gn: julia packages upstreamed

2 files changed, 1 insertions, 391 deletions

diff --git a/VERSION b/VERSION
index 9ee1073..78cb503 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-2ca982ff41270288913ad6b7d5d9e1cad87b06d9
+7b59508ca711d1fe299de3f8d9710da36aeb6829
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)))