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build-system/julia: Enable Julia Pkg to find installed packages.

Browse source 
Julia's built-in package manager (Pkg) looks for packages in
JULIA_DEPOT_PATH/packages/PACKAGENAME/XXXX, where XXXX is a string
encoding package UUID and SHA1 of files.  The link-depot phase creates
a link at the correct location to allow Pkg to find packages that were
already installed by Guix.

* guix/build/julia-build-system.scm (link-depot): New phase.
(%package-path): Modified package path from packages/ to loadpath/.
(project.toml->uuid): New procedure, retrive package uuid from TOML file.
(precompile, check): Adjust to the change in paths.
(%standard-phases): Add link-depot phase.
(julia-build): Add julia-package-uuid keyword.
* guix/build-system/julia.scm (julia-build): Also use the
julia-package-uuid keyword.
* gnu/packages/julia-jll.scm (julia-bzip2-jll, julia-cairo-jll,
julia-compilersupportlibraries-jll, julia-expat-jll, julia-ffmpeg-jll,
julia-fontconfig-jll, julia-freetype2-jll, julia-fribidi-jll,
julia-gettext-jll, julia-glib-jll, julia-gr-jll, julia-gumbo-jll,
julia-imagemagick-jll, julia-jllwrappers-jll, julia-jpegturbo-jll,
julia-lame-jll, julia-libass-jll, julia-libfdk-aac-jll,
julia-libffi-jll, julia-libgcrypt-jll, julia-libglvnd-jll,
julia-libgpg-error-jll, juli-libiconv-jll, julia-libmount-jll,
julia-libpng-jll, julia-libsass-jll, julia-libtiff-jll,
julia-libuuid-jll, julia-libvorbis-jll, julia-lzo-jll,
julia-mbedtls-jll, julia-ogg-jll, julia-openspecfun-jll,
julia-openssl-jll, julia-opus-jll, julia-pcre-jll, julia-pixman-jll,
julia-qt5base-jll, julia-wayland-jll, julia-wayland-protocols-jll,
julia-x264-jll, julia-x265-jll, julia-xkbcommon-jll, julia-xml2-jll,
julia-xorg-libpthread-stubs-jll, julia-xorg-libx11-jll,
julia-xorg-libxau-jll, julia-xorg-libxcb-jll, julia-xorg-libxcursor-jll,
julia-xorg-libxdmcp-jll, julia-xorg-libxext-jll,
julia-xorg-libxfixes-jll, julia-xorg-libxi-jll,
julia-xorg-libxinerama-jll, julia-xorg-libxkbfile-jll,
julia-xorg-libxrandr-jll, julia-xorg-libxrender-jll,
julia-xorg-xcb-util-jll, julia-xorg-xcb-util-keysyms-jll,
julia-xorg-xcb-util-renderutil-jll, julia-xorg-xcb-util-wm-jll,
julia-xorg-xkbcomp-jll, julia-xorg-xkeyboard-config-jll,
julia-xorg-xtrans-jll, julia-xslt-jll, julia-zlib-jll, julia-zstd-jll)
[argument]: Adjust the order of the phases to the change in the
julia-build-system.
* gnu/packages/julia-xyz.scm (julia-bufferedstreams, julia-calculus,
julia-dataframes, julia-datavalues, julia-distances, julia-documenter,
julia-dualnumbers, julia-ellipsisnotation, julia-expronicon,
julia-fileio, julia-fixedpointnumbers, julia-functionwrappers,
julia-fuzzycompletions, julia-genericlinearalgebra, julia-genericschur,
julia-geometrybasics, julia-imagemagick, julia-infinity,
julia-matrixfactorizations, julia-media, julia-missings, julia-nnlib,
julia-optimtestproblems, julia-orderedcollections, julia-prettytables,
julia-pycall, julia-quadmath, julia-safetests, julia-stackviews)
[arguments]: Correct paths to reflect change of %package-path modify
order of phases as link-depot needs to run on an unmodified src
directory add package-name-uuid keyword argument to packages without
Project.toml file.
* gnu/packages/julia.scm (julia)[native-search-paths]: Correct paths to
reflect change of %package-path modify order of phases as link-depot
needs to run on an unmodified src directory.

Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
This commit is contained in:
Jean-Baptiste Volatier 2021-11-12 14:23:52 +00:00 committed by Efraim Flashner
parent e31d48d8db
commit 3af351a7de
No known key found for this signature in database
GPG key ID: 41AAE7DCCA3D8351
5 changed files with 154 additions and 108 deletions
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138
gnu/packages/julia-jll.scm
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@ -77,7 +77,7 @@ (define-public julia-bzip2-jll
'(#:tests? #f ; No runtests.jl
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -117,7 +117,7 @@ (define-public julia-cairo-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -163,7 +163,7 @@ (define-public julia-compilersupportlibraries-jll
`(#:tests? #f ; no runtests.jl
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -205,7 +205,7 @@ (define-public julia-expat-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -243,7 +243,7 @@ (define-public julia-ffmpeg-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -292,7 +292,7 @@ (define-public julia-fontconfig-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -335,7 +335,7 @@ (define-public julia-freetype2-jll
'(#:tests? #f ; No runtests.jl
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -377,7 +377,7 @@ (define-public julia-fribidi-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -413,7 +413,7 @@ (define-public julia-gettext-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -454,7 +454,7 @@ (define-public julia-glfw-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -497,7 +497,7 @@ (define-public julia-glib-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -541,7 +541,7 @@ (define-public julia-gr-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -590,7 +590,7 @@ (define-public julia-gumbo-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(let ((gumbo (string-append (assoc-ref inputs "gumbo-parser"))))
(for-each
@ -630,7 +630,7 @@ (define-public julia-imagemagick-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -672,7 +672,7 @@ (define-public julia-jllwrappers
'(#:tests? #f
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'custom-override-path
(add-after 'link-depot 'custom-override-path
(lambda* (#:key inputs #:allow-other-keys)
;; Make @generate_wrapper_header take an optional argument that
;; guix packagers can pass to override the default "override"
@ -718,7 +718,7 @@ (define-public julia-jpegturbo-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -754,7 +754,7 @@ (define-public julia-lame-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -790,7 +790,7 @@ (define-public julia-libass-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -830,7 +830,7 @@ (define-public julia-libfdk-aac-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -866,7 +866,7 @@ (define-public julia-libffi-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -903,7 +903,7 @@ (define-public julia-libgcrypt-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -942,7 +942,7 @@ (define-public julia-libglvnd-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -980,7 +980,7 @@ (define-public julia-libgpg-error-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -1018,7 +1018,7 @@ (define-public julia-libiconv-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -1056,7 +1056,7 @@ (define-public julia-libmount-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -1095,7 +1095,7 @@ (define-public julia-libpng-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -1133,7 +1133,7 @@ (define-public julia-libsass-jll
`(#:tests? #f ; no runtests.jl
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -1175,7 +1175,7 @@ (define-public julia-libtiff-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -1214,7 +1214,7 @@ (define-public julia-libuuid-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -1252,7 +1252,7 @@ (define-public julia-libvorbis-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -1290,7 +1290,7 @@ (define-public julia-lzo-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -1328,7 +1328,7 @@ (define-public julia-mbedtls-jll
'(#:tests? #f ; No runtests.jl
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -1366,7 +1366,7 @@ (define-public julia-ogg-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -1403,7 +1403,7 @@ (define-public julia-openspecfun-jll
`(#:tests? #f ; no runtests.jl
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -1446,7 +1446,7 @@ (define-public julia-openssl-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -1482,7 +1482,7 @@ (define-public julia-opus-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -1518,7 +1518,7 @@ (define-public julia-pcre-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -1556,7 +1556,7 @@ (define-public julia-pixman-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -1594,7 +1594,7 @@ (define-public julia-qt5base-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -1645,7 +1645,7 @@ (define-public julia-wayland-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -1684,7 +1684,7 @@ (define-public julia-wayland-protocols-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -1721,7 +1721,7 @@ (define-public julia-x264-jll
`(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(let ((libx264 (assoc-ref inputs "libx264")))
(map
@ -1762,7 +1762,7 @@ (define-public julia-x265-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -1798,7 +1798,7 @@ (define-public julia-xkbcommon-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -1838,7 +1838,7 @@ (define-public julia-xml2-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -1878,7 +1878,7 @@ (define-public julia-xorg-libpthread-stubs-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -1915,7 +1915,7 @@ (define-public julia-xorg-libx11-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -1953,7 +1953,7 @@ (define-public julia-xorg-libxau-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -1989,7 +1989,7 @@ (define-public julia-xorg-libxcb-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -2029,7 +2029,7 @@ (define-public julia-xorg-libxcursor-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -2067,7 +2067,7 @@ (define-public julia-xorg-libxdmcp-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -2103,7 +2103,7 @@ (define-public julia-xorg-libxext-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -2140,7 +2140,7 @@ (define-public julia-xorg-libxfixes-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -2177,7 +2177,7 @@ (define-public julia-xorg-libxi-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -2215,7 +2215,7 @@ (define-public julia-xorg-libxinerama-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -2252,7 +2252,7 @@ (define-public julia-xorg-libxkbfile-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -2289,7 +2289,7 @@ (define-public julia-xorg-libxrandr-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -2327,7 +2327,7 @@ (define-public julia-xorg-libxrender-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -2364,7 +2364,7 @@ (define-public julia-xorg-xcb-util-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -2401,7 +2401,7 @@ (define-public julia-xorg-xcb-util-image-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -2438,7 +2438,7 @@ (define-public julia-xorg-xcb-util-keysyms-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -2475,7 +2475,7 @@ (define-public julia-xorg-xcb-util-renderutil-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -2512,7 +2512,7 @@ (define-public julia-xorg-xcb-util-wm-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -2549,7 +2549,7 @@ (define-public julia-xorg-xkbcomp-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -2586,7 +2586,7 @@ (define-public julia-xorg-xkeyboard-config-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -2623,7 +2623,7 @@ (define-public julia-xorg-xtrans-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -2659,7 +2659,7 @@ (define-public julia-xslt-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -2702,7 +2702,7 @@ (define-public julia-zlib-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)
@ -2740,7 +2740,7 @@ (define-public julia-zstd-jll
'(#:tests? #f ; no runtests
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'override-binary-path
(add-after 'link-depot 'override-binary-path
(lambda* (#:key inputs #:allow-other-keys)
(map
(lambda (wrapper)

69
gnu/packages/julia-xyz.scm
View file

@ -410,7 +410,8 @@ (define-public julia-bufferedstreams
;; https://travis-ci.org/BioJulia/BufferedStreams.jl/jobs/491050182
(arguments
'(#:tests? #f
#:julia-package-name "BufferedStreams"))
#:julia-package-name "BufferedStreams"
#:julia-package-uuid "e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d"))
(propagated-inputs `(("julia-compat" ,julia-compat)))
(home-page "https://github.com/BioJulia/BufferedStreams.jl")
(synopsis "Fast composable IO streams")
@ -778,12 +779,12 @@ (define-public julia-configurations
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-tests
(add-after 'link-depot 'fix-tests
(lambda _
(substitute* "test/runtests.jl"
(("option.toml") "test/option.toml"))
#t))
(add-after 'unpack 'dont-use-exproniconlite
(add-after 'link-depot 'dont-use-exproniconlite
(lambda _
(substitute* '("Project.toml"
"src/Configurations.jl"
@ -919,7 +920,7 @@ (define-public julia-dataframes
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'skip-failing-test
(add-after 'link-depot 'skip-failing-test
(lambda _
;; Tests with non-standard colors.
(substitute* "test/show.jl"
@ -1022,7 +1023,7 @@ (define-public julia-datavalues
`(#:tests? #f ; Tests need upgrading with newer Julia version.
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'skip-known-failing-tests
(add-after 'link-depot 'skip-known-failing-tests
(lambda _
;; See upstream report:
;; https://github.com/queryverse/DataValues.jl/issues/83
@ -1100,7 +1101,7 @@ (define-public julia-distances
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'skip-flakey-tests
(add-after 'link-depot 'skip-flakey-tests
(lambda _
;; Some combination of these tests fail nondeterministically
;; each of the times this package is built.
@ -1166,14 +1167,14 @@ (define-public julia-documenter
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'patch-source
(add-after 'link-depot '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
(add-after 'link-depot 'remove-javascript-downloads
(lambda _
(substitute* "src/Writers/HTMLWriter.jl"
(("cdnjs.cloudflare.com") "example.com"))
@ -1352,7 +1353,7 @@ (define-public julia-dualnumbers
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'adjust-test-suite
(add-after 'link-depot 'adjust-test-suite
(lambda _
(substitute* "test/runtests.jl"
;; Seems to not play nicely with SpecialFunctions
@ -1386,7 +1387,7 @@ (define-public julia-ellipsisnotation
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'adjust-test-suite
(add-after 'link-depot 'adjust-test-suite
(lambda _
(substitute* "test/runtests.jl"
;; Seems to not play nicely with Julia-1.6.
@ -1438,7 +1439,7 @@ (define-public julia-expronicon
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'skip-network-tests
(add-after 'link-depot 'skip-network-tests
(lambda _
(substitute* "test/runtests.jl"
;; This test tries to access the Julia package registry.
@ -1517,7 +1518,7 @@ (define-public julia-fileio
`(#:phases
(modify-phases %standard-phases
(delete 'reset-gzip-timestamps)
(add-after 'unpack 'skip-network-tests
(add-after 'link-depot 'skip-network-tests
(lambda _
;; These tests try to download audio/video files.
(substitute* "test/query.jl"
@ -1677,7 +1678,7 @@ (define-public julia-fixedpointnumbers
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'disable-failing-test
(add-after 'link-depot 'disable-failing-test
(lambda* (#:key outputs #:allow-other-keys)
(substitute* "test/fixed.jl"
;; A deprecation warning is not thrown
@ -1764,7 +1765,7 @@ (define-public julia-functionwrappers
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'adjust-tests
(add-after 'link-depot 'adjust-tests
(lambda _
(substitute* "test/runtests.jl"
(("testset \\\"Abstract.*" all)
@ -1817,7 +1818,7 @@ (define-public julia-fuzzycompletions
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'skip-failing-test
(add-after 'link-depot 'skip-failing-test
(lambda _
(substitute* "test/runtests.jl"
((".*RPLE.*") "")))))))
@ -1844,7 +1845,7 @@ (define-public julia-genericlinearalgebra
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'adjust-test-suite
(add-after 'link-depot 'adjust-test-suite
(lambda _
(substitute* "test/runtests.jl"
((".*lapack.*") "")))))))
@ -1875,7 +1876,7 @@ (define-public julia-genericschur
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'adjust-test-suite
(add-after 'link-depot 'adjust-test-suite
(lambda _
(substitute* "test/complex.jl"
;; expected Array{Int32,1}, got a value of type Array{Int64,1}
@ -1912,13 +1913,13 @@ (define-public julia-geometrybasics
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'remove-earcut
(add-after 'link-depot 'remove-earcut
(lambda _
(substitute* '("Project.toml"
"src/GeometryBasics.jl")
((".*EarCut.*") ""))
#t))
(add-after 'unpack 'skip-incompatible-test
(add-after 'link-depot 'skip-incompatible-test
(lambda _
(substitute* "test/runtests.jl"
(("@testset.*MetaT and heterogeneous data.*" all)
@ -2268,7 +2269,7 @@ (define-public julia-imagemagick
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'skip-failing-test
(add-after 'link-depot 'skip-failing-test
(lambda _
;; These tests try to download from the imagemagick.org
(substitute* "test/runtests.jl"
@ -2465,7 +2466,7 @@ (define-public julia-infinity
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'remove-timezones.jl
(add-after 'link-depot 'remove-timezones.jl
(lambda _
(substitute* "test/runtests.jl"
(("using TimeZones.*") "")
@ -2864,7 +2865,7 @@ (define-public julia-matrixfactorizations
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'skip-failing-test
(add-after 'link-depot 'skip-failing-test
(lambda _
;; Tests with math functions are hard.
(substitute* "test/test_ul.jl"
@ -2981,7 +2982,8 @@ (define-public julia-media
(build-system julia-build-system)
;; Package without Project.toml
(arguments
'(#:julia-package-name "Media"))
'(#:julia-package-name "Media"
#:julia-package-uuid "e89f7d12-3494-54d1-8411-f7d8b9ae1f27"))
(propagated-inputs
`(("julia-macrotools" ,julia-macrotools)))
(home-page "https://github.com/JunoLab/Media.jl")
@ -3202,7 +3204,7 @@ (define-public julia-nnlib
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'skip-cuda-tests
(add-after 'link-depot 'skip-cuda-tests
(lambda _
(substitute* "test/runtests.jl"
(("using CUDA") "")
@ -3238,7 +3240,8 @@ (define-public julia-optimtestproblems
(base32 "10h47x5ws42pkqjccimaz0yxfvz41w0yazq6inamfk4lg5g2g3d9"))))
(build-system julia-build-system)
(arguments
`(#:julia-package-name "OptimTestProblems"))
`(#:julia-package-name "OptimTestProblems"
#:julia-package-uuid "cec144fc-5a64-5bc6-99fb-dde8f63e154c"))
(home-page "https://github.com/JuliaNLSolvers/OptimTestProblems.jl")
(synopsis "Collection of optimization test problems")
(description "The purpose of this package is to provide test problems for
@ -3528,7 +3531,7 @@ (define-public julia-prettytables
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'skip-color-tests
(add-after 'link-depot 'skip-color-tests
(lambda _
(substitute* "test/text_backend.jl"
((".*colors\\.jl.*") ""))
@ -3567,7 +3570,7 @@ (define-public julia-pycall
((guix build python-build-system) #:prefix python:))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'remove-conda
(add-after 'link-depot 'remove-conda
(lambda _
(substitute* "Project.toml"
((".*Conda.*") ""))
@ -3577,7 +3580,7 @@ (define-public julia-pycall
(substitute* "deps/depsutils.jl"
(("Conda.PYTHONDIR") "\"/\""))
#t))
(add-after 'unpack 'set-python
(add-after 'link-depot 'set-python
(lambda* (#:key inputs outputs #:allow-other-keys)
(let ((python (assoc-ref inputs "python")))
(setenv "PYCALL_JL_RUNTIME_PYTHON"
@ -3690,7 +3693,7 @@ (define-public julia-quadmath
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'hardcode-libmath-location
(add-after 'link-depot 'hardcode-libmath-location
(lambda* (#:key inputs #:allow-other-keys)
(let ((gcclib (assoc-ref inputs "gcc:lib")))
(substitute* "src/Quadmath.jl"
@ -4082,7 +4085,8 @@ (define-public julia-safetestsets
(base32 "1fb1dfdmiw2ggx60hf70954xlps0r48fcb3k3dvxynlz7ylphp96"))))
(build-system julia-build-system)
(arguments
`(#:julia-package-name "SafeTestsets"))
`(#:julia-package-name "SafeTestsets"
#:julia-package-uuid "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"))
(native-inputs
`(("julia-staticarrays" ,julia-staticarrays)))
(home-page "https://github.com/YingboMa/SafeTestsets.jl")
@ -4308,7 +4312,7 @@ (define-public julia-stackviews
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'skip-doctest
(add-after 'link-depot 'skip-doctest
(lambda _
(substitute* "test/runtests.jl"
((".*doctest.*") ""))
@ -4811,6 +4815,7 @@ (define-public julia-uris
(build-system julia-build-system)
(arguments
'(#:julia-package-name "URIs" ;required to run tests
#:julia-package-uuid "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4"
#:phases
(modify-phases %standard-phases
(add-before 'check 'change-dir
@ -4818,7 +4823,7 @@ (define-public julia-uris
(lambda* (#:key source outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(chdir
(string-append out "/share/julia/packages/URIs/test")))
(string-append out "/share/julia/loadpath/URIs/test")))
#t)))))
;; required for tests
(inputs `(("julia-json" ,julia-json)))

2
gnu/packages/julia.scm
View file

@ -673,7 +673,7 @@ (define-public julia
(native-search-paths
(list (search-path-specification
(variable "JULIA_LOAD_PATH")
(files (list "share/julia/packages/")))
(files (list "share/julia/loadpath/")))
(search-path-specification
(variable "JULIA_DEPOT_PATH")
(files (list "share/julia/")))))

5
guix/build-system/julia.scm
View file

@ -1,5 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2019 Nicolò Balzarotti <nicolo@nixo.xyz>
;;; Copyright © 2021 Jean-Baptiste Volatier <jbv@pm.me>
;;;
;;; This file is part of GNU Guix.
;;;
@ -83,6 +84,7 @@ (define* (julia-build store name inputs
(system (%current-system))
(guile #f)
(julia-package-name #f)
(julia-package-uuid #f)
(imported-modules %julia-build-system-modules)
(modules '((guix build julia-build-system)
(guix build utils))))
@ -105,7 +107,8 @@ (define builder
#:search-paths ',(map search-path-specification->sexp
search-paths)
#:inputs %build-inputs
#:julia-package-name ,julia-package-name)))
#:julia-package-name ,julia-package-name
#:julia-package-uuid ,julia-package-uuid)))
(define guile-for-build
(match guile

48
guix/build/julia-build-system.scm
View file

@ -1,5 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2019, 2020 Nicolò Balzarotti <nicolo@nixo.xyz>
;;; Copyright © 2021 Jean-Baptiste Volatier <jbv@pm.me>
;;;
;;; This file is part of GNU Guix.
;;;
@ -20,9 +21,11 @@
(define-module (guix build julia-build-system)
#:use-module ((guix build gnu-build-system) #:prefix gnu:)
#:use-module (guix build utils)
#:use-module (rnrs io ports)
#:use-module (ice-9 match)
#:use-module (ice-9 regex)
#:use-module (ice-9 rdelim)
#:use-module (ice-9 popen)
#:export (%standard-phases
julia-create-package-toml
julia-build))
@ -37,7 +40,7 @@ (define (invoke-julia code)
(invoke "julia" "-e" code))
;; subpath where we store the package content
(define %package-path "/share/julia/packages/")
(define %package-path "/share/julia/loadpath/")
(define (project.toml->name file)
"Look for Julia package name in the TOML file FILE (usually named
@ -51,6 +54,18 @@ (define (project.toml->name file)
(if m (match:substring m 1)
(loop (read-line in 'concat)))))))))
(define (project.toml->uuid file)
"Look for Julia package uuid in the TOML file FILE (usually named
Project.toml)."
(call-with-input-file file
(lambda (in)
(let loop ((line (read-line in 'concat)))
(if (eof-object? line)
#f
(let ((m (string-match "uuid\\s*=\\s*\"(.*)\"" line)))
(if m (match:substring m 1)
(loop (read-line in 'concat)))))))))
(define* (install #:key source inputs outputs julia-package-name
#:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
@ -73,7 +88,7 @@ (define* (precompile #:key source inputs outputs julia-package-name
(setenv "JULIA_DEPOT_PATH" builddir)
;; Add new package dir to the load path.
(setenv "JULIA_LOAD_PATH"
(string-append builddir "packages/" ":"
(string-append builddir "loadpath/" ":"
(or (getenv "JULIA_LOAD_PATH")
"")))
;; Actual precompilation:
@ -97,15 +112,36 @@ (define* (check #:key tests? source inputs outputs julia-package-name
(setenv "SOURCE_DATE_EPOCH" "1")
(setenv "JULIA_DEPOT_PATH" builddir)
(setenv "JULIA_LOAD_PATH"
(string-append builddir "packages/" ":"
(string-append builddir "loadpath/" ":"
(or (getenv "JULIA_LOAD_PATH")
"")))
(setenv "HOME" "/tmp")
(invoke "julia" "--depwarn=yes"
(string-append builddir "packages/"
(string-append builddir "loadpath/"
package "/test/runtests.jl"))))
#t)
(define* (link-depot #:key source inputs outputs julia-package-name julia-package-uuid
#:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(package-name (or
julia-package-name
(project.toml->name "Project.toml")))
(package-dir (string-append out %package-path package-name))
(uuid (or julia-package-uuid (project.toml->uuid "Project.toml")))
(pipe (open-pipe* OPEN_READ "julia" "-e"
(format #f "using Pkg;
println(Base.version_slug(Base.UUID(\"~a\"),
Base.SHA1(Pkg.GitTools.tree_hash(\".\"))))" uuid)))
(slug (string-trim-right (get-string-all pipe))))
;; When installing a package, julia looks first at in the JULIA_DEPOT_PATH
;; for a path like packages/PACKAGE/XXXX
;; Where XXXX is a slug encoding the package UUID and SHA1 of the files
;; Here we create a link with the correct path to enable julia to find the package
(mkdir-p (string-append out "/share/julia/packages/" package-name))
(symlink package-dir (string-append out "/share/julia/packages/" package-name "/" slug)))
#t)
(define (julia-create-package-toml outputs source
name uuid version
deps)
@ -138,6 +174,7 @@ (define %standard-phases
(delete 'check) ; tests must be run after installation
(replace 'install install)
(add-after 'install 'precompile precompile)
(add-after 'unpack 'link-depot link-depot)
(add-after 'install 'check check)
;; TODO: In the future we could add a "system-image-generation" phase
;; where we use PackageCompiler.jl to speed up package loading times
@ -146,11 +183,12 @@ (define %standard-phases
(delete 'patch-usr-bin-file)
(delete 'build)))
(define* (julia-build #:key inputs julia-package-name
(define* (julia-build #:key inputs julia-package-name julia-package-uuid
(phases %standard-phases)
#:allow-other-keys #:rest args)
"Build the given Julia package, applying all of PHASES in order."
(apply gnu:gnu-build
#:inputs inputs #:phases phases
#:julia-package-name julia-package-name
#:julia-package-uuid julia-package-uuid
args))