Package: guix-patches;
Reported by: Jean-Baptiste Volatier <jbv <at> pm.me>
Date: Thu, 21 Oct 2021 13:08:01 UTC
Severity: normal
Tags: patch
Done: zimoun <zimon.toutoune <at> gmail.com>
Bug is archived. No further changes may be made.
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guix-patches <at> gnu.org:bug#51319; Package guix-patches.
(Thu, 21 Oct 2021 13:08:02 GMT) Full text and rfc822 format available.Jean-Baptiste Volatier <jbv <at> pm.me>:guix-patches <at> gnu.org.
(Thu, 21 Oct 2021 13:08:02 GMT) Full text and rfc822 format available.Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
From: Jean-Baptiste Volatier <jbv <at> pm.me> To: guix-patches <at> gnu.org Cc: Jean-Baptiste Volatier <jbv <at> pm.me> Subject: [PATCH 0/2] Better interoperability between guix and Julia built-in package manager Date: Thu, 21 Oct 2021 13:06:56 +0000
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
guix-patches <at> gnu.org:bug#51319; Package guix-patches.
(Thu, 21 Oct 2021 13:11:02 GMT) Full text and rfc822 format available.Message #8 received at 51319 <at> debbugs.gnu.org (full text, mbox):
From: Jean-Baptiste Volatier <jbv <at> pm.me> To: 51319 <at> debbugs.gnu.org Cc: Jean-Baptiste Volatier <jbv <at> pm.me> Subject: [PATCH 0/2] Better interoperability between guix and Julia built-in package manager Date: Thu, 21 Oct 2021 13:09:55 +0000
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
guix-patches <at> gnu.org:bug#51319; Package guix-patches.
(Thu, 21 Oct 2021 13:11:02 GMT) Full text and rfc822 format available.Message #11 received at 51319 <at> debbugs.gnu.org (full text, mbox):
From: Jean-Baptiste Volatier <jbv <at> pm.me> To: 51319 <at> debbugs.gnu.org Cc: Jean-Baptiste Volatier <jbv <at> pm.me> Subject: [PATCH 2/2] gnu: Add julia-sundials-jull Date: Thu, 21 Oct 2021 13:10:06 +0000
* 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(+)
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
guix-patches <at> gnu.org:bug#51319; Package guix-patches.
(Thu, 21 Oct 2021 13:11:02 GMT) Full text and rfc822 format available.Message #14 received at 51319 <at> debbugs.gnu.org (full text, mbox):
From: Jean-Baptiste Volatier <jbv <at> pm.me> To: 51319 <at> debbugs.gnu.org Cc: Jean-Baptiste Volatier <jbv <at> pm.me> Subject: [PATCH 1/2] build-system/julia: Enable Julia Pkg to find installed packages Date: Thu, 21 Oct 2021 13:09:58 +0000
* 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(-)
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 <at> nixo.xyz>
+;;; Copyright © 2021 Jean-Baptiste Volatier <jbv <at> 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
guix-patches <at> gnu.org:bug#51319; Package guix-patches.
(Mon, 08 Nov 2021 07:32:02 GMT) Full text and rfc822 format available.Message #17 received at 51319 <at> debbugs.gnu.org (full text, mbox):
From: Efraim Flashner <efraim <at> flashner.co.il> To: Jean-Baptiste Volatier <jbv <at> pm.me> Cc: 51319 <at> debbugs.gnu.org Subject: Re: [bug#51319] [PATCH 1/2] build-system/julia: Enable Julia Pkg to find installed packages Date: Mon, 8 Nov 2021 09:30:31 +0200
[Message part 1 (text/plain, inline)]
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.
A couple of comments inline in the patch:
On Thu, Oct 21, 2021 at 01:09:58PM +0000, Jean-Baptiste Volatier via Guix-patches via wrote:
> * 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(-)
>
> 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 <at> nixo.xyz>
> +;;; Copyright © 2021 Jean-Baptiste Volatier <jbv <at> 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)
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.
> + (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)))
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?
> + (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 <efraim <at> flashner.co.il> רנשלפ םירפא
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guix-patches <at> gnu.org:bug#51319; Package guix-patches.
(Fri, 12 Nov 2021 14:25:01 GMT) Full text and rfc822 format available.Message #20 received at 51319 <at> debbugs.gnu.org (full text, mbox):
From: Jean-Baptiste Volatier <jbv <at> pm.me> To: 51319 <at> debbugs.gnu.org, efraim <at> flashner.co.il Cc: Jean-Baptiste Volatier <jbv <at> pm.me> Subject: [PATCH v2 0/2] Better interoperability between guix and Julia built-in package manager Date: Fri, 12 Nov 2021 14:23:46 +0000
On Monday, November 8th, 2021 at 8:30 AM, Efraim Flashner <efraim <at> 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
guix-patches <at> gnu.org:bug#51319; Package guix-patches.
(Fri, 12 Nov 2021 14:25:02 GMT) Full text and rfc822 format available.Message #23 received at 51319 <at> debbugs.gnu.org (full text, mbox):
From: Jean-Baptiste Volatier <jbv <at> pm.me> To: 51319 <at> debbugs.gnu.org, efraim <at> flashner.co.il Cc: Jean-Baptiste Volatier <jbv <at> pm.me> Subject: [PATCH v2 1/2] build-system/julia: Enable Julia Pkg to find installed packages Date: Fri, 12 Nov 2021 14:23:52 +0000
* 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(-)
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
(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)
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 @@ (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)))
diff --git a/gnu/packages/julia.scm b/gnu/packages/julia.scm
index fe31e545c9..8bf2c8e25e 100644
--- a/gnu/packages/julia.scm
+++ b/gnu/packages/julia.scm
@@ -670,7 +670,7 @@ (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-system/julia.scm b/guix/build-system/julia.scm
index 63cb7cd864..8ceac090c7 100644
--- a/guix/build-system/julia.scm
+++ b/guix/build-system/julia.scm
@@ -1,5 +1,6 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2019 Nicolò Balzarotti <nicolo <at> nixo.xyz>
+;;; Copyright © 2021 Jean-Baptiste Volatier <jbv <at> 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
diff --git a/guix/build/julia-build-system.scm b/guix/build/julia-build-system.scm
index d74acf2a05..a23f241ba6 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 <at> nixo.xyz>
+;;; Copyright © 2021 Jean-Baptiste Volatier <jbv <at> 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 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 +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
@@ -146,11 +184,12 @@ (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))
--
2.33.1
guix-patches <at> gnu.org:bug#51319; Package guix-patches.
(Fri, 12 Nov 2021 14:25:02 GMT) Full text and rfc822 format available.Message #26 received at 51319 <at> debbugs.gnu.org (full text, mbox):
From: Jean-Baptiste Volatier <jbv <at> pm.me> To: 51319 <at> debbugs.gnu.org, efraim <at> flashner.co.il Cc: Jean-Baptiste Volatier <jbv <at> pm.me> Subject: [PATCH v2 2/2] gnu: Add julia-sundials-jull Date: Fri, 12 Nov 2021 14:24:05 +0000
* 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(+)
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
guix-patches <at> gnu.org:bug#51319; Package guix-patches.
(Wed, 09 Mar 2022 23:34:01 GMT) Full text and rfc822 format available.Message #29 received at 51319 <at> debbugs.gnu.org (full text, mbox):
From: Ludovic Courtès <ludo <at> gnu.org> To: efraim <at> flashner.co.il, zimoun <zimon.toutoune <at> gmail.com> Cc: 51319 <at> debbugs.gnu.org, Jean-Baptiste Volatier <jbv <at> pm.me> Subject: Re: bug#51319: [PATCH 0/2] Better interoperability between guix and Julia built-in package manager Date: Thu, 10 Mar 2022 00:33:24 +0100
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 <at> pm.me> skribis: > On Monday, November 8th, 2021 at 8:30 AM, Efraim Flashner <efraim <at> 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 <zimon.toutoune <at> gmail.com>:Jean-Baptiste Volatier <jbv <at> pm.me>:Message #34 received at 51319-done <at> debbugs.gnu.org (full text, mbox):
From: zimoun <zimon.toutoune <at> gmail.com> To: Ludovic Courtès <ludo <at> gnu.org> Cc: 51319-done <at> debbugs.gnu.org, Jean-Baptiste Volatier <jbv <at> pm.me>, efraim <at> flashner.co.il Subject: Re: bug#51319: [PATCH 0/2] Better interoperability between guix and Julia built-in package manager Date: Thu, 10 Mar 2022 00:59:35 +0100
Hi Ludo, On Thu, 10 Mar 2022 at 00:33, Ludovic Courtès <ludo <at> gnu.org> wrote: > 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. ;-)
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(Thu, 07 Apr 2022 11:24:04 GMT) Full text and rfc822 format available.
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