* [PATCH] Update biopython to 1.66.
@ 2015-11-11 11:28 Ben Woodcroft
2015-12-09 21:23 ` Ludovic Courtès
0 siblings, 1 reply; 5+ messages in thread
From: Ben Woodcroft @ 2015-11-11 11:28 UTC (permalink / raw)
To: guix-devel@gnu.org
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I also figure with the shiny new updaters it might make things easier if
pypi is used instead of the biopython site.
thanks.
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From bb6e9ba482ea8602afafd9f6a310a8053544bd80 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Wed, 11 Nov 2015 21:27:02 +1000
Subject: [PATCH] gnu: python-biopython, python2-biopython: Update to 1.66.
* gnu/packages/bioinformatics.scm (python-biopython, python2-biopython): Update to 1.66.
[source]: Use PyPi instead of biopython.org.
---
gnu/packages/bioinformatics.scm | 9 ++++-----
1 file changed, 4 insertions(+), 5 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f13e405..706a871 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -348,15 +348,14 @@ provide a coordinated and extensible framework to do computational biology.")
(define-public python-biopython
(package
(name "python-biopython")
- (version "1.65")
+ (version "1.66")
(source (origin
(method url-fetch)
- (uri (string-append
- "http://biopython.org/DIST/biopython-"
- version ".tar.gz"))
+ ;; use PyPi rather than biopython.org to ease updating
+ (uri (pypi-uri "biopython" version))
(sha256
(base32
- "13m8s9jkrw40zvdp1rl709n6lmgdh4f52aann7gzr6sfp0fwhg26"))))
+ "1gdv92593klimg22icf5j9by7xiq86jnwzkpz4abaa05ylkdf6hp"))))
(build-system python-build-system)
(inputs
`(("python-numpy" ,python-numpy)))
--
2.5.0
^ permalink raw reply related [flat|nested] 5+ messages in thread
* Re: [PATCH] Update biopython to 1.66.
2015-11-11 11:28 [PATCH] Update biopython to 1.66 Ben Woodcroft
@ 2015-12-09 21:23 ` Ludovic Courtès
2015-12-10 9:31 ` Ricardo Wurmus
2015-12-10 13:18 ` Ricardo Wurmus
0 siblings, 2 replies; 5+ messages in thread
From: Ludovic Courtès @ 2015-12-09 21:23 UTC (permalink / raw)
To: Ben Woodcroft; +Cc: guix-devel@gnu.org
Hi Ben,
It seems that this ~1 month old message fell through the cracks, sorry
about that!
Ben Woodcroft <b.woodcroft@uq.edu.au> skribis:
> I also figure with the shiny new updaters it might make things easier
> if pypi is used instead of the biopython site.
I think so. Is it the same archive that is served on both sites? For
instance, does the pypi version include tests and doc as well?
> From bb6e9ba482ea8602afafd9f6a310a8053544bd80 Mon Sep 17 00:00:00 2001
> From: Ben Woodcroft <donttrustben@gmail.com>
> Date: Wed, 11 Nov 2015 21:27:02 +1000
> Subject: [PATCH] gnu: python-biopython, python2-biopython: Update to 1.66.
>
> * gnu/packages/bioinformatics.scm (python-biopython, python2-biopython): Update to 1.66.
> [source]: Use PyPi instead of biopython.org.
That looks good. Ricardo?
Thanks!
Ludo’.
^ permalink raw reply [flat|nested] 5+ messages in thread
* Re: [PATCH] Update biopython to 1.66.
2015-12-09 21:23 ` Ludovic Courtès
@ 2015-12-10 9:31 ` Ricardo Wurmus
2015-12-10 11:04 ` Ben Woodcroft
2015-12-10 13:18 ` Ricardo Wurmus
1 sibling, 1 reply; 5+ messages in thread
From: Ricardo Wurmus @ 2015-12-10 9:31 UTC (permalink / raw)
To: Ludovic Courtès; +Cc: guix-devel@gnu.org
Ludovic Courtès <ludo@gnu.org> writes:
>> From bb6e9ba482ea8602afafd9f6a310a8053544bd80 Mon Sep 17 00:00:00 2001
>> From: Ben Woodcroft <donttrustben@gmail.com>
>> Date: Wed, 11 Nov 2015 21:27:02 +1000
>> Subject: [PATCH] gnu: python-biopython, python2-biopython: Update to 1.66.
>>
>> * gnu/packages/bioinformatics.scm (python-biopython, python2-biopython): Update to 1.66.
>> [source]: Use PyPi instead of biopython.org.
>
> That looks good. Ricardo?
Yes, this should be okay. Thank you, Ben!
~~ Ricardo
^ permalink raw reply [flat|nested] 5+ messages in thread
* Re: [PATCH] Update biopython to 1.66.
2015-12-10 9:31 ` Ricardo Wurmus
@ 2015-12-10 11:04 ` Ben Woodcroft
0 siblings, 0 replies; 5+ messages in thread
From: Ben Woodcroft @ 2015-12-10 11:04 UTC (permalink / raw)
To: Ricardo Wurmus, Ludovic Courtès; +Cc: guix-devel@gnu.org
On 10/12/15 19:31, Ricardo Wurmus wrote:
> Ludovic Courtès <ludo@gnu.org> writes:
>
>>> From bb6e9ba482ea8602afafd9f6a310a8053544bd80 Mon Sep 17 00:00:00 2001
>>> From: Ben Woodcroft <donttrustben@gmail.com>
>>> Date: Wed, 11 Nov 2015 21:27:02 +1000
>>> Subject: [PATCH] gnu: python-biopython, python2-biopython: Update to 1.66.
>>>
>>> * gnu/packages/bioinformatics.scm (python-biopython, python2-biopython): Update to 1.66.
>>> [source]: Use PyPi instead of biopython.org.
>> That looks good. Ricardo?
> Yes, this should be okay. Thank you, Ben!
No problem. I assume one of you will push - thanks in advance.
^ permalink raw reply [flat|nested] 5+ messages in thread
* Re: [PATCH] Update biopython to 1.66.
2015-12-09 21:23 ` Ludovic Courtès
2015-12-10 9:31 ` Ricardo Wurmus
@ 2015-12-10 13:18 ` Ricardo Wurmus
1 sibling, 0 replies; 5+ messages in thread
From: Ricardo Wurmus @ 2015-12-10 13:18 UTC (permalink / raw)
To: Ludovic Courtès; +Cc: guix-devel@gnu.org
Ludovic Courtès <ludo@gnu.org> writes:
>> I also figure with the shiny new updaters it might make things easier
>> if pypi is used instead of the biopython site.
>
> I think so. Is it the same archive that is served on both sites? For
> instance, does the pypi version include tests and doc as well?
Yes. They are virtually identical. The only difference between the two
tarballs is this:
$ diff -r biopython-1.66 biopython-1.66-pypi/
diff -r biopython-1.66/PKG-INFO biopython-1.66-pypi/PKG-INFO
1c1
< Metadata-Version: 1.1
---
> Metadata-Version: 1.0
I’ll rebase a couple of things in my local repository and will push this
commit within a couple of hours unless someone else gets to it earlier.
~~ Ricardo
^ permalink raw reply [flat|nested] 5+ messages in thread
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2015-11-11 11:28 [PATCH] Update biopython to 1.66 Ben Woodcroft
2015-12-09 21:23 ` Ludovic Courtès
2015-12-10 9:31 ` Ricardo Wurmus
2015-12-10 11:04 ` Ben Woodcroft
2015-12-10 13:18 ` Ricardo Wurmus
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