[PATCH 0/2] Better interoperability between guix and Julia built-in package manager

Done

Details

4 participants

Efraim Flashner
Jean-Baptiste Volatier
Ludovic Courtès
zimoun

Owner: unassigned

Submitted by: Jean-Baptiste Volatier

Severity: normal

Jean-Baptiste Volatier wrote on 21 Oct 2021 15:06

Recipients:(address . guix-patches@gnu.org)(name . Jean-Baptiste Volatier)(address . jbv@pm.me)

Message-ID:20211021130648.14594-1-jbv@pm.me

With this patch, when a user install a package using Julia package manager,

the package manager finds packages that were already installed in the guix

profile and use them.

First patch of the serie does the implementation, the second patch is an example using

sundials_jll package.

Sundials_jll is a julia package that wraps the sundials library, it is typically not

installed on its own but as a dependency of DifferentialEquations.jl for example.

As DifferentialEquations.jl is not currently packaged in julia, a fallback is to

install it with julia package manager. Unfortunately that will also install

sundials_jll and downloads some .so that will fail to load on Guix because of

linker incompatilibities.

Now with the proposed patch, the user can install sundials_jll using guix,

and then julia package manager will use this package instead of downloading some

binary files.

As for the patch itself, it works by following more closely the directory

structure that Julia expects in JULIA_DEPOT_PATH. Namely the packages

subfolder should not contain packages but packages/XXXX/ where XXXX is

a string encoding package uuid and sha1 of package files.

$JULIA_DEPOT_PATH/packages was also used as JULIA_LOAD_PATH, this will not

work anymore as packages are behind a layer of XXXX sub directories.

So instead I added a new subfolder $JULIA_DEPOT_PATH/loadpath where the package

is installed and $JULIA_DEPOT_PATH/packages/XXXX is a symlink to it.

Jean-Baptiste Volatier (2):

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

gnu: Add julia-sundials-jull

gnu/packages/julia-jll.scm | 38 +++++++++++++++++++++++++

gnu/packages/julia-xyz.scm | 2 +-

gnu/packages/julia.scm | 2 +-

gnu/packages/maths.scm | 24 ++++++++++++++++

guix/build/julia-build-system.scm | 46 ++++++++++++++++++++++++++++---

5 files changed, 106 insertions(+), 6 deletions(-)

2.33.1

Jean-Baptiste Volatier wrote on 21 Oct 2021 15:09

Recipients:(address . 51319@debbugs.gnu.org)(name . Jean-Baptiste Volatier)(address . jbv@pm.me)

Message-ID:20211021130952.14696-1-jbv@pm.me

With this patch, when a user install a package using Julia package manager,

the package manager finds packages that were already installed in the guix

profile and use them.

First patch of the serie does the implementation, the second patch is an example using

sundials_jll package.

Sundials_jll is a julia package that wraps the sundials library, it is typically not

installed on its own but as a dependency of DifferentialEquations.jl for example.

As DifferentialEquations.jl is not currently packaged in julia, a fallback is to

install it with julia package manager. Unfortunately that will also install

sundials_jll and downloads some .so that will fail to load on Guix because of

linker incompatilibities.

Now with the proposed patch, the user can install sundials_jll using guix,

and then julia package manager will use this package instead of downloading some

binary files.

As for the patch itself, it works by following more closely the directory

structure that Julia expects in JULIA_DEPOT_PATH. Namely the packages

subfolder should not contain packages but packages/XXXX/ where XXXX is

a string encoding package uuid and sha1 of package files.

$JULIA_DEPOT_PATH/packages was also used as JULIA_LOAD_PATH, this will not

work anymore as packages are behind a layer of XXXX sub directories.

So instead I added a new subfolder $JULIA_DEPOT_PATH/loadpath where the package

is installed and $JULIA_DEPOT_PATH/packages/XXXX is a symlink to it.

Jean-Baptiste Volatier (2):

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

gnu: Add julia-sundials-jull

gnu/packages/julia-jll.scm | 38 +++++++++++++++++++++++++

gnu/packages/julia-xyz.scm | 2 +-

gnu/packages/julia.scm | 2 +-

gnu/packages/maths.scm | 24 ++++++++++++++++

guix/build/julia-build-system.scm | 46 ++++++++++++++++++++++++++++---

5 files changed, 106 insertions(+), 6 deletions(-)

2.33.1

Jean-Baptiste Volatier wrote on 21 Oct 2021 15:10

[PATCH 2/2] gnu: Add julia-sundials-jull

Recipients:(address . 51319@debbugs.gnu.org)(name . Jean-Baptiste Volatier)(address . jbv@pm.me)

Message-ID:20211021130952.14696-3-jbv@pm.me

* gnu/packages/julia-jll.scm (julia-sundials-jll): New variable.
* gnu/packages/maths.scm (sundials-julia): New variable.
---
 gnu/packages/julia-jll.scm | 38 ++++++++++++++++++++++++++++++++++++++
 gnu/packages/maths.scm     | 24 ++++++++++++++++++++++++
 2 files changed, 62 insertions(+)

Toggle diff (81 lines)diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm
index d3677d0a33..e1c33903dd 100644
--- a/gnu/packages/julia-jll.scm
+++ b/gnu/packages/julia-jll.scm
@@ -2709,3 +2709,41 @@ (define-public julia-zstd-jll
     (synopsis "Zstd library wrappers")
     (description "This package provides a wrapper for the zstd library.")
     (license license:expat)))
+
+(define-public julia-sundials-jll
+  (package
+    (name "julia-sundials-jll")
+    (version "5.2.1+0")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/JuliaBinaryWrappers/Sundials_jll.jl")
+               (commit (string-append "Sundials-v" version))))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "0cijb9frq8gj8bjpqf2lr5d0jxlj262y6h6xi4z3536dingrvffc"))))
+    (build-system julia-build-system)
+    (arguments
+     '(#:tests? #f  ; no runtests
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'link-depot 'override-binary-path
+           (lambda* (#:key inputs #:allow-other-keys)
+             (map
+               (lambda (wrapper)
+                 (substitute* wrapper
+                   (("global artifact_dir.*")
+                    (string-append
+                     "global artifact_dir = \""
+                      (assoc-ref inputs "sundials") "\"\n"))))
+               ;; There's a Julia file for each platform, override them all
+               (find-files "src/wrappers/" "\\.jl$")))))))
+    (inputs
+     `(("sundials" ,sundials-julia)))
+    (propagated-inputs
+     `(("julia-jllwrappers" ,julia-jllwrappers)))
+    (home-page "https://github.com/JuliaBinaryWrappers/Sundials_jll.jl")
+    (synopsis "SUndials library wrappers")
+    (description "This package provides a wrapper for the sundials library.")
+    (license license:expat)))
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 038ca5518c..54f44a3b55 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -5943,6 +5943,30 @@ (define-public sundials-openmpi
 	     ,%openmpi-setup)))))
     (synopsis "SUNDIALS with OpenMPI support")))

+(define-public sundials-julia
+  (package
+    (inherit sundials)
+    (name "sundials-julia")
+    (version "5.2.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/LLNL/sundials.git")
+             (commit (string-append "v" version))))
+       (sha256
+        (base32
+         "08q9svjdl6fmqrwyd9p12m98n0wd2lws38yh223wyp6590zi3i49"))))
+    (inputs
+     `(("lapack" ,lapack)
+       ,@(package-inputs sundials)))
+    (arguments
+     (substitute-keyword-arguments (package-arguments sundials)
+       ((#:configure-flags flags '())
+        `(cons* "-DLAPACK_ENABLE:BOOL=ON"
+                ,flags))))
+    (synopsis "SUNDIALS with lapack support as required by julia-sundials-jll")))
+
 (define-public combinatorial-blas
   (package
     (name "combinatorial-blas")

2.33.1

Jean-Baptiste Volatier wrote on 21 Oct 2021 15:09

[PATCH 1/2] build-system/julia: Enable Julia Pkg to find installed packages

Recipients:(address . 51319@debbugs.gnu.org)(name . Jean-Baptiste Volatier)(address . jbv@pm.me)

Message-ID:20211021130952.14696-2-jbv@pm.me

* guix/build/julia-build-system.scm (link-depot): New phase.
Julia 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.
(%package-path): modified package path from packages/ to
loadpath/
(project.toml->uuid): retrive package uuid from TOML file

* gnu/packages/julia-xyz.scm: correct paths to reflect
change of %package-path

* gnu/packages/julia.scm: correct paths to reflect change of
%package-path
---
 gnu/packages/julia-xyz.scm        |  2 +-
 gnu/packages/julia.scm            |  2 +-
 guix/build/julia-build-system.scm | 46 ++++++++++++++++++++++++++++---
 3 files changed, 44 insertions(+), 6 deletions(-)

Toggle diff (135 lines)diff --git a/gnu/packages/julia-xyz.scm b/gnu/packages/julia-xyz.scm
index c1ebc0fba1..1e407a2277 100644
--- a/gnu/packages/julia-xyz.scm
+++ b/gnu/packages/julia-xyz.scm
@@ -4610,7 +4610,7 @@ (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)))
diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm
index 411f2e2e10..5b9bf91ed6 100644
--- a/gnu/packages/julia.scm
+++ b/gnu/packages/julia.scm
@@ -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/")))))
diff --git a/guix/build/julia-build-system.scm b/guix/build/julia-build-system.scm
index d74acf2a05..c7f2119974 100644
--- a/guix/build/julia-build-system.scm
+++ b/guix/build/julia-build-system.scm
@@ -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.
 ;;;
@@ -20,10 +21,13 @@
 (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
+            %package-path
             julia-create-package-toml
             julia-build))

@@ -37,7 +41,7 @@ (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 +55,18 @@ (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 +89,7 @@ (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 +113,36 @@ (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
+                     #: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 (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 package-dir)))
+         (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 +175,7 @@ (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

2.33.1

Efraim Flashner wrote on 8 Nov 2021 08:30

Recipients:(name . Jean-Baptiste Volatier)(address . jbv@pm.me)(address . 51319@debbugs.gnu.org)

Message-ID:YYjSF2CewB3kkAhg@3900XT

Attachment: file

Jean-Baptiste Volatier wrote on 12 Nov 2021 15:23

[PATCH v2 0/2] Better interoperability between guix and Julia built-in package manager

Recipients:(name . Jean-Baptiste Volatier)(address . jbv@pm.me)

Message-ID:20211112142328.28400-1-jbv@pm.me

On Monday, November 8th, 2021 at 8:30 AM, Efraim Flashner <efraim@flashner.co.il> wrote:

Toggle quote (4 lines)

> Thanks for the patch series! I'm really looking forward to this working

> out in Guix, being able to use Julia to download as-yet unpackaged julia

> packages will make using Julia much easier.

Me too! Then we can concentrate first on the JLL packages since

source only packages are likely to work as is.

I forgot to mention that for this patch to work, the link-depot

phase needs to be called before the source is modified.

So in this new version, I have modified all packages that where

modifiying the source after unpack to do it after link-depot instead.

Toggle quote (5 lines)

> I had to wrap this with '(when (file-exists? "Project.toml")' since we

> do have some packages that pre-date the use of Project.toml. Building

> julia-bufferedstreams will test both a package with and without a

> Project.toml.

I added a julia-package-uuid keyword argument like julia-package-name

for packages without a Project.toml. I also modified the packages

that needed it.

Toggle quote (3 lines)

> Here you have a '~a' to use uuid but package-dir isn't used anywhere. Is

> package-dir not needed or is there a missing substitution?

This was some left over from a previous iteration.

Jean-Baptiste Volatier (2):

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

gnu: Add julia-sundials-jull

gnu/packages/julia-jll.scm | 176 ++++++++++++++++++------------

gnu/packages/julia-xyz.scm | 69 ++++++------

gnu/packages/julia.scm | 2 +-

gnu/packages/maths.scm | 24 ++++

guix/build-system/julia.scm | 5 +-

guix/build/julia-build-system.scm | 49 ++++++++-

6 files changed, 217 insertions(+), 108 deletions(-)

base-commit: 6e67c701a88064babd1aef93b58890aed2dcd0aa

2.33.1

Jean-Baptiste Volatier wrote on 12 Nov 2021 15:23

[PATCH v2 1/2] build-system/julia: Enable Julia Pkg to find installed packages

Recipients:(name . Jean-Baptiste Volatier)(address . jbv@pm.me)

Message-ID:20211112142328.28400-2-jbv@pm.me

* guix/build/julia-build-system.scm (link-depot): New phase.
Julia 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.
(%package-path): modified package path from packages/ to
loadpath/
(project.toml->uuid): retrive package uuid from TOML file

* gnu/packages/julia-xyz.scm: 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: correct paths to reflect change of
%package-path
modify order of phases as link-depot needs to run on an
unmodified src directory
---
 gnu/packages/julia-jll.scm        | 138 +++++++++++++++---------------
 gnu/packages/julia-xyz.scm        |  69 ++++++++-------
 gnu/packages/julia.scm            |   2 +-
 guix/build-system/julia.scm       |   5 +-
 guix/build/julia-build-system.scm |  49 +++++++++--
 5 files changed, 155 insertions(+), 108 deletions(-)

Toggle diff (461 lines)diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm
index 51643819ae..d8cf5b9eaf 100644
--- a/gnu/packages/julia-jll.scm
+++ b/gnu/packages/julia-jll.scm
@@ -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
     

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Jean-Baptiste Volatier wrote on 12 Nov 2021 15:24

[PATCH v2 2/2] gnu: Add julia-sundials-jull

Recipients:(name . Jean-Baptiste Volatier)(address . jbv@pm.me)

Message-ID:20211112142328.28400-3-jbv@pm.me

* gnu/packages/julia-jll.scm (julia-sundials-jll): New variable.
* gnu/packages/maths.scm (sundials-julia): New variable.
---
 gnu/packages/julia-jll.scm | 38 ++++++++++++++++++++++++++++++++++++++
 gnu/packages/maths.scm     | 24 ++++++++++++++++++++++++
 2 files changed, 62 insertions(+)

Toggle diff (81 lines)diff --git a/gnu/packages/julia-jll.scm b/gnu/packages/julia-jll.scm
index d8cf5b9eaf..097d2f1123 100644
--- a/gnu/packages/julia-jll.scm
+++ b/gnu/packages/julia-jll.scm
@@ -2759,3 +2759,41 @@ (define-public julia-zstd-jll
     (synopsis "Zstd library wrappers")
     (description "This package provides a wrapper for the zstd library.")
     (license license:expat)))
+
+(define-public julia-sundials-jll
+  (package
+    (name "julia-sundials-jll")
+    (version "5.2.1+0")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/JuliaBinaryWrappers/Sundials_jll.jl")
+               (commit (string-append "Sundials-v" version))))
+        (file-name (git-file-name name version))
+        (sha256
+         (base32 "0cijb9frq8gj8bjpqf2lr5d0jxlj262y6h6xi4z3536dingrvffc"))))
+    (build-system julia-build-system)
+    (arguments
+     '(#:tests? #f  ; no runtests
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'link-depot 'override-binary-path
+           (lambda* (#:key inputs #:allow-other-keys)
+             (map
+               (lambda (wrapper)
+                 (substitute* wrapper
+                   (("global artifact_dir.*")
+                    (string-append
+                     "global artifact_dir = \""
+                      (assoc-ref inputs "sundials") "\"\n"))))
+               ;; There's a Julia file for each platform, override them all
+               (find-files "src/wrappers/" "\\.jl$")))))))
+    (inputs
+     `(("sundials" ,sundials-julia)))
+    (propagated-inputs
+     `(("julia-jllwrappers" ,julia-jllwrappers)))
+    (home-page "https://github.com/JuliaBinaryWrappers/Sundials_jll.jl")
+    (synopsis "SUndials library wrappers")
+    (description "This package provides a wrapper for the sundials library.")
+    (license license:expat)))
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 5152fe6942..eba45cd6b6 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -6159,6 +6159,30 @@ (define-public sundials-openmpi
 	     ,%openmpi-setup)))))
     (synopsis "SUNDIALS with OpenMPI support")))

+(define-public sundials-julia
+  (package
+    (inherit sundials)
+    (name "sundials-julia")
+    (version "5.2.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/LLNL/sundials.git")
+             (commit (string-append "v" version))))
+       (sha256
+        (base32
+         "08q9svjdl6fmqrwyd9p12m98n0wd2lws38yh223wyp6590zi3i49"))))
+    (inputs
+     `(("lapack" ,lapack)
+       ,@(package-inputs sundials)))
+    (arguments
+     (substitute-keyword-arguments (package-arguments sundials)
+       ((#:configure-flags flags '())
+        `(cons* "-DLAPACK_ENABLE:BOOL=ON"
+                ,flags))))
+    (synopsis "SUNDIALS with lapack support as required by julia-sundials-jll")))
+
 (define-public combinatorial-blas
   (package
     (name "combinatorial-blas")

2.33.1

Ludovic Courtès wrote on 10 Mar 2022 00:33

Re: bug#51319: [PATCH 0/2] Better interoperability between guix and Julia built-in package manager

Recipients:

Message-ID:87sfrq1z23.fsf_-_@gnu.org

Hello!

Efraim, zimoun: I just stumbled upon this patch series by Jean-Baptiste,

which seems to have fallen through the cracks:

https://issues.guix.gnu.org/51319

Could you take a look and apply them if appropriate?

Thanks in advance!

Ludo’.

Jean-Baptiste Volatier <jbv@pm.me> skribis:

Toggle quote (45 lines)> On Monday, November 8th, 2021 at 8:30 AM, Efraim Flashner <efraim@flashner.co.il> wrote:
>
>> Thanks for the patch series! I'm really looking forward to this working
>> out in Guix, being able to use Julia to download as-yet unpackaged julia
>> packages will make using Julia much easier.
>
> Me too! Then we can concentrate first on the JLL packages since
> source only packages are likely to work as is.
>
> I forgot to mention that for this patch to work, the link-depot
> phase needs to be called before the source is modified.
> So in this new version, I have modified all packages that where
> modifiying the source after unpack to do it after link-depot instead.
>
>> I had to wrap this with '(when (file-exists? "Project.toml")' since we
>> do have some packages that pre-date the use of Project.toml. Building
>> julia-bufferedstreams will test both a package with and without a
>> Project.toml.
>
> I added a julia-package-uuid keyword argument like julia-package-name
> for packages without a Project.toml. I also modified the packages
> that needed it.
>
>> Here you have a '~a' to use uuid but package-dir isn't used anywhere. Is
>> package-dir not needed or is there a missing substitution?
>
> This was some left over from a previous iteration.
>
>
> Jean-Baptiste Volatier (2):
>   build-system/julia: Enable Julia Pkg to find installed packages
>   gnu: Add julia-sundials-jull
>
>  gnu/packages/julia-jll.scm        | 176 ++++++++++++++++++------------
>  gnu/packages/julia-xyz.scm        |  69 ++++++------
>  gnu/packages/julia.scm            |   2 +-
>  gnu/packages/maths.scm            |  24 ++++
>  guix/build-system/julia.scm       |   5 +-
>  guix/build/julia-build-system.scm |  49 ++++++++-
>  6 files changed, 217 insertions(+), 108 deletions(-)
>
>
> base-commit: 6e67c701a88064babd1aef93b58890aed2dcd0aa
> --
> 2.33.1

zimoun wrote on 10 Mar 2022 00:59

Recipients:(name . Ludovic Courtès)(address . ludo@gnu.org)

Message-ID:86pmmusmmw.fsf_-_@gmail.com

Hi Ludo,

On Thu, 10 Mar 2022 at 00:33, Ludovic Courtès <ludo@gnu.org> wrote:

Toggle quote (4 lines)

> https://issues.guix.gnu.org/51319

> Could you take a look and apply them if appropriate?

From my understanding, already applied with

3af351a7de41b8d50f27f3623c46392f571b9a4e and

546f8537aad3ac03fef43e036d3cab3abc943915. Therefore, I am closing.

Thanks for taking care.

Cheers,

simon

PS: The feature pointed in the Guix-HPC report, IIRC. ;-)

Closed

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