-i686 - (lambda _ - (substitute* "test/utilities.jl" - ;; Non-deterministic returned value, e.g., - ;; Expression: n == @allocated(f()) - ;; Evaluated: 240 == 120 - ;; and for some other values: - ;; Got correct result, please change to @test - ;; so @test_broken is not enough. - (("@test n == @allocated f\\(\\)") - " ")))))) - '(%standard-phases)))) + (list + #:phases + (if (target-x86-32?) + #~(modify-phases %standard-phases + (add-after 'unpack 'remove-failing-test-i686 + (lambda _ + (substitute* "test/utilities.jl" + ;; Non-deterministic returned value, e.g., + ;; Expression: n == @allocated(f()) + ;; Evaluated: 240 == 120 + ;; and for some other values: + ;; Got correct result, please change to @test + ;; so @test_broken is not enough. + (("@test n == @allocated f\\(\\)") + " "))))) + #~%standard-phases))) (propagated-inputs (list julia-offsetarrays)) (home-page "https://github.com/jump-dev/MutableArithmetics.jl") @@ -3584,14 +3749,15 @@ interface to interact with these types.") (base32 "16vn5w5274kcywh1xp0zqjk5q10xrk125aznz5av6wifwrvghk8s")))) (build-system julia-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'link-depot 'skip-cuda-tests - (lambda _ - (substitute* "test/runtests.jl" - (("using CUDA") "") - (("&& CUDA\\.functional\\(\\)") "")) - (setenv "NNLIB_TEST_CUDA" "false")))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'link-depot 'skip-cuda-tests + (lambda _ + (substitute* "test/runtests.jl" + (("using CUDA") "") + (("&& CUDA\\.functional\\(\\)") "")) + (setenv "NNLIB_TEST_CUDA" "false")))))) (propagated-inputs (list julia-adapt julia-chainrulescore @@ -3607,6 +3773,53 @@ machine learning, such as softmax, sigmoid, convolutions and pooling. It doesn't provide any other \"high-level\" functionality like layers or AD.") (license license:expat))) +(define-public julia-optim + (package + (name "julia-optim") + (version "1.6.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaNLSolvers/Optim.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0nvl3xp9c6r80y9n7fic4zyq2443apfmbcpnx0wvgkv4vsy08x5j")))) + (build-system julia-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'adjust-tests + (lambda _ + ;; TODO: Figure out why this test fails. + (substitute* "test/runtests.jl" + ((".*l_bfgs.*") ""))))))) + (propagated-inputs + (list julia-compat + julia-fillarrays + julia-forwarddiff + julia-linesearches + julia-nanmath + julia-nlsolversbase + julia-parameters + julia-positivefactorizations + julia-statsbase)) + (native-inputs + (list julia-linesearches + julia-measurements + julia-nlsolversbase + julia-optimtestproblems + julia-positivefactorizations + julia-recursivearraytools + julia-stablerngs)) + (home-page "https://github.com/JuliaNLSolvers/Optim.jl") + (synopsis "Optimization functions for Julia") + (description "@code{Optim.jl} is a package for univariate and multivariate +optimization of functions.") + (license license:expat))) + (define-public julia-optimtestproblems (package (name "julia-optimtestproblems") @@ -3622,8 +3835,9 @@ doesn't provide any other \"high-level\" functionality like layers or AD.") (base32 "10h47x5ws42pkqjccimaz0yxfvz41w0yazq6inamfk4lg5g2g3d9")))) (build-system julia-build-system) (arguments - `(#:julia-package-name "OptimTestProblems" - #:julia-package-uuid "cec144fc-5a64-5bc6-99fb-dde8f63e154c")) + (list + #:julia-package-name "OptimTestProblems" + #:julia-package-uuid "cec144fc-5a64-5bc6-99fb-dde8f63e154c")) (home-page "https://github.com/JuliaNLSolvers/OptimTestProblems.jl") (synopsis "Collection of optimization test problems") (description "The purpose of this package is to provide test problems for @@ -3669,7 +3883,7 @@ which they were added to the collection.") (propagated-inputs (list julia-adapt)) ;; CatIndices depends on OffsetArrays, introducing a recursive dependency - (arguments '(#:tests? #f)) + (arguments (list #: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 @@ -3886,7 +4100,7 @@ definite.") (base32 "1cail43iqzbi6m9v6981rhz47zf2lcvhs5ds5gdqvc9nx5frghxq")))) (build-system julia-build-system) (arguments - `(#:tests? #f)) ; Tests try to mkdir /.julia + (list #:tests? #f)) ; Tests try to mkdir /.julia (home-page "https://github.com/JuliaPackaging/Preferences.jl") (synopsis "Store configuration switches to TOML files") (description "The @code{Preferences} package provides an integrated way for @@ -3911,13 +4125,13 @@ everything from run time algorithm choice to code generation at compile time.") (base32 "1d1sd87kkwbar3l608h0adzws42cwdrmp1idxx7an6mfqcsdrijw")))) (build-system julia-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'link-depot 'skip-color-tests - (lambda _ - (substitute* "test/text_backend.jl" - ((".*colors\\.jl.*") "")) - #t))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'link-depot 'skip-color-tests + (lambda _ + (substitute* "test/text_backend.jl" + ((".*colors\\.jl.*") ""))))))) (propagated-inputs (list julia-crayons julia-formatting @@ -3945,49 +4159,47 @@ human-readable format.") "1fj5d1ihnhnm0pl4hbx6hcd2bpdyhm8jiaqah2axsbd069j70saf")))) (build-system julia-build-system) (arguments - `(#:imported-modules ((guix build python-build-system) + (list + #:imported-modules `((guix build python-build-system) ,@%julia-build-system-modules) - #:modules ((guix build julia-build-system) + #:modules '((guix build julia-build-system) (guix build utils) ((guix build python-build-system) #:prefix python:)) - #:phases - (modify-phases %standard-phases - (add-after 'link-depot 'remove-conda - (lambda _ - (substitute* "Project.toml" - ((".*Conda.*") "")) - (substitute* (list "src/PyCall.jl" - "test/runtests.jl") - (("import Conda") "")) - (substitute* "deps/depsutils.jl" - (("Conda.PYTHONDIR") "\"/\"")) - #t)) - (add-after 'link-depot 'set-python - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((python (assoc-ref inputs "python"))) - (setenv "PYCALL_JL_RUNTIME_PYTHON" - (string-append python "/bin/python3")) - (with-output-to-file "deps/deps.jl" - (lambda _ - (format #t - "const python = \"~a/bin/python3\"~@ + #:phases + #~(modify-phases %standard-phases + (add-after 'link-depot 'remove-conda + (lambda _ + (substitute* "Project.toml" + ((".*Conda.*") "")) + (substitute* (list "src/PyCall.jl" + "test/runtests.jl") + (("import Conda") "")) + (substitute* "deps/depsutils.jl" + (("Conda.PYTHONDIR") "\"/\"")))) + (add-after 'link-depot 'set-python + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((python (assoc-ref inputs "python"))) + (setenv "PYCALL_JL_RUNTIME_PYTHON" + (string-append python "/bin/python3")) + (with-output-to-file "deps/deps.jl" + (lambda _ + (format #t + "const python = \"~a/bin/python3\"~@ const pyprogramname = \"~a/bin/python3\"~@ const libpython = \"~a/lib/libpython~a.so.1.0\"~@ const PYTHONHOME = \"~a\"~@ const pyversion_build = v\"~a\"~@ const conda = false~%" - python - python - python - (python:python-version python) - python - ,(package-version python)))) - #t))) - (add-before 'check 'pre-check - (lambda _ - (setenv "CI" "true") - (setenv "JULIA_PKGEVAL" "true") - #t))))) + python + python + python + (python:python-version python) + python + #$(package-version python))))))) + (add-before 'check 'pre-check + (lambda _ + (setenv "CI" "true") + (setenv "JULIA_PKGEVAL" "true")))))) (propagated-inputs (list julia-macrotools julia-versionparsing)) @@ -4073,15 +4285,15 @@ arbitrary normed vector spaces (e.g. matrix-valued integrands).") (base32 "051biw4b9zni7cmh2f1yzifp1v8wazlfxrdz4p44lyd1wba6379w")))) (build-system julia-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'link-depot 'hardcode-libmath-location - (lambda* (#:key inputs #:allow-other-keys) - (let ((gcclib (assoc-ref inputs "gcc:lib"))) - (substitute* "src/Quadmath.jl" - (("libgcc_s.so.1" lib) (string-append gcclib "/lib/" lib)) - (("libquadmath.so.0" lib) (string-append gcclib "/lib/" lib))) - #t)))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'link-depot 'hardcode-libmath-location + (lambda* (#:key inputs #:allow-other-keys) + (let ((gcclib (assoc-ref inputs "gcc:lib"))) + (substitute* "src/Quadmath.jl" + (("libgcc_s.so.1" lib) (string-append gcclib "/lib/" lib)) + (("libquadmath.so.0" lib) (string-append gcclib "/lib/" lib))))))))) (propagated-inputs (list julia-requires)) (inputs @@ -4222,7 +4434,7 @@ more complex visualizations.") (base32 "0zq4bzxvq36zr0va6iip3x97mgq5b4fwza8avszx1ryfqm3lg1f7")))) (build-system julia-build-system) (arguments - `(#:tests? #f)) ; Cycle with Plots.jl. + (list #:tests? #f)) ; Cycle with Plots.jl. (propagated-inputs (list julia-nanmath julia-plotutils @@ -4252,7 +4464,7 @@ recipes to full specifications for a plot.") (base32 "0vx8ndxrii53na7jsc2lki47wfpi77rn3y2r6xhiysx1qwr14msf")))) (build-system julia-build-system) (arguments - `(#:tests? #f)) ; Cycle with OrdinaryDiffEq.jl. + (list #:tests? #f)) ; Cycle with OrdinaryDiffEq.jl. (propagated-inputs (list julia-arrayinterface julia-chainrulescore @@ -4307,7 +4519,7 @@ recursive arrays like arrays of arrays.") (base32 "0mm6bjhs8a21pippww6b08b5frmnb9m6k8xrszrwq9zhc879zpc9")))) (build-system julia-build-system) (arguments - `(#:tests? #f)) ; Cycle with ImageCore.jl through ImageMagick.jl. + (list #:tests? #f)) ; Cycle with ImageCore.jl through ImageMagick.jl. (propagated-inputs (list julia-deepdiffs julia-distances @@ -4345,7 +4557,7 @@ package can help create and update if need be.") (base32 "03hyfy7c0ma45b0y756j76awi3az2ii4bz4s8cxm3xw9yy1z7b01")))) (build-system julia-build-system) (arguments - `(#:parallel-tests? #f)) + (list #:parallel-tests? #f)) (inputs ;required for test (list julia-example)) (propagated-inputs @@ -4377,7 +4589,7 @@ can be avoided.") ;; Expression: hash(tr_float, hash(1)) === hash(v_float, hash(1)) ;; MethodError: no method matching decompose(::ReverseDiff.TrackedReal{Float64, Float64, Nothing}) ;; Disable as stopgap. - `(#:tests? ,(not (target-x86-32?)))) + (list #:tests? (not (target-x86-32?)))) (propagated-inputs (list julia-diffresults julia-diffrules @@ -4475,8 +4687,9 @@ through matrix-vector multiplication.") (base32 "1fb1dfdmiw2ggx60hf70954xlps0r48fcb3k3dvxynlz7ylphp96")))) (build-system julia-build-system) (arguments - `(#:julia-package-name "SafeTestsets" - #:julia-package-uuid "1bc83da4-3b8d-516f-aca4-4fe02f6d838f")) + (list + #:julia-package-name "SafeTestsets" + #:julia-package-uuid "1bc83da4-3b8d-516f-aca4-4fe02f6d838f")) (native-inputs (list julia-staticarrays)) (home-page "https://github.com/YingboMa/SafeTestsets.jl") @@ -4546,7 +4759,7 @@ bytes in a chunk of memory. Think of it like a much faster version of "09xni9rrrax17fxjz04j1b48mk9ffww5rcbagh66jklr89mrkqhx")))) (build-system julia-build-system) (arguments - `(#:tests? #f)) ; Test suite tries to access the Julia package registry. + (list #:tests? #f)) ; Test suite tries to access the Julia package registry. (home-page "https://github.com/JuliaPackaging/Scratch.jl") (synopsis "Scratch spaces for all your persistent mutable data needs") (description "This repository implements the scratch spaces API for @@ -4667,7 +4880,7 @@ beginners.") (base32 "173x77a80xnh99viqa3r7rgdaksvxaw8xyfqw09gwvp4p2zrxivb")))) (build-system julia-build-system) (arguments - `(#:tests? #f)) ; cycle with StatsBase.jl + (list #:tests? #f)) ; cycle with StatsBase.jl (propagated-inputs (list julia-datastructures)) ;(native-inputs @@ -4771,13 +4984,13 @@ some performance improvements).") (base32 "1fwiaxdpx1z9dli3jr8kyraych0jbdiny3qklynf0r13px25r6i7")))) (build-system julia-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'link-depot 'skip-doctest - (lambda _ - (substitute* "test/runtests.jl" - ((".*doctest.*") "")) - #t))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'link-depot 'skip-doctest + (lambda _ + (substitute* "test/runtests.jl" + ((".*doctest.*") ""))))))) (propagated-inputs (list julia-offsetarrays)) (native-inputs @@ -4936,14 +5149,15 @@ applied to any distance.") (base32 "1qwc5ll68ng80b5921ww6fvifxbsmiylakfgsbsjbzg7lzyb5i67")))) (build-system julia-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'skip-failing-test - (lambda _ - ;; https://github.com/JuliaStrings/StringEncodings.jl/issues/49 - (substitute* "test/runtests.jl" - (("\"SHIFT_JIS\", \"SHIFT_JISX0213\"") - " "))))))) + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'skip-failing-test + (lambda _ + ;; https://github.com/JuliaStrings/StringEncodings.jl/issues/49 + (substitute* "test/runtests.jl" + (("\"SHIFT_JIS\", \"SHIFT_JISX0213\"") + " "))))))) (propagated-inputs (list julia-libiconv-jll)) (home-page "https://github.com/JuliaStrings/StringEncodings.jl") @@ -4968,15 +5182,16 @@ texts between multiple character encodings. It is currently based on the (base32 "0rjcpyjwzg70n87q5r9c5i1qzigavncslxssm3rk5a3y549py56v")))) (build-system julia-build-system) (arguments - `(#:phases - ,@(if (target-64bit?) - '(%standard-phases) - '((modify-phases %standard-phases - (add-after 'unpack 'fix-tests-int32-i686 - (lambda _ - (substitute* '("src/utils.jl" - "test/runtests.jl") - (("Int64") "Int32"))))))))) + (list + #:phases + (if (target-64bit?) + #~%standard-phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-tests-int32-i686 + (lambda _ + (substitute* '("src/utils.jl" + "test/runtests.jl") + (("Int64") "Int32")))))))) (propagated-inputs (list julia-dataapi julia-staticarrays @@ -5174,7 +5389,7 @@ dimensions}.") (base32 "1lnfsmx33qspyvxw0cykwh7il8xykjpcw1080sisn95ngz2qhdmy")))) (build-system julia-build-system) (arguments - `(#:tests? #f)) ; cycle with ImageMagick.jl + (list #:tests? #f)) ; cycle with ImageMagick.jl (propagated-inputs (list julia-axisarrays julia-colortypes @@ -5243,7 +5458,7 @@ automatic differentiation for its machine learning platform.") (base32 "1w3klii293caqiclfh28jggv7f53xclm9fr6xmw38brwrn1hjb48")))) (build-system julia-build-system) (arguments - `(#:tests? #f)) ; Circular dependency with various codecs. + (list #:tests? #f)) ; Circular dependency with various codecs. (home-page "https://github.com/JuliaIO/TranscodingStreams.jl") (synopsis "Fast I/O transcoding data streams") (description "This package provides tools for transcoding data streams @@ -5338,17 +5553,17 @@ types, modules, and dictionaries.") (base32 "0kp4hg3kknkm2smlcizqfd33l9x4vkahc2714gnbjp39fj285b92")))) (build-system julia-build-system) (arguments - '(#:julia-package-name "URIs" ;required to run tests - #:julia-package-uuid "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" - #:phases - (modify-phases %standard-phases - (add-before 'check 'change-dir - ;; Tests must be run from the testdir - (lambda* (#:key source outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (chdir - (string-append out "/share/julia/loadpath/URIs/test"))) - #t))))) + (list + #:julia-package-name "URIs" ;required to run tests + #:julia-package-uuid "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" + #:phases + #~(modify-phases %standard-phases + (add-before 'check 'change-dir + ;; Tests must be run from the testdir + (lambda* (#:key source outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (chdir + (string-append out "/share/julia/loadpath/URIs/test")))))))) ;; required for tests (inputs (list julia-json)) (home-page "https://github.com/JuliaWeb/URIs.jl") @@ -5373,7 +5588,7 @@ working with @acronym{URIs,Uniform Resource Identifiers}, as defined in RFC (base32 "10qwscd15dnmvx116dwvg99m7kmwgmj5ahdkq7psiq48lcc554gq")))) (build-system julia-build-system) (arguments - `(#:parallel-tests? #f)) + (list #:parallel-tests? #f)) (propagated-inputs (list julia-constructionbase)) (home-page "https://painterqubits.github.io/Unitful.jl/stable/") @@ -5445,15 +5660,16 @@ allows for efficient string representation and transfer") (base32 "04yykivi8zrbryxlmb0p5xa6lma8iq22r5s863117dnnqj5gaffd")))) (build-system julia-build-system) (arguments - `(#:phases - ,@(if (target-x86-32?) - '((modify-phases %standard-phases - (add-after 'unpack 'remove-failing-test-i686 - (lambda _ - (substitute* "test/woodbury.jl" - (("@test logdet\\(W\\)") - "@test_broken logdet(W)")))))) - '(%standard-phases)))) + (list + #:phases + (if (target-x86-32?) + #~(modify-phases %standard-phases + (add-after 'unpack 'remove-failing-test-i686 + (lambda _ + (substitute* "test/woodbury.jl" + (("@test logdet\\(W\\)") + "@test_broken logdet(W)"))))) + #~%standard-phases))) (home-page "https://github.com/timholy/WoodburyMatrices.jl") (synopsis "Support for the Woodbury matrix identity for Julia") (description "This package provides support for the Woodbury matrix identity @@ -5548,7 +5764,7 @@ Zygote, without depending on Zygote itself.") (base32 "1cx66sp30s34ln6p0fpqk1ggjxfxg2gp8791zz3cl85dmk4dl14b")))) (build-system julia-build-system) (arguments - `(#:tests? #f)) ;require CUDA, not packaged yet + (list #:tests? #f)) ;require CUDA, not packaged yet (propagated-inputs (list julia-abstractffts julia-chainrules |