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authorEfraim Flashner2021-09-10 17:19:58 +0300
committerEfraim Flashner2021-09-10 17:19:58 +0300
commit8bd585606b67c09a91912307026a68bacc0fb1d9 (patch)
treef4f2467dd4d09aad0c1135a41ec34bb7bd907579 /gn/packages
parent6b358542f5832376be16a165b897ea43270e2323 (diff)
downloadguix-bioinformatics-8bd585606b67c09a91912307026a68bacc0fb1d9.tar.gz
gn: julia updates
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/julia.scm149
1 files changed, 128 insertions, 21 deletions
diff --git a/gn/packages/julia.scm b/gn/packages/julia.scm
index 1e546bf..dc904ee 100644
--- a/gn/packages/julia.scm
+++ b/gn/packages/julia.scm
@@ -440,11 +440,10 @@ properties
;; TODO: Unbundle extra assets? assets/html/
;; see also: js inputs: src/Writers/HTMLWriter.jl
;; latex inputs: src/Writers/LaTeXWriter.jl
-;; needs pip: src/Deps.jl
(define-public julia-documenter
(package
(name "julia-documenter")
- (version "0.27.2")
+ (version "0.27.6")
(source
(origin
(method git-fetch)
@@ -453,16 +452,32 @@ properties
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32
- "0x99ns9fvnpm5jrqgfssfxdspxlx82qx7w5g0jy1x530yknk8ijq"))))
+ (base32 "1y6rql7cxc7hfhc8rfq1mdmffp70sqzyh4vnnq93fziwrc8c8sbj"))))
(build-system julia-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'patch-source
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "src/Deps.jl"
+ (("pip install")
+ (string-append (assoc-ref inputs "python") "/bin/pip install")))
+ #t))
+ )
+ ))
(propagated-inputs
- `(("julia-docstringextensions" ,julia-docstringextensions)
+ `(("julia-ansicoloredprinters" ,julia-ansicoloredprinters)
+ ("julia-docstringextensions" ,julia-docstringextensions)
("julia-iocapture" ,julia-iocapture)
("julia-json" ,julia-json)))
+ (inputs
+ `(
+ ("python" ,python-wrapper)
+ ))
(native-inputs
`(("git" ,(S "git-minimal"))
- ("julia-documentermarkdown" ,julia-documentermarkdown)))
+ ("julia-documentermarkdown" ,julia-documentermarkdown)
+ ("julia-documentertools" ,julia-documentertools)))
(home-page "https://juliadocs.github.io/Documenter.jl")
(synopsis "Documentation generator for Julia")
(description "This package provides a documentation generator for Julia.")
@@ -542,22 +557,112 @@ properties
(sha256
(base32 "05p57p8xlkn42m1lv9gq4hl96vp7hpj19d51p828ai1rbpcpi3a6"))))
(build-system julia-build-system)
+ (arguments
+ `(#:tests? #f)) ; Tests require network.
(inputs
;; We don't want to propagate the bootstrap version.
;; Cycle with Documenter.jl in later versions.
`(("julia-documenter" ,julia-documenter-0.22)))
(propagated-inputs
- `(
- ("julia-docstringextensions" ,julia-docstringextensions)
+ `(("julia-docstringextensions" ,julia-docstringextensions)
("julia-gumbo" ,julia-gumbo)
- ;("julia-sass" ,julia-sass)
- ))
+ ("julia-sass" ,julia-sass)))
+ (native-inputs
+ `(("julia-example" ,julia-example)))
(home-page "https://github.com/JuliaDocs/DocumenterTools.jl")
(synopsis "Extra tools for setting up Documenter")
(description "This package contains utilities for setting up documentation
generation with @code{Documenter.jl}.")
(license license:expat)))
+;; raedy to upstream
+(define-public julia-ansicoloredprinters
+ (package
+ (name "julia-ansicoloredprinters")
+ (version "0.0.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/JuliaDocs/ANSIColoredPrinters.jl")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0dp5agljr0g50s5gn0pr70wrz01ggck6pb40ay3l4szhswq7mqzf"))))
+ (build-system julia-build-system)
+ (home-page "https://github.com/JuliaDocs/ANSIColoredPrinters.jl")
+ (synopsis "ANSI escape code translator")
+ (description "@code{ANSIColoredPrinters.jl} converts a text qualified by
+ANSI escape codes to another format.")
+ (license license:expat)))
+
+;; ready to upstream
+(define-public julia-sass
+ (package
+ (name "julia-sass")
+ (version "0.2.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/piever/Sass.jl")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0y7kkkj717h5cj659ssry89i5r64symr6pvhr6vv4qmaxrnjxj92"))))
+ (build-system julia-build-system)
+ (propagated-inputs
+ `(("julia-libsass-jll" ,julia-libsass-jll)))
+ (home-page "https://github.com/piever/Sass.jl")
+ (synopsis "Compile scss and sass file to css in Julia")
+ (description "This library provides a simple Julian API to use the
+@code{libsass} library to compile scss and sass files to css.")
+ (license license:expat)))
+
+;; ready to upstream
+(define-public julia-libsass-jll
+ (let ((commit "69bf10603aad0ebf1f6df088c5fd7c4a5d1eb0ca"))
+ (package
+ (name "julia-libsass-jll")
+ (version "3.5.5+0") ;tag not created upstream
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/JuliaBinaryWrappers/libsass_jll.jl")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1fb6rf422533bsmfslvc20ag1hr50bf9xaj32rvh7nv593sbiygn"))))
+ (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(\"libsass\", \""
+ (assoc-ref inputs "libsass") "\")\n"))))
+ ;; There's a Julia file for each platform, override them all
+ (find-files "src/wrappers/" "\\.jl$"))
+ #t)))))
+ (inputs
+ `(("libsass" ,(@ (gnu packages web) libsass))))
+ (propagated-inputs
+ `(("julia-jllwrappers" ,julia-jllwrappers)))
+ (home-page "https://github.com/JuliaBinaryWrappers/libsass_jll.jl")
+ (synopsis "Julia wrapper for libsass")
+ (description "This package provides a wrapper for libsass It is an
+autogenerated source package constructed using @code{BinaryBuilder.jl}. The
+originating @code{build_tarballs.jl} script can be found on the community
+build tree Yggdrasil.")
+ (license license:expat))))
+
;; ready to upstream
;; if the test suite passes
(define-public julia-optim
@@ -1106,7 +1211,7 @@ implemented in Julia.")
(define-public julia-doublefloats
(package
(name "julia-doublefloats")
- (version "1.1.21")
+ (version "1.1.23")
(source
(origin
(method git-fetch)
@@ -1115,10 +1220,11 @@ implemented in Julia.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "0bpx2y05mmnk77lsg3gnxcjvag5h75nk5pyv0xrw53a8b62ja57y"))))
+ (base32 "0qdkcmjknlan25dbgqw101zvgb5ly8v4pf1xikj6k2x96k8c6c8g"))))
(build-system julia-build-system)
(propagated-inputs
- `(("julia-polynomials" ,julia-polynomials)
+ `(("julia-genericlinearalgebra" ,julia-genericlinearalgebra)
+ ("julia-polynomials" ,julia-polynomials)
("julia-quadmath" ,julia-quadmath)
("julia-requires" ,julia-requires)
("julia-specialfunctions" ,julia-specialfunctions)))
@@ -1136,7 +1242,7 @@ floats and complex types.")
(define-public julia-polynomials
(package
(name "julia-polynomials")
- (version "2.0.12")
+ (version "2.0.14")
(source
(origin
(method git-fetch)
@@ -1145,7 +1251,7 @@ floats and complex types.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "1ydxw1ich5gkd6mlrr6x4clyjkr0xkmlf0l054g4k73symw2bc7x"))))
+ (base32 "07yb98fm9yhhan0n3iwmd9dz7zpj4kal99z5h1px1q5zpmjn68xa"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-intervals" ,julia-intervals)
@@ -1153,7 +1259,8 @@ floats and complex types.")
("julia-recipesbase" ,julia-recipesbase)))
(native-inputs
`(("julia-offsetarrays" ,julia-offsetarrays)
- ("julia-specialfunctions" ,julia-specialfunctions)))
+ ("julia-specialfunctions" ,julia-specialfunctions)
+ ("julia-staticarrays" ,julia-staticarrays)))
(home-page "https://github.com/JuliaMath/Polynomials.jl")
(synopsis "Polynomial manipulations in Julia")
(description "This package provides basic arithmetic, integration,
@@ -1197,7 +1304,7 @@ polynomials.")
(define-public julia-infinity
(package
(name "julia-infinity")
- (version "0.2.3")
+ (version "0.2.4")
(source
(origin
(method git-fetch)
@@ -1206,7 +1313,7 @@ polynomials.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "1bw7p88l8svb7455srz0jmw8ap17r2wwgz5y02vr9s8cg4lbsps5"))))
+ (base32 "1941lwvrdjnrynigzixxin3chpg1ba6xplvcwc89x0f6z658hwmm"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-compat" ,julia-compat)
@@ -1219,7 +1326,7 @@ polynomials.")
(synopsis "Representation of infinity in Julia")
(description "This package provides representations for infinity and
negative infinity in Julia.")
- (license license:gpl3)))
+ (license license:expat)))
;; TODO: Keep this in sync with tzdata in base.scm
;; Package can use more work
@@ -1387,7 +1494,7 @@ that still support Julia versions older than 1.6.")
(define-public julia-structarrays
(package
(name "julia-structarrays")
- (version "0.6.0")
+ (version "0.6.1")
(source
(origin
(method git-fetch)
@@ -1396,7 +1503,7 @@ that still support Julia versions older than 1.6.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "05yxsmzi82fp9f0bg5kihpcls4xjxdy4chnnflmg8h4i457pbr5v"))))
+ (base32 "1scmwv016pqdl6mx6i3c2bkqf1kwbzcymgwzdq9hp6bq627zmr3v"))))
(build-system julia-build-system)
(propagated-inputs
`(("julia-dataapi" ,julia-dataapi)