Toggle diff (441 lines)
diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 4090d6d9c4..14c8c30751 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -139,7 +139,7 @@ (define-public julia-aqua
(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},
@@ -165,7 +165,7 @@ (define-public julia-arrayinterface
;; 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
@@ -335,24 +335,25 @@ (define-public julia-benchmarktools
(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")
@@ -405,15 +406,16 @@ (define-public julia-bioalignments
(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
@@ -498,13 +500,14 @@ (define-public julia-biosymbols
(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")
@@ -528,14 +531,15 @@ (define-public julia-blockarrays
(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))
@@ -627,9 +631,10 @@ (define-public julia-bufferedstreams
;; 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")
@@ -815,14 +820,15 @@ (define-public julia-codeczlib
(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$"))
- #t))))))
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-before 'reset-gzip-timestamps 'make-files-writable
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (for-each make-file-writable
+ (find-files out "\\.gz$"))
+ #t))))))
(propagated-inputs
(list julia-transcodingstreams
julia-zlib-jll))
@@ -1015,27 +1021,28 @@ (define-public julia-configurations
(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
@@ -1160,21 +1167,22 @@ (define-public julia-dataframes
(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)))
+ #t)))))
(propagated-inputs
(list julia-dataapi
julia-invertedindices
@@ -1220,18 +1228,19 @@ (define-public julia-datastructures
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,
@@ -1275,17 +1284,18 @@ (define-public julia-datavalues
(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.*") ""))
+ #t)))))
(propagated-inputs
(list julia-datavalueinterfaces))
(home-page "https://github.com/queryverse/DataValues.jl")
@@ -1354,17 +1364,18 @@ (define-public julia-distances
(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
@@ -1393,7 +1404,7 @@ (define-public julia-docstringextensions
(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
@@ -1420,22 +1431,23 @@ (define-public julia-documenter
(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
@@ -1505,7 +1517,7 @@ (define-public julia-documentertools
(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.
@@ -1604,13 +1616,14 @@ (define-public julia-dualnumbers
(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
@@ -1638,13 +1651,14 @@ (define-public julia-ellipsisnotation
(base32 "0py46kxl702r8pw3v7x4cqllf7yc91b0dr7vb60xh2qi7d6y3jc7"))))
(build-system julia-build-system)
(arguments