diff options
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/julia.scm | 274 |
1 files changed, 131 insertions, 143 deletions
diff --git a/gn/packages/julia.scm b/gn/packages/julia.scm index 0423451..0b10145 100644 --- a/gn/packages/julia.scm +++ b/gn/packages/julia.scm @@ -386,7 +386,7 @@ equations in string literals in the Julia language.") (define-public julia-distributions (package (name "julia-distributions") - (version "0.25.1") + (version "0.25.6") (source (origin (method git-fetch) @@ -395,18 +395,17 @@ equations in string literals in the Julia language.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0p3998sh667f1bskd011z9hfdkbdw5kgh9n1771jx4madxscy7dq")))) + (base32 "07n7g5zxp1b82k6yvqa5kh51jww2cy1f5pyvh60k3fp6rdp8sy1j")))) (build-system julia-build-system) (arguments `(;#:tests? #f )) (propagated-inputs `( - ;("julia-fillarrays" ,julia-fillarrays) - ;("julia-distributed" ,julia-distributed) + ("julia-fillarrays" ,julia-fillarrays) ("julia-pdmats" ,julia-pdmats) ;("julia-quadgk" ,julia-quadgk) - ;("julia-specialfunctions" ,julia-specialfunctions) + ("julia-specialfunctions" ,julia-specialfunctions) ("julia-statsbase" ,julia-statsbase) ("julia-statsfuns" ,julia-statsfuns) ; fix Rmath.jl )) @@ -429,7 +428,7 @@ equations in string literals in the Julia language.") (define-public julia-documenter (package (name "julia-documenter") - (version "0.26.3") + (version "0.27.2") (source (origin (method git-fetch) @@ -439,12 +438,11 @@ equations in string literals in the Julia language.") (file-name (git-file-name name version)) (sha256 (base32 - "1d4mdjc56w0hrc50qia361zfp8zapq163cqgagkbbjn0k83zp21x")))) + "0x99ns9fvnpm5jrqgfssfxdspxlx82qx7w5g0jy1x530yknk8ijq")))) (build-system julia-build-system) (propagated-inputs `(("julia-docstringextensions" ,julia-docstringextensions) - ;; TODO: Switch to julia-iocapture after 0.27. - ("julia-iocapture" ,julia-iocapture-0.1) + ("julia-iocapture" ,julia-iocapture) ("julia-json" ,julia-json))) (native-inputs `(("git" ,(S "git-minimal")) @@ -454,22 +452,6 @@ equations in string literals in the Julia language.") (description "This package provides a documentation generator for Julia.") (license license:expat))) -;; Upstream with julia-documenter -(define-public julia-iocapture-0.1 - (package - (inherit julia-iocapture) - (name "julia-iocapture") - (version "0.1.1") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/JuliaDocs/IOCapture.jl") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "0wm8pag5mk46064h3qpvgz8m63138104rq0smx1za7lh7j32925h")))))) - ;; ready to upstream with julia-documenter (define-public julia-documenter-0.22 (package @@ -509,7 +491,7 @@ equations in string literals in the Julia language.") (define-public julia-documentermarkdown (package (name "julia-documentermarkdown") - (version "0.2.1") + (version "0.2.2") (source (origin (method git-fetch) @@ -518,8 +500,7 @@ equations in string literals in the Julia language.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 - "11l7yrifg8pdr4q6h75zydfw5i8vww07p5bci5mi8gwwcpi3jksb")))) + (base32 "0sx89hi5p2f8zi2rp5qrv06m270d90pxj5d2y5cxls1spax7wqx8")))) (build-system julia-build-system) (inputs ;; We don't want to propagate the bootstrap version. @@ -527,10 +508,40 @@ equations in string literals in the Julia language.") `(("julia-documenter" ,julia-documenter-0.22))) (home-page "https://github.com/JuliaDocs/DocumenterMarkdown.jl") (synopsis "Documenter's Markdown") - (description "his package enables the Markdown / MkDocs backend of + (description "This package enables the Markdown / MkDocs backend of @code{Documenter.jl}.") (license license:expat))) +(define-public julia-documentertools + (package + (name "julia-documentertools") + (version "0.1.13") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaDocs/DocumenterTools.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "05p57p8xlkn42m1lv9gq4hl96vp7hpj19d51p828ai1rbpcpi3a6")))) + (build-system julia-build-system) + (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-gumbo" ,julia-gumbo) + ;("julia-sass" ,julia-sass) + )) + (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))) + (define-public julia-optim (package (name "julia-optim") @@ -571,7 +582,7 @@ optimization of functions.") (define-public julia-plots (package (name "julia-plots") - (version "1.15.1") + (version "1.16.6") (source (origin (method git-fetch) @@ -580,8 +591,7 @@ optimization of functions.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 - "1bw76zzrq4zlwglhr7nkr1h0w0wl1i49rp35nnbbdqkdj46bz52y")))) + (base32 "0ipv9408r4czsx1j01sv2f7ww52b329jc0v79npn4x2mf827nsik")))) (build-system julia-build-system) (arguments `(#:tests? #f ; for now @@ -610,19 +620,19 @@ optimization of functions.") (native-inputs `( ;("julia-distributions" ,julia-distributions) - ;("julia-fileio" ,julia-fileio) + ("julia-fileio" ,julia-fileio) ;("julia-gtk" ,julia-gtk) ;("julia-hdf5" ,julia-hdf5) ("julia-imagemagick" ,julia-imagemagick) ;("julia-images" ,julia-images) - ;("julia-offsetarrays" ,julia-offsetarrays) + ("julia-offsetarrays" ,julia-offsetarrays) ;("julia-pgfplotsx" ,julia-pgfplotsx) ;("julia-plotlyjs" ,julia-plotlyjs) ;("julia-rdatasets" ,julia-rdatasets) - ;("julia-stablerngs" ,julia-stablerngs) - ;("julia-staticarrays" ,julia-staticarrays) + ("julia-stablerngs" ,julia-stablerngs) + ("julia-staticarrays" ,julia-staticarrays) ;("julia-statsplots" ,julia-statsplots) - ;("julia-testimages" ,julia-testimages) + ("julia-testimages" ,julia-testimages) ;("julia-unicodeplots" ,julia-unicodeplots) ;("julia-visualregressiontests" ,julia-visualregressiontests) )) @@ -743,7 +753,7 @@ variables, both with unordered (nominal variables) and ordered categories (define-public julia-pluto (package (name "julia-pluto") - (version "0.14.7") + (version "0.14.8") (source (origin (method git-fetch) @@ -752,8 +762,7 @@ variables, both with unordered (nominal variables) and ordered categories (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 - "0b2g3j78kpkayhrm3am855cc5kjb3w73ygcvjbvhz2p5i1ivji7b")))) + (base32 "0kzl70fgb6q23yxifkadxrxp7nhc26pqnklna83bqdczk0543q3w")))) (build-system julia-build-system) (arguments `(#:tests? #f ; Many tests need network connectivity or a browser. @@ -805,10 +814,11 @@ dependencies between them and takes care of execution.") native to Julia. Use it with the @code{@@bind} macro in Pluto.") (license license:expat))) +;; ready to upstream (define-public julia-configurations (package (name "julia-configurations") - (version "0.15.4") + (version "0.16.0") (source (origin (method git-fetch) @@ -817,19 +827,36 @@ 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 - "1dz1h64nqgcv6ai70pfv2dv4mqx9rqmh08196k7j73bqlc6r00w1")))) + (base32 "033wc6bqslvv6fkknlc725432j2vc2wcji2167klnx3qwlac2965")))) (build-system julia-build-system) (arguments - `(#:tests? #f)) ; cannot find test/option.toml + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-tests + (lambda _ + (substitute* "test/runtests.jl" + (("option.toml") "test/option.toml")) + #t)) + (add-after 'unpack 'dont-use-exproniconlite + (lambda _ + (substitute* '("Project.toml" + "src/Configurations.jl" + "test/runtests.jl") + (("ExproniconLite") "Expronicon")) + (substitute* "Project.toml" + (("55351af7-c7e9-48d6-89ff-24e801d99491") + "6b7a57c9-7cc1-4fdf-b7f5-e857abae3636")) + #t))))) (propagated-inputs `(("julia-crayons" ,julia-crayons) - ("julia-exproniconlite" ,julia-exproniconlite) + ("julia-expronicon" ,julia-expronicon) ("julia-orderedcollections" ,julia-orderedcollections) ("julia-toml" ,julia-toml))) - (home-page "https://configurations.rogerluo.dev/stable") - (synopsis "Options & Configurations made easy") - (description "Configurations is a Julia Language package.") + (home-page "https://configurations.rogerluo.dev/stable/") + (synopsis "Options and configurations in Julia") + (description "@code{Configurations.jl} provides a macro @code{@@option} to +let you define @code{structs} to represent options/configurations, and serialize +between different option/configuration file formats such as @code{TOML}.") (license license:expat))) ;; XXX: Part of base Julia as of 1.6+ @@ -853,6 +880,8 @@ native to Julia. Use it with the @code{@@bind} macro in Pluto.") (description "TOML v1.0.0 parser for Julia.") (license license:expat))) +;; ready to upstream +;; ExproniconLite.jl is autogenerated from this package. (define-public julia-expronicon (package (name "julia-expronicon") @@ -865,44 +894,41 @@ 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 - "0lbzfn1li2ph02z6hl5286bj6bf17g63vfp6qn4cz40d760fcw8a")))) + (base32 "0lbzfn1li2ph02z6hl5286bj6bf17g63vfp6qn4cz40d760fcw8a")))) (build-system julia-build-system) - (arguments - `(;#:tests? #f - )) (propagated-inputs - `( - ;("julia-mlstyle" ,julia-mlstyle) - )) - (home-page "https://expronicon.rogerluo.dev/") + `(("julia-mlstyle" ,julia-mlstyle) + ("julia-toml" ,julia-toml))) + (native-inputs + `(("julia-documenter" ,julia-documenter))) + (home-page "https://expronicon.rogerluo.dev/dev/") (synopsis "Collective tools for metaprogramming on Julia Expr") - (description "Collective tools for metaprogramming on Julia Expr.") + (description "This package provides a collection of tools for +metaprogramming on Julia Expr, the meta programming standard library for +@code{MLStyle}.") (license license:expat))) -;; autogenerated package? -(define-public julia-exproniconlite +;; ready to upstream +(define-public julia-mlstyle (package - (name "julia-exproniconlite") - (version "0.6.8") + (name "julia-mlstyle") + (version "0.4.10") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/Roger-luo/ExproniconLite.jl") + (url "https://github.com/thautwarm/MLStyle.jl") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 - "02zm5r3fi7zx4fnr2ikxpapb9rvmnqvklrfyd4j9418q1mryh04l")))) + (base32 "0h1cd7cr4c4cnpqyj3180113gdbvcc047lqphp8a8gq5smp3c059")))) (build-system julia-build-system) (native-inputs - `(("julia-documenter" ,julia-documenter))) - (home-page "https://expronicon.rogerluo.dev/") - (synopsis "Collective tools for metaprogramming on Julia Expr") - (description "no fancy pattern matching, no dependencies, Light-weight Expronicon for low latency. - - this package is generated by Expronicon, please refer to Expronicon for any issues") + `(("julia-datastructures" ,julia-datastructures))) + (home-page "https://thautwarm.github.io/MLStyle.jl/latest/") + (synopsis "Julia functional programming infrastructures") + (description "This package provides consistent and extensible functional +programming infrastructures, and metaprogramming facilities.") (license license:expat))) (define-public julia-statsfuns @@ -943,13 +969,15 @@ native to Julia. Use it with the @code{@@bind} macro in Pluto.") (method git-fetch) (uri (git-reference (url "https://github.com/JuliaStats/Rmath-julia") - (commit (string-append "v" version)))) + ;(commit (string-append "v" version)))) + (commit "5c5dfd6baca358103fbb47cc03dc0ecee04fb1ff"))) (file-name (git-file-name name version)) (sha256 - (base32 "11a6h3wwmpnb2d55pkm6av111b3pxlvxfnbz8b0n77afpllgb8j2")))) + ;(base32 "11a6h3wwmpnb2d55pkm6av111b3pxlvxfnbz8b0n77afpllgb8j2")))) + (base32 "04lf8gfnfcppckk9d7hss0ja91yxaax6qz1gzqya9w0shjr386s5")))) (build-system julia-build-system) (arguments - `(#:tests? #f ; Test not defined, tests not often run upstream. + `(;#:tests? #f ; Test not defined, tests not often run upstream. #:phases (modify-phases %standard-phases (delete 'precompile) @@ -978,7 +1006,6 @@ native to Julia. Use it with the @code{@@bind} macro in Pluto.") (package (name "julia-rmath") (version "0.7.0") - ;(version "0.6.1") (source (origin (method git-fetch) @@ -988,30 +1015,27 @@ native to Julia. Use it with the @code{@@bind} macro in Pluto.") (file-name (git-file-name name version)) (sha256 (base32 "0cam16ff4v2fl7c9j1wx2ahgjhwba9mk2q6qv3zdknnnqj6w664s")))) - ;(base32 "1745xajy5c8hdcy1hgi2rr9lrapr55hp0jm2dcb1ksyskvm5drsr")))) (build-system julia-build-system) (arguments - `(;#:tests? #f ; Test not defined - #:phases + `(#:phases (modify-phases %standard-phases - ;(add-after 'unpack 'patch-source - ; (lambda _ - ; ;; see upstream julia bug - ; ;; ERROR: LoadError: InitError: UndefVarError: libRmath_path not defined - ; (substitute* "src/Rmath.jl" - ; (("libRmath\\)") "libRmath_path)")) - ; #t)) - ) - )) + (add-after 'unpack 'link-to-librmath-directly + (lambda* (#:key inputs #:allow-other-keys) + (let* ((rmath (assoc-ref inputs "rmath")) + (librmath (string-append rmath "/lib/libRmath-julia.so"))) + ;; see upstream julia bug + ;; ERROR: LoadError: InitError: UndefVarError: libRmath_path not defined + (substitute* "src/Rmath.jl" + (("libRmath\\)") (string-append "\"" librmath "\")"))) + ;(substitute* "test/runtests.jl" + ; (("Rmath\\.libRmath\\)") (string-append "\"" librmath "\")"))) + #t)))))) (propagated-inputs - `( - ("julia-rmath-jll" ,julia-rmath-jll) - ;("julia-rmath-jll" ,julia-rmath-jll-0.2) - )) + `(("julia-rmath-jll" ,julia-rmath-jll))) + (inputs + `(("rmath" ,rmath-julia))) (native-inputs - `( - ;("julia-offsetarrays" ,julia-offsetarrays) - )) + `(("rmath" ,rmath-julia))) (home-page "https://github.com/JuliaStats/Rmath.jl") (synopsis "functions that emulate R's d-p-q-r functions for probability distributions") (description " @@ -1019,6 +1043,7 @@ native to Julia. Use it with the @code{@@bind} macro in Pluto.") Archive of functions that emulate R's d-p-q-r functions for probability distributions.") (license license:expat))) +;; This package seems to be bugged, doesn't load libRmath-julia.so correctly. (define-public julia-rmath-jll (package (name "julia-rmath-jll") @@ -1050,8 +1075,7 @@ native to Julia. Use it with the @code{@@bind} macro in Pluto.") ;; There's a Julia file for each platform, override them all (find-files "src/wrappers/" "\\.jl$"))))))) (inputs - `( - ;; It wants the custom rmath. + `(;; It wants the custom rmath. ("rmath" ,rmath-julia) ;("rmath" ,(S "rmath-standalone")) )) @@ -1062,42 +1086,6 @@ native to Julia. Use it with the @code{@@bind} macro in Pluto.") (description "This package provides a wrapper for Rmath.") (license license:expat))) -(define-public julia-rmath-jll-0.2 - (package - (name "julia-rmath-jll") - (version "0.2.2+2") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/JuliaBinaryWrappers/Rmath_jll.jl") - (commit (string-append "Rmath-v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "13wvx4n0ai7bsda3rvlw8xbqwdbdwhjijbgjgl0k2yzq5l8x5dmh")))) - (build-system julia-build-system) - (arguments - '(#:tests? #f ; no runtests - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'override-binary-path - (lambda* (#:key inputs #:allow-other-keys) - (map - (lambda (wrapper) - (substitute* wrapper - (("artifact\"Rmath\"") - (string-append "\"" (assoc-ref inputs "rmath") "\"")))) - ;; There's a Julia file for each platform, override them all - (find-files "src/wrappers/" "\\.jl$"))))))) - (inputs - `(("rmath" ,rmath-julia))) - (propagated-inputs - `(("julia-jllwrappers" ,julia-jllwrappers))) - (home-page "https://github.com/JuliaBinaryWrappers/Rmath_jll.jl") - (synopsis "Rmath library wrappers") - (description "This package provides a wrapper for Rmath.") - (license license:expat))) - ;; ready to upstream (define-public julia-linesearches (package @@ -1170,7 +1158,7 @@ floats and complex types.") (define-public julia-polynomials (package (name "julia-polynomials") - (version "2.0.10") + (version "2.0.12") (source (origin (method git-fetch) @@ -1179,7 +1167,7 @@ floats and complex types.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0mz7ls281d6166w9808lwgn007dsk8pqi4qmdf0jiiipy5a0a4ji")))) + (base32 "1ydxw1ich5gkd6mlrr6x4clyjkr0xkmlf0l054g4k73symw2bc7x")))) (build-system julia-build-system) (propagated-inputs `(("julia-intervals" ,julia-intervals) @@ -1378,7 +1366,7 @@ that still support Julia versions older than 1.6.") (define-public julia-geometrybasics (package (name "julia-geometrybasics") - (version "0.3.12") + (version "0.3.13") (source (origin (method git-fetch) @@ -1387,7 +1375,7 @@ that still support Julia versions older than 1.6.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1wsx287i1hlzkw7ljfc929ssla6b4qn647nsa3j32v2f8gzd86ag")))) + (base32 "05wq41s6c69zay2awgdhjld8gsycdb5jbvf6a785i3f12av6ndk0")))) (build-system julia-build-system) (arguments `(;#:tests? #f @@ -1421,7 +1409,7 @@ that still support Julia versions older than 1.6.") (define-public julia-structarrays (package (name "julia-structarrays") - (version "0.5.1") + (version "0.6.0") (source (origin (method git-fetch) @@ -1430,10 +1418,11 @@ that still support Julia versions older than 1.6.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0i1h3pbjp04dwic786yjnx81ifppgcbdysvgjs00cd9zmpn3xnqw")))) + (base32 "05yxsmzi82fp9f0bg5kihpcls4xjxdy4chnnflmg8h4i457pbr5v")))) (build-system julia-build-system) (propagated-inputs `(("julia-dataapi" ,julia-dataapi) + ("julia-staticarrays" ,julia-staticarrays) ("julia-tables" ,julia-tables))) (native-inputs `(("julia-documenter" ,julia-documenter) @@ -1551,7 +1540,7 @@ is column based (meaning each field of the @code{struct} is stored in a separate (define-public julia-gr (package (name "julia-gr") - (version "0.57.4") + (version "0.57.5") (source (origin (method git-fetch) @@ -1560,8 +1549,7 @@ is column based (meaning each field of the @code{struct} is stored in a separate (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 - "0hwzxwnak3sixm8jlm2zz6578gn713sbbznq49s11h38n0aczjx2")))) + (base32 "14nra7fx2g8y2ll3saxgccanzbcl5s58qzgd2jlha3r0ngfhrvxg")))) (build-system julia-build-system) (propagated-inputs `(("julia-gr-jll" ,julia-gr-jll))) @@ -1625,7 +1613,7 @@ in Julia).") (define-public julia-gr-jll (package (name "julia-gr-jll") - (version "0.57.2+0") + (version "0.57.3+0") (source (origin (method git-fetch) @@ -1634,7 +1622,7 @@ in Julia).") (commit (string-append "GR-v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1fqm531s5pm8q2rqz0gmrbj2qsivmc6x04sgn8gzfpz9jrmglbzq")))) + (base32 "0a568qxxdrfi951s0lhy5081yw8pw6sv39vfkzxw5cxic92w6rbs")))) (build-system julia-build-system) (arguments '(#:tests? #f ; no runtests |