[PATCH] gnu: Add Biopython.

[PATCH] gnu: Add Biopython.

[Ricardo Wurmus]

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From ca3474b1a639e43d708aad4385057cd84e3cce8b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Wed, 15 Apr 2015 17:46:35 +0200
Subject: [PATCH] gnu: Add Biopython.

* gnu/packages/bioinformatics.scm (python-biopython, python2-biopython): New
  variables.
---
 gnu/packages/bioinformatics.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0239e97..6d53e4e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -187,6 +187,35 @@ pybedtools extends BEDTools by offering feature-level manipulations from with
 Python.")
     (license license:gpl2+)))
 
+(define-public python-biopython
+  (package
+    (name "python-biopython")
+    (version "1.65")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "http://biopython.org/DIST/biopython-"
+                    version ".tar.gz"))
+              (sha256
+               (base32
+                "13m8s9jkrw40zvdp1rl709n6lmgdh4f52aann7gzr6sfp0fwhg26"))))
+    (build-system python-build-system)
+    (inputs
+     `(("python-numpy" ,python-numpy)))
+    (native-inputs
+     `(("python-setuptools" ,python2-setuptools)))
+    (home-page "http://biopython.org/")
+    (synopsis "Set of tools for biological computation in Python")
+    (description
+     "Biopython is a set of tools for biological computation written in Python
+by an international team of developers.")
+    (license license:expat)))
+
+(define-public python2-biopython
+  (package (inherit (package-with-python2 python-biopython))
+    (inputs
+     `(("python2-numpy" ,python2-numpy)))))
+
 (define-public bowtie
   (package
     (name "bowtie")
-- 
2.1.0

Re: [PATCH] gnu: Add Biopython.

[Ludovic Courtès]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:

> From ca3474b1a639e43d708aad4385057cd84e3cce8b Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Wed, 15 Apr 2015 17:46:35 +0200
> Subject: [PATCH] gnu: Add Biopython.
>
> * gnu/packages/bioinformatics.scm (python-biopython, python2-biopython): New
>   variables.

[...]

> +    (home-page "http://biopython.org/")
> +    (synopsis "Set of tools for biological computation in Python")

s/Set of//

> +    (description
> +     "Biopython is a set of tools for biological computation written in Python
> +by an international team of developers.")

What about removing “written ...” and instead giving a few keywords of
the features/algorithms it implements?

OK to push with these changes.

Thank you!

Ludo’.

Re: [PATCH] gnu: Add Biopython.

[Ricardo Wurmus]

Ludovic Courtès writes:

> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
>
>> From ca3474b1a639e43d708aad4385057cd84e3cce8b Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
>> Date: Wed, 15 Apr 2015 17:46:35 +0200
>> Subject: [PATCH] gnu: Add Biopython.
>>
>> * gnu/packages/bioinformatics.scm (python-biopython, python2-biopython): New
>>   variables.
>
> [...]
>
>> +    (home-page "http://biopython.org/")
>> +    (synopsis "Set of tools for biological computation in Python")
>
> s/Set of//

Okay.

>> +    (description
>> +     "Biopython is a set of tools for biological computation written in Python
>> +by an international team of developers.")
>
> What about removing “written ...” and instead giving a few keywords of
> the features/algorithms it implements?

I've changed the description to this:

     "Biopython is a set of tools for biological computation including parsers
for bioinformatics files into Python data structures; interfaces to common
bioinformatics programs; a standard sequence class and tools for performing
common operations on them; code to perform data classification; code for
dealing with alignments; code making it easy to split up parallelizable tasks
into separate processes; and more."

After checking the license again, I have doubts whether it really is
Expat.  The wording of the license differs from that of the Expat
license, though the meaning is very similar.

  http://www.biopython.org/DIST/LICENSE
  http://directory.fsf.org/wiki/License:Expat

FWIW, Fedora names the license "MIT" in their python-biopython package.
Is it really okay for me to use "license:expat" or should I use a
different one?

~~ Ricardo

Re: [PATCH] gnu: Add Biopython.

[Andreas Enge]

On Thu, Apr 16, 2015 at 10:46:11AM +0200, Ricardo Wurmus wrote:
>   http://www.biopython.org/DIST/LICENSE

It starts like this:
"Permission to use, copy, modify, and distribute this software and its
documentation with or without modifications and for any purpose and
without fee is hereby granted"

Does the provision "without fee" make it non-free?

Otherwise, I think you could use "non-copyleft" (which takes additional
arguments just like "x11-style").

Andreas

Re: [PATCH] gnu: Add Biopython.

[Ludovic Courtès]

Andreas Enge <andreas@enge.fr> skribis:

> On Thu, Apr 16, 2015 at 10:46:11AM +0200, Ricardo Wurmus wrote:
>>   http://www.biopython.org/DIST/LICENSE
>
> It starts like this:
> "Permission to use, copy, modify, and distribute this software and its
> documentation with or without modifications and for any purpose and
> without fee is hereby granted"
>
> Does the provision "without fee" make it non-free?

Good point, you may be right.  Biopython is in Debian and derivatives
AFAICS though, but it could have slipped through the cracks.

Ricardo: could you check with licensing@gnu.org?

We’ll have to await an answer.

Thanks,
Ludo’.

Re: [PATCH] gnu: Add Biopython.

[Ricardo Wurmus]

Ludovic Courtès writes:

> Andreas Enge <andreas@enge.fr> skribis:
>
>> On Thu, Apr 16, 2015 at 10:46:11AM +0200, Ricardo Wurmus wrote:
>>>   http://www.biopython.org/DIST/LICENSE
>>
>> It starts like this:
>> "Permission to use, copy, modify, and distribute this software and its
>> documentation with or without modifications and for any purpose and
>> without fee is hereby granted"
>>
>> Does the provision "without fee" make it non-free?
>
> Good point, you may be right.  Biopython is in Debian and derivatives
> AFAICS though, but it could have slipped through the cracks.
>
> Ricardo: could you check with licensing@gnu.org?

Sure, I'll write them and post an update here when I get a reply.

~~ Ricardo

Re: [PATCH] gnu: Add Biopython.

[Ricardo Wurmus]

>>> Does the provision "without fee" make it non-free?
>>
>> Good point, you may be right.  Biopython is in Debian and derivatives
>> AFAICS though, but it could have slipped through the cracks.
>>
>> Ricardo: could you check with licensing@gnu.org?

I received the following reply from licensing@gnu.org:

    > http://www.biopython.org/DIST/LICENSE

    Yes, this is a free software license typically used with Python and
    compatible with the GNU GPL. Please see:

    http://www.gnu.org/licenses/license-list.html#Python

This is good.  I'll push the commit if there are no further objections.
Thanks, everyone!

~~ Ricardo

Re: [PATCH] gnu: Add Biopython.

[Andreas Enge]

On Sat, Apr 18, 2015 at 06:01:40PM +0200, Ricardo Wurmus wrote:
> I received the following reply from licensing@gnu.org:
>     > http://www.biopython.org/DIST/LICENSE
>     http://www.gnu.org/licenses/license-list.html#Python

Great news!

Andreas

Re: [PATCH] gnu: Add Biopython.

[John Darrington]

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On Thu, Apr 16, 2015 at 11:00:30AM +0200, Andreas Enge wrote:
     
     It starts like this:
     "Permission to use, copy, modify, and distribute this software and its
     documentation with or without modifications and for any purpose and
     without fee is hereby granted"
     
     Does the provision "without fee" make it non-free?
     
I don't think it does.

From a native English speaker's perspective, I think it is free.  It 
says "for any purpose".    Ipso facto, "any purpose" embraces for the purpose
of pecuniary gain through charges for distribution.

The important words are: "Permission ... without fee ... is hereby granted."
In other words, the licensor does not demand a fee before granting that permission.
If it had said "Permission ... upon payment of fee ... will be granted". Then that
would have made the thing non-free.

I think the confusion is arising because some people might interpret 
"for any purpose and without fee" to mean: "for any purpose except distribution 
in exchange for a fee ..."

Maybe the licensors should amend the text just to avoid this possible 
misunderstanding, but in the meantime I don't think it is a problem.

(I am not a lawyer.  But I am also not illiterate.)

J'

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Re: [PATCH] gnu: Add Biopython.

[Ludovic Courtès]

John Darrington <john@darrington.wattle.id.au> skribis:

> On Thu, Apr 16, 2015 at 11:00:30AM +0200, Andreas Enge wrote:
>      
>      It starts like this:
>      "Permission to use, copy, modify, and distribute this software and its
>      documentation with or without modifications and for any purpose and
>      without fee is hereby granted"
>      
>      Does the provision "without fee" make it non-free?
>      
> I don't think it does.
>
> From a native English speaker's perspective, I think it is free.  It 
> says "for any purpose".    Ipso facto, "any purpose" embraces for the purpose
> of pecuniary gain through charges for distribution.
>
> The important words are: "Permission ... without fee ... is hereby granted."
> In other words, the licensor does not demand a fee before granting that permission.
> If it had said "Permission ... upon payment of fee ... will be granted". Then that
> would have made the thing non-free.

Oooh.  IOW “without fee” applies to “Permission”, not to “to use, copy,
modify, and distribute”, right?

That makes sense.  I think I was fooled in the past by similar wording.

Does it sound like 100% non-ambiguous to native speakers reading here?

Thanks,
Ludo’.

Re: [PATCH] gnu: Add Biopython.

[Andreas Enge]

On Thu, Apr 16, 2015 at 03:16:36PM +0200, Ludovic Courtès wrote:
> Oooh.  IOW “without fee” applies to “Permission”, not to “to use, copy,
> modify, and distribute”, right?
> That makes sense.  I think I was fooled in the past by similar wording.

Hm, I also read it as "... distribute ... without fee".

Andreas