diff options
| -rw-r--r-- | gn/packages/julia.scm | 1462 | ||||
| -rw-r--r-- | gn/services/pluto.scm | 55 |
2 files changed, 1332 insertions, 185 deletions
diff --git a/gn/packages/julia.scm b/gn/packages/julia.scm index 355a498..2150d52 100644 --- a/gn/packages/julia.scm +++ b/gn/packages/julia.scm @@ -7,6 +7,7 @@ #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) #:use-module (guix build-system julia) + #:use-module (gnu packages) #:use-module (gn packages cran) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages compression) @@ -17,6 +18,8 @@ #:use-module (gnu packages video) #:use-module (ice-9 match)) +(define S specification->package) + (define-public julia-visuals (let ((commit "e7d670eb045a9f8e3a839476dc166318da7fe9dc") (revision "1")) @@ -38,23 +41,30 @@ (modify-phases %standard-phases (add-after 'unpack 'patch-source (lambda* (#:key inputs #:allow-other-keys) - (chmod "runpluto.sh" #o755) ; it starts as #o444 + (chmod "runpluto.sh" #o555) ; it starts as #o444 (substitute* "runpluto.sh" - ;(("julia") - ; (string-append (assoc-ref inputs "julia") "/bin/julia")) - ;(("basename") - ; (string-append (assoc-ref inputs "coreutils") "/bin/basename")) - ;; The arguments don't pass through the wrapper - (("\\$\\{1\\}") "4343") - ) + ;; The arguments don't pass through the wrapper so we hardcode the port. + (("\\$\\{1\\}") "4343")) #t)) (replace 'install (lambda* (#:key outputs #:allow-other-keys) - (copy-recursively "." (assoc-ref outputs "out")) - #t)) + (let ((out (assoc-ref outputs "out"))) + ;; Copied from the Dockerfile. + (for-each + (lambda (file) + (copy-recursively file (string-append out "/" file))) + (list "plutoserver" + "environment.yml" + "setup.py" + "runpluto.sh" + "notebooks" + "Project.toml" + "Manifest.toml")) + #t))) (add-after 'install 'wrap-program (lambda* (#:key inputs outputs #:allow-other-keys) (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"))) @@ -63,26 +73,23 @@ (replace 'precompile (lambda _ (invoke "julia" "-e" "\"import Pkg; Pkg.instantiate(); Pkg.status(); Pkg.precompile()\"") - #t)) - ) - )) + #t))))) (propagated-inputs `( - ("julia" ,(@ (gnu packages julia) julia)) + ;; and from setup.py + ("python-jupyter-server-proxy" ,(@ (gn packages python) python-jupyter-server-proxy-1)) + )) + (inputs + `( + ;("julia-distributions" ,julia-distributions) + ;("julia-interactiveutils" ,julia-interactiveutils) ; Part of stdlib as of XXXX ("julia-latexstrings" ,julia-latexstrings) + ;("julia-markdown" ,julia-markdown) ; Part of stdlib as of XXXX ("julia-optim" ,julia-optim) ("julia-plots" ,julia-plots) ("julia-pluto" ,julia-pluto) ("julia-plutoui" ,julia-plutoui) - ;; Additional packages in generate.jl - ;("julia-markdown" ,julia-markdown) - ;("julia-interactiveutils" ,julia-interactiveutils) - ;("julia-distributions" ,julia-distributions) - ;; and from setup.py - ("python-jupyter-server-proxy" ,(@ (gn packages python) python-jupyter-server-proxy-1)) - )) - (inputs - `(("guile" ,(@ (gnu packages guile) guile-3.0)))) ; for wrap-script + ("guile" ,(@ (gnu packages guile) guile-3.0)))) ; for wrap-script (home-page "https://github.com/senresearch/LiteQTL.jl") (synopsis "Visualizations using Pluto.jl notebooks") (description "Visualizations using Pluto.jl notebooks.") @@ -368,7 +375,7 @@ distributed computing.") )) (native-inputs `( - ("conda" ,(@ (gnu packages package-management) conda)) + ("conda" ,(S "conda")) ("python" ,(@ (gnu packages python) python-wrapper)) )) (propagated-inputs @@ -406,7 +413,7 @@ distributed computing.") (define-public julia-distributions (package (name "julia-distributions") - (version "0.25.0") + (version "0.25.1") (source (origin (method git-fetch) @@ -415,8 +422,7 @@ distributed computing.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 - "1rxv9cml5r8gp0qgqdp61hqbgvv55ncyfzbim4iqfmbaj4ji9fmp")))) + (base32 "0p3998sh667f1bskd011z9hfdkbdw5kgh9n1771jx4madxscy7dq")))) (build-system julia-build-system) (arguments `(;#:tests? #f @@ -429,7 +435,7 @@ distributed computing.") ;("julia-quadgk" ,julia-quadgk) ;("julia-specialfunctions" ,julia-specialfunctions) ("julia-statsbase" ,julia-statsbase) - ("julia-statsfuns" ,julia-statsfuns) + ("julia-statsfuns" ,julia-statsfuns) ; fix Rmath.jl )) (home-page "https://github.com/JuliaStats/Distributions.jl") (synopsis "probability distributions and associated functions") @@ -1550,6 +1556,10 @@ it with the @code{@@bind} macro in Pluto.") ("julia-rmath" ,julia-rmath) ("julia-specialfunctions" ,julia-specialfunctions) )) + (native-inputs + `( + ("julia-forwarddiff" ,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 and numerical functions for statistical computing.") @@ -1622,6 +1632,7 @@ 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) @@ -1631,6 +1642,7 @@ 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 @@ -1639,6 +1651,7 @@ it with the @code{@@bind} macro in Pluto.") ;(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)) @@ -1647,6 +1660,7 @@ it with the @code{@@bind} macro in Pluto.") (propagated-inputs `( ("julia-rmath-jll" ,julia-rmath-jll) + ;("julia-rmath-jll" ,julia-rmath-jll-0.2) )) (native-inputs `( @@ -1680,12 +1694,53 @@ it with the @code{@@bind} macro in Pluto.") (add-after 'unpack 'override-binary-path (lambda* (#:key inputs #:allow-other-keys) (map + (lambda (wrapper) + (substitute* wrapper + ;(("libRmath-julia") "libRmath") + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"Rmath\", \"" + (assoc-ref inputs "rmath") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `( + ;; It wants the custom rmath. + ("rmath" ,rmath-julia) + ;("rmath" ,(S "rmath-standalone")) + )) + (propagated-inputs + `(("julia-jllwrappers" ,julia-jllwrappers))) + (home-page "https://github.com/JuliaBinaryWrappers/Rmath_jll.jl") + (synopsis "Rmath library wrappers") + (description "This package provides a wrapper for Rmath.") + (license license:expat))) + +(define-public julia-rmath-jll-0.2 + (package + (name "julia-rmath-jll") + (version "0.2.2+2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Rmath_jll.jl") + (commit (string-append "Rmath-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "13wvx4n0ai7bsda3rvlw8xbqwdbdwhjijbgjgl0k2yzq5l8x5dmh")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map (lambda (wrapper) (substitute* wrapper - (("generate_wrapper_header.*") - (string-append - "generate_wrapper_header(\"Rmath\", \"" - (assoc-ref inputs "rmath") "\")\n")))) + (("artifact\"Rmath\"") + (string-append "\"" (assoc-ref inputs "rmath") "\"")))) ;; There's a Julia file for each platform, override them all (find-files "src/wrappers/" "\\.jl$"))))))) (inputs @@ -3766,16 +3821,6 @@ polynomials.") (sha256 (base32 "1s7bz5aaj9sx753pcaixq83jgbk33adxgybpinjgzb9lzdv1ddgx")))) (build-system julia-build-system) - ;(arguments - ; `(#:tests? #f)) - (propagated-inputs - `( - ;("julia-indexing" ,julia-indexing) - )) - (native-inputs - `( - ;("julia-pooledarrays" ,julia-pooledarrays) - )) (home-page "https://github.com/andyferris/Indexing.jl") (synopsis "Generalized indexing for Julia") (description "This package defines functions for getting multiple indices out of dictionaries, tuples, etc, extending this ability beyond @code{AbstractArray}.") @@ -3795,16 +3840,8 @@ polynomials.") (sha256 (base32 "1j88f6qa5hqm64n5q3jy08a02gwp7by401s03n5x7575p58iqqh2")))) (build-system julia-build-system) - ;(arguments - ; `(#:tests? #f)) (propagated-inputs - `( - ("julia-indexing" ,julia-indexing) - )) - (native-inputs - `( - ;("julia-pooledarrays" ,julia-pooledarrays) - )) + `(("julia-indexing" ,julia-indexing))) (home-page "https://github.com/andyferris/Dictionaries.jl") (synopsis "An alternative interface for dictionaries in Julia, for improved productivity and performance") (description "An alternative interface for dictionaries in Julia, for improved productivity and performance.") @@ -3922,17 +3959,9 @@ polynomials.") (sha256 (base32 "1kwqixwhnnxs59xsw2k44xxnkx5fn4y49g58l5snfbszycxq7lls")))) (build-system julia-build-system) - ;(arguments - ; `(#:tests? #f)) (propagated-inputs - `( - ("julia-ffmpeg-jll" ,julia-ffmpeg-jll) - ("julia-x264-jll" ,julia-x264-jll) - )) - (native-inputs - `( - ;("julia-pooledarrays" ,julia-pooledarrays) - )) + `(("julia-ffmpeg-jll" ,julia-ffmpeg-jll) + ("julia-x264-jll" ,julia-x264-jll))) (home-page "https://github.com/JuliaIO/FFMPEG.jl") (synopsis "Julia Package for the FFMPEG builder binaries") (description "This package is made to be included into packages that just need the ffmpeg binaries + executables, and don't want to take on the 3.6 second load time of VideoIO.") @@ -3969,9 +3998,7 @@ polynomials.") ;; There's a Julia file for each platform, override them all (find-files "src/wrappers/" "\\.jl$"))))))) (propagated-inputs - `( - ("julia-jllwrappers" ,julia-jllwrappers) - )) + `(("julia-jllwrappers" ,julia-jllwrappers))) (inputs `(("x264" ,libx264))) (home-page "https://github.com/JuliaBinaryWrappers/x264_jll.jl") @@ -4195,14 +4222,7 @@ wrappers.") ;; There's a Julia file for each platform, override them all (find-files "src/wrappers/" "\\.jl$"))))))) (propagated-inputs - `( - ("julia-jllwrappers" ,julia-jllwrappers) - - ("julia-bzip2-jll" ,julia-bzip2-jll) - ("julia-freetype2-jll" ,julia-freetype2-jll) - ;("julia-fribidi-jll" ,julia-fribidi-jll) - ;("julia-zlib-jll" ,julia-zlib-jll) - )) + `(("julia-jllwrappers" ,julia-jllwrappers))) (inputs `(("fribidi" ,(@ (gnu packages fribidi) fribidi)))) (home-page "https://github.com/JuliaBinaryWrappers/FriBidi_jll.jl") @@ -4357,10 +4377,7 @@ wrappers.") ;; There's a Julia file for each platform, override them all (find-files "src/wrappers/" "\\.jl$"))))))) (propagated-inputs - `( - ("julia-jllwrappers" ,julia-jllwrappers) - ;("julia-ogg-jll" ,julia-ogg-jll) - )) + `(("julia-jllwrappers" ,julia-jllwrappers))) (inputs `(("libogg" ,(@ (gnu packages xiph) libogg)))) (home-page "https://github.com/JuliaBinaryWrappers/Ogg_jll.jl") @@ -4728,24 +4745,14 @@ wrappers.") (base32 "0hwzxwnak3sixm8jlm2zz6578gn713sbbznq49s11h38n0aczjx2")))) (build-system julia-build-system) - (arguments - `(#:tests? #f - )) (propagated-inputs - `( - ;; Only commented out to keep down the build times. - ;("julia-gr-jll" ,julia-gr-jll) - )) - (native-inputs - `( - ;("julia-distributions" ,julia-distributions) - )) + `(("julia-gr-jll" ,julia-gr-jll))) (home-page "https://github.com/jheinen/GR.jl") (synopsis "Plotting for Julia based on GR, a framework for visualisation applications") (description "This module provides a Julia interface to GR, a framework for visualisation applications.") (license license:expat))) -;; TODO: Unbundle fonts, add inputs? +;; TODO: Unbundle fonts (define-public gr-framework (package (name "gr-framework") @@ -4759,58 +4766,35 @@ wrappers.") (file-name (git-file-name name version)) (sha256 (base32 "05qch57acgj6bs1l634wczj0agj2v0b3j221iyk47zqhbimhk45y")) + (modules '((guix build utils))) + (snippet + '(begin + (delete-file-recursively "3rdparty") + #t)) )) (build-system cmake-build-system) (arguments - `(#:tests? #f ; no test target - ;#:configure-flags '("-DEARCUT_BUILD_BENCH=OFF" - ; "-DEARCUT_BUILD_VIZ=OFF" - ; ) - #:phases - (modify-phases %standard-phases - ;(delete 'configure) ; no configure script - (add-after 'unpack 'patch-source - (lambda* (#:key outputs #:allow-other-keys) - ;; Force using the shared library, -fPIC errors otherwise - (substitute* "cmake/FindQhull.cmake" - (("qhullstatic") "qhull_r")) - #t)) - ; (replace 'check - ; (lambda* (#:key tests? #:allow-other-keys) - ; (when tests? - ; (invoke "./tests")) - ; #t)) - ;; no install target, but no shared library either - ;(replace 'install - ; (lambda* (#:key outputs #:allow-other-keys) - ; (let ((out (assoc-ref outputs "out"))) - ) - )) - (propagated-inputs - `( - ;("julia-indexing" ,julia-indexing) - )) + `(#:tests? #f)) ; no test target (inputs `( - ;("glfw" ,(@ (gnu packages gl) glfw)) ; for VIZ - )) - (native-inputs - `( - ;("boost" ,(@ (gnu packages boost) boost)) ; not needed for tests? - ;;("julia-pooledarrays" ,julia-pooledarrays) + ("cairo" ,(S "cairo")) + ("ffmpeg" ,(S "ffmpeg")) ("freetype" ,(@ (gnu packages fontutils) freetype)) + ("glfw" ,(S "glfw")) ("libjpeg-turbo" ,(@ (gnu packages image) libjpeg-turbo)) ("libpng" ,(@ (gnu packages image) libpng)) - ;("libx11" ,(@ (gnu packages xorg) libx11)) - ;("libxft" ,(@ (gnu packages xorg) libxft)) - ;("libxt" ,(@ (gnu packages xorg) libxt)) - ("qhull" ,(@ (gnu packages maths) qhull)) + ("libtiff" ,(S "libtiff")) + ("libx11" ,(@ (gnu packages xorg) libx11)) + ("libxft" ,(@ (gnu packages xorg) libxft)) + ("libxt" ,(@ (gnu packages xorg) libxt)) + ("pixman" ,(S "pixman")) ("qtbase" ,(@ (gnu packages qt) qtbase)) + ("qhull" ,(@ (gnu packages maths) qhull)) ("zlib" ,zlib) )) (home-page "https://gr-framework.org/") - (synopsis "") - (description "") + (synopsis "Graphics library for visualisation applications") + (description "GR is a universal framework for cross-platform visualization applications. It offers developers a compact, portable and consistent graphics library for their programs. Applications range from publication quality 2D graphs to the representation of complex 3D scenes. GR is essentially based on an implementation of a @acronym{GKS, Graphical Kernel System}. As a self-contained system it can quickly and easily be integrated into existing applications (i.e. using the @code{ctypes} mechanism in Python or @code{ccall} in Julia).") (license license:expat))) (define-public julia-gr-jll @@ -4852,12 +4836,12 @@ wrappers.") ("julia-cairo-jll" ,julia-cairo-jll) ("julia-ffmpeg-jll" ,julia-ffmpeg-jll) ("julia-fontconfig-jll" ,julia-fontconfig-jll) - ;("julia-glfw-jll" ,julia-glfw-jll) + ("julia-glfw-jll" ,julia-glfw-jll) ("julia-jpegturbo-jll" ,julia-jpegturbo-jll) - ;("julia-libtiff-jll" ,julia-libtiff-jll) ("julia-libpng-jll" ,julia-libpng-jll) + ("julia-libtiff-jll" ,julia-libtiff-jll) ("julia-pixman-jll" ,julia-pixman-jll) - ;("julia-qt5base-jll" ,julia-qt5base-jll) + ("julia-qt5base-jll" ,julia-qt5base-jll) ("julia-zlib-jll" ,julia-zlib-jll) )) (home-page "https://github.com/JuliaBinaryWrappers/GR_jll.jl") @@ -4903,9 +4887,9 @@ wrappers.") ("julia-fontconfig-jll" ,julia-fontconfig-jll) ("julia-glib-jll" ,julia-glib-jll) ("julia-libpng-jll" ,julia-libpng-jll) - ;("julia-lzo-jll" ,julia-lzo-jll) + ("julia-lzo-jll" ,julia-lzo-jll) ("julia-pixman-jll" ,julia-pixman-jll) - ;("julia-xorg-libxrender-jll" ,julia-xorg-libxrender-jll) + ("julia-xorg-libxrender-jll" ,julia-xorg-libxrender-jll) ("julia-xorg-libxext-jll" ,julia-xorg-libxext-jll) ("julia-zlib-jll" ,julia-zlib-jll) )) @@ -5444,7 +5428,7 @@ wrappers.") `( ("julia-jllwrappers" ,julia-jllwrappers) ("julia-xorg-libxcb-jll" ,julia-xorg-libxcb-jll) - ;("julia-xorg-xtrans-jll" ,julia-xorg-xtrans-jll) + ("julia-xorg-xtrans-jll" ,julia-xorg-xtrans-jll) )) (home-page "https://github.com/JuliaBinaryWrappers/Xorg_libX11_jll.jl") (synopsis "LibX11 library wrappers") @@ -5454,7 +5438,7 @@ wrappers.") (define-public julia-xorg-libxcb-jll (package (name "julia-xorg-libxcb-jll") - (version "1.13.0+1") + (version "1.13.0+2") (source (origin (method git-fetch) @@ -5463,7 +5447,7 @@ wrappers.") (commit (string-append "Xorg_libxcb-v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0ahqkn7d4kjg929iy124pzz3w0r9kvz1nz0sy4d7a048i3r1ajwh")))) + (base32 "109m4r4v6ww31rq0klyqd3rf3j1yiycvld82d514d040w5027ssk")))) (build-system julia-build-system) (arguments '(#:tests? #f ; no runtests @@ -5483,12 +5467,1210 @@ wrappers.") (propagated-inputs `( ("julia-jllwrappers" ,julia-jllwrappers) - ;("julia-xorg-libxau-jll" ,julia-xorg-libxau-jll) - ;("julia-xorg-libpthreads-stubs-jll" ,julia-xorg-libpthreads-stubs-jll) - ;("julia-xorg-libxdcmp-jll" ,julia-xorg-libxdcmp-jll) - ;("julia-xslt-jll" ,julia-xslt-jll) + ("julia-xorg-libxau-jll" ,julia-xorg-libxau-jll) + ("julia-xorg-libpthread-stubs-jll" ,julia-xorg-libpthread-stubs-jll) + ("julia-xorg-libxdmcp-jll" ,julia-xorg-libxdmcp-jll) + ("julia-xslt-jll" ,julia-xslt-jll) )) (home-page "https://github.com/JuliaBinaryWrappers/Xorg_libxcb_jll.jl") (synopsis "Libxcb library wrappers") (description "This package provides a wrapper for the libxcb library.") (license license:expat))) + +(define-public julia-binaryprovider + (package + (name "julia-binaryprovider") + (version "0.5.10") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaPackaging/BinaryProvider.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "00kin10n3fv5352fx3a4wh8l581702iqqhfz2sng773hkljndi9v")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; test suite attempts to download packages + )) + (inputs + `( + ("busybox" ,(S "busybox")) + )) + (propagated-inputs + `( + )) + (home-page "https://github.com/JuliaPackaging/BinaryProvider.jl") + (synopsis "binary provider for Julia") + (description "Packages are installed to a Prefix; a folder that acts similar to the /usr/local directory on Unix-like systems, containing a bin folder for binaries, a lib folder for libraries, etc... Prefix objects can have tarballs install()'ed within them, uninstall()'ed from them, etc...") + (license license:expat))) + +(define-public julia-xorg-libxau-jll + (package + (name "julia-xorg-libxau-jll") + (version "1.0.9+3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_libXau_jll.jl") + (commit (string-append "Xorg_libXau-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1bc59hzg4jgdy0lwykp6avxsb87fq9j79c30yxprwjvxq8xm3p8z")))) + (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\"Xorg_libXau\"") + (string-append "\"" (assoc-ref inputs "libxau") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libxau" ,(@ (gnu packages xorg) libxau)))) + (propagated-inputs + `( + ("julia-jllwrappers" ,julia-jllwrappers) + )) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_libXau_jll.jl") + (synopsis "Libxau library wrappers") + (description "This package provides a wrapper for the libxau library.") + (license license:expat))) + +(define-public julia-xorg-libxdmcp-jll + (package + (name "julia-xorg-libxdmcp-jll") + (version "1.1.3+3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_libXdmcp_jll.jl") + (commit (string-append "Xorg_libXdmcp-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1ghw8c7ibkm2hv4h38qyhbxfmyizxszqv6fv8qzlb5031dmshnap")))) + (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\"Xorg_libXdmcp\"") + (string-append "\"" (assoc-ref inputs "libxdmcp") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libxdmcp" ,(@ (gnu packages xorg) libxdmcp)))) + (propagated-inputs + `( + ("julia-jllwrappers" ,julia-jllwrappers) + )) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_libXdmcp_jll.jl") + (synopsis "Libxdmcp library wrappers") + (description "This package provides a wrapper for the libxdmcp library.") + (license license:expat))) + +(define-public julia-xslt-jll + (package + (name "julia-xslt-jll") + (version "1.1.34+0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/XSLT_jll.jl") + (commit (string-append "XSLT-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0wjkfnrgpd7c6i4ga5xzsqqmfrxcdkr1kjsxmd9bff8cqvyknnhq")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"XSLT\", \"" + (assoc-ref inputs "libxslt") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libxslt" ,(S "libxslt")))) + (propagated-inputs + `( + ("julia-jllwrappers" ,julia-jllwrappers) + ("julia-libiconv-jll" ,julia-libiconv-jll) + ("julia-libgcrypt-jll" ,julia-libgcrypt-jll) + ("julia-libgpg-error-jll" ,julia-libgpg-error-jll) + ("julia-xml2-jll" ,julia-xml2-jll) + ("julia-zlib-jll" ,julia-zlib-jll) + )) + (home-page "https://github.com/JuliaBinaryWrappers/XSLT_jll.jl") + (synopsis "Xslt library wrappers") + (description "This package provides a wrapper for the libxslt library.") + (license license:expat))) + +(define-public julia-libgpg-error-jll + (package + (name "julia-libgpg-error-jll") + (version "1.42.0+0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Libgpg_error_jll.jl") + (commit (string-append "Libgpg_error-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0jmsn0mhn6b35b5awbrlpjjszknsplr62li574fkgwfxlfixb8iy")))) + (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 + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"Libgpg_error\", \"" + (assoc-ref inputs "libgpg-error") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libgpg-error" ,(S "libgpg-error")))) + (propagated-inputs + `( + ("julia-jllwrappers" ,julia-jllwrappers) + )) + (home-page "https://github.com/JuliaBinaryWrappers/Libgpg_error_jll.jl") + (synopsis "libgpg-error library wrappers") + (description "This package provides a wrapper for the libgpg-error library.") + (license license:expat))) + +(define-public julia-libgcrypt-jll + (package + (name "julia-libgcrypt-jll") + (version "1.8.7+0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Libgcrypt_jll.jl") + (commit (string-append "Libgcrypt-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "06fsdwrfw3f4cdbg1ssswznvj8ar3w5w4vxxag1hacs14pxlm5gi")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"Libgcrypt\", \"" + (assoc-ref inputs "libgcrypt") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libgcrypt" ,(S "libgcrypt")))) + (propagated-inputs + `( + ("julia-jllwrappers" ,julia-jllwrappers) + ("julia-libgpg-error-jll" ,julia-libgpg-error-jll) + )) + (home-page "https://github.com/JuliaBinaryWrappers/Libgcrypt_jll.jl") + (synopsis "libgcrypt library wrappers") + (description "This package provides a wrapper for the libgcrypt library.") + (license license:expat))) + +(define-public julia-xorg-libpthread-stubs-jll + (package + (name "julia-xorg-libpthread-stubs-jll") + (version "0.1.0+2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_libpthread_stubs_jll.jl") + (commit (string-append "Xorg_libpthread_stubs-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "161f4111xsb8xq4zs59jw95s94xfn1yxpii0p0dhn3yqgligggvx")))) + (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\"Xorg_libpthread_stubs\"") + (string-append "\"" (assoc-ref inputs "libpthread-stubs") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libpthread-stubs" ,(@ (gnu packages xorg) libpthread-stubs)))) + (propagated-inputs + `( + ("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xslt-jll" ,julia-xslt-jll) + )) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_libpthread_stubs_jll.jl") + (synopsis "Libpthread_stubs library wrappers") + (description "This package provides a wrapper for the libpthread_stubs library.") + (license license:expat))) + +(define-public julia-xorg-xtrans-jll + (package + (name "julia-xorg-xtrans-jll") + (version "1.4.0+2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_xtrans_jll.jl") + (commit (string-append "Xorg_xtrans-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "16rzkgc7l1j57l43v5ffrak164bdff7h1amm0y3mcnwjqmkig9dn")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Xorg_xtrans\"") + (string-append "\"" (assoc-ref inputs "xtrans") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("xtrans" ,(@ (gnu packages xorg) xtrans)))) + (propagated-inputs + `( + ("julia-jllwrappers" ,julia-jllwrappers) + )) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_xtrans_jll.jl") + (synopsis "xtrans library wrappers") + (description "This package provides a wrapper for the xtrans library.") + (license license:expat))) + +(define-public julia-xorg-libxrender-jll + (package + (name "julia-xorg-libxrender-jll") + (version "0.9.10+3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_libXrender_jll.jl") + (commit (string-append "Xorg_libXrender-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "041kjqpkgcjf72msg4zm4wja623wfsy9gmkqjvsj46lj885qizz7")))) + (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\"Xorg_libXrender\"") + (string-append "\"" (assoc-ref inputs "libxrender") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libxrender" ,(@ (gnu packages xorg) libxrender)))) + (propagated-inputs + `( + ("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-libx11-jll" ,julia-xorg-libx11-jll) + )) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_libXrender_jll.jl") + (synopsis "libXrender library wrappers") + (description "This package provides a wrapper for the libXrender library.") + (license license:expat))) + +(define-public julia-lzo-jll + (package + (name "julia-lzo-jll") + (version "2.10.1+0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/LZO_jll.jl") + (commit (string-append "LZO-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1gy57znz3b6pk902vgdzlrwrxib0bcfl0zr1prinfbr9vfmiv1h0")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"LZO\", \"" + (assoc-ref inputs "lzo") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("lzo" ,(S "lzo")))) + (propagated-inputs + `( + ("julia-jllwrappers" ,julia-jllwrappers) + )) + (home-page "https://github.com/JuliaBinaryWrappers/LZO_jll.jl") + (synopsis "lzo library wrappers") + (description "This package provides a wrapper for the lzo library.") + (license license:expat))) + +(define-public julia-glfw-jll + (package + (name "julia-glfw-jll") + (version "3.3.4+0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/GLFW_jll.jl") + (commit (string-append "GLFW-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "12r4g8x1pgfrx53wq1a2q0rj4p08q352mmci2px1j4bd0pwi8rc4")))) + (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 + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"GLFW\", \"" + (assoc-ref inputs "glfw") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("glfw" ,(S "glfw")))) + (propagated-inputs + `( + ("julia-jllwrappers" ,julia-jllwrappers) + ("julia-libglvnd-jll" ,julia-libglvnd-jll) + ("julia-xorg-libxcursor-jll" ,julia-xorg-libxcursor-jll) + ("julia-xorg-libxinerama-jll" ,julia-xorg-libxinerama-jll) + ("julia-xorg-libxrandr-jll" ,julia-xorg-libxrandr-jll) + ("julia-xorg-libxi-jll" ,julia-xorg-libxi-jll) + )) + (home-page "https://github.com/JuliaBinaryWrappers/GLFW_jll.jl") + (synopsis "glfw library wrappers") + (description "This package provides a wrapper for the glfw library.") + (license license:expat))) + +(define-public julia-libglvnd-jll + (package + (name "julia-libglvnd-jll") + (version "1.3.0+2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Libglvnd_jll.jl") + (commit (string-append "Libglvnd-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1lrppqj836saryqxj9xrqn0cih513qhijkhgqdww5azw8w917d3w")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Libglvnd\"") + (string-append "\"" (assoc-ref inputs "libglvnd") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libglvnd" ,(S "libglvnd")))) + (propagated-inputs + `( + ("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-libx11-jll" ,julia-xorg-libx11-jll) + ("julia-xorg-libxext-jll" ,julia-xorg-libxext-jll) + )) + (home-page "https://github.com/JuliaBinaryWrappers/Libglvnd_jll.jl") + (synopsis "libglvnd library wrappers") + (description "This package provides a wrapper for the libglvnd library.") + (license license:expat))) + +(define-public julia-xorg-libxcursor-jll + (package + (name "julia-xorg-libxcursor-jll") + (version "1.2.0+3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_libXcursor_jll.jl") + (commit (string-append "Xorg_libXcursor-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0hxhpsjw1zk30qphrp90g1wvqfs1hr47qifn1gqgx73ci5nmq0y7")))) + (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\"Xorg_libXcursor\"") + (string-append "\"" (assoc-ref inputs "libxcursor") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libxcursor" ,(S "libxcursor")))) + (propagated-inputs + `( + ("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-libxfixes-jll" ,julia-xorg-libxfixes-jll) + ("julia-xorg-libxrender-jll" ,julia-xorg-libxrender-jll) + )) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_libXcursor_jll.jl") + (synopsis "xorg-libxcursor library wrappers") + (description "This package provides a wrapper for the xorg-libxcursor library.") + (license license:expat))) + +(define-public julia-xorg-libxfixes-jll + (package + (name "julia-xorg-libxfixes-jll") + (version "5.0.3+3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_libXfixes_jll.jl") + (commit (string-append "Xorg_libXfixes-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0sjpclxinbcq3msnaqdfqlpfhnlvl15qn7dam968i4qwrpyv43dv")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Xorg_libXfixes\"") + (string-append "\"" (assoc-ref inputs "libxfixes") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libxfixes" ,(S "libxfixes")))) + (propagated-inputs + `( + ("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-libx11-jll" ,julia-xorg-libx11-jll) + )) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_libXfixes_jll.jl") + (synopsis "xorg-libxfixes library wrappers") + (description "This package provides a wrapper for the xorg-libxfixes library.") + (license license:expat))) + +(define-public julia-xorg-libxi-jll + (package + (name "julia-xorg-libxi-jll") + (version "1.7.10+3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_libXi_jll.jl") + (commit (string-append "Xorg_libXi-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1jhrng5sf44880x3pnw1gpb88z21c7nznfyzhs4a5z910ndrynd7")))) + (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\"Xorg_libXi\"") + (string-append "\"" (assoc-ref inputs "libxi") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libxi" ,(S "libxi")))) + (propagated-inputs + `( + ("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-libxext-jll" ,julia-xorg-libxext-jll) + ("julia-xorg-libxfixes-jll" ,julia-xorg-libxfixes-jll) + )) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_libXi_jll.jl") + (synopsis "xorg-libxi library wrappers") + (description "This package provides a wrapper for the xorg-libxi library.") + (license license:expat))) + +(define-public julia-xorg-libxinerama-jll + (package + (name "julia-xorg-libxinerama-jll") + (version "1.1.4+3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_libXinerama_jll.jl") + (commit (string-append "Xorg_libXinerama-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0jybxbqxd4jc9ka3rk3v5yh8ps2fapdibldr7bymllzw1w2i25rn")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Xorg_libXinerama\"") + (string-append "\"" (assoc-ref inputs "libxinerama") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libxinerama" ,(S "libxinerama")))) + (propagated-inputs + `( + ("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-libxext-jll" ,julia-xorg-libxext-jll) + )) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_libXinerama_jll.jl") + (synopsis "xorg-libxinerama library wrappers") + (description "This package provides a wrapper for the xorg-libxinerama library.") + (license license:expat))) + +(define-public julia-xorg-libxrandr-jll + (package + (name "julia-xorg-libxrandr-jll") + (version "1.5.2+3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_libXrandr_jll.jl") + (commit (string-append "Xorg_libXrandr-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0y4gsw5x643qdamf932agzdlyayzp63pn8j7j0lckd6dzqfdz46g")))) + (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\"Xorg_libXrandr\"") + (string-append "\"" (assoc-ref inputs "libxrandr") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libxrandr" ,(S "libxrandr")))) + (propagated-inputs + `( + ("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-libxext-jll" ,julia-xorg-libxext-jll) + ("julia-xorg-libxrender-jll" ,julia-xorg-libxrender-jll) + )) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_libXrandr_jll.jl") + (synopsis "xorg-libxrandr library wrappers") + (description "This package provides a wrapper for the xorg-libxrandr library.") + (license license:expat))) + +(define-public julia-libtiff-jll + (package + (name "julia-libtiff-jll") + (version "4.1.0+1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Libtiff_jll.jl") + (commit (string-append "Libtiff-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "07zzhmwmh2g4645ghv76z40hza2ghlb7sw15b1pii7f9kfcsgf45")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Libtiff\"") + (string-append "\"" (assoc-ref inputs "libtiff") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libtiff" ,(S "libtiff")))) + (propagated-inputs + `( + ("julia-jllwrappers" ,julia-jllwrappers) + ("julia-jpegturbo-jll" ,julia-jpegturbo-jll) + ("julia-zlib-jll" ,julia-zlib-jll) + ("julia-zstd-jll" ,julia-zstd-jll) + )) + (home-page "https://github.com/JuliaBinaryWrappers/Libtiff_jll.jl") + (synopsis "libtiff library wrappers") + (description "This package provides a wrapper for the libtiff library.") + (license license:expat))) + +(define-public julia-qt5base-jll + (package + (name "julia-qt5base-jll") + (version "5.15.2+0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Qt5Base_jll.jl") + (commit (string-append "Qt5Base-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1hhs316dl2jy56y2j4809vwpfj6ffbjchl1a27x44mmh9bj7vxzy")))) + (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 + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"Qt5Base\", \"" + (assoc-ref inputs "qtbase") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("qtbase" ,(S "qtbase")))) + (propagated-inputs + `( + ("julia-jllwrappers" ,julia-jllwrappers) + ("julia-libglvnd-jll" ,julia-libglvnd-jll) + ("julia-compilersupportlibraries-jll" ,julia-compilersupportlibraries-jll) + ("julia-fontconfig-jll" ,julia-fontconfig-jll) + ("julia-glib-jll" ,julia-glib-jll) + ("julia-openssl-jll" ,julia-openssl-jll) + ("julia-xkbcommon-jll" ,julia-xkbcommon-jll) + ("julia-xorg-libxcb-jll" ,julia-xorg-libxcb-jll) + ("julia-xorg-libxext-jll" ,julia-xorg-libxext-jll) + ("julia-xorg-xcb-util-image-jll" ,julia-xorg-xcb-util-image-jll) + ("julia-xorg-xcb-util-keysyms-jll" ,julia-xorg-xcb-util-keysyms-jll) + ("julia-xorg-xcb-util-renderutil-jll" ,julia-xorg-xcb-util-renderutil-jll) + ("julia-xorg-xcb-util-wm-jll" ,julia-xorg-xcb-util-wm-jll) + ("julia-zlib-jll" ,julia-zlib-jll) + )) + (home-page "https://github.com/JuliaBinaryWrappers/Qt5Base_jll.jl") + (synopsis "qt5base library wrappers") + (description "This package provides a wrapper for the qt5base library.") + (license license:expat))) + +(define-public julia-xkbcommon-jll + (package + (name "julia-xkbcommon-jll") + (version "0.9.1+3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/xkbcommon_jll.jl") + (commit (string-append "xkbcommon-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1g2gmd3mj1p369kzvrd02ldgr9s712vs9774v1phb59jxlshc0zc")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"xkbcommon\"") + (string-append "\"" (assoc-ref inputs "libxkbcommon") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libxkbcommon" ,(S "libxkbcommon")))) + (propagated-inputs + `( + ("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-xkeyboard-config-jll" ,julia-xorg-xkeyboard-config-jll) + ("julia-xorg-libxcb-jll" ,julia-xorg-libxcb-jll) + ("julia-wayland-jll" ,julia-wayland-jll) + ("julia-wayland-protocols-jll" ,julia-wayland-protocols-jll) + )) + (home-page "https://github.com/JuliaBinaryWrappers/xkbcommon_jll.jl") + (synopsis "xkbcommon library wrappers") + (description "This package provides a wrapper for the xkbcommon library.") + (license license:expat))) + +(define-public julia-xorg-xkeyboard-config-jll + (package + (name "julia-xorg-xkeyboard-config-jll") + (version "2.27.0+3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_xkeyboard_config_jll.jl") + (commit (string-append "Xorg_xkeyboard_config-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1lgynzxd0mn64zbf0njqkd1hz1illqnl3p7hi9abwh5vbdf4pwhw")))) + (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\"Xorg_xkeyboard_config\"") + (string-append "\"" (assoc-ref inputs "xkeyboard-config") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("xkeyboard-config" ,(S "xkeyboard-config")))) + (propagated-inputs + `( + ("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-xkbcomp-jll" ,julia-xorg-xkbcomp-jll) + )) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_xkeyboard_config_jll.jl") + (synopsis "xkeyboard-config library wrappers") + (description "This package provides a wrapper for the xkeyboard-config library.") + (license license:expat))) + +(define-public julia-xorg-xkbcomp-jll + (package + (name "julia-xorg-xkbcomp-jll") + (version "1.4.2+3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_xkbcomp_jll.jl") + (commit (string-append "Xorg_xkbcomp-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1rkb9525iq0jjpq8v333b728kfillgixxsim37mqdplad85l36wl")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Xorg_xkbcomp\"") + (string-append "\"" (assoc-ref inputs "xkbcomp") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("xkbcomp" ,(S "xkbcomp")))) + (propagated-inputs + `( + ("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-libxkbfile-jll" ,julia-xorg-libxkbfile-jll) + )) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_xkbcomp_jll.jl") + (synopsis "libxkbcomp library wrappers") + (description "This package provides a wrapper for the libxkbcomp library.") + (license license:expat))) + +(define-public julia-xorg-libxkbfile-jll + (package + (name "julia-xorg-libxkbfile-jll") + (version "1.1.0+3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_libxkbfile_jll.jl") + (commit (string-append "Xorg_libxkbfile-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0zrnrixz34h54n0c06ziaxcajvndydzgxxh5jbvqx1xrij5rw5gy")))) + (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\"Xorg_libxkbfile\"") + (string-append "\"" (assoc-ref inputs "libxkbfile") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("libxkbfile" ,(S "libxkbfile")))) + (propagated-inputs + `( + ("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-libx11-jll" ,julia-xorg-libx11-jll) + )) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_libxkbfile_jll.jl") + (synopsis "libxkbfile library wrappers") + (description "This package provides a wrapper for the libxkbfile library.") + (license license:expat))) + +(define-public julia-wayland-jll + (package + (name "julia-wayland-jll") + (version "1.17.0+3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Wayland_jll.jl") + (commit (string-append "Wayland-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1w53inz62va3f022pgw3rfw5z5vgiv8z9dg3lfzpjrdb0lcd6ab6")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Wayland\"") + (string-append "\"" (assoc-ref inputs "wayland") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("wayland" ,(S "wayland")))) + (propagated-inputs + `( + ("julia-jllwrappers" ,julia-jllwrappers) + ("julia-expat-jll" ,julia-expat-jll) + ("julia-libffi-jll" ,julia-libffi-jll) + ("julia-xml2-jll" ,julia-xml2-jll) + )) + (home-page "https://github.com/JuliaBinaryWrappers/Wayland_jll.jl") + (synopsis "wayland library wrappers") + (description "This package provides a wrapper for the wayland library.") + (license license:expat))) + +(define-public julia-wayland-protocols-jll + (package + (name "julia-wayland-protocols-jll") + (version "1.18.0+3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Wayland_protocols_jll.jl") + (commit (string-append "Wayland_protocols-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1dc9d2wzgybqjlg8l7f4ridkv2d66dg3lb3zihnl0k64psibn4x9")))) + (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\"Wayland_protocols\"") + (string-append "\"" (assoc-ref inputs "wayland-protocols") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("wayland-protocols" ,(S "wayland-protocols")))) + (propagated-inputs + `( + ("julia-jllwrappers" ,julia-jllwrappers) + ("julia-wayland-jll" ,julia-wayland-jll) + )) + (home-page "https://github.com/JuliaBinaryWrappers/Wayland_protocols_jll.jl") + (synopsis "wayland-protocols library wrappers") + (description "This package provides a wrapper for the wayland-protocols library.") + (license license:expat))) + +(define-public julia-xorg-xcb-util-wm-jll + (package + (name "julia-xorg-xcb-util-wm-jll") + (version "0.4.1+1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_xcb_util_wm_jll.jl") + (commit (string-append "Xorg_xcb_util_wm-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0g6jhfb3l04lrx3cm3b8wc0pp5271dpncwin5pg94nljdj4mgj53")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Xorg_xcb_util_wm\"") + (string-append "\"" (assoc-ref inputs "xcb-util-wm") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("xcb-util-wm" ,(S "xcb-util-wm")))) + (propagated-inputs + `( + ("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-xcb-util-jll" ,julia-xorg-xcb-util-jll) + )) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_xcb_util_wm_jll.jl") + (synopsis "xcb-util-wm library wrappers") + (description "This package provides a wrapper for the xcb-util-wm library.") + (license license:expat))) + +(define-public julia-xorg-xcb-util-jll + (package + (name "julia-xorg-xcb-util-jll") + (version "0.4.0+1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_xcb_util_jll.jl") + (commit (string-append "Xorg_xcb_util-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0jywbxwf9x2naqsh9hh231bqpphh15v7cdhijcspjfggwkyq1npi")))) + (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\"Xorg_xcb_util\"") + (string-append "\"" (assoc-ref inputs "xcb-util") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("xcb-util" ,(S "xcb-util")))) + (propagated-inputs + `( + ("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-libxcb-jll" ,julia-xorg-libxcb-jll) + )) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_xcb_util_jll.jl") + (synopsis "xcb-util library wrappers") + (description "This package provides a wrapper for the xcb-util library.") + (license license:expat))) + +(define-public julia-xorg-xcb-util-image-jll + (package + (name "julia-xorg-xcb-util-image-jll") + (version "0.4.0+1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_xcb_util_image_jll.jl") + (commit (string-append "Xorg_xcb_util_image-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1f9xx094nylg7dcfxm0qmph4xy492rd3yxa8arijqyi6rs8zrgxz")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Xorg_xcb_util_image\"") + (string-append "\"" (assoc-ref inputs "xcb-util-image") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("xcb-util-image" ,(S "xcb-util-image")))) + (propagated-inputs + `( + ("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-xcb-util-jll" ,julia-xorg-xcb-util-jll) + )) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_xcb_util_image_jll.jl") + (synopsis "xcb-util-image library wrappers") + (description "This package provides a wrapper for the xcb-util-image library.") + (license license:expat))) + +(define-public julia-xorg-xcb-util-keysyms-jll + (package + (name "julia-xorg-xcb-util-keysyms-jll") + (version "0.4.0+1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_xcb_util_keysyms_jll.jl") + (commit (string-append "Xorg_xcb_util_keysyms-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "03i3fw9p16rpjnki80w4rhmaiqvjlfsr94bf9yizndqsw1lcq42l")))) + (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\"Xorg_xcb_util_keysyms\"") + (string-append "\"" (assoc-ref inputs "xcb-util-keysyms") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("xcb-util-keysyms" ,(S "xcb-util-keysyms")))) + (propagated-inputs + `( + ("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-xcb-util-jll" ,julia-xorg-xcb-util-jll) + )) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_xcb_util_keysyms_jll.jl") + (synopsis "xcb-util-keysyms library wrappers") + (description "This package provides a wrapper for the xcb-util-keysyms library.") + (license license:expat))) + +(define-public julia-xorg-xcb-util-renderutil-jll + (package + (name "julia-xorg-xcb-util-renderutil-jll") + (version "0.3.9+1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Xorg_xcb_util_renderutil_jll.jl") + (commit (string-append "Xorg_xcb_util_renderutil-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1zxz459sxma7cv32x2y8fnvwdz1f37fq0xhkihdsnkfdl761gn1a")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("artifact\"Xorg_xcb_util_renderutil\"") + (string-append "\"" (assoc-ref inputs "xcb-util-renderutil") "\"")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + `(("xcb-util-renderutil" ,(S "xcb-util-renderutil")))) + (propagated-inputs + `( + ("julia-jllwrappers" ,julia-jllwrappers) + ("julia-xorg-xcb-util-jll" ,julia-xorg-xcb-util-jll) + )) + (home-page "https://github.com/JuliaBinaryWrappers/Xorg_xcb_util_renderutil_jll.jl") + (synopsis "xcb-util-renderutil library wrappers") + (description "This package provides a wrapper for the xcb-util-renderutil library.") + (license license:expat))) diff --git a/gn/services/pluto.scm b/gn/services/pluto.scm index 3df804c..76a45c2 100644 --- a/gn/services/pluto.scm +++ b/gn/services/pluto.scm @@ -16,42 +16,21 @@ pluto-configuration? (package pluto-configuration-package ; package (default julia-visuals)) + ;; TODO: Currently port 4343 is hardcoded in the package definition. (port pluto-configuration-port ; integer (default 80))) (define %julia-account (list (user-group (name "julia") - ;(system? #t) - ) + (system? #t)) (user-account (name "julia") (group "julia") - ;(system? #t) + (system? #t) (comment "Julia User") (home-directory "/home/jovyan") - ;(shell (file-append shadow "/sbin/nologin")) - ))) - -;(define pluto-activation -; (match-lambda -; (($ <ratspub-configuration> package) -; #~(begin -; (let ((nltk_data "/var/cache/nltk_data/tokenizers") -; (data_dir "/export/ratspub")) -; (unless (file-exists? "/export2/PubMed") -; (mkdir-p "/export2/PubMed")) -; (unless (file-exists? nltk_data) -; (begin -; ;; The correct way would be to use python-nltk to download the data -; ;; python3 -m nltk.downloader -d /var/cache/nltk_data punkt -; (mkdir-p nltk_data) -; (chdir nltk_data) -; (invoke #$(file-append unzip "/bin/unzip") "-q" #$%punkt.zip))) -; (unless (file-exists? (string-append data_dir "/userspub.sqlite")) -; (begin -; (install-file #$(file-append package "/userspub.sqlite") data_dir) -; (chmod (string-append data_dir "/userspub.sqlite") #o554)))))))) + (shell (file-append shadow "/sbin/nologin"))))) (define pluto-shepherd-service (match-lambda @@ -66,22 +45,15 @@ (gnu system file-systems))) (start #~(make-forkexec-constructor/container (list #$(file-append package "/runpluto.sh") #$port) - ;; Needs to run from the directory it is located in. - ;#:directory #$package #:log-file "/var/log/pluto.log" - ;; We don't need to set TMPDIR because we're inside a container. #:user "julia" #:group "julia" - #:environment-variables - '(;"JULIA_PROJECT=/home/jovyan" - ;"JULIA_LOAD_PATH=/run/current-system/profile/share/julia/packages/" - ) + ;; This needs to exist. Unclear why. + #:environment-variables '() #:mappings (list (file-system-mapping (source "/home/jovyan") (target source) - (writable? #t)) - ) - )) + (writable? #t))))) (stop #~(make-kill-destructor)))))))) (define pluto-service-type @@ -91,13 +63,8 @@ (list (service-extension shepherd-root-service-type pluto-shepherd-service) - ;(service-extension activation-service-type - ; ratspub-activation) (service-extension account-service-type - (const %julia-account)) - ;; Make sure we get all the dependencies of julia-visuals. - (service-extension profile-service-type - (compose list pluto-configuration-package)))) + (const %julia-account)))) (default-value (pluto-configuration)) (description "Run a Pluto Jupyter Webserver."))) @@ -118,9 +85,7 @@ ;; (kernel linux-libre-vm) ;; No firmware for VMs. (firmware '()) - (packages ;(list nss-certs) - %base-packages - ) + (packages (list nss-certs)) (services (list (service pluto-service-type (pluto-configuration @@ -130,5 +95,5 @@ ;; For docker it isn't necessary to list the shared folders at build time. ;; guix system docker-image -L /path/to/guix-bioinformatics/ -L /path/to/guix-past/modules/ /path/to/guix-bioinformatics/gn/services/pluto.scm --network ;; Docker instructions: -;; docker load --input pluto-docker-image.tar.gz +;; docker load --input guix-docker-image.tar.gz ;; docker run -d --privileged --net=host --name pluto guix |