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authorEfraim Flashner2023-02-07 18:17:07 +0200
committerEfraim Flashner2023-03-19 11:44:38 +0200
commit9fe470438af4139e1f23070198e716ab2c6adf4c (patch)
tree480be24b928997180783233ea72a34bf21279111 /gn
parentd530a17d2a699e7fbd6dc173949532274d9557e5 (diff)
downloadguix-bioinformatics-9fe470438af4139e1f23070198e716ab2c6adf4c.tar.gz
updates to julia packages
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/julia.scm150
1 files changed, 119 insertions, 31 deletions
diff --git a/gn/packages/julia.scm b/gn/packages/julia.scm
index 03425b2..36d9e31 100644
--- a/gn/packages/julia.scm
+++ b/gn/packages/julia.scm
@@ -23,8 +23,8 @@
(define S specification->package)
(define-public julia-visuals
- (let ((commit "e7d670eb045a9f8e3a839476dc166318da7fe9dc")
- (revision "1"))
+ (let ((commit "e8e2b601f40a76c8f20f0ddfe80c56257dd9a294")
+ (revision "2"))
(package
(name "julia-visuals")
(version (git-version "0.0.0" revision commit))
@@ -35,7 +35,7 @@
(commit commit)))
(file-name (git-file-name name version))
(sha256
- (base32 "15hshm5qrig5qbj02xy4ji79kfc72n93nna5nvxkhvb8gw3vvx07"))))
+ (base32 "0lm9yhk0mq5cvvkcbsgcjc1y7fzhr8qz2nxn38cy1zdxd8vfknsx"))))
(build-system julia-build-system)
(arguments
`(#:tests? #f ; no test suite
@@ -67,25 +67,29 @@
(let ((out (assoc-ref outputs "out")))
;; Do we need to wrap this with PYTHONPATH too?
(wrap-script (string-append out "/runpluto.sh")
- `("PATH" ":" prefix (,(string-append (assoc-ref inputs "julia") "/bin")
- ,(string-append (assoc-ref inputs "coreutils") "/bin")))
- `("JULIA_LOAD_PATH" ":" prefix (,(getenv "JULIA_LOAD_PATH")))))))
+ `("PATH" ":" prefix (,(string-append (assoc-ref inputs "julia") "/bin")
+ ,(string-append (assoc-ref inputs "coreutils") "/bin")))
+ `("JULIA_LOAD_PATH" ":" prefix (,(getenv "JULIA_LOAD_PATH")))))))
(replace 'precompile
(lambda _
(invoke "julia" "-e" "\"import Pkg; Pkg.instantiate(); Pkg.status(); Pkg.precompile()\""))))))
- ;;
- ;; (propagated-inputs
- ;; `( ;; from setup.py
- ;; ("python-jupyter-server-proxy"
- ;; ,(@ (gn packages python) python-jupyter-server-proxy-1)))
+
+ (propagated-inputs
+ `(;; from setup.py
+ ("python-jupyter-server-proxy"
+ ,(@ (gn packages python) python-jupyter-server-proxy-1))))
(inputs
- `(("julia-distributions" ,julia-distributions)
- ("julia-latexstrings" ,julia-latexstrings)
- ("julia-optim" ,julia-optim)
- ("julia-plots" ,julia-plots)
- ("julia-pluto" ,julia-pluto)
- ("julia-plutoui" ,julia-plutoui)
+ `(;("julia-cairomakie" ,julia-cairomakie) ; ~0.8.13
+ ("julia-distributions" ,julia-distributions) ; ~0.25.76
+ ("julia-latexstrings" ,julia-latexstrings) ; ~1.3.0
+ ("julia-optim" ,julia-optim) ; ~1.7.2
+ ("julia-plots" ,julia-plots) ; ~1.35.3
+ ("julia-pluto" ,julia-pluto) ; ~0.19.11
+ ("julia-plutoui" ,julia-plutoui) ; ~0.7.46
+ ("julia-prettytables" ,julia-prettytables) ; ~2.1.0
+ ("julia-quadgk" ,julia-quadgk) ; ~2.5.0
+ ;("julia-roots" ,julia-roots) ; ~2.0.3
("guile" ,(@ (gnu packages guile) guile-3.0)))) ; for wrap-script
(home-page "https://github.com/sens/visuals")
(synopsis "Visualizations using Pluto.jl notebooks")
@@ -264,7 +268,7 @@ distributed computing.")
(define-public julia-distributions
(package
(name "julia-distributions")
- (version "0.25.11")
+ (version "0.25.80")
(source
(origin
(method git-fetch)
@@ -273,12 +277,14 @@ distributed computing.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "0n5xgdpzrpb4s0g23rjggk7c7x8677hbhq0sam7xbw9mn2w79m7n"))))
+ (base32 "0nqlnkh8grxfm8d1mivi7dnrvb31bznj9s540a10d2v396ikfggn"))))
(build-system julia-build-system)
(arguments
`(#:tests? #f)) ; Some failed tests
(propagated-inputs
- `(("julia-fillarrays" ,julia-fillarrays)
+ `(("julia-chainrulescore" ,julia-chainrulescore)
+ ("julia-densityinterface" ,julia-densityinterface)
+ ("julia-fillarrays" ,julia-fillarrays)
("julia-pdmats" ,julia-pdmats)
("julia-quadgk" ,julia-quadgk)
("julia-specialfunctions" ,julia-specialfunctions)
@@ -286,9 +292,11 @@ distributed computing.")
("julia-statsfuns" ,julia-statsfuns)))
(native-inputs
`(("julia-calculus" ,julia-calculus)
+ ("julia-chainrulestestutils" ,julia-chainrulestestutils)
("julia-finitedifferences" ,julia-finitedifferences)
("julia-forwarddiff" ,julia-forwarddiff)
("julia-json" ,julia-json)
+ ("julia-offsetarrays" ,julia-offsetarrays)
("julia-stablerngs" ,julia-stablerngs)
("julia-staticarrays" ,julia-staticarrays)))
(home-page "https://github.com/JuliaStats/Distributions.jl")
@@ -305,6 +313,31 @@ properties
@end enumerate")
(license license:expat)))
+;; ready to upstream
+(define-public julia-densityinterface
+ (package
+ (name "julia-densityinterface")
+ (version "0.4.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/JuliaMath/DensityInterface.jl")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "10yr69lndh4jdyhjnpm421zvbw8v48bimxjawz05lqkd7k4w4lw6"))))
+ (build-system julia-build-system)
+ (propagated-inputs
+ (list julia-inversefunctions))
+ (native-inputs
+ (list julia-documenter))
+ (home-page "https://github.com/JuliaMath/DensityInterface.jl")
+ (synopsis "Interface for mathematical/statistical densities")
+ (description "This package defines an interface for mathematical/statistical
+densities and objects associated with a density in Julia.")
+ (license license:expat)))
+
(define-public julia-plots
(package
(name "julia-plots")
@@ -444,7 +477,7 @@ native to Julia. Use it with the @code{@@bind} macro in Pluto.")
(define-public julia-statsfuns
(package
(name "julia-statsfuns")
- (version "0.9.8")
+ (version "0.9.18")
(source
(origin
(method git-fetch)
@@ -453,21 +486,19 @@ native to Julia. Use it with the @code{@@bind} macro in Pluto.")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "1zl46p9gbx9xkjnnpd45csshqvq2i94mxw10karpr8xkx8msyk3k"))))
+ (base32 "1y71gz4skp6hxw8k5vjbjayplxmdfh3m3yjfw4ggi0azav6c9hrk"))))
(build-system julia-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'link-depot 'adjust-test-suite
- (lambda _
- (substitute* "test/misc.jl"
- (("test logmvbeta\\(1") "test_nowarn logmvbeta(1")))))))
(propagated-inputs
- (list julia-logexpfunctions
+ (list julia-chainrulescore
+ julia-inversefunctions
+ julia-irrationalconstants
+ julia-logexpfunctions
+ julia-reexport
julia-rmath
julia-specialfunctions))
(native-inputs
- (list julia-forwarddiff))
+ (list julia-chainrulestestutils
+ julia-forwarddiff))
(home-page "https://github.com/JuliaStats/StatsFuns.jl")
(synopsis "Mathematical functions related to statistics")
(description "This package provides a collection of mathematical constants
@@ -475,6 +506,29 @@ and numerical functions for statistical computing.")
(license license:expat)))
;; ready to upstream
+(define-public julia-inversefunctions
+ (package
+ (name "julia-inversefunctions")
+ (version "0.1.8")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/JuliaMath/InverseFunctions.jl")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "05g9f6i735x7syfr56l4yf4fy71kgdisjc6cfxi4jkf46iq86a69"))))
+ (build-system julia-build-system)
+ (native-inputs
+ (list julia-documenter))
+ (home-page "https://github.com/JuliaMath/InverseFunctions.jl")
+ (synopsis "Interface for function inversion in Julia")
+ (description
+ "This package provides an interface to invert functions in Julia.")
+ (license license:expat)))
+
+;; ready to upstream
(define-public rmath-for-julia-rmath-jll
;; More recent commits fix various build issues
(let ((commit "5c5dfd6baca358103fbb47cc03dc0ecee04fb1ff")
@@ -693,6 +747,40 @@ polynomials.")
AbstractInterval, along with its subtypes Interval and AnchoredInterval, and also Bound.")
(license license:expat)))
+(define-public julia-infinity
+ (package
+ (name "julia-infinity")
+ (version "0.2.4")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/cjdoris/Infinity.jl")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1941lwvrdjnrynigzixxin3chpg1ba6xplvcwc89x0f6z658hwmm"))))
+ (build-system julia-build-system)
+ (arguments
+ (list
+ #:tests? #f ; TODO: Fix tests!
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'link-depot 'remove-timezones.jl
+ (lambda _
+ (substitute* "test/runtests.jl"
+ (("using TimeZones.*") "")
+ ((".*infextendedtime.*") "")))))))
+ (propagated-inputs
+ (list julia-requires))
+ (native-inputs
+ (list julia-compat))
+ (home-page "https://docs.juliahub.com/Infinity/")
+ (synopsis "Representation of infinity in Julia")
+ (description "This package provides representations for infinity and
+negative infinity in Julia.")
+ (license license:expat)))
+
;; TODO: There is talk upstream about separating out the timezone data into a
;; separate package which can allow this to actually be packaged in a sane way.
;; As of 1.7.1 there are 257 items in Artifact.toml