path: root/gnu/packages/julia-xyz.scm

;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2020, 2021 Nicolò Balzarotti <nicolo@nixo.xyz>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

(define-module (gnu packages julia-xyz)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix git-download)
  #:use-module (guix build-system julia)
  #:use-module (gnu packages tls))

(define-public julia-adapt
  (package
    (name "julia-adapt")
    (version "3.1.1")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/JuliaGPU/Adapt.jl")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "1lks6k3a1gvwlplld47nh6xfy3nnlpc0vhkzg6zg0qn33qdmavrg"))))
    (build-system julia-build-system)
    (home-page "https://github.com/JuliaGPU/Adapt.jl")
    (synopsis "Package providing the @code{adapt} function, similar to @code{convert}")
    (description "This Julia package provides the @code{adapt(T, x)} function
acts like @code{convert(T, x)}, but without the restriction of returning a
@code{T}.  This allows you to \"convert\" wrapper types like @code{Adjoint} to
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-compat
  (package
    (name "julia-compat")
    (version "3.25.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/JuliaLang/Compat.jl")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "1m4r5i8mq29xjp3mllh6047n5a78sdyld57m15anrnsjgaapcgby"))))
    (build-system julia-build-system)
    (home-page "https://github.com/JuliaLang/Compat.jl")
    (synopsis "Compatibility across Julia versions")
    (description "The Compat package is designed to ease interoperability
between older and newer versions of the Julia language.  The Compat package
provides a macro that lets you use the latest syntax in a backwards-compatible
way.")
    (license license:expat)))

(define-public julia-datastructures
  (package
    (name "julia-datastructures")
    (version "0.18.9")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/JuliaCollections/DataStructures.jl")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "0hdqp8ipsqdw5bqqkdvz4j6n67x80sj5azr9vzyxwjfsgkfbnk2l"))))
    (propagated-inputs
     `(("julia-compat" ,julia-compat)
       ("julia-orderedcollections" ,julia-orderedcollections)))
    (build-system julia-build-system)
    (home-page "https://github.com/JuliaCollections/DataStructures.jl")
    (synopsis "Julia module providing different data structures")
    (description "This package implements a variety of data structures,
including, @code{CircularBuffer}, @code{Queue}, @code{Stack},
@code{Accumulators}, @code{LinkedLists}, @code{SortedDicts} and many others.")
    (license license:expat)))

(define-public julia-fixedpointnumbers
  (package
    (name "julia-fixedpointnumbers")
    (version "0.8.4")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/JuliaMath/FixedPointNumbers.jl")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "0j0n40n04q9sk68wh9jq90m6c67k4ws02k41djjzkrqmpzv4rcdi"))))
    (build-system julia-build-system)
    (arguments
     `(#:phases
       (modify-phases %standard-phases
         (add-after 'unpack 'disable-failing-test
           (lambda* (#:key outputs #:allow-other-keys)
             (substitute* "test/fixed.jl"
               ;; A deprecation warning is not thrown
               (("@test_logs.*:warn" all) (string-append "# " all)))
             #t)))))
    (propagated-inputs `(("julia-compat" ,julia-compat)))
    (home-page "https://github.com/JuliaMath/FixedPointNumbers.jl")
    (synopsis "Fixed point types for Julia")
    (description "@code{FixedPointNumbers.jl} implements fixed-point number
types for Julia.  A fixed-point number represents a fractional, or
non-integral, number.  In contrast with the more widely known floating-point
numbers, with fixed-point numbers the decimal point doesn't \"float\":
fixed-point numbers are effectively integers that are interpreted as being
scaled by a constant factor.  Consequently, they have a fixed number of
digits (bits) after the decimal (radix) point.")
    (license license:expat)))

(define-public julia-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-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")
    (version "0.21.1")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/JuliaIO/JSON.jl")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "1f9k613kbknmp4fgjxvjaw4d5sfbx8a5hmcszmp1w9rqfqngjx9m"))))
    (build-system julia-build-system)
    (propagated-inputs
     `(("julia-datastructures" ,julia-datastructures)
       ("julia-fixedpointnumbers" ,julia-fixedpointnumbers)
       ("julia-parsers" ,julia-parsers)
       ("julia-offsetarrays" ,julia-offsetarrays)))
    (home-page "https://github.com/JuliaIO/JSON.jl")
    (synopsis "JSON parsing and printing library for Julia")
    (description "@code{JSON.jl} is a pure Julia module which supports parsing
and printing JSON documents.")
    (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-orderedcollections
  (package
    (name "julia-orderedcollections")
    (version "1.3.2")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/JuliaCollections/OrderedCollections.jl")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "0sfip1ixghsz91q2s7d62rgzw3gppg42fg6bccxlplqa3hfmbycf"))))
    (build-system julia-build-system)
    (home-page "https://github.com/JuliaCollections/OrderedCollections.jl")
    (synopsis "Associative containers that preserve insertion order")
    (description "This package implements @code{OrderedDicts} and
@code{OrderedSets}, which are similar to containers in base Julia.  However,
during iteration the @code{Ordered*} containers return items in the order in
which they were added to the collection.")
    (license license:expat)))

(define-public julia-offsetarrays
  (package
    (name "julia-offsetarrays")
    (version "1.5.2")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/JuliaArrays/OffsetArrays.jl")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "1y3fnssw2hzyghrk6jfcxslab0f8sjkjszh482snfq4k6mkrhy77"))))
    (build-system julia-build-system)
    (propagated-inputs
     `(("julia-adapt" ,julia-adapt)))
    ;; CatIndices depends on OffsetArrays, introducing a recursive dependency
    (arguments '(#:tests? #f))
    (home-page "https://juliaarrays.github.io/OffsetArrays.jl/stable/")
    (synopsis "Fortran-like arrays with arbitrary, zero or negative indices")
    (description "@code{OffsetArrays.jl} provides Julia users with arrays that
have arbitrary indices, similar to those found in some other programming
languages like Fortran.")
    (license license:expat)))

(define-public julia-parsers
  (package
    (name "julia-parsers")
    (version "1.0.15")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/JuliaData/Parsers.jl")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32 "16iffl6l28kspgqch48mhi1s8qhspr3cpqcwsph3rqi72lbfqygx"))))
    (build-system julia-build-system)
    (home-page "https://github.com/JuliaData/Parsers.jl")
    (synopsis "Fast parsing machinery for basic types in Julia")
    (description "@code{Parsers.jl} is a collection of type parsers and
utilities for Julia.")
    (license license:expat)))

(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)))