[PATCH] gnu: flexbar: Enable tests.

[PATCH] gnu: flexbar: Enable tests.

[Ricardo Wurmus]

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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

Re: [PATCH] gnu: flexbar: Enable tests.

[David Thompson]

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

Re: [PATCH] gnu: flexbar: Enable tests.

[Ricardo Wurmus]

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