* [PATCH] gnu: flexbar: Enable tests.
@ 2015-04-27 9:49 Ricardo Wurmus
2015-04-27 10:57 ` David Thompson
0 siblings, 1 reply; 3+ messages in thread
From: Ricardo Wurmus @ 2015-04-27 9:49 UTC (permalink / raw)
To: guix-devel
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Hi Guix,
this patch enables the tests of flexbar. There is no check target but a
validation script and some test data, so I'm just running the script
instead of "make check".
~~ Ricardo
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From 7568ba7f62bcbc8ac50a892d8bb58782603a2c70 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Mon, 27 Apr 2015 11:48:00 +0200
Subject: [PATCH] gnu: flexbar: Enable tests.
* gnu/packages/bioinformatics.scm (flexbar): Enable tests.
---
gnu/packages/bioinformatics.scm | 15 ++++++++++-----
1 file changed, 10 insertions(+), 5 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fc07bcf..42b1f4f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -623,15 +623,20 @@ results. The FASTX-Toolkit tools perform some of these preprocessing tasks.")
"13jaykc3y1x8y5nn9j8ljnb79s5y51kyxz46hdmvvjj6qhyympmf"))))
(build-system cmake-build-system)
(arguments
- `(;; There is no test target, although there is a directory containing
- ;; test data and scripts (launched by flexbar_validate.sh).
- #:tests? #f
- #:configure-flags (list
+ `(#:configure-flags (list
(string-append "-DFLEXBAR_BINARY_DIR="
(assoc-ref %outputs "out")
"/bin/"))
#:phases
- (alist-delete 'install %standard-phases)))
+ (alist-replace
+ 'check
+ (lambda* (#:key outputs #:allow-other-keys)
+ (setenv "PATH" (string-append
+ (assoc-ref outputs "out") "/bin:"
+ (getenv "PATH")))
+ (chdir "../flexbar_v2.5_src/test")
+ (zero? (system* "bash" "flexbar_validate.sh")))
+ (alist-delete 'install %standard-phases))))
(inputs
`(("tbb" ,tbb)
("zlib" ,zlib)))
--
2.1.0
^ permalink raw reply related [flat|nested] 3+ messages in thread
* Re: [PATCH] gnu: flexbar: Enable tests.
2015-04-27 9:49 [PATCH] gnu: flexbar: Enable tests Ricardo Wurmus
@ 2015-04-27 10:57 ` David Thompson
2015-04-27 12:37 ` Ricardo Wurmus
0 siblings, 1 reply; 3+ messages in thread
From: David Thompson @ 2015-04-27 10:57 UTC (permalink / raw)
To: Ricardo Wurmus, guix-devel
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:
> this patch enables the tests of flexbar. There is no check target but a
> validation script and some test data, so I'm just running the script
> instead of "make check".
Looks fine to me! Minor critique below:
> From 7568ba7f62bcbc8ac50a892d8bb58782603a2c70 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Mon, 27 Apr 2015 11:48:00 +0200
> Subject: [PATCH] gnu: flexbar: Enable tests.
>
> * gnu/packages/bioinformatics.scm (flexbar): Enable tests.
> ---
> gnu/packages/bioinformatics.scm | 15 ++++++++++-----
> 1 file changed, 10 insertions(+), 5 deletions(-)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index fc07bcf..42b1f4f 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -623,15 +623,20 @@ results. The FASTX-Toolkit tools perform some of these preprocessing tasks.")
> "13jaykc3y1x8y5nn9j8ljnb79s5y51kyxz46hdmvvjj6qhyympmf"))))
> (build-system cmake-build-system)
> (arguments
> - `(;; There is no test target, although there is a directory containing
> - ;; test data and scripts (launched by flexbar_validate.sh).
> - #:tests? #f
> - #:configure-flags (list
> + `(#:configure-flags (list
> (string-append "-DFLEXBAR_BINARY_DIR="
> (assoc-ref %outputs "out")
> "/bin/"))
> #:phases
> - (alist-delete 'install %standard-phases)))
> + (alist-replace
> + 'check
> + (lambda* (#:key outputs #:allow-other-keys)
> + (setenv "PATH" (string-append
> + (assoc-ref outputs "out") "/bin:"
> + (getenv "PATH")))
> + (chdir "../flexbar_v2.5_src/test")
> + (zero? (system* "bash" "flexbar_validate.sh")))
> + (alist-delete 'install %standard-phases))))
Consider rewriting using 'modify-phases' syntax.
> (inputs
> `(("tbb" ,tbb)
> ("zlib" ,zlib)))
> --
> 2.1.0
>
--
David Thompson
Web Developer - Free Software Foundation - http://fsf.org
GPG Key: 0FF1D807
Support the FSF: https://fsf.org/donate
^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: [PATCH] gnu: flexbar: Enable tests.
2015-04-27 10:57 ` David Thompson
@ 2015-04-27 12:37 ` Ricardo Wurmus
0 siblings, 0 replies; 3+ messages in thread
From: Ricardo Wurmus @ 2015-04-27 12:37 UTC (permalink / raw)
To: David Thompson; +Cc: guix-devel
David Thompson writes:
> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:
>
>> this patch enables the tests of flexbar. There is no check target but a
>> validation script and some test data, so I'm just running the script
>> instead of "make check".
>
> Looks fine to me! Minor critique below:
Thanks.
>> #:phases
>> - (alist-delete 'install %standard-phases)))
>> + (alist-replace
>> + 'check
>> + (lambda* (#:key outputs #:allow-other-keys)
>> + (setenv "PATH" (string-append
>> + (assoc-ref outputs "out") "/bin:"
>> + (getenv "PATH")))
>> + (chdir "../flexbar_v2.5_src/test")
>> + (zero? (system* "bash" "flexbar_validate.sh")))
>> + (alist-delete 'install %standard-phases))))
>
> Consider rewriting using 'modify-phases' syntax.
I think in this particular case, using "modify-phases" wouldn't be much
clearer. Here we're just deleting one and replacing another phase and I
think it's as clear as things can be. Or is the use of "alist-*" in
package definitions deprecated?
(I should rewrite my icedtea7 patch, however, to use "modify-phases"
syntax. With so many custom phases it really makes sense.)
~~ Ricardo
^ permalink raw reply [flat|nested] 3+ messages in thread
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