[bug#53017] [PATCH 00/17] Add julia-biosequences and julia-bioalignments

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* [bug#53017] [PATCH 00/17] Add julia-biosequences and julia-bioalignments
@ 2022-01-04 22:45 zimoun
  2022-01-04 22:47 ` [bug#53017] [PATCH 01/17] gnu: julia-xyz: Adjust style zimoun
  0 siblings, 1 reply; 19+ messages in thread
From: zimoun @ 2022-01-04 22:45 UTC (permalink / raw)
  To: 53017; +Cc: zimoun, Efraim Flashner

Hi,

This series adds two useful packages for bioinformatics.

The first patch sets one inputs per line.  It is justified because a) Julia
package name can be long and often similar and b) uniformity helps.  For
instance of a)

--8<---------------cut here---------------start------------->8---
-     (list julia-arraylayouts julia-bandedmatrices julia-blockarrays
-           julia-fillarrays julia-matrixfactorizations))
+     (list julia-arraylayouts
+           julia-bandedmatrices
+           julia-blockarrays
+           julia-fillarrays
--8<---------------cut here---------------end--------------->8---

and this first patch does not trigger any rebuild.

The 3 other "adjust style" triggers some rebuild.

The second patch fixes packages without Project.toml file which are then
propagated.  Sadly, it implies the rebuild of all Julia packages for only one
problematic package: julia-indexablebitvectors.

Last, the tests of the package julia-biosymbols are still failing and I have
no clue why.  Therefore, they are turned off.  The package is correct because
used by julia-sequences and julia-alignments, both passing their test suite.

Cheers,
simon

zimoun (17):
  gnu: julia-xyz: Adjust style.
  build: julia-build-system: Create 'Project.toml' file when missing.
  gnu: julia-zygote: Adjust style.
  gnu: julia-documentertools: Adjust style.
  gnu: julia-documenter: Adjust style.
  gnu: Add julia-biogenerics.
  gnu: Add julia-indexablebitvectors.
  gnu: Add julia-twiddle.
  gnu: Add julia-simd.
  gnu: Add julia-scanbyte.
  gnu: Add julia-automa.
  gnu: Add julia-stringencodings.
  gnu: Add julia-yaml.
  gnu: Add julia-biosymbols.
  gnu: Add julia-biosequences.
  gnu: Add julia-intervaltrees.
  gnu: Add julia-bioalignments.

 doc/guix.texi                     |  19 +-
 gnu/packages/julia-xyz.scm        | 690 +++++++++++++++++++++++++-----
 guix/build/julia-build-system.scm |  33 +-
 3 files changed, 607 insertions(+), 135 deletions(-)

base-commit: b9c5dff57ff961a16c8fc24843a4535ea817e732
-- 
2.33.1

^ permalink raw reply	[flat|nested] 19+ messages in thread

* [bug#53017] [PATCH 01/17] gnu: julia-xyz: Adjust style.
  2022-01-04 22:45 [bug#53017] [PATCH 00/17] Add julia-biosequences and julia-bioalignments zimoun
@ 2022-01-04 22:47 ` zimoun
  2022-01-04 22:47   ` [bug#53017] [PATCH 02/17] build: julia-build-system: Create 'Project.toml' file when missing zimoun
                     ` (16 more replies)
  0 siblings, 17 replies; 19+ messages in thread
From: zimoun @ 2022-01-04 22:47 UTC (permalink / raw)
  To: 53017; +Cc: efraim, zimoun

* gnu/packages/julia-xyz: Align all inputs.
---
 gnu/packages/julia-xyz.scm | 313 ++++++++++++++++++++++++++-----------
 1 file changed, 224 insertions(+), 89 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 2ad1c4cd5d..3701bf3996 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -166,7 +166,9 @@ (define-public julia-arrayinterface
      ;; Disable as stopgap.
      `(#:tests? ,(not (target-x86-32?))))
     (propagated-inputs
-     (list julia-ifelse julia-requires julia-static))
+     (list julia-ifelse
+           julia-requires
+           julia-static))
     (native-inputs
      (list julia-aqua
            julia-bandedmatrices
@@ -248,9 +250,12 @@ (define-public julia-axisarrays
          (base32 "03kzan1lm4fxfhzv1xjg3ysf6y7nagcc61vfz15kvdrp1dqxlynk"))))
     (build-system julia-build-system)
     (propagated-inputs
-     (list julia-rangearrays julia-intervalsets julia-itertools))
+     (list julia-rangearrays
+           julia-intervalsets
+           julia-itertools))
     (native-inputs
-     (list julia-offsetarrays julia-unitful))
+     (list julia-offsetarrays
+           julia-unitful))
     (home-page "http://juliaarrays.github.io/AxisArrays.jl/latest/")
     (synopsis "Arrays where each dimension can have a named axis with values")
     (description "This package for the Julia language provides an array type
@@ -276,7 +281,8 @@ (define-public julia-bandedmatrices
          (base32 "0rlfj9gr9ss621v5kw5b06206yaak21s2vq9vk7r8a7p2ylncism"))))
     (build-system julia-build-system)
     (propagated-inputs
-     (list julia-arraylayouts julia-fillarrays))
+     (list julia-arraylayouts
+           julia-fillarrays))
     (native-inputs
      (list julia-genericlinearalgebra))
     (home-page "https://github.com/JuliaMatrices/BandedMatrices.jl")
@@ -318,7 +324,8 @@ (define-public julia-benchmarktools
                      (("@test @ballocated\\(Ref\\(1\\)\\)")
                       "@test_broken @ballocated(Ref(1))"))))))
            '(%standard-phases))))
-    (propagated-inputs (list julia-json))
+    (propagated-inputs
+     (list 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
@@ -350,9 +357,12 @@ (define-public julia-blockarrays
                    (substitute* "test/test_blockarrays.jl"
                      (("Int64") "Int32")))))))))
     (propagated-inputs
-     (list julia-arraylayouts julia-fillarrays))
+     (list julia-arraylayouts
+           julia-fillarrays))
     (native-inputs
-     (list julia-lazyarrays julia-offsetarrays julia-staticarrays))
+     (list julia-lazyarrays
+           julia-offsetarrays
+           julia-staticarrays))
     (home-page "https://github.com/JuliaArrays/BlockArrays.jl")
     (synopsis "BlockArrays for Julia")
     (description "A block array is a partition of an array into blocks or
@@ -383,8 +393,11 @@ (define-public julia-blockbandedmatrices
          (base32 "10n1r6kmmv2wa307jfg9y2m6p16j8hngjp3fjavpbdy1r5haasm9"))))
     (build-system julia-build-system)
     (propagated-inputs
-     (list julia-arraylayouts julia-bandedmatrices julia-blockarrays
-           julia-fillarrays julia-matrixfactorizations))
+     (list julia-arraylayouts
+           julia-bandedmatrices
+           julia-blockarrays
+           julia-fillarrays
+           julia-matrixfactorizations))
     (home-page "https://github.com/JuliaMatrices/BlockBandedMatrices.jl")
     (synopsis "Block-banded matrices and banded-block-banded matrices")
     (description "This package supports representing block-banded and
@@ -437,7 +450,8 @@ (define-public julia-bufferedstreams
      '(#:tests? #f
        #:julia-package-name "BufferedStreams"
        #:julia-package-uuid "e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d"))
-    (propagated-inputs (list julia-compat))
+    (propagated-inputs
+     (list julia-compat))
     (home-page "https://github.com/BioJulia/BufferedStreams.jl")
     (synopsis "Fast composable IO streams")
     (description "@code{BufferedStreams.jl} provides buffering for IO
@@ -514,10 +528,14 @@ (define-public julia-chainrules
         (base32 "0if93pd3b3scg2x3gmk1cbwjk0ax1n792vy8c38y3xl7jpd5cb70"))))
     (build-system julia-build-system)
     (inputs                             ;required for test
-     (list julia-chainrulestestutils julia-finitedifferences julia-nanmath
+     (list julia-chainrulestestutils
+           julia-finitedifferences
+           julia-nanmath
            julia-specialfunctions))
     (propagated-inputs
-     (list julia-chainrulescore julia-compat julia-reexport
+     (list julia-chainrulescore
+           julia-compat
+           julia-reexport
            julia-requires))
     (home-page "https://github.com/JuliaDiff/ChainRules.jl")
     (synopsis "Common utilities for automatic differentiation")
@@ -541,7 +559,8 @@ (define-public julia-chainrulescore
         (base32 "1866xv30h1bi7f2m993nljzf58wwmv8zlgn6ffn9j3wckch1nfpb"))))
     (build-system julia-build-system)
     (inputs                             ;required for tests
-     (list julia-benchmarktools julia-staticarrays))
+     (list julia-benchmarktools
+           julia-staticarrays))
     (propagated-inputs
      (list julia-compat))
     (home-page "https://github.com/JuliaDiff/ChainRulesCore.jl")
@@ -565,7 +584,9 @@ (define-public julia-chainrulestestutils
         (base32 "1vlkyp72d514gyb4k3yhjl1g7f24ncmz61j56p4sdi9f76rk9fx9"))))
     (build-system julia-build-system)
     (propagated-inputs
-     (list julia-chainrulescore julia-compat julia-finitedifferences))
+     (list julia-chainrulescore
+           julia-compat
+           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
@@ -604,7 +625,8 @@ (define-public julia-codeczlib
                          (find-files out "\\.gz$"))
                #t))))))
     (propagated-inputs
-     (list julia-zlib-jll julia-transcodingstreams))
+     (list julia-zlib-jll
+           julia-transcodingstreams))
     (home-page "https://github.com/JuliaIO/CodecZlib.jl")
     (synopsis "Zlib codecs for @code{TranscodingStreams.jl}")
     (description "This package provides zlib codecs for
@@ -626,7 +648,9 @@ (define-public julia-colors
         (base32 "0kx3hq7rf8p5zx6ly9k5j90zijmc7yrwmy96cgkl2ibdfbnhmya3"))))
     (build-system julia-build-system)
     (propagated-inputs
-     (list julia-colortypes julia-fixedpointnumbers julia-reexport))
+     (list julia-colortypes
+           julia-fixedpointnumbers
+           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
@@ -650,7 +674,9 @@ (define-public julia-colorschemes
          (base32 "0kpjhmqd5cj8dh8bmh9b5g6bscyp7h23hzpr2s93pnrp57q1wvhq"))))
     (build-system julia-build-system)
     (propagated-inputs
-     (list julia-colors julia-colortypes julia-fixedpointnumbers
+     (list julia-colors
+           julia-colortypes
+           julia-fixedpointnumbers
            julia-staticarrays))
     (home-page "https://github.com/JuliaGraphics/ColorSchemes.jl")
     (synopsis "Colorschemes, colormaps, gradients, and palettes")
@@ -698,7 +724,9 @@ (define-public julia-colorvectorspace
          (base32 "02gk7f5g5wjxdasbjf8bvv1m7clksh7mw1xmygjdirjz1q0d6dwi"))))
     (build-system julia-build-system)
     (propagated-inputs
-     (list julia-colortypes julia-specialfunctions julia-tensorcore))
+     (list julia-colortypes
+           julia-specialfunctions
+           julia-tensorcore))
     (native-inputs
      (list julia-colors))
     (home-page "https://github.com/JuliaGraphics/ColorVectorSpace.jl")
@@ -810,7 +838,9 @@ (define-public julia-configurations
                    (substitute* "test/runtests.jl"
                      (("Int64") "Int32")))))))))
     (propagated-inputs
-     (list julia-crayons julia-expronicon julia-orderedcollections))
+     (list julia-crayons
+           julia-expronicon
+           julia-orderedcollections))
     (home-page "https://configurations.rogerluo.dev/stable/")
     (synopsis "Tools for options and configurations in Julia")
     (description "@code{Configurations.jl} provides a macro @code{@@option} to
@@ -855,7 +885,9 @@ (define-public julia-coordinatetransformations
     (propagated-inputs
      (list julia-staticarrays))
     (native-inputs
-    (list julia-documenter julia-forwarddiff julia-unitful))
+    (list julia-documenter
+          julia-forwarddiff
+          julia-unitful))
     (home-page "https://github.com/JuliaGeometry/CoordinateTransformations.jl")
     (synopsis "Coordinate transformations in Julia")
     (description "@code{CoordinateTransformations} is a Julia package to manage
@@ -985,7 +1017,8 @@ (define-public julia-datastructures
        (sha256
         (base32 "0hdqp8ipsqdw5bqqkdvz4j6n67x80sj5azr9vzyxwjfsgkfbnk2l"))))
     (propagated-inputs
-     (list julia-compat julia-orderedcollections))
+     (list julia-compat
+           julia-orderedcollections))
     (build-system julia-build-system)
     (arguments
      `(#:phases
@@ -1136,7 +1169,8 @@ (define-public julia-distances
     (propagated-inputs
      (list julia-statsapi))
     (native-inputs
-     (list julia-offsetarrays julia-unitful))
+     (list julia-offsetarrays
+           julia-unitful))
     (home-page "https://github.com/JuliaStats/Distances.jl")
     (synopsis "Julia package for evaluating distances (metrics) between vectors")
     (description "A Julia package for evaluating distances(metrics) between
@@ -1300,9 +1334,9 @@ (define-public julia-diffresults
        (file-name (git-file-name name version))
        (sha256
         (base32 "1w6p3yxajvclax5b9g7cr2jmbc7lvr5nk4gq0aljxdycdq1d2y3v"))))
+    (build-system julia-build-system)
     (propagated-inputs
      (list 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
@@ -1322,9 +1356,10 @@ (define-public julia-diffrules
        (file-name (git-file-name name version))
        (sha256
         (base32 "0cwjvj4gma7924fm3yas0nf0jlnwwx4v7fi79ii3s290lkdldzfl"))))
-    (propagated-inputs
-     (list julia-nanmath julia-specialfunctions))
     (build-system julia-build-system)
+    (propagated-inputs
+     (list julia-nanmath
+           julia-specialfunctions))
     (home-page "https://github.com/JuliaDiff/DiffRules.jl")
     (synopsis "Primitive differentiation rules")
     (description "This package provides primitive differentiation rules that
@@ -1376,7 +1411,9 @@ (define-public julia-dualnumbers
                ;; Seems to not play nicely with SpecialFunctions
                ((".*isempty.*") "")))))))
     (propagated-inputs
-     (list julia-calculus julia-nanmath julia-specialfunctions))
+     (list julia-calculus
+           julia-nanmath
+           julia-specialfunctions))
     (home-page "https://github.com/JuliaDiff/DualNumbers.jl")
     (synopsis "Represent dual numbers and for perform dual algebra")
     (description "The @code{DualNumbers} Julia package defines the @code{Dual}
@@ -1506,7 +1543,8 @@ (define-public julia-ffmpeg
          (base32 "1ldxbp0kq3ip67x7sp82dz56aq4p5i0chspbgx2zgskr6jcbjj1b"))))
     (build-system julia-build-system)
     (propagated-inputs
-     (list julia-ffmpeg-jll julia-x264-jll))
+     (list julia-ffmpeg-jll
+           julia-x264-jll))
     (home-page "https://github.com/JuliaIO/FFMPEG.jl")
     (synopsis "Julia Package for ffmpeg")
     (description "This package is made to be included into packages that just
@@ -1552,7 +1590,9 @@ (define-public julia-fileio
     (propagated-inputs
      (list julia-requires))
     (native-inputs
-     (list julia-colortypes julia-filepathsbase julia-http))
+     (list julia-colortypes
+           julia-filepathsbase
+           julia-http))
     (home-page "https://github.com/JuliaIO/FileIO.jl")
     (synopsis "Main Package for IO, loading all different kind of files")
     (description "@code{FileIO} aims to provide a common framework for detecting
@@ -1632,9 +1672,12 @@ (define-public julia-finitediff
              (setenv "GROUP" "Core")
              #t)))))
     (propagated-inputs
-     (list julia-arrayinterface julia-requires julia-staticarrays))
+     (list julia-arrayinterface
+           julia-requires
+           julia-staticarrays))
     (native-inputs
-     (list julia-bandedmatrices julia-blockbandedmatrices
+     (list julia-bandedmatrices
+           julia-blockbandedmatrices
            julia-safetestsets))
     (home-page "https://github.com/JuliaDiff/FiniteDiff.jl")
     (synopsis "Calculations of gradients, Jacobians, and Hessians")
@@ -1672,7 +1715,9 @@ (define-public julia-finitedifferences
     (inputs
      (list julia-benchmarktools))
     (propagated-inputs
-     (list julia-chainrulescore julia-richardson julia-staticarrays))
+     (list julia-chainrulescore
+           julia-richardson
+           julia-staticarrays))
     (home-page "https://github.com/JuliaDiff/FiniteDifferences.jl")
     (synopsis "Estimates derivatives with finite differences")
     (description "This package calculates approximate derivatives numerically
@@ -1702,7 +1747,8 @@ (define-public julia-fixedpointnumbers
                ;; A deprecation warning is not thrown
                (("@test_logs.*:warn" all) (string-append "# " all)))
              #t)))))
-    (propagated-inputs (list julia-compat))
+    (propagated-inputs
+     (list julia-compat))
     (home-page "https://github.com/JuliaMath/FixedPointNumbers.jl")
     (synopsis "Fixed point types for Julia")
     (description "@code{FixedPointNumbers.jl} implements fixed-point number
@@ -1755,7 +1801,8 @@ (define-public julia-forwarddiff
      ;; Disable as stopgap.
      `(#:tests? ,(not (target-x86-32?))))
     (inputs                             ;required for tests
-     (list julia-calculus julia-difftests))
+     (list julia-calculus
+           julia-difftests))
     (propagated-inputs
      (list julia-commonsubexpressions
            julia-diffresults
@@ -1953,7 +2000,9 @@ (define-public julia-geometrybasics
                    (substitute* "test/runtests.jl"
                      (("Int64") "Int32")))))))))
     (propagated-inputs
-     (list julia-itertools julia-staticarrays julia-structarrays
+     (list julia-itertools
+           julia-staticarrays
+           julia-structarrays
            julia-tables))
     (native-inputs
      (list julia-offsetarrays))
@@ -2003,7 +2052,8 @@ (define-public julia-graphics
          (base32 "10h1s09v7qkvrjr6l678zamb1p248n8jv4rrwkf8g7d2bpfz9amn"))))
     (build-system julia-build-system)
     (propagated-inputs
-     (list julia-colors julia-nanmath))
+     (list julia-colors
+           julia-nanmath))
     (home-page "https://github.com/JuliaGraphics/Graphics.jl")
     (synopsis "Base graphics in Julia")
     (description "@code{Graphics.jl} is an abstraction layer for graphical
@@ -2025,7 +2075,8 @@ (define-public julia-gumbo
         (base32 "1g22dv3v7caakspv3pdahnqn937fzzsg9y87rj72hid9g8lxl1gm"))))
     (build-system julia-build-system)
     (propagated-inputs
-     (list julia-abstracttrees julia-gumbo-jll))
+     (list julia-abstracttrees
+           julia-gumbo-jll))
     (home-page "https://github.com/JuliaWeb/Gumbo.jl")
     (synopsis "Julia wrapper around Google's gumbo C library for parsing HTML")
     (description "@code{Gumbo.jl} is a Julia wrapper around Google's gumbo
@@ -2077,10 +2128,13 @@ (define-public julia-http
                 (string-append all "return\n")))
              #t)))))
     (propagated-inputs
-     (list julia-inifile julia-mbedtls julia-uris))
+     (list julia-inifile
+           julia-mbedtls
+           julia-uris))
     ;; required for tests
     (inputs
-     (list julia-json julia-bufferedstreams))
+     (list julia-json
+           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,
@@ -2148,7 +2202,9 @@ (define-public julia-imageaxes
          (base32 "15zqxani1jjh8849s7rdps6b6prqdwv8yxx893y536vkpk7i07qd"))))
     (build-system julia-build-system)
     (propagated-inputs
-     (list julia-axisarrays julia-imagecore julia-reexport
+     (list julia-axisarrays
+           julia-imagecore
+           julia-reexport
            julia-simpletraits))
     (native-inputs
      (list julia-unitful))
@@ -2176,7 +2232,8 @@ (define-public julia-imagebase
     (arguments
      `(#:tests? #f))    ; Cycle with ImageMagick.jl.
     (propagated-inputs
-     (list julia-imagecore julia-reexport))
+     (list julia-imagecore
+           julia-reexport))
     ;(native-inputs
     ; `(("julia-imagemagick" ,julia-imagemagick)
     ;   ("julia-offsetarrays" ,julia-offsetarrays)
@@ -2248,7 +2305,10 @@ (define-public julia-imageinterminal
     (arguments
      `(#:tests? #f))    ; Cycle with ReferenceTests.jl.
     (propagated-inputs
-     (list julia-crayons julia-imagebase julia-imagecore julia-requires))
+     (list julia-crayons
+           julia-imagebase
+           julia-imagecore
+           julia-requires))
     ;(native-inputs
     ; `(("julia-coordinatetransformations" ,julia-coordinatetransformations)
     ;   ("julia-imagemagick" ,julia-imagemagick)
@@ -2294,7 +2354,9 @@ (define-public julia-imagemagick
                (("test (B == map)" _ test) (string-append "test_nowarn " test)))
              #t)))))
     (propagated-inputs
-     (list julia-fileio julia-imagecore julia-imagemagick-jll))
+     (list julia-fileio
+           julia-imagecore
+           julia-imagemagick-jll))
     (native-inputs
      (list julia-colors
            julia-colorvectorspace
@@ -2325,10 +2387,14 @@ (define-public julia-imagemetadata
          (base32 "0iv154ms370xgcr56bwsjl13iwmy671cbxjl9ld5yfj85pclcwi1"))))
     (build-system julia-build-system)
     (propagated-inputs
-     (list julia-axisarrays julia-imageaxes julia-imagecore
+     (list julia-axisarrays
+           julia-imageaxes
+           julia-imagecore
            julia-indirectarrays))
     (native-inputs
-     (list julia-offsetarrays julia-simpletraits julia-unitful))
+     (list julia-offsetarrays
+           julia-simpletraits
+           julia-unitful))
     (home-page "https://github.com/JuliaImages/ImageMetadata.jl")
     (synopsis "Julia package for images having metadata")
     (description "@code{ImageMetadata} is a simple package providing utilities
@@ -2355,8 +2421,11 @@ (define-public julia-imageshow
     (arguments
      `(#:tests? #f))    ; cycle with ImageMagick.jl.
     (propagated-inputs
-     (list julia-fileio julia-imagebase julia-imagecore
-           julia-offsetarrays julia-stackviews))
+     (list julia-fileio
+           julia-imagebase
+           julia-imagecore
+           julia-offsetarrays
+           julia-stackviews))
     ;(native-inputs
     ; `(("julia-imagedistances" ,julia-imagedistances)
     ;   ("julia-imagemagick" ,julia-imagemagick)
@@ -2442,7 +2511,9 @@ (define-public julia-indirectarrays
          (base32 "0l0jq0jnr9z3k431ni82xycq7mqapgxrbrx4yyk6lycvi41ipm4s"))))
     (build-system julia-build-system)
     (native-inputs
-     (list julia-colors julia-fixedpointnumbers julia-mappedarrays))
+     (list julia-colors
+           julia-fixedpointnumbers
+           julia-mappedarrays))
     (home-page "https://github.com/JuliaArrays/IndirectArrays.jl")
     (synopsis "Julia implementation of indexed arrays")
     (description "An @code{IndirectArray} is one that encodes data using a
@@ -2534,7 +2605,9 @@ (define-public julia-interpolations
            julia-staticarrays
            julia-woodburymatrices))
     (native-inputs
-     (list julia-dualnumbers julia-forwarddiff julia-offsetarrays
+     (list julia-dualnumbers
+           julia-forwarddiff
+           julia-offsetarrays
            julia-unitful julia-zygote))
     (home-page "https://github.com/JuliaMath/Interpolations.jl")
     (synopsis "Continuous interpolation of discrete datasets")
@@ -2727,7 +2800,9 @@ (define-public julia-json
         (base32 "1f9k613kbknmp4fgjxvjaw4d5sfbx8a5hmcszmp1w9rqfqngjx9m"))))
     (build-system julia-build-system)
     (propagated-inputs
-     (list julia-datastructures julia-fixedpointnumbers julia-parsers
+     (list julia-datastructures
+           julia-fixedpointnumbers
+           julia-parsers
            julia-offsetarrays))
     (home-page "https://github.com/JuliaIO/JSON.jl")
     (synopsis "JSON parsing and printing library for Julia")
@@ -2750,7 +2825,8 @@ (define-public julia-json3
          (base32 "11z5maz7v50wd99id8z7838higza0cllh2amkdkrlskbri3v2f17"))))
     (build-system julia-build-system)
     (propagated-inputs
-     (list julia-parsers julia-structtypes))
+     (list julia-parsers
+           julia-structtypes))
     (home-page "https://github.com/quinnj/JSON3.jl")
     (synopsis "JSON package for Julia")
     (description "This package provides another JSON package for Julia, with a
@@ -2803,8 +2879,11 @@ (define-public julia-lazyarrays
                    (substitute* "test/multests.jl"
                      (("Int64") "Int32")))))))))
     (propagated-inputs
-     (list julia-arraylayouts julia-fillarrays julia-macrotools
-           julia-matrixfactorizations julia-staticarrays))
+     (list julia-arraylayouts
+           julia-fillarrays
+           julia-macrotools
+           julia-matrixfactorizations
+           julia-staticarrays))
     (native-inputs
      (list julia-tracker))
     (home-page "https://github.com/JuliaArrays/LazyArrays.jl")
@@ -2887,7 +2966,9 @@ (define-public julia-mappedarrays
     (propagated-inputs
      (list julia-fixedpointnumbers))
     (native-inputs
-     (list julia-colortypes julia-fixedpointnumbers julia-offsetarrays))
+     (list julia-colortypes
+           julia-fixedpointnumbers
+           julia-offsetarrays))
     (home-page "https://github.com/JuliaArrays/MappedArrays.jl")
     (synopsis "Lazy in-place transformations of arrays")
     (description "This package implements \"lazy\" in-place elementwise
@@ -2956,7 +3037,8 @@ (define-public julia-mbedtls
              (substitute* "test/runtests.jl"
                (("testhost =") "return #"))
              #t)))))
-    (propagated-inputs (list julia-mbedtls-jll))
+    (propagated-inputs
+     (list 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
@@ -2978,9 +3060,13 @@ (define-public julia-measurements
          (base32 "05p3f0gr4sv4maq8cix5fi8ldq0zagswqsd43xn6fhy046f936mz"))))
     (build-system julia-build-system)
     (propagated-inputs
-     (list julia-calculus julia-recipesbase julia-requires))
+     (list julia-calculus
+           julia-recipesbase
+           julia-requires))
     (native-inputs
-     (list julia-quadgk julia-specialfunctions julia-unitful))
+     (list julia-quadgk
+           julia-specialfunctions
+           julia-unitful))
     (home-page "https://juliaphysics.github.io/Measurements.jl/stable/")
     (synopsis "Error propagation calculator and library")
     (description "@code{Measurements.jl} is an error propagation calculator and
@@ -3121,7 +3207,8 @@ (define-public julia-mocking
          (base32 "1cg2is83bjmrchmmxcgx57k8c9b9vlamrw38v4fdhbb6d4six5cg"))))
     (build-system julia-build-system)
     (propagated-inputs
-     (list julia-compat julia-exprtools))
+     (list julia-compat
+           julia-exprtools))
     (home-page "https://github.com/invenia/Mocking.jl")
     (synopsis "Overload Julia function calls")
     (description "The purpose of this package is to allow Julia function calls
@@ -3145,7 +3232,9 @@ (define-public julia-mosaicviews
     (arguments
      `(#:tests? #f))    ; Cycle with ImageCore.jl
     (propagated-inputs
-     (list julia-mappedarrays julia-paddedviews julia-stackviews))
+     (list julia-mappedarrays
+           julia-paddedviews
+           julia-stackviews))
     ;(native-inputs
     ; `(("julia-colorvectorspace" ,julia-colorvectorspace)
     ;   ("julia-imagecore" ,julia-imagecore)))
@@ -3255,9 +3344,12 @@ (define-public julia-nlsolversbase
          (base32 "0n8qh5a2ghjx1j70zxn0hmh8gzpa46kmjg8di879y9974bfk0f98"))))
     (build-system julia-build-system)
     (propagated-inputs
-     (list julia-diffresults julia-finitediff julia-forwarddiff))
+     (list julia-diffresults
+           julia-finitediff
+           julia-forwarddiff))
     (native-inputs
-     (list julia-optimtestproblems julia-recursivearraytools))
+     (list julia-optimtestproblems
+           julia-recursivearraytools))
     (home-page "https://github.com/JuliaNLSolvers/NLSolversBase.jl")
     (synopsis "Optimization and equation solver software in JuliaNLSolvers")
     (description "This package aims at establishing common ground for Optim.jl,
@@ -3290,9 +3382,13 @@ (define-public julia-nnlib
                (("&& CUDA\\.functional\\(\\)") ""))
              (setenv "NNLIB_TEST_CUDA" "false"))))))
     (propagated-inputs
-     (list julia-adapt julia-chainrulescore julia-requires))
+     (list julia-adapt
+           julia-chainrulescore
+           julia-requires))
     (native-inputs
-     (list julia-chainrulestestutils julia-stablerngs julia-zygote))
+     (list julia-chainrulestestutils
+           julia-stablerngs
+           julia-zygote))
     (home-page "https://github.com/FluxML/NNlib.jl")
     (synopsis "Neural Network primitives with multiple backends")
     (description "This package will provide a library of functions useful for
@@ -3412,7 +3508,8 @@ (define-public julia-parameters
          (base32 "0b8lawi7kcws4axfsdf023gyxca15irl648ciyi1kw3wghz3pfi2"))))
     (build-system julia-build-system)
     (propagated-inputs
-     (list julia-orderedcollections julia-unpack))
+     (list julia-orderedcollections
+           julia-unpack))
     (home-page "https://github.com/mauro3/Parameters.jl")
     (synopsis "Numerical-model parameter helpers")
     (description "This package contains types with default field values, keyword
@@ -3480,7 +3577,8 @@ (define-public julia-plotthemes
          (base32 "1fd27w9z1vhz0d1bzrs5vcavpb5r5jviyh27d9c4ka37phz4xvmh"))))
     (build-system julia-build-system)
     (propagated-inputs
-     (list julia-plotutils julia-requires))
+     (list julia-plotutils
+           julia-requires))
     (home-page "https://github.com/JuliaPlots/PlotThemes.jl")
     (synopsis "Themes for the Julia plotting package Plots.jl")
     (description
@@ -3502,7 +3600,9 @@ (define-public julia-plotutils
          (base32 "12aw5gkkcfhpczv2w510k65w1j0hjnh825ihimi223v8plsi5105"))))
     (build-system julia-build-system)
     (propagated-inputs
-     (list julia-colors julia-colorschemes julia-reexport))
+     (list julia-colors
+           julia-colorschemes
+           julia-reexport))
     (native-inputs
      (list julia-stablerngs))
     (home-page "https://github.com/JuliaPlots/PlotUtils.jl")
@@ -3548,7 +3648,8 @@ (define-public julia-positivefactorizations
          (base32 "1wxy6ak7f3hvibcgc8q88cgkf9zvi649mmjy1zlkx1qk80hgvz23"))))
     (build-system julia-build-system)
     (native-inputs
-     (list julia-forwarddiff julia-reversediff))
+     (list julia-forwarddiff
+           julia-reversediff))
     (home-page "https://github.com/timholy/PositiveFactorizations.jl")
     (synopsis "Positive-definite \"approximations\" to matrices")
     (description "@code{PositiveFactorizations} is a package for computing a
@@ -3607,7 +3708,10 @@ (define-public julia-prettytables
                ((".*colors\\.jl.*") ""))
              #t)))))
     (propagated-inputs
-     (list julia-crayons julia-formatting julia-reexport julia-tables))
+     (list julia-crayons
+           julia-formatting
+           julia-reexport
+           julia-tables))
     (home-page "https://github.com/ronisbr/PrettyTables.jl")
     (synopsis "Print data in formatted tables")
     (description "This package has the purpose to print data in matrices in a
@@ -3674,7 +3778,8 @@ (define-public julia-pycall
              (setenv "JULIA_PKGEVAL" "true")
              #t)))))
     (propagated-inputs
-     (list julia-macrotools julia-versionparsing))
+     (list julia-macrotools
+           julia-versionparsing))
     (inputs
      (list python))
     (native-inputs
@@ -3817,7 +3922,8 @@ (define-public julia-queryoperators
          (base32 "06zm4cbn3x49lbpgshhdfvvmgz066qkc8q0d57igm5p8bcp6js22"))))
     (build-system julia-build-system)
     (propagated-inputs
-     (list julia-datastructures julia-iteratorinterfaceextensions
+     (list julia-datastructures
+           julia-iteratorinterfaceextensions
            julia-tableshowutils))
     (home-page "https://github.com/queryverse/QueryOperators.jl")
     (synopsis "Query operators for Julia")
@@ -3907,7 +4013,9 @@ (define-public julia-recipespipeline
     (arguments
      `(#:tests? #f))    ; Cycle with Plots.jl.
     (propagated-inputs
-     (list julia-nanmath julia-plotutils julia-recipesbase))
+     (list julia-nanmath
+           julia-plotutils
+           julia-recipesbase))
     (home-page "http://juliaplots.org/RecipesPipeline.jl/dev/")
     (synopsis "Utilities for processing recipes")
     (description "This package was factored out of @code{Plots.jl} to allow any
@@ -3990,7 +4098,10 @@ (define-public julia-referencetests
     (arguments
      `(#:tests? #f))    ; Cycle with ImageCore.jl through ImageMagick.jl.
     (propagated-inputs
-     (list julia-deepdiffs julia-distances julia-fileio julia-imagecore
+     (list julia-deepdiffs
+           julia-distances
+           julia-fileio
+           julia-imagecore
            julia-imageinterminal))
     ;(native-inputs
     ; `(("julia-csvfiles" ,julia-csvfiles)
@@ -4066,7 +4177,8 @@ (define-public julia-reversediff
            julia-specialfunctions
            julia-staticarrays))
     (native-inputs
-     (list julia-difftests julia-fillarrays))
+     (list julia-difftests
+           julia-fillarrays))
     (home-page "https://github.com/JuliaDiff/ReverseDiff.jl")
     (synopsis "Reverse Mode Automatic Differentiation for Julia")
     (description "@code{ReverseDiff.jl} is a fast and compile-able tape-based
@@ -4122,7 +4234,9 @@ (define-public julia-rotations
       (propagated-inputs
        (list julia-staticarrays))
       (native-inputs
-       (list julia-benchmarktools julia-forwarddiff julia-unitful))
+       (list julia-benchmarktools
+             julia-forwarddiff
+             julia-unitful))
       (home-page "https://github.com/JuliaGeometry/Rotations.jl")
       (synopsis "Julia implementations for different rotation parameterisations")
       (description "This package implements various 3D rotation parameterizations
@@ -4323,7 +4437,8 @@ (define-public julia-specialfunctions
     (inputs
      (list julia-chainrulestestutils))
     (propagated-inputs
-     (list julia-chainrulescore julia-logexpfunctions
+     (list julia-chainrulescore
+           julia-logexpfunctions
            julia-openspecfun-jll))
     (home-page "https://github.com/JuliaMath/SpecialFunctions.jl")
     (synopsis "Special mathematical functions")
@@ -4348,7 +4463,8 @@ (define-public julia-splitapplycombine
          (base32 "1qzaqvk57b0s5krzn8bxkzmr5kz6hi9dm3jbf2sl7z4vznsgbn9x"))))
     (build-system julia-build-system)
     (propagated-inputs
-     (list julia-dictionaries julia-indexing))
+     (list julia-dictionaries
+           julia-indexing))
     (home-page "https://github.com/JuliaData/SplitApplyCombine.jl")
     (synopsis "Split-apply-combine strategies for Julia")
     (description "@code{SplitApplyCombine.jl} provides high-level, generic tools
@@ -4406,7 +4522,8 @@ (define-public julia-stackviews
     (propagated-inputs
      (list julia-offsetarrays))
     (native-inputs
-    (list julia-aqua julia-documenter))
+    (list julia-aqua
+          julia-documenter))
     (home-page "https://github.com/JuliaArrays/StackViews.jl")
     (synopsis "No more catcat")
     (description "StackViews provides only one array type: @code{StackView}.
@@ -4506,8 +4623,11 @@ (define-public julia-statsbase
          (base32 "02y4pm5yvg713a2pn970bbcfkrn2h133rxbxk1da18svhqw3czhi"))))
     (build-system julia-build-system)
     (propagated-inputs
-     (list julia-dataapi julia-datastructures julia-missings
-           julia-sortingalgorithms julia-statsapi))
+     (list julia-dataapi
+           julia-datastructures
+           julia-missings
+           julia-sortingalgorithms
+           julia-statsapi))
     (native-inputs
      (list julia-stablerngs))
     (home-page "https://github.com/JuliaStats/StatsBase.jl")
@@ -4567,10 +4687,15 @@ (define-public julia-structarrays
                                   "test/runtests.jl")
                      (("Int64") "Int32")))))))))
     (propagated-inputs
-     (list julia-dataapi julia-staticarrays julia-tables))
+     (list julia-dataapi
+           julia-staticarrays
+           julia-tables))
     (native-inputs
-     (list julia-documenter julia-offsetarrays julia-pooledarrays
-           julia-typedtables julia-weakrefstrings))
+     (list julia-documenter
+           julia-offsetarrays
+           julia-pooledarrays
+           julia-typedtables
+           julia-weakrefstrings))
     (home-page "https://github.com/JuliaArrays/StructArrays.jl")
     (synopsis "Efficient implementation of struct arrays in Julia")
     (description "This package introduces the type @code{StructArray} which is
@@ -4659,10 +4784,13 @@ (define-public julia-tables
          (base32 "1sqqagzqvav8b1rv5ywwbgy9ixvlmipq95fkwfwn0m8769i8jwzb"))))
     (build-system julia-build-system)
     (propagated-inputs
-     (list julia-dataapi julia-datavalueinterfaces
-           julia-iteratorinterfaceextensions julia-tabletraits))
+     (list julia-dataapi
+           julia-datavalueinterfaces
+           julia-iteratorinterfaceextensions
+           julia-tabletraits))
     (native-inputs
-     (list julia-datavalues julia-queryoperators))
+     (list julia-datavalues
+           julia-queryoperators))
     (home-page "https://github.com/JuliaData/Tables.jl")
     (synopsis "Interface for tables in Julia")
     (description "The @code{Tables.jl} package provides simple, yet powerful
@@ -4687,7 +4815,8 @@ (define-public julia-tableshowutils
            (base32 "0gp3hpj3jvzfhkp9r345vfic2j2n2s60729wv38hwn75csp74cg5"))))
       (build-system julia-build-system)
       (propagated-inputs
-       (list julia-datavalues julia-json))
+       (list julia-datavalues
+             julia-json))
       (home-page "https://github.com/queryverse/TableShowUtils.jl")
       (synopsis "Implement show for TableTraits.jl types")
       (description "This package provides some common helper functions that make
@@ -4756,8 +4885,11 @@ (define-public julia-testimages
     (arguments
      `(#:tests? #f))    ; cycle with ImageMagick.jl
     (propagated-inputs
-     (list julia-axisarrays julia-colortypes julia-fileio
-           julia-offsetarrays julia-stringdistances))
+     (list julia-axisarrays
+           julia-colortypes
+           julia-fileio
+           julia-offsetarrays
+           julia-stringdistances))
     ;(native-inputs
     ; `(("julia-colors" ,julia-colors)
     ;   ("julia-fixedpointnumbers" ,julia-fixedpointnumbers)
@@ -4848,7 +4980,9 @@ (define-public julia-typedtables
          (base32 "0nk6zhqvl2r8yhjdhb59kxq0srd3vy4ysg4d8rszj9a43dnn3w3i"))))
     (build-system julia-build-system)
     (propagated-inputs
-     (list julia-adapt julia-splitapplycombine julia-tables))
+     (list julia-adapt
+           julia-splitapplycombine
+           julia-tables))
     (home-page "https://github.com/JuliaData/TypedTables.jl")
     (synopsis "Column-based storage for data analysis in Julia")
     (description "@code{TypedTables.jl} provides two column-based storage
@@ -4976,7 +5110,8 @@ (define-public julia-weakrefstrings
          (base32 "14h1vdnc3rx87w6v2rr59lgb4kai2hd1wzqpxhmzsi8karg2z219"))))
     (build-system julia-build-system)
     (propagated-inputs
-     (list julia-dataapi julia-parsers))
+     (list julia-dataapi
+           julia-parsers))
     (home-page "https://github.com/JuliaData/WeakRefStrings.jl")
     (synopsis "Efficient string representation and transfer in Julia")
     (description "This package provides a minimal String type for Julia that
-- 
2.33.1





^ permalink raw reply related	[flat|nested] 19+ messages in thread

* [bug#53017] [PATCH 02/17] build: julia-build-system: Create 'Project.toml' file when missing.
  2022-01-04 22:47 ` [bug#53017] [PATCH 01/17] gnu: julia-xyz: Adjust style zimoun
@ 2022-01-04 22:47   ` zimoun
  2022-01-04 22:47   ` [bug#53017] [PATCH 03/17] gnu: julia-zygote: Adjust style zimoun
                     ` (15 subsequent siblings)
  16 siblings, 0 replies; 19+ messages in thread
From: zimoun @ 2022-01-04 22:47 UTC (permalink / raw)
  To: 53017; +Cc: efraim, zimoun

* guix/build/julia-build-system.scm (link-depot): Create 'Project.toml' file
when missing using data provided by the user.
(julia-create-package-toml): Remove from export.
* doc/guix.texi (Build Systems): Update julia-build-system section.
---
 doc/guix.texi                     | 19 +++++++++---------
 guix/build/julia-build-system.scm | 33 ++++++++++++++++++++-----------
 2 files changed, 30 insertions(+), 22 deletions(-)

diff --git a/doc/guix.texi b/doc/guix.texi
index dfb94be74e..603f8dcca3 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -71,7 +71,7 @@ Copyright @copyright{} 2019 Kyle Andrews@*
 Copyright @copyright{} 2019 Alex Griffin@*
 Copyright @copyright{} 2019, 2020, 2021 Guillaume Le Vaillant@*
 Copyright @copyright{} 2020 Liliana Marie Prikler@*
-Copyright @copyright{} 2019, 2020, 2021 Simon Tournier@*
+Copyright @copyright{} 2019, 2020, 2021, 2022 Simon Tournier@*
 Copyright @copyright{} 2020 Wiktor Żelazny@*
 Copyright @copyright{} 2020 Damien Cassou@*
 Copyright @copyright{} 2020 Jakub Kądziołka@*
@@ -8363,9 +8363,10 @@ julia} packages, which essentially is similar to running @samp{julia -e
 @env{JULIA_LOAD_PATH} contains the paths to all Julia package inputs.
 Tests are run by calling @code{/test/runtests.jl}.
 
-The Julia package name is read from the file @file{Project.toml}.  This
-value can be overridden by passing the argument @code{#:julia-package-name}
-(which must be correctly capitalized).
+The Julia package name and uuid is read from the file
+@file{Project.toml}.  These values can be overridden by passing the
+argument @code{#:julia-package-name} (which must be correctly
+capitalized) or @code{#:julia-package-uuid}.
 
 Julia packages usually manage their binary dependencies via
 @code{JLLWrappers.jl}, a Julia package that creates a module (named
@@ -8393,12 +8394,10 @@ MbedTLS package:
               (find-files "src/wrappers/" "\\.jl$"))))
 @end lisp
 
-Some older packages that aren't using @file{Package.toml} yet, will require
-this file to be created, too.  The function @code{julia-create-package-toml}
-helps creating the file.  You need to pass the outputs and the source of the
-package, its name (the same as the @code{file-name} parameter), the package
-uuid, the package version, and a list of dependencies specified by their name
-and their uuid.
+Some older packages that aren't using @file{Project.toml} yet, will
+require this file to be created, too.  It is internally done if the
+arguments @code{#:julia-package-name} and @code{#:julia-package-uuid}
+are provided.
 @end defvr
 
 @defvr {Scheme Variable} maven-build-system
diff --git a/guix/build/julia-build-system.scm b/guix/build/julia-build-system.scm
index b4e0044567..03d669be64 100644
--- a/guix/build/julia-build-system.scm
+++ b/guix/build/julia-build-system.scm
@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2019, 2020 Nicolò Balzarotti <nicolo@nixo.xyz>
 ;;; Copyright © 2021 Jean-Baptiste Volatier <jbv@pm.me>
-;;; Copyright © 2021 Simon Tournier <zimon.toutoune@gmail.com>
+;;; Copyright © 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -27,8 +27,8 @@ (define-module (guix build julia-build-system)
   #:use-module (ice-9 regex)
   #:use-module (ice-9 rdelim)
   #:use-module (ice-9 popen)
+  #:use-module (srfi srfi-1)
   #:export (%standard-phases
-            julia-create-package-toml
             julia-build))
 
 ;; Commentary:
@@ -138,6 +138,8 @@ (define* (check #:key tests? source inputs outputs julia-package-name
 (define* (link-depot #:key source inputs outputs
                      julia-package-name julia-package-uuid  #:allow-other-keys)
   (let* ((out (assoc-ref outputs "out"))
+         (name+version (strip-store-file-name out))
+         (version (last (string-split name+version #\-)))
          (package-name (or
                         julia-package-name
                         (project.toml->name "Project.toml")))
@@ -148,6 +150,14 @@ (define* (link-depot #:key source inputs outputs
 println(Base.version_slug(Base.UUID(\"~a\"),
                           Base.SHA1(Pkg.GitTools.tree_hash(\".\"))))" uuid)))
          (slug (string-trim-right (get-string-all pipe))))
+    ;; Few packages do not have the regular Project.toml file, then when they
+    ;; are propagated, dependencies do not find them and an raise error.
+    (unless (file-exists? "Project.toml")
+        (julia-create-package-toml (getcwd)
+                                   julia-package-name julia-package-uuid
+                                   version
+                                   #:file "Project.toml"))
+
     ;; When installing a package, julia looks first at in the JULIA_DEPOT_PATH
     ;; for a path like packages/PACKAGE/XXXX
     ;; Where XXXX is a slug encoding the package UUID and SHA1 of the files
@@ -157,17 +167,16 @@ (define* (link-depot #:key source inputs outputs
     (symlink package-dir (string-append out "/share/julia/packages/"
                                         package-name "/" slug))))
 
-(define (julia-create-package-toml outputs source
-                                   name uuid version
-                                   deps)
-  "Some packages are not using the new Package.toml dependency specifications.
-Write this file manually, so that Julia can find its dependencies."
+(define* (julia-create-package-toml location
+                                    name uuid version
+                                    #:optional
+                                    (deps '())
+                                    #:key
+                                    (file "Project.toml"))
+  "Some packages are not using the new Project.toml dependency specifications.
+Write this FILE manually, so that Julia can find its dependencies."
   (let ((f (open-file
-            (string-append
-             (assoc-ref outputs "out")
-             %package-path
-             (string-append
-              name "/Project.toml"))
+            (string-append location "/" file)
             "w")))
     (display (string-append
               "
-- 
2.33.1





^ permalink raw reply related	[flat|nested] 19+ messages in thread

* [bug#53017] [PATCH 03/17] gnu: julia-zygote: Adjust style.
  2022-01-04 22:47 ` [bug#53017] [PATCH 01/17] gnu: julia-xyz: Adjust style zimoun
  2022-01-04 22:47   ` [bug#53017] [PATCH 02/17] build: julia-build-system: Create 'Project.toml' file when missing zimoun
@ 2022-01-04 22:47   ` zimoun
  2022-01-04 22:47   ` [bug#53017] [PATCH 04/17] gnu: julia-documentertools: " zimoun
                     ` (14 subsequent siblings)
  16 siblings, 0 replies; 19+ messages in thread
From: zimoun @ 2022-01-04 22:47 UTC (permalink / raw)
  To: 53017; +Cc: efraim, zimoun

* gnu/packages/julia-xyz.scm (julia-zygote)[propagated-inputs]: Remove labels.
---
 gnu/packages/julia-xyz.scm | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 3701bf3996..e6733fce92 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -5213,17 +5213,17 @@ (define-public julia-zygote
     (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)))
+     (list julia-abstractffts
+           julia-chainrules
+           julia-diffrules
+           julia-fillarrays
+           julia-forwarddiff
+           julia-irtools
+           julia-macrotools
+           julia-nanmath
+           julia-requires
+           julia-specialfunctions
+           julia-zygoterules))
     (home-page "https://fluxml.ai/Zygote.jl")
     (synopsis "Automatic differentiation in Julia")
     (description "Zygote provides source-to-source automatic
-- 
2.33.1





^ permalink raw reply related	[flat|nested] 19+ messages in thread

* [bug#53017] [PATCH 04/17] gnu: julia-documentertools: Adjust style.
  2022-01-04 22:47 ` [bug#53017] [PATCH 01/17] gnu: julia-xyz: Adjust style zimoun
  2022-01-04 22:47   ` [bug#53017] [PATCH 02/17] build: julia-build-system: Create 'Project.toml' file when missing zimoun
  2022-01-04 22:47   ` [bug#53017] [PATCH 03/17] gnu: julia-zygote: Adjust style zimoun
@ 2022-01-04 22:47   ` zimoun
  2022-01-04 22:47   ` [bug#53017] [PATCH 05/17] gnu: julia-documenter: " zimoun
                     ` (13 subsequent siblings)
  16 siblings, 0 replies; 19+ messages in thread
From: zimoun @ 2022-01-04 22:47 UTC (permalink / raw)
  To: 53017; +Cc: efraim, zimoun

* gnu/packages/julia-xyz.scm (julia-documentertools)[inputs]: Remove label.
[propagated-inputs]: Adjust.
---
 gnu/packages/julia-xyz.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index e6733fce92..928fd39c37 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -1310,9 +1310,11 @@ (define-public julia-documentertools
     (inputs
      ;; We don't want to propagate the bootstrap version.
      ;; Cycle with Documenter.jl in later versions.
-     `(("julia-documenter" ,julia-documenter-bootstrap)))
+     (list julia-documenter-bootstrap))
     (propagated-inputs
-     (list julia-docstringextensions julia-gumbo julia-sass))
+     (list julia-docstringextensions
+           julia-gumbo
+           julia-sass))
     (native-inputs
      (list julia-example))
     (home-page "https://github.com/JuliaDocs/DocumenterTools.jl")
-- 
2.33.1





^ permalink raw reply related	[flat|nested] 19+ messages in thread

* [bug#53017] [PATCH 05/17] gnu: julia-documenter: Adjust style.
  2022-01-04 22:47 ` [bug#53017] [PATCH 01/17] gnu: julia-xyz: Adjust style zimoun
                     ` (2 preceding siblings ...)
  2022-01-04 22:47   ` [bug#53017] [PATCH 04/17] gnu: julia-documentertools: " zimoun
@ 2022-01-04 22:47   ` zimoun
  2022-01-04 22:47   ` [bug#53017] [PATCH 06/17] gnu: Add julia-biogenerics zimoun
                     ` (12 subsequent siblings)
  16 siblings, 0 replies; 19+ messages in thread
From: zimoun @ 2022-01-04 22:47 UTC (permalink / raw)
  To: 53017; +Cc: efraim, zimoun

* gnu/packages/julia-xyz.scm (julia-documenter)[propagated-inputs] Remove labels.
[inputs, native-inputs]: Remove labels.
[arguments]: Remove unnecessary return '#t'.
---
 gnu/packages/julia-xyz.scm | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 928fd39c37..26a1f31c25 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -1228,8 +1228,7 @@ (define-public julia-documenter
              (substitute* "src/Deps.jl"
                (("pip install")
                 (string-append (assoc-ref inputs "python")
-                               "/bin/pip install")))
-             #t))
+                               "/bin/pip install")))))
          (add-after 'link-depot 'remove-javascript-downloads
            (lambda _
              (substitute* "src/Writers/HTMLWriter.jl"
@@ -1237,17 +1236,18 @@ (define-public julia-documenter
              ;; Removing the javascript downloads causes these tests fail.
              (substitute* "test/examples/tests.jl"
                ((".*Main\\.examples_html_doc.*") "")
-               ((".*Main\\.examples_html_mathjax3_doc.*") ""))
-             #t)))))
+               ((".*Main\\.examples_html_mathjax3_doc.*") "")))))))
     (propagated-inputs
-     (list julia-ansicoloredprinters julia-docstringextensions
-           julia-iocapture julia-json))
+     (list julia-ansicoloredprinters
+           julia-docstringextensions
+           julia-iocapture
+           julia-json))
     (inputs
-     `(("python" ,python-wrapper)))
+     (list python-wrapper))
     (native-inputs
-     `(("git" ,git-minimal)
-       ("julia-documentermarkdown" ,julia-documentermarkdown)
-       ("julia-documentertools" ,julia-documentertools)))
+     (list git-minimal
+           julia-documentermarkdown
+           julia-documentertools))
     (home-page "https://juliadocs.github.io/Documenter.jl")
     (synopsis "Documentation generator for Julia")
     (description "This package provides a documentation generator for Julia.")
-- 
2.33.1





^ permalink raw reply related	[flat|nested] 19+ messages in thread

* [bug#53017] [PATCH 06/17] gnu: Add julia-biogenerics.
  2022-01-04 22:47 ` [bug#53017] [PATCH 01/17] gnu: julia-xyz: Adjust style zimoun
                     ` (3 preceding siblings ...)
  2022-01-04 22:47   ` [bug#53017] [PATCH 05/17] gnu: julia-documenter: " zimoun
@ 2022-01-04 22:47   ` zimoun
  2022-01-04 22:47   ` [bug#53017] [PATCH 07/17] gnu: Add julia-indexablebitvectors zimoun
                     ` (11 subsequent siblings)
  16 siblings, 0 replies; 19+ messages in thread
From: zimoun @ 2022-01-04 22:47 UTC (permalink / raw)
  To: 53017; +Cc: efraim, zimoun

* gnu/packages/julia-xyz.scm (julia-biogenerics): New variable.
---
 gnu/packages/julia-xyz.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 26a1f31c25..49bf6ae26f 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -333,6 +333,32 @@ (define-public julia-benchmarktools
 benchmarks as well as comparing benchmark results.")
     (license license:expat)))
 
+(define-public julia-biogenerics
+  ;; No upstream release
+  (let ((commit "a75abaf459250e2b5e22b4d9adf25fd36d2acab6")
+        (revision "0"))
+    (package
+      (name "julia-biogenerics")
+      (version (git-version "0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/BioJulia/BioGenerics.jl")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "17d222vi9nssjwr5l349fss7jnglnjimp1z62kmfmxa4fsn8lk8l"))))
+      (build-system julia-build-system)
+      (inputs
+       (list julia-transcodingstreams))
+      (home-page "https://github.com/BioJulia/BioGenerics.jl")
+      (synopsis "Generic methods used by BioJulia packages")
+      (description "This package provides generic methods and modules used in
+many of the other BioJulia packages.  This package defines IO, exceptions, and
+other types or methods used by other BioJulia packages.")
+      (license license:expat))))
+
 (define-public julia-blockarrays
   (package
     (name "julia-blockarrays")
-- 
2.33.1





^ permalink raw reply related	[flat|nested] 19+ messages in thread

* [bug#53017] [PATCH 07/17] gnu: Add julia-indexablebitvectors.
  2022-01-04 22:47 ` [bug#53017] [PATCH 01/17] gnu: julia-xyz: Adjust style zimoun
                     ` (4 preceding siblings ...)
  2022-01-04 22:47   ` [bug#53017] [PATCH 06/17] gnu: Add julia-biogenerics zimoun
@ 2022-01-04 22:47   ` zimoun
  2022-01-04 22:47   ` [bug#53017] [PATCH 08/17] gnu: Add julia-twiddle zimoun
                     ` (10 subsequent siblings)
  16 siblings, 0 replies; 19+ messages in thread
From: zimoun @ 2022-01-04 22:47 UTC (permalink / raw)
  To: 53017; +Cc: efraim, zimoun

* gnu/packages/julia-xyz.scm (julia-indexablebitvectors): New variable.
---
 gnu/packages/julia-xyz.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 49bf6ae26f..1508a86dd1 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -2503,6 +2503,39 @@ (define-public julia-imagetransformations
 rotation, and other spatial transformations of arrays.")
     (license license:expat)))
 
+(define-public julia-indexablebitvectors
+  (package
+    (name "julia-indexablebitvectors")
+    (version "1.0.0")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/BioJulia/IndexableBitVectors.jl")
+               (commit (string-append "v" version))))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "1khaycydwa31sxwvrrvvlylpzdb77kkxfmb8cax3i22ix0c2nmlc"))))
+    (build-system julia-build-system)
+    ;; Package without Project.toml
+    (arguments
+     '(#:julia-package-name "IndexableBitVectors"
+       #:julia-package-uuid "1cb3b9ac-1ffd-5777-9e6b-a3d42300664d"))
+    (home-page "https://github.com/BioJulia/IndexableBitVectors.jl")
+    (synopsis "Bit vectors operations with extremely fast speed")
+    (description "This package exports following operations over bit vectors
+with extremely fast speed while keeping extra memory usage small:
+@itemize
+@item @code{getindex(bv::IndexableBitVectors, i::Integer)}: @code{i}-th
+element of @code{bv}
+@item @code{rank(b::Bool, bv::AbstractIndexableBitVector, i::Integer)}: the
+number of occurrences of bit @code{b} in @code{bv[1:i]}
+@item @code{select(b::Bool, bv::AbstractIndexableBitVector, i::Integer)}: the
+index of i-th occurrence of @code{b} in @code{bv}.
+@end itemize
+and other shortcuts or types.")
+    (license license:expat)))
+
 (define-public julia-indexing
   (package
     (name "julia-indexing")
-- 
2.33.1





^ permalink raw reply related	[flat|nested] 19+ messages in thread

* [bug#53017] [PATCH 08/17] gnu: Add julia-twiddle.
  2022-01-04 22:47 ` [bug#53017] [PATCH 01/17] gnu: julia-xyz: Adjust style zimoun
                     ` (5 preceding siblings ...)
  2022-01-04 22:47   ` [bug#53017] [PATCH 07/17] gnu: Add julia-indexablebitvectors zimoun
@ 2022-01-04 22:47   ` zimoun
  2022-01-04 22:47   ` [bug#53017] [PATCH 09/17] gnu: Add julia-simd zimoun
                     ` (9 subsequent siblings)
  16 siblings, 0 replies; 19+ messages in thread
From: zimoun @ 2022-01-04 22:47 UTC (permalink / raw)
  To: 53017; +Cc: efraim, zimoun

* gnu/packages/julia-xyz.scm (julia-twiddle): New variable.
---
 gnu/packages/julia-xyz.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 1508a86dd1..e407b1aec5 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -5026,6 +5026,27 @@ (define-public julia-transcodingstreams
 @end itemize")
     (license license:expat)))
 
+(define-public julia-twiddle
+  (package
+    (name "julia-twiddle")
+    (version "1.1.2")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/BenJWard/Twiddle.jl")
+               (commit (string-append "v" version))))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "1c2gdv7sy4n1d8687w2q0yzwmwmanf4p6mvzvkz5gm4baxyzmbh2"))))
+    (build-system julia-build-system)
+    (home-page "https://ben-ward.science/Twiddle.jl/stable")
+    (synopsis "Ready to use bit-twiddling tricks")
+    (description "This package provides a collection of useful bit-twiddling
+tricks, ready to use as functions, with detailed documentation and example
+real-world use cases.")
+    (license license:expat)))
+
 (define-public julia-typedtables
   (package
     (name "julia-typedtables")
-- 
2.33.1





^ permalink raw reply related	[flat|nested] 19+ messages in thread

* [bug#53017] [PATCH 09/17] gnu: Add julia-simd.
  2022-01-04 22:47 ` [bug#53017] [PATCH 01/17] gnu: julia-xyz: Adjust style zimoun
                     ` (6 preceding siblings ...)
  2022-01-04 22:47   ` [bug#53017] [PATCH 08/17] gnu: Add julia-twiddle zimoun
@ 2022-01-04 22:47   ` zimoun
  2022-01-04 22:47   ` [bug#53017] [PATCH 10/17] gnu: Add julia-scanbyte zimoun
                     ` (8 subsequent siblings)
  16 siblings, 0 replies; 19+ messages in thread
From: zimoun @ 2022-01-04 22:47 UTC (permalink / raw)
  To: 53017; +Cc: efraim, zimoun

* gnu/packages/julia-xyz.scm (julia-simd): New variable.
---
 gnu/packages/julia-xyz.scm | 27 ++++++++++++++++++++++++++-
 1 file changed, 26 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index e407b1aec5..4a3ca18666 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -1,6 +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>
+;;; Copyright © 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2021 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2021 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2021 jgart <jgart@dismail.de>
@@ -4406,6 +4406,31 @@ (define-public julia-showoff
 in @code{Gadfly}, @code{Plots} and @code{Makie} to label axes and keys.")
     (license license:expat)))
 
+(define-public julia-simd
+  (package
+    (name "julia-simd")
+    (version "3.3.1")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/eschnett/SIMD.jl")
+               (commit (string-append "v" version))))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "1jiic2hcl9l6zh6jgqzbd3ik2girmgvni4bq65kdci5l12k9la68"))))
+    (build-system julia-build-system)
+    (home-page "https://github.com/eschnett/SIMD.jl")
+    (synopsis "Explicit SIMD vectorization")
+    (description "This package allows programmers to explicitly SIMD-vectorize
+their Julia code.  By exposing SIMD vector types and corresponding operations,
+the programmer can explicitly vectorize their code.  While this does not
+guarantee that the generated machine code is efficient, it relieves the
+compiler from determining whether it is legal to vectorize the code, deciding
+whether it is beneficial to do so, and rearranging the code to synthesize
+vector instructions.")
+    (license license:expat)))
+
 (define-public julia-simpletraits
   (package
     (name "julia-simpletraits")
-- 
2.33.1





^ permalink raw reply related	[flat|nested] 19+ messages in thread

* [bug#53017] [PATCH 10/17] gnu: Add julia-scanbyte.
  2022-01-04 22:47 ` [bug#53017] [PATCH 01/17] gnu: julia-xyz: Adjust style zimoun
                     ` (7 preceding siblings ...)
  2022-01-04 22:47   ` [bug#53017] [PATCH 09/17] gnu: Add julia-simd zimoun
@ 2022-01-04 22:47   ` zimoun
  2022-01-04 22:47   ` [bug#53017] [PATCH 11/17] gnu: Add julia-automa zimoun
                     ` (7 subsequent siblings)
  16 siblings, 0 replies; 19+ messages in thread
From: zimoun @ 2022-01-04 22:47 UTC (permalink / raw)
  To: 53017; +Cc: efraim, zimoun

* gnu/packages/julia-xyz.scm (julia-scanbyte): New variable.
---
 gnu/packages/julia-xyz.scm | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 4a3ca18666..524e5c3fb4 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -4357,6 +4357,29 @@ (define-public julia-sass
 @code{libsass} library to compile scss and sass files to css.")
     (license license:expat)))
 
+(define-public julia-scanbyte
+  (package
+    (name "julia-scanbyte")
+    (version "0.3")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/jakobnissen/ScanByte.jl")
+               (commit (string-append "v" version))))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "0dqqa3d7c87358144pji6ik8xlki2hj0hkvjs72j5aypfms8rwn3"))))
+    (build-system julia-build-system)
+    (propagated-inputs
+     (list julia-simd))
+    (home-page "https://github.com/JuliaPackaging/Scratch.jl")
+    (synopsis "Find the first occurrence of set of bytes in a chunk of memory")
+    (description "This package finds the first occurrence of a byte or set of
+bytes in a chunk of memory.  Think of it like a much faster version of
+@code{findfirst} that only iterates over bytes in memory.")
+    (license license:expat)))
+
 (define-public julia-scratch
   (package
     (name "julia-scratch")
-- 
2.33.1





^ permalink raw reply related	[flat|nested] 19+ messages in thread

* [bug#53017] [PATCH 11/17] gnu: Add julia-automa.
  2022-01-04 22:47 ` [bug#53017] [PATCH 01/17] gnu: julia-xyz: Adjust style zimoun
                     ` (8 preceding siblings ...)
  2022-01-04 22:47   ` [bug#53017] [PATCH 10/17] gnu: Add julia-scanbyte zimoun
@ 2022-01-04 22:47   ` zimoun
  2022-01-04 22:47   ` [bug#53017] [PATCH 12/17] gnu: Add julia-stringencodings zimoun
                     ` (6 subsequent siblings)
  16 siblings, 0 replies; 19+ messages in thread
From: zimoun @ 2022-01-04 22:47 UTC (permalink / raw)
  To: 53017; +Cc: efraim, zimoun

* gnu/packages/julia-xyz.scm (julia-automa): New variable.
---
 gnu/packages/julia-xyz.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 524e5c3fb4..757030301d 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -211,6 +211,34 @@ (define-public julia-arraylayouts
 much wider class of matrix types than Julia's in-built @code{StridedArray}.")
     (license license:expat)))
 
+(define-public julia-automa
+  (package
+    (name "julia-automa")
+    (version "0.8.2")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/BioJulia/Automa.jl")
+               (commit (string-append "v" version))))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "0hmwvk3qw54p7f63a2dnzlmvkynfs62x9n8x952bcmczp35csgq0"))))
+    (build-system julia-build-system)
+    (propagated-inputs
+     (list julia-scanbyte
+           julia-transcodingstreams))
+    (home-page "https://github.com/BioJulia/Automa.jl")
+    (synopsis "Validation, parsing, and tokenizing based on state machine compiler.")
+    (description "This package compiles regular expressions into Julia code,
+which is then compiled into low-level machine code by the Julia compiler.  The
+package is designed to generate very efficient code to scan large text data,
+which is often much faster than handcrafted code.  @code{Automa.jl} can insert
+arbitrary Julia code that will be executed in state transitions.  This makes
+it possible, for example, to extract substrings that match a part of a regular
+expression.")
+    (license license:expat)))
+
 (define-public julia-axisalgorithms
   (package
     (name "julia-axisalgorithms")
-- 
2.33.1





^ permalink raw reply related	[flat|nested] 19+ messages in thread

* [bug#53017] [PATCH 12/17] gnu: Add julia-stringencodings.
  2022-01-04 22:47 ` [bug#53017] [PATCH 01/17] gnu: julia-xyz: Adjust style zimoun
                     ` (9 preceding siblings ...)
  2022-01-04 22:47   ` [bug#53017] [PATCH 11/17] gnu: Add julia-automa zimoun
@ 2022-01-04 22:47   ` zimoun
  2022-01-04 22:47   ` [bug#53017] [PATCH 13/17] gnu: Add julia-yaml zimoun
                     ` (5 subsequent siblings)
  16 siblings, 0 replies; 19+ messages in thread
From: zimoun @ 2022-01-04 22:47 UTC (permalink / raw)
  To: 53017; +Cc: efraim, zimoun

* gnu/packages/julia-xyz.scm (julia-stringencodings): New variable.
---
 gnu/packages/julia-xyz.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 757030301d..84a6fef3a6 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -4799,6 +4799,38 @@ (define-public julia-stringdistances
 applied to any distance.")
     (license license:expat)))
 
+(define-public julia-stringencodings
+  (package
+    (name "julia-stringencodings")
+    (version "0.3.5")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/JuliaStrings/StringEncodings.jl")
+               (commit (string-append "v" version))))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "1qwc5ll68ng80b5921ww6fvifxbsmiylakfgsbsjbzg7lzyb5i67"))))
+    (build-system julia-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'skip-failing-test
+           (lambda _
+             ;; https://github.com/JuliaStrings/StringEncodings.jl/issues/49
+             (substitute* "test/runtests.jl"
+               (("\"SHIFT_JIS\", \"SHIFT_JISX0213\"")
+                " ")))))))
+    (propagated-inputs
+     (list julia-libiconv-jll))
+    (home-page "https://github.com/JuliaStrings/StringEncodings.jl")
+    (synopsis "Support for decoding and encoding texts ")
+    (description "This package provides support for decoding and encoding
+texts between multiple character encodings.  It is currently based on the
+@code{iconv} interface, and supports all major platforms using GNU libiconv.")
+    (license license:expat)))
+
 (define-public julia-structarrays
   (package
     (name "julia-structarrays")
-- 
2.33.1





^ permalink raw reply related	[flat|nested] 19+ messages in thread

* [bug#53017] [PATCH 13/17] gnu: Add julia-yaml.
  2022-01-04 22:47 ` [bug#53017] [PATCH 01/17] gnu: julia-xyz: Adjust style zimoun
                     ` (10 preceding siblings ...)
  2022-01-04 22:47   ` [bug#53017] [PATCH 12/17] gnu: Add julia-stringencodings zimoun
@ 2022-01-04 22:47   ` zimoun
  2022-01-04 22:47   ` [bug#53017] [PATCH 14/17] gnu: Add julia-biosymbols zimoun
                     ` (4 subsequent siblings)
  16 siblings, 0 replies; 19+ messages in thread
From: zimoun @ 2022-01-04 22:47 UTC (permalink / raw)
  To: 53017; +Cc: efraim, zimoun

* gnu/packages/julia-xyz.scm (julia-yaml): New variable.
---
 gnu/packages/julia-xyz.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 84a6fef3a6..404c35627c 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -5341,6 +5341,31 @@ (define-public julia-woodburymatrices
 inaccuracy in the result.")
     (license license:expat)))
 
+(define-public julia-yaml
+  (package
+    (name "julia-yaml")
+    (version "0.4.7")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/JuliaData/YAML.jl")
+               (commit (string-append "v" version))))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "00k8456ffldbf75k2q5yxim7cgz3p0pbshsvmpm1331g8qy6liin"))))
+    (build-system julia-build-system)
+    (propagated-inputs
+     (list julia-stringencodings))
+    (native-inputs
+     (list julia-datastructures
+           julia-orderedcollections))
+    (home-page "https://github.com/JuliaData/YAML.jl")
+    (synopsis "Parses YAML documents into native Julia types")
+    (description "This package parses YAML documents into native Julia types
+and dumps them back into YAML documents.")
+    (license license:expat)))
+
 (define-public julia-zipfile
   (package
     (name "julia-zipfile")
-- 
2.33.1





^ permalink raw reply related	[flat|nested] 19+ messages in thread

* [bug#53017] [PATCH 14/17] gnu: Add julia-biosymbols.
  2022-01-04 22:47 ` [bug#53017] [PATCH 01/17] gnu: julia-xyz: Adjust style zimoun
                     ` (11 preceding siblings ...)
  2022-01-04 22:47   ` [bug#53017] [PATCH 13/17] gnu: Add julia-yaml zimoun
@ 2022-01-04 22:47   ` zimoun
  2022-01-04 22:47   ` [bug#53017] [PATCH 15/17] gnu: Add julia-biosequences zimoun
                     ` (3 subsequent siblings)
  16 siblings, 0 replies; 19+ messages in thread
From: zimoun @ 2022-01-04 22:47 UTC (permalink / raw)
  To: 53017; +Cc: efraim, zimoun

* gnu/packages/julia-xyz.scm (julia-biosymbols): New variable.
---
 gnu/packages/julia-xyz.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 404c35627c..04d0beeb96 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -387,6 +387,30 @@ (define-public julia-biogenerics
 other types or methods used by other BioJulia packages.")
       (license license:expat))))
 
+(define-public julia-biosymbols
+  (package
+    (name "julia-biosymbols")
+    (version "4.0.4")  ;Older release for compatibility with julia-biosequence
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/BioJulia/BioSymbols.jl")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1222rwdndi777lai8a6dwrh35i5rgmj75kcrhn8si72sxgz0syjm"))))
+    (build-system julia-build-system)
+    (arguments
+     `(#:tests? #f))
+    (propagated-inputs
+     (list julia-automa))
+    (home-page "https://github.com/BioJulia/BioSymbols.jl")
+    (synopsis "Primitive types for nucleic acids and amino acids")
+    (description "This package defines the primitive types for nucleic acids
+and amino acids that are used ny otherBioJulia packages.")
+    (license license:expat)))
+
 (define-public julia-blockarrays
   (package
     (name "julia-blockarrays")
-- 
2.33.1





^ permalink raw reply related	[flat|nested] 19+ messages in thread

* [bug#53017] [PATCH 15/17] gnu: Add julia-biosequences.
  2022-01-04 22:47 ` [bug#53017] [PATCH 01/17] gnu: julia-xyz: Adjust style zimoun
                     ` (12 preceding siblings ...)
  2022-01-04 22:47   ` [bug#53017] [PATCH 14/17] gnu: Add julia-biosymbols zimoun
@ 2022-01-04 22:47   ` zimoun
  2022-01-04 22:47   ` [bug#53017] [PATCH 16/17] gnu: Add julia-intervaltrees zimoun
                     ` (2 subsequent siblings)
  16 siblings, 0 replies; 19+ messages in thread
From: zimoun @ 2022-01-04 22:47 UTC (permalink / raw)
  To: 53017; +Cc: efraim, zimoun

* gnu/packages/julia-xyz.scm (julia-biosequences): New variable.
---
 gnu/packages/julia-xyz.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 04d0beeb96..e028f37a28 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -387,6 +387,37 @@ (define-public julia-biogenerics
 other types or methods used by other BioJulia packages.")
       (license license:expat))))
 
+(define-public julia-biosequences
+  (package
+    (name "julia-biosequences")
+    (version "2.0.5")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/BioJulia/BioSequences.jl")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0ns6zk0zvnsf4hlsys9ck2xrn20qck0b0aghh484vc6n458zq2gw"))))
+    (build-system julia-build-system)
+    (propagated-inputs
+     (list julia-biogenerics
+           julia-biosymbols
+           julia-combinatorics
+           julia-indexablebitvectors
+           julia-stablerngs
+           julia-twiddle))
+    (native-inputs
+     (list julia-statsbase
+           julia-yaml))
+    (home-page "https://biojulia.net/BioSequences.jl/stable/")
+    (synopsis "Data types and methods for common operations with biological sequences")
+    (description "This package provides Data types and methods for common
+operations with biological sequences, including DNA, RNA, and amino acid
+sequences.")
+    (license license:expat)))
+
 (define-public julia-biosymbols
   (package
     (name "julia-biosymbols")
-- 
2.33.1





^ permalink raw reply related	[flat|nested] 19+ messages in thread

* [bug#53017] [PATCH 16/17] gnu: Add julia-intervaltrees.
  2022-01-04 22:47 ` [bug#53017] [PATCH 01/17] gnu: julia-xyz: Adjust style zimoun
                     ` (13 preceding siblings ...)
  2022-01-04 22:47   ` [bug#53017] [PATCH 15/17] gnu: Add julia-biosequences zimoun
@ 2022-01-04 22:47   ` zimoun
  2022-01-04 22:47   ` [bug#53017] [PATCH 17/17] gnu: Add julia-bioalignments zimoun
  2022-01-10 13:20   ` bug#53017: [PATCH 01/17] gnu: julia-xyz: Adjust style Efraim Flashner
  16 siblings, 0 replies; 19+ messages in thread
From: zimoun @ 2022-01-04 22:47 UTC (permalink / raw)
  To: 53017; +Cc: efraim, zimoun

* gnu/packages/julia-xyz.scm (julia-intervaltrees): New variable.
---
 gnu/packages/julia-xyz.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index e028f37a28..2e726aed23 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -2800,6 +2800,30 @@ (define-public julia-intervalsets
 unambiguously define the @code{..} and @code{±} operators.")
     (license license:expat)))
 
+(define-public julia-intervaltrees
+  ;; Last upstream release on May 2020 and this last release does not contain
+  ;; the file Project.toml.
+  (let ((commit "e37edab61568d08141a3e9c25ec55caac21e5aa5"))
+    (package
+      (name "julia-intervaltrees")
+      (version (git-version "1.0.0" "0" commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/BioJulia/IntervalTrees.jl")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "01x48a5zrx0833s1kjhf0ml4x9xz8xja4ymran770akmf6968yl9"))))
+      (build-system julia-build-system)
+      (home-page "https://github.com/BioJulia/IntervalTrees.jl")
+      (synopsis "Interval Trees for Julia")
+      (description "This package provides an implementation of an associative
+container mapping @code{(K,V)} pairs via the type @code{IntervalTree{K, V}}.
+The type @code{K} may be any ordered type.")
+      (license license:expat))))
+
 (define-public julia-invertedindices
   (package
     (name "julia-invertedindices")
-- 
2.33.1





^ permalink raw reply related	[flat|nested] 19+ messages in thread

* [bug#53017] [PATCH 17/17] gnu: Add julia-bioalignments.
  2022-01-04 22:47 ` [bug#53017] [PATCH 01/17] gnu: julia-xyz: Adjust style zimoun
                     ` (14 preceding siblings ...)
  2022-01-04 22:47   ` [bug#53017] [PATCH 16/17] gnu: Add julia-intervaltrees zimoun
@ 2022-01-04 22:47   ` zimoun
  2022-01-10 13:20   ` bug#53017: [PATCH 01/17] gnu: julia-xyz: Adjust style Efraim Flashner
  16 siblings, 0 replies; 19+ messages in thread
From: zimoun @ 2022-01-04 22:47 UTC (permalink / raw)
  To: 53017; +Cc: efraim, zimoun

* gnu/packages/julia-xyz.scm (julia-bioalignments): New variable.
---
 gnu/packages/julia-xyz.scm | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 2e726aed23..b7a4224694 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -361,6 +361,41 @@ (define-public julia-benchmarktools
 benchmarks as well as comparing benchmark results.")
     (license license:expat)))
 
+(define-public julia-bioalignments
+  (package
+    (name "julia-bioalignments")
+    (version "2.0.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/BioJulia/BioAlignments.jl")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1wf6qgsada59r2fykxfj9hcr635wl8maqxbd3w8qpa01k9glxa0k"))))
+    (build-system julia-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'skip-test
+           (lambda _
+             ;; Test fails because an unexpected type representation from
+             ;; BioSequences.  The aligned value is correct though.
+             (substitute* "test/runtests.jl"
+               (("@test sprint\\(show, aln\\)")
+                "@test_broken sprint(show, aln)")))))))
+    (propagated-inputs
+     (list julia-biogenerics
+           julia-biosequences
+           julia-biosymbols
+           julia-intervaltrees))
+    (home-page "https://github.com/BioJulia/BioAlignments.jl")
+    (synopsis "Sequence alignement algorithm and data structures")
+    (description "This package provides alignement algorithms and data
+structures for sequence of DNA, RNA, and amino acid sequences.")
+    (license license:expat)))
+
 (define-public julia-biogenerics
   ;; No upstream release
   (let ((commit "a75abaf459250e2b5e22b4d9adf25fd36d2acab6")
-- 
2.33.1





^ permalink raw reply related	[flat|nested] 19+ messages in thread

* bug#53017: [PATCH 01/17] gnu: julia-xyz: Adjust style.
  2022-01-04 22:47 ` [bug#53017] [PATCH 01/17] gnu: julia-xyz: Adjust style zimoun
                     ` (15 preceding siblings ...)
  2022-01-04 22:47   ` [bug#53017] [PATCH 17/17] gnu: Add julia-bioalignments zimoun
@ 2022-01-10 13:20   ` Efraim Flashner
  16 siblings, 0 replies; 19+ messages in thread
From: Efraim Flashner @ 2022-01-10 13:20 UTC (permalink / raw)
  To: zimoun; +Cc: 53017-done

[-- Attachment #1: Type: text/plain, Size: 238 bytes --]

Patches pushed. Thanks!

-- 
Efraim Flashner   <efraim@flashner.co.il>   רנשלפ םירפא
GPG key = A28B F40C 3E55 1372 662D  14F7 41AA E7DC CA3D 8351
Confidentiality cannot be guaranteed on emails sent or received unencrypted

[-- Attachment #2: signature.asc --]
[-- Type: application/pgp-signature, Size: 833 bytes --]

^ permalink raw reply	[flat|nested] 19+ messages in thread

end of thread, other threads:[~2022-01-10 13:23 UTC | newest]

Thread overview: 19+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2022-01-04 22:45 [bug#53017] [PATCH 00/17] Add julia-biosequences and julia-bioalignments zimoun
2022-01-04 22:47 ` [bug#53017] [PATCH 01/17] gnu: julia-xyz: Adjust style zimoun
2022-01-04 22:47   ` [bug#53017] [PATCH 02/17] build: julia-build-system: Create 'Project.toml' file when missing zimoun
2022-01-04 22:47   ` [bug#53017] [PATCH 03/17] gnu: julia-zygote: Adjust style zimoun
2022-01-04 22:47   ` [bug#53017] [PATCH 04/17] gnu: julia-documentertools: " zimoun
2022-01-04 22:47   ` [bug#53017] [PATCH 05/17] gnu: julia-documenter: " zimoun
2022-01-04 22:47   ` [bug#53017] [PATCH 06/17] gnu: Add julia-biogenerics zimoun
2022-01-04 22:47   ` [bug#53017] [PATCH 07/17] gnu: Add julia-indexablebitvectors zimoun
2022-01-04 22:47   ` [bug#53017] [PATCH 08/17] gnu: Add julia-twiddle zimoun
2022-01-04 22:47   ` [bug#53017] [PATCH 09/17] gnu: Add julia-simd zimoun
2022-01-04 22:47   ` [bug#53017] [PATCH 10/17] gnu: Add julia-scanbyte zimoun
2022-01-04 22:47   ` [bug#53017] [PATCH 11/17] gnu: Add julia-automa zimoun
2022-01-04 22:47   ` [bug#53017] [PATCH 12/17] gnu: Add julia-stringencodings zimoun
2022-01-04 22:47   ` [bug#53017] [PATCH 13/17] gnu: Add julia-yaml zimoun
2022-01-04 22:47   ` [bug#53017] [PATCH 14/17] gnu: Add julia-biosymbols zimoun
2022-01-04 22:47   ` [bug#53017] [PATCH 15/17] gnu: Add julia-biosequences zimoun
2022-01-04 22:47   ` [bug#53017] [PATCH 16/17] gnu: Add julia-intervaltrees zimoun
2022-01-04 22:47   ` [bug#53017] [PATCH 17/17] gnu: Add julia-bioalignments zimoun
2022-01-10 13:20   ` bug#53017: [PATCH 01/17] gnu: julia-xyz: Adjust style Efraim Flashner

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