diff options
Diffstat (limited to 'gnu/packages/julia-xyz.scm')
| -rw-r--r-- | gnu/packages/julia-xyz.scm | 1044 |
1 files changed, 1042 insertions, 2 deletions
diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm index 34dba958ce..85949ec9e8 100644 --- a/gnu/packages/julia-xyz.scm +++ b/gnu/packages/julia-xyz.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2020, 2021 Nicolò Balzarotti <nicolo@nixo.xyz> +;;; Copyright © 2021 Simon Tournier <zimon.toutoune@gmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -20,7 +21,35 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix git-download) - #:use-module (guix build-system julia)) + #:use-module (guix build-system julia) + #:use-module (gnu packages gcc) + #:use-module (gnu packages maths) + #:use-module (gnu packages tls)) + +(define-public julia-abstractffts + (package + (name "julia-abstractffts") + (version "1.0.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaMath/AbstractFFTS.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0083pwdyxjb04i330ir9pc8kmp4bwk59lx1jgc9qi05y8j7xzbp0")))) + (build-system julia-build-system) + (inputs ;required for tests + `(("julia-unitful" ,julia-unitful))) + (home-page "https://github.com/JuliaGPU/Adapt.jl") + (synopsis "General framework for fast Fourier transforms (FFTs)") + (description "This package allows multiple FFT packages to co-exist with +the same underlying @code{fft(x)} and @code{plan_fft(x)} interface. It is +mainly not intended to be used directly. Instead, developers of packages that +implement FFTs (such as @code{FFTW.jl} or @code{FastTransforms.jl}) extend the +types/functions defined in AbstractFFTs.") + (license license:expat))) (define-public julia-adapt (package @@ -32,7 +61,7 @@ (uri (git-reference (url "https://github.com/JuliaGPU/Adapt.jl") (commit (string-append "v" version)))) - (file-name "Adapt") + (file-name (git-file-name name version)) (sha256 (base32 "1lks6k3a1gvwlplld47nh6xfy3nnlpc0vhkzg6zg0qn33qdmavrg")))) (build-system julia-build-system) @@ -44,6 +73,242 @@ acts like @code{convert(T, x)}, but without the restriction of returning a be GPU compatible without throwing away the wrapper.") (license license:expat))) +(define-public julia-benchmarktools + (package + (name "julia-benchmarktools") + (version "0.5.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaCI/BenchmarkTools.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0nsx21m3i5h22lkgyrmfj6r085va6ag40khwssqs8y7l0wz98lvp")))) + (build-system julia-build-system) + (propagated-inputs `(("julia-json" ,julia-json))) + (home-page "https://github.com/JuliaCI/BenchmarkTools.jl") + (synopsis "Benchmarking framework for the Julia language") + (description "@code{BenchmarkTools.jl} makes performance tracking of Julia +code easy by supplying a framework for writing and running groups of +benchmarks as well as comparing benchmark results.") + (license license:expat))) + +(define-public julia-bufferedstreams + (package + (name "julia-bufferedstreams") + (version "1.0.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/BioJulia/BufferedStreams.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0sf4sxbq55mg2pwxyxf0c839z1lk0yxg8nmb7617bfbvw31cp88z")))) + (build-system julia-build-system) + ;; The package is old and tests are using undefined functions. They also + ;; freeze, see + ;; https://travis-ci.org/BioJulia/BufferedStreams.jl/jobs/491050182 + (arguments + '(#:tests? #f + #:julia-package-name "BufferedStreams")) + (propagated-inputs `(("julia-compat" ,julia-compat))) + (home-page "https://github.com/BioJulia/BufferedStreams.jl") + (synopsis "Fast composable IO streams") + (description "@code{BufferedStreams.jl} provides buffering for IO +operations. It can wrap any @code{IO} type automatically making incremental +reading and writing faster.") + (license license:expat))) + +(define-public julia-calculus + (package + (name "julia-calculus") + (version "0.5.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaMath/Calculus.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0xh0ak2ycsjw2h86ja24ch3kn2d18zx3frrds78aimwdnqb1gdc2")))) + (build-system julia-build-system) + (home-page "https://github.com/JuliaMath/Calculus.jl") + (synopsis "Common utilities for automatic differentiation") + (description "This package provides tools for working with the basic +calculus operations of differentiation and integration. The @code{Calculus} +package produces approximate derivatives by several forms of finite +differencing or produces exact derivative using symbolic differentiation. It +can also be used to compute definite integrals by different numerical +methods.") + (license license:expat))) + +(define-public julia-chainrules + (package + (name "julia-chainrules") + (version "0.7.54") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaDiff/ChainRules.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1x4w71v8cw0vpba47h8f5xq4gyjfxbcvayzf7m41yg8gf49s9pkf")))) + (build-system julia-build-system) + (inputs ;required for test + `(("julia-chainrulestestutils" ,julia-chainrulestestutils) + ("julia-finitedifferences" ,julia-finitedifferences) + ("julia-nanmath" ,julia-nanmath) + ("julia-specialfunctions" ,julia-specialfunctions))) + (propagated-inputs + `(("julia-chainrulescore" ,julia-chainrulescore) + ("julia-compat" ,julia-compat) + ("julia-reexport" ,julia-reexport) + ("julia-requires" ,julia-requires))) + (home-page "https://github.com/JuliaDiff/ChainRules.jl") + (synopsis "Common utilities for automatic differentiation") + (description "The is package provides a variety of common utilities that +can be used by downstream automatic differentiation (AD) tools to define and +execute forward-, reverse-, and mixed-mode primitives.") + (license license:expat))) + +(define-public julia-chainrulescore + (package + (name "julia-chainrulescore") + (version "0.9.29") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaDiff/ChainRulesCore.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1k0iayw39n1ikkkhvyi4498vsnzc94skqs41gnd15632gxjfvki4")))) + (build-system julia-build-system) + (inputs ;required for tests + `(("julia-benchmarktools" ,julia-benchmarktools) + ("julia-staticarrays" ,julia-staticarrays))) + (propagated-inputs + `(("julia-compat" ,julia-compat))) + (home-page "https://github.com/JuliaDiff/ChainRulesCore.jl") + (synopsis "Common utilities used by downstream automatic differentiation tools") + (description "The package provides a light-weight dependency for defining +sensitivities for functions without the need to depend on ChainRules itself.") + (license license:expat))) + +(define-public julia-chainrulestestutils + (package + (name "julia-chainrulestestutils") + (version "0.6.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaDiff/ChainRulesTestUtils.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1pzs947adnb3cx1qd0cxp2fidk9szz0zsqbas90z1lhydykkvkil")))) + (build-system julia-build-system) + (propagated-inputs + `(("julia-chainrulescore" ,julia-chainrulescore) + ("julia-compat" ,julia-compat) + ("julia-finitedifference" ,julia-finitedifferences))) + (home-page "https://github.com/JuliaDiff/ChainRulesTestUtils.jl") + (synopsis "Common utilities used by downstream automatic differentiation tools") + (description "This package is designed to help in testing +@code{ChainRulesCore.frule} and @code{ChainRulesCore.rrule} methods. The main +entry points are @code{ChainRulesTestUtils.frule_test}, +@code{ChainRulesTestUtils.rrule_test}, and +@code{ChainRulesTestUtils.test_scalar}. Currently this is done via testing the +rules against numerical differentiation (using @code{FiniteDifferences.jl}). + +@code{ChainRulesTestUtils.jl} is separated from @code{ChainRulesCore.jl} so that it +can be a test-only dependency, allowing it to have potentially heavy +dependencies, while keeping @code{ChainRulesCore.jl} as light-weight as possible.") + (license license:expat))) + +(define-public julia-colors + (package + (name "julia-colors") + (version "0.12.6") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaGraphics/Colors.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "156zsszgwh6bmznsan0zyha6yvcxw3c5mvc5vr2qfsgxbyh36ln6")))) + (build-system julia-build-system) + (propagated-inputs + `(("julia-colortypes" ,julia-colortypes) + ("julia-fixedpointnumbers" ,julia-fixedpointnumbers) + ("julia-reexport" ,julia-reexport))) + (home-page "https://github.com/JuliaGraphics/Colors.jl") + (synopsis "Tools for dealing with color") + (description "This package provides a wide array of functions for dealing +with color. This includes conversion between colorspaces, measuring distance +between colors, simulating color blindness, parsing colors, and generating +color scales for graphics.") + (license license:expat))) + +(define-public julia-colortypes + (package + (name "julia-colortypes") + (version "0.10.12") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaGraphics/ColorTypes.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "176hr3qbz7lncmykks2qaj3cqisnzim7wi5jwsca9ld26wwyvyqq")))) + (arguments + '(#:tests? #f)) ;require Documenter, not packaged yet + (build-system julia-build-system) + (propagated-inputs + `(("julia-fixedpointnumbers" ,julia-fixedpointnumbers))) + (home-page "https://github.com/JuliaGraphics/ColorTypes.jl") + (synopsis "Basic color types and constructor") + (description "This minimalistic package serves as the foundation for +working with colors in Julia. It defines basic color types and their +constructors, and sets up traits and show methods to make them easier to work +with.") + (license license:expat))) + +(define-public julia-commonsubexpressions + (package + (name "julia-commonsubexpressions") + (version "0.3.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rdeits/CommonSubexpressions.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0mgy90kk8ksv3l720kkk04gnhn4aqhh2dj4sp3x8yy3limngfjay")))) + (build-system julia-build-system) + (propagated-inputs + `(("julia-macrotools" ,julia-macrotools))) + (home-page "https://github.com/rdeits/CommonSubexpressions.jl") + (synopsis "@code{@@cse} macro for Julia") + (description "This package provides the @code{@@cse} macro, which performs +common subexpression elimination.") + (license license:expat))) + (define-public julia-compat (package (name "julia-compat") @@ -66,6 +331,71 @@ provides a macro that lets you use the latest syntax in a backwards-compatible way.") (license license:expat))) +;;; TODO: Remove this autogenerated source package +;;; and build it from realse source using <https://github.com/JuliaPackaging/Yggdrasil/> +(define-public julia-compilersupportlibraries-jll + (package + (name "julia-compilersupportlibraries-jll") + (version "0.4.0+1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/CompilerSupportLibraries_jll.jl") + (commit (string-append "CompilerSupportLibraries-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "03j6xdvps259mhdzpjqf41l65w2l9sahvxg4wrp34hcf69wkrzpy")))) + (build-system julia-build-system) + (arguments + `(#:tests? #f ; no runtests.jl + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"CompilerSupportLibraries\", \"" + (assoc-ref inputs "gfortran:lib") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$")) + #t))))) + (inputs ;required by artifacts + `(("gfortran:lib" ,gfortran "lib"))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers))) + (home-page "https://github.com/JuliaBinaryWrappers/CompilerSupportLibraries_jll.jl") + (synopsis "Internal wrappers") + (description "This package provides compiler support for libraries. It is +an autogenerated source package constructed using @code{BinaryBuilder.jl}. The +originating @code{build_tarballs.jl} script can be found on the community +build tree Yggdrasil.") + (license license:expat))) + +(define-public julia-constructionbase + (let ((commit "de77e2865b554f9b078fd8c35b593cce0554ae02")) + (package + (name "julia-constructionbase") + (version "1.1.0") ;tag not created upstream + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaObjects/ConstructionBase.jl") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1y79sfj0rds1skl9j16p9161hwa9khm0xc2m4hgjcbh5zzvyr57v")))) + (build-system julia-build-system) + (home-page "https://juliaobjects.github.io/ConstructionBase.jl/dev/") + (synopsis "Primitive functions for construction of objects") + (description "This very lightweight package provides primitive functions +for construction of objects.") + (license license:expat)))) + (define-public julia-datastructures (package (name "julia-datastructures") @@ -90,6 +420,143 @@ including, @code{CircularBuffer}, @code{Queue}, @code{Stack}, @code{Accumulators}, @code{LinkedLists}, @code{SortedDicts} and many others.") (license license:expat))) +(define-public julia-diffresults + (package + (name "julia-diffresults") + (version "1.0.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaDiff/DiffResults.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1w6p3yxajvclax5b9g7cr2jmbc7lvr5nk4gq0aljxdycdq1d2y3v")))) + (propagated-inputs + `(("julia-staticarrays" ,julia-staticarrays))) + (build-system julia-build-system) + (home-page "https://github.com/JuliaDiff/DiffResults.jl") + (synopsis "In-place differentiation methods of primal values at multi-order") + (description "This package provides the @code{DiffResult} type, which can +be passed to in-place differentiation methods instead of an output buffer.") + (license license:expat))) + +(define-public julia-diffrules + (package + (name "julia-diffrules") + (version "1.0.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaDiff/DiffRules.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0cwjvj4gma7924fm3yas0nf0jlnwwx4v7fi79ii3s290lkdldzfl")))) + (propagated-inputs + `(("julia-nanmath" ,julia-nanmath) + ("julia-specialfunctions" ,julia-specialfunctions))) + (build-system julia-build-system) + (home-page "https://github.com/JuliaDiff/DiffRules.jl") + (synopsis "Primitive differentiation rules") + (description "This package provides primitive differentiation rules that +can be composed via various formulations of the chain rule. Using +@code{DiffRules}, new differentiation rules can defined, query whether or not +a given rule exists, and symbolically apply rules to simple Julia expressions.") + (license license:expat))) + +(define-public julia-difftests + (package + (name "julia-difftests") + (version "0.1.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaDiff/DiffTests.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1rxpnd5zi3pxgdd38l5jm2sxc3q6p7g57fqgll2dsiin07y3my57")))) + (build-system julia-build-system) + (home-page "https://github.com/JuliaDiff/DiffTests.jl") + (synopsis "Common test functions for differentiation tools") + (description "This package contains a common suite of test functions for +stressing the robustness of differentiation tools.") + (license license:expat))) + +(define-public julia-example + (let ((commit "f968c69dea24f851d0c7e686db23fa55826b5388")) + (package + (name "julia-example") + (version "0.5.4") ;tag not created upstream + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaLang/Example.jl") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1v3z0d6gh6wfbypffy9m9rhh36px6fm5wjzq0y6rbmc95r0qpqlx")))) + (build-system julia-build-system) + (home-page "https://github.com/JuliaLang/Example.jl") + (synopsis "Module providing examples") + (description "This package provides various examples.") + (license license:expat)))) + +(define-public julia-fillarrays + (package + (name "julia-fillarrays") + (version "0.11.7") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaArrays/FillArrays.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1q1qn9pb5dmppddnmf8gggdqyvivqh3ffvbblhn37smcf9r5sy7d")))) + (build-system julia-build-system) + (inputs ;required by tests + `(("julia-staticarrays" ,julia-staticarrays))) + (home-page "https://github.com/JuliaArrays/FillArrays.jl") + (synopsis "Lazy matrix representation") + (description "This package allows to lazily represent matrices filled with +a single entry, as well as identity matrices. This package exports the +following types: @code{Eye}, @code{Fill}, @code{Ones}, @code{Zeros}, +@code{Trues} and @code{Falses}.") + (license license:expat))) + +(define-public julia-finitedifferences + (package + (name "julia-finitedifferences") + (version "0.12.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaDiff/FiniteDifferences.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0dcx34026xdpfmbjls3mrknl8ww62kxxfr77kfihbazsfg2gp5b4")))) + (build-system julia-build-system) + (inputs + `(("julia-benchmarktools" ,julia-benchmarktools))) + (propagated-inputs + `(("julia-chainrulescore" ,julia-chainrulescore) + ("julia-richardson" ,julia-richardson) + ("julia-staticarrays" ,julia-staticarrays))) + (home-page "https://github.com/JuliaDiff/FiniteDifferences.jl") + (synopsis "Estimates derivatives with finite differences") + (description "This package calculates approximate derivatives numerically +using finite difference.") + (license license:expat))) + (define-public julia-fixedpointnumbers (package (name "julia-fixedpointnumbers") @@ -125,6 +592,185 @@ scaled by a constant factor. Consequently, they have a fixed number of digits (bits) after the decimal (radix) point.") (license license:expat))) +(define-public julia-forwarddiff + (package + (name "julia-forwarddiff") + (version "0.10.17") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaDiff/ForwardDiff.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "17xaz4v0zr46p7w873w1fwf31phdnhr0vbdym9yr4flmpzi528jw")))) + (build-system julia-build-system) + (inputs ;required for tests + `(("julia-calculus" ,julia-calculus) + ("julia-difftests" ,julia-difftests))) + (propagated-inputs + `(("julia-commonsubexpressions" ,julia-commonsubexpressions) + ("julia-diffresults" ,julia-diffresults) + ("julia-diffrules" ,julia-diffrules) + ("julia-nanmath" ,julia-nanmath) + ("julia-specialfunctions" ,julia-specialfunctions) + ("julia-staticarrays" ,julia-staticarrays))) + (home-page "https://github.com/JuliaDiff/ForwardDiff.jl") + (synopsis "Methods to take multidimensional derivatives") + (description "This package implements methods to take derivatives, +gradients, Jacobians, Hessians, and higher-order derivatives of native Julia +functions (or any callable object, really) using forward mode automatic +differentiation (AD).") + (license license:expat))) + +(define-public julia-http + (package + (name "julia-http") + (version "0.9.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaWeb/HTTP.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0ij0yci13c46p92m4zywvcs02nn8pm0abyfffiyhxvva6hq48lyl")))) + (build-system julia-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'install 'disable-network-tests + (lambda _ + (substitute* "test/runtests.jl" + (("\"async.jl") "# \"async.jl") + (("\"client.jl") "# \"client.jl")) + (substitute* "test/aws4.jl" + (("@testset.*HTTP.request with AWS authentication.*" all) + (string-append all "return\n"))) + (substitute* "test/insert_layers.jl" + (("@testset.*Inserted final layer runs handler.*" all) + (string-append all "return\n"))) + (substitute* "test/multipart.jl" + (("@testset \"Setting of Content-Type.*" all) + (string-append all "return\n")) + (("@testset \"Deprecation of .*" all) + (string-append all "return\n"))) + (substitute* "test/websockets.jl" + (("@testset.*External Host.*" all) + (string-append all "return\n"))) + (substitute* "test/messages.jl" + (("@testset.*Read methods.*" all) + (string-append all "return\n")) + (("@testset.*Body - .*" all) + (string-append all "return\n")) + (("@testset.*Write to file.*" all) + (string-append all "return\n"))) + #t))))) + (propagated-inputs + `(("julia-inifile" ,julia-inifile) + ("julia-mbedtls" ,julia-mbedtls) + ("julia-uris" ,julia-uris))) + ;; required for tests + (inputs + `(("julia-json" ,julia-json) + ("julia-bufferedstreams" ,julia-bufferedstreams))) + (home-page "https://juliaweb.github.io/HTTP.jl/") + (synopsis "HTTP support for Julia") + (description "@code{HTTP.jl} is a Julia library for HTTP Messages, +implementing both a client and a server.") + (license license:expat))) + +(define-public julia-inifile + (package + (name "julia-inifile") + (version "0.5.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaIO/IniFile.jl") + (commit "8ba59958495fa276d6489d2c3903e765d75e0bc0"))) + (file-name (git-file-name name version)) + (sha256 + (base32 "11h6f99jpbg729lplw841m68jprka7q3n8yw390bndlmcdsjabpd")))) + (build-system julia-build-system) + (home-page "https://github.com/JuliaIO/IniFile.jl") + (synopsis "Reading Windows-style INI files") + (description "This is a Julia package that defines an IniFile type that +allows to interface with @file{.ini} files.") + (license license:expat))) + +(define-public julia-irtools + (package + (name "julia-irtools") + (version "0.4.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/FluxML/IRTools.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0wwzy77jcdnffnd5fr6xan7162g4wydz67igrq82wflwnrhlcx5y")))) + (arguments + '(#:tests? #f)) ;require Documenter, not packaged yet + (build-system julia-build-system) + (propagated-inputs + `(("julia-macrotools" ,julia-macrotools))) + (home-page "https://github.com/FluxML/IRTools.jl") + (synopsis "Simple and flexible IR format") + (description "This package provides a simple and flexible IR format, +expressive enough to work with both lowered and typed Julia code, as well as +external IRs. It can be used with Julia metaprogramming tools such as +Cassette.") + (license license:expat))) + +(define-public julia-jllwrappers + (package + (name "julia-jllwrappers") + (version "1.2.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaPackaging/JLLWrappers.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1sj3mi2dcc13apqfpy401wic5n0pgbck1p98b2g3zw0mln9s83m4")))) + (arguments + ;; Wants to download stuff + '(#:tests? #f + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'custom-override-path + (lambda* (#:key inputs #:allow-other-keys) + ;; Make @generate_wrapper_header take an optional argument that + ;; guix packagers can pass to override the default "override" + ;; binary path. This won't be needed when something like + ;; https://github.com/JuliaPackaging/JLLWrappers.jl/pull/27 + ;; will be merged. + (substitute* "src/wrapper_generators.jl" + (("generate_wrapper_header.*") + "generate_wrapper_header(src_name, override_path = nothing)\n") + (("pkg_dir = .*" all) + (string-append + all "\n" "override = something(override_path," + "joinpath(dirname(pkg_dir), \"override\"))\n")) + (("@static if isdir.*") "@static if isdir($override)\n") + (("return joinpath.*") "return $override\n")) + #t))))) + (build-system julia-build-system) + (home-page "https://github.com/JuliaPackaging/JLLWrappers.jl") + (synopsis "Julia macros used by JLL packages") + (description "This package contains Julia macros that enable JLL packages +to generate themselves. It is not intended to be used by users, but rather is +used in autogenerated packages via @code{BinaryBuilder.jl}.") + (license license:expat))) + (define-public julia-json (package (name "julia-json") @@ -150,6 +796,117 @@ digits (bits) after the decimal (radix) point.") and printing JSON documents.") (license license:expat))) +(define-public julia-macrotools + (package + (name "julia-macrotools") + (version "0.5.6") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/FluxML/MacroTools.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0k4z2hyasd9cwxf4l61zk3w4ajs44k69wx6z1ghdn8f5p8xy217f")))) + (build-system julia-build-system) + (home-page "https://fluxml.ai/MacroTools.jl") + (synopsis "Tools for working with Julia code and expressions") + (description "This library provides tools for working with Julia code and +expressions. This includes a template-matching system and code-walking tools +that let you do deep transformations of code.") + (license license:expat))) + +(define-public julia-mbedtls + (package + (name "julia-mbedtls") + (version "1.0.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaLang/MbedTLS.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0zjzf2r57l24n3k0gcqkvx3izwn5827iv9ak0lqix0aa5967wvfb")))) + (build-system julia-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'install 'disable-network-tests + ;; Tries to connect to httpbin.org + (lambda _ + (substitute* "test/runtests.jl" + (("testhost =") "return #")) + #t))))) + (propagated-inputs `(("julia-mbedtls-jll" ,julia-mbedtls-jll))) + (home-page "https://github.com/JuliaLang/MbedTLS.jl") + (synopsis "Apache's mbed TLS library wrapper") + (description "@code{MbedTLS.jl} provides a wrapper around the @code{mbed +TLS} and cryptography C libary for Julia.") + (license license:expat))) + +(define-public julia-mbedtls-jll + (package + (name "julia-mbedtls-jll") + ;; version 2.25.0+0 is not compatible with current mbedtls 2.23.0, + ;; upgrade this when mbedtls is updated in guix + (version "2.24.0+1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/MbedTLS_jll.jl") + (commit (string-append "MbedTLS-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0kk9dlxdh7yms21npgrdfmjbj8q8ng6kdhrzw3jr2d7rp696kp99")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; No runtests.jl + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"MbedTLS\", \"" + (assoc-ref inputs "mbedtls-apache") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$")) + #t))))) + (inputs `(("mbedtls-apache" ,mbedtls-apache))) + (propagated-inputs `(("julia-jllwrappers" ,julia-jllwrappers))) + (home-page "https://github.com/JuliaBinaryWrappers/MbedTLS_jll.jl") + (synopsis "Apache's mbed TLS binary wrappers") + (description "This Julia module provides @code{mbed TLS} libraries and +wrappers.") + (license license:expat))) + +(define-public julia-nanmath + (package + (name "julia-nanmath") + (version "0.3.5") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mlubin/NaNMath.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1hczhz00qj99w63vp627kwk02l2sr2qmzc2rkwwkdwvzy670p25q")))) + (build-system julia-build-system) + (home-page "https://github.com/mlubin/NaNMath.jl") + (synopsis "Implementations of basic math functions") + (description "Implementations of basic math functions which return +@code{NaN} instead of throwing a @code{DomainError}.") + (license license:expat))) + (define-public julia-orderedcollections (package (name "julia-orderedcollections") @@ -197,6 +954,52 @@ have arbitrary indices, similar to those found in some other programming languages like Fortran.") (license license:expat))) +;;; TODO: Remove this autogenerated source package +;;; and build it from realse source using <https://github.com/JuliaPackaging/Yggdrasil/> +(define-public julia-openspecfun-jll +(let ((commit "6c505cce3bdcd9cd2b15b4f9362ec3a42c4da71c")) + (package + (name "julia-openspecfun-jll") + (version "0.5.3+4") ;tag not created upstream + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/OpenSpecFun_jll.jl") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0bl2gcgndsbiwhwy8fl070cjm1fyf9kxj6gkikgirmzgjl29iakn")))) + (build-system julia-build-system) + (arguments + `(#:tests? #f ; no runtests.jl + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"OpenSpecFun\", \"" + (assoc-ref inputs "openspecfun") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$")) + #t))))) + (inputs + `(("openspecfun" ,openspecfun))) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers) + ("julia-compilersupportlibraries-jll" ,julia-compilersupportlibraries-jll))) + (home-page "https://github.com/JuliaBinaryWrappers/OpenSpecFun_jll.jl") + (synopsis "Internal wrappers") + (description "This package provides a wrapper for OpenSpecFun. It is an +autogenerated source package constructed using @code{BinaryBuilder.jl}. The +originating @code{build_tarballs.jl} script can be found on the community +build tree Yggdrasil.") + (license license:expat)))) + (define-public julia-parsers (package (name "julia-parsers") @@ -216,3 +1019,240 @@ languages like Fortran.") (description "@code{Parsers.jl} is a collection of type parsers and utilities for Julia.") (license license:expat))) + +(define-public julia-reexport + (package + (name "julia-reexport") + (version "1.0.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/simonster/Reexport.jl") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1yhhja1zz6dy5f4fd19bdwd6jwgj7q4w3avzgyg1hjhmdl8jrh0s")))) + (build-system julia-build-system) + (home-page "https://github.com/simonster/Reexport.jl") + (synopsis "Re-export modules and symbols") + (description "This package provides tools to re-export modules and symbols.") + (license license:expat))) + +(define-public julia-requires + (package + (name "julia-requires") + (version "1.1.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaPackaging/Requires.jl/") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "03hyfy7c0ma45b0y756j76awi3az2ii4bz4s8cxm3xw9yy1z7b01")))) + (build-system julia-build-system) + (inputs ;required for test + `(("julia-example" ,julia-example))) + (propagated-inputs + `(("julia-colors" ,julia-colors))) + (home-page "https://github.com/JuliaPackaging/Requires.jl/") + (synopsis "Faster package loader") + (description "This package make loading packages faster, maybe. It +supports specifying glue code in packages which will load automatically when +another package is loaded, so that explicit dependencies (and long load times) +can be avoided.") + (license license:expat))) + +(define-public julia-richardson + (package + (name "julia-richardson") + (version "1.4.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaMath/Richardson.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "06v9ii3d7hh41fsrfklaa8ap55z5s017f888mrd1c18y4fx9i4nx")))) + (build-system julia-build-system) + (home-page "https://juliapackages.com/p/richardson") + (synopsis "Extrapolate function using Richardson method") + (description "This package provides a function extrapolate that +extrapolates a given function @code{f(x)} to @code{f(x0)}, evaluating @code{f} +only at a geometric sequence of points @code{> x0} (or optionally @code{< +x0}). The key algorithm is Richardson extrapolation using a Neville–Aitken +tableau, which adaptively increases the degree of an extrapolation polynomial +until convergence is achieved to a desired tolerance (or convergence stalls +due to e.g. floating-point errors). This allows one to obtain @code{f(x0)} to +high-order accuracy, assuming that @code{f(x0+h)} has a Taylor series or some +other power series in @code{h}.") + (license license:expat))) + +(define-public julia-specialfunctions + (package + (name "julia-specialfunctions") + (version "1.3.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaMath/SpecialFunctions.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1rfhrrkzi3ils7fklbn35ki1yp5x88fi71qknfwqyw4pk8cf8p80")))) + (build-system julia-build-system) + (inputs + `(("julia-chainrulestestutils" ,julia-chainrulestestutils))) + (propagated-inputs + `(("julia-chainrulescore" ,julia-chainrulescore) + ("julia-openspecfun-jll" ,julia-openspecfun-jll))) + (home-page "https://github.com/JuliaMath/SpecialFunctions.jl") + (synopsis "Special mathematical functions") + (description "This package provides special mathematical functions, +including Bessel, Hankel, Airy, error, Dawson, exponential (or sine and +cosine) integrals, eta, zeta, digamma, inverse digamma, trigamma, and +polygamma functions.") + (license license:expat))) + +(define-public julia-staticarrays + (package + (name "julia-staticarrays") + (version "1.0.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaArrays/StaticArrays.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "01z8bcqwpfkp8p1h1r36pr5cc3798y76zkas7g3206pcsdhvlkz1")))) + (build-system julia-build-system) + (inputs + `(("julia-benchmarktools" ,julia-benchmarktools))) + (home-page "https://github.com/JuliaArrays/StaticArrays.jl") + (synopsis "Statically sized arrays") + (description "This package provides a framework for implementing +statically sized arrays in Julia, using the abstract type +@code{StaticArray{Size,T,N} <: AbstractArray{T,N}}. Subtypes of +@code{StaticArray} will provide fast implementations of common array and +linear algebra operations.") + (license license:expat))) + +(define-public julia-uris + (package + (name "julia-uris") + (version "1.2.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaWeb/URIs.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0fqyagsqks5za7m0czafr34m2xh5501f689k9cn5x3npajdnh2r3")))) + (build-system julia-build-system) + (arguments + '(#:julia-package-name "URIs" ;required to run tests + #:phases + (modify-phases %standard-phases + (add-before 'check 'change-dir + ;; Tests must be run from the testdir + (lambda* (#:key source outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (chdir + (string-append out "/share/julia/packages/URIs/test"))) + #t))))) + ;; required for tests + (inputs `(("julia-json" ,julia-json))) + (home-page "https://github.com/JuliaWeb/URIs.jl") + (synopsis "URI parsing in Julia") + (description "@code{URIs.jl} is a Julia package that allows parsing and +working with @acronym{URIs,Uniform Resource Identifiers}, as defined in RFC +3986.") + (license license:expat))) + +(define-public julia-unitful + (package + (name "julia-unitful") + (version "1.6.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/PainterQubits/Unitful.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0g5bhlvay9yk11c5dqwbzmb3q7lzj0cq5zchyk39d59fkvvmxvq3")))) + (build-system julia-build-system) + (propagated-inputs + `(("julia-constructionbase" ,julia-constructionbase))) + (home-page "https://painterqubits.github.io/Unitful.jl/stable/") + (synopsis "Physical units in Julia") + (description "This package supports SI units and also many other unit +system.") + (license license:expat))) + +(define-public julia-zygoterules + (package + (name "julia-zygoterules") + (version "0.2.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/FluxML/ZygoteRules.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "07i2mf6rr5b8i6l82qgwl5arsb5pwyyzyfasgnszhdqllk9501bs")))) + (build-system julia-build-system) + (propagated-inputs + `(("julia-macrotools" ,julia-macrotools))) + (home-page "https://github.com/FluxML/ZygoteRules.jl") + (synopsis "Add minimal custom gradients to Zygote") + (description "Minimal package which enables to add custom gradients to +Zygote, without depending on Zygote itself.") + (license license:expat))) + +(define-public julia-zygote + (package + (name "julia-zygote") + (version "0.6.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/FluxML/Zygote.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1h2ph0lsisbkh8y4xgwzgw9p5zi243q8zzp5gfh3zw9pzkx6a1rf")))) + (build-system julia-build-system) + (arguments + `(#:tests? #f)) ;require CUDA, not packaged yet + (propagated-inputs + `(("julia-abstractffs" ,julia-abstractffts) + ("julia-chainrules" ,julia-chainrules) + ("julia-diffrules" ,julia-diffrules) + ("julia-fillarrays" ,julia-fillarrays) + ("julia-forwarddiff" ,julia-forwarddiff) + ("julia-irtools" ,julia-irtools) + ("julia-macrotools" ,julia-macrotools) + ("julia-nanmath" ,julia-nanmath) + ("julia-requires" ,julia-requires) + ("julia-specialfunctions" ,julia-specialfunctions) + ("julia-zygote-rules" ,julia-zygoterules))) + (home-page "https://fluxml.ai/Zygote.jl") + (synopsis "Automatic differentiation in Julia") + (description "Zygote provides source-to-source automatic +differentiation (AD) in Julia, and is the next-generation AD system for the +Flux differentiable programming framework.") + (license license:expat))) |