[PATCH] Update biopython to 1.66.

[PATCH] Update biopython to 1.66.

[Ben Woodcroft]

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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

Re: [PATCH] Update biopython to 1.66.

[Ludovic Courtès]

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’.

Re: [PATCH] Update biopython to 1.66.

[Ricardo Wurmus]

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

Re: [PATCH] Update biopython to 1.66.

[Ben Woodcroft]

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.

Re: [PATCH] Update biopython to 1.66.

[Ricardo Wurmus]

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