diff options
| -rw-r--r-- | gn/packages/julia.scm | 150 |
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 |