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authorEfraim Flashner2021-09-30 14:28:51 +0300
committerEfraim Flashner2021-09-30 14:28:51 +0300
commitdd13ae09c669a8af2360eede90e2b9cc453fe82d (patch)
tree6204673393aaa34d6a97892768867c890cefeeb8 /gn/packages
parent8e59af5447699a26518427e0a761437e2e5cc9fa (diff)
downloadguix-bioinformatics-dd13ae09c669a8af2360eede90e2b9cc453fe82d.tar.gz
gn: julia packages upstreamed
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/julia.scm390
1 files changed, 0 insertions, 390 deletions
diff --git a/gn/packages/julia.scm b/gn/packages/julia.scm
index 8042fac..7e181a9 100644
--- a/gn/packages/julia.scm
+++ b/gn/packages/julia.scm
@@ -236,82 +236,6 @@ module. PyPlot uses the Julia PyCall package to call Matplotlib directly from
Julia with little or no overhead (arrays are passed without making a copy).")
(license license:expat))))
-;; ready to upstream
-(define-public julia-pycall
- (package
- (name "julia-pycall")
- (version "1.92.3")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/JuliaPy/PyCall.jl")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "07r99ni6nkxpyrp3wsb5qg4jxz7i2r08dyqbiffy2zm3g0bn88jq"))))
- (build-system julia-build-system)
- (arguments
- `(#:imported-modules ((guix build python-build-system)
- ,@%julia-build-system-modules)
- #:modules ((guix build julia-build-system)
- (guix build utils)
- ((guix build python-build-system) #:prefix python:))
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'remove-conda
- (lambda _
- (substitute* "Project.toml"
- ((".*Conda.*") ""))
- (substitute* (list "src/PyCall.jl"
- "test/runtests.jl")
- (("import Conda") ""))
- (substitute* "deps/depsutils.jl"
- (("Conda.PYTHONDIR") "\"/\""))
- #t))
- (add-after 'unpack 'set-python
- (lambda* (#:key inputs outputs #:allow-other-keys)
- (let ((python (assoc-ref inputs "python")))
- (setenv "PYCALL_JL_RUNTIME_PYTHON"
- (string-append python "/bin/python3"))
- (with-output-to-file "deps/deps.jl"
- (lambda _
- (format #t
- "const python = \"~a/bin/python3\"~@
- const pyprogramname = \"~a/bin/python3\"~@
- const libpython = \"~a/lib/libpython~a.so.1.0\"~@
- const PYTHONHOME = \"~a\"~@
- const pyversion_build = v\"~a\"~@
- const conda = false~%"
- python
- python
- python
- (python:python-version python)
- python
- ,(package-version python))))
- #t)))
- (add-before 'check 'pre-check
- (lambda _
- (setenv "CI" "true")
- (setenv "JULIA_PKGEVAL" "true")
- #t)))))
- (propagated-inputs
- `(("julia-macrotools" ,julia-macrotools)
- ("julia-versionparsing" ,julia-versionparsing)))
- (inputs
- `(("python" ,python)))
- (native-inputs
- `(("python-numpy" ,(@ (gnu packages python-xyz) python-numpy))))
- (home-page "https://github.com/JuliaPy/PyCall.jl")
- (synopsis "Call Python functions from the Julia language")
- (description "This package provides the ability to directly call and fully
-interoperate with Python from the Julia language. You can import arbitrary
-Python modules from Julia, call Python functions (with automatic conversion of
-types between Julia and Python), define Python classes from Julia methods, and
-share large data structures between Julia and Python without copying them.")
- (license license:expat)))
-
(define-public julia-conda
(package
(name "julia-conda")
@@ -439,239 +363,6 @@ properties
@end enumerate")
(license license:expat)))
-;; ready to upstream!
-;; By removing all the javascript and css downloads any HTML documentation
-;; produced by this package will not be very useful.
-(define-public julia-documenter
- (package
- (name "julia-documenter")
- (version "0.27.6")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/JuliaDocs/Documenter.jl")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32 "1y6rql7cxc7hfhc8rfq1mdmffp70sqzyh4vnnq93fziwrc8c8sbj"))))
- (build-system julia-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'patch-source
- (lambda* (#:key inputs #:allow-other-keys)
- (substitute* "src/Deps.jl"
- (("pip install")
- (string-append (assoc-ref inputs "python")
- "/bin/pip install")))
- #t))
- (add-after 'unpack 'remove-javascript-downloads
- (lambda _
- (substitute* "src/Writers/HTMLWriter.jl"
- (("cdnjs.cloudflare.com") "example.com"))
- ;; Removing the javascript downloads causes these tests fail.
- (substitute* "test/examples/tests.jl"
- ((".*Main\\.examples_html_doc.*") "")
- ((".*Main\\.examples_html_mathjax3_doc.*") ""))
- #t)))))
- (propagated-inputs
- `(("julia-ansicoloredprinters" ,julia-ansicoloredprinters)
- ("julia-docstringextensions" ,julia-docstringextensions)
- ("julia-iocapture" ,julia-iocapture)
- ("julia-json" ,julia-json)))
- (inputs
- `(("python" ,python-wrapper)))
- (native-inputs
- `(("git" ,(S "git-minimal"))
- ("julia-documentermarkdown" ,julia-documentermarkdown)
- ("julia-documentertools" ,julia-documentertools)))
- (home-page "https://juliadocs.github.io/Documenter.jl")
- (synopsis "Documentation generator for Julia")
- (description "This package provides a documentation generator for Julia.")
- (license license:expat)))
-
-;; ready to upstream with julia-documenter
-(define-public julia-documenter-0.22
- (package
- (inherit julia-documenter)
- (name "julia-documenter")
- (version "0.22.6")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/JuliaDocs/Documenter.jl")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "1z8b7267y7yn5nx8sjwkmc0ph97vmv42q52jg7s89ghqb9xx3wv5"))))
- (arguments
- `(#:tests? #f ; Some tests require network.
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'remove-javascript-downloads
- (lambda _
- ;; This isn't problematic because we only use
- ;; this package for bootstrapping.
- (substitute* '("assets/html/documenter.js"
- "assets/html/search.js"
- "src/Writers/HTMLWriter.jl")
- (("cdnjs.cloudflare.com") "example.com"))
- #t)))))
- (propagated-inputs
- `(("julia-docstringextensions" ,julia-docstringextensions)
- ("julia-json" ,julia-json)))
- (inputs `())
- (native-inputs `())
- (properties '((hidden? . #t)))))
-
-;; ready to upstream; depends on julia-documenter
-(define-public julia-documentermarkdown
- (package
- (name "julia-documentermarkdown")
- (version "0.2.2")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/JuliaDocs/DocumenterMarkdown.jl")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32 "0sx89hi5p2f8zi2rp5qrv06m270d90pxj5d2y5cxls1spax7wqx8"))))
- (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)))
- (home-page "https://github.com/JuliaDocs/DocumenterMarkdown.jl")
- (synopsis "Documenter's Markdown")
- (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)
- (arguments
- `(#:tests? #f)) ; Tests require network.
- (inputs
- ;; We don't want to propagate the bootstrap version.
- ;; Cycle with Documenter.jl in later versions.
- `(("julia-documenter" ,julia-documenter-0.22)))
- (propagated-inputs
- `(("julia-docstringextensions" ,julia-docstringextensions)
- ("julia-gumbo" ,julia-gumbo)
- ("julia-sass" ,julia-sass)))
- (native-inputs
- `(("julia-example" ,julia-example)))
- (home-page "https://github.com/JuliaDocs/DocumenterTools.jl")
- (synopsis "Extra tools for setting up Documenter")
- (description "This package contains utilities for setting up documentation
-generation with @code{Documenter.jl}.")
- (license license:expat)))
-
-;; raedy to upstream
-(define-public julia-ansicoloredprinters
- (package
- (name "julia-ansicoloredprinters")
- (version "0.0.1")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/JuliaDocs/ANSIColoredPrinters.jl")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32 "0dp5agljr0g50s5gn0pr70wrz01ggck6pb40ay3l4szhswq7mqzf"))))
- (build-system julia-build-system)
- (home-page "https://github.com/JuliaDocs/ANSIColoredPrinters.jl")
- (synopsis "ANSI escape code translator")
- (description "@code{ANSIColoredPrinters.jl} converts a text qualified by
-ANSI escape codes to another format.")
- (license license:expat)))
-
-;; ready to upstream
-(define-public julia-sass
- (package
- (name "julia-sass")
- (version "0.2.0")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/piever/Sass.jl")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32 "0y7kkkj717h5cj659ssry89i5r64symr6pvhr6vv4qmaxrnjxj92"))))
- (build-system julia-build-system)
- (propagated-inputs
- `(("julia-libsass-jll" ,julia-libsass-jll)))
- (home-page "https://github.com/piever/Sass.jl")
- (synopsis "Compile scss and sass file to css in Julia")
- (description "This library provides a simple Julian API to use the
-@code{libsass} library to compile scss and sass files to css.")
- (license license:expat)))
-
-;; ready to upstream
-(define-public julia-libsass-jll
- (let ((commit "69bf10603aad0ebf1f6df088c5fd7c4a5d1eb0ca"))
- (package
- (name "julia-libsass-jll")
- (version "3.5.5+0") ;tag not created upstream
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/JuliaBinaryWrappers/libsass_jll.jl")
- (commit commit)))
- (file-name (git-file-name name version))
- (sha256
- (base32 "1fb6rf422533bsmfslvc20ag1hr50bf9xaj32rvh7nv593sbiygn"))))
- (build-system julia-build-system)
- (arguments
- `(#:tests? #f ; no runtests.jl
- #:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'override-binary-path
- (lambda* (#:key inputs #:allow-other-keys)
- (map
- (lambda (wrapper)
- (substitute* wrapper
- (("generate_wrapper_header.*")
- (string-append
- "generate_wrapper_header(\"libsass\", \""
- (assoc-ref inputs "libsass") "\")\n"))))
- ;; There's a Julia file for each platform, override them all
- (find-files "src/wrappers/" "\\.jl$"))
- #t)))))
- (inputs
- `(("libsass" ,(@ (gnu packages web) libsass))))
- (propagated-inputs
- `(("julia-jllwrappers" ,julia-jllwrappers)))
- (home-page "https://github.com/JuliaBinaryWrappers/libsass_jll.jl")
- (synopsis "Julia wrapper for libsass")
- (description "This package provides a wrapper for libsass. It is an
-autogenerated source package constructed using @code{BinaryBuilder.jl}. The
-originating @code{build_tarballs.jl} script can be found on the community
-build tree Yggdrasil.")
- (license license:expat))))
-
;; ready to upstream
;; if the test suite passes
(define-public julia-optim
@@ -998,29 +689,6 @@ metaprogramming on Julia Expr, the meta programming standard library for
(license license:expat)))
;; ready to upstream
-(define-public julia-mlstyle
- (package
- (name "julia-mlstyle")
- (version "0.4.10")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/thautwarm/MLStyle.jl")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32 "0h1cd7cr4c4cnpqyj3180113gdbvcc047lqphp8a8gq5smp3c059"))))
- (build-system julia-build-system)
- (native-inputs
- `(("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)))
-
-;; ready to upstream
(define-public julia-statsfuns
(package
(name "julia-statsfuns")
@@ -1778,61 +1446,3 @@ in Julia).")
(synopsis "binary provider for Julia")
(description "Packages are installed to a @code{Prefix}; a folder that acts similar to the @code{/usr/local} directory on Unix-like systems, containing a @code{bin} folder for binaries, a @code{lib} folder for libraries, etc... @code{Prefix} objects can have tarballs @code{install()}'ed within them, @code{uninstall()}'ed from them, etc...")
(license license:expat)))
-
-;; ready to upstream
-(define-public julia-measurements
- (package
- (name "julia-measurements")
- (version "2.6.0")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/JuliaPhysics/Measurements.jl")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32 "05p3f0gr4sv4maq8cix5fi8ldq0zagswqsd43xn6fhy046f936mz"))))
- (build-system julia-build-system)
- (propagated-inputs
- `(("julia-calculus" ,julia-calculus)
- ("julia-recipesbase" ,julia-recipesbase)
- ("julia-requires" ,julia-requires)))
- (native-inputs
- `(("julia-specialfunctions" ,julia-specialfunctions)
- ("julia-quadgk" ,julia-quadgk)
- ("julia-unitful" ,julia-unitful)))
- (home-page "https://juliaphysics.github.io/Measurements.jl/stable/")
- (synopsis "Error propagation calculator and library")
- (description "@code{Measurements.jl} is an error propagation calculator and
-library for physical measurements. It supports real and complex numbers with
-uncertainty, arbitrary precision calculations, operations with arrays, and
-numerical integration. The linear error propagation theory is employed to
-propagate the errors.")
- (license license:expat)))
-
-;; ready to upstream
-(define-public julia-quadgk
- (package
- (name "julia-quadgk")
- (version "2.4.1")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/JuliaMath/QuadGK.jl")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32 "1hy0629yai6xflgxaflk9764lzr1lzhlghimxk1aqi212q9c6n33"))))
- (build-system julia-build-system)
- (propagated-inputs
- `(("julia-datastructures" ,julia-datastructures)))
- (home-page "https://github.com/JuliaMath/QuadGK.jl")
- (synopsis "Adaptive 1d numerical Gauss–Kronrod integration in Julia")
- (description "This package provides support for one-dimensional numerical
-integration in Julia using adaptive Gauss-Kronrod quadrature. The code was
-originally part of Base Julia. It supports integration of arbitrary numeric
-types, including arbitrary precision (@code{BigFloat}), and even integration of
-arbitrary normed vector spaces (e.g. matrix-valued integrands).")
- (license license:expat)))