* [PATCH 2/2] gnu: multiqc: Update to 0.8.
@ 2016-12-18 21:36 Ra
0 siblings, 0 replies; 4+ messages in thread
From: Ra @ 2016-12-18 21:36 UTC (permalink / raw)
To: guix-devel@gnu.org
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[PATCH] gnu: multiqc: Update to 0.8.
is [PATCH 1/2] for this message, sorry for the mistake.
Running multiqc without [PATCH 2/2] systems say that matplotlib requires
nose>=0.11.1, so I added it to the propagated inputs.
---
gnu/packages/bioinformatics.scm | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/bioinformatics.scm
b/gnu/packages/bioinformatics.scm
index 43bf701..1167df5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7863,7 +7863,8 @@ replacement for strverscmp.")
("python-pyyaml" ,python-pyyaml)
("python-click" ,python-click)
("python-matplotlib" ,python-matplotlib)
- ("python-numpy" ,python-numpy)))
+ ("python-numpy" ,python-numpy)
+ ("python-nose" ,python-nose )))
(home-page "http://multiqc.info")
(synopsis "Aggregate bioinformatics analysis reports")
(description
--
1.9.1
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^ permalink raw reply related [flat|nested] 4+ messages in thread
* Re: [PATCH 2/2] gnu: multiqc: Update to 0.8.
2016-12-26 10:45 ` Ra
@ 2016-12-26 12:18 ` Ben Woodcroft
2016-12-28 13:13 ` Ra
0 siblings, 1 reply; 4+ messages in thread
From: Ben Woodcroft @ 2016-12-26 12:18 UTC (permalink / raw)
To: Ra, guix-devel@gnu.org
Hi Raoul,
On 26/12/16 20:45, Ra wrote:
> Hi Ben,
> thanks I will investigate. Does it mean that multiqc is in stand by
> for now ?
It would be ideal I think to add tests, and because they are failing it
would be good to know why. I thought the easiest simply to ask the
maintainers if they knew why the tests were failing:
https://github.com/ewels/MultiQC/issues/376
I also submitted the exception catching patch here, which we should add
to our patch if we decide to keep it before pushing our changes.
https://github.com/ewels/MultiQC/pull/377
I figure it makes sense to give them a week or two to respond, and
reevaluate after that. I presume you have not observed any problems
using multiqc after this update?
Thanks,
ben
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: [PATCH 2/2] gnu: multiqc: Update to 0.8.
2016-12-26 12:18 ` Ben Woodcroft
@ 2016-12-28 13:13 ` Ra
2016-12-30 7:37 ` Ben Woodcroft
0 siblings, 1 reply; 4+ messages in thread
From: Ra @ 2016-12-28 13:13 UTC (permalink / raw)
To: Ben Woodcroft, guix-devel@gnu.org
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Hi Ben,
reading the comments from https://github.com/ewels/MultiQC/issues/376
it seems that in the upcoming release they will solve the problem.
Are we going to wait for the next v. 1.0 or include it now and update later
?
--
Ra
On Mon, Dec 26, 2016 at 1:18 PM Ben Woodcroft <b.woodcroft@uq.edu.au> wrote:
> Hi Raoul,
>
>
> On 26/12/16 20:45, Ra wrote:
> > Hi Ben,
> > thanks I will investigate. Does it mean that multiqc is in stand by
> > for now ?
>
> It would be ideal I think to add tests, and because they are failing it
> would be good to know why. I thought the easiest simply to ask the
> maintainers if they knew why the tests were failing:
> https://github.com/ewels/MultiQC/issues/376
>
> I also submitted the exception catching patch here, which we should add
> to our patch if we decide to keep it before pushing our changes.
> https://github.com/ewels/MultiQC/pull/377
>
> I figure it makes sense to give them a week or two to respond, and
> reevaluate after that. I presume you have not observed any problems
> using multiqc after this update?
> Thanks,
> ben
>
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^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: [PATCH 2/2] gnu: multiqc: Update to 0.8.
2016-12-28 13:13 ` Ra
@ 2016-12-30 7:37 ` Ben Woodcroft
0 siblings, 0 replies; 4+ messages in thread
From: Ben Woodcroft @ 2016-12-30 7:37 UTC (permalink / raw)
To: Ra, guix-devel@gnu.org
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Hi Raoul,
On 28/12/16 23:13, Ra wrote:
> Hi Ben,
> reading the comments from https://github.com/ewels/MultiQC/issues/376
> it seems that in the upcoming release they will solve the problem.
> Are we going to wait for the next v. 1.0 or include it now and update
> later ?
I just pushed an update to 0.9 as
a29929b32caf9e437d18bdb0cd4d1b22bc096fed. I did not add nose as an input
because the issue seems to be with matplotlib, not multiqc.
Specifically, nose is listed in the 'requires.txt' file of matplotlib
when should only be needed for testing.
So to test the updated package I ran
$ ./pre-inst-env guix environment --ad-hoc multiqc python python-nose
glibc-locales -C --no-grafts --no-substitutes
[env] # LC_ALL=en_AU.UTF-8 LANG=en_AU.UTF-8
GUIX_LOCPATH=/gnu/store/hyi7svs0ds79wrcg5l0nr36zzjikqj7i-glibc-locales-2.24/lib/locale/
multiqc -h
The use of click with python3 means that we must set locales or it will
refuse to run. Please do tell if you find any issues with the update -
I've not used this tool before so I only tested it superficially.
ben
PS. In future would you mind please bottom-posting your emails if
possible? Around here, we've chosen a side of that debate :)
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^ permalink raw reply [flat|nested] 4+ messages in thread
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2016-12-18 21:36 [PATCH 2/2] gnu: multiqc: Update to 0.8 Ra
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2016-12-23 13:30 ` Fwd: " Ben Woodcroft
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2016-12-26 12:18 ` Ben Woodcroft
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