julia-xyz.scm 253 KB

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  1. ;;; GNU Guix --- Functional package management for GNU
  2. ;;; Copyright © 2020, 2021 Nicolò Balzarotti <nicolo@nixo.xyz>
  3. ;;; Copyright © 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
  4. ;;; Copyright © 2021-2023 Efraim Flashner <efraim@flashner.co.il>
  5. ;;; Copyright © 2021 Vinicius Monego <monego@posteo.net>
  6. ;;; Copyright © 2021 jgart <jgart@dismail.de>
  7. ;;; Copyright © 2023 Sharlatan Hellseher <sharlatanus@gmail.com>
  8. ;;;
  9. ;;; This file is part of GNU Guix.
  10. ;;;
  11. ;;; GNU Guix is free software; you can redistribute it and/or modify it
  12. ;;; under the terms of the GNU General Public License as published by
  13. ;;; the Free Software Foundation; either version 3 of the License, or (at
  14. ;;; your option) any later version.
  15. ;;;
  16. ;;; GNU Guix is distributed in the hope that it will be useful, but
  17. ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  18. ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
  19. ;;; GNU General Public License for more details.
  20. ;;;
  21. ;;; You should have received a copy of the GNU General Public License
  22. ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
  23. (define-module (gnu packages julia-xyz)
  24. #:use-module ((guix licenses) #:prefix license:)
  25. #:use-module (gnu packages)
  26. #:use-module (guix gexp)
  27. #:use-module (guix utils)
  28. #:use-module (guix packages)
  29. #:use-module (guix git-download)
  30. #:use-module (guix build-system julia)
  31. #:use-module (gnu packages gcc)
  32. #:use-module (gnu packages julia-jll)
  33. #:use-module (gnu packages python)
  34. #:use-module (gnu packages python-xyz)
  35. #:use-module (gnu packages version-control))
  36. (define-public julia-abstractffts
  37. (package
  38. (name "julia-abstractffts")
  39. (version "1.0.1")
  40. (source
  41. (origin
  42. (method git-fetch)
  43. (uri (git-reference
  44. (url "https://github.com/JuliaMath/AbstractFFTS.jl")
  45. (commit (string-append "v" version))))
  46. (file-name (git-file-name name version))
  47. (sha256
  48. (base32 "0083pwdyxjb04i330ir9pc8kmp4bwk59lx1jgc9qi05y8j7xzbp0"))))
  49. (build-system julia-build-system)
  50. (inputs ;required for tests
  51. (list julia-unitful))
  52. (home-page "https://github.com/JuliaGPU/Adapt.jl")
  53. (synopsis "General framework for fast Fourier transforms (FFTs)")
  54. (description "This package allows multiple FFT packages to co-exist with
  55. the same underlying @code{fft(x)} and @code{plan_fft(x)} interface. It is
  56. mainly not intended to be used directly. Instead, developers of packages that
  57. implement FFTs (such as @code{FFTW.jl} or @code{FastTransforms.jl}) extend the
  58. types/functions defined in AbstractFFTs.")
  59. (license license:expat)))
  60. (define-public julia-abstracttrees
  61. (package
  62. (name "julia-abstracttrees")
  63. (version "0.4.3")
  64. (source
  65. (origin
  66. (method git-fetch)
  67. (uri (git-reference
  68. (url "https://github.com/JuliaCollections/AbstractTrees.jl")
  69. (commit (string-append "v" version))))
  70. (file-name (git-file-name name version))
  71. (sha256
  72. (base32 "04g3b6j4nvxs36rcjm743gwhy0vv0d6pvgx771agjljx109bciyr"))))
  73. (build-system julia-build-system)
  74. (home-page "https://juliacollections.github.io/AbstractTrees.jl/stable/")
  75. (synopsis "Abstract Julia interfaces for working with trees")
  76. (description "This Julia package provides several utilities for working
  77. with tree-like data structures. Most importantly, it defines the
  78. @code{children} method that any package that contains such a data structure
  79. may import and extend in order to take advantage of any generic tree algorithm
  80. in this package.")
  81. (license license:expat)))
  82. (define-public julia-adapt
  83. (package
  84. (name "julia-adapt")
  85. (version "3.3.1")
  86. (source
  87. (origin
  88. (method git-fetch)
  89. (uri (git-reference
  90. (url "https://github.com/JuliaGPU/Adapt.jl")
  91. (commit (string-append "v" version))))
  92. (file-name (git-file-name name version))
  93. (sha256
  94. (base32 "009fj59fzhvfsyw35kakllsh36k3xlwyzq8qa5f5k598i3pq14i7"))))
  95. (build-system julia-build-system)
  96. (home-page "https://github.com/JuliaGPU/Adapt.jl")
  97. (synopsis "Package providing the @code{adapt} function, similar to @code{convert}")
  98. (description "This Julia package provides the @code{adapt(T, x)} function
  99. acts like @code{convert(T, x)}, but without the restriction of returning a
  100. @code{T}. This allows you to \"convert\" wrapper types like @code{Adjoint} to
  101. be GPU compatible without throwing away the wrapper.")
  102. (license license:expat)))
  103. (define-public julia-ansicoloredprinters
  104. (package
  105. (name "julia-ansicoloredprinters")
  106. (version "0.0.1")
  107. (source
  108. (origin
  109. (method git-fetch)
  110. (uri (git-reference
  111. (url "https://github.com/JuliaDocs/ANSIColoredPrinters.jl")
  112. (commit (string-append "v" version))))
  113. (file-name (git-file-name name version))
  114. (sha256
  115. (base32 "0dp5agljr0g50s5gn0pr70wrz01ggck6pb40ay3l4szhswq7mqzf"))))
  116. (build-system julia-build-system)
  117. (home-page "https://github.com/JuliaDocs/ANSIColoredPrinters.jl")
  118. (synopsis "ANSI escape code translator")
  119. (description "@code{ANSIColoredPrinters.jl} converts a text qualified by
  120. ANSI escape codes to another format.")
  121. (license license:expat)))
  122. (define-public julia-aqua
  123. (package
  124. (name "julia-aqua")
  125. (version "0.5.5")
  126. (source
  127. (origin
  128. (method git-fetch)
  129. (uri (git-reference
  130. (url "https://github.com/JuliaTesting/Aqua.jl")
  131. (commit (string-append "v" version))))
  132. (file-name (git-file-name name version))
  133. (sha256
  134. (base32 "12hng8czkgynsn1pshavma2wijypl6k05hhgivc3rqiyclfpi89z"))))
  135. (build-system julia-build-system)
  136. (arguments
  137. (list #:parallel-tests? #f))
  138. (home-page "https://github.com/JuliaTesting/Aqua.jl")
  139. (synopsis "Automated quality assurance for Julia packages")
  140. (description "@acronym{Aqua.jl, Auto QUality Assurance for Julia packages},
  141. provides functions to run a few automatable checks for Julia packages.")
  142. (license license:expat)))
  143. (define-public julia-arnoldimethod
  144. (package
  145. (name "julia-arnoldimethod")
  146. (version "0.2.0")
  147. (source
  148. (origin
  149. (method git-fetch)
  150. (uri (git-reference
  151. (url "https://github.com/JuliaLinearAlgebra/ArnoldiMethod.jl")
  152. (commit (string-append "v" version))))
  153. (file-name (git-file-name name version))
  154. (sha256
  155. (base32 "1gs7pikgdg436srxxfywpnp12ay1mf45f7z80wym92rfrjzakwh2"))))
  156. (build-system julia-build-system)
  157. (propagated-inputs
  158. (list julia-genericschur julia-staticarrays))
  159. (home-page "https://github.com/JuliaLinearAlgebra/ArnoldiMethod.jl")
  160. (synopsis "Implicitly Restarted Arnoldi Method, natively in Julia")
  161. (description
  162. "@code{ArnoldiMethod.jl} provides an iterative method to find a few
  163. approximate solutions to the eigenvalue problem in standard form with main
  164. goals:
  165. @itemize
  166. @item Having a native Julia implementation of the @code{eigs} function that
  167. performs as well as ARPACK. With native we mean that its implementation should
  168. be generic and support any number type. Currently the partialschur function
  169. does not depend on LAPACK, and removing the last remnants of direct calls to
  170. BLAS is in the pipeline.
  171. @item Removing the dependency of the Julia language on ARPACK. This goal was
  172. already achieved before the package was stable enough, since ARPACK moved to a
  173. separate repository @code{Arpack.jl}.
  174. @end itemize")
  175. (license license:expat)))
  176. (define-public julia-arrayinterface
  177. (package
  178. (name "julia-arrayinterface")
  179. (version "5.0.8")
  180. (source
  181. (origin
  182. (method git-fetch)
  183. (uri (git-reference
  184. (url "https://github.com/JuliaArrays/ArrayInterface.jl")
  185. (commit (string-append "v" version))))
  186. (file-name (git-file-name name version))
  187. (sha256
  188. (base32 "0b0h4ihc8sykd96rn16vpk5kfk0p1si5iim61cixk9x12ma8ia3h"))))
  189. (build-system julia-build-system)
  190. (arguments
  191. ;; XXXX: Unexpected failures for i686, e.g.,
  192. ;; Expression: @inferred(ArrayInterface.size(Rnr)) === (StaticInt(4),)
  193. ;; Evaluated: (static(2),) === (static(4),)
  194. ;; Disable as stopgap.
  195. (list #:tests? (not (or (%current-target-system)
  196. (target-x86-32?)))))
  197. (propagated-inputs
  198. (list julia-compat
  199. julia-ifelse
  200. julia-requires
  201. julia-static-0.6))
  202. (native-inputs
  203. (list julia-aqua
  204. julia-bandedmatrices
  205. julia-blockbandedmatrices
  206. julia-ifelse
  207. julia-offsetarrays
  208. julia-static-0.6
  209. julia-staticarrays))
  210. (home-page "https://github.com/JuliaArrays/ArrayInterface.jl")
  211. (synopsis "Base array interface primitives")
  212. (description "The purpose of this library is to solidify extensions to the
  213. current @code{AbstractArray} interface, which are put to use in package
  214. ecosystems like @code{DifferentialEquations.jl}. Since these libraries are
  215. live, this package will serve as a staging ground for ideas before they are
  216. merged into Base Julia. For this reason, no functionality is exported so that
  217. if such functions are added and exported in a future Base Julia, there will be
  218. no issues with the upgrade.")
  219. (license license:expat)))
  220. (define-public julia-arraylayouts
  221. (package
  222. (name "julia-arraylayouts")
  223. (version "0.8.16")
  224. (source
  225. (origin
  226. (method git-fetch)
  227. (uri (git-reference
  228. (url "https://github.com/JuliaMatrices/ArrayLayouts.jl")
  229. (commit (string-append "v" version))))
  230. (file-name (git-file-name name version))
  231. (sha256
  232. (base32 "1j11jid4scw9icrbr8g6myp17nabjzmf4f40cichb20lzf1agz8l"))))
  233. (build-system julia-build-system)
  234. (arguments
  235. (list
  236. #:phases
  237. #~(modify-phases %standard-phases
  238. (add-after 'unpack 'adjust-tests
  239. (lambda _
  240. (substitute* "test/test_layoutarray.jl"
  241. (("@test all\\(B") "@test_broken all(B")))))))
  242. (propagated-inputs
  243. (list julia-fillarrays))
  244. (native-inputs
  245. (list julia-stablerngs))
  246. (home-page "https://github.com/JuliaMatrices/ArrayLayouts.jl")
  247. (synopsis "Array layouts and general fast linear algebra")
  248. (description "This package implements a trait-based framework for describing
  249. array layouts such as column major, row major, etc. that can be dispatched to
  250. appropriate BLAS or optimised Julia linear algebra routines. This supports a
  251. much wider class of matrix types than Julia's in-built @code{StridedArray}.")
  252. (license license:expat)))
  253. (define-public julia-astrotime
  254. (package
  255. (name "julia-astrotime")
  256. (version "0.7.0")
  257. (source
  258. (origin
  259. (method git-fetch)
  260. (uri (git-reference
  261. (url "https://github.com/JuliaAstro/AstroTime.jl")
  262. (commit (string-append "v" version))))
  263. (file-name (git-file-name name version))
  264. (sha256
  265. (base32 "032hlanan49ypqh4lwlf91pg7052c8h5sgbxqc1771b8j9srbyd2"))))
  266. (build-system julia-build-system)
  267. (native-inputs
  268. (list julia-measurements))
  269. (propagated-inputs
  270. (list julia-erfa
  271. julia-earthorientation
  272. julia-itemgraphs
  273. julia-macrotools
  274. julia-muladdmacro
  275. julia-reexport))
  276. (home-page "https://github.com/JuliaAstro/AstroTime.jl")
  277. (synopsis "Astronomical time keeping in Julia")
  278. (description "@code{AstroTime.jl} provides a high-precision, time-scale
  279. aware, @code{DateTime}-like data type which supports all commonly used
  280. astronomical time scales.")
  281. (license license:expat)))
  282. (define-public julia-automa
  283. (package
  284. (name "julia-automa")
  285. (version "0.8.2")
  286. (source
  287. (origin
  288. (method git-fetch)
  289. (uri (git-reference
  290. (url "https://github.com/BioJulia/Automa.jl")
  291. (commit (string-append "v" version))))
  292. (file-name (git-file-name name version))
  293. (sha256
  294. (base32 "0hmwvk3qw54p7f63a2dnzlmvkynfs62x9n8x952bcmczp35csgq0"))))
  295. (build-system julia-build-system)
  296. (propagated-inputs
  297. (list julia-scanbyte
  298. julia-transcodingstreams))
  299. (home-page "https://github.com/BioJulia/Automa.jl")
  300. (synopsis "Validation, parsing, and tokenizing based on state machine compiler")
  301. (description "This package compiles regular expressions into Julia code,
  302. which is then compiled into low-level machine code by the Julia compiler. The
  303. package is designed to generate very efficient code to scan large text data,
  304. which is often much faster than handcrafted code. @code{Automa.jl} can insert
  305. arbitrary Julia code that will be executed in state transitions. This makes
  306. it possible, for example, to extract substrings that match a part of a regular
  307. expression.")
  308. (license license:expat)))
  309. (define-public julia-axisalgorithms
  310. (package
  311. (name "julia-axisalgorithms")
  312. (version "1.0.0")
  313. (source
  314. (origin
  315. (method git-fetch)
  316. (uri (git-reference
  317. (url "https://github.com/timholy/AxisAlgorithms.jl")
  318. (commit (string-append "v" version))))
  319. (file-name (git-file-name name version))
  320. (sha256
  321. (base32 "00x85lnfln7xkfnirpplzyi8r6q92nfqwya8il156bf7b1pa20gk"))))
  322. (build-system julia-build-system)
  323. (propagated-inputs
  324. (list julia-woodburymatrices))
  325. (home-page "https://github.com/timholy/AxisAlgorithms.jl")
  326. (synopsis "Filtering and linear algebra routines for multidimensional arrays")
  327. (description "@code{AxisAlgorithms} is a collection of filtering and linear
  328. algebra algorithms for multidimensional arrays. For algorithms that would
  329. typically apply along the columns of a matrix, you can instead pick an arbitrary
  330. axis (dimension).")
  331. (license license:expat)))
  332. (define-public julia-axisarrays
  333. (package
  334. (name "julia-axisarrays")
  335. (version "0.4.6")
  336. (source
  337. (origin
  338. (method git-fetch)
  339. (uri (git-reference
  340. (url "https://github.com/JuliaArrays/AxisArrays.jl")
  341. (commit (string-append "v" version))))
  342. (file-name (git-file-name name version))
  343. (sha256
  344. (base32 "1bsd6y866ldfb4072hfm8fvc2k0vy72z2blcwfy2mpj8dlyskx3n"))))
  345. (build-system julia-build-system)
  346. (propagated-inputs
  347. (list julia-rangearrays
  348. julia-intervalsets
  349. julia-itertools))
  350. (native-inputs
  351. (list julia-offsetarrays
  352. julia-unitful))
  353. (home-page "http://juliaarrays.github.io/AxisArrays.jl/latest/")
  354. (synopsis "Arrays where each dimension can have a named axis with values")
  355. (description "This package for the Julia language provides an array type
  356. (the AxisArray) that knows about its dimension names and axis values. This
  357. allows for indexing by name without incurring any runtime overhead. This
  358. permits one to implement algorithms that are oblivious to the storage order of
  359. the underlying arrays. AxisArrays can also be indexed by the values along their
  360. axes, allowing column names or interval selections.")
  361. (license license:expat)))
  362. (define-public julia-bandedmatrices
  363. (package
  364. (name "julia-bandedmatrices")
  365. (version "0.17.9")
  366. (source
  367. (origin
  368. (method git-fetch)
  369. (uri (git-reference
  370. (url "https://github.com/JuliaMatrices/BandedMatrices.jl")
  371. (commit (string-append "v" version))))
  372. (file-name (git-file-name name version))
  373. (sha256
  374. (base32 "0nrcasjdpwf15z7l2lzyhxjqxlnqk5if78s15sh4gdgxf9kzj3a6"))))
  375. (build-system julia-build-system)
  376. (propagated-inputs
  377. (list julia-aqua
  378. julia-arraylayouts
  379. julia-fillarrays))
  380. (native-inputs
  381. (list julia-aqua
  382. julia-genericlinearalgebra))
  383. (home-page "https://github.com/JuliaMatrices/BandedMatrices.jl")
  384. (synopsis "Julia package for representing banded matrices")
  385. (description "This package supports representing banded matrices by only
  386. the entries on the bands.")
  387. (license license:expat)))
  388. (define-public julia-benchmarktools
  389. (package
  390. (name "julia-benchmarktools")
  391. (version "1.3.2")
  392. (source
  393. (origin
  394. (method git-fetch)
  395. (uri (git-reference
  396. (url "https://github.com/JuliaCI/BenchmarkTools.jl")
  397. (commit (string-append "v" version))))
  398. (file-name (git-file-name name version))
  399. (sha256
  400. (base32 "02n2pi71jvhsnc25a888i6imimd2c1phg6iyr73b12595lrz175d"))))
  401. (build-system julia-build-system)
  402. (arguments
  403. (list
  404. #:phases
  405. (if (target-x86-32?)
  406. #~(modify-phases %standard-phases
  407. (add-after 'unpack 'remove-failing-tests-i686
  408. (lambda _
  409. (substitute* "test/GroupsTests.jl"
  410. (("@test sprint\\(show, g1\\)")
  411. "@test_broken sprint(show, g1)")
  412. (("@test sprint\\(show, g1; context = :boundto => 1\\)")
  413. "@test_broken sprint(show, g1; context = :boundto => 1)")
  414. (("@test sprint\\(show, g1; context = :limit => false\\)")
  415. "@test_broken sprint(show, g1; context = :limit => false)")
  416. (("@test @test_deprecated") "@test_broken"))
  417. (substitute* "test/ExecutionTests.jl"
  418. ;; Evaluated: 12 == 8
  419. (("@test @ballocated\\(Ref\\(1\\)\\)")
  420. "@test_broken @ballocated(Ref(1))")))))
  421. #~%standard-phases)))
  422. (propagated-inputs
  423. (list julia-json))
  424. (home-page "https://github.com/JuliaCI/BenchmarkTools.jl")
  425. (synopsis "Benchmarking framework for the Julia language")
  426. (description "@code{BenchmarkTools.jl} makes performance tracking of Julia
  427. code easy by supplying a framework for writing and running groups of
  428. benchmarks as well as comparing benchmark results.")
  429. (license license:expat)))
  430. (define-public julia-bfloat16s
  431. (package
  432. (name "julia-bfloat16s")
  433. (version "0.4.0")
  434. (source
  435. (origin
  436. (method git-fetch)
  437. (uri (git-reference
  438. (url "https://github.com/JuliaMath/BFloat16s.jl")
  439. (commit (string-append "v" version))))
  440. (file-name (git-file-name name version))
  441. (sha256
  442. (base32 "12d5dv5jy8vphczlbnks0qa6wmlz0czxq7gc48bcb94f9qvq0r1n"))))
  443. (build-system julia-build-system)
  444. (home-page "https://github.com/JuliaMath/BFloat16s.jl")
  445. (synopsis "Define BFloat16 data type")
  446. (description "This package defines the @code{BFloat16} data type. The
  447. only currently available hardware implementation of this datatype are Google's
  448. Cloud TPUs. As such, this package is suitable to evaluate whether using TPUs
  449. would cause precision problems for any particular algorithm, even without
  450. access to TPU hardware. Note that this package is designed for functionality,
  451. not performance, so this package should be used for precision experiments
  452. only, not performance experiments.")
  453. (license license:expat)))
  454. (define-public julia-bioalignments
  455. (package
  456. (name "julia-bioalignments")
  457. (version "2.0.0")
  458. (source
  459. (origin
  460. (method git-fetch)
  461. (uri (git-reference
  462. (url "https://github.com/BioJulia/BioAlignments.jl")
  463. (commit (string-append "v" version))))
  464. (file-name (git-file-name name version))
  465. (sha256
  466. (base32 "1wf6qgsada59r2fykxfj9hcr635wl8maqxbd3w8qpa01k9glxa0k"))))
  467. (build-system julia-build-system)
  468. (arguments
  469. (list
  470. #:phases
  471. #~(modify-phases %standard-phases
  472. (add-after 'unpack 'skip-test
  473. (lambda _
  474. ;; Test fails because an unexpected type representation from
  475. ;; BioSequences. The aligned value is correct though.
  476. (substitute* "test/runtests.jl"
  477. (("@test sprint\\(show, aln\\)")
  478. "@test_broken sprint(show, aln)")))))))
  479. (propagated-inputs
  480. (list julia-biogenerics
  481. julia-biosequences
  482. julia-biosymbols
  483. julia-intervaltrees))
  484. (home-page "https://github.com/BioJulia/BioAlignments.jl")
  485. (synopsis "Sequence alignment algorithm and data structures")
  486. (description "This package provides alignment algorithms and data
  487. structures for sequence of DNA, RNA, and amino acid sequences.")
  488. (license license:expat)))
  489. (define-public julia-biogenerics
  490. ;; No upstream release
  491. (let ((commit "a75abaf459250e2b5e22b4d9adf25fd36d2acab6")
  492. (revision "1"))
  493. (package
  494. (name "julia-biogenerics")
  495. (version (git-version "0.0.0" revision commit))
  496. (source
  497. (origin
  498. (method git-fetch)
  499. (uri (git-reference
  500. (url "https://github.com/BioJulia/BioGenerics.jl")
  501. (commit commit)))
  502. (file-name (git-file-name name version))
  503. (sha256
  504. (base32 "17d222vi9nssjwr5l349fss7jnglnjimp1z62kmfmxa4fsn8lk8l"))))
  505. (build-system julia-build-system)
  506. (inputs
  507. (list julia-transcodingstreams))
  508. (home-page "https://github.com/BioJulia/BioGenerics.jl")
  509. (synopsis "Generic methods used by BioJulia packages")
  510. (description "This package provides generic methods and modules used in
  511. many of the other BioJulia packages. This package defines IO, exceptions, and
  512. other types or methods used by other BioJulia packages.")
  513. (license license:expat))))
  514. (define-public julia-biosequences
  515. (package
  516. (name "julia-biosequences")
  517. (version "2.0.5")
  518. (source
  519. (origin
  520. (method git-fetch)
  521. (uri (git-reference
  522. (url "https://github.com/BioJulia/BioSequences.jl")
  523. (commit (string-append "v" version))))
  524. (file-name (git-file-name name version))
  525. (sha256
  526. (base32 "0ns6zk0zvnsf4hlsys9ck2xrn20qck0b0aghh484vc6n458zq2gw"))))
  527. (build-system julia-build-system)
  528. (propagated-inputs
  529. (list julia-biogenerics
  530. julia-biosymbols
  531. julia-combinatorics
  532. julia-indexablebitvectors
  533. julia-stablerngs
  534. julia-twiddle))
  535. (native-inputs
  536. (list julia-statsbase
  537. julia-yaml))
  538. (home-page "https://biojulia.net/BioSequences.jl/stable/")
  539. (synopsis "Data types and methods for common operations with biological sequences")
  540. (description "This package provides Data types and methods for common
  541. operations with biological sequences, including DNA, RNA, and amino acid
  542. sequences.")
  543. (license license:expat)))
  544. (define-public julia-biosymbols
  545. (package
  546. (name "julia-biosymbols")
  547. ;; Older release for compatibility with julia-biosequences.
  548. (version "4.0.4")
  549. (source
  550. (origin
  551. (method git-fetch)
  552. (uri (git-reference
  553. (url "https://github.com/BioJulia/BioSymbols.jl")
  554. (commit (string-append "v" version))))
  555. (file-name (git-file-name name version))
  556. (sha256
  557. (base32 "1222rwdndi777lai8a6dwrh35i5rgmj75kcrhn8si72sxgz0syjm"))))
  558. (build-system julia-build-system)
  559. (arguments
  560. (list
  561. #:phases
  562. #~(modify-phases %standard-phases
  563. (add-after 'unpack 'adjust-tests
  564. (lambda _
  565. (substitute* "test/runtests.jl"
  566. (("\\@testset \\\"Range.*" all)
  567. (string-append all " return\n"))))))))
  568. (propagated-inputs
  569. (list julia-automa))
  570. (home-page "https://github.com/BioJulia/BioSymbols.jl")
  571. (synopsis "Primitive types for nucleic acids and amino acids")
  572. (description "This package defines the primitive types for nucleic acids
  573. and amino acids that are used ny otherBioJulia packages.")
  574. (license license:expat)))
  575. (define-public julia-blockarrays
  576. (package
  577. (name "julia-blockarrays")
  578. (version "0.16.23")
  579. (source
  580. (origin
  581. (method git-fetch)
  582. (uri (git-reference
  583. (url "https://github.com/JuliaArrays/BlockArrays.jl")
  584. (commit (string-append "v" version))))
  585. (file-name (git-file-name name version))
  586. (sha256
  587. (base32 "14gby25ixbp9ha0y2aj4gnjkzha4c7v4y3sicicgbkysnq921qd0"))))
  588. (build-system julia-build-system)
  589. (arguments
  590. (list
  591. #:phases
  592. (if (target-64bit?)
  593. #~%standard-phases
  594. #~(modify-phases %standard-phases
  595. (add-after 'unpack 'fix-tests-int32-i686
  596. (lambda _
  597. (substitute* "test/test_blockarrays.jl"
  598. (("Int64") "Int32"))))))))
  599. (propagated-inputs
  600. (list julia-arraylayouts
  601. julia-fillarrays))
  602. (native-inputs
  603. (list julia-aqua
  604. julia-offsetarrays
  605. julia-staticarrays))
  606. (home-page "https://github.com/JuliaArrays/BlockArrays.jl")
  607. (synopsis "BlockArrays for Julia")
  608. (description "A block array is a partition of an array into blocks or
  609. subarrays. This package has two purposes. Firstly, it defines an interface for
  610. an @code{AbstractBlockArray} block arrays that can be shared among types
  611. representing different types of block arrays. The advantage to this is that it
  612. provides a consistent API for block arrays.
  613. Secondly, it also implements two different type of block arrays that follow the
  614. @code{AbstractBlockArray} interface. The type @code{BlockArray} stores each
  615. block contiguously while the type @code{PseudoBlockArray} stores the full matrix
  616. contiguously. This means that @code{BlockArray} supports fast non copying
  617. extraction and insertion of blocks while @code{PseudoBlockArray} supports fast
  618. access to the full matrix to use in in for example a linear solver.")
  619. (license license:expat)))
  620. (define-public julia-blockbandedmatrices
  621. (package
  622. (name "julia-blockbandedmatrices")
  623. (version "0.11.9")
  624. (source
  625. (origin
  626. (method git-fetch)
  627. (uri (git-reference
  628. (url "https://github.com/JuliaMatrices/BlockBandedMatrices.jl")
  629. (commit (string-append "v" version))))
  630. (file-name (git-file-name name version))
  631. (sha256
  632. (base32 "1qag5awl8cmsyhpajv6llhpqbzxfii1bacppbjvmb1fqs9s0lifd"))))
  633. (build-system julia-build-system)
  634. (propagated-inputs
  635. (list julia-arraylayouts
  636. julia-bandedmatrices
  637. julia-blockarrays
  638. julia-fillarrays
  639. julia-matrixfactorizations))
  640. (home-page "https://github.com/JuliaMatrices/BlockBandedMatrices.jl")
  641. (synopsis "Block-banded matrices and banded-block-banded matrices")
  642. (description "This package supports representing block-banded and
  643. banded-block-banded matrices by only storing the entries in the non-zero bands.
  644. A @code{BlockBandedMatrix} is a subtype of @code{BlockMatrix} of
  645. @code{BlockArrays.jl} whose layout of non-zero blocks is banded.")
  646. (license license:expat)))
  647. (define-public julia-bson
  648. (package
  649. (name "julia-bson")
  650. (version "0.3.6")
  651. (source
  652. (origin
  653. (method git-fetch)
  654. (uri (git-reference
  655. (url "https://github.com/JuliaIO/BSON.jl")
  656. (commit (string-append "v" version))))
  657. (file-name (git-file-name name version))
  658. (sha256
  659. (base32 "1accra3casg66fhn5r07hz3rgs7qf9ld9ajnz8f80aid85zyp891"))))
  660. (build-system julia-build-system)
  661. (native-inputs
  662. (list julia-dataframes))
  663. (home-page "https://github.com/JuliaIO/BSON.jl")
  664. (synopsis "Binary JSON serialisation format")
  665. (description "@code{BSON.jl} is a Julia package for working with the Binary
  666. JSON serialisation format. It can be used as a general store for Julia data
  667. structures.")
  668. (license license:expat)))
  669. (define-public julia-bufferedstreams
  670. (package
  671. (name "julia-bufferedstreams")
  672. (version "1.0.0")
  673. (source
  674. (origin
  675. (method git-fetch)
  676. (uri (git-reference
  677. (url "https://github.com/BioJulia/BufferedStreams.jl")
  678. (commit (string-append "v" version))))
  679. (file-name (git-file-name name version))
  680. (sha256
  681. (base32 "0sf4sxbq55mg2pwxyxf0c839z1lk0yxg8nmb7617bfbvw31cp88z"))))
  682. (build-system julia-build-system)
  683. ;; The package is old and tests are using undefined functions. They also
  684. ;; freeze, see
  685. ;; https://travis-ci.org/BioJulia/BufferedStreams.jl/jobs/491050182
  686. (arguments
  687. (list
  688. #:tests? #f
  689. #:julia-package-name "BufferedStreams"
  690. #:julia-package-uuid "e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d"))
  691. (propagated-inputs
  692. (list julia-compat))
  693. (home-page "https://github.com/BioJulia/BufferedStreams.jl")
  694. (synopsis "Fast composable IO streams")
  695. (description "@code{BufferedStreams.jl} provides buffering for IO
  696. operations. It can wrap any @code{IO} type automatically making incremental
  697. reading and writing faster.")
  698. (license license:expat)))
  699. (define-public julia-calculus
  700. (package
  701. (name "julia-calculus")
  702. (version "0.5.1")
  703. (source
  704. (origin
  705. (method git-fetch)
  706. (uri (git-reference
  707. (url "https://github.com/JuliaMath/Calculus.jl")
  708. (commit (string-append "v" version))))
  709. (file-name (git-file-name name version))
  710. (sha256
  711. (base32 "0xh0ak2ycsjw2h86ja24ch3kn2d18zx3frrds78aimwdnqb1gdc2"))))
  712. (build-system julia-build-system)
  713. (home-page "https://github.com/JuliaMath/Calculus.jl")
  714. (synopsis "Common utilities for automatic differentiation")
  715. (description "This package provides tools for working with the basic
  716. calculus operations of differentiation and integration. The @code{Calculus}
  717. package produces approximate derivatives by several forms of finite
  718. differencing or produces exact derivative using symbolic differentiation. It
  719. can also be used to compute definite integrals by different numerical
  720. methods.")
  721. (license license:expat)))
  722. (define-public julia-categoricalarrays
  723. (package
  724. (name "julia-categoricalarrays")
  725. (version "0.10.7")
  726. (source
  727. (origin
  728. (method git-fetch)
  729. (uri (git-reference
  730. (url "https://github.com/JuliaData/CategoricalArrays.jl")
  731. (commit (string-append "v" version))))
  732. (file-name (git-file-name name version))
  733. (sha256
  734. (base32 "17fix7wlwqbif5jbcrbi0a0ghdl3429km3l6lqa962p7jf1gjd2d"))))
  735. (build-system julia-build-system)
  736. (arguments
  737. (list
  738. #:phases
  739. #~(modify-phases %standard-phases
  740. (add-after 'unpack 'adjust-tests
  741. (lambda _
  742. ;; Plots.jl isn't packaged yet.
  743. (substitute* "test/runtests.jl"
  744. ((".*13_arraycommon\\.jl.*") "")))))))
  745. (native-inputs
  746. (list julia-json
  747. julia-json3
  748. ;julia-plots
  749. julia-pooledarrays
  750. julia-recipesbase
  751. julia-sentinelarrays
  752. julia-structtypes))
  753. (propagated-inputs
  754. (list julia-dataapi
  755. julia-json
  756. julia-json3
  757. julia-missings
  758. julia-recipesbase
  759. julia-requires
  760. julia-sentinelarrays
  761. julia-structtypes))
  762. (home-page "https://github.com/JuliaData/CategoricalArrays.jl")
  763. (synopsis "Arrays for working with categorical data")
  764. (description "This package provides tools for working with categorical
  765. variables, both with unordered (nominal variables) and ordered categories
  766. (ordinal variables), optionally with missing values.")
  767. (license license:expat)))
  768. (define-public julia-cenum
  769. (package
  770. (name "julia-cenum")
  771. (version "0.4.1")
  772. (source
  773. (origin
  774. (method git-fetch)
  775. (uri (git-reference
  776. (url "https://github.com/JuliaInterop/CEnum.jl")
  777. (commit (string-append "v" version))))
  778. (file-name (git-file-name name version))
  779. (sha256
  780. (base32 "0h079mggvv420bw87j8s3hsgk7vavjgm4j1cvk0pnzrrh8ib1381"))))
  781. (build-system julia-build-system)
  782. (home-page "https://github.com/JuliaInterop/CEnum.jl")
  783. (synopsis "C-compatible enum for Julia")
  784. (description "This package provides a C-compatible enum for Julia.")
  785. (license license:expat)))
  786. (define-public julia-cfitsio
  787. (package
  788. (name "julia-cfitsio")
  789. (version "1.4.1")
  790. (source
  791. (origin
  792. (method git-fetch)
  793. (uri (git-reference
  794. (url "https://github.com/JuliaAstro/CFITSIO.jl")
  795. (commit (string-append "v" version))))
  796. (file-name (git-file-name name version))
  797. (sha256
  798. (base32 "05bxzzjcc021p3hi092h06r2q7qnvql0xz1alggi83i0pp1mxp6d"))))
  799. (build-system julia-build-system)
  800. (native-inputs (list julia-aqua))
  801. (propagated-inputs (list julia-cfitsio-jll))
  802. (home-page "https://github.com/JuliaAstro/CFITSIO.jl")
  803. (synopsis "C-style interface to the libcfitsio library")
  804. (description "This package provides Julia implementation of C-style
  805. interface to CFITSIO functions with following features:
  806. @itemize
  807. @item Function names closely mirror the C interface (e.g.,
  808. @code{fits_open_file()}).
  809. @item Functions operate on @code{FITSFile}, a thin wrapper for fitsfile C
  810. struct (@code{FITSFile} has concept of \"current HDU\", as in CFITSIO).
  811. @item Wrapper functions do check the return status from CFITSIO and throw an
  812. error with the appropriate message.
  813. @end itemize")
  814. (license license:expat)))
  815. (define-public julia-chainrules
  816. (package
  817. (name "julia-chainrules")
  818. (version "1.35.0")
  819. (source
  820. (origin
  821. (method git-fetch)
  822. (uri (git-reference
  823. (url "https://github.com/JuliaDiff/ChainRules.jl")
  824. (commit (string-append "v" version))))
  825. (file-name (git-file-name name version))
  826. (sha256
  827. (base32 "17irgz3gamyrmzsjhq4s1n1sblvhkj10yg5y5y53yr631cl2fr6a"))))
  828. (build-system julia-build-system)
  829. (arguments
  830. (list #:tests? #f)) ; JuliaInterpreter.jl not packaged yet.
  831. ;(inputs ;required for test
  832. ; (list julia-chainrulestestutils
  833. ; julia-finitedifferences
  834. ; julia-juliainterpreter))
  835. (propagated-inputs
  836. (list julia-chainrulescore
  837. julia-compat
  838. julia-irrationalconstants
  839. julia-realdot))
  840. (home-page "https://github.com/JuliaDiff/ChainRules.jl")
  841. (synopsis "Common utilities for automatic differentiation")
  842. (description "The is package provides a variety of common utilities that
  843. can be used by downstream automatic differentiation (AD) tools to define and
  844. execute forward-, reverse-, and mixed-mode primitives.")
  845. (license license:expat)))
  846. (define-public julia-chainrulescore
  847. (package
  848. (name "julia-chainrulescore")
  849. (version "1.12.2")
  850. (source
  851. (origin
  852. (method git-fetch)
  853. (uri (git-reference
  854. (url "https://github.com/JuliaDiff/ChainRulesCore.jl")
  855. (commit (string-append "v" version))))
  856. (file-name (git-file-name name version))
  857. (sha256
  858. (base32 "0lgfcsb7f6c7knhiz5dbqh8x47d370pn71y9ys2y6763g0b4pm61"))))
  859. (build-system julia-build-system)
  860. (arguments
  861. (list
  862. #:phases
  863. #~(modify-phases %standard-phases
  864. (add-after 'unpack 'adjust-tests
  865. (lambda _
  866. (substitute* "test/tangent_types/tangent.jl"
  867. ;; This test is disabled after the release.
  868. (("@test haskey.*Float.*") "")
  869. (("@test (.*construct)" _ test)
  870. (string-append "@test_broken " test))))))))
  871. (inputs ;required for tests
  872. (list julia-benchmarktools
  873. julia-staticarrays))
  874. (propagated-inputs
  875. (list julia-compat))
  876. (home-page "https://github.com/JuliaDiff/ChainRulesCore.jl")
  877. (synopsis "Common utilities used by downstream automatic differentiation tools")
  878. (description "The package provides a light-weight dependency for defining
  879. sensitivities for functions without the need to depend on ChainRules itself.")
  880. (license license:expat)))
  881. (define-public julia-chainrulestestutils
  882. (package
  883. (name "julia-chainrulestestutils")
  884. (version "1.5.1")
  885. (source
  886. (origin
  887. (method git-fetch)
  888. (uri (git-reference
  889. (url "https://github.com/JuliaDiff/ChainRulesTestUtils.jl")
  890. (commit (string-append "v" version))))
  891. (file-name (git-file-name name version))
  892. (sha256
  893. (base32 "0vk7cpp049pjj7g5zqxr7djp5v0swhvhq3wvkxyw8m8xvqlnfncc"))))
  894. (build-system julia-build-system)
  895. (propagated-inputs
  896. (list julia-chainrulescore
  897. julia-compat
  898. julia-finitedifferences))
  899. (home-page "https://github.com/JuliaDiff/ChainRulesTestUtils.jl")
  900. (synopsis "Common utilities used by downstream automatic differentiation tools")
  901. (description "This package is designed to help in testing
  902. @code{ChainRulesCore.frule} and @code{ChainRulesCore.rrule} methods. The main
  903. entry points are @code{ChainRulesTestUtils.frule_test},
  904. @code{ChainRulesTestUtils.rrule_test}, and
  905. @code{ChainRulesTestUtils.test_scalar}. Currently this is done via testing the
  906. rules against numerical differentiation (using @code{FiniteDifferences.jl}).
  907. @code{ChainRulesTestUtils.jl} is separated from @code{ChainRulesCore.jl} so that it
  908. can be a test-only dependency, allowing it to have potentially heavy
  909. dependencies, while keeping @code{ChainRulesCore.jl} as light-weight as possible.")
  910. (license license:expat)))
  911. (define-public julia-changesofvariables
  912. (package
  913. (name "julia-changesofvariables")
  914. (version "0.1.4")
  915. (source
  916. (origin
  917. (method git-fetch)
  918. (uri (git-reference
  919. (url "https://github.com/JuliaMath/ChangesOfVariables.jl")
  920. (commit (string-append "v" version))))
  921. (file-name (git-file-name name version))
  922. (sha256
  923. (base32 "1migyhiqr1rq496302wlkb0s5l8zwqs97ajfkip0jzpvrk2s2xxy"))))
  924. (build-system julia-build-system)
  925. (arguments
  926. ;; Pulls in ForwardDiff, would have a cyclical
  927. ;; dependency with LogExpFunctions.
  928. (list #:tests? #f))
  929. (propagated-inputs
  930. (list julia-chainrulescore))
  931. (home-page "https://github.com/JuliaMath/ChangesOfVariables.jl")
  932. (synopsis "Interface for transformation functions in Julia")
  933. (description "This package defines functionality to calculate volume element
  934. changes for functions that perform a change of variables (like coordinate
  935. transformations).")
  936. (license license:expat)))
  937. (define-public julia-codeczlib
  938. (package
  939. (name "julia-codeczlib")
  940. (version "0.7.0")
  941. (source
  942. (origin
  943. (method git-fetch)
  944. (uri (git-reference
  945. (url "https://github.com/JuliaIO/CodecZlib.jl")
  946. (commit (string-append "v" version))))
  947. (file-name (git-file-name name version))
  948. (sha256
  949. (base32 "0xm603nylkwk4bzx66zv1g3syzrvn3jh9spdx7kvcvgszzyrrgh4"))))
  950. (build-system julia-build-system)
  951. (propagated-inputs
  952. (list julia-transcodingstreams
  953. julia-zlib-jll))
  954. (home-page "https://github.com/JuliaIO/CodecZlib.jl")
  955. (synopsis "Zlib codecs for @code{TranscodingStreams.jl}")
  956. (description "This package provides zlib codecs for
  957. @code{TranscodingStreams.jl}.")
  958. (license license:expat)))
  959. (define-public julia-colors
  960. (package
  961. (name "julia-colors")
  962. (version "0.12.9")
  963. (source
  964. (origin
  965. (method git-fetch)
  966. (uri (git-reference
  967. (url "https://github.com/JuliaGraphics/Colors.jl")
  968. (commit (string-append "v" version))))
  969. (file-name (git-file-name name version))
  970. (sha256
  971. (base32 "1g0fvvz09pfk6jxqrdplwkw1yywcqvwjd3ga24hblq71mah367n6"))))
  972. (build-system julia-build-system)
  973. (arguments
  974. (list
  975. #:phases
  976. #~(modify-phases %standard-phases
  977. (add-after 'unpack 'adjust-tests
  978. (lambda _
  979. (substitute* "test/runtests.jl"
  980. ((".*detect_ambiguities.*") "")))))))
  981. (propagated-inputs
  982. (list julia-colortypes
  983. julia-fixedpointnumbers
  984. julia-reexport))
  985. (native-inputs
  986. (list julia-abstracttrees))
  987. (home-page "https://github.com/JuliaGraphics/Colors.jl")
  988. (synopsis "Tools for dealing with color")
  989. (description "This package provides a wide array of functions for dealing
  990. with color. This includes conversion between colorspaces, measuring distance
  991. between colors, simulating color blindness, parsing colors, and generating
  992. color scales for graphics.")
  993. (license license:expat)))
  994. (define-public julia-colorschemes
  995. (package
  996. (name "julia-colorschemes")
  997. (version "3.15.0")
  998. (source
  999. (origin
  1000. (method git-fetch)
  1001. (uri (git-reference
  1002. (url "https://github.com/JuliaGraphics/ColorSchemes.jl")
  1003. (commit (string-append "v" version))))
  1004. (file-name (git-file-name name version))
  1005. (sha256
  1006. (base32 "0kpjhmqd5cj8dh8bmh9b5g6bscyp7h23hzpr2s93pnrp57q1wvhq"))))
  1007. (build-system julia-build-system)
  1008. (propagated-inputs
  1009. (list julia-colors
  1010. julia-colortypes
  1011. julia-fixedpointnumbers
  1012. julia-staticarrays))
  1013. (home-page "https://github.com/JuliaGraphics/ColorSchemes.jl")
  1014. (synopsis "Colorschemes, colormaps, gradients, and palettes")
  1015. (description "This package provides a collection of colorschemes.")
  1016. (license license:expat)))
  1017. (define-public julia-colortypes
  1018. (package
  1019. (name "julia-colortypes")
  1020. (version "0.11.1")
  1021. (source
  1022. (origin
  1023. (method git-fetch)
  1024. (uri (git-reference
  1025. (url "https://github.com/JuliaGraphics/ColorTypes.jl")
  1026. (commit (string-append "v" version))))
  1027. (file-name (git-file-name name version))
  1028. (sha256
  1029. (base32 "0cp5wbi2bhnxp4h7wpzkx341d47744f4c9a8n0w0kn016qa16m86"))))
  1030. (build-system julia-build-system)
  1031. (arguments
  1032. (list
  1033. #:phases
  1034. #~(modify-phases %standard-phases
  1035. (add-after 'unpack 'skip-failing-test
  1036. (lambda _
  1037. (substitute* "test/conversions.jl"
  1038. (("@test promote\\(RGB\\{N0f8")
  1039. "@test_broken promote(RGB{N0f8")))))))
  1040. (propagated-inputs
  1041. (list julia-fixedpointnumbers))
  1042. (native-inputs
  1043. (list julia-documenter))
  1044. (home-page "https://github.com/JuliaGraphics/ColorTypes.jl")
  1045. (synopsis "Basic color types and constructor")
  1046. (description "This minimalistic package serves as the foundation for
  1047. working with colors in Julia. It defines basic color types and their
  1048. constructors, and sets up traits and show methods to make them easier to work
  1049. with.")
  1050. (license license:expat)))
  1051. (define-public julia-colorvectorspace
  1052. (package
  1053. (name "julia-colorvectorspace")
  1054. (version "0.9.9")
  1055. (source
  1056. (origin
  1057. (method git-fetch)
  1058. (uri (git-reference
  1059. (url "https://github.com/JuliaGraphics/ColorVectorSpace.jl")
  1060. (commit (string-append "v" version))))
  1061. (file-name (git-file-name name version))
  1062. (sha256
  1063. (base32 "07scws2bn2z3f2crhnx1zxk3zk3vzfv9iz6lv3i9785nplmsgdx9"))))
  1064. (build-system julia-build-system)
  1065. (arguments
  1066. (list
  1067. #:tests? #f)) ; TODO: Reenable the test suite.
  1068. (propagated-inputs
  1069. (list julia-colortypes
  1070. julia-fixedpointnumbers
  1071. julia-specialfunctions
  1072. julia-tensorcore))
  1073. (native-inputs
  1074. (list julia-colors))
  1075. (home-page "https://github.com/JuliaGraphics/ColorVectorSpace.jl")
  1076. (synopsis "Treat colors as n-vectors for the purposes of arithmetic")
  1077. (description "This package is an add-on to @code{ColorTypes.jl} and provides
  1078. fast mathematical operations for objects with types such as RGB and Gray.
  1079. Specifically, with this package both grayscale and RGB colors are treated as if
  1080. they are points in a normed vector space.")
  1081. (license license:expat)))
  1082. (define-public julia-combinatorics
  1083. (package
  1084. (name "julia-combinatorics")
  1085. (version "1.0.2")
  1086. (source
  1087. (origin
  1088. (method git-fetch)
  1089. (uri (git-reference
  1090. (url "https://github.com/JuliaMath/Combinatorics.jl")
  1091. (commit (string-append "v" version))))
  1092. (file-name (git-file-name name version))
  1093. (sha256
  1094. (base32 "0gafqkqi874zfm9h99akw9q95lk3ih5gip2h8p12fj9h7rvyf4j5"))))
  1095. (build-system julia-build-system)
  1096. (home-page "https://github.com/JuliaMath/Combinatorics.jl")
  1097. (synopsis "Combinatorics library for Julia")
  1098. (description "This package provides a combinatorics library for Julia,
  1099. focusing mostly (as of now) on enumerative combinatorics and permutations.")
  1100. (license license:expat)))
  1101. (define-public julia-commonsubexpressions
  1102. (package
  1103. (name "julia-commonsubexpressions")
  1104. (version "0.3.0")
  1105. (source
  1106. (origin
  1107. (method git-fetch)
  1108. (uri (git-reference
  1109. (url "https://github.com/rdeits/CommonSubexpressions.jl")
  1110. (commit (string-append "v" version))))
  1111. (file-name (git-file-name name version))
  1112. (sha256
  1113. (base32 "0mgy90kk8ksv3l720kkk04gnhn4aqhh2dj4sp3x8yy3limngfjay"))))
  1114. (build-system julia-build-system)
  1115. (propagated-inputs
  1116. (list julia-macrotools))
  1117. (home-page "https://github.com/rdeits/CommonSubexpressions.jl")
  1118. (synopsis "@code{@@cse} macro for Julia")
  1119. (description "This package provides the @code{@@cse} macro, which performs
  1120. common subexpression elimination.")
  1121. (license license:expat)))
  1122. (define-public julia-compat
  1123. (package
  1124. (name "julia-compat")
  1125. (version "3.39.0")
  1126. (source
  1127. (origin
  1128. (method git-fetch)
  1129. (uri (git-reference
  1130. (url "https://github.com/JuliaLang/Compat.jl")
  1131. (commit (string-append "v" version))))
  1132. (file-name (git-file-name name version))
  1133. (sha256
  1134. (base32 "0qzvaqi5gqgc747fnajbvvf5vqbh6cwykwky00c7glvmvdsgk3z0"))))
  1135. (build-system julia-build-system)
  1136. (arguments
  1137. (list
  1138. #:phases
  1139. #~(modify-phases %standard-phases
  1140. (add-after 'unpack 'patch-shell-invocation
  1141. (lambda* (#:key inputs #:allow-other-keys)
  1142. (substitute* "test/runtests.jl"
  1143. (("shcmd = `sh`") (string-append "shcmd = `" (which "sh") "`"))))))))
  1144. (home-page "https://github.com/JuliaLang/Compat.jl")
  1145. (synopsis "Compatibility across Julia versions")
  1146. (description "The Compat package is designed to ease interoperability
  1147. between older and newer versions of the Julia language. The Compat package
  1148. provides a macro that lets you use the latest syntax in a backwards-compatible
  1149. way.")
  1150. (license license:expat)))
  1151. (define-public julia-configurations
  1152. (package
  1153. (name "julia-configurations")
  1154. (version "0.16.4")
  1155. (source
  1156. (origin
  1157. (method git-fetch)
  1158. (uri (git-reference
  1159. (url "https://github.com/Roger-luo/Configurations.jl")
  1160. (commit (string-append "v" version))))
  1161. (file-name (git-file-name name version))
  1162. (sha256
  1163. (base32 "1b23p0zk8dx2sf01cnw177mqci7qd81b9s32ixz9clsh0r0icl1b"))))
  1164. (build-system julia-build-system)
  1165. (arguments
  1166. (list
  1167. #:phases
  1168. #~(modify-phases %standard-phases
  1169. (add-after 'link-depot 'fix-tests
  1170. (lambda _
  1171. (substitute* "test/runtests.jl"
  1172. (("option.toml") "test/option.toml"))))
  1173. (add-after 'link-depot 'dont-use-exproniconlite
  1174. (lambda _
  1175. (substitute* '("Project.toml"
  1176. "src/Configurations.jl"
  1177. "test/runtests.jl")
  1178. (("ExproniconLite") "Expronicon"))
  1179. (substitute* "Project.toml"
  1180. (("55351af7-c7e9-48d6-89ff-24e801d99491")
  1181. "6b7a57c9-7cc1-4fdf-b7f5-e857abae3636"))))
  1182. #$@(if (target-64bit?)
  1183. '()
  1184. '((add-after 'unpack 'fix-tests-int32-i686
  1185. (lambda _
  1186. (substitute* "test/runtests.jl"
  1187. (("Int64") "Int32")))))))))
  1188. (propagated-inputs
  1189. (list julia-crayons
  1190. julia-expronicon
  1191. julia-orderedcollections))
  1192. (home-page "https://configurations.rogerluo.dev/stable/")
  1193. (synopsis "Tools for options and configurations in Julia")
  1194. (description "@code{Configurations.jl} provides a macro @code{@@option} to
  1195. let you define @code{structs} to represent options/configurations, and serialize
  1196. between different option/configuration file formats such as @code{TOML}.")
  1197. (license license:expat)))
  1198. (define-public julia-constructionbase
  1199. (package
  1200. (name "julia-constructionbase")
  1201. (version "1.3.0")
  1202. (source
  1203. (origin
  1204. (method git-fetch)
  1205. (uri (git-reference
  1206. (url "https://github.com/JuliaObjects/ConstructionBase.jl")
  1207. (commit (string-append "v" version))))
  1208. (file-name (git-file-name name version))
  1209. (sha256
  1210. (base32 "1jk3h446vkv4yaavgm1hf1az7cwhppvhklvr08s49hhg02cm750q"))))
  1211. (build-system julia-build-system)
  1212. (home-page "https://juliaobjects.github.io/ConstructionBase.jl/dev/")
  1213. (synopsis "Primitive functions for construction of objects")
  1214. (description "This very lightweight package provides primitive functions
  1215. for construction of objects.")
  1216. (license license:expat)))
  1217. (define-public julia-coordinatetransformations
  1218. ;; Test suite fixed after the last release.
  1219. (let ((commit "78f5a5cc8cf77f21407b4f175673fa4f6bf86633")
  1220. (revision "1"))
  1221. (package
  1222. (name "julia-coordinatetransformations")
  1223. (version (git-version "0.6.2" revision commit))
  1224. (source
  1225. (origin
  1226. (method git-fetch)
  1227. (uri (git-reference
  1228. (url "https://github.com/JuliaGeometry/CoordinateTransformations.jl")
  1229. (commit commit)))
  1230. (file-name (git-file-name name version))
  1231. (sha256
  1232. (base32 "026g3b2m2z509jdlqvd46yhnhg8y6m00plr3k7cjlbzrfi2yjjn8"))))
  1233. (build-system julia-build-system)
  1234. (propagated-inputs
  1235. (list julia-staticarrays))
  1236. (native-inputs
  1237. (list julia-documenter
  1238. julia-forwarddiff
  1239. julia-unitful))
  1240. (home-page "https://github.com/JuliaGeometry/CoordinateTransformations.jl")
  1241. (synopsis "Coordinate transformations in Julia")
  1242. (description "@code{CoordinateTransformations} is a Julia package to manage
  1243. simple or complex networks of coordinate system transformations.
  1244. Transformations can be easily applied, inverted, composed, and differentiated
  1245. (both with respect to the input coordinates and with respect to transformation
  1246. parameters such as rotation angle). Transformations are designed to be
  1247. light-weight and efficient enough for, e.g., real-time graphical applications,
  1248. while support for both explicit and automatic differentiation makes it easy to
  1249. perform optimization and therefore ideal for computer vision applications such
  1250. as SLAM (simultaneous localization and mapping).")
  1251. (license license:expat))))
  1252. (define-public julia-crayons
  1253. (package
  1254. (name "julia-crayons")
  1255. (version "4.1.1")
  1256. (source
  1257. (origin
  1258. (method git-fetch)
  1259. (uri (git-reference
  1260. (url "https://github.com/KristofferC/Crayons.jl")
  1261. (commit (string-append "v" version))))
  1262. (file-name (git-file-name name version))
  1263. (sha256
  1264. (base32 "0vfbb02pclwlbpcl7rhr98a495kga5wydf5wz1gp1xn1wxgpgxpd"))))
  1265. (build-system julia-build-system)
  1266. (home-page "https://github.com/KristofferC/Crayons.jl")
  1267. (synopsis "Colored and styled strings for terminals")
  1268. (description "Crayons is a package that makes it simple to write strings in
  1269. different colors and styles to terminals. It supports the 16 system colors,
  1270. both the 256 color and 24 bit true color extensions, and the different text
  1271. styles available to terminals.")
  1272. (license license:expat)))
  1273. (define-public julia-cstparser
  1274. (package
  1275. (name "julia-cstparser")
  1276. (version "3.3.4")
  1277. (source
  1278. (origin
  1279. (method git-fetch)
  1280. (uri (git-reference
  1281. (url "https://github.com/julia-vscode/CSTParser.jl")
  1282. (commit (string-append "v" version))))
  1283. (file-name (git-file-name name version))
  1284. (sha256
  1285. (base32 "162jpcdph26ybg7rajbvfcbpnngygybpzk5bry4c4ppda3m1dl1i"))))
  1286. (build-system julia-build-system)
  1287. (arguments
  1288. (list
  1289. #:phases
  1290. #~(modify-phases %standard-phases
  1291. (add-after 'unpack 'fix-or-ignore-tests
  1292. (lambda _
  1293. (substitute* "test/iterate.jl"
  1294. (("parser.jl")
  1295. (string-append #$output "/share/julia/loadpath/CSTParser/test/parser.jl"))
  1296. (("../src")
  1297. (string-append #$output "/share/julia/loadpath/CSTParser/src")))
  1298. (substitute* "test/check_base.jl"
  1299. (("testset.*" all)
  1300. (string-append all "return\n"))))))))
  1301. (inputs (list julia-tokenize))
  1302. (home-page "https://github.com/julia-vscode/CSTParser.jl")
  1303. (synopsis "Parser for Julia")
  1304. (description "This package provides a parser for Julia code.")
  1305. (license license:expat)))
  1306. (define-public julia-csv
  1307. (package
  1308. (name "julia-csv")
  1309. (version "0.10.4")
  1310. (source
  1311. (origin
  1312. (method git-fetch)
  1313. (uri (git-reference
  1314. (url "https://github.com/JuliaData/CSV.jl")
  1315. (commit (string-append "v" version))))
  1316. (file-name (git-file-name name version))
  1317. (sha256
  1318. (base32 "15kjh5wa6ravb10n9n9bsh7ggmarqmw8s57p35l4b3dqk9d8qafh"))))
  1319. (build-system julia-build-system)
  1320. (arguments
  1321. (list #:phases
  1322. #~(modify-phases %standard-phases
  1323. (add-after 'unpack 'fix-reference-to-cat
  1324. (lambda _
  1325. (substitute* "test/basics.jl"
  1326. ;; XXXX: Test fail to read using CVS.Chunk; raising:
  1327. ;; ArgumentError: unable to iterate chunks from input file source
  1328. ;; Disable and the two tests using it.
  1329. (("chunks = CSV.Chunks") "# chunks = CSV.Chunks")
  1330. (("@test sum\\(length, chunks\\) == 10000")
  1331. "# @test sum(length, chunks) == 10000")
  1332. (("@test Tables.partitions\\(chunks\\) === chunks")
  1333. "# @test Tables.partitions(chunks) === chunks")))))))
  1334. (propagated-inputs
  1335. (list julia-codeczlib
  1336. julia-filepathsbase
  1337. julia-inlinestrings
  1338. julia-parsers
  1339. julia-pooledarrays
  1340. julia-sentinelarrays
  1341. julia-tables
  1342. julia-weakrefstrings))
  1343. (home-page "https://github.com/JuliaData/CSV.jl")
  1344. (synopsis "Fast and flexible delimited-file reader/writer")
  1345. (description "This package provides reader/writer for delimited text data,
  1346. as comma-delimited (csv), tab-delimited (tsv), or otherwise.")
  1347. (license license:expat)))
  1348. (define-public julia-dataapi
  1349. (package
  1350. (name "julia-dataapi")
  1351. (version "1.13.0")
  1352. (source
  1353. (origin
  1354. (method git-fetch)
  1355. (uri (git-reference
  1356. (url "https://github.com/JuliaData/DataAPI.jl")
  1357. (commit (string-append "v" version))))
  1358. (file-name (git-file-name name version))
  1359. (sha256
  1360. (base32 "1x5pdpjlbk29766ark7rmzjbl0rhxmsb1cp04lc891aknh30rn3i"))))
  1361. (build-system julia-build-system)
  1362. (home-page "https://github.com/JuliaData/DataAPI.jl")
  1363. (synopsis "Data-focused namespace for packages to share functions")
  1364. (description "This package provides a namespace for data-related generic
  1365. function definitions to solve the optional dependency problem; packages wishing
  1366. to share and/or extend functions can avoid depending directly on each other by
  1367. moving the function definition to DataAPI.jl and each package taking a
  1368. dependency on it.")
  1369. (license license:expat)))
  1370. (define-public julia-dataframes
  1371. (package
  1372. (name "julia-dataframes")
  1373. (version "1.3.6")
  1374. (source
  1375. (origin
  1376. (method git-fetch)
  1377. (uri (git-reference
  1378. (url "https://github.com/JuliaData/DataFrames.jl")
  1379. (commit (string-append "v" version))))
  1380. (file-name (git-file-name name version))
  1381. (sha256
  1382. (base32 "01ybc1ckn5wi7kwp29g5ms4m3g650856z4xv71racbdr8475pmg5"))))
  1383. (build-system julia-build-system)
  1384. (arguments
  1385. (list
  1386. #:phases
  1387. #~(modify-phases %standard-phases
  1388. (add-after 'link-depot 'skip-failing-test
  1389. (lambda _
  1390. ;; Tests with non-standard colors.
  1391. (substitute* "test/show.jl"
  1392. (("test (sprint\\(show, df, context=:color=>true)" _ test)
  1393. (string-append "test_nowarn " test)))
  1394. (substitute* "test/io.jl"
  1395. (("testset \\\"improved.*" all)
  1396. (string-append all "return\n")))
  1397. (substitute* "test/join.jl"
  1398. (("test (levels\\(outerjoin\\(B)" _ test)
  1399. (string-append "test_nowarn " test)))
  1400. ;; Compat with julia-1.8, remove with next package update.
  1401. (substitute* "test/indexing_offset.jl"
  1402. (("@test_throws ErrorException")
  1403. "@test_throws Base.CanonicalIndexError")))))))
  1404. (propagated-inputs
  1405. (list julia-categoricalarrays
  1406. julia-compat
  1407. julia-dataapi
  1408. julia-invertedindices
  1409. julia-iteratorinterfaceextensions
  1410. julia-missings
  1411. julia-pooledarrays
  1412. julia-prettytables
  1413. julia-reexport
  1414. julia-shiftedarrays
  1415. julia-sortingalgorithms
  1416. julia-tables
  1417. julia-tabletraits
  1418. julia-unitful))
  1419. (native-inputs
  1420. (list julia-categoricalarrays
  1421. julia-combinatorics
  1422. julia-datastructures
  1423. julia-datavalues
  1424. julia-offsetarrays
  1425. julia-shiftedarrays
  1426. julia-unitful))
  1427. (home-page "https://dataframes.juliadata.org/stable/")
  1428. (synopsis "In-memory tabular data")
  1429. (description "This package provides a set of tools for working with tabular
  1430. data in Julia. Its design and functionality are similar to those of Pandas from
  1431. Python or @code{data.frame}, @code{data.table} and @code{dplyr} from R, making
  1432. it a great general purpose data science tool, especially for those coming to
  1433. Julia from R or Python.")
  1434. (license license:expat)))
  1435. (define-public julia-datastructures
  1436. (package
  1437. (name "julia-datastructures")
  1438. (version "0.18.13")
  1439. (source
  1440. (origin
  1441. (method git-fetch)
  1442. (uri (git-reference
  1443. (url "https://github.com/JuliaCollections/DataStructures.jl")
  1444. (commit (string-append "v" version))))
  1445. (file-name (git-file-name name version))
  1446. (sha256
  1447. (base32 "1ikrgc4d39980nrr77yzcnr1v74wrjh9xvyi2ajfzbcim58vrcqg"))))
  1448. (propagated-inputs
  1449. (list julia-compat
  1450. julia-orderedcollections))
  1451. (build-system julia-build-system)
  1452. (arguments
  1453. (list
  1454. #:phases
  1455. (if (target-x86-32?)
  1456. #~(modify-phases %standard-phases
  1457. (add-after 'unpack 'remove-failing-test-i686
  1458. (lambda _
  1459. ;; The evaluation returns the correct value,
  1460. ;; Evaluated: "Accumulator(1 => 3, 3 => 4)"
  1461. ;; but, for some reasons, is considered as failed.
  1462. (substitute* "test/test_accumulator.jl"
  1463. (("@test sprint\\(show,Accumulator\\(1 => 3, 3 => 4\\)\\)")
  1464. "@test_broken sprint(show, Accumulator(1 => 3, 3 => 4))")))))
  1465. #~%standard-phases)))
  1466. (home-page "https://github.com/JuliaCollections/DataStructures.jl")
  1467. (synopsis "Julia module providing different data structures")
  1468. (description "This package implements a variety of data structures,
  1469. including, @code{CircularBuffer}, @code{Queue}, @code{Stack},
  1470. @code{Accumulators}, @code{LinkedLists}, @code{SortedDicts} and many others.")
  1471. (license license:expat)))
  1472. (define-public julia-datavalueinterfaces
  1473. (package
  1474. (name "julia-datavalueinterfaces")
  1475. (version "1.0.0")
  1476. (source
  1477. (origin
  1478. (method git-fetch)
  1479. (uri (git-reference
  1480. (url "https://github.com/queryverse/DataValueInterfaces.jl")
  1481. (commit (string-append "v" version))))
  1482. (file-name (git-file-name name version))
  1483. (sha256
  1484. (base32 "0g2wj6q7jj956nx6g7dk8x7w1c4l2xcmnr1kq5x8s8fild9kslg8"))))
  1485. (build-system julia-build-system)
  1486. (home-page "https://github.com/queryverse/DataValueInterfaces.jl")
  1487. (synopsis "Interface for DataValues.jl")
  1488. (description "This package allows a few \"forward\" definitions for the
  1489. @code{DataValues.jl} package that other packages can utilize for integration
  1490. without having to take direct dependencies.")
  1491. (license license:expat)))
  1492. (define-public julia-datavalues
  1493. (package
  1494. (name "julia-datavalues")
  1495. (version "0.4.13")
  1496. (source
  1497. (origin
  1498. (method git-fetch)
  1499. (uri (git-reference
  1500. (url "https://github.com/queryverse/DataValues.jl")
  1501. (commit (string-append "v" version))))
  1502. (file-name (git-file-name name version))
  1503. (sha256
  1504. (base32 "15j3hrqq6nazn533bfsvg32xznacbzsl303j1qs48av59ppnvhhv"))))
  1505. (build-system julia-build-system)
  1506. (arguments
  1507. (list
  1508. #:tests? #f ; Tests need upgrading with newer Julia version.
  1509. #:phases
  1510. #~(modify-phases %standard-phases
  1511. (add-after 'link-depot 'skip-known-failing-tests
  1512. (lambda _
  1513. ;; See upstream report:
  1514. ;; https://github.com/queryverse/DataValues.jl/issues/83
  1515. (substitute* "test/array/test_reduce.jl"
  1516. ((".*DataValue\\(mapreduce.*") "")
  1517. ((".*DataValue\\(method\\(f.*") "")))))))
  1518. (propagated-inputs
  1519. (list julia-datavalueinterfaces))
  1520. (home-page "https://github.com/queryverse/DataValues.jl")
  1521. (synopsis "Missing values for Julia")
  1522. (description "This package provides the type @code{DataValue} that is used
  1523. to represent missing data.")
  1524. (license license:expat)))
  1525. (define-public julia-deepdiffs
  1526. (package
  1527. (name "julia-deepdiffs")
  1528. (version "1.2.0")
  1529. (source
  1530. (origin
  1531. (method git-fetch)
  1532. (uri (git-reference
  1533. (url "https://github.com/ssfrr/DeepDiffs.jl")
  1534. (commit (string-append "v" version))))
  1535. (file-name (git-file-name name version))
  1536. (sha256
  1537. (base32 "1gsbxb1d67g05h5bvzz3swdfih6404jrydy724a8dvbdgqvm3sds"))))
  1538. (build-system julia-build-system)
  1539. (home-page "https://github.com/ssfrr/DeepDiffs.jl")
  1540. (synopsis "Compute and pretty-print diffs for data structures")
  1541. (description "@code{DeepDiffs.jl} provides the @code{deepdiff} function,
  1542. which finds and displays differences (diffs) between Julia data structures. It
  1543. supports @code{Vectors}, @code{Dicts}, and @code{String}s. When diffing
  1544. dictionaries where values associated with a particular key may change,
  1545. @code{deepdiff} will recurse into value to provide a more detailed diff.")
  1546. (license license:expat)))
  1547. (define-public julia-dictionaries
  1548. (package
  1549. (name "julia-dictionaries")
  1550. (version "0.3.10")
  1551. (source
  1552. (origin
  1553. (method git-fetch)
  1554. (uri (git-reference
  1555. (url "https://github.com/andyferris/Dictionaries.jl")
  1556. (commit (string-append "v" version))))
  1557. (file-name (git-file-name name version))
  1558. (sha256
  1559. (base32 "1mm43hm8hd6sgmkkpqhbqhvap7mpkjwzmz5algxi6manp580gkr5"))))
  1560. (build-system julia-build-system)
  1561. (propagated-inputs
  1562. (list julia-indexing))
  1563. (home-page "https://github.com/andyferris/Dictionaries.jl")
  1564. (synopsis "Alternative interface for dictionaries in Julia")
  1565. (description "This package provides an alternative interface for
  1566. dictionaries in Julia, for improved productivity and performance.")
  1567. (license license:expat)))
  1568. (define-public julia-distances
  1569. (package
  1570. (name "julia-distances")
  1571. (version "0.10.7")
  1572. (source
  1573. (origin
  1574. (method git-fetch)
  1575. (uri (git-reference
  1576. (url "https://github.com/JuliaStats/Distances.jl")
  1577. (commit (string-append "v" version))))
  1578. (file-name (git-file-name name version))
  1579. (sha256
  1580. (base32 "0sgrh3bzhmqqz0m28lmk66xhnl62i5r2miaiqml8nhbkaapbwc06"))))
  1581. (build-system julia-build-system)
  1582. (arguments
  1583. (list
  1584. #:phases
  1585. #~(modify-phases %standard-phases
  1586. (add-after 'link-depot 'skip-flakey-tests
  1587. (lambda _
  1588. ;; Some combination of these tests fail nondeterministically
  1589. ;; each of the times this package is built.
  1590. (substitute* "test/test_dists.jl"
  1591. (("test dyz ≥") "test_nowarn dyz ≥")
  1592. (("test dist\\(y, x") "test_nowarn dist(y, x")
  1593. (("test dist\\(z, x") "test_nowarn dist(z, x")
  1594. (("test dist\\(z, y") "test_nowarn dist(z, y"))
  1595. #$@(if (not (target-64bit?))
  1596. ;; A little too much precision
  1597. ;; Evaluated: 1.8839055991209719 === 1.8839055991209717
  1598. `((substitute* "test/test_dists.jl"
  1599. (("@test whamming\\(a, b, w\\) === sum")
  1600. "@test_skip whamming(a, b, w) === sum")))
  1601. '()))))))
  1602. (propagated-inputs
  1603. (list julia-statsapi))
  1604. (native-inputs
  1605. (list julia-offsetarrays
  1606. julia-unitful))
  1607. (home-page "https://github.com/JuliaStats/Distances.jl")
  1608. (synopsis "Julia package for evaluating distances (metrics) between vectors")
  1609. (description "A Julia package for evaluating distances(metrics) between
  1610. vectors. This package also provides optimized functions to compute column-wise
  1611. and pairwise distances, which are often substantially faster than a
  1612. straightforward loop implementation.")
  1613. (license license:expat)))
  1614. (define-public julia-docstringextensions
  1615. (package
  1616. (name "julia-docstringextensions")
  1617. (version "0.8.5")
  1618. (source
  1619. (origin
  1620. (method git-fetch)
  1621. (uri (git-reference
  1622. (url "https://github.com/JuliaDocs/DocStringExtensions.jl")
  1623. (commit (string-append "v" version))))
  1624. (file-name (git-file-name name version))
  1625. (sha256
  1626. (base32 "0fy4kfnfacyfmlly6nqxn77dk2gqw80b69zb4m1i0i39zv3cpqfb"))))
  1627. (build-system julia-build-system)
  1628. (arguments
  1629. (list #:tests? #f)) ; Tests try to read SSL certificates.
  1630. (home-page "https://juliadocs.github.io/DocStringExtensions.jl/latest/")
  1631. (synopsis "Extensions for Julia's docsystem")
  1632. (description "This package provides a collection of useful extensions for
  1633. Julia's built-in docsystem. These are features that are not yet mature enough
  1634. to be considered for inclusion in Base, or that have sufficiently niche use
  1635. cases that including them with the default Julia installation is not seen as
  1636. valuable enough at this time.")
  1637. (license license:expat)))
  1638. ;; By removing all the javascript and css downloads any HTML documentation
  1639. ;; produced by this package will not be very useful.
  1640. (define-public julia-documenter
  1641. (package
  1642. (name "julia-documenter")
  1643. (version "0.27.7")
  1644. (source
  1645. (origin
  1646. (method git-fetch)
  1647. (uri (git-reference
  1648. (url "https://github.com/JuliaDocs/Documenter.jl")
  1649. (commit (string-append "v" version))))
  1650. (file-name (git-file-name name version))
  1651. (sha256
  1652. (base32 "00ai3c24i3fkn5plmavampcxm0ijhwk0v5cn9xwm7rvbjnnvaaam"))))
  1653. (build-system julia-build-system)
  1654. (arguments
  1655. (list
  1656. #:phases
  1657. #~(modify-phases %standard-phases
  1658. (add-after 'link-depot 'patch-source
  1659. (lambda* (#:key inputs #:allow-other-keys)
  1660. (substitute* "src/Deps.jl"
  1661. (("pip install")
  1662. (string-append (search-input-file inputs "bin/pip")
  1663. " install")))))
  1664. (add-after 'link-depot 'fix-test-git-submodule
  1665. ;; Git v2.38.1 fixes security issues and changes the default
  1666. ;; behaviour of `git submodule`. This substitution is a backport
  1667. ;; of the upstream patch, not yet released, fixing the test suite.
  1668. ;; https://github.com/JuliaDocs/Documenter.jl/commit/b5a5c65d02d136743e7c18ffebf8baba900484fc
  1669. (lambda* (#:key inputs #:allow-other-keys)
  1670. (substitute* "test/utilities.jl"
  1671. (("submodule add")
  1672. "-c protocol.file.allow=always submodule add"))))
  1673. (add-after 'link-depot 'remove-javascript-downloads
  1674. (lambda _
  1675. (substitute* "src/Writers/HTMLWriter.jl"
  1676. (("cdnjs.cloudflare.com") "example.com"))
  1677. ;; Removing the javascript downloads causes these tests fail.
  1678. (substitute* "test/examples/tests.jl"
  1679. ((".*Main\\.examples_html_doc.*") "")
  1680. ((".*Main\\.examples_html_mathjax3_doc.*") "")))))))
  1681. (propagated-inputs
  1682. (list julia-ansicoloredprinters
  1683. julia-docstringextensions
  1684. julia-iocapture
  1685. julia-json))
  1686. (inputs
  1687. (list python-wrapper))
  1688. (native-inputs
  1689. (list git-minimal/pinned ;needed for the "Utilities" test
  1690. julia-documentermarkdown
  1691. julia-documentertools))
  1692. (home-page "https://juliadocs.github.io/Documenter.jl")
  1693. (synopsis "Documentation generator for Julia")
  1694. (description "This package provides a documentation generator for Julia.")
  1695. (license license:expat)))
  1696. (define julia-documenter-bootstrap
  1697. (package
  1698. (inherit julia-documenter)
  1699. (name "julia-documenter-bootstrap")
  1700. (arguments
  1701. (substitute-keyword-arguments (package-arguments julia-documenter)
  1702. ((#:phases phases)
  1703. `(modify-phases ,phases
  1704. (delete 'patch-source)))
  1705. ;; Not all dependencies available in bootstrap version.
  1706. ((#:tests? _ #f) #f)))
  1707. (inputs `())
  1708. (native-inputs `())))
  1709. (define-public julia-documentermarkdown
  1710. (package
  1711. (name "julia-documentermarkdown")
  1712. (version "0.2.2")
  1713. (source
  1714. (origin
  1715. (method git-fetch)
  1716. (uri (git-reference
  1717. (url "https://github.com/JuliaDocs/DocumenterMarkdown.jl")
  1718. (commit (string-append "v" version))))
  1719. (file-name (git-file-name name version))
  1720. (sha256
  1721. (base32 "0sx89hi5p2f8zi2rp5qrv06m270d90pxj5d2y5cxls1spax7wqx8"))))
  1722. (build-system julia-build-system)
  1723. (inputs
  1724. ;; We don't want to propagate the bootstrap version.
  1725. ;; Cycle with Documenter.jl in later versions.
  1726. (list julia-documenter-bootstrap))
  1727. (home-page "https://github.com/JuliaDocs/DocumenterMarkdown.jl")
  1728. (synopsis "Documenter's Markdown")
  1729. (description "This package enables the Markdown / MkDocs backend of
  1730. @code{Documenter.jl}.")
  1731. (license license:expat)))
  1732. (define-public julia-documentertools
  1733. (package
  1734. (name "julia-documentertools")
  1735. (version "0.1.13")
  1736. (source
  1737. (origin
  1738. (method git-fetch)
  1739. (uri (git-reference
  1740. (url "https://github.com/JuliaDocs/DocumenterTools.jl")
  1741. (commit (string-append "v" version))))
  1742. (file-name (git-file-name name version))
  1743. (sha256
  1744. (base32 "05p57p8xlkn42m1lv9gq4hl96vp7hpj19d51p828ai1rbpcpi3a6"))))
  1745. (build-system julia-build-system)
  1746. (arguments
  1747. (list #:tests? #f)) ; Tests require network.
  1748. (inputs
  1749. ;; We don't want to propagate the bootstrap version.
  1750. ;; Cycle with Documenter.jl in later versions.
  1751. (list julia-documenter-bootstrap))
  1752. (propagated-inputs
  1753. (list julia-docstringextensions
  1754. julia-gumbo
  1755. julia-sass))
  1756. (native-inputs
  1757. (list julia-example))
  1758. (home-page "https://github.com/JuliaDocs/DocumenterTools.jl")
  1759. (synopsis "Extra tools for setting up Documenter.jl")
  1760. (description "This package contains utilities for setting up documentation
  1761. generation with @code{Documenter.jl}.")
  1762. (license license:expat)))
  1763. (define-public julia-diffresults
  1764. (package
  1765. (name "julia-diffresults")
  1766. (version "1.0.3")
  1767. (source
  1768. (origin
  1769. (method git-fetch)
  1770. (uri (git-reference
  1771. (url "https://github.com/JuliaDiff/DiffResults.jl")
  1772. (commit (string-append "v" version))))
  1773. (file-name (git-file-name name version))
  1774. (sha256
  1775. (base32 "1w6p3yxajvclax5b9g7cr2jmbc7lvr5nk4gq0aljxdycdq1d2y3v"))))
  1776. (build-system julia-build-system)
  1777. (propagated-inputs
  1778. (list julia-staticarrays))
  1779. (home-page "https://github.com/JuliaDiff/DiffResults.jl")
  1780. (synopsis "In-place differentiation methods of primal values at multi-order")
  1781. (description "This package provides the @code{DiffResult} type, which can
  1782. be passed to in-place differentiation methods instead of an output buffer.")
  1783. (license license:expat)))
  1784. (define-public julia-diffrules
  1785. (package
  1786. (name "julia-diffrules")
  1787. (version "1.12.2")
  1788. (source
  1789. (origin
  1790. (method git-fetch)
  1791. (uri (git-reference
  1792. (url "https://github.com/JuliaDiff/DiffRules.jl")
  1793. (commit (string-append "v" version))))
  1794. (file-name (git-file-name name version))
  1795. (sha256
  1796. (base32 "0l983kzy01y7qqw42pi0ihpvx3yzfnwrhcmk38avw7y513qlm7vf"))))
  1797. (build-system julia-build-system)
  1798. (propagated-inputs
  1799. (list julia-irrationalconstants
  1800. julia-logexpfunctions
  1801. julia-nanmath
  1802. julia-specialfunctions))
  1803. (native-inputs
  1804. (list julia-finitedifferences))
  1805. (home-page "https://github.com/JuliaDiff/DiffRules.jl")
  1806. (synopsis "Primitive differentiation rules")
  1807. (description "This package provides primitive differentiation rules that
  1808. can be composed via various formulations of the chain rule. Using
  1809. @code{DiffRules}, new differentiation rules can defined, query whether or not
  1810. a given rule exists, and symbolically apply rules to simple Julia expressions.")
  1811. (license license:expat)))
  1812. (define-public julia-difftests
  1813. (package
  1814. (name "julia-difftests")
  1815. (version "0.1.1")
  1816. (source
  1817. (origin
  1818. (method git-fetch)
  1819. (uri (git-reference
  1820. (url "https://github.com/JuliaDiff/DiffTests.jl")
  1821. (commit (string-append "v" version))))
  1822. (file-name (git-file-name name version))
  1823. (sha256
  1824. (base32 "1rxpnd5zi3pxgdd38l5jm2sxc3q6p7g57fqgll2dsiin07y3my57"))))
  1825. (build-system julia-build-system)
  1826. (home-page "https://github.com/JuliaDiff/DiffTests.jl")
  1827. (synopsis "Common test functions for differentiation tools")
  1828. (description "This package contains a common suite of test functions for
  1829. stressing the robustness of differentiation tools.")
  1830. (license license:expat)))
  1831. (define-public julia-dualnumbers
  1832. (package
  1833. (name "julia-dualnumbers")
  1834. (version "0.6.5")
  1835. (source
  1836. (origin
  1837. (method git-fetch)
  1838. (uri (git-reference
  1839. (url "https://github.com/JuliaDiff/DualNumbers.jl")
  1840. (commit (string-append "v" version))))
  1841. (file-name (git-file-name name version))
  1842. (sha256
  1843. (base32 "05vr5wbzqpchnb96b3pmn67x196mbfnkv7r9bdlz3gm56if4awk5"))))
  1844. (build-system julia-build-system)
  1845. (arguments
  1846. (list
  1847. #:phases
  1848. #~(modify-phases %standard-phases
  1849. (add-after 'link-depot 'adjust-test-suite
  1850. (lambda _
  1851. (substitute* "test/runtests.jl"
  1852. ;; Seems to not play nicely with SpecialFunctions
  1853. ((".*isempty.*") "")))))))
  1854. (propagated-inputs
  1855. (list julia-calculus
  1856. julia-nanmath
  1857. julia-specialfunctions))
  1858. (home-page "https://github.com/JuliaDiff/DualNumbers.jl")
  1859. (synopsis "Represent dual numbers and for perform dual algebra")
  1860. (description "The @code{DualNumbers} Julia package defines the @code{Dual}
  1861. type to represent dual numbers, and supports standard mathematical operations on
  1862. them. Conversions and promotions are defined to allow performing operations on
  1863. combinations of dual numbers with predefined Julia numeric types.")
  1864. (license license:expat)))
  1865. (define-public julia-earthorientation
  1866. (package
  1867. (name "julia-earthorientation")
  1868. (version "0.7.1")
  1869. (source
  1870. (origin
  1871. (method git-fetch)
  1872. (uri (git-reference
  1873. (url "https://github.com/JuliaAstro/EarthOrientation.jl")
  1874. (commit (string-append "v" version))))
  1875. (file-name (git-file-name name version))
  1876. (sha256
  1877. (base32 "1fschx4qmfd83q0ymgbzqi1dl0drbh45cd7hlcbqnm9lfmw2d847"))))
  1878. (build-system julia-build-system)
  1879. (propagated-inputs
  1880. (list julia-leapseconds
  1881. julia-optionaldata
  1882. julia-remotefiles))
  1883. (home-page "https://github.com/JuliaAstro/EarthOrientation.jl")
  1884. (synopsis "Calculate Earth orientation parameters from IERS tables in Julia")
  1885. (description
  1886. "This package provides a functionality to calculate Earth orientation parameters
  1887. with data retrieved from @acronym{IERS, International Earth Rotation Service}.")
  1888. (license license:expat)))
  1889. (define-public julia-ellipsisnotation
  1890. (package
  1891. (name "julia-ellipsisnotation")
  1892. (version "1.6.0")
  1893. (source
  1894. (origin
  1895. (method git-fetch)
  1896. (uri (git-reference
  1897. (url "https://github.com/ChrisRackauckas/EllipsisNotation.jl")
  1898. (commit (string-append "v" version))))
  1899. (file-name (git-file-name name version))
  1900. (sha256
  1901. (base32 "0l4fc180chhxlq9d67122c0lgq2hfsxsmcgml2bfl2rnh13gya2b"))))
  1902. (build-system julia-build-system)
  1903. (propagated-inputs
  1904. (list julia-arrayinterface))
  1905. (home-page "https://github.com/ChrisRackauckas/EllipsisNotation.jl")
  1906. (synopsis "Ellipsis notation implementation")
  1907. (description "This implements the notation @code{..} for indexing arrays.
  1908. It's similar to the Python @code{...} in that it means \"all of the columns
  1909. before (or after)\".")
  1910. (license license:expat)))
  1911. (define-public julia-erfa
  1912. (package
  1913. (name "julia-erfa")
  1914. (version "1.1.0")
  1915. (source
  1916. (origin
  1917. (method git-fetch)
  1918. (uri (git-reference
  1919. (url "https://github.com/JuliaAstro/ERFA.jl")
  1920. (commit (string-append "v" version))))
  1921. (file-name (git-file-name name version))
  1922. (sha256
  1923. (base32 "1f63kyqpsx9n4dh54hzy1bvm3fpl4vf8wi1279vfiza3vhh2ggx5"))))
  1924. (build-system julia-build-system)
  1925. (propagated-inputs
  1926. (list julia-erfa-jll julia-staticarrays))
  1927. (home-page "https://github.com/JuliaAstro/ERFA.jl")
  1928. (synopsis "Julia wrapper for liberfa")
  1929. (description "This package provides a Julia wrapper for astronomical library ERFA.")
  1930. (license license:expat)))
  1931. (define-public julia-example
  1932. (let ((commit "f968c69dea24f851d0c7e686db23fa55826b5388"))
  1933. (package
  1934. (name "julia-example")
  1935. (version "0.5.4") ;tag not created upstream
  1936. (source
  1937. (origin
  1938. (method git-fetch)
  1939. (uri (git-reference
  1940. (url "https://github.com/JuliaLang/Example.jl")
  1941. (commit commit)))
  1942. (file-name (git-file-name name version))
  1943. (sha256
  1944. (base32 "1v3z0d6gh6wfbypffy9m9rhh36px6fm5wjzq0y6rbmc95r0qpqlx"))))
  1945. (build-system julia-build-system)
  1946. (home-page "https://github.com/JuliaLang/Example.jl")
  1947. (synopsis "Module providing examples")
  1948. (description "This package provides various examples.")
  1949. (license license:expat))))
  1950. ;; ExproniconLite.jl is autogenerated from this package.
  1951. (define-public julia-expronicon
  1952. (package
  1953. (name "julia-expronicon")
  1954. (version "0.6.10")
  1955. (source
  1956. (origin
  1957. (method git-fetch)
  1958. (uri (git-reference
  1959. (url "https://github.com/Roger-luo/Expronicon.jl")
  1960. (commit (string-append "v" version))))
  1961. (file-name (git-file-name name version))
  1962. (sha256
  1963. (base32 "0h8aaynqlxrkn8575k5vqmhzil4vvxchhf0bcxa6zwawp558gj2y"))))
  1964. (build-system julia-build-system)
  1965. (arguments
  1966. (list
  1967. #:phases
  1968. #~(modify-phases %standard-phases
  1969. (add-after 'link-depot 'skip-network-tests
  1970. (lambda _
  1971. (substitute* "test/runtests.jl"
  1972. ;; This test tries to access the Julia package registry.
  1973. ((".*expand\\.jl.*") "")))))))
  1974. (propagated-inputs
  1975. (list julia-mlstyle))
  1976. (native-inputs
  1977. (list julia-documenter))
  1978. (home-page "https://expronicon.rogerluo.dev/dev/")
  1979. (synopsis "Collective tools for metaprogramming on Julia Expr")
  1980. (description "This package provides a collection of tools for
  1981. metaprogramming on Julia Expr, the meta programming standard library for
  1982. @code{MLStyle}.")
  1983. (license license:expat)))
  1984. (define-public julia-exprtools
  1985. (package
  1986. (name "julia-exprtools")
  1987. (version "0.1.8")
  1988. (source
  1989. (origin
  1990. (method git-fetch)
  1991. (uri (git-reference
  1992. (url "https://github.com/invenia/ExprTools.jl")
  1993. (commit (string-append "v" version))))
  1994. (file-name (git-file-name name version))
  1995. (sha256
  1996. (base32 "0sxrhc5dz1v53zs8sym4csfy28ki00b7x7aihm2zmkrx48if63gb"))))
  1997. (build-system julia-build-system)
  1998. (home-page "https://github.com/invenia/ExprTools.jl")
  1999. (synopsis "Light-weight expression manipulation tools")
  2000. (description "@code{ExprTools} provides tooling for working with Julia
  2001. expressions during metaprogramming. This package aims to provide light-weight
  2002. performant tooling without requiring additional package dependencies.")
  2003. (license license:expat)))
  2004. (define-public julia-ffmpeg
  2005. (package
  2006. (name "julia-ffmpeg")
  2007. (version "0.4.1")
  2008. (source
  2009. (origin
  2010. (method git-fetch)
  2011. (uri (git-reference
  2012. (url "https://github.com/JuliaIO/FFMPEG.jl")
  2013. (commit (string-append "v" version))))
  2014. (file-name (git-file-name name version))
  2015. (sha256
  2016. (base32 "1ldxbp0kq3ip67x7sp82dz56aq4p5i0chspbgx2zgskr6jcbjj1b"))))
  2017. (build-system julia-build-system)
  2018. (propagated-inputs
  2019. (list julia-ffmpeg-jll
  2020. julia-x264-jll))
  2021. (home-page "https://github.com/JuliaIO/FFMPEG.jl")
  2022. (synopsis "Julia Package for ffmpeg")
  2023. (description "This package is made to be included into packages that just
  2024. need the ffmpeg binaries + executables, and don't want the overhead of
  2025. @code{VideoIO.jl}.")
  2026. (license license:expat)))
  2027. (define-public julia-fileio
  2028. (package
  2029. (name "julia-fileio")
  2030. (version "1.9.1")
  2031. (source
  2032. (origin
  2033. (method git-fetch)
  2034. (uri (git-reference
  2035. (url "https://github.com/JuliaIO/FileIO.jl")
  2036. (commit (string-append "v" version))))
  2037. (file-name (git-file-name name version))
  2038. (sha256
  2039. (base32 "1b18x43i737g5q41n9818xbnc2pgd98q1m6yw3h29yri0clg4gfx"))))
  2040. (build-system julia-build-system)
  2041. (arguments
  2042. (list
  2043. #:phases
  2044. #~(modify-phases %standard-phases
  2045. (delete 'reset-gzip-timestamps)
  2046. (add-after 'link-depot 'skip-network-tests
  2047. (lambda _
  2048. ;; These tests try to download audio/video files.
  2049. (substitute* "test/query.jl"
  2050. (("testset.*(MP4|OGG|MATROSKA).*" all)
  2051. (string-append all "return\n")))
  2052. (substitute* "test/loadsave.jl"
  2053. (("testset.*CSVFiles.*" all)
  2054. (string-append all "return\n")))
  2055. ;; This test tries to download a Julia package.
  2056. (substitute* "test/error_handling.jl"
  2057. (("testset.*Not installed.*" all)
  2058. (string-append all "return\n")))
  2059. ;; This test tries to write to the store.
  2060. ;; (Error says can't find User 0)
  2061. (substitute* "test/runtests.jl"
  2062. ((".*test_mimesave.*") "")))))))
  2063. (propagated-inputs
  2064. (list julia-requires))
  2065. (native-inputs
  2066. (list julia-colortypes
  2067. julia-filepathsbase
  2068. julia-http))
  2069. (home-page "https://github.com/JuliaIO/FileIO.jl")
  2070. (synopsis "Main Package for IO, loading all different kind of files")
  2071. (description "@code{FileIO} aims to provide a common framework for detecting
  2072. file formats and dispatching to appropriate readers/writers. The two core
  2073. functions in this package are called @code{load} and @code{save}, and offer
  2074. high-level support for formatted files (in contrast with Julia's low-level
  2075. @code{read} and @code{write}).")
  2076. (license license:expat)))
  2077. (define-public julia-filepathsbase
  2078. (package
  2079. (name "julia-filepathsbase")
  2080. (version "0.9.10")
  2081. (source
  2082. (origin
  2083. (method git-fetch)
  2084. (uri (git-reference
  2085. (url "https://github.com/rofinn/FilePathsBase.jl")
  2086. (commit (string-append "v" version))))
  2087. (file-name (git-file-name name version))
  2088. (sha256
  2089. (base32 "136wm4ik6isrdanmpi4gdr1qw0qhr15i925qzjxbawk5hnyzwng9"))))
  2090. (build-system julia-build-system)
  2091. (arguments
  2092. (list #:tests? #f)) ; Cycle with JLSO.jl
  2093. (home-page "https://github.com/rofinn/FilePathsBase.jl")
  2094. (synopsis "Filesystem path types in Julia")
  2095. (description "@code{FilePathsBase.jl} provides a type based approach to
  2096. working with filesystem paths in Julia.")
  2097. (license license:expat)))
  2098. (define-public julia-fillarrays
  2099. (package
  2100. (name "julia-fillarrays")
  2101. (version "0.13.6")
  2102. (source
  2103. (origin
  2104. (method git-fetch)
  2105. (uri (git-reference
  2106. (url "https://github.com/JuliaArrays/FillArrays.jl")
  2107. (commit (string-append "v" version))))
  2108. (file-name (git-file-name name version))
  2109. (sha256
  2110. (base32 "1c4i8awmw9qq8dqfhxwjh76mc1nlmzrl5j754fpnbajv8p49gdv5"))))
  2111. (build-system julia-build-system)
  2112. (propagated-inputs
  2113. (list julia-aqua))
  2114. (inputs ;required by tests
  2115. (list julia-staticarrays))
  2116. (home-page "https://github.com/JuliaArrays/FillArrays.jl")
  2117. (synopsis "Lazy matrix representation")
  2118. (description "This package lazily represents matrices filled with
  2119. a single entry, as well as identity matrices. This package exports the
  2120. following types: @code{Eye}, @code{Fill}, @code{Ones}, @code{Zeros},
  2121. @code{Trues} and @code{Falses}.")
  2122. (license license:expat)))
  2123. (define-public julia-finitediff
  2124. (package
  2125. (name "julia-finitediff")
  2126. (version "2.8.1")
  2127. (source
  2128. (origin
  2129. (method git-fetch)
  2130. (uri (git-reference
  2131. (url "https://github.com/JuliaDiff/FiniteDiff.jl")
  2132. (commit (string-append "v" version))))
  2133. (file-name (git-file-name name version))
  2134. (sha256
  2135. (base32 "105f6r0hq97n9mxf1nacmz94dpca66vzqj5p3zh4h0brshmggqnq"))))
  2136. (build-system julia-build-system)
  2137. (arguments
  2138. (list
  2139. #:phases
  2140. #~(modify-phases %standard-phases
  2141. (add-before 'check 'pre-check
  2142. (lambda _
  2143. ;; We don't want to run all the tests; the Downstream tests
  2144. ;; try to download the package registry.
  2145. (setenv "GROUP" "Core"))))))
  2146. (propagated-inputs
  2147. (list julia-arrayinterface
  2148. julia-requires
  2149. julia-staticarrays))
  2150. (native-inputs
  2151. (list julia-bandedmatrices
  2152. julia-blockbandedmatrices
  2153. julia-safetestsets))
  2154. (home-page "https://github.com/JuliaDiff/FiniteDiff.jl")
  2155. (synopsis "Calculations of gradients, Jacobians, and Hessians")
  2156. (description "This package is for calculating derivatives, gradients,
  2157. Jacobians, Hessians, etc. numerically. This library is for maximizing speed
  2158. while giving a usable interface to end users in a way that specializes on array
  2159. types and sparsity.")
  2160. (license license:expat)))
  2161. (define-public julia-finitedifferences
  2162. (package
  2163. (name "julia-finitedifferences")
  2164. (version "0.12.17")
  2165. (source
  2166. (origin
  2167. (method git-fetch)
  2168. (uri (git-reference
  2169. (url "https://github.com/JuliaDiff/FiniteDifferences.jl")
  2170. (commit (string-append "v" version))))
  2171. (file-name (git-file-name name version))
  2172. (sha256
  2173. (base32 "09nsf9cgk49yrvprflnhd9h5rrgs280rgj8sad3csghxdx6jqk5c"))))
  2174. (build-system julia-build-system)
  2175. (arguments
  2176. (list
  2177. #:phases
  2178. (if (target-x86-32?)
  2179. #~(modify-phases %standard-phases
  2180. (add-after 'unpack 'remove-failing-test-i686
  2181. (lambda _
  2182. ;; Machine Precision incorrectly handled
  2183. (substitute* "test/methods.jl"
  2184. (("@test central_fdm\\(15, 5, adapt=2\\)\\(exp, 1.0\\)")
  2185. "@test_broken central_fdm(15, 5, adapt=2)(exp, 1.0)")))))
  2186. #~%standard-phases)))
  2187. (inputs
  2188. (list julia-benchmarktools))
  2189. (propagated-inputs
  2190. (list julia-chainrulescore
  2191. julia-richardson
  2192. julia-staticarrays))
  2193. (home-page "https://github.com/JuliaDiff/FiniteDifferences.jl")
  2194. (synopsis "Estimates derivatives with finite differences")
  2195. (description "This package calculates approximate derivatives numerically
  2196. using finite difference.")
  2197. (license license:expat)))
  2198. (define-public julia-fitsio
  2199. (package
  2200. (name "julia-fitsio")
  2201. (version "0.17.0")
  2202. (source
  2203. (origin
  2204. (method git-fetch)
  2205. (uri (git-reference
  2206. (url "https://github.com/JuliaAstro/FITSIO.jl")
  2207. (commit (string-append "v" version))))
  2208. (file-name (git-file-name name version))
  2209. (sha256
  2210. (base32 "10w7cdb2cvcwpkcfdz2fwl4ji5rfdv8w9msc9gfd8d34k58bk8c5"))))
  2211. (build-system julia-build-system)
  2212. (native-inputs
  2213. (list julia-aqua julia-orderedcollections))
  2214. (propagated-inputs
  2215. (list julia-cfitsio julia-reexport julia-tables))
  2216. (home-page "https://github.com/JuliaAstro/CFITSIO.jl")
  2217. (synopsis "Astronomical FITS file support for Julia")
  2218. (description "This package provides Julia implementation for reading and
  2219. writing @acronym{FITS, Flexible Image Transport System} files, based on the
  2220. @code{cfitsio} library.")
  2221. (license license:expat)))
  2222. (define-public julia-fixedpointnumbers
  2223. (let ((commit "59ee94b93f2f1ee75544ef44187fc0e440cd8015")
  2224. (revision "1"))
  2225. (package
  2226. (name "julia-fixedpointnumbers")
  2227. (version (git-version "0.8.4" revision commit))
  2228. (source
  2229. (origin
  2230. (method git-fetch)
  2231. (uri (git-reference
  2232. (url "https://github.com/JuliaMath/FixedPointNumbers.jl")
  2233. (commit commit)))
  2234. (file-name (git-file-name name version))
  2235. (sha256
  2236. (base32 "1ghriy7p2fj7mwdx11ssjg28jmwz8pi13c3j8p1grvwb4nvc0jnq"))))
  2237. (build-system julia-build-system)
  2238. (arguments
  2239. (list #:tests? #f)) ; Cycle with julia-documenter
  2240. (propagated-inputs
  2241. (list julia-compat))
  2242. (home-page "https://github.com/JuliaMath/FixedPointNumbers.jl")
  2243. (synopsis "Fixed point types for Julia")
  2244. (description "@code{FixedPointNumbers.jl} implements fixed-point number
  2245. types for Julia. A fixed-point number represents a fractional, or
  2246. non-integral, number. In contrast with the more widely known floating-point
  2247. numbers, with fixed-point numbers the decimal point doesn't \"float\":
  2248. fixed-point numbers are effectively integers that are interpreted as being
  2249. scaled by a constant factor. Consequently, they have a fixed number of
  2250. digits (bits) after the decimal (radix) point.")
  2251. (license license:expat))))
  2252. (define-public julia-formatting
  2253. (package
  2254. (name "julia-formatting")
  2255. (version "0.4.2")
  2256. (source
  2257. (origin
  2258. (method git-fetch)
  2259. (uri (git-reference
  2260. (url "https://github.com/JuliaIO/Formatting.jl")
  2261. (commit (string-append "v" version))))
  2262. (file-name (git-file-name name version))
  2263. (sha256
  2264. (base32 "0ma3q9my51rr38bb5712xkc4h3rq0wsfjb4ac6mdh9ywn8rqvrmh"))))
  2265. (build-system julia-build-system)
  2266. (home-page "https://github.com/JuliaIO/Formatting.jl")
  2267. (synopsis "Julia package to provide Python-like formatting support")
  2268. (description "This package offers Python-style general formatting and
  2269. c-style numerical formatting.")
  2270. (license license:expat)))
  2271. (define-public julia-forwarddiff
  2272. (package
  2273. (name "julia-forwarddiff")
  2274. (version "0.10.34")
  2275. (source
  2276. (origin
  2277. (method git-fetch)
  2278. (uri (git-reference
  2279. (url "https://github.com/JuliaDiff/ForwardDiff.jl")
  2280. (commit (string-append "v" version))))
  2281. (file-name (git-file-name name version))
  2282. (sha256
  2283. (base32 "1lwjw2jzkffwk06hfc30vxhv36ng3gf12qjc43swmqiakkd3m5jx"))))
  2284. (build-system julia-build-system)
  2285. (arguments
  2286. ;; XXXX: Unexpected and non-deterministic failures for i686, e.g.,
  2287. ;; Expression: dual_isapprox(FDNUM ^ PRIMAL, exp(PRIMAL * log(FDNUM)))
  2288. ;; ERROR: LoadError: LoadError: There was an error during testing
  2289. ;; Disable as stopgap.
  2290. (list #:tests? (not (or (%current-target-system)
  2291. (target-x86-32?)))))
  2292. (inputs ;required for tests
  2293. (list julia-calculus
  2294. julia-difftests))
  2295. (propagated-inputs
  2296. (list julia-calculus
  2297. julia-commonsubexpressions
  2298. julia-diffresults
  2299. julia-diffrules
  2300. julia-difftests
  2301. julia-nanmath
  2302. julia-specialfunctions
  2303. julia-staticarrays))
  2304. (home-page "https://github.com/JuliaDiff/ForwardDiff.jl")
  2305. (synopsis "Methods to take multidimensional derivatives")
  2306. (description "This package implements methods to take derivatives,
  2307. gradients, Jacobians, Hessians, and higher-order derivatives of native Julia
  2308. functions (or any callable object, really) using forward mode automatic
  2309. differentiation (AD).")
  2310. (license license:expat)))
  2311. (define-public julia-functionwrappers
  2312. (package
  2313. (name "julia-functionwrappers")
  2314. (version "1.1.2")
  2315. (source
  2316. (origin
  2317. (method git-fetch)
  2318. (uri (git-reference
  2319. (url "https://github.com/yuyichao/FunctionWrappers.jl")
  2320. (commit (string-append "v" version))))
  2321. (file-name (git-file-name name version))
  2322. (sha256
  2323. (base32 "02jilpjr7px6138dx2w7ixricvfgsxqdk84d9dgviranibhnjcxa"))))
  2324. (build-system julia-build-system)
  2325. (arguments
  2326. (list
  2327. #:phases
  2328. #~(modify-phases %standard-phases
  2329. (add-after 'link-depot 'adjust-tests
  2330. (lambda _
  2331. (substitute* "test/runtests.jl"
  2332. (("testset \\\"Abstract.*" all)
  2333. (string-append all "return\n"))))))))
  2334. (home-page "https://github.com/yuyichao/FunctionWrappers.jl")
  2335. (synopsis "Type stable and efficient wrapper of arbitrary functions")
  2336. (description "This package provides a type stable and efficient wrapper of
  2337. arbitrary functions.")
  2338. (license license:expat)))
  2339. (define-public julia-functors
  2340. (package
  2341. (name "julia-functors")
  2342. (version "0.4.1")
  2343. (source
  2344. (origin
  2345. (method git-fetch)
  2346. (uri (git-reference
  2347. (url "https://github.com/FluxML/Functors.jl")
  2348. (commit (string-append "v" version))))
  2349. (file-name (git-file-name name version))
  2350. (sha256
  2351. (base32 "00rzbj2rs2lq91wz8qyxq14bg7p9i49dq7y44fvxn6jaikha2ymw"))))
  2352. (build-system julia-build-system)
  2353. (native-inputs
  2354. (list julia-documenter
  2355. julia-staticarrays
  2356. julia-zygote))
  2357. (home-page "https://fluxml.ai/Functors.jl/stable/")
  2358. (synopsis "Design pattern for structures as in machine learning")
  2359. (description "This package provides tools to express a design pattern for
  2360. dealing with large/ nested structures, as in machine learning and
  2361. optimisation. For large machine learning models it can be cumbersome or
  2362. inefficient to work with parameters as one big, flat vector, and structs help
  2363. in managing complexity; but it is also desirable to easily operate over all
  2364. parameters at once, e.g. for changing precision or applying an optimiser
  2365. update step.")
  2366. (license license:expat)))
  2367. (define-public julia-fuzzycompletions
  2368. (package
  2369. (name "julia-fuzzycompletions")
  2370. (version "0.4.1")
  2371. (source
  2372. (origin
  2373. (method git-fetch)
  2374. (uri (git-reference
  2375. (url "https://github.com/JunoLab/FuzzyCompletions.jl")
  2376. (commit (string-append "v" version))))
  2377. (file-name (git-file-name name version))
  2378. (sha256
  2379. (base32 "07sv88c472n6w4x7diy952igbcfm1s104ysnnvprld83312siw06"))))
  2380. (build-system julia-build-system)
  2381. (arguments
  2382. (list
  2383. #:phases
  2384. #~(modify-phases %standard-phases
  2385. (add-after 'link-depot 'skip-failing-test
  2386. (lambda _
  2387. (substitute* "test/runtests.jl"
  2388. ((".*RPLE.*") "")))))))
  2389. (home-page "https://github.com/JunoLab/FuzzyCompletions.jl")
  2390. (synopsis "Fuzzy completion provider for Julia")
  2391. (description
  2392. "FuzzyCompletions provides fuzzy completions for a Julia runtime session.")
  2393. (license license:expat)))
  2394. (define-public julia-genericlinearalgebra
  2395. (package
  2396. (name "julia-genericlinearalgebra")
  2397. (version "0.2.5")
  2398. (source
  2399. (origin
  2400. (method git-fetch)
  2401. (uri (git-reference
  2402. (url "https://github.com/JuliaLinearAlgebra/GenericLinearAlgebra.jl")
  2403. (commit (string-append "v" version))))
  2404. (file-name (git-file-name name version))
  2405. (sha256
  2406. (base32 "0ndwypa397z3pwzdgc3s9plaqlqf63g3d4px5pvym5psgr6lnm3l"))))
  2407. (build-system julia-build-system)
  2408. (arguments
  2409. (list
  2410. #:phases
  2411. #~(modify-phases %standard-phases
  2412. (add-after 'link-depot 'adjust-test-suite
  2413. (lambda _
  2414. (substitute* "test/runtests.jl"
  2415. ((".*lapack.*") "")))))))
  2416. (native-inputs
  2417. (list julia-quaternions))
  2418. (home-page "https://github.com/JuliaLinearAlgebra/GenericLinearAlgebra.jl")
  2419. (synopsis "Generic numerical linear algebra")
  2420. (description "The purpose of this package is partly to extend linear algebra
  2421. functionality in base to cover generic element types, e.g. @code{BigFloat} and
  2422. @code{Quaternion}, and partly to be a place to experiment with fast linear
  2423. algebra routines written in Julia (except for optimized BLAS).")
  2424. (license license:expat)))
  2425. (define-public julia-genericschur
  2426. (package
  2427. (name "julia-genericschur")
  2428. (version "0.5.3")
  2429. (source
  2430. (origin
  2431. (method git-fetch)
  2432. (uri (git-reference
  2433. (url "https://github.com/RalphAS/GenericSchur.jl")
  2434. (commit (string-append "v" version))))
  2435. (file-name (git-file-name name version))
  2436. (sha256
  2437. (base32 "02f2azi6036ca8nlgyvvfagwbks8jxfz4k0d8a709ixr1n0ylwap"))))
  2438. (build-system julia-build-system)
  2439. (arguments
  2440. (list
  2441. #:phases
  2442. #~(modify-phases %standard-phases
  2443. (add-after 'link-depot 'adjust-test-suite
  2444. (lambda _
  2445. (substitute* "test/complex.jl"
  2446. ;; expected Vector{Int32,1}, got a value of type Vector{Int64,1}
  2447. (("A = _example") "#A = _example")
  2448. (("schurtest\\(A,20\\)") ""))
  2449. (substitute* "test/runtests.jl"
  2450. ;; Test errors relating to liblapack.so
  2451. ((".*complex\\.jl.*") "")
  2452. ((".*real\\.jl.*") "")
  2453. ;; GenericSVD is deprecated upstream
  2454. ((".*gordschur\\.jl.*") "")))))))
  2455. (home-page "https://github.com/RalphAS/GenericSchur.jl")
  2456. (synopsis "Schur decomposition of matrices with generic element types")
  2457. (description "The Schur decomposition is the workhorse for eigensystem
  2458. analysis of dense matrices. The diagonal eigen-decomposition of normal
  2459. (especially Hermitian) matrices is an important special case, but for non-normal
  2460. matrices the Schur form is often more useful.")
  2461. (license license:expat)))
  2462. (define-public julia-geometrybasics
  2463. (package
  2464. (name "julia-geometrybasics")
  2465. (version "0.4.2")
  2466. (source
  2467. (origin
  2468. (method git-fetch)
  2469. (uri (git-reference
  2470. (url "https://github.com/JuliaGeometry/GeometryBasics.jl")
  2471. (commit (string-append "v" version))))
  2472. (file-name (git-file-name name version))
  2473. (sha256
  2474. (base32 "0kxn7gzv4sm3017qbng70iqb4wzy1k2fj5w6lkz1kn7lx7z7m33x"))))
  2475. (build-system julia-build-system)
  2476. (arguments
  2477. (list
  2478. #:phases
  2479. #~(modify-phases %standard-phases
  2480. (add-after 'link-depot 'remove-earcut
  2481. (lambda _
  2482. (substitute* '("Project.toml"
  2483. "src/GeometryBasics.jl")
  2484. ((".*EarCut.*") ""))))
  2485. (add-after 'link-depot 'skip-incompatible-test
  2486. (lambda _
  2487. (substitute* "test/runtests.jl"
  2488. (("@testset.*MetaT and heterogeneous data.*" all)
  2489. (string-append all "return\n")))))
  2490. #$@(if (target-64bit?)
  2491. '()
  2492. '((add-after 'unpack 'fix-tests-int32-i686
  2493. (lambda _
  2494. (substitute* "test/runtests.jl"
  2495. (("Int64") "Int32")))))))))
  2496. (propagated-inputs
  2497. (list julia-itertools
  2498. julia-staticarrays
  2499. julia-structarrays
  2500. julia-tables))
  2501. (native-inputs
  2502. (list julia-offsetarrays))
  2503. (home-page "https://github.com/JuliaGeometry/GeometryBasics.jl")
  2504. (synopsis "Basic Geometry Types")
  2505. (description "This package aims to offer a standard set of Geometry types,
  2506. which easily work with metadata, query frameworks on geometries and different
  2507. memory layouts. The aim is to create a solid basis for Graphics/Plotting,
  2508. finite elements analysis, Geo applications, and general geometry manipulations
  2509. - while offering a Julian API, that still allows performant C-interop.")
  2510. (license license:expat)))
  2511. (define-public julia-gpuarrays
  2512. (package
  2513. (name "julia-gpuarrays")
  2514. (version "8.1.3")
  2515. (source
  2516. (origin
  2517. (method git-fetch)
  2518. (uri (git-reference
  2519. (url "https://github.com/JuliaGPU/GPUArrays.jl")
  2520. (commit (string-append "v" version))))
  2521. (file-name (git-file-name name version))
  2522. (sha256
  2523. (base32 "129q8m94b2xq3vij28pkb7dry3r7qbiqrz72a26ma9kilcr35gk4"))))
  2524. (build-system julia-build-system)
  2525. (inputs
  2526. (list julia-adapt))
  2527. (home-page "https://github.com/JuliaGPU/GPUArrays.jl")
  2528. (synopsis "Reusable GPU array functionality for various GPU backends")
  2529. (description "This package is the counterpart of AbstractArray interface,
  2530. but for GPU array types. It provides functionality and tooling to speed-up
  2531. development of new GPU array types. This package is not intended for end
  2532. users; instead, you should use one of the packages that builds on
  2533. @code{GPUArrays.jl}, such as @code{CUDA.jl}, @code{oneAPI.jl} or
  2534. @code{AMDGPU.jl}.")
  2535. (license license:expat)))
  2536. (define-public julia-gr
  2537. (package
  2538. (name "julia-gr")
  2539. (version "0.58.1")
  2540. (source
  2541. (origin
  2542. (method git-fetch)
  2543. (uri (git-reference
  2544. (url "https://github.com/jheinen/GR.jl")
  2545. (commit (string-append "v" version))))
  2546. (file-name (git-file-name name version))
  2547. (sha256
  2548. (base32 "18zxa1w2wmrf44c5l10qbh99zjdp7h94gxlymh47cf5kj5fc4xmx"))))
  2549. (build-system julia-build-system)
  2550. (propagated-inputs
  2551. (list julia-gr-jll))
  2552. (home-page "https://github.com/jheinen/GR.jl")
  2553. (synopsis "Plotting for Julia based on GR")
  2554. (description "This module provides a Julia interface to GR, a framework for
  2555. visualisation applications.")
  2556. (license license:expat)))
  2557. (define-public julia-graphics
  2558. (package
  2559. (name "julia-graphics")
  2560. (version "1.1.2")
  2561. (source
  2562. (origin
  2563. (method git-fetch)
  2564. (uri (git-reference
  2565. (url "https://github.com/JuliaGraphics/Graphics.jl")
  2566. (commit (string-append "v" version))))
  2567. (file-name (git-file-name name version))
  2568. (sha256
  2569. (base32 "083fppcbmchgnqp4xqdsd4asavq51jq31w8ak35ns701534hr82p"))))
  2570. (build-system julia-build-system)
  2571. (propagated-inputs
  2572. (list julia-colors
  2573. julia-nanmath))
  2574. (home-page "https://github.com/JuliaGraphics/Graphics.jl")
  2575. (synopsis "Base graphics in Julia")
  2576. (description "@code{Graphics.jl} is an abstraction layer for graphical
  2577. operations in Julia.")
  2578. (license license:expat)))
  2579. (define-public julia-gumbo
  2580. (package
  2581. (name "julia-gumbo")
  2582. (version "0.8.0")
  2583. (source
  2584. (origin
  2585. (method git-fetch)
  2586. (uri (git-reference
  2587. (url "https://github.com/JuliaWeb/Gumbo.jl")
  2588. (commit (string-append "v" version))))
  2589. (file-name (git-file-name name version))
  2590. (sha256
  2591. (base32 "1g22dv3v7caakspv3pdahnqn937fzzsg9y87rj72hid9g8lxl1gm"))))
  2592. (build-system julia-build-system)
  2593. (propagated-inputs
  2594. (list julia-abstracttrees
  2595. julia-gumbo-jll))
  2596. (home-page "https://github.com/JuliaWeb/Gumbo.jl")
  2597. (synopsis "Julia wrapper around Google's gumbo C library for parsing HTML")
  2598. (description "@code{Gumbo.jl} is a Julia wrapper around Google's gumbo
  2599. library for parsing HTML.")
  2600. (license license:expat)))
  2601. (define-public julia-http
  2602. (package
  2603. (name "julia-http")
  2604. (version "0.9.17")
  2605. (source
  2606. (origin
  2607. (method git-fetch)
  2608. (uri (git-reference
  2609. (url "https://github.com/JuliaWeb/HTTP.jl")
  2610. (commit (string-append "v" version))))
  2611. (file-name (git-file-name name version))
  2612. (sha256
  2613. (base32 "1ynzcl30sf5r42l75l5x1a8z0643hlck2kysyhag9795gzafxzv3"))))
  2614. (build-system julia-build-system)
  2615. (arguments
  2616. (list
  2617. #:phases
  2618. #~(modify-phases %standard-phases
  2619. (add-before 'install 'disable-network-tests
  2620. (lambda _
  2621. (substitute* "test/runtests.jl"
  2622. (("\"async.jl") "# \"async.jl")
  2623. (("\"client.jl") "# \"client.jl"))
  2624. (substitute* "test/aws4.jl"
  2625. (("@testset.*HTTP.request with AWS authentication.*" all)
  2626. (string-append all "return\n")))
  2627. (substitute* "test/insert_layers.jl"
  2628. (("@testset.*Inserted final layer runs handler.*" all)
  2629. (string-append all "return\n")))
  2630. (substitute* "test/multipart.jl"
  2631. (("@testset \"Setting of Content-Type.*" all)
  2632. (string-append all "return\n"))
  2633. (("@testset \"Deprecation of .*" all)
  2634. (string-append all "return\n")))
  2635. (substitute* "test/websockets.jl"
  2636. (("@testset.*External Host.*" all)
  2637. (string-append all "return\n")))
  2638. (substitute* "test/messages.jl"
  2639. (("@testset.*Read methods.*" all)
  2640. (string-append all "return\n"))
  2641. (("@testset.*Body - .*" all)
  2642. (string-append all "return\n"))
  2643. (("@testset.*Write to file.*" all)
  2644. (string-append all "return\n")))
  2645. (substitute* "test/cookies.jl"
  2646. (("@testset.*Set-Cookie casing.*" all)
  2647. (string-append all "return\n"))))))))
  2648. (propagated-inputs
  2649. (list julia-inifile
  2650. julia-mbedtls
  2651. julia-uris))
  2652. ;; required for tests
  2653. (inputs
  2654. (list julia-json
  2655. julia-bufferedstreams))
  2656. (home-page "https://juliaweb.github.io/HTTP.jl/")
  2657. (synopsis "HTTP support for Julia")
  2658. (description "@code{HTTP.jl} is a Julia library for HTTP Messages,
  2659. implementing both a client and a server.")
  2660. (license license:expat)))
  2661. (define-public julia-ifelse
  2662. (package
  2663. (name "julia-ifelse")
  2664. (version "0.1.0")
  2665. (source
  2666. (origin
  2667. (method git-fetch)
  2668. (uri (git-reference
  2669. (url "https://github.com/sciml/ifelse.jl")
  2670. (commit (string-append "v" version))))
  2671. (file-name (git-file-name name version))
  2672. (sha256
  2673. (base32 "1wrw842r8708fryf2ihp9mkmdrg27saa9nix2c31vs995k2fgr9w"))))
  2674. (build-system julia-build-system)
  2675. (home-page "https://github.com/sciml/ifelse.jl")
  2676. (synopsis "Function form of the if-else conditional statement")
  2677. (description "This package provides a convenient function form of the
  2678. conditional ifelse. It is similar to @code{Core.ifelse} but it is extendable.")
  2679. (license license:expat)))
  2680. (define-public julia-imageaxes
  2681. (package
  2682. (name "julia-imageaxes")
  2683. (version "0.6.10")
  2684. (source
  2685. (origin
  2686. (method git-fetch)
  2687. (uri (git-reference
  2688. (url "https://github.com/JuliaImages/ImageAxes.jl")
  2689. (commit (string-append "v" version))))
  2690. (file-name (git-file-name name version))
  2691. (sha256
  2692. (base32 "15f3y46vcr88fplr7rlibrm3k852p8rzwid5dgmbhc03a8xqd50s"))))
  2693. (build-system julia-build-system)
  2694. (arguments
  2695. (list
  2696. #:phases
  2697. #~(modify-phases %standard-phases
  2698. (add-after 'unpack 'adjust-tests
  2699. (lambda _
  2700. (substitute* "test/runtests.jl"
  2701. ;; Skip the constantly failing grayscale test.
  2702. (("@test summary") "@test_broken summary")))))))
  2703. (propagated-inputs
  2704. (list julia-axisarrays
  2705. julia-imagebase
  2706. julia-imagecore
  2707. julia-reexport
  2708. julia-simpletraits))
  2709. (native-inputs
  2710. (list julia-aqua
  2711. julia-documenter
  2712. julia-unitful))
  2713. (home-page "https://github.com/JuliaImages/ImageAxes.jl")
  2714. (synopsis "Julia package for giving \"meaning\" to the axes of an image")
  2715. (description "This small package supports the representation of images as
  2716. @code{AxisArrays} to endow the axes with \"meaning,\" and makes programming with
  2717. such arrays easy via traits.")
  2718. (license license:expat)))
  2719. (define-public julia-imagebase
  2720. (package
  2721. (name "julia-imagebase")
  2722. (version "0.1.5")
  2723. (source
  2724. (origin
  2725. (method git-fetch)
  2726. (uri (git-reference
  2727. (url "https://github.com/JuliaImages/ImageBase.jl")
  2728. (commit (string-append "v" version))))
  2729. (file-name (git-file-name name version))
  2730. (sha256
  2731. (base32 "00gi268jsyhlkadkkbyiffph6c8yb7zw34px76n6hs7dkfzp6jm3"))))
  2732. (build-system julia-build-system)
  2733. (arguments
  2734. (list #:tests? #f)) ; Cycle with ImageMagick.jl.
  2735. (propagated-inputs
  2736. (list julia-imagecore
  2737. julia-reexport))
  2738. ;(native-inputs
  2739. ; (list julia-aqua
  2740. ; julia-documenter
  2741. ; julia-imagefiltering
  2742. ; julia-imageio
  2743. ; julia-imagemagick
  2744. ; julia-offsetarrays
  2745. ; jula-statistics
  2746. ; julia-testimages))
  2747. (home-page "https://github.com/JuliaImages/ImageBase.jl")
  2748. (synopsis "Wrapper package around ImageCore")
  2749. (description "This is a twin package to @code{ImageCore} with functions that
  2750. are used among many of the packages in JuliaImages. The main purpose of this
  2751. package is to reduce unnecessary compilation overhead from external
  2752. dependencies.")
  2753. (license license:expat)))
  2754. (define-public julia-imagecore
  2755. (package
  2756. (name "julia-imagecore")
  2757. (version "0.9.4")
  2758. (source
  2759. (origin
  2760. (method git-fetch)
  2761. (uri (git-reference
  2762. (url "https://github.com/JuliaImages/ImageCore.jl")
  2763. (commit (string-append "v" version))))
  2764. (file-name (git-file-name name version))
  2765. (sha256
  2766. (base32 "0a6m3cszgh2bfsgs08i64f1h1pwh6by4267rvwyvdk470z0ayc8q"))))
  2767. (build-system julia-build-system)
  2768. (arguments
  2769. (list #:tests? #f)) ; Cycle with ImageMagick.jl.
  2770. (propagated-inputs
  2771. (list julia-abstractffts
  2772. julia-colors
  2773. julia-colorvectorspace
  2774. julia-fixedpointnumbers
  2775. julia-graphics
  2776. julia-mappedarrays
  2777. julia-mosaicviews
  2778. julia-offsetarrays
  2779. julia-paddedviews
  2780. julia-reexport))
  2781. ;(native-inputs
  2782. ; `(("julia-aqua" ,julia-aqua)
  2783. ; ("julia-blockarrays" ,julia-blockarrays)
  2784. ; ("julia-documenter" ,julia-documenter)
  2785. ; ("julia-fftw" ,julia-fftw)
  2786. ; ("julia-imageinterminal" ,julia-imageinterminal)
  2787. ; ("julia-imagemagick" ,julia-imagemagick)
  2788. ; ("julia-referencetests" ,julia-referencetests)
  2789. ; ("julia-statistics" ,julia-statistics)))
  2790. (home-page "https://github.com/JuliaImages/ImageCore.jl")
  2791. (synopsis "Julia types for representing images")
  2792. (description "@code{ImageCore} is the lowest-level component of the system
  2793. of packages designed to support image processing and computer vision.")
  2794. (license license:expat)))
  2795. (define-public julia-imageinterminal
  2796. (package
  2797. (name "julia-imageinterminal")
  2798. (version "0.4.7")
  2799. (source
  2800. (origin
  2801. (method git-fetch)
  2802. (uri (git-reference
  2803. (url "https://github.com/JuliaImages/ImageInTerminal.jl")
  2804. (commit (string-append "v" version))))
  2805. (file-name (git-file-name name version))
  2806. (sha256
  2807. (base32 "0bbpzi7bv8jdiggq1wmcn67vnf96qagvwg0fk95s125wy5980xsl"))))
  2808. (build-system julia-build-system)
  2809. (arguments
  2810. (list #:tests? #f)) ; Cycle with ReferenceTests.jl.
  2811. (propagated-inputs
  2812. (list julia-crayons
  2813. julia-imagebase
  2814. julia-imagecore
  2815. julia-requires))
  2816. ;(native-inputs
  2817. ; `(("julia-coordinatetransformations" ,julia-coordinatetransformations)
  2818. ; ("julia-imagemagick" ,julia-imagemagick)
  2819. ; ("julia-imagetransformations" ,julia-imagetransformations)
  2820. ; ("julia-offsetarrays" ,julia-offsetarrays)
  2821. ; ("julia-referencetests" ,julia-referencetests)
  2822. ; ("julia-rotations" ,julia-rotations)
  2823. ; ("julia-sparsearrays" ,julia-sparsearrays)
  2824. ; ("julia-testimages" ,julia-testimages)))
  2825. (home-page "https://github.com/JuliaImages/ImageInTerminal.jl")
  2826. (synopsis "Julia package for displaying images in the terminal")
  2827. (description "@code{ImageInTerminal.jl} is a drop-in package that once
  2828. imported changes a how a single @code{Colorant} and whole @code{Colorant} arrays
  2829. (i.e. Images) are displayed in the interactive REPL. The displayed images will
  2830. be downscaled to fit into the size of your active terminal session.")
  2831. (license license:expat)))
  2832. (define-public julia-imagemagick
  2833. (package
  2834. (name "julia-imagemagick")
  2835. (version "1.2.1")
  2836. (source
  2837. (origin
  2838. (method git-fetch)
  2839. (uri (git-reference
  2840. (url "https://github.com/JuliaIO/ImageMagick.jl")
  2841. (commit (string-append "v" version))))
  2842. (file-name (git-file-name name version))
  2843. (sha256
  2844. (base32 "05vzv4jsj3l9pv6yrix28hlw7wnag0mqdfjwv8shn4x71hcfxl1p"))))
  2845. (build-system julia-build-system)
  2846. (arguments
  2847. (list
  2848. #:phases
  2849. #~(modify-phases %standard-phases
  2850. (add-after 'link-depot 'skip-failing-test
  2851. (lambda _
  2852. ;; These tests try to download from the imagemagick.org
  2853. (substitute* "test/runtests.jl"
  2854. ((".*readremote\\.jl.*") ""))
  2855. ;; Tests with the color gray are hard.
  2856. (substitute* "test/constructed_images.jl"
  2857. (("test (b == aa)" _ test) (string-append "test_nowarn " test))
  2858. (("test (B == map)" _ test) (string-append "test_nowarn " test))))))))
  2859. (propagated-inputs
  2860. (list julia-fileio
  2861. julia-imagecore
  2862. julia-imagemagick-jll))
  2863. (native-inputs
  2864. (list julia-colors
  2865. julia-colorvectorspace
  2866. julia-imagemetadata
  2867. julia-imageshow
  2868. julia-imagetransformations
  2869. julia-indirectarrays
  2870. julia-offsetarrays
  2871. julia-zipfile))
  2872. (home-page "https://github.com/JuliaIO/ImageMagick.jl")
  2873. (synopsis "Thin wrapper for ImageMagick")
  2874. (description "This package provides a wrapper around ImageMagick version 6.
  2875. It was split off from @code{Images.jl} to make image I/O more modular.")
  2876. (license license:expat)))
  2877. (define-public julia-imagemetadata
  2878. (package
  2879. (name "julia-imagemetadata")
  2880. (version "0.9.8")
  2881. (source
  2882. (origin
  2883. (method git-fetch)
  2884. (uri (git-reference
  2885. (url "https://github.com/JuliaImages/ImageMetadata.jl")
  2886. (commit (string-append "v" version))))
  2887. (file-name (git-file-name name version))
  2888. (sha256
  2889. (base32 "0rdzvya5szlkg5ds3fw7lpk47hn16655i6265czwf8fxs3hb1gvf"))))
  2890. (build-system julia-build-system)
  2891. (arguments
  2892. (list
  2893. #:phases
  2894. #~(modify-phases %standard-phases
  2895. (add-after 'unpack 'adjust-tests
  2896. (lambda _
  2897. (substitute* "test/operations.jl"
  2898. ;; Skip the constantly failing greyscale test.
  2899. (("\\@testset \\\"operations.*" all)
  2900. (string-append all " return\n"))))))))
  2901. (propagated-inputs
  2902. (list julia-axisarrays
  2903. julia-imageaxes
  2904. julia-imagebase
  2905. julia-imagecore))
  2906. (native-inputs
  2907. (list julia-indirectarrays
  2908. julia-offsetarrays
  2909. julia-simpletraits
  2910. julia-unitful))
  2911. (home-page "https://github.com/JuliaImages/ImageMetadata.jl")
  2912. (synopsis "Julia package for images having metadata")
  2913. (description "@code{ImageMetadata} is a simple package providing utilities
  2914. for working with images that have metadata attached. For example, you might
  2915. want to associate an image with the date on which the picture was taken, or an
  2916. MRI scan with patient data, or an astronomical image with sky coordinates and
  2917. information about the detector used to acquire the image.")
  2918. (license license:expat)))
  2919. (define-public julia-imageshow
  2920. (package
  2921. (name "julia-imageshow")
  2922. (version "0.3.2")
  2923. (source
  2924. (origin
  2925. (method git-fetch)
  2926. (uri (git-reference
  2927. (url "https://github.com/JuliaImages/ImageShow.jl")
  2928. (commit (string-append "v" version))))
  2929. (file-name (git-file-name name version))
  2930. (sha256
  2931. (base32 "00wq3ab8y6nyhxwc5lpz9dnslsmcr1vg3cjdkh7wb7k6a8bw98mh"))))
  2932. (build-system julia-build-system)
  2933. (arguments
  2934. (list #:tests? #f)) ; cycle with ImageMagick.jl.
  2935. (propagated-inputs
  2936. (list julia-fileio
  2937. julia-imagebase
  2938. julia-imagecore
  2939. julia-offsetarrays
  2940. julia-stackviews))
  2941. ;(native-inputs
  2942. ; `(("julia-imagedistances" ,julia-imagedistances)
  2943. ; ("julia-imagemagick" ,julia-imagemagick)
  2944. ; ("julia-suppressor" ,julia-suppressor)
  2945. ; ("julia-testimages" ,julia-testimages)))
  2946. (home-page "https://github.com/JuliaImages/ImageShow.jl")
  2947. (synopsis
  2948. "Inline graphical display of images in Julia graphical environments")
  2949. (description "This package implements image @code{show} methods suitable
  2950. for graphical platforms such as IJulia. It is intended to provide convenient
  2951. inline presentation of greyscale or color images.")
  2952. (license license:expat)))
  2953. (define-public julia-imagetransformations
  2954. (package
  2955. (name "julia-imagetransformations")
  2956. (version "0.9.5")
  2957. (source
  2958. (origin
  2959. (method git-fetch)
  2960. (uri (git-reference
  2961. (url "https://github.com/JuliaImages/ImageTransformations.jl")
  2962. (commit (string-append "v" version))))
  2963. (file-name (git-file-name name version))
  2964. (sha256
  2965. (base32 "1wavfs5chq8s9ma0k8fxfaqam4560w4l2j3lhbd9aqsjlgvi3swc"))))
  2966. (build-system julia-build-system)
  2967. (arguments
  2968. (list #:tests? #f)) ; Cycle with ImageMagick.jl.
  2969. (propagated-inputs
  2970. (list julia-axisalgorithms
  2971. julia-colorvectorspace
  2972. julia-coordinatetransformations
  2973. julia-imagebase
  2974. julia-imagecore
  2975. julia-interpolations
  2976. julia-offsetarrays
  2977. julia-rotations
  2978. julia-staticarrays))
  2979. ;(native-inputs
  2980. ; (list julia-endpointranges
  2981. ; julia-imageio
  2982. ; julia-imagemagick
  2983. ; julia-referencetests
  2984. ; julia-tau
  2985. ; julia-testimages))
  2986. (home-page "https://github.com/JuliaImages/ImageTransformations.jl")
  2987. (synopsis "Geometric transformations on images for Julia")
  2988. (description "This package provides support for image resizing, image
  2989. rotation, and other spatial transformations of arrays.")
  2990. (license license:expat)))
  2991. (define-public julia-indexablebitvectors
  2992. (package
  2993. (name "julia-indexablebitvectors")
  2994. (version "1.0.0")
  2995. (source
  2996. (origin
  2997. (method git-fetch)
  2998. (uri (git-reference
  2999. (url "https://github.com/BioJulia/IndexableBitVectors.jl")
  3000. (commit (string-append "v" version))))
  3001. (file-name (git-file-name name version))
  3002. (sha256
  3003. (base32 "1khaycydwa31sxwvrrvvlylpzdb77kkxfmb8cax3i22ix0c2nmlc"))))
  3004. (build-system julia-build-system)
  3005. ;; Package without Project.toml
  3006. (arguments
  3007. (list
  3008. #:julia-package-name "IndexableBitVectors"
  3009. #:julia-package-uuid "1cb3b9ac-1ffd-5777-9e6b-a3d42300664d"))
  3010. (home-page "https://github.com/BioJulia/IndexableBitVectors.jl")
  3011. (synopsis "Bit vectors operations with extremely fast speed")
  3012. (description "This package exports following operations over bit vectors
  3013. with extremely fast speed while keeping extra memory usage small:
  3014. @itemize
  3015. @item @code{getindex(bv::IndexableBitVectors, i::Integer)}: @code{i}-th
  3016. element of @code{bv}
  3017. @item @code{rank(b::Bool, bv::AbstractIndexableBitVector, i::Integer)}: the
  3018. number of occurrences of bit @code{b} in @code{bv[1:i]}
  3019. @item @code{select(b::Bool, bv::AbstractIndexableBitVector, i::Integer)}: the
  3020. index of i-th occurrence of @code{b} in @code{bv}.
  3021. @end itemize
  3022. and other shortcuts or types.")
  3023. ;; There are plenty of places in the code which rely on the
  3024. ;; length of an Integer in a 64-bit system.
  3025. (supported-systems %64bit-supported-systems)
  3026. (license license:expat)))
  3027. (define-public julia-indexing
  3028. (package
  3029. (name "julia-indexing")
  3030. (version "1.1.1")
  3031. (source
  3032. (origin
  3033. (method git-fetch)
  3034. (uri (git-reference
  3035. (url "https://github.com/andyferris/Indexing.jl")
  3036. (commit (string-append "v" version))))
  3037. (file-name (git-file-name name version))
  3038. (sha256
  3039. (base32 "1s7bz5aaj9sx753pcaixq83jgbk33adxgybpinjgzb9lzdv1ddgx"))))
  3040. (build-system julia-build-system)
  3041. (home-page "https://github.com/andyferris/Indexing.jl")
  3042. (synopsis "Generalized indexing for Julia")
  3043. (description "This package defines functions for getting multiple indices
  3044. out of dictionaries, tuples, etc, extending this ability beyond
  3045. @code{AbstractArray}.")
  3046. (license license:expat)))
  3047. (define-public julia-indirectarrays
  3048. (package
  3049. (name "julia-indirectarrays")
  3050. (version "0.5.1")
  3051. (source
  3052. (origin
  3053. (method git-fetch)
  3054. (uri (git-reference
  3055. (url "https://github.com/JuliaArrays/IndirectArrays.jl")
  3056. (commit (string-append "v" version))))
  3057. (file-name (git-file-name name version))
  3058. (sha256
  3059. (base32 "0l0jq0jnr9z3k431ni82xycq7mqapgxrbrx4yyk6lycvi41ipm4s"))))
  3060. (build-system julia-build-system)
  3061. (native-inputs
  3062. (list julia-colors
  3063. julia-fixedpointnumbers
  3064. julia-mappedarrays))
  3065. (home-page "https://github.com/JuliaArrays/IndirectArrays.jl")
  3066. (synopsis "Julia implementation of indexed arrays")
  3067. (description "An @code{IndirectArray} is one that encodes data using a
  3068. combination of an @code{index} and a @code{value} table. Each element is
  3069. assigned its own index, which is used to retrieve the value from the
  3070. @code{value} table. Among other uses, @code{IndirectArrays} can represent
  3071. indexed images, sometimes called \"colormap images\" or \"paletted images.\"")
  3072. (license license:expat)))
  3073. (define-public julia-inflate
  3074. (package
  3075. (name "julia-inflate")
  3076. (version "0.1.2")
  3077. (source
  3078. (origin
  3079. (method git-fetch)
  3080. (uri (git-reference
  3081. (url "https://github.com/GunnarFarneback/Inflate.jl")
  3082. (commit (string-append "v" version))))
  3083. (file-name (git-file-name name version))
  3084. (sha256
  3085. (base32 "16nbl40b819yzmfqs860xbcbx8nnxm0pkvzj49qmxibv5jnsj47q"))))
  3086. (build-system julia-build-system)
  3087. (arguments
  3088. ;; FIXME: Tests fail hard with a lot of errors.
  3089. '(#:tests? #f))
  3090. (propagated-inputs
  3091. (list julia-codeczlib))
  3092. (home-page "https://github.com/GunnarFarneback/Inflate.jl")
  3093. (synopsis "Julia implementation of zlib decompression")
  3094. (description "Inflate provides a pure Julia implementation of zlib decompression
  3095. functionality, with both in- memory and streaming interfaces. This covers
  3096. decompression of the Deflate algorithm and the Zlib and Gzip wrapper formats, as
  3097. specified in RFC 1950, RFC 1951, and RFC 1952.")
  3098. (license license:expat)))
  3099. (define-public julia-infinity
  3100. (package
  3101. (name "julia-infinity")
  3102. (version "0.2.4")
  3103. (source
  3104. (origin
  3105. (method git-fetch)
  3106. (uri (git-reference
  3107. (url "https://github.com/cjdoris/Infinity.jl")
  3108. (commit (string-append "v" version))))
  3109. (file-name (git-file-name name version))
  3110. (sha256
  3111. (base32 "1941lwvrdjnrynigzixxin3chpg1ba6xplvcwc89x0f6z658hwmm"))))
  3112. (build-system julia-build-system)
  3113. (arguments
  3114. (list
  3115. #:phases
  3116. #~(modify-phases %standard-phases
  3117. (add-after 'link-depot 'remove-timezones.jl
  3118. (lambda _
  3119. (substitute* "test/runtests.jl"
  3120. (("using TimeZones.*") "")
  3121. ((".*infextendedtime.*") "")))))))
  3122. (propagated-inputs
  3123. (list julia-requires))
  3124. (native-inputs
  3125. (list julia-compat))
  3126. (home-page "https://docs.juliahub.com/Infinity/")
  3127. (synopsis "Representation of infinity in Julia")
  3128. (description "This package provides representations for infinity and
  3129. negative infinity in Julia.")
  3130. (license license:expat)))
  3131. (define-public julia-inifile
  3132. (package
  3133. (name "julia-inifile")
  3134. (version "0.5.0")
  3135. (source
  3136. (origin
  3137. (method git-fetch)
  3138. (uri (git-reference
  3139. (url "https://github.com/JuliaIO/IniFile.jl")
  3140. (commit "8ba59958495fa276d6489d2c3903e765d75e0bc0")))
  3141. (file-name (git-file-name name version))
  3142. (sha256
  3143. (base32 "11h6f99jpbg729lplw841m68jprka7q3n8yw390bndlmcdsjabpd"))))
  3144. (build-system julia-build-system)
  3145. (home-page "https://github.com/JuliaIO/IniFile.jl")
  3146. (synopsis "Reading Windows-style INI files")
  3147. (description "This is a Julia package that defines an IniFile type that
  3148. interfaces with @file{.ini} files.")
  3149. (license license:expat)))
  3150. (define-public julia-inlinestrings
  3151. (package
  3152. (name "julia-inlinestrings")
  3153. (version "1.1.3")
  3154. (source
  3155. (origin
  3156. (method git-fetch)
  3157. (uri (git-reference
  3158. (url "https://github.com/JuliaStrings/InlineStrings.jl")
  3159. (commit (string-append "v" version))))
  3160. (file-name (git-file-name name version))
  3161. (sha256
  3162. (base32 "1dcdpxlphjliqlnkcri7mhg9bqqzpsdj80h9gkw8xhzr3ls473zr"))))
  3163. (build-system julia-build-system)
  3164. (propagated-inputs
  3165. (list julia-parsers))
  3166. (home-page "https://github.com/JuliaStrings/InlineStrings.jl")
  3167. (synopsis "Fixed-width string types")
  3168. (description "This package provides a set of custom string types of
  3169. various fixed sizes. Each inline string is a custom primitive type and can
  3170. benefit from being stack friendly by avoiding allocations/heap tracking in the
  3171. GC. When used in an array, the elements are able to be stored inline since
  3172. each one has a fixed size. Currently support inline strings from 1 byte up to
  3173. 255 bytes.")
  3174. (license license:expat)))
  3175. (define-public julia-interpolations
  3176. (package
  3177. (name "julia-interpolations")
  3178. (version "0.13.6")
  3179. (source
  3180. (origin
  3181. (method git-fetch)
  3182. (uri (git-reference
  3183. (url "https://github.com/JuliaMath/Interpolations.jl")
  3184. (commit (string-append "v" version))))
  3185. (file-name (git-file-name name version))
  3186. (sha256
  3187. (base32 "1skzvgd63rhj1zpn45gi3974rbrir9p2y17zyfmkz6c6nird7bkj"))))
  3188. (build-system julia-build-system)
  3189. (arguments
  3190. (list
  3191. #:parallel-tests? #f
  3192. ;; XXXX: Unexpected failures for i686, e.g.,
  3193. ;; Got exception outside of a @test
  3194. ;; OverflowError: 96908232 * 106943408 overflowed for type Int32
  3195. ;; Disable as stopgap.
  3196. #:tests? (not (or (%current-target-system)
  3197. (target-x86-32?)))))
  3198. (propagated-inputs
  3199. (list julia-axisalgorithms
  3200. julia-chainrulescore
  3201. julia-offsetarrays
  3202. julia-ratios
  3203. julia-requires
  3204. julia-staticarrays
  3205. julia-woodburymatrices))
  3206. (native-inputs
  3207. (list julia-colorvectorspace
  3208. julia-dualnumbers
  3209. julia-forwarddiff
  3210. julia-offsetarrays
  3211. julia-unitful
  3212. julia-zygote))
  3213. (home-page "https://github.com/JuliaMath/Interpolations.jl")
  3214. (synopsis "Continuous interpolation of discrete datasets")
  3215. (description "This package implements a variety of interpolation schemes for
  3216. the Julia language. It has the goals of ease-of-use, broad algorithmic support,
  3217. and exceptional performance.")
  3218. (license license:expat)))
  3219. (define-public julia-intervalsets
  3220. (package
  3221. (name "julia-intervalsets")
  3222. (version "0.5.3")
  3223. (source
  3224. (origin
  3225. (method git-fetch)
  3226. (uri (git-reference
  3227. (url "https://github.com/JuliaMath/IntervalSets.jl")
  3228. (commit (string-append "v" version))))
  3229. (file-name (git-file-name name version))
  3230. (sha256
  3231. (base32 "0gsz89cd3iygbl5qr389k9vwpg7w1nk0s90g25nsmk34y9hifxag"))))
  3232. (build-system julia-build-system)
  3233. (arguments
  3234. (list
  3235. #:phases
  3236. (if (target-x86-32?)
  3237. #~(modify-phases %standard-phases
  3238. (add-after 'unpack 'remove-failing-test-i686
  3239. (lambda _
  3240. (substitute* "test/runtests.jl"
  3241. ;; For some reason, the output is correct but the test
  3242. ;; is considered as failed:
  3243. ;; Expression: duration(ClosedInterval(A, B)) ≡ 60
  3244. ;; Evaluated: 60 ≡ 60
  3245. (("@test duration\\(ClosedInterval")
  3246. "@test_broken duration(ClosedInterval")))))
  3247. #~%standard-phases)))
  3248. (propagated-inputs
  3249. (list julia-ellipsisnotation))
  3250. (native-inputs
  3251. (list julia-offsetarrays))
  3252. (home-page "https://github.com/JuliaMath/IntervalSets.jl")
  3253. (synopsis "Interval Sets for Julia")
  3254. (description "This package is intended to implement a \"minimal\" foundation
  3255. for intervals upon which other packages might build. In particular, we
  3256. encourage type-piracy for the reason that only one interval package can
  3257. unambiguously define the @code{..} and @code{±} operators.")
  3258. (license license:expat)))
  3259. (define-public julia-intervaltrees
  3260. ;; Last upstream release on May 2020 and this last release does not contain
  3261. ;; the file Project.toml.
  3262. (let ((commit "e37edab61568d08141a3e9c25ec55caac21e5aa5")
  3263. (revision "1"))
  3264. (package
  3265. (name "julia-intervaltrees")
  3266. (version (git-version "1.0.0" revision commit))
  3267. (source
  3268. (origin
  3269. (method git-fetch)
  3270. (uri (git-reference
  3271. (url "https://github.com/BioJulia/IntervalTrees.jl")
  3272. (commit commit)))
  3273. (file-name (git-file-name name version))
  3274. (sha256
  3275. (base32 "01x48a5zrx0833s1kjhf0ml4x9xz8xja4ymran770akmf6968yl9"))))
  3276. (build-system julia-build-system)
  3277. (home-page "https://github.com/BioJulia/IntervalTrees.jl")
  3278. (synopsis "Interval Trees for Julia")
  3279. (description "This package provides an implementation of an associative
  3280. container mapping @code{(K,V)} pairs via the type @code{IntervalTree{K, V}}.
  3281. The type @code{K} may be any ordered type.")
  3282. (license license:expat))))
  3283. (define-public julia-inversefunctions
  3284. (package
  3285. (name "julia-inversefunctions")
  3286. (version "0.1.8")
  3287. (source
  3288. (origin
  3289. (method git-fetch)
  3290. (uri (git-reference
  3291. (url "https://github.com/JuliaMath/InverseFunctions.jl")
  3292. (commit (string-append "v" version))))
  3293. (file-name (git-file-name name version))
  3294. (sha256
  3295. (base32 "05g9f6i735x7syfr56l4yf4fy71kgdisjc6cfxi4jkf46iq86a69"))))
  3296. (build-system julia-build-system)
  3297. (native-inputs
  3298. (list julia-documenter))
  3299. (home-page "https://github.com/JuliaMath/InverseFunctions.jl")
  3300. (synopsis "Interface for function inversion")
  3301. (description "This package provides an interface to invert functions.")
  3302. (license license:expat)))
  3303. (define-public julia-invertedindices
  3304. (package
  3305. (name "julia-invertedindices")
  3306. (version "1.1.0")
  3307. (source
  3308. (origin
  3309. (method git-fetch)
  3310. (uri (git-reference
  3311. (url "https://github.com/mbauman/InvertedIndices.jl")
  3312. (commit (string-append "v" version))))
  3313. (file-name (git-file-name name version))
  3314. (sha256
  3315. (base32 "15ym4dzyi4fkz0dznni032w3c84zmfa6mrzj2ljqvlqx1i6agqis"))))
  3316. (build-system julia-build-system)
  3317. (native-inputs
  3318. (list julia-offsetarrays))
  3319. (home-page "https://github.com/mbauman/InvertedIndices.jl")
  3320. (synopsis "Index type that allows for inverted selections")
  3321. (description "This package just exports one type: the @code{InvertedIndex},
  3322. or @code{Not} for short. It can wrap any supported index type and may be used
  3323. as an index into any @code{AbstractArray} subtype, including OffsetArrays.")
  3324. (license license:expat)))
  3325. (define-public julia-iocapture
  3326. (package
  3327. (name "julia-iocapture")
  3328. (version "0.2.2")
  3329. (source
  3330. (origin
  3331. (method git-fetch)
  3332. (uri (git-reference
  3333. (url "https://github.com/JuliaDocs/IOCapture.jl")
  3334. (commit (string-append "v" version))))
  3335. (file-name (git-file-name name version))
  3336. (sha256
  3337. (base32 "0v76wbvg80g9nx0rjbcna82zk61krly1y9yhyfrjv2pf7mcr4idb"))))
  3338. (build-system julia-build-system)
  3339. (home-page "https://github.com/JuliaDocs/IOCapture.jl")
  3340. (synopsis "Capture standard output and error streams")
  3341. (description "This package provides the @code{IOCapture.capture(f)}
  3342. function, which captures the standard output and standard error, and returns it
  3343. as a string together with the return value.")
  3344. (license license:expat)))
  3345. (define-public julia-irrationalconstants
  3346. (package
  3347. (name "julia-irrationalconstants")
  3348. (version "0.1.1")
  3349. (source
  3350. (origin
  3351. (method git-fetch)
  3352. (uri (git-reference
  3353. (url "https://github.com/JuliaMath/IrrationalConstants.jl")
  3354. (commit (string-append "v" version))))
  3355. (file-name (git-file-name name version))
  3356. (sha256
  3357. (base32 "1a007iyh26x67a1bj6fcz7pfxa43kn2v7jpmnz727jkk3xgppg2s"))))
  3358. (build-system julia-build-system)
  3359. (home-page "https://github.com/JuliaMath/IrrationalConstants.jl")
  3360. (synopsis "Additional irrationals for Julia")
  3361. (description "This package provides these irrational constants:
  3362. @itemize
  3363. @item
  3364. @item twoπ = 2π
  3365. @item fourπ = 4π
  3366. @item halfπ = π / 2
  3367. @item quartπ = π / 4
  3368. @item invπ = 1 / π
  3369. @item twoinvπ = 2 / π
  3370. @item fourinvπ = 4 / π
  3371. @item inv2π = 1 / (2π)
  3372. @item inv4π = 1 / (4π)
  3373. @item sqrt2 = √2
  3374. @item sqrt3 = √3
  3375. @item sqrtπ = √π
  3376. @item sqrt2π = √2π
  3377. @item sqrt4π = √4π
  3378. @item sqrthalfπ = √(π / 2)
  3379. @item invsqrt2 = 1 / √2
  3380. @item invsqrtπ = 1 / √π
  3381. @item invsqrt2π = 1 / √2π
  3382. @item loghalf = log(1 / 2)
  3383. @item logtwo = log(2)
  3384. @item logten = log(10)
  3385. @item logπ = log(π)
  3386. @item log2π = log(2π)
  3387. @item log4π = log(4π)
  3388. @end itemize")
  3389. (license license:expat)))
  3390. (define-public julia-irtools
  3391. (package
  3392. (name "julia-irtools")
  3393. (version "0.4.7")
  3394. (source
  3395. (origin
  3396. (method git-fetch)
  3397. (uri (git-reference
  3398. (url "https://github.com/FluxML/IRTools.jl")
  3399. (commit (string-append "v" version))))
  3400. (file-name (git-file-name name version))
  3401. (sha256
  3402. (base32 "1faddim4gp9pgyadgxi7zdqpdn6qkh7acqpdy29ixpbnb0wgla5r"))))
  3403. (build-system julia-build-system)
  3404. (propagated-inputs
  3405. (list julia-macrotools))
  3406. (native-inputs
  3407. (list julia-documenter))
  3408. (home-page "https://github.com/FluxML/IRTools.jl")
  3409. (synopsis "Simple and flexible IR format")
  3410. (description "This package provides a simple and flexible IR format,
  3411. expressive enough to work with both lowered and typed Julia code, as well as
  3412. external IRs. It can be used with Julia metaprogramming tools such as
  3413. Cassette.")
  3414. (license license:expat)))
  3415. (define-public julia-itemgraphs
  3416. (package
  3417. (name "julia-itemgraphs")
  3418. (version "0.4.0")
  3419. (source
  3420. (origin
  3421. (method git-fetch)
  3422. (uri (git-reference
  3423. (url "https://github.com/helgee/ItemGraphs.jl")
  3424. (commit (string-append "v" version))))
  3425. (file-name (git-file-name name version))
  3426. (sha256
  3427. (base32 "16w30y7s922dzp7i64wxdrafv4gy13v3rl4k1z5jkvnmnw68kygg"))))
  3428. (build-system julia-build-system)
  3429. (propagated-inputs
  3430. (list julia-lightgraphs))
  3431. (home-page "https://github.com/helgee/ItemGraphs.jl")
  3432. (synopsis "Shortest paths between items")
  3433. (description
  3434. "ItemGraphs is a simple wrapper around LightGraphs that enables most
  3435. common use case for graph-like data structures: with collection of items that
  3436. are in relations between each other providing the shortest path between two
  3437. items.")
  3438. (license license:expat)))
  3439. (define-public julia-iteratorinterfaceextensions
  3440. (package
  3441. (name "julia-iteratorinterfaceextensions")
  3442. (version "1.0.0")
  3443. (source
  3444. (origin
  3445. (method git-fetch)
  3446. (uri (git-reference
  3447. (url "https://github.com/queryverse/IteratorInterfaceExtensions.jl")
  3448. (commit (string-append "v" version))))
  3449. (file-name (git-file-name name version))
  3450. (sha256
  3451. (base32 "1slpay1dhja8f9gy6z7b3psgvgcknn963dvfqqakvg1grk9ppa09"))))
  3452. (build-system julia-build-system)
  3453. (home-page "https://github.com/queryverse/IteratorInterfaceExtensions.jl")
  3454. (synopsis "Traits for Julia iterators")
  3455. (description "IteratorInterfaceExtensions defines a small number of
  3456. extensions to the iterator interface.")
  3457. (license license:expat)))
  3458. (define-public julia-itertools
  3459. (package
  3460. (name "julia-itertools")
  3461. (version "1.3.0")
  3462. (source
  3463. (origin
  3464. (method git-fetch)
  3465. (uri (git-reference
  3466. (url "https://github.com/JuliaCollections/IterTools.jl")
  3467. (commit (string-append "v" version))))
  3468. (file-name (git-file-name name version))
  3469. (sha256
  3470. (base32 "0haf974kcqj6arv4if97ahs4w3dmvslh6ab3hl57r9s41ic36xdq"))))
  3471. (build-system julia-build-system)
  3472. (home-page "https://github.com/JuliaCollections/IterTools.jl")
  3473. (synopsis "Common functional iterator patterns")
  3474. (description
  3475. "Common functional iterator patterns (formerly @code{Iterators.jl}).")
  3476. (license license:expat)))
  3477. (define-public julia-jive
  3478. (package
  3479. (name "julia-jive")
  3480. (version "0.2.27")
  3481. (source
  3482. (origin
  3483. (method git-fetch)
  3484. (uri (git-reference
  3485. (url "https://github.com/wookay/Jive.jl")
  3486. (commit (string-append "v" version))))
  3487. (file-name (git-file-name name version))
  3488. (sha256
  3489. (base32 "010dxs9p5ab97h80kw12bx5mkraf0584wi0ggk8wnhg10jf3lpam"))))
  3490. (build-system julia-build-system)
  3491. (home-page "https://github.com/wookay/Jive.jl")
  3492. (synopsis "Julia package to help with writing tests")
  3493. (description "@code{Jive.jl} is a Julia package to help with writing tests.")
  3494. (license license:expat)))
  3495. (define-public julia-json
  3496. (package
  3497. (name "julia-json")
  3498. (version "0.21.3")
  3499. (source
  3500. (origin
  3501. (method git-fetch)
  3502. (uri (git-reference
  3503. (url "https://github.com/JuliaIO/JSON.jl")
  3504. (commit (string-append "v" version))))
  3505. (file-name (git-file-name name version))
  3506. (sha256
  3507. (base32 "1l2p852sxq6h5fif3dqshvbw17gb06jmq2nkr88spvp7s0n0nslz"))))
  3508. (build-system julia-build-system)
  3509. (propagated-inputs
  3510. (list julia-datastructures
  3511. julia-fixedpointnumbers
  3512. julia-parsers
  3513. julia-offsetarrays))
  3514. (home-page "https://github.com/JuliaIO/JSON.jl")
  3515. (synopsis "JSON parsing and printing library for Julia")
  3516. (description "@code{JSON.jl} is a pure Julia module which supports parsing
  3517. and printing JSON documents.")
  3518. (license license:expat)))
  3519. (define-public julia-json3
  3520. (package
  3521. (name "julia-json3")
  3522. (version "1.9.0")
  3523. (source
  3524. (origin
  3525. (method git-fetch)
  3526. (uri (git-reference
  3527. (url "https://github.com/quinnj/JSON3.jl")
  3528. (commit (string-append "v" version))))
  3529. (file-name (git-file-name name version))
  3530. (sha256
  3531. (base32 "11z5maz7v50wd99id8z7838higza0cllh2amkdkrlskbri3v2f17"))))
  3532. (build-system julia-build-system)
  3533. (propagated-inputs
  3534. (list julia-parsers
  3535. julia-structtypes))
  3536. (home-page "https://github.com/quinnj/JSON3.jl")
  3537. (synopsis "JSON package for Julia")
  3538. (description "This package provides another JSON package for Julia, with a
  3539. focus on speed and slick struct mapping.")
  3540. (license license:expat)))
  3541. (define-public julia-juno
  3542. (package
  3543. (name "julia-juno")
  3544. (version "0.8.4")
  3545. (source
  3546. (origin
  3547. (method git-fetch)
  3548. (uri (git-reference
  3549. (url "https://github.com/JunoLab/Juno.jl")
  3550. (commit (string-append "v" version))))
  3551. (file-name (git-file-name name version))
  3552. (sha256
  3553. (base32 "02ryj5blnrmck3jisrpwn1x563i7rsg65d7zms52njsvv499gygk"))))
  3554. (build-system julia-build-system)
  3555. (inputs
  3556. (list julia-media))
  3557. (home-page "https://github.com/JunoLab/Juno.jl")
  3558. (synopsis "Integrated Development Environment (IDE) for Julia")
  3559. (description "This package provides tools to help you develop code. Juno
  3560. is built on the Atom text editor. Juno consists of both Julia and Atom
  3561. packages in order to add Julia-specific enhancements, such as syntax
  3562. highlighting, a plot pane, integration with Julia's debugger, a console for
  3563. running code, and much more.
  3564. Consider that the package is “maintenance-only mode” and only receives bug
  3565. fixes. The Julia IDE effort is pointed to extension for VSCode.")
  3566. (license license:expat)))
  3567. (define-public julia-latexstrings
  3568. (package
  3569. (name "julia-latexstrings")
  3570. (version "1.3.0")
  3571. (source
  3572. (origin
  3573. (method git-fetch)
  3574. (uri (git-reference
  3575. (url "https://github.com/stevengj/LaTeXStrings.jl")
  3576. (commit (string-append "v" version))))
  3577. (file-name (git-file-name name version))
  3578. (sha256
  3579. (base32 "0iijp96ca9mqg5skr6ps7q0lvqaa374lr2zkbbia5q6qgpq0j5ww"))))
  3580. (build-system julia-build-system)
  3581. (native-inputs
  3582. (list julia-documenter))
  3583. (home-page "https://github.com/stevengj/LaTeXStrings.jl")
  3584. (synopsis "Input and display of LaTeX equation strings")
  3585. (description "This is a small package to make it easier to type LaTeX
  3586. equations in string literals in the Julia language.")
  3587. (license license:expat)))
  3588. (define-public julia-lazyarrays
  3589. (package
  3590. (name "julia-lazyarrays")
  3591. (version "0.22.16")
  3592. (source
  3593. (origin
  3594. (method git-fetch)
  3595. (uri (git-reference
  3596. (url "https://github.com/JuliaArrays/LazyArrays.jl")
  3597. (commit (string-append "v" version))))
  3598. (file-name (git-file-name name version))
  3599. (sha256
  3600. (base32 "127yld4f26lchw5jwp30g2jkjbm7narfsxwcbggy7dfp43s531c5"))))
  3601. (build-system julia-build-system)
  3602. (arguments
  3603. (list
  3604. #:phases
  3605. (if (target-64bit?)
  3606. #~%standard-phases
  3607. #~(modify-phases %standard-phases
  3608. (add-after 'unpack 'fix-tests-int32-i686
  3609. (lambda _
  3610. (substitute* "test/multests.jl"
  3611. (("Int64") "Int32"))))))))
  3612. (propagated-inputs
  3613. (list julia-aqua
  3614. julia-arraylayouts
  3615. julia-fillarrays
  3616. julia-macrotools
  3617. julia-matrixfactorizations
  3618. julia-staticarrays))
  3619. (native-inputs
  3620. (list julia-aqua
  3621. julia-tracker))
  3622. (home-page "https://github.com/JuliaArrays/LazyArrays.jl")
  3623. (synopsis "Lazy arrays and linear algebra")
  3624. (description "This package supports lazy analogues of array operations like
  3625. @code{vcat}, @code{hcat}, and multiplication. This helps with the
  3626. implementation of matrix-free methods for iterative solvers.")
  3627. (license license:expat)))
  3628. (define-public julia-leapseconds
  3629. (package
  3630. (name "julia-leapseconds")
  3631. (version "1.1.0")
  3632. (source
  3633. (origin
  3634. (method git-fetch)
  3635. (uri (git-reference
  3636. (url "https://github.com/JuliaTime/LeapSeconds.jl")
  3637. (commit (string-append "v" version))))
  3638. (file-name (git-file-name name version))
  3639. (sha256
  3640. (base32 "13xa49dx11n7ii77rw6300h1rfl4qlq05ypsprvfmvyww81angkp"))))
  3641. (build-system julia-build-system)
  3642. (native-inputs
  3643. (list julia-erfa))
  3644. (home-page "https://github.com/JuliaTime/LeapSeconds.jl")
  3645. (synopsis "Leap seconds in Julia")
  3646. (description
  3647. "@code{LeapSeconds} provides a functionality to return the difference
  3648. between @acronym{TAI, International Atomic Time} and @acronym{UTC, Coordinated
  3649. Universal Time} or vice versa for a given date. For dates after 1972-01-01, this
  3650. is the number of leap seconds.")
  3651. (license license:expat)))
  3652. (define-public julia-lightgraphs
  3653. (package
  3654. (name "julia-lightgraphs")
  3655. (version "1.3.5")
  3656. (source
  3657. (origin
  3658. (method git-fetch)
  3659. (uri (git-reference
  3660. (url "https://github.com/sbromberger/LightGraphs.jl")
  3661. (commit (string-append "v" version))))
  3662. (file-name (git-file-name name version))
  3663. (sha256
  3664. (base32 "0ygnbzx32b9ciwgg0rn5i0m33dvrb6dh3an6bnmzac1w67sy2vxq"))))
  3665. (build-system julia-build-system)
  3666. (arguments
  3667. (list
  3668. #:phases
  3669. #~(modify-phases %standard-phases
  3670. ;; FIXME: 8x tests fails adjusting for now.
  3671. ;; ERROR: LoadError: Some tests did not pass: 29548 passed, 0 failed,
  3672. ;; 8 errored, 0 broken.
  3673. (add-after 'unpack 'adjust-tests
  3674. (lambda _
  3675. (substitute* "test/runtests.jl"
  3676. ;; Got exception outside of a @test BoundsError: attempt to
  3677. ;; access 1-element Vector{SubString{String}} at index [2]
  3678. ((".*degeneracy.*") "")
  3679. ;; Got exception outside of a @test type DataType has no field
  3680. ;; mutable
  3681. ((".*shortestpaths.*") ""))
  3682. (substitute* "test/experimental/experimental.jl"
  3683. ;; Got exception outside of a @test type DataType has no field mutable
  3684. (("\"shortestpaths\",") ""))
  3685. (substitute* "test/linalg/runtests.jl"
  3686. ;; ArgumentError: Illegal buffers for SparseMatrixCSC
  3687. ;; construction 5 [1, 3, 5, 7, 9, 10] [1, 2, 1, 3, 2, 4, 3, 5,
  3688. ;; 4] [1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
  3689. ;;
  3690. ;; ArgumentError: Illegal buffers for SparseMatrixCSC
  3691. ;; construction 5 UInt16[0x0001, 0x0003, 0x0005, 0x0007,
  3692. ;; 0x0009, 0x000a] UInt16[0x0001, 0x0002, 0x0001, 0x0003,
  3693. ;; 0x0002, 0x0004, 0x0003, 0x0005, 0x0004] [1, 1, 1, 1, 1, 1,
  3694. ;; 1, 1, 1, 1]
  3695. ;;
  3696. ;; ArgumentError: Illegal buffers for SparseMatrixCSC
  3697. ;; construction 5 Int32[1, 3, 5, 7, 9, 10] Int32[1, 2, 1, 3,
  3698. ;; 2, 4, 3, 5, 4] [1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
  3699. ((".*spectral.*") ""))
  3700. (substitute* "test/parallel/runtests.jl"
  3701. ;; Got exception outside of a @test type DataType has no field
  3702. ;; mutable
  3703. ((".*shortestpaths/johnson.*") "")
  3704. ;; Got exception outside of a @test TaskFailedException nested
  3705. ;; task error: On worker 2: UndefVarError: nv not defined
  3706. ((".*utils.*") "")))))))
  3707. (propagated-inputs
  3708. (list julia-arnoldimethod
  3709. julia-datastructures
  3710. julia-inflate
  3711. julia-simpletraits))
  3712. (home-page "https://github.com/sbromberger/LightGraphs.jl")
  3713. (synopsis "Optimized graphs package for Julia")
  3714. (description
  3715. "LightGraphs offers both (a) a set of simple, concrete graph implementations --
  3716. Graph (for undirected graphs) and DiGraph (for directed graphs), and (b) an API
  3717. for the development of more sophisticated graph implementations under the
  3718. AbstractGraph type.")
  3719. (license license:bsd-2)))
  3720. (define-public julia-linesearches
  3721. (package
  3722. (name "julia-linesearches")
  3723. (version "7.1.1")
  3724. (source
  3725. (origin
  3726. (method git-fetch)
  3727. (uri (git-reference
  3728. (url "https://github.com/JuliaNLSolvers/LineSearches.jl")
  3729. (commit (string-append "v" version))))
  3730. (file-name (git-file-name name version))
  3731. (sha256
  3732. (base32 "1qc4la07w6s1xhcyd0hvbnpr31zc1a2ssgyybc8biv5m00g0dnr0"))))
  3733. (build-system julia-build-system)
  3734. (arguments
  3735. (list
  3736. #:phases
  3737. #~(modify-phases %standard-phases
  3738. (add-after 'link-depot 'skip-optim-tests
  3739. (lambda _
  3740. (substitute* "test/examples.jl"
  3741. ;; Prevent a cycle with Optim.jl.
  3742. (("^ SKIPFILE.*") "")
  3743. (("^ #SKIPFILE") " SKIPFILE"))))
  3744. (add-after 'link-depot 'skip-doublefloats-tests
  3745. (lambda _
  3746. (substitute* "test/runtests.jl"
  3747. (("using DoubleFloats.*") "")
  3748. ((".*arbitrary_precision\\.jl.*") "")))))))
  3749. (propagated-inputs
  3750. (list julia-nlsolversbase
  3751. julia-nanmath
  3752. julia-parameters))
  3753. (native-inputs
  3754. ;; DoubleFloats.jl transitively depends on TimeZones.jl, which is currently
  3755. ;; unpackageable due to its oversized Artifacts.toml.
  3756. (list ;julia-doublefloats
  3757. julia-optimtestproblems))
  3758. (home-page "https://github.com/JuliaNLSolvers/LineSearches.jl")
  3759. (synopsis "Line search methods for optimization and root-finding")
  3760. (description "This package provides an interface to line search algorithms
  3761. implemented in Julia.")
  3762. (license license:expat)))
  3763. (define-public julia-logexpfunctions
  3764. (package
  3765. (name "julia-logexpfunctions")
  3766. (version "0.3.17")
  3767. (source
  3768. (origin
  3769. (method git-fetch)
  3770. (uri (git-reference
  3771. (url "https://github.com/JuliaStats/LogExpFunctions.jl")
  3772. (commit (string-append "v" version))))
  3773. (file-name (git-file-name name version))
  3774. (sha256
  3775. (base32 "0272c1256r42y6g4wsjmgpwcl5s7z98b8sfmyycckqf0zp5dzxg4"))))
  3776. (build-system julia-build-system)
  3777. (propagated-inputs
  3778. (list julia-chainrulescore
  3779. julia-changesofvariables
  3780. julia-docstringextensions
  3781. julia-inversefunctions
  3782. julia-irrationalconstants))
  3783. (native-inputs
  3784. (list julia-chainrulestestutils
  3785. julia-offsetarrays))
  3786. (home-page "https://github.com/JuliaStats/LogExpFunctions.jl")
  3787. (synopsis "Special functions based on @code{log} and @code{exp}")
  3788. (description "Various special functions based on log and exp moved from
  3789. @code{StatsFuns.jl} into a separate package, to minimize dependencies. These
  3790. functions only use native Julia code, so there is no need to depend on
  3791. @code{librmath} or similar libraries.")
  3792. (license license:expat)))
  3793. (define-public julia-macrotools
  3794. (package
  3795. (name "julia-macrotools")
  3796. (version "0.5.6")
  3797. (source
  3798. (origin
  3799. (method git-fetch)
  3800. (uri (git-reference
  3801. (url "https://github.com/FluxML/MacroTools.jl")
  3802. (commit (string-append "v" version))))
  3803. (file-name (git-file-name name version))
  3804. (sha256
  3805. (base32 "0k4z2hyasd9cwxf4l61zk3w4ajs44k69wx6z1ghdn8f5p8xy217f"))))
  3806. (build-system julia-build-system)
  3807. (home-page "https://fluxml.ai/MacroTools.jl")
  3808. (synopsis "Tools for working with Julia code and expressions")
  3809. (description "This library provides tools for working with Julia code and
  3810. expressions. This includes a template-matching system and code-walking tools
  3811. that let you do deep transformations of code.")
  3812. (license license:expat)))
  3813. (define-public julia-mappedarrays
  3814. (package
  3815. (name "julia-mappedarrays")
  3816. (version "0.4.1")
  3817. (source
  3818. (origin
  3819. (method git-fetch)
  3820. (uri (git-reference
  3821. (url "https://github.com/JuliaArrays/MappedArrays.jl")
  3822. (commit (string-append "v" version))))
  3823. (file-name (git-file-name name version))
  3824. (sha256
  3825. (base32 "08kb28dv1zzqbbxblhyllgs4sjxyp76dgjqhdizcq4zg4i1kls6p"))
  3826. (snippet
  3827. #~(begin
  3828. (use-modules (guix build utils))
  3829. ;; Fix deprecation warning
  3830. ;; https://github.com/JuliaArrays/MappedArrays.jl/pull/51
  3831. (substitute* "src/MappedArrays.jl"
  3832. (("Vararg\\{<:AbstractArray") "Vararg{AbstractArray"))
  3833. ;; Fix test failures
  3834. ;; https://github.com/JuliaArrays/MappedArrays.jl/pull/50
  3835. (substitute* "test/runtests.jl"
  3836. (("_zero\\(x\\) = x > 0 \\? x : 0")
  3837. "_zero(x) = ismissing(x) ? x : (x > 0 ? x : 0)"))))))
  3838. (build-system julia-build-system)
  3839. (arguments
  3840. (list
  3841. #:phases
  3842. #~(modify-phases %standard-phases
  3843. (add-after 'unpack 'adjust-tests
  3844. (lambda _
  3845. (substitute* "test/runtests.jl"
  3846. ((".*@test_throws ErrorException b.*") ""))
  3847. (when #$(not (target-64bit?))
  3848. (substitute* "test/runtests.jl"
  3849. (("Int64") "Int32"))))))))
  3850. (propagated-inputs
  3851. (list julia-fixedpointnumbers))
  3852. (native-inputs
  3853. (list julia-colors
  3854. julia-fixedpointnumbers
  3855. julia-offsetarrays))
  3856. (home-page "https://github.com/JuliaArrays/MappedArrays.jl")
  3857. (synopsis "Lazy in-place transformations of arrays")
  3858. (description "This package implements \"lazy\" in-place elementwise
  3859. transformations of arrays for the Julia programming language. Explicitly, it
  3860. provides a \"view\" M of an array A so that @code{M[i] = f(A[i])} for a
  3861. specified (but arbitrary) function f, without ever having to compute M
  3862. explicitly (in the sense of allocating storage for M). The name of the package
  3863. comes from the fact that @code{M == map(f, A)}.")
  3864. (license license:expat)))
  3865. (define-public julia-matrixfactorizations
  3866. (package
  3867. (name "julia-matrixfactorizations")
  3868. (version "0.9.3")
  3869. (source
  3870. (origin
  3871. (method git-fetch)
  3872. (uri (git-reference
  3873. (url "https://github.com/JuliaMatrices/MatrixFactorizations.jl")
  3874. (commit (string-append "v" version))))
  3875. (file-name (git-file-name name version))
  3876. (sha256
  3877. (base32 "0sqmig01irmvh617h2rsw44hl39qwv2913nlqjsdz9si5vli2hsl"))))
  3878. (build-system julia-build-system)
  3879. (arguments
  3880. (list
  3881. #:phases
  3882. #~(modify-phases %standard-phases
  3883. (add-after 'link-depot 'skip-failing-test
  3884. (lambda _
  3885. (substitute* "test/test_ul.jl"
  3886. ;; Don't warn on the REPL test.
  3887. (("test String") "test_nowarn String")))))))
  3888. (propagated-inputs
  3889. (list julia-arraylayouts))
  3890. (home-page "https://github.com/JuliaMatrices/MatrixFactorizations.jl")
  3891. (synopsis "Julia package to contain non-standard matrix factorizations")
  3892. (description "A Julia package to contain non-standard matrix factorizations.
  3893. At the moment it implements the QL, RQ, and UL factorizations, a combined
  3894. Cholesky factorization with inverse, and polar decompositions. In the future it
  3895. may include other factorizations such as the LQ factorization.")
  3896. (license license:expat)))
  3897. (define-public julia-mbedtls
  3898. (package
  3899. (name "julia-mbedtls")
  3900. (version "1.0.3")
  3901. (source
  3902. (origin
  3903. (method git-fetch)
  3904. (uri (git-reference
  3905. (url "https://github.com/JuliaLang/MbedTLS.jl")
  3906. (commit (string-append "v" version))))
  3907. (file-name (git-file-name name version))
  3908. (sha256
  3909. (base32 "0zjzf2r57l24n3k0gcqkvx3izwn5827iv9ak0lqix0aa5967wvfb"))))
  3910. (build-system julia-build-system)
  3911. (arguments
  3912. (list
  3913. #:phases
  3914. #~(modify-phases %standard-phases
  3915. (add-before 'install 'disable-network-tests
  3916. ;; Tries to connect to httpbin.org
  3917. (lambda _
  3918. (substitute* "test/runtests.jl"
  3919. (("testhost =") "return #")))))))
  3920. (propagated-inputs
  3921. (list julia-mbedtls-jll))
  3922. (home-page "https://github.com/JuliaLang/MbedTLS.jl")
  3923. (synopsis "Apache's mbed TLS library wrapper")
  3924. (description "@code{MbedTLS.jl} provides a wrapper around the @code{mbed
  3925. TLS} and cryptography C library for Julia.")
  3926. (license license:expat)))
  3927. (define-public julia-measurements
  3928. (package
  3929. (name "julia-measurements")
  3930. (version "2.8.0")
  3931. (source
  3932. (origin
  3933. (method git-fetch)
  3934. (uri (git-reference
  3935. (url "https://github.com/JuliaPhysics/Measurements.jl")
  3936. (commit (string-append "v" version))))
  3937. (file-name (git-file-name name version))
  3938. (sha256
  3939. (base32 "1rn7qaf2s3l7awm8q5fjxlp1503g9mjgmsnvrbhjjvwyyn1k705r"))))
  3940. (build-system julia-build-system)
  3941. (propagated-inputs
  3942. (list julia-calculus
  3943. julia-recipesbase
  3944. julia-requires))
  3945. (native-inputs
  3946. (list julia-aqua
  3947. julia-quadgk
  3948. julia-specialfunctions
  3949. julia-unitful))
  3950. (home-page "https://juliaphysics.github.io/Measurements.jl/stable/")
  3951. (synopsis "Error propagation calculator and library")
  3952. (description "@code{Measurements.jl} is an error propagation calculator and
  3953. library for physical measurements. It supports real and complex numbers with
  3954. uncertainty, arbitrary precision calculations, operations with arrays, and
  3955. numerical integration. The linear error propagation theory is employed to
  3956. propagate the errors.")
  3957. (license license:expat)))
  3958. (define-public julia-measures
  3959. (package
  3960. (name "julia-measures")
  3961. (version "0.3.1")
  3962. (source
  3963. (origin
  3964. (method git-fetch)
  3965. (uri (git-reference
  3966. (url "https://github.com/JuliaGraphics/Measures.jl")
  3967. (commit (string-append "v" version))))
  3968. (file-name (git-file-name name version))
  3969. (sha256
  3970. (base32 "0j34psrdijnqqn9zv0r2sknr1p9q0mmbjvjhmjra37bb5fh2gk8l"))))
  3971. (build-system julia-build-system)
  3972. (home-page "https://github.com/JuliaGraphics/Measures.jl")
  3973. (synopsis "Unified measure and coordinates types")
  3974. (description "This library generalizes and unifies the notion of measures
  3975. used in Compose, Compose3D, and Escher. It allows building up and representing
  3976. expressions involving differing types of units that are then evaluated,
  3977. resolving them into absolute units.")
  3978. (license license:expat)))
  3979. (define-public julia-media
  3980. (package
  3981. (name "julia-media")
  3982. (version "0.5.0")
  3983. (source
  3984. (origin
  3985. (method git-fetch)
  3986. (uri (git-reference
  3987. (url "https://github.com/JunoLab/Media.jl")
  3988. (commit (string-append "v" version))))
  3989. (file-name (git-file-name name version))
  3990. (sha256
  3991. (base32 "05jq9j3vs8yfj2lwz3sh1vk5rha06xdcikp9s2q3dn316vryy6di"))))
  3992. (build-system julia-build-system)
  3993. ;; Package without Project.toml
  3994. (arguments
  3995. (list
  3996. #:julia-package-name "Media"
  3997. #:julia-package-uuid "e89f7d12-3494-54d1-8411-f7d8b9ae1f27"
  3998. #:julia-package-dependencies
  3999. #~(list '("MacroTools" . "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"))))
  4000. (propagated-inputs
  4001. (list julia-macrotools))
  4002. (home-page "https://github.com/JunoLab/Media.jl")
  4003. (synopsis "Unified measure and coordinates types")
  4004. (description "This package provides a display system which enables the
  4005. user handle multiple input/output devices and decide what media types get
  4006. displayed where.")
  4007. (license license:expat)))
  4008. (define-public julia-millboard
  4009. (package
  4010. (name "julia-millboard")
  4011. (version "0.2.5")
  4012. (source
  4013. (origin
  4014. (method git-fetch)
  4015. (uri (git-reference
  4016. (url "https://github.com/wookay/Millboard.jl")
  4017. (commit (string-append "v" version))))
  4018. (file-name (git-file-name name version))
  4019. (sha256
  4020. (base32 "0k9jqgp285qhckldvvsmfk6s69dcr8s74m2fijgm2vxjj2gqjs1n"))))
  4021. (build-system julia-build-system)
  4022. (native-inputs
  4023. (list julia-jive))
  4024. (home-page "https://github.com/wookay/Millboard.jl")
  4025. (synopsis "Displaying data in tables for Julia")
  4026. (description
  4027. "@code{Millboard.jl} provides a library for getting data in a tablized
  4028. format to arrange into rows and columns of cells.")
  4029. (license license:expat)))
  4030. (define-public julia-missings
  4031. (package
  4032. (name "julia-missings")
  4033. (version "1.0.2")
  4034. (source
  4035. (origin
  4036. (method git-fetch)
  4037. (uri (git-reference
  4038. (url "https://github.com/JuliaData/Missings.jl")
  4039. (commit (string-append "v" version))))
  4040. (file-name (git-file-name name version))
  4041. (sha256
  4042. (base32 "1k481rm5lahmjyh34j177d4n10svgr0wm7ps5m3ar3xx6nr26ad5"))))
  4043. (build-system julia-build-system)
  4044. (propagated-inputs
  4045. (list julia-dataapi))
  4046. (home-page "https://github.com/JuliaData/Missings.jl")
  4047. (synopsis "Additional missing value support for Julia")
  4048. (description "This package provides additional functionality for working
  4049. with @code{missing} values in Julia.")
  4050. (license license:expat)))
  4051. (define-public julia-mlstyle
  4052. (package
  4053. (name "julia-mlstyle")
  4054. (version "0.4.10")
  4055. (source
  4056. (origin
  4057. (method git-fetch)
  4058. (uri (git-reference
  4059. (url "https://github.com/thautwarm/MLStyle.jl")
  4060. (commit (string-append "v" version))))
  4061. (file-name (git-file-name name version))
  4062. (sha256
  4063. (base32 "0h1cd7cr4c4cnpqyj3180113gdbvcc047lqphp8a8gq5smp3c059"))))
  4064. (build-system julia-build-system)
  4065. (native-inputs
  4066. (list julia-datastructures))
  4067. (home-page "https://thautwarm.github.io/MLStyle.jl/latest/")
  4068. (synopsis "Julia functional programming infrastructures")
  4069. (description "This package provides consistent and extensible functional
  4070. programming infrastructures, and metaprogramming facilities.")
  4071. (license license:expat)))
  4072. (define-public julia-mocking
  4073. (package
  4074. (name "julia-mocking")
  4075. (version "0.7.3")
  4076. (source
  4077. (origin
  4078. (method git-fetch)
  4079. (uri (git-reference
  4080. (url "https://github.com/invenia/Mocking.jl")
  4081. (commit (string-append "v" version))))
  4082. (file-name (git-file-name name version))
  4083. (sha256
  4084. (base32 "1cg2is83bjmrchmmxcgx57k8c9b9vlamrw38v4fdhbb6d4six5cg"))))
  4085. (build-system julia-build-system)
  4086. (propagated-inputs
  4087. (list julia-compat
  4088. julia-exprtools))
  4089. (home-page "https://github.com/invenia/Mocking.jl")
  4090. (synopsis "Overload Julia function calls")
  4091. (description "The purpose of this package is to allow Julia function calls
  4092. to be temporarily overloaded for the purpose of testing.")
  4093. (license license:expat)))
  4094. (define-public julia-mosaicviews
  4095. (package
  4096. (name "julia-mosaicviews")
  4097. (version "0.3.3")
  4098. (source
  4099. (origin
  4100. (method git-fetch)
  4101. (uri (git-reference
  4102. (url "https://github.com/JuliaArrays/MosaicViews.jl")
  4103. (commit (string-append "v" version))))
  4104. (file-name (git-file-name name version))
  4105. (sha256
  4106. (base32 "04fgxghyb7n2ji76xkb1r1fjhzsdbgmp5wsfyyn3yjcsdqbyp8pz"))))
  4107. (build-system julia-build-system)
  4108. (arguments
  4109. (list #:tests? #f)) ; Cycle with ImageCore.jl
  4110. (propagated-inputs
  4111. (list julia-mappedarrays
  4112. julia-paddedviews
  4113. julia-stackviews))
  4114. ;(native-inputs
  4115. ; `(("julia-colorvectorspace" ,julia-colorvectorspace)
  4116. ; ("julia-imagecore" ,julia-imagecore)))
  4117. (home-page "https://github.com/JuliaArrays/MosaicViews.jl")
  4118. (synopsis
  4119. "Lazily view a 3D or 4D array as an expanded 2D array as a matrix of slices")
  4120. (description "When visualizing images, it is not uncommon to provide a 2D
  4121. view of different image sources. For example, comparing multiple images of
  4122. different sizes, getting a preview of machine learning dataset. This package
  4123. aims to provide easy-to-use tools for such tasks.")
  4124. (license license:expat)))
  4125. (define-public julia-msgpack
  4126. (package
  4127. (name "julia-msgpack")
  4128. (version "1.1.0")
  4129. (source
  4130. (origin
  4131. (method git-fetch)
  4132. (uri (git-reference
  4133. (url "https://github.com/JuliaIO/MsgPack.jl")
  4134. (commit (string-append "v" version))))
  4135. (file-name (git-file-name name version))
  4136. (sha256
  4137. (base32 "1layiqjf9si38pfdcszppgcy4zbfqgld7jlw8x645sm9b17b19fg"))))
  4138. (build-system julia-build-system)
  4139. (home-page "https://github.com/JuliaIO/MsgPack.jl")
  4140. (synopsis "Julia MsgPack implementation")
  4141. (description "@code{MsgPack.jl} is a MessagePack implementation in pure
  4142. Julia, with type-driven, overloadable packing/unpacking functionality.")
  4143. (license license:expat)))
  4144. (define-public julia-muladdmacro
  4145. (package
  4146. (name "julia-muladdmacro")
  4147. (version "0.2.4")
  4148. (source
  4149. (origin
  4150. (method git-fetch)
  4151. (uri (git-reference
  4152. (url "https://github.com/SciML/MuladdMacro.jl")
  4153. (commit (string-append "v" version))))
  4154. (file-name (git-file-name name version))
  4155. (sha256
  4156. (base32 "0pvmfw7f3igpwx0w8c8i40pls0wfm248b1i662wnlrkqiw56j0yq"))))
  4157. (build-system julia-build-system)
  4158. (home-page "https://github.com/SciML/MuladdMacro.jl")
  4159. (synopsis "Julia macro to convert expressions to use muladd calls and FMA operations")
  4160. (description
  4161. "This package provides the @code{@@muladd} macro. It automatically converts
  4162. expressions with multiplications and additions or subtractions to calls with
  4163. muladd which then fuse via FMA when it would increase the performance of the
  4164. code. The @code{@@muladd} macro can be placed on code blocks and it will automatically
  4165. find the appropriate expressions and nest muladd expressions when necessary. In
  4166. mixed expressions summands without multiplication will be grouped together and
  4167. evaluated first but otherwise the order of evaluation of multiplications and
  4168. additions is not changed.")
  4169. (license license:expat)))
  4170. (define-public julia-mutablearithmetics
  4171. (package
  4172. (name "julia-mutablearithmetics")
  4173. (version "0.2.20")
  4174. (source
  4175. (origin
  4176. (method git-fetch)
  4177. (uri (git-reference
  4178. (url "https://github.com/jump-dev/MutableArithmetics.jl")
  4179. (commit (string-append "v" version))))
  4180. (file-name (git-file-name name version))
  4181. (sha256
  4182. (base32 "1isyj8h4nx96cr6892d154v8pw1nhr7mjyz5bd6ffr2mkzb2bq4f"))))
  4183. (build-system julia-build-system)
  4184. (arguments
  4185. (list
  4186. #:phases
  4187. (if (target-x86-32?)
  4188. #~(modify-phases %standard-phases
  4189. (add-after 'unpack 'remove-failing-test-i686
  4190. (lambda _
  4191. (substitute* "test/utilities.jl"
  4192. ;; Non-deterministic returned value, e.g.,
  4193. ;; Expression: n == @allocated(f())
  4194. ;; Evaluated: 240 == 120
  4195. ;; and for some other values:
  4196. ;; Got correct result, please change to @test
  4197. ;; so @test_broken is not enough.
  4198. (("@test n == @allocated f\\(\\)")
  4199. " ")))))
  4200. #~%standard-phases)))
  4201. (propagated-inputs
  4202. (list julia-offsetarrays))
  4203. (home-page "https://github.com/jump-dev/MutableArithmetics.jl")
  4204. (synopsis "Interface for arithmetics on mutable types in Julia")
  4205. (description "MutableArithmetics is a Julia package which allows:
  4206. @itemize
  4207. @item mutable types to implement mutable arithmetics
  4208. @item algorithms that could exploit mutable arithmetics to exploit them while
  4209. still being completely generic
  4210. @end itemize")
  4211. (license license:mpl2.0)))
  4212. (define-public julia-nanmath
  4213. (package
  4214. (name "julia-nanmath")
  4215. (version "0.3.7")
  4216. (source
  4217. (origin
  4218. (method git-fetch)
  4219. (uri (git-reference
  4220. (url "https://github.com/mlubin/NaNMath.jl")
  4221. (commit (string-append "v" version))))
  4222. (file-name (git-file-name name version))
  4223. (sha256
  4224. (base32 "1fwqa2fzl84a86ppjb2xaqh93b5gg42zyrclbjfdm5l0044hwii6"))))
  4225. (build-system julia-build-system)
  4226. (home-page "https://github.com/mlubin/NaNMath.jl")
  4227. (synopsis "Implementations of basic math functions")
  4228. (description "Implementations of basic math functions which return
  4229. @code{NaN} instead of throwing a @code{DomainError}.")
  4230. (license license:expat)))
  4231. (define-public julia-nlsolversbase
  4232. (package
  4233. (name "julia-nlsolversbase")
  4234. (version "7.8.0")
  4235. (source
  4236. (origin
  4237. (method git-fetch)
  4238. (uri (git-reference
  4239. (url "https://github.com/JuliaNLSolvers/NLSolversBase.jl")
  4240. (commit (string-append "v" version))))
  4241. (file-name (git-file-name name version))
  4242. (sha256
  4243. (base32 "0n8qh5a2ghjx1j70zxn0hmh8gzpa46kmjg8di879y9974bfk0f98"))))
  4244. (build-system julia-build-system)
  4245. (propagated-inputs
  4246. (list julia-diffresults
  4247. julia-finitediff
  4248. julia-forwarddiff))
  4249. (native-inputs
  4250. (list julia-optimtestproblems
  4251. julia-recursivearraytools))
  4252. (home-page "https://github.com/JuliaNLSolvers/NLSolversBase.jl")
  4253. (synopsis "Optimization and equation solver software in JuliaNLSolvers")
  4254. (description "This package aims at establishing common ground for Optim.jl,
  4255. LineSearches.jl, and NLsolve.jl. The common ground is mainly the types used to
  4256. hold objective related callables, information about the objectives, and an
  4257. interface to interact with these types.")
  4258. (license license:expat)))
  4259. (define-public julia-nnlib
  4260. (package
  4261. (name "julia-nnlib")
  4262. (version "0.7.34")
  4263. (source
  4264. (origin
  4265. (method git-fetch)
  4266. (uri (git-reference
  4267. (url "https://github.com/FluxML/NNlib.jl")
  4268. (commit (string-append "v" version))))
  4269. (file-name (git-file-name name version))
  4270. (sha256
  4271. (base32 "1xzlh7pj6aqmbkrskqgwvifprg9a6xkkdh00ls6f6xnzqfrnhwna"))))
  4272. (build-system julia-build-system)
  4273. (arguments
  4274. (list
  4275. #:phases
  4276. #~(modify-phases %standard-phases
  4277. (add-after 'link-depot 'skip-some-tests
  4278. (lambda _
  4279. (substitute* "test/runtests.jl"
  4280. ;; Skip the CUDA tests
  4281. (("using CUDA") "")
  4282. (("&& CUDA\\.functional\\(\\)") "")
  4283. ;; UnicodePlots is only used for the doctests
  4284. (("if VERSION <.*") "if true\n"))
  4285. (setenv "NNLIB_TEST_CUDA" "false"))))))
  4286. (propagated-inputs
  4287. (list julia-adapt
  4288. julia-chainrulescore
  4289. julia-compat
  4290. julia-requires))
  4291. (native-inputs
  4292. (list julia-chainrulestestutils
  4293. julia-stablerngs
  4294. julia-zygote))
  4295. (home-page "https://github.com/FluxML/NNlib.jl")
  4296. (synopsis "Neural Network primitives with multiple backends")
  4297. (description "This package will provide a library of functions useful for
  4298. machine learning, such as softmax, sigmoid, convolutions and pooling. It
  4299. doesn't provide any other \"high-level\" functionality like layers or AD.")
  4300. (license license:expat)))
  4301. (define-public julia-optim
  4302. (package
  4303. (name "julia-optim")
  4304. (version "1.7.4")
  4305. (source
  4306. (origin
  4307. (method git-fetch)
  4308. (uri (git-reference
  4309. (url "https://github.com/JuliaNLSolvers/Optim.jl")
  4310. (commit (string-append "v" version))))
  4311. (file-name (git-file-name name version))
  4312. (sha256
  4313. (base32 "0pdwa2xm08c3g979qgsmcr343j4kkh4l6x5rdj1blhqh5gw8172b"))))
  4314. (build-system julia-build-system)
  4315. (arguments
  4316. (list
  4317. #:phases
  4318. #~(modify-phases %standard-phases
  4319. (add-after 'unpack 'adjust-tests
  4320. (lambda _
  4321. (substitute* "test/runtests.jl"
  4322. ;; Distributions.jl isn't packaged yet.
  4323. ((".*newton_trust_region.*") ""))
  4324. (substitute*
  4325. "test/multivariate/solvers/constrained/ipnewton/constraints.jl"
  4326. ;; TODO: Figure out why this test fails.
  4327. (("@test Optim\\.converged") "@test_skip Optim.converged")
  4328. (("@test Optim\\.minimum") "@test_skip Optim.minimum")))))))
  4329. (propagated-inputs
  4330. (list julia-compat
  4331. julia-fillarrays
  4332. julia-forwarddiff
  4333. julia-linesearches
  4334. julia-nanmath
  4335. julia-nlsolversbase
  4336. julia-parameters
  4337. julia-positivefactorizations
  4338. julia-statsbase))
  4339. (native-inputs
  4340. (list julia-linesearches
  4341. julia-measurements
  4342. julia-nlsolversbase
  4343. julia-optimtestproblems
  4344. julia-positivefactorizations
  4345. julia-recursivearraytools
  4346. julia-stablerngs))
  4347. (home-page "https://github.com/JuliaNLSolvers/Optim.jl")
  4348. (synopsis "Optimization functions for Julia")
  4349. (description "@code{Optim.jl} is a package for univariate and multivariate
  4350. optimization of functions.")
  4351. (license license:expat)))
  4352. (define-public julia-optimisers
  4353. (package
  4354. (name "julia-optimisers")
  4355. (version "0.2.13")
  4356. (source
  4357. (origin
  4358. (method git-fetch)
  4359. (uri (git-reference
  4360. (url "https://github.com/FluxML/Optimisers.jl")
  4361. (commit (string-append "v" version))))
  4362. (file-name (git-file-name name version))
  4363. (sha256
  4364. (base32 "1xs51r365l6r56rpm08kba00nfcl5jlglwy8494w06vbi22ysbq7"))))
  4365. (build-system julia-build-system)
  4366. (propagated-inputs
  4367. (list julia-chainrulescore
  4368. julia-functors
  4369. julia-zygote))
  4370. (native-inputs
  4371. (list julia-staticarrays
  4372. julia-zygote))
  4373. (home-page "https://github.com/FluxML/Optimisers.jl")
  4374. (synopsis "Optimisers and utilities for learning loops")
  4375. (description "@code{Optimisers.jl} defines many standard gradient-based
  4376. optimisation rules, and tools for applying them to deeply nested models.")
  4377. (license license:expat)))
  4378. (define-public julia-optimtestproblems
  4379. (package
  4380. (name "julia-optimtestproblems")
  4381. (version "2.0.2")
  4382. (source
  4383. (origin
  4384. (method git-fetch)
  4385. (uri (git-reference
  4386. (url "https://github.com/JuliaNLSolvers/OptimTestProblems.jl")
  4387. (commit (string-append "v" version))))
  4388. (file-name (git-file-name name version))
  4389. (sha256
  4390. (base32 "10h47x5ws42pkqjccimaz0yxfvz41w0yazq6inamfk4lg5g2g3d9"))))
  4391. (build-system julia-build-system)
  4392. (arguments
  4393. (list
  4394. #:julia-package-name "OptimTestProblems"
  4395. #:julia-package-uuid "cec144fc-5a64-5bc6-99fb-dde8f63e154c"
  4396. #:julia-package-dependencies
  4397. #~(list '("LinearAlgebra" . "37e2e46d-f89d-539d-b4ee-838fcccc9c8e")
  4398. '("SparseArrays" . "2f01184e-e22b-5df5-ae63-d93ebab69eaf")
  4399. '("Test" . "8dfed614-e22c-5e08-85e1-65c5234f0b40"))))
  4400. (home-page "https://github.com/JuliaNLSolvers/OptimTestProblems.jl")
  4401. (synopsis "Collection of optimization test problems")
  4402. (description "The purpose of this package is to provide test problems for
  4403. JuliaNLSolvers packages.")
  4404. (license license:expat)))
  4405. (define-public julia-optionaldata
  4406. (package
  4407. (name "julia-optionaldata")
  4408. (version "1.0.0")
  4409. (source
  4410. (origin
  4411. (method git-fetch)
  4412. (uri (git-reference
  4413. (url "https://github.com/helgee/OptionalData.jl")
  4414. (commit (string-append "v" version))))
  4415. (file-name (git-file-name name version))
  4416. (sha256
  4417. (base32 "11js258j7cz6362ijsi24nih3lx90aalf8k1n3fv6v7iqas8bz5s"))))
  4418. (build-system julia-build-system)
  4419. (home-page "https://github.com/helgee/OptionalData.jl")
  4420. (synopsis "Work with global data that might not be available")
  4421. (description
  4422. "This package provides the @code{@@OptionalData} macro and the corresponding
  4423. OptData type which is a thin wrapper around a nullable value (of type @code{Union{T,
  4424. Nothing} where T)}. It allows you to load and access globally available data at
  4425. runtime in a type-stable way.")
  4426. (license license:expat)))
  4427. (define-public julia-orderedcollections
  4428. (package
  4429. (name "julia-orderedcollections")
  4430. (version "1.4.1")
  4431. (source
  4432. (origin
  4433. (method git-fetch)
  4434. (uri (git-reference
  4435. (url "https://github.com/JuliaCollections/OrderedCollections.jl")
  4436. (commit (string-append "v" version))))
  4437. (file-name (git-file-name name version))
  4438. (sha256
  4439. (base32 "0jaxcmvkp8zpqrz101yikdigz90s70i7in5wn8kybwzf0na3lhwf"))))
  4440. (build-system julia-build-system)
  4441. (home-page "https://github.com/JuliaCollections/OrderedCollections.jl")
  4442. (synopsis "Associative containers that preserve insertion order")
  4443. (description "This package implements @code{OrderedDicts} and
  4444. @code{OrderedSets}, which are similar to containers in base Julia. However,
  4445. during iteration the @code{Ordered*} containers return items in the order in
  4446. which they were added to the collection.")
  4447. (license license:expat)))
  4448. (define-public julia-offsetarrays
  4449. (package
  4450. (name "julia-offsetarrays")
  4451. (version "1.12.8")
  4452. (source
  4453. (origin
  4454. (method git-fetch)
  4455. (uri (git-reference
  4456. (url "https://github.com/JuliaArrays/OffsetArrays.jl")
  4457. (commit (string-append "v" version))))
  4458. (file-name (git-file-name name version))
  4459. (sha256
  4460. (base32 "09cidr42q0xwp6wwyaw09hl580vqi85wb5f78pxrxcfm75yg3xki"))))
  4461. (build-system julia-build-system)
  4462. (propagated-inputs
  4463. (list julia-adapt))
  4464. ;; CatIndices depends on OffsetArrays, introducing a recursive dependency
  4465. (arguments (list #:tests? #f))
  4466. (home-page "https://juliaarrays.github.io/OffsetArrays.jl/stable/")
  4467. (synopsis "Fortran-like arrays with arbitrary, zero or negative indices")
  4468. (description "@code{OffsetArrays.jl} provides Julia users with arrays that
  4469. have arbitrary indices, similar to those found in some other programming
  4470. languages like Fortran.")
  4471. (license license:expat)))
  4472. (define-public julia-paddedviews
  4473. (package
  4474. (name "julia-paddedviews")
  4475. (version "0.5.11")
  4476. (source
  4477. (origin
  4478. (method git-fetch)
  4479. (uri (git-reference
  4480. (url "https://github.com/JuliaArrays/PaddedViews.jl")
  4481. (commit (string-append "v" version))))
  4482. (file-name (git-file-name name version))
  4483. (sha256
  4484. (base32 "1835q06g6ymqh1k7625ssahwm46j08370v2inb61y1lw8vd99f3x"))))
  4485. (build-system julia-build-system)
  4486. (propagated-inputs
  4487. (list julia-offsetarrays))
  4488. (native-inputs
  4489. (list julia-documenter))
  4490. (home-page "https://github.com/JuliaArrays/PaddedViews.jl")
  4491. (synopsis "Add virtual padding to the edges of an array")
  4492. (description "@code{PaddedViews} provides a simple wrapper type,
  4493. @code{PaddedView}, to add \"virtual\" padding to any array without copying data.
  4494. Edge values not specified by the array are assigned a @code{fillvalue}.
  4495. Multiple arrays may be \"promoted\" to have common indices using the
  4496. @code{paddedviews} function.")
  4497. (license license:expat)))
  4498. (define-public julia-parameters
  4499. (package
  4500. (name "julia-parameters")
  4501. (version "0.12.2")
  4502. (source
  4503. (origin
  4504. (method git-fetch)
  4505. (uri (git-reference
  4506. (url "https://github.com/mauro3/Parameters.jl")
  4507. (commit (string-append "v" version))))
  4508. (file-name (git-file-name name version))
  4509. (sha256
  4510. (base32 "0b8lawi7kcws4axfsdf023gyxca15irl648ciyi1kw3wghz3pfi2"))))
  4511. (build-system julia-build-system)
  4512. (propagated-inputs
  4513. (list julia-orderedcollections
  4514. julia-unpack))
  4515. (home-page "https://github.com/mauro3/Parameters.jl")
  4516. (synopsis "Numerical-model parameter helpers")
  4517. (description "This package contains types with default field values, keyword
  4518. constructors and (un-)pack macros. Keyword functions can be slow in Julia,
  4519. however, the normal positional constructor is also provided and could be used in
  4520. performance critical code.")
  4521. (license license:expat)))
  4522. (define-public julia-parsers
  4523. (package
  4524. (name "julia-parsers")
  4525. (version "2.2.4")
  4526. (source
  4527. (origin
  4528. (method git-fetch)
  4529. (uri (git-reference
  4530. (url "https://github.com/JuliaData/Parsers.jl")
  4531. (commit (string-append "v" version))))
  4532. (file-name (git-file-name name version))
  4533. (sha256
  4534. (base32 "09v2x9yd1wdp74hzsf6218dpamlf2hb5nkmixqb4bc53ll8hpw4i"))))
  4535. (build-system julia-build-system)
  4536. (home-page "https://github.com/JuliaData/Parsers.jl")
  4537. (synopsis "Fast parsing machinery for basic types in Julia")
  4538. (description "@code{Parsers.jl} is a collection of type parsers and
  4539. utilities for Julia.")
  4540. (license license:expat)))
  4541. (define-public julia-pdmats
  4542. (package
  4543. (name "julia-pdmats")
  4544. (version "0.11.1")
  4545. (source
  4546. (origin
  4547. (method git-fetch)
  4548. (uri (git-reference
  4549. (url "https://github.com/JuliaStats/PDMats.jl")
  4550. (commit (string-append "v" version))))
  4551. (file-name (git-file-name name version))
  4552. (sha256
  4553. (base32 "0bc2gmpd30rkclvxyfnssjllp0pk63h0vvgr8862phm5ia83r8j0"))))
  4554. (build-system julia-build-system)
  4555. (home-page "https://github.com/JuliaStats/PDMats.jl")
  4556. (synopsis
  4557. "Uniform Interface for positive definite matrices of various structures")
  4558. (description "PDMats.jl supports efficient computation on positive definite
  4559. matrices of various structures. In particular, it provides uniform interfaces
  4560. to use positive definite matrices of various structures for writing generic
  4561. algorithms, while ensuring that the most efficient implementation is used in
  4562. actual computation.")
  4563. (license license:expat)))
  4564. (define-public julia-plotthemes
  4565. (package
  4566. (name "julia-plotthemes")
  4567. (version "2.0.1")
  4568. (source
  4569. (origin
  4570. (method git-fetch)
  4571. (uri (git-reference
  4572. (url "https://github.com/JuliaPlots/PlotThemes.jl")
  4573. (commit (string-append "v" version))))
  4574. (file-name (git-file-name name version))
  4575. (sha256
  4576. (base32 "1fd27w9z1vhz0d1bzrs5vcavpb5r5jviyh27d9c4ka37phz4xvmh"))))
  4577. (build-system julia-build-system)
  4578. (propagated-inputs
  4579. (list julia-plotutils
  4580. julia-requires))
  4581. (home-page "https://github.com/JuliaPlots/PlotThemes.jl")
  4582. (synopsis "Themes for the Julia plotting package Plots.jl")
  4583. (description
  4584. "PlotThemes is a package to spice up the plots made with @code{Plots.jl}.")
  4585. (license license:expat)))
  4586. (define-public julia-plotutils
  4587. (package
  4588. (name "julia-plotutils")
  4589. (version "1.2.0")
  4590. (source
  4591. (origin
  4592. (method git-fetch)
  4593. (uri (git-reference
  4594. (url "https://github.com/JuliaPlots/PlotUtils.jl")
  4595. (commit (string-append "v" version))))
  4596. (file-name (git-file-name name version))
  4597. (sha256
  4598. (base32 "1yml9ayaniqnzx5r8sfjckifcm99ck7qhc19cd8fs0bwzkh7nza7"))))
  4599. (build-system julia-build-system)
  4600. (arguments
  4601. (list
  4602. #:phases
  4603. #~(modify-phases %standard-phases
  4604. (add-after 'unpack 'adjust-test-suite
  4605. (lambda _
  4606. (substitute* "test/runtests.jl"
  4607. (("(@test_throws) ErrorException (.*notacolor)" _ @test notacolor)
  4608. (string-append @test " ArgumentError " notacolor))))))))
  4609. (propagated-inputs
  4610. (list julia-colors
  4611. julia-colorschemes
  4612. julia-reexport))
  4613. (native-inputs
  4614. (list julia-stablerngs))
  4615. (home-page "https://github.com/JuliaPlots/PlotUtils.jl")
  4616. (synopsis "Helper algorithms for building plotting components")
  4617. (description "This package contains generic helper algorithms for building
  4618. plotting components.")
  4619. (license license:expat)))
  4620. (define-public julia-pooledarrays
  4621. (package
  4622. (name "julia-pooledarrays")
  4623. (version "1.4.2")
  4624. (source
  4625. (origin
  4626. (method git-fetch)
  4627. (uri (git-reference
  4628. (url "https://github.com/JuliaData/PooledArrays.jl")
  4629. (commit (string-append "v" version))))
  4630. (file-name (git-file-name name version))
  4631. (sha256
  4632. (base32 "0g30d46n8cc8vr9icjhfkqz2il2185ijh7xhfy9vhcnmllzpd0yg"))))
  4633. (build-system julia-build-system)
  4634. (propagated-inputs
  4635. (list julia-dataapi))
  4636. (native-inputs
  4637. (list julia-offsetarrays))
  4638. (home-page "https://github.com/JuliaData/PooledArrays.jl")
  4639. (synopsis "Pooled representation of arrays in Julia")
  4640. (description "This package provides a pooled representation of arrays for
  4641. purposes of compression when there are few unique elements.")
  4642. (license license:expat)))
  4643. (define-public julia-positivefactorizations
  4644. (package
  4645. (name "julia-positivefactorizations")
  4646. (version "0.2.4")
  4647. (source
  4648. (origin
  4649. (method git-fetch)
  4650. (uri (git-reference
  4651. (url "https://github.com/timholy/PositiveFactorizations.jl")
  4652. (commit (string-append "v" version))))
  4653. (file-name (git-file-name name version))
  4654. (sha256
  4655. (base32 "1wxy6ak7f3hvibcgc8q88cgkf9zvi649mmjy1zlkx1qk80hgvz23"))))
  4656. (build-system julia-build-system)
  4657. (native-inputs
  4658. (list julia-forwarddiff
  4659. julia-reversediff))
  4660. (home-page "https://github.com/timholy/PositiveFactorizations.jl")
  4661. (synopsis "Positive-definite \"approximations\" to matrices")
  4662. (description "@code{PositiveFactorizations} is a package for computing a
  4663. positive definite matrix decomposition (factorization) from an arbitrary
  4664. symmetric input. The motivating application is optimization (Newton or
  4665. quasi-Newton methods), in which the canonical search direction -H/g (H being the
  4666. Hessian and g the gradient) may not be a descent direction if H is not positive
  4667. definite.")
  4668. (license license:expat)))
  4669. (define-public julia-preferences
  4670. (package
  4671. (name "julia-preferences")
  4672. (version "1.2.2")
  4673. (source
  4674. (origin
  4675. (method git-fetch)
  4676. (uri (git-reference
  4677. (url "https://github.com/JuliaPackaging/Preferences.jl")
  4678. (commit (string-append "v" version))))
  4679. (file-name (git-file-name name version))
  4680. (sha256
  4681. (base32 "1cail43iqzbi6m9v6981rhz47zf2lcvhs5ds5gdqvc9nx5frghxq"))))
  4682. (build-system julia-build-system)
  4683. (arguments
  4684. (list #:tests? #f)) ; Tests try to mkdir /.julia
  4685. (home-page "https://github.com/JuliaPackaging/Preferences.jl")
  4686. (synopsis "Store configuration switches to TOML files")
  4687. (description "The @code{Preferences} package provides an integrated way for
  4688. packages to store configuration switches to persistent TOML files, and use those
  4689. pieces of information at both run time and compile time in Julia. This enables
  4690. the user to modify the behavior of a package, and have that choice reflected in
  4691. everything from run time algorithm choice to code generation at compile time.")
  4692. (license license:expat)))
  4693. (define-public julia-prettytables
  4694. (package
  4695. (name "julia-prettytables")
  4696. (version "1.0.1")
  4697. (source
  4698. (origin
  4699. (method git-fetch)
  4700. (uri (git-reference
  4701. (url "https://github.com/ronisbr/PrettyTables.jl")
  4702. (commit (string-append "v" version))))
  4703. (file-name (git-file-name name version))
  4704. (sha256
  4705. (base32 "1d1sd87kkwbar3l608h0adzws42cwdrmp1idxx7an6mfqcsdrijw"))))
  4706. (build-system julia-build-system)
  4707. (arguments
  4708. (list
  4709. #:phases
  4710. #~(modify-phases %standard-phases
  4711. (add-after 'link-depot 'skip-color-tests
  4712. (lambda _
  4713. (substitute* "test/text_backend.jl"
  4714. ((".*colors\\.jl.*") "")))))))
  4715. (propagated-inputs
  4716. (list julia-crayons
  4717. julia-formatting
  4718. julia-reexport
  4719. julia-tables))
  4720. (home-page "https://github.com/ronisbr/PrettyTables.jl")
  4721. (synopsis "Print data in formatted tables")
  4722. (description "This package has the purpose to print data in matrices in a
  4723. human-readable format.")
  4724. (license license:expat)))
  4725. (define-public julia-pycall
  4726. (package
  4727. (name "julia-pycall")
  4728. (version "1.92.5")
  4729. (source
  4730. (origin
  4731. (method git-fetch)
  4732. (uri (git-reference
  4733. (url "https://github.com/JuliaPy/PyCall.jl")
  4734. (commit (string-append "v" version))))
  4735. (file-name (git-file-name name version))
  4736. (sha256
  4737. (base32
  4738. "1fj5d1ihnhnm0pl4hbx6hcd2bpdyhm8jiaqah2axsbd069j70saf"))))
  4739. (build-system julia-build-system)
  4740. (arguments
  4741. (list
  4742. #:imported-modules `((guix build python-build-system)
  4743. ,@%julia-build-system-modules)
  4744. #:modules '((guix build julia-build-system)
  4745. (guix build utils)
  4746. ((guix build python-build-system) #:prefix python:))
  4747. #:phases
  4748. #~(modify-phases %standard-phases
  4749. (add-after 'link-depot 'remove-conda
  4750. (lambda _
  4751. (substitute* "Project.toml"
  4752. ((".*Conda.*") ""))
  4753. (substitute* (list "src/PyCall.jl"
  4754. "test/runtests.jl")
  4755. (("import Conda") ""))
  4756. (substitute* "deps/depsutils.jl"
  4757. (("Conda.PYTHONDIR") "\"/\""))))
  4758. (add-after 'link-depot 'set-python
  4759. (lambda* (#:key inputs outputs #:allow-other-keys)
  4760. (let ((python (assoc-ref inputs "python")))
  4761. (setenv "PYCALL_JL_RUNTIME_PYTHON"
  4762. (string-append python "/bin/python3"))
  4763. (with-output-to-file "deps/deps.jl"
  4764. (lambda _
  4765. (format #t
  4766. "const python = \"~a/bin/python3\"~@
  4767. const pyprogramname = \"~a/bin/python3\"~@
  4768. const libpython = \"~a/lib/libpython~a.so.1.0\"~@
  4769. const PYTHONHOME = \"~a\"~@
  4770. const pyversion_build = v\"~a\"~@
  4771. const conda = false~%"
  4772. python
  4773. python
  4774. python
  4775. (python:python-version python)
  4776. python
  4777. #$(package-version python)))))))
  4778. (add-before 'check 'pre-check
  4779. (lambda _
  4780. (setenv "CI" "true")
  4781. (setenv "JULIA_PKGEVAL" "true"))))))
  4782. (propagated-inputs
  4783. (list julia-macrotools
  4784. julia-versionparsing))
  4785. (inputs
  4786. (list python))
  4787. (native-inputs
  4788. (list python-numpy))
  4789. (home-page "https://github.com/JuliaPy/PyCall.jl")
  4790. (synopsis "Call Python functions from the Julia language")
  4791. (description "This package provides the ability to directly call and fully
  4792. interoperate with Python from the Julia language. You can import arbitrary
  4793. Python modules from Julia, call Python functions (with automatic conversion of
  4794. types between Julia and Python), define Python classes from Julia methods, and
  4795. share large data structures between Julia and Python without copying them.")
  4796. (license license:expat)))
  4797. (define-public julia-pyplot
  4798. (package
  4799. (name "julia-pyplot")
  4800. (version "2.10.0")
  4801. (source
  4802. (origin
  4803. (method git-fetch)
  4804. (uri (git-reference
  4805. (url "https://github.com/JuliaPy/PyPlot.jl")
  4806. (commit (string-append "v" version))))
  4807. (file-name (git-file-name name version))
  4808. (sha256
  4809. (base32 "007zs0imfgs69f30pp2a3rc93kl0qiq7qjx6ig35z4wzkmps4skd"))))
  4810. (build-system julia-build-system)
  4811. (propagated-inputs
  4812. (list julia-colors
  4813. julia-latexstrings
  4814. julia-pycall
  4815. julia-versionparsing
  4816. ;; python-matplotlib is expected to be available at runtime.
  4817. python-matplotlib))
  4818. (home-page "https://github.com/JuliaPy/PyPlot.jl")
  4819. (synopsis "Plotting for Julia based on matplotlib.pyplot")
  4820. (description "This package provides a Julia interface to the Matplotlib
  4821. plotting library from Python, and specifically to the @code{matplotlib.pyplot}
  4822. module. PyPlot uses the Julia PyCall package to call Matplotlib directly from
  4823. Julia with little or no overhead (arrays are passed without making a copy).")
  4824. (license license:expat)))
  4825. (define-public julia-quadgk
  4826. (package
  4827. (name "julia-quadgk")
  4828. (version "2.5.0")
  4829. (source
  4830. (origin
  4831. (method git-fetch)
  4832. (uri (git-reference
  4833. (url "https://github.com/JuliaMath/QuadGK.jl")
  4834. (commit (string-append "v" version))))
  4835. (file-name (git-file-name name version))
  4836. (sha256
  4837. (base32 "0f14dhn0f7ln2j96qvmnsyy9ffzqsngd16ikc136snlxv4k4whiv"))))
  4838. (build-system julia-build-system)
  4839. (propagated-inputs
  4840. (list julia-datastructures))
  4841. (home-page "https://github.com/JuliaMath/QuadGK.jl")
  4842. (synopsis "Adaptive 1d numerical Gauss–Kronrod integration")
  4843. (description "This package provides support for one-dimensional numerical
  4844. integration in Julia using adaptive Gauss-Kronrod quadrature. The code was
  4845. originally part of Base Julia. It supports integration of arbitrary numeric
  4846. types, including arbitrary precision (@code{BigFloat}), and even integration of
  4847. arbitrary normed vector spaces (e.g. matrix-valued integrands).")
  4848. (license license:expat)))
  4849. (define-public julia-quadmath
  4850. (package
  4851. (name "julia-quadmath")
  4852. (version "0.5.5")
  4853. (source
  4854. (origin
  4855. (method git-fetch)
  4856. (uri (git-reference
  4857. (url "https://github.com/JuliaMath/Quadmath.jl")
  4858. (commit (string-append "v" version))))
  4859. (file-name (git-file-name name version))
  4860. (sha256
  4861. (base32 "051biw4b9zni7cmh2f1yzifp1v8wazlfxrdz4p44lyd1wba6379w"))))
  4862. (build-system julia-build-system)
  4863. (arguments
  4864. (list
  4865. #:phases
  4866. #~(modify-phases %standard-phases
  4867. (add-after 'link-depot 'hardcode-libmath-location
  4868. (lambda* (#:key inputs #:allow-other-keys)
  4869. (let ((gcclib (assoc-ref inputs "gcc:lib")))
  4870. (substitute* "src/Quadmath.jl"
  4871. (("libgcc_s.so.1" lib) (string-append gcclib "/lib/" lib))
  4872. (("libquadmath.so.0" lib) (string-append gcclib "/lib/" lib)))))))))
  4873. (propagated-inputs
  4874. (list julia-requires))
  4875. (inputs
  4876. `(("gcc:lib" ,gcc "lib")))
  4877. (native-inputs
  4878. (list julia-specialfunctions))
  4879. (home-page "https://github.com/JuliaMath/Quadmath.jl")
  4880. (synopsis "Float128 and libquadmath for the Julia language")
  4881. (description "This is a Julia interface to @code{libquadmath}, providing a
  4882. @code{Float128} type corresponding to the IEEE754 binary128 floating point
  4883. format.")
  4884. (license license:expat)))
  4885. (define-public julia-quaternions
  4886. (package
  4887. (name "julia-quaternions")
  4888. (version "0.4.2")
  4889. (source
  4890. (origin
  4891. (method git-fetch)
  4892. (uri (git-reference
  4893. (url "https://github.com/JuliaGeometry/Quaternions.jl")
  4894. (commit (string-append "v" version))))
  4895. (file-name (git-file-name name version))
  4896. (sha256
  4897. (base32 "1zhynyvchc50hywws2jznpkwydr3njh8cv84d2ylyabhcwwmil9s"))))
  4898. (build-system julia-build-system)
  4899. (propagated-inputs
  4900. (list julia-dualnumbers))
  4901. (home-page "https://github.com/JuliaGeometry/Quaternions.jl")
  4902. (synopsis "Quaternion and dual-quaternion functionality")
  4903. (description "Quaternions are best known for their suitability as
  4904. representations of 3D rotational orientation. They can also be viewed as an
  4905. extension of complex numbers.")
  4906. (license license:expat)))
  4907. (define-public julia-queryoperators
  4908. (package
  4909. (name "julia-queryoperators")
  4910. (version "0.9.3")
  4911. (source
  4912. (origin
  4913. (method git-fetch)
  4914. (uri (git-reference
  4915. (url "https://github.com/queryverse/QueryOperators.jl")
  4916. (commit (string-append "v" version))))
  4917. (file-name (git-file-name name version))
  4918. (sha256
  4919. (base32 "06zm4cbn3x49lbpgshhdfvvmgz066qkc8q0d57igm5p8bcp6js22"))))
  4920. (build-system julia-build-system)
  4921. (propagated-inputs
  4922. (list julia-datastructures
  4923. julia-iteratorinterfaceextensions
  4924. julia-tableshowutils))
  4925. (home-page "https://github.com/queryverse/QueryOperators.jl")
  4926. (synopsis "Query operators for Julia")
  4927. (description "This package contains the underlying query operators that are
  4928. exposed to users in @code{Query.jl}.")
  4929. (license license:expat)))
  4930. (define-public julia-rangearrays
  4931. (package
  4932. (name "julia-rangearrays")
  4933. (version "0.3.2")
  4934. (source
  4935. (origin
  4936. (method git-fetch)
  4937. (uri (git-reference
  4938. (url "https://github.com/JuliaArrays/RangeArrays.jl")
  4939. (commit (string-append "v" version))))
  4940. (file-name (git-file-name name version))
  4941. (sha256
  4942. (base32 "1ihzfyfq1xihkjcvn7xmzfbn6igzidb4fkzdcxwfr5qkvi52gnmg"))))
  4943. (build-system julia-build-system)
  4944. (home-page "https://github.com/JuliaArrays/RangeArrays.jl")
  4945. (synopsis "Array data structures with autogenerated columns")
  4946. (description "The goal of RangeArrays is to provide efficient and convenient
  4947. array data structures where the columns of the arrays are generated (on the fly)
  4948. by Ranges.")
  4949. (license license:expat)))
  4950. (define-public julia-ratios
  4951. (package
  4952. (name "julia-ratios")
  4953. (version "0.4.0")
  4954. (source
  4955. (origin
  4956. (method git-fetch)
  4957. (uri (git-reference
  4958. (url "https://github.com/timholy/Ratios.jl")
  4959. (commit (string-append "v" version))))
  4960. (file-name (git-file-name name version))
  4961. (sha256
  4962. (base32 "1a4fd4jq4qjply29rkwg3m1clfndjsbckj1b1dab1bc35h2c6yxh"))))
  4963. (build-system julia-build-system)
  4964. (home-page "https://github.com/timholy/Ratios.jl")
  4965. (synopsis "Faster Rational-like types for Julia")
  4966. (description "This package provides types similar to Julia's @code{Rational}
  4967. type, which make some sacrifices but have better computational performance.")
  4968. (license license:expat)))
  4969. (define-public julia-realdot
  4970. (package
  4971. (name "julia-realdot")
  4972. (version "0.1.0")
  4973. (source
  4974. (origin
  4975. (method git-fetch)
  4976. (uri (git-reference
  4977. (url "https://github.com/JuliaMath/RealDot.jl")
  4978. (commit (string-append "v" version))))
  4979. (file-name (git-file-name name version))
  4980. (sha256
  4981. (base32 "1jr8dq110j8axjfz936b1lqqcnqg3979rfg11w76rq1iz7zgi691"))))
  4982. (build-system julia-build-system)
  4983. (home-page "https://github.com/JuliaMath/RealDot.jl")
  4984. (synopsis "Compute realdot efficiently")
  4985. (description "This package only contains and exports a single function
  4986. @code{realdot(x, y)}. It computes @code{real(LinearAlgebra.dot(x, y))} while
  4987. avoiding computing the imaginary part of @code{LinearAlgebra.dot(x, y)} if
  4988. possible. The real dot product is useful when one treats complex numbers as
  4989. embedded in a real vector space.")
  4990. (license license:expat)))
  4991. (define-public julia-recipesbase
  4992. (package
  4993. (name "julia-recipesbase")
  4994. (version "1.1.1")
  4995. (source
  4996. (origin
  4997. (method git-fetch)
  4998. (uri (git-reference
  4999. (url "https://github.com/JuliaPlots/RecipesBase.jl")
  5000. (commit (string-append "v" version))))
  5001. (file-name (git-file-name name version))
  5002. (sha256
  5003. (base32 "1b6m5rz6wprj30rwvlxz4r1jv5gl0ay0f52kfmy2w7lqly7zhap5"))))
  5004. (build-system julia-build-system)
  5005. (home-page "https://github.com/JuliaPlots/RecipesBase.jl")
  5006. (synopsis "Define transformation recipes on user types")
  5007. (description "This package implements handy macros @code{@@recipe} and
  5008. @code{@@series} which will define a custom transformation and attach attributes
  5009. for user types. Its design is an attempt to simplify and generalize the summary
  5010. and display of types and data from external packages. With this package it is
  5011. possible to describe visualization routines that can be used as components in
  5012. more complex visualizations.")
  5013. (license license:expat)))
  5014. (define-public julia-recipespipeline
  5015. (package
  5016. (name "julia-recipespipeline")
  5017. (version "0.3.4")
  5018. (source
  5019. (origin
  5020. (method git-fetch)
  5021. (uri (git-reference
  5022. (url "https://github.com/JuliaPlots/RecipesPipeline.jl")
  5023. (commit (string-append "v" version))))
  5024. (file-name (git-file-name name version))
  5025. (sha256
  5026. (base32 "0zq4bzxvq36zr0va6iip3x97mgq5b4fwza8avszx1ryfqm3lg1f7"))))
  5027. (build-system julia-build-system)
  5028. (arguments
  5029. (list #:tests? #f)) ; Cycle with Plots.jl.
  5030. (propagated-inputs
  5031. (list julia-nanmath
  5032. julia-plotutils
  5033. julia-recipesbase))
  5034. (home-page "https://juliaplots.org/RecipesPipeline.jl/dev/")
  5035. (synopsis "Utilities for processing recipes")
  5036. (description "This package was factored out of @code{Plots.jl} to allow any
  5037. other plotting package to use the recipe pipeline. In short, the extremely
  5038. lightweight @code{RecipesBase.jl} package can be depended on by any package to
  5039. define \"recipes\": plot specifications of user-defined types, as well as custom
  5040. plot types. @code{RecipePipeline.jl} contains the machinery to translate these
  5041. recipes to full specifications for a plot.")
  5042. (license license:expat)))
  5043. (define-public julia-recursivearraytools
  5044. (package
  5045. (name "julia-recursivearraytools")
  5046. (version "2.16.1")
  5047. (source
  5048. (origin
  5049. (method git-fetch)
  5050. (uri (git-reference
  5051. (url "https://github.com/SciML/RecursiveArrayTools.jl")
  5052. (commit (string-append "v" version))))
  5053. (file-name (git-file-name name version))
  5054. (sha256
  5055. (base32 "0vx8ndxrii53na7jsc2lki47wfpi77rn3y2r6xhiysx1qwr14msf"))))
  5056. (build-system julia-build-system)
  5057. (arguments
  5058. (list #:tests? #f)) ; Cycle with OrdinaryDiffEq.jl.
  5059. (propagated-inputs
  5060. (list julia-arrayinterface
  5061. julia-chainrulescore
  5062. julia-docstringextensions
  5063. julia-recipesbase
  5064. julia-requires
  5065. julia-staticarrays
  5066. julia-zygoterules))
  5067. ;(native-inputs
  5068. ; `(("julia-forwarddiff" ,julia-forwarddiff)
  5069. ; ("julia-nlsolve" ,julia-nlsolve)
  5070. ; ("julia-ordinarydiffeq" ,julia-ordinarydiffeq)
  5071. ; ("julia-structarrays" ,julia-structarrays)
  5072. ; ("julia-zygote" ,julia-zygote)))
  5073. (home-page "https://github.com/SciML/RecursiveArrayTools.jl")
  5074. (synopsis "Tools for handling objects like arrays of arrays and deeper nestings")
  5075. (description "@code{RecursiveArrayTools.jl} is a set of tools for dealing with
  5076. recursive arrays like arrays of arrays.")
  5077. (license license:expat)))
  5078. (define-public julia-reexport
  5079. (package
  5080. (name "julia-reexport")
  5081. (version "1.2.2")
  5082. (source
  5083. (origin
  5084. (method git-fetch)
  5085. (uri (git-reference
  5086. (url "https://github.com/simonster/Reexport.jl")
  5087. (commit (string-append "v" version))))
  5088. (file-name (git-file-name name version))
  5089. (sha256
  5090. (base32 "0inf5q6f01ncd5c5wm8mwzv2hs627ng6xlh8dhrlflp321hbamwf"))))
  5091. (build-system julia-build-system)
  5092. (home-page "https://github.com/simonster/Reexport.jl")
  5093. (synopsis "Re-export modules and symbols")
  5094. (description "This package provides tools to re-export modules and symbols.")
  5095. (license license:expat)))
  5096. (define-public julia-remotefiles
  5097. (package
  5098. (name "julia-remotefiles")
  5099. (version "0.5.0")
  5100. (source
  5101. (origin
  5102. (method git-fetch)
  5103. (uri (git-reference
  5104. (url "https://github.com/helgee/RemoteFiles.jl")
  5105. (commit (string-append "v" version))))
  5106. (file-name (git-file-name name version))
  5107. (sha256
  5108. (base32 "1zpklzpd4ckp7s4wbf93qmq3dyyrx4pzl41x5i9zbiskadhniqnh"))))
  5109. (build-system julia-build-system)
  5110. (arguments
  5111. '(#:tests? #f)) ; Tests try to download from Internet.
  5112. (propagated-inputs
  5113. (list julia-fileio julia-http))
  5114. (home-page "https://github.com/helgee/RemoteFiles.jl")
  5115. (synopsis "Download files from the Internet and keep them up-to-date")
  5116. (description
  5117. "This package provides a functionality of files download with cURL, wget or
  5118. @code{HTTP.jl} backends.")
  5119. (license license:expat)))
  5120. (define-public julia-referencetests
  5121. (package
  5122. (name "julia-referencetests")
  5123. (version "0.9.7")
  5124. (source
  5125. (origin
  5126. (method git-fetch)
  5127. (uri (git-reference
  5128. (url "https://github.com/JuliaTesting/ReferenceTests.jl")
  5129. (commit (string-append "v" version))))
  5130. (file-name (git-file-name name version))
  5131. (sha256
  5132. (base32 "0mm6bjhs8a21pippww6b08b5frmnb9m6k8xrszrwq9zhc879zpc9"))))
  5133. (build-system julia-build-system)
  5134. (arguments
  5135. (list #:tests? #f)) ; Cycle with ImageCore.jl through ImageMagick.jl.
  5136. (propagated-inputs
  5137. (list julia-deepdiffs
  5138. julia-distances
  5139. julia-fileio
  5140. julia-imagecore
  5141. julia-imageinterminal))
  5142. ;(native-inputs
  5143. ; `(("julia-csvfiles" ,julia-csvfiles)
  5144. ; ("julia-dataframes" ,julia-dataframes)
  5145. ; ("julia-gr" ,julia-gr)
  5146. ; ("julia-imagemagick" ,julia-imagemagick)
  5147. ; ("julia-imagetransformations" ,julia-imagetransformations)
  5148. ; ("julia-plots" ,julia-plots)
  5149. ; ("julia-testimages" ,julia-testimages)))
  5150. (home-page "https://juliatesting.github.io/ReferenceTests.jl/latest/")
  5151. (synopsis "Utility package for comparing data against reference files")
  5152. (description "@code{ReferenceTests.jl} is a Julia package that adds a couple
  5153. of additional macros to your testing toolbox. In particular, it focuses on
  5154. functionality for testing values against reference files, which in turn the
  5155. package can help create and update if need be.")
  5156. (license license:expat)))
  5157. (define-public julia-requires
  5158. (package
  5159. (name "julia-requires")
  5160. (version "1.3.0")
  5161. (source
  5162. (origin
  5163. (method git-fetch)
  5164. (uri (git-reference
  5165. (url "https://github.com/JuliaPackaging/Requires.jl/")
  5166. (commit (string-append "v" version))))
  5167. (file-name (git-file-name name version))
  5168. (sha256
  5169. (base32 "0gmqs7f17aq500lbdff4ibws00f8m0pnzskvf4b3ig520xv3n3nm"))))
  5170. (build-system julia-build-system)
  5171. (arguments
  5172. (list #:parallel-tests? #f)) ; Test suite has race conditions.
  5173. (native-inputs
  5174. (list julia-colors
  5175. julia-example))
  5176. (home-page "https://github.com/JuliaPackaging/Requires.jl/")
  5177. (synopsis "Faster package loader")
  5178. (description "This package make loading packages faster, maybe. It
  5179. supports specifying glue code in packages which will load automatically when
  5180. another package is loaded, so that explicit dependencies (and long load times)
  5181. can be avoided.")
  5182. (license license:expat)))
  5183. (define-public julia-reversediff
  5184. (package
  5185. (name "julia-reversediff")
  5186. (version "1.14.4")
  5187. (source
  5188. (origin
  5189. (method git-fetch)
  5190. (uri (git-reference
  5191. (url "https://github.com/JuliaDiff/ReverseDiff.jl")
  5192. (commit (string-append "v" version))))
  5193. (file-name (git-file-name name version))
  5194. (sha256
  5195. (base32 "0hwsjmr4wiscqa5kaj4mw0i4agyyzdcmq4r1gp2i563nc1ziaylg"))))
  5196. (build-system julia-build-system)
  5197. (arguments
  5198. ;; XXXX: Test suite failing for i686, e.g.,
  5199. ;; Expression: hash(tr_float, hash(1)) === hash(v_float, hash(1))
  5200. ;; MethodError: no method matching decompose(::ReverseDiff.TrackedReal{Float64, Float64, Nothing})
  5201. ;; Disable as stopgap.
  5202. (list #:tests? (not (or (%current-target-system)
  5203. (target-x86-32?)))))
  5204. (propagated-inputs
  5205. (list julia-chainrulescore
  5206. julia-diffresults
  5207. julia-diffrules
  5208. julia-difftests
  5209. julia-forwarddiff
  5210. julia-functionwrappers
  5211. julia-logexpfunctions
  5212. julia-macrotools
  5213. julia-nanmath
  5214. julia-specialfunctions
  5215. julia-staticarrays))
  5216. (native-inputs
  5217. (list julia-difftests
  5218. julia-fillarrays))
  5219. (home-page "https://github.com/JuliaDiff/ReverseDiff.jl")
  5220. (synopsis "Reverse Mode Automatic Differentiation for Julia")
  5221. (description "@code{ReverseDiff.jl} is a fast and compile-able tape-based
  5222. reverse mode @acronym{AD, automatic differentiation}, that implements methods to
  5223. take gradients, Jacobians, Hessians, and higher-order derivatives of native
  5224. Julia functions (or any callable object, really).")
  5225. (license license:expat)))
  5226. (define-public julia-richardson
  5227. (package
  5228. (name "julia-richardson")
  5229. (version "1.4.0")
  5230. (source
  5231. (origin
  5232. (method git-fetch)
  5233. (uri (git-reference
  5234. (url "https://github.com/JuliaMath/Richardson.jl")
  5235. (commit (string-append "v" version))))
  5236. (file-name (git-file-name name version))
  5237. (sha256
  5238. (base32 "06v9ii3d7hh41fsrfklaa8ap55z5s017f888mrd1c18y4fx9i4nx"))))
  5239. (build-system julia-build-system)
  5240. (home-page "https://juliapackages.com/p/richardson")
  5241. (synopsis "Extrapolate function using Richardson method")
  5242. (description "This package provides a function extrapolate that
  5243. extrapolates a given function @code{f(x)} to @code{f(x0)}, evaluating @code{f}
  5244. only at a geometric sequence of points @code{> x0} (or optionally @code{<
  5245. x0}). The key algorithm is Richardson extrapolation using a Neville–Aitken
  5246. tableau, which adaptively increases the degree of an extrapolation polynomial
  5247. until convergence is achieved to a desired tolerance (or convergence stalls
  5248. due to e.g. floating-point errors). This allows one to obtain @code{f(x0)} to
  5249. high-order accuracy, assuming that @code{f(x0+h)} has a Taylor series or some
  5250. other power series in @code{h}.")
  5251. (license license:expat)))
  5252. (define-public julia-rotations
  5253. ;; This is the first commit with support for julia-1.6.
  5254. (let ((commit "b599102535bc3534252c76f3fd4cf521f4741788")
  5255. (revision "1"))
  5256. (package
  5257. (name "julia-rotations")
  5258. (version (git-version "1.0.2" revision commit))
  5259. (source
  5260. (origin
  5261. (method git-fetch)
  5262. (uri (git-reference
  5263. (url "https://github.com/JuliaGeometry/Rotations.jl")
  5264. (commit commit)))
  5265. (file-name (git-file-name name version))
  5266. (sha256
  5267. (base32 "01wwqbdmj61yiz7rkmams4xg7gb9hbmg325173846ky4b9x1wb19"))))
  5268. (build-system julia-build-system)
  5269. (propagated-inputs
  5270. (list julia-staticarrays))
  5271. (native-inputs
  5272. (list julia-benchmarktools
  5273. julia-forwarddiff
  5274. julia-unitful))
  5275. (home-page "https://github.com/JuliaGeometry/Rotations.jl")
  5276. (synopsis "Julia implementations for different rotation parameterisations")
  5277. (description "This package implements various 3D rotation parameterizations
  5278. and defines conversions between them. At their heart, each rotation
  5279. parameterization is a 3×3 unitary (orthogonal) matrix (based on the
  5280. @code{StaticArrays.jl} package), and acts to rotate a 3-vector about the origin
  5281. through matrix-vector multiplication.")
  5282. (license license:expat))))
  5283. (define-public julia-safetestsets
  5284. ;; The only release tag is the first commit in the repository.
  5285. (let ((commit "e553edc4c753344d38349304b9ff5483c3b8ff21")
  5286. (revision "1"))
  5287. (package
  5288. (name "julia-safetestsets")
  5289. (version (git-version "0.0.1" revision commit))
  5290. (source
  5291. (origin
  5292. (method git-fetch)
  5293. (uri (git-reference
  5294. (url "https://github.com/YingboMa/SafeTestsets.jl")
  5295. (commit commit)))
  5296. (file-name (git-file-name name version))
  5297. (sha256
  5298. (base32 "1fb1dfdmiw2ggx60hf70954xlps0r48fcb3k3dvxynlz7ylphp96"))))
  5299. (build-system julia-build-system)
  5300. (arguments
  5301. (list
  5302. #:julia-package-name "SafeTestsets"
  5303. #:julia-package-uuid "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
  5304. #:phases
  5305. #~(modify-phases %standard-phases
  5306. (add-after 'link-depot 'fix-package-toml
  5307. (lambda _
  5308. (substitute* "Project.toml"
  5309. (("version = .*") "version = \"0.0.1\"\n")))))))
  5310. (native-inputs
  5311. (list julia-staticarrays))
  5312. (home-page "https://github.com/YingboMa/SafeTestsets.jl")
  5313. (synopsis "Julia's testset in a module")
  5314. (description "This package contains the testset from Julia, packaged into
  5315. a loadable module.")
  5316. (license license:expat))))
  5317. (define-public julia-sass
  5318. (package
  5319. (name "julia-sass")
  5320. (version "0.2.0")
  5321. (source
  5322. (origin
  5323. (method git-fetch)
  5324. (uri (git-reference
  5325. (url "https://github.com/piever/Sass.jl")
  5326. (commit (string-append "v" version))))
  5327. (file-name (git-file-name name version))
  5328. (sha256
  5329. (base32 "0y7kkkj717h5cj659ssry89i5r64symr6pvhr6vv4qmaxrnjxj92"))))
  5330. (build-system julia-build-system)
  5331. (propagated-inputs
  5332. (list julia-libsass-jll))
  5333. (home-page "https://github.com/piever/Sass.jl")
  5334. (synopsis "Compile scss and sass file to css")
  5335. (description "This package provides a simple Julian API to use the
  5336. @code{libsass} library to compile scss and sass files to css.")
  5337. (license license:expat)))
  5338. (define-public julia-scanbyte
  5339. (package
  5340. (name "julia-scanbyte")
  5341. (version "0.3.2")
  5342. (source
  5343. (origin
  5344. (method git-fetch)
  5345. (uri (git-reference
  5346. (url "https://github.com/jakobnissen/ScanByte.jl")
  5347. (commit (string-append "v" version))))
  5348. (file-name (git-file-name name version))
  5349. (sha256
  5350. (base32 "1c18hkcb0h6l437v2s02kijjkyly91mqark84czvh8yzxm19hr7k"))))
  5351. (build-system julia-build-system)
  5352. (propagated-inputs
  5353. (list julia-simd))
  5354. (home-page "https://github.com/jakobnissen/ScanByte.jl")
  5355. (synopsis "Find the first occurrence of set of bytes in a chunk of memory")
  5356. (description "This package finds the first occurrence of a byte or set of
  5357. bytes in a chunk of memory. Think of it like a much faster version of
  5358. @code{findfirst} that only iterates over bytes in memory.")
  5359. ;; https://github.com/jakobnissen/ScanByte.jl/issues/2
  5360. (supported-systems '("x86_64-linux"))
  5361. (license license:expat)))
  5362. (define-public julia-scratch
  5363. (package
  5364. (name "julia-scratch")
  5365. (version "1.1.0")
  5366. (source
  5367. (origin
  5368. (method git-fetch)
  5369. (uri (git-reference
  5370. (url "https://github.com/JuliaPackaging/Scratch.jl")
  5371. (commit (string-append "v" version))))
  5372. (file-name (git-file-name name version))
  5373. (sha256
  5374. (base32
  5375. "09xni9rrrax17fxjz04j1b48mk9ffww5rcbagh66jklr89mrkqhx"))))
  5376. (build-system julia-build-system)
  5377. (arguments
  5378. (list #:tests? #f)) ; Test suite tries to access the Julia package registry.
  5379. (home-page "https://github.com/JuliaPackaging/Scratch.jl")
  5380. (synopsis "Scratch spaces for all your persistent mutable data needs")
  5381. (description "This repository implements the scratch spaces API for
  5382. package-specific mutable containers of data. These spaces can contain datasets,
  5383. text, binaries, or any other kind of data that would be convenient to store in
  5384. a location specific to your package. As compared to Artifacts, these containers
  5385. of data are mutable. Because the scratch space location on disk is not very
  5386. user-friendly, scratch spaces should, in general, not be used for a storing
  5387. files that the user must interact with through a file browser.")
  5388. (license license:expat)))
  5389. (define-public julia-sentinelarrays
  5390. (package
  5391. (name "julia-sentinelarrays")
  5392. (version "1.3.13")
  5393. (source
  5394. (origin
  5395. (method git-fetch)
  5396. (uri (git-reference
  5397. (url "https://github.com/JuliaData/SentinelArrays.jl")
  5398. (commit (string-append "v" version))))
  5399. (file-name (git-file-name name version))
  5400. (sha256
  5401. (base32 "1h3vpz7xskbf2a60imdg0irwh9bybkahjpnb6b3wyk0j9a97nqkr"))))
  5402. (build-system julia-build-system)
  5403. (home-page "https://github.com/JuliaData/SentinelArrays.jl")
  5404. (synopsis "Array types using sentinel values")
  5405. (description "This package provides @code{SentinelArray{T}} that wraps an
  5406. @code{AbstractArray} of type @code{T}, and accepts a sentinel and value
  5407. argument.")
  5408. (license license:expat)))
  5409. (define-public julia-shiftedarrays
  5410. (package
  5411. (name "julia-shiftedarrays")
  5412. (version "1.0.0")
  5413. (source
  5414. (origin
  5415. (method git-fetch)
  5416. (uri (git-reference
  5417. (url "https://github.com/JuliaArrays/ShiftedArrays.jl")
  5418. (commit (string-append "v" version))))
  5419. (file-name (git-file-name name version))
  5420. (sha256
  5421. (base32 "0wy7k29qx2lvj587kiz31fzdc60808mjsgpp41h6b682ypz8rw0c"))))
  5422. (build-system julia-build-system)
  5423. (home-page "https://github.com/JuliaArrays/ShiftedArrays.jl")
  5424. (synopsis "Lazy shifted arrays for data analysis in Julia")
  5425. (description
  5426. "This package provides an implementation of shifted arrays for Julia.")
  5427. (license license:expat)))
  5428. (define-public julia-showoff
  5429. (package
  5430. (name "julia-showoff")
  5431. (version "1.0.2")
  5432. (source
  5433. (origin
  5434. (method git-fetch)
  5435. (uri (git-reference
  5436. (url "https://github.com/JuliaGraphics/Showoff.jl")
  5437. (commit (string-append "v" version))))
  5438. (file-name (git-file-name name version))
  5439. (sha256
  5440. (base32 "1g4hqvjjpwbrs7fnllyl5w66yj6qlvpvzpygym2nvf01m1ps6m53"))))
  5441. (build-system julia-build-system)
  5442. (home-page "https://github.com/JuliaGraphics/Showoff.jl")
  5443. (synopsis "Nicely format an array of n things for tables and plots")
  5444. (description "@code{Showoff} provides an interface for consistently
  5445. formatting an array of n things, e.g. numbers, dates, unitful values. It's used
  5446. in @code{Gadfly}, @code{Plots} and @code{Makie} to label axes and keys.")
  5447. (license license:expat)))
  5448. (define-public julia-simd
  5449. (package
  5450. (name "julia-simd")
  5451. (version "3.4.2")
  5452. (source
  5453. (origin
  5454. (method git-fetch)
  5455. (uri (git-reference
  5456. (url "https://github.com/eschnett/SIMD.jl")
  5457. (commit (string-append "v" version))))
  5458. (file-name (git-file-name name version))
  5459. (sha256
  5460. (base32 "02pbrg2qa20pqnckbnbg5jyic2ahydql09f3xhzd1xnxicp77lw5"))))
  5461. (build-system julia-build-system)
  5462. (home-page "https://github.com/eschnett/SIMD.jl")
  5463. (synopsis "Explicit SIMD vectorization")
  5464. (description "This package allows programmers to explicitly SIMD-vectorize
  5465. their Julia code. By exposing SIMD vector types and corresponding operations,
  5466. the programmer can explicitly vectorize their code. While this does not
  5467. guarantee that the generated machine code is efficient, it relieves the
  5468. compiler from determining whether it is legal to vectorize the code, deciding
  5469. whether it is beneficial to do so, and rearranging the code to synthesize
  5470. vector instructions.")
  5471. (license license:expat)))
  5472. (define-public julia-simpletraits
  5473. (package
  5474. (name "julia-simpletraits")
  5475. (version "0.9.4")
  5476. (source
  5477. (origin
  5478. (method git-fetch)
  5479. (uri (git-reference
  5480. (url "https://github.com/mauro3/SimpleTraits.jl")
  5481. (commit (string-append "v" version))))
  5482. (file-name (git-file-name name version))
  5483. (sha256
  5484. (base32 "1qvmkqcvhc2nilvkk36szccxdlcv9ls2i0ksxgl2yfjr3b3qlr05"))))
  5485. (build-system julia-build-system)
  5486. (propagated-inputs
  5487. (list julia-macrotools))
  5488. (home-page "https://github.com/mauro3/SimpleTraits.jl")
  5489. (synopsis "Simple Traits for Julia")
  5490. (description "This package provides a macro-based implementation of traits.
  5491. The main idea behind traits is to group types outside the type-hierarchy and to
  5492. make dispatch work with that grouping. The difference to Union-types is that
  5493. types can be added to a trait after the creation of the trait, whereas Union
  5494. types are fixed after creation.")
  5495. (license license:expat)))
  5496. (define-public julia-softglobalscope
  5497. (package
  5498. (name "julia-softglobalscope")
  5499. (version "1.1.0")
  5500. (source
  5501. (origin
  5502. (method git-fetch)
  5503. (uri (git-reference
  5504. (url "https://github.com/stevengj/SoftGlobalScope.jl")
  5505. (commit (string-append "v" version))))
  5506. (file-name (git-file-name name version))
  5507. (sha256
  5508. (base32 "1n3l0al1vw5jpb4k9a29a71666cdb617nmiqg34wcmyfzrxpvv39"))))
  5509. (build-system julia-build-system)
  5510. (home-page "https://github.com/stevengj/SoftGlobalScope.jl")
  5511. (synopsis "Utilities for soft global scope in interactive Julia environments")
  5512. (description
  5513. "SoftGlobalScope is a package for the Julia language that simplifies the
  5514. variable scoping rules for code in global scope. It is intended for interactive
  5515. shells to make it easier to work interactively with Julia, especially for
  5516. beginners.")
  5517. (license license:expat)))
  5518. (define-public julia-sortingalgorithms
  5519. (package
  5520. (name "julia-sortingalgorithms")
  5521. (version "1.0.1")
  5522. (source
  5523. (origin
  5524. (method git-fetch)
  5525. (uri (git-reference
  5526. (url "https://github.com/JuliaCollections/SortingAlgorithms.jl")
  5527. (commit (string-append "v" version))))
  5528. (file-name (git-file-name name version))
  5529. (sha256
  5530. (base32 "173x77a80xnh99viqa3r7rgdaksvxaw8xyfqw09gwvp4p2zrxivb"))))
  5531. (build-system julia-build-system)
  5532. (arguments
  5533. (list #:tests? #f)) ; cycle with StatsBase.jl
  5534. (propagated-inputs
  5535. (list julia-datastructures))
  5536. ;(native-inputs
  5537. ; `(("julia-statsbase" ,julia-statsbase)))
  5538. (home-page "https://github.com/JuliaCollections/SortingAlgorithms.jl")
  5539. (synopsis "Extra sorting algorithms extending Julia's sorting API")
  5540. (description "The SortingAlgorithms package provides three sorting
  5541. algorithms that can be used with Julia's standard sorting API: heapsort,
  5542. timsort and radixsort.")
  5543. (license license:expat)))
  5544. (define-public julia-specialfunctions
  5545. (package
  5546. (name "julia-specialfunctions")
  5547. (version "1.8.7")
  5548. (source
  5549. (origin
  5550. (method git-fetch)
  5551. (uri (git-reference
  5552. (url "https://github.com/JuliaMath/SpecialFunctions.jl")
  5553. (commit (string-append "v" version))))
  5554. (file-name (git-file-name name version))
  5555. (sha256
  5556. (base32 "0shlgx9lkbjb1awdf5lrbkq06bmkyahc92qay2a049b4lvqrhj7a"))))
  5557. (build-system julia-build-system)
  5558. (inputs
  5559. (list julia-chainrulestestutils))
  5560. (propagated-inputs
  5561. (list julia-chainrulescore
  5562. julia-irrationalconstants
  5563. julia-logexpfunctions
  5564. julia-openspecfun-jll))
  5565. (home-page "https://github.com/JuliaMath/SpecialFunctions.jl")
  5566. (synopsis "Special mathematical functions")
  5567. (description "This package provides special mathematical functions,
  5568. including Bessel, Hankel, Airy, error, Dawson, exponential (or sine and
  5569. cosine) integrals, eta, zeta, digamma, inverse digamma, trigamma, and
  5570. polygamma functions.")
  5571. (license license:expat)))
  5572. (define-public julia-splitapplycombine
  5573. (package
  5574. (name "julia-splitapplycombine")
  5575. (version "1.1.4")
  5576. (source
  5577. (origin
  5578. (method git-fetch)
  5579. (uri (git-reference
  5580. (url "https://github.com/JuliaData/SplitApplyCombine.jl")
  5581. (commit (string-append "v" version))))
  5582. (file-name (git-file-name name version))
  5583. (sha256
  5584. (base32 "1qzaqvk57b0s5krzn8bxkzmr5kz6hi9dm3jbf2sl7z4vznsgbn9x"))))
  5585. (build-system julia-build-system)
  5586. (propagated-inputs
  5587. (list julia-dictionaries
  5588. julia-indexing))
  5589. (home-page "https://github.com/JuliaData/SplitApplyCombine.jl")
  5590. (synopsis "Split-apply-combine strategies for Julia")
  5591. (description "@code{SplitApplyCombine.jl} provides high-level, generic tools
  5592. for manipulating data - particularly focussing on data in nested containers. An
  5593. emphasis is placed on ensuring split-apply-combine strategies are easy to apply,
  5594. and work reliably for arbitrary iterables and in an optimized way with the data
  5595. structures included in Julia's standard library.")
  5596. (license license:expat)))
  5597. (define-public julia-stablerngs
  5598. (package
  5599. (name "julia-stablerngs")
  5600. (version "1.0.0")
  5601. (source
  5602. (origin
  5603. (method git-fetch)
  5604. (uri (git-reference
  5605. (url "https://github.com/JuliaRandom/StableRNGs.jl")
  5606. (commit (string-append "v" version))))
  5607. (file-name (git-file-name name version))
  5608. (sha256
  5609. (base32 "1cw4wc38qbgmrrx0jjwjhynnarrzjkh0yyz242zj272brbci7p1r"))))
  5610. (build-system julia-build-system)
  5611. (home-page "https://github.com/JuliaRandom/StableRNGs.jl")
  5612. (synopsis "Julia RNG with stable streams")
  5613. (description "This package intends to provide a simple RNG with stable
  5614. streams, suitable for tests in packages which need reproducible streams of
  5615. random numbers across Julia versions. Indeed, the Julia RNGs provided by
  5616. default are documented to have non-stable streams (which for example enables
  5617. some performance improvements).")
  5618. (license license:expat)))
  5619. (define-public julia-stackviews
  5620. (package
  5621. (name "julia-stackviews")
  5622. (version "0.1.1")
  5623. (source
  5624. (origin
  5625. (method git-fetch)
  5626. (uri (git-reference
  5627. (url "https://github.com/JuliaArrays/StackViews.jl")
  5628. (commit (string-append "v" version))))
  5629. (file-name (git-file-name name version))
  5630. (sha256
  5631. (base32 "1fwiaxdpx1z9dli3jr8kyraych0jbdiny3qklynf0r13px25r6i7"))))
  5632. (build-system julia-build-system)
  5633. (arguments
  5634. (list
  5635. #:phases
  5636. #~(modify-phases %standard-phases
  5637. (add-after 'link-depot 'skip-doctest
  5638. (lambda _
  5639. (substitute* "test/runtests.jl"
  5640. ((".*doctest.*") "")))))))
  5641. (propagated-inputs
  5642. (list julia-offsetarrays))
  5643. (native-inputs
  5644. (list julia-aqua
  5645. julia-documenter))
  5646. (home-page "https://github.com/JuliaArrays/StackViews.jl")
  5647. (synopsis "No more catcat")
  5648. (description "StackViews provides only one array type: @code{StackView}.
  5649. There are multiple ways to understand @code{StackView}:
  5650. @itemize
  5651. @item inverse of @code{eachslice}
  5652. @item @code{cat} variant
  5653. @item view object
  5654. @item lazy version of @code{repeat} special case
  5655. @end itemize")
  5656. (license license:expat)))
  5657. (define-public julia-static
  5658. (package
  5659. (name "julia-static")
  5660. (version "0.8.3")
  5661. (source
  5662. (origin
  5663. (method git-fetch)
  5664. (uri (git-reference
  5665. (url "https://github.com/SciML/Static.jl")
  5666. (commit (string-append "v" version))))
  5667. (file-name (git-file-name name version))
  5668. (sha256
  5669. (base32 "1ilmging187w37vjff8ilnz1f0qygyhbwl6nhq91z3b5vxyf13zr"))))
  5670. (build-system julia-build-system)
  5671. (propagated-inputs
  5672. (list julia-ifelse))
  5673. (native-inputs
  5674. (list julia-aqua))
  5675. (home-page "https://github.com/SciML/Static.jl")
  5676. (synopsis "Static types useful for dispatch and generated functions")
  5677. (description "Static.jl defines a limited set of statically parameterized
  5678. types and a common interface that is shared between them.")
  5679. (license license:expat)))
  5680. (define-public julia-static-0.6
  5681. (package
  5682. (inherit julia-static)
  5683. (name "julia-static")
  5684. (version "0.6.6")
  5685. (source
  5686. (origin
  5687. (method git-fetch)
  5688. (uri (git-reference
  5689. (url "https://github.com/SciML/Static.jl")
  5690. (commit (string-append "v" version))))
  5691. (file-name (git-file-name name version))
  5692. (sha256
  5693. (base32 "03ri8nl046cz7l433p0nlr84yywxvjykyymqparm8lxxwkv0rxqd"))))))
  5694. (define-public julia-staticarrays
  5695. (package
  5696. (name "julia-staticarrays")
  5697. (version "1.2.13")
  5698. (source
  5699. (origin
  5700. (method git-fetch)
  5701. (uri (git-reference
  5702. (url "https://github.com/JuliaArrays/StaticArrays.jl")
  5703. (commit (string-append "v" version))))
  5704. (file-name (git-file-name name version))
  5705. (sha256
  5706. (base32 "041mijzgzm8r61a3gwspr2wcxjikqksvj2rbnl4gmcy41alqmx79"))))
  5707. (build-system julia-build-system)
  5708. (inputs
  5709. (list julia-benchmarktools))
  5710. (home-page "https://github.com/JuliaArrays/StaticArrays.jl")
  5711. (synopsis "Statically sized arrays")
  5712. (description "This package provides a framework for implementing
  5713. statically sized arrays in Julia, using the abstract type
  5714. @code{StaticArray{Size,T,N} <: AbstractArray{T,N}}. Subtypes of
  5715. @code{StaticArray} will provide fast implementations of common array and
  5716. linear algebra operations.")
  5717. (license license:expat)))
  5718. (define-public julia-statsapi
  5719. (package
  5720. (name "julia-statsapi")
  5721. (version "1.0.0")
  5722. (source
  5723. (origin
  5724. (method git-fetch)
  5725. (uri (git-reference
  5726. (url "https://github.com/JuliaStats/StatsAPI.jl")
  5727. (commit (string-append "v" version))))
  5728. (file-name (git-file-name name version))
  5729. (sha256
  5730. (base32 "1k1c3s7i5wzkz4r9fyy4gd7wb97p0qgbc7bmaajm16zqipfmy2bv"))))
  5731. (build-system julia-build-system)
  5732. (home-page "https://juliastats.org/")
  5733. (synopsis "Statistics-focused namespace for packages to share functions")
  5734. (description "This package provides a namespace for data-related generic
  5735. function definitions to solve the optional dependency problem; packages wishing
  5736. to share and/or extend functions can avoid depending directly on each other by
  5737. moving the function definition to @code{StatsAPI.jl} and each package taking a
  5738. dependency on it.")
  5739. (license license:expat)))
  5740. (define-public julia-statsbase
  5741. (package
  5742. (name "julia-statsbase")
  5743. (version "0.33.10")
  5744. (source
  5745. (origin
  5746. (method git-fetch)
  5747. (uri (git-reference
  5748. (url "https://github.com/JuliaStats/StatsBase.jl")
  5749. (commit (string-append "v" version))))
  5750. (file-name (git-file-name name version))
  5751. (sha256
  5752. (base32 "0pjsn531zdz3s34pa418pvyqvrx8nbcc8j0fgwfnadssihqah6g7"))))
  5753. (build-system julia-build-system)
  5754. (propagated-inputs
  5755. (list julia-dataapi
  5756. julia-datastructures
  5757. julia-missings
  5758. julia-sortingalgorithms
  5759. julia-statsapi))
  5760. (native-inputs
  5761. (list julia-stablerngs))
  5762. (home-page "https://github.com/JuliaStats/StatsBase.jl")
  5763. (synopsis "Basic statistics for Julia")
  5764. (description "StatsBase.jl is a Julia package that provides basic support
  5765. for statistics. Particularly, it implements a variety of statistics-related
  5766. functions, such as scalar statistics, high-order moment computation, counting,
  5767. ranking, covariances, sampling, and empirical density estimation.")
  5768. (license license:expat)))
  5769. (define-public julia-stringdistances
  5770. (package
  5771. (name "julia-stringdistances")
  5772. (version "0.10.0")
  5773. (source
  5774. (origin
  5775. (method git-fetch)
  5776. (uri (git-reference
  5777. (url "https://github.com/matthieugomez/StringDistances.jl")
  5778. (commit (string-append "v" version))))
  5779. (file-name (git-file-name name version))
  5780. (sha256
  5781. (base32 "0n5707wplbibzhhv1xmshvc025d7xk6mnikclc3hvq5cdc0gy9f7"))))
  5782. (build-system julia-build-system)
  5783. (propagated-inputs
  5784. (list julia-distances))
  5785. (home-page "https://github.com/matthieugomez/StringDistances.jl")
  5786. (synopsis "String Distances in Julia")
  5787. (description "This package provides string distances in Julia. Distances
  5788. are defined for @code{AbstractStrings}, and any iterator that define
  5789. @code{length()}. The package also defines Distance \"modifiers\" that can be
  5790. applied to any distance.")
  5791. (license license:expat)))
  5792. (define-public julia-stringencodings
  5793. (package
  5794. (name "julia-stringencodings")
  5795. (version "0.3.5")
  5796. (source
  5797. (origin
  5798. (method git-fetch)
  5799. (uri (git-reference
  5800. (url "https://github.com/JuliaStrings/StringEncodings.jl")
  5801. (commit (string-append "v" version))))
  5802. (file-name (git-file-name name version))
  5803. (sha256
  5804. (base32 "1qwc5ll68ng80b5921ww6fvifxbsmiylakfgsbsjbzg7lzyb5i67"))))
  5805. (build-system julia-build-system)
  5806. (arguments
  5807. (list
  5808. #:phases
  5809. #~(modify-phases %standard-phases
  5810. (add-after 'unpack 'skip-failing-test
  5811. (lambda _
  5812. ;; https://github.com/JuliaStrings/StringEncodings.jl/issues/49
  5813. (substitute* "test/runtests.jl"
  5814. (("\"SHIFT_JIS\", \"SHIFT_JISX0213\"")
  5815. " ")))))))
  5816. (propagated-inputs
  5817. (list julia-libiconv-jll))
  5818. (home-page "https://github.com/JuliaStrings/StringEncodings.jl")
  5819. (synopsis "Support for decoding and encoding texts")
  5820. (description "This package provides support for decoding and encoding
  5821. texts between multiple character encodings. It is currently based on the
  5822. @code{iconv} interface, and supports all major platforms using GNU libiconv.")
  5823. (license license:expat)))
  5824. (define-public julia-structarrays
  5825. (package
  5826. (name "julia-structarrays")
  5827. (version "0.6.3")
  5828. (source
  5829. (origin
  5830. (method git-fetch)
  5831. (uri (git-reference
  5832. (url "https://github.com/JuliaArrays/StructArrays.jl")
  5833. (commit (string-append "v" version))))
  5834. (file-name (git-file-name name version))
  5835. (sha256
  5836. (base32 "0rjcpyjwzg70n87q5r9c5i1qzigavncslxssm3rk5a3y549py56v"))))
  5837. (build-system julia-build-system)
  5838. (arguments
  5839. (list
  5840. #:phases
  5841. (if (target-64bit?)
  5842. #~%standard-phases
  5843. #~(modify-phases %standard-phases
  5844. (add-after 'unpack 'fix-tests-int32-i686
  5845. (lambda _
  5846. (substitute* '("src/utils.jl"
  5847. "test/runtests.jl")
  5848. (("Int64") "Int32"))))))))
  5849. (propagated-inputs
  5850. (list julia-dataapi
  5851. julia-staticarrays
  5852. julia-tables))
  5853. (native-inputs
  5854. (list julia-documenter
  5855. julia-offsetarrays
  5856. julia-pooledarrays
  5857. julia-typedtables
  5858. julia-weakrefstrings))
  5859. (home-page "https://github.com/JuliaArrays/StructArrays.jl")
  5860. (synopsis "Efficient implementation of struct arrays in Julia")
  5861. (description "This package introduces the type @code{StructArray} which is
  5862. an @code{AbstractArray} whose elements are @code{struct} (for example
  5863. @code{NamedTuples}, or @code{ComplexF64}, or a custom user defined
  5864. @code{struct}). While a @code{StructArray} iterates @code{structs}, the layout
  5865. is column based (meaning each field of the @code{struct} is stored in a separate
  5866. @code{Array}).")
  5867. (license license:expat)))
  5868. (define-public julia-structtypes
  5869. (package
  5870. (name "julia-structtypes")
  5871. (version "1.7.2")
  5872. (source
  5873. (origin
  5874. (method git-fetch)
  5875. (uri (git-reference
  5876. (url "https://github.com/JuliaData/StructTypes.jl")
  5877. (commit (string-append "v" version))))
  5878. (file-name (git-file-name name version))
  5879. (sha256
  5880. (base32 "02mn4kkhn3927dk7945c9bjwlldihydxgn5ilmqqvs8dknvbw8p1"))))
  5881. (build-system julia-build-system)
  5882. (home-page "https://juliadata.github.io/StructTypes.jl/stable/")
  5883. (synopsis "Abstract definitions and convenience methods for Julia objects")
  5884. (description "This package provides the @code{StructTypes.StructType} trait
  5885. for Julia types to declare the kind of \"struct\" they are, providing
  5886. serialization/deserialization packages patterns and strategies to automatically
  5887. construct objects.")
  5888. (license license:expat)))
  5889. (define-public julia-suppressor
  5890. (package
  5891. (name "julia-suppressor")
  5892. (version "0.2.0")
  5893. (source
  5894. (origin
  5895. (method git-fetch)
  5896. (uri (git-reference
  5897. (url "https://github.com/JuliaIO/Suppressor.jl")
  5898. (commit (string-append "v" version))))
  5899. (file-name (git-file-name name version))
  5900. (sha256
  5901. (base32 "0v6pxvf8lzrqjc676snvlszh14ridl442g2h6syfjiy75pk7mdyc"))))
  5902. (build-system julia-build-system)
  5903. (home-page "https://github.com/JuliaIO/Suppressor.jl")
  5904. (synopsis "Capture stdout and sterr")
  5905. (description "Julia macros for suppressing and/or capturing output (stdout),
  5906. warnings (stderr) or both streams at the same time.")
  5907. (license license:expat)))
  5908. (define-public julia-tableiointerface
  5909. (package
  5910. (name "julia-tableiointerface")
  5911. (version "0.1.6")
  5912. (source
  5913. (origin
  5914. (method git-fetch)
  5915. (uri (git-reference
  5916. (url "https://github.com/lungben/TableIOInterface.jl")
  5917. (commit (string-append "v" version))))
  5918. (file-name (git-file-name name version))
  5919. (sha256
  5920. (base32 "0p2fi9jbyfg2j6rysv4if7dx8qw2mssb04i75j1zq607j8707kvn"))))
  5921. (build-system julia-build-system)
  5922. (home-page "https://github.com/lungben/TableIOInterface.jl")
  5923. (synopsis "File formats based on file extensions")
  5924. (description "This package determines tabular file formats based on file
  5925. extensions. It is intended to be the base both for @code{TableIO.jl} and for
  5926. the @code{Pluto.jl} tabular data import functionality.")
  5927. (license license:expat)))
  5928. (define-public julia-tables
  5929. (package
  5930. (name "julia-tables")
  5931. (version "1.4.4")
  5932. (source
  5933. (origin
  5934. (method git-fetch)
  5935. (uri (git-reference
  5936. (url "https://github.com/JuliaData/Tables.jl")
  5937. (commit (string-append "v" version))))
  5938. (file-name (git-file-name name version))
  5939. (sha256
  5940. (base32 "1sqqagzqvav8b1rv5ywwbgy9ixvlmipq95fkwfwn0m8769i8jwzb"))))
  5941. (build-system julia-build-system)
  5942. (propagated-inputs
  5943. (list julia-dataapi
  5944. julia-datavalueinterfaces
  5945. julia-iteratorinterfaceextensions
  5946. julia-tabletraits))
  5947. (native-inputs
  5948. (list julia-datavalues
  5949. julia-queryoperators))
  5950. (home-page "https://github.com/JuliaData/Tables.jl")
  5951. (synopsis "Interface for tables in Julia")
  5952. (description "The @code{Tables.jl} package provides simple, yet powerful
  5953. interface functions for working with all kinds tabular data.")
  5954. (license license:expat)))
  5955. (define-public julia-tableshowutils
  5956. ;; The 0.2.5 release is not fully compatable with newer versions of Julia.
  5957. (let ((commit "c4e02d8b9bbb31fc81ed6618955e9b1c7cb04460")
  5958. (revision "1"))
  5959. (package
  5960. (name "julia-tableshowutils")
  5961. (version "0.2.5")
  5962. (source
  5963. (origin
  5964. (method git-fetch)
  5965. (uri (git-reference
  5966. (url "https://github.com/queryverse/TableShowUtils.jl")
  5967. (commit commit)))
  5968. (file-name (git-file-name name version))
  5969. (sha256
  5970. (base32 "0gp3hpj3jvzfhkp9r345vfic2j2n2s60729wv38hwn75csp74cg5"))))
  5971. (build-system julia-build-system)
  5972. (propagated-inputs
  5973. (list julia-datavalues
  5974. julia-json))
  5975. (home-page "https://github.com/queryverse/TableShowUtils.jl")
  5976. (synopsis "Implement show for TableTraits.jl types")
  5977. (description "This package provides some common helper functions that make
  5978. it easier to implement various @code{Base.show} functions for types that
  5979. participate in the @code{TableTraits.jl} ecosystem.")
  5980. (license license:expat))))
  5981. (define-public julia-tabletraits
  5982. (package
  5983. (name "julia-tabletraits")
  5984. (version "1.0.1")
  5985. (source
  5986. (origin
  5987. (method git-fetch)
  5988. (uri (git-reference
  5989. (url "https://github.com/queryverse/TableTraits.jl")
  5990. (commit (string-append "v" version))))
  5991. (file-name (git-file-name name version))
  5992. (sha256
  5993. (base32 "08ssb2630wm6j8f2qa985mn2vfibfm5kjcn4ayl2qkhfcyp8daw4"))))
  5994. (build-system julia-build-system)
  5995. (propagated-inputs
  5996. (list julia-iteratorinterfaceextensions))
  5997. (home-page "https://github.com/queryverse/TableTraits.jl")
  5998. (synopsis "Traits for Julia tables")
  5999. (description "TableTraits defines a generic interface for tabular data.")
  6000. (license license:expat)))
  6001. (define-public julia-tensorcore
  6002. (package
  6003. (name "julia-tensorcore")
  6004. (version "0.1.1")
  6005. (source
  6006. (origin
  6007. (method git-fetch)
  6008. (uri (git-reference
  6009. (url "https://github.com/JuliaMath/TensorCore.jl")
  6010. (commit (string-append "v" version))))
  6011. (file-name (git-file-name name version))
  6012. (sha256
  6013. (base32 "1sy3in4a1rl3l2vk0cm9mzg2nkva7syhr7i35si0kbzhkdwpbqjy"))))
  6014. (build-system julia-build-system)
  6015. (home-page "https://github.com/JuliaMath/TensorCore.jl")
  6016. (synopsis "Tensor-algebra definitions")
  6017. (description "This package is intended as a lightweight foundation for
  6018. tensor operations across the Julia ecosystem. Currently it exports three
  6019. operations: @acronym{hadamard, elementwise multiplication}, @acronym{tensor,
  6020. product preserves all dimensions}, and @acronym{boxdot, contracts neighboring
  6021. dimensions}.")
  6022. (license license:expat)))
  6023. (define-public julia-testimages
  6024. (package
  6025. (name "julia-testimages")
  6026. (version "1.5.0")
  6027. (source
  6028. (origin
  6029. (method git-fetch)
  6030. (uri (git-reference
  6031. (url "https://github.com/JuliaImages/TestImages.jl")
  6032. (commit (string-append "v" version))))
  6033. (file-name (git-file-name name version))
  6034. (sha256
  6035. (base32 "1lnfsmx33qspyvxw0cykwh7il8xykjpcw1080sisn95ngz2qhdmy"))))
  6036. (build-system julia-build-system)
  6037. (arguments
  6038. (list #:tests? #f)) ; cycle with ImageMagick.jl
  6039. (propagated-inputs
  6040. (list julia-axisarrays
  6041. julia-colortypes
  6042. julia-fileio
  6043. julia-offsetarrays
  6044. julia-stringdistances))
  6045. ;(native-inputs
  6046. ; `(("julia-colors" ,julia-colors)
  6047. ; ("julia-fixedpointnumbers" ,julia-fixedpointnumbers)
  6048. ; ("julia-imagecontrastadjustment" ,julia-imagecontrastadjustment)
  6049. ; ("julia-imagemagick" ,julia-imagemagick)
  6050. ; ("julia-ometiff" ,julia-ometiff)
  6051. ; ("julia-referencetests" ,julia-referencetests)))
  6052. (home-page "https://testimages.juliaimages.org/")
  6053. (synopsis "Standard test images for Julia")
  6054. (description "This package provides a convenient Julia interface for loading
  6055. standard named test images and example images for the internal usage in
  6056. @code{JuliaImages}. This can be used in conjunction with the @code{Images}
  6057. package.")
  6058. (license license:expat)))
  6059. (define-public julia-tokenize
  6060. (package
  6061. (name "julia-tokenize")
  6062. (version "0.5.24")
  6063. (source
  6064. (origin
  6065. (method git-fetch)
  6066. (uri (git-reference
  6067. (url "https://github.com/JuliaLang/Tokenize.jl")
  6068. (commit (string-append "v" version))))
  6069. (file-name (git-file-name name version))
  6070. (sha256
  6071. (base32 "1l3dy6nad0viavzy26lfnhzpd3gcxgaq7yvm7h1ja280xsh60p3i"))))
  6072. (build-system julia-build-system)
  6073. (home-page "https://github.com/JuliaGPU/Tokenize.jl")
  6074. (synopsis "Tokenize a string or buffer containing Julia code")
  6075. (description "This package takes a string or buffer containing Julia code,
  6076. performs lexical analysis and returns a stream of tokens.")
  6077. (license license:expat)))
  6078. (define-public julia-tracker
  6079. (package
  6080. (name "julia-tracker")
  6081. (version "0.2.22")
  6082. (source
  6083. (origin
  6084. (method git-fetch)
  6085. (uri (git-reference
  6086. (url "https://github.com/FluxML/Tracker.jl")
  6087. (commit (string-append "v" version))))
  6088. (file-name (git-file-name name version))
  6089. (sha256
  6090. (base32 "0sxncn999dc5j15y0h3cw28x41pv5qjaw64drhy1y4rn3na48504"))))
  6091. (build-system julia-build-system)
  6092. (propagated-inputs
  6093. (list julia-adapt
  6094. julia-diffrules
  6095. julia-forwarddiff
  6096. julia-functors
  6097. julia-logexpfunctions
  6098. julia-macrotools
  6099. julia-nanmath
  6100. julia-nnlib
  6101. julia-optimisers
  6102. julia-requires
  6103. julia-specialfunctions))
  6104. (native-inputs
  6105. (list julia-pdmats))
  6106. (home-page "https://github.com/FluxML/Tracker.jl")
  6107. (synopsis "Operator overloading reverse-mode automatic differentiator")
  6108. (description "@code{Tracker.jl} previously provided @code{Flux.jl} with
  6109. automatic differentiation for its machine learning platform.")
  6110. (license license:expat)))
  6111. (define-public julia-transcodingstreams
  6112. (package
  6113. (name "julia-transcodingstreams")
  6114. (version "0.9.6")
  6115. (source
  6116. (origin
  6117. (method git-fetch)
  6118. (uri (git-reference
  6119. (url "https://github.com/JuliaIO/TranscodingStreams.jl")
  6120. (commit (string-append "v" version))))
  6121. (file-name (git-file-name name version))
  6122. (sha256
  6123. (base32 "1w3klii293caqiclfh28jggv7f53xclm9fr6xmw38brwrn1hjb48"))))
  6124. (build-system julia-build-system)
  6125. (arguments
  6126. (list #:tests? #f)) ; Circular dependency with various codecs.
  6127. (home-page "https://github.com/JuliaIO/TranscodingStreams.jl")
  6128. (synopsis "Fast I/O transcoding data streams")
  6129. (description "This package provides tools for transcoding data streams
  6130. which are:
  6131. @itemize
  6132. @item fast: small overhead and specialized methods
  6133. @item consistent: basic I/O operations work as expected
  6134. @item generic: support any I/O objects like files, buffers, pipes, etc.
  6135. @item extensible: easy definition for new codec to transcode data
  6136. @end itemize")
  6137. (license license:expat)))
  6138. (define-public julia-twiddle
  6139. (package
  6140. (name "julia-twiddle")
  6141. (version "1.1.2")
  6142. (source
  6143. (origin
  6144. (method git-fetch)
  6145. (uri (git-reference
  6146. (url "https://github.com/SabrinaJaye/Twiddle.jl")
  6147. (commit (string-append "v" version))))
  6148. (file-name (git-file-name name version))
  6149. (sha256
  6150. (base32 "1c2gdv7sy4n1d8687w2q0yzwmwmanf4p6mvzvkz5gm4baxyzmbh2"))))
  6151. (build-system julia-build-system)
  6152. (home-page "https://ben-ward.science/Twiddle.jl/stable")
  6153. (synopsis "Ready to use bit-twiddling tricks")
  6154. (description "This package provides a collection of useful bit-twiddling
  6155. tricks, ready to use as functions, with detailed documentation and example
  6156. real-world use cases.")
  6157. (license license:expat)))
  6158. (define-public julia-typedtables
  6159. (package
  6160. (name "julia-typedtables")
  6161. (version "1.4.0")
  6162. (source
  6163. (origin
  6164. (method git-fetch)
  6165. (uri (git-reference
  6166. (url "https://github.com/JuliaData/TypedTables.jl")
  6167. (commit (string-append "v" version))))
  6168. (file-name (git-file-name name version))
  6169. (sha256
  6170. (base32 "0nk6zhqvl2r8yhjdhb59kxq0srd3vy4ysg4d8rszj9a43dnn3w3i"))))
  6171. (build-system julia-build-system)
  6172. (propagated-inputs
  6173. (list julia-adapt
  6174. julia-splitapplycombine
  6175. julia-tables))
  6176. (home-page "https://github.com/JuliaData/TypedTables.jl")
  6177. (synopsis "Column-based storage for data analysis in Julia")
  6178. (description "@code{TypedTables.jl} provides two column-based storage
  6179. containers: @code{Table} and @code{FlexTable}, both of which represent an array
  6180. of @code{NamedTuples}. This package is designed to be lightweight, easy-to-use
  6181. and fast, and presents a very minimal new interface to learn.")
  6182. (license license:expat)))
  6183. (define-public julia-unpack
  6184. (package
  6185. (name "julia-unpack")
  6186. (version "1.0.2")
  6187. (source
  6188. (origin
  6189. (method git-fetch)
  6190. (uri (git-reference
  6191. (url "https://github.com/mauro3/UnPack.jl")
  6192. (commit (string-append "v" version))))
  6193. (file-name (git-file-name name version))
  6194. (sha256
  6195. (base32 "066v1px72zidnvhl0rczhh07rcfwvli0jx5nprrgyi1dvj3mps2a"))))
  6196. (build-system julia-build-system)
  6197. (home-page "https://github.com/mauro3/UnPack.jl")
  6198. (synopsis "Pack and Unpack macros for Julia")
  6199. (description "The @code{@@unpack} and @code{@@pack!} macros work to unpack
  6200. types, modules, and dictionaries.")
  6201. (license license:expat)))
  6202. (define-public julia-uris
  6203. (package
  6204. (name "julia-uris")
  6205. (version "1.3.0")
  6206. (source
  6207. (origin
  6208. (method git-fetch)
  6209. (uri (git-reference
  6210. (url "https://github.com/JuliaWeb/URIs.jl")
  6211. (commit (string-append "v" version))))
  6212. (file-name (git-file-name name version))
  6213. (sha256
  6214. (base32 "0kp4hg3kknkm2smlcizqfd33l9x4vkahc2714gnbjp39fj285b92"))))
  6215. (build-system julia-build-system)
  6216. (arguments
  6217. (list
  6218. #:julia-package-name "URIs" ;required to run tests
  6219. #:julia-package-uuid "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4"
  6220. #:phases
  6221. #~(modify-phases %standard-phases
  6222. (add-before 'check 'change-dir
  6223. ;; Tests must be run from the testdir
  6224. (lambda* (#:key source outputs #:allow-other-keys)
  6225. (let ((out (assoc-ref outputs "out")))
  6226. (chdir
  6227. (string-append out "/share/julia/loadpath/URIs/test"))))))))
  6228. ;; required for tests
  6229. (inputs (list julia-json))
  6230. (home-page "https://github.com/JuliaWeb/URIs.jl")
  6231. (synopsis "URI parsing in Julia")
  6232. (description "@code{URIs.jl} is a Julia package that allows parsing and
  6233. working with @acronym{URIs,Uniform Resource Identifiers}, as defined in RFC
  6234. 3986.")
  6235. (license license:expat)))
  6236. (define-public julia-unitful
  6237. (package
  6238. (name "julia-unitful")
  6239. (version "1.12.2")
  6240. (source
  6241. (origin
  6242. (method git-fetch)
  6243. (uri (git-reference
  6244. (url "https://github.com/PainterQubits/Unitful.jl")
  6245. (commit (string-append "v" version))))
  6246. (file-name (git-file-name name version))
  6247. (sha256
  6248. (base32 "1b8w6wqc7azqzg2f8zc3bmc72fb01sx0rqh6dv3k54wj01ph15p7"))))
  6249. (build-system julia-build-system)
  6250. (arguments
  6251. (list #:parallel-tests? #f))
  6252. (propagated-inputs
  6253. (list julia-constructionbase))
  6254. (home-page "https://painterqubits.github.io/Unitful.jl/stable/")
  6255. (synopsis "Physical units in Julia")
  6256. (description "This package supports SI units and also many other unit
  6257. system.")
  6258. (license license:expat)))
  6259. (define-public julia-versionparsing
  6260. (package
  6261. (name "julia-versionparsing")
  6262. (version "1.2.0")
  6263. (source
  6264. (origin
  6265. (method git-fetch)
  6266. (uri (git-reference
  6267. (url "https://github.com/JuliaInterop/VersionParsing.jl")
  6268. (commit (string-append "v" version))))
  6269. (file-name (git-file-name name version))
  6270. (sha256
  6271. (base32 "060s72dsnpavgilf7f7315lw2sn4npk8lkndmj6bg7i23hppiwva"))))
  6272. (build-system julia-build-system)
  6273. (home-page "https://github.com/JuliaInterop/VersionParsing.jl")
  6274. (synopsis "Flexible VersionNumber parsing in Julia")
  6275. (description "The @code{VersionParsing} package implements flexible parsing
  6276. of version-number strings into Julia's built-in @code{VersionNumber} type, via
  6277. the @code{vparse(string)} function. Unlike the @code{VersionNumber(string)}
  6278. constructor, @code{vparse(string)} can handle version-number strings in a much
  6279. wider range of formats than are encompassed by the semver standard. This is
  6280. useful in order to support @code{VersionNumber} comparisons applied to
  6281. \"foreign\" version numbers from external packages.")
  6282. (license license:expat)))
  6283. (define-public julia-wcs
  6284. (package
  6285. (name "julia-wcs")
  6286. (version "0.6.2")
  6287. (source
  6288. (origin
  6289. (method git-fetch)
  6290. (uri (git-reference
  6291. (url "https://github.com/JuliaAstro/WCS.jl")
  6292. (commit (string-append "v" version))))
  6293. (file-name (git-file-name name version))
  6294. (sha256
  6295. (base32 "0ala8j4mh51gh14k3npcxmnlj2f00l0pij74qz453iqadb2283mi"))))
  6296. (build-system julia-build-system)
  6297. (propagated-inputs
  6298. (list julia-constructionbase julia-wcs-jll))
  6299. (home-page "https://github.com/JuliaAstro/WCS.jl")
  6300. (synopsis "Astronomical WCS library for Julia")
  6301. (description "Astronomical @url{World Coordinate System,
  6302. https://www.atnf.csiro.au/people/mcalabre/WCS/} library for Julia. This package
  6303. wraps the WCSLIB C library.")
  6304. (license license:expat)))
  6305. (define-public julia-weakrefstrings
  6306. (package
  6307. (name "julia-weakrefstrings")
  6308. (version "1.4.0")
  6309. (source
  6310. (origin
  6311. (method git-fetch)
  6312. (uri (git-reference
  6313. (url "https://github.com/JuliaData/WeakRefStrings.jl")
  6314. (commit (string-append "v" version))))
  6315. (file-name (git-file-name name version))
  6316. (sha256
  6317. (base32 "1ca94bpsjqrap2y9wlixspnisfkcms7aax0kpv7yn0v2vs9481wk"))))
  6318. (build-system julia-build-system)
  6319. (propagated-inputs
  6320. (list julia-dataapi
  6321. julia-inlinestrings
  6322. julia-parsers))
  6323. (home-page "https://github.com/JuliaData/WeakRefStrings.jl")
  6324. (synopsis "Efficient string representation and transfer in Julia")
  6325. (description "This package provides a minimal String type for Julia that
  6326. allows for efficient string representation and transfer")
  6327. (license license:expat)))
  6328. (define-public julia-woodburymatrices
  6329. (package
  6330. (name "julia-woodburymatrices")
  6331. (version "0.5.5")
  6332. (source
  6333. (origin
  6334. (method git-fetch)
  6335. (uri (git-reference
  6336. (url "https://github.com/timholy/WoodburyMatrices.jl")
  6337. (commit (string-append "v" version))))
  6338. (file-name (git-file-name name version))
  6339. (sha256
  6340. (base32 "1vwy8nlhvjh0ndia4ni40iq4pf2nhwy5iy3rmf4i2jff13vc6aqn"))))
  6341. (build-system julia-build-system)
  6342. (home-page "https://github.com/timholy/WoodburyMatrices.jl")
  6343. (synopsis "Support for the Woodbury matrix identity for Julia")
  6344. (description "This package provides support for the Woodbury matrix identity
  6345. for the Julia programming language. This is a generalization of the
  6346. Sherman-Morrison formula. Note that the Woodbury matrix identity is notorious
  6347. for floating-point roundoff errors, so be prepared for a certain amount of
  6348. inaccuracy in the result.")
  6349. (license license:expat)))
  6350. (define-public julia-yaml
  6351. (package
  6352. (name "julia-yaml")
  6353. (version "0.4.7")
  6354. (source
  6355. (origin
  6356. (method git-fetch)
  6357. (uri (git-reference
  6358. (url "https://github.com/JuliaData/YAML.jl")
  6359. (commit (string-append "v" version))))
  6360. (file-name (git-file-name name version))
  6361. (sha256
  6362. (base32 "00k8456ffldbf75k2q5yxim7cgz3p0pbshsvmpm1331g8qy6liin"))))
  6363. (build-system julia-build-system)
  6364. (propagated-inputs
  6365. (list julia-stringencodings))
  6366. (native-inputs
  6367. (list julia-datastructures
  6368. julia-orderedcollections))
  6369. (home-page "https://github.com/JuliaData/YAML.jl")
  6370. (synopsis "Parses YAML documents into native Julia types")
  6371. (description "This package parses YAML documents into native Julia types
  6372. and dumps them back into YAML documents.")
  6373. (license license:expat)))
  6374. (define-public julia-zipfile
  6375. (package
  6376. (name "julia-zipfile")
  6377. (version "0.9.3")
  6378. (source
  6379. (origin
  6380. (method git-fetch)
  6381. (uri (git-reference
  6382. (url "https://github.com/fhs/ZipFile.jl")
  6383. (commit (string-append "v" version))))
  6384. (file-name (git-file-name name version))
  6385. (sha256
  6386. (base32
  6387. "15bm3ki5mb9nvqs2byznrryq0bilnjcvsfy3k05hxhk9vapilw7k"))))
  6388. (build-system julia-build-system)
  6389. (propagated-inputs
  6390. (list julia-zlib-jll))
  6391. (home-page "https://github.com/fhs/ZipFile.jl")
  6392. (synopsis "Read/Write ZIP archives in Julia")
  6393. (description "This module provides support for reading and writing ZIP
  6394. archives in Julia.")
  6395. (license license:expat)))
  6396. (define-public julia-zygoterules
  6397. (package
  6398. (name "julia-zygoterules")
  6399. (version "0.2.2")
  6400. (source
  6401. (origin
  6402. (method git-fetch)
  6403. (uri (git-reference
  6404. (url "https://github.com/FluxML/ZygoteRules.jl")
  6405. (commit (string-append "v" version))))
  6406. (file-name (git-file-name name version))
  6407. (sha256
  6408. (base32 "0h9m9ibxfcw9cqa7p0aylpvibvlxsn5nlfzkz1pk68jy58vkzhca"))))
  6409. (build-system julia-build-system)
  6410. (propagated-inputs
  6411. (list julia-macrotools))
  6412. (home-page "https://github.com/FluxML/ZygoteRules.jl")
  6413. (synopsis "Add minimal custom gradients to Zygote")
  6414. (description "Minimal package which enables to add custom gradients to
  6415. Zygote, without depending on Zygote itself.")
  6416. (license license:expat)))
  6417. (define-public julia-zygote
  6418. (package
  6419. (name "julia-zygote")
  6420. (version "0.6.41")
  6421. (source
  6422. (origin
  6423. (method git-fetch)
  6424. (uri (git-reference
  6425. (url "https://github.com/FluxML/Zygote.jl")
  6426. (commit (string-append "v" version))))
  6427. (file-name (git-file-name name version))
  6428. (sha256
  6429. (base32 "02bgj6m1j25sm3pa5sgmds706qpxk1qsbm0s2j3rjlrz9xn7glgk"))))
  6430. (build-system julia-build-system)
  6431. (arguments
  6432. (list #:tests? #f)) ;require CUDA, not packaged yet
  6433. (propagated-inputs
  6434. (list julia-abstractffts
  6435. julia-chainrules
  6436. julia-chainrulescore
  6437. julia-diffrules
  6438. julia-fillarrays
  6439. julia-forwarddiff
  6440. julia-irtools
  6441. julia-logexpfunctions
  6442. julia-macrotools
  6443. julia-nanmath
  6444. julia-requires
  6445. julia-specialfunctions
  6446. julia-zygoterules))
  6447. (home-page "https://fluxml.ai/Zygote.jl")
  6448. (synopsis "Automatic differentiation in Julia")
  6449. (description "Zygote provides source-to-source automatic
  6450. differentiation (AD) in Julia, and is the next-generation AD system for the
  6451. Flux differentiable programming framework.")
  6452. (license license:expat)))
  6453. ;;;
  6454. ;;; Avoid adding new packages to the end of this file. To reduce the chances
  6455. ;;; of a merge conflict, place them above by existing packages with similar
  6456. ;;; functionality or similar names.
  6457. ;;;