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

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>

1 files changed, 37 insertions, 32 deletions

diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index 93fadf318c..73768317b8 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -410,7 +410,8 @@ structures.")
     ;; 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 @@ way.")
     (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 @@ dependency on it.")
     (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 @@ without having to take direct dependencies.")
      `(#: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 @@ dictionaries in Julia, for improved productivity and performance.")
     (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 @@ valuable enough at this time.")
     (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 @@ stressing the robustness of differentiation tools.")
     (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 @@ combinations of dual numbers with predefined Julia numeric types.")
     (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 @@ before (or after)\".")
     (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 @@ need the ffmpeg binaries + executables, and don't want the overhead of
      `(#: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 @@ using finite difference.")
     (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 @@ differentiation (AD).")
     (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 @@ update step.")
     (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 @@ update step.")
     (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 @@ algebra routines written in Julia (except for optimized BLAS).")
     (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 @@ matrices the Schur form is often more useful.")
     (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 @@ be downscaled to fit into the size of your active terminal session.")
     (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 @@ indexed images, sometimes called \"colormap images\" or \"paletted images.\"")
     (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 @@ comes from the fact that @code{M == map(f, A)}.")
     (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 @@ resolving them into absolute units.")
     (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 @@ interface to interact with these types.")
     (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 @@ doesn't provide any other \"high-level\" functionality like layers or AD.")
          (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 @@ everything from run time algorithm choice to code generation at compile time.")
     (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 @@ human-readable format.")
                   ((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 @@ human-readable format.")
              (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 @@ arbitrary normed vector spaces (e.g. matrix-valued integrands).")
     (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 @@ through matrix-vector multiplication.")
            (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 @@ some performance improvements).")
     (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 @@ types, modules, and dictionaries.")
     (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 @@ types, modules, and dictionaries.")
            (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)))