guix-bioinformatics
/
guix
mirror of http://git.savannah.gnu.org/git/guix.git
3
0
Fork 0
Code Issues Projects Releases Wiki Activity
Browse Source

build: Add julia-build-system. 

* guix/build/julia-build-system.scm: New file.
* guix/build-system/julia.scm: New file.
* Makefile.am (MODULES): Add them.
* doc/guix.texi (Build Systems): Document julia-build-system.

Signed-off-by: Julien Lepiller <julien@lepiller.eu>
wip-system-bootstrap
nixo 3 years ago
committed by Julien Lepiller
parent
4ab97ef18f
commit
a44a535ebe
No known key found for this signature in database GPG Key ID: 43111F4520086A0C
4 changed files with 292 additions and 0 deletions
Whitespace
Show all changes Ignore whitespace when comparing lines Ignore changes in amount of whitespace Ignore changes in whitespace at EOL
Split View
Diff Options
Show Stats Download Patch File Download Diff File
  1. 2
      Makefile.am
  2. 23
      doc/guix.texi
  3. 132
      guix/build-system/julia.scm
  4. 135
      guix/build/julia-build-system.scm

2
Makefile.am
View File

@ -126,6 +126,7 @@ MODULES = \
guix/build-system/gnu.scm \
guix/build-system/guile.scm \
guix/build-system/haskell.scm \
guix/build-system/julia.scm \
guix/build-system/linux-module.scm \
guix/build-system/node.scm \
guix/build-system/perl.scm \
@ -184,6 +185,7 @@ MODULES = \
guix/build/texlive-build-system.scm \
guix/build/waf-build-system.scm \
guix/build/haskell-build-system.scm \
guix/build/julia-build-system.scm \
guix/build/linux-module-build-system.scm \
guix/build/store-copy.scm \
guix/build/json.scm \

23
doc/guix.texi
View File

@ -6034,6 +6034,29 @@ Packages built with @code{guile-build-system} must provide a Guile package in
their @code{native-inputs} field.
@end defvr
@defvr {Scheme Variable} julia-build-system
This variable is exported by @code{(guix build-system julia)}. It implements
the build procedure used by @uref{https://julialang.org/, julia} packages,
which essentially is similar to running @command{julia -e 'using Pkg;
Pkg.add(package)'} in an environment where @code{JULIA_LOAD_PATH} contains the
paths to all Julia package inputs. Tests are run not run.
Julia packages require the source @code{file-name} to be the real name of the
package, correctly capitalized.
For packages requiring shared library dependencies, you may need to write the
@file{/deps/deps.jl} file manually. It's usually a line of @code{const
variable = /gnu/store/libary.so} for each dependency, plus a void function
@code{check_deps() = nothing}.
Some older packages that aren't using @file{Package.toml} yet, will require
this file to be created, too. The function @code{julia-create-package-toml}
helps creating the file. You need to pass the outputs and the source of the
package, it's name (the same as the @code{file-name} parameter), the package
uuid, the package version, and a list of dependencies specified by their name
and their uuid.
@end defvr
@defvr {Scheme Variable} minify-build-system
This variable is exported by @code{(guix build-system minify)}. It
implements a minification procedure for simple JavaScript packages.

132
guix/build-system/julia.scm
View File

@ -0,0 +1,132 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2019 Nicolò Balzarotti <nicolo@nixo.xyz>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (guix build-system julia)
#:use-module ((guix build julia-build-system))
#:use-module (gnu packages julia)
#:use-module (guix store)
#:use-module (guix utils)
#:use-module (guix packages)
#:use-module (guix derivations)
#:use-module (guix search-paths)
#:use-module (guix build-system)
#:use-module (guix build-system gnu)
#:use-module (ice-9 match)
#:use-module (srfi srfi-26)
#:export (%julia-build-system-modules
julia-build
julia-build-system))
;; Commentary:
;;
;; Standard build procedure for Julia packages.
;;
;; Code:
(define %julia-build-system-modules
;; Build-side modules imported by default.
`((guix build julia-build-system)
,@%gnu-build-system-modules))
(define (default-julia)
"Return the default Julia package."
;; Lazily resolve the binding to avoid a circular dependency.
(let ((julia-mod (resolve-interface '(gnu packages julia))))
(module-ref julia-mod 'julia)))
(define* (lower name
#:key source inputs native-inputs outputs system target
(julia julia)
#:allow-other-keys
#:rest arguments)
"Return a bag for NAME."
(define private-keywords
'(#:target #:julia #:inputs #:native-inputs))
(and (not target) ;XXX: no cross-compilation
(bag
(name name)
(system system)
(host-inputs `(,@(if source
`(("source" ,source))
'())
,@inputs
;; Keep the standard inputs of 'gnu-build-system'.
,@(standard-packages)))
(build-inputs `(("julia" ,julia)
,@native-inputs))
(outputs outputs)
(build julia-build)
(arguments (strip-keyword-arguments private-keywords arguments)))))
(define* (julia-build store name inputs
#:key source
(tests? #f)
(phases '(@ (guix build julia-build-system)
%standard-phases))
(outputs '("out"))
(search-paths '())
(system (%current-system))
(guile #f)
(imported-modules %julia-build-system-modules)
(modules '((guix build julia-build-system)
(guix build utils))))
"Build SOURCE using Julia, and with INPUTS."
(define builder
`(begin
(use-modules ,@modules)
(julia-build #:name ,name
#:source ,(match (assoc-ref inputs "source")
(((? derivation? source))
(derivation->output-path source))
((source)
source)
(source
source))
#:system ,system
#:tests? ,tests?
#:phases ,phases
#:outputs %outputs
#:search-paths ',(map search-path-specification->sexp
search-paths)
#:inputs %build-inputs)))
(define guile-for-build
(match guile
((? package?)
(package-derivation store guile system #:graft? #f))
(#f ; the default
(let* ((distro (resolve-interface '(gnu packages commencement)))
(guile (module-ref distro 'guile-final)))
(package-derivation store guile system #:graft? #f)))))
(build-expression->derivation store name builder
#:inputs inputs
#:system system
#:modules imported-modules
#:outputs outputs
#:guile-for-build guile-for-build))
(define julia-build-system
(build-system
(name 'julia)
(description "The build system for Julia packages")
(lower lower)))
;;; julia.scm ends here

135
guix/build/julia-build-system.scm
View File

@ -0,0 +1,135 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2019 Nicolò Balzarotti <nicolo@nixo.xyz>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (guix build julia-build-system)
#:use-module ((guix build gnu-build-system) #:prefix gnu:)
#:use-module (guix build utils)
#:use-module (ice-9 match)
#:export (%standard-phases
julia-create-package-toml
julia-build))
;; Commentary:
;;
;; Builder-side code of the standard build procedure for Julia packages.
;;
;; Code:
(define (invoke-julia code)
(invoke "julia" "-e" code))
;; subpath where we store the package content
(define %package-path "/share/julia/packages/")
(define (generate-load-path inputs outputs)
(string-append
(string-join (map (match-lambda
((_ . path)
(string-append path %package-path)))
;; Restrict to inputs beginning with "julia-".
(filter (match-lambda
((name . _)
(string-prefix? "julia-" name)))
inputs))
":")
(string-append ":" (assoc-ref outputs "out") %package-path)
;; stdlib is always required to find Julia's standard libraries.
;; usually there are other two paths in this variable:
;; "@" and "@v#.#"
":@stdlib"))
(define* (install #:key source inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(package-dir (string-append out %package-path
(string-append
(strip-store-file-name source)))))
(setenv "JULIA_LOAD_PATH" (generate-load-path inputs outputs))
(mkdir-p package-dir)
(copy-recursively source package-dir))
#t)
;; TODO: Precompilation is working, but I don't know how to tell
;; julia to use use it. If (on rantime) we set HOME to
;; store path, julia tries to write files there (failing)
(define* (precompile #:key source inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(builddir (string-append out "/share/julia/"))
(package (strip-store-file-name source)))
(mkdir-p builddir)
(setenv "JULIA_DEPOT_PATH" builddir)
(setenv "JULIA_LOAD_PATH" (generate-load-path inputs outputs))
;; Actual precompilation
(invoke-julia (string-append "using " package)))
#t)
(define* (check #:key source inputs outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(package (strip-store-file-name source))
(builddir (string-append out "/share/julia/")))
(setenv "JULIA_DEPOT_PATH" builddir)
(setenv "JULIA_LOAD_PATH" (generate-load-path inputs outputs))
(invoke-julia (string-append "using Pkg;Pkg.test(\"" package "\")")))
#t)
(define (julia-create-package-toml outputs source
name uuid version
deps)
"Some packages are not using the new Package.toml dependency specifications.
Write this file manually, so that Julia can find its dependencies."
(let ((f (open-file
(string-append
(assoc-ref outputs "out")
%package-path
(string-append
name "/Project.toml"))
"w")))
(display (string-append
"
name = \"" name "\"
uuid = \"" uuid "\"
version = \"" version "\"
") f)
(when (not (null? deps))
(display "[deps]\n" f)
(for-each (lambda dep
(display (string-append (car (car dep)) " = \"" (cdr (car dep)) "\"\n")
f))
deps))
(close-port f))
#t)
(define %standard-phases
(modify-phases gnu:%standard-phases
(delete 'check) ; tests must be run after installation
(replace 'install install)
(add-after 'install 'precompile precompile)
;; (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
(delete 'configure)
(delete 'bootstrap)
(delete 'patch-usr-bin-file)
(delete 'build)))
(define* (julia-build #:key inputs (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
args))
Write Preview
Loading…
Cancel
Save