On 18/09/15 01:51, Ricardo Wurmus wrote:
> Hi Ben,
>
> thank you very much for your patch!
and you sir, for the review.
>> +    (inputs
>> +     `(("python-setuptools" ,python2-setuptools)
> I think this should be a native input instead.
ok
>> +       ("python-biopython" ,python2-biopython)))
> And this looks like it should be a propagated input instead.  Have you
> tried running seqmagick after installing it with this package recipe?  I
> found that Python executables often require either propagated inputs or
> wrapping in PYTHONPATH to work without runtime errors.
I did, although not well enough to pick up the error you point out. 
Actually I'm a bit confused as to the difference between the input types 
even after reading the manual. Is this a fair summary?

native-inputs: required for building but not runtime - installing a 
package through a substitute won't install these inputs
inputs: installed in the store but not in the profile, as well as being 
present at build time
propagated-inputs: installed in the store and in the profile, as well as 
being present at build time


Anyway, it seems as if the package would have worked because a wrapper 
is generated with PYTHONPATH including inputs, propagated-inputs and 
native-inputs. But this seems a bit strange - why would native inputs be 
in the runtime wrapper?

$ cat /tmp/a.fa
 >a
ATGG
$ ./pre-inst-env guix environment --ad-hoc seqmagick --pure -E 'echo 
$PATH; echo $PYTHONPATH; seqmagick info /tmp/a.fa'
;;; note: source file /home/ben/git/guix/gnu/packages/bioinformatics.scm
;;;       newer than compiled 
/home/ben/git/guix/gnu/packages/bioinformatics.go
/gnu/store/bjd27hqk0wnh28nzmawjymdh3gfk98pn-seqmagick-0.6.1/bin

name      alignment    min_len   max_len   avg_len  num_seqs
/tmp/a.fa FALSE              4         4      4.00         1



$ cat 
/gnu/store/bjd27hqk0wnh28nzmawjymdh3gfk98pn-seqmagick-0.6.1/bin/.seqmagick-wrap-01 

#!/gnu/store/cpx9iibpdwi3wb81glpnnlxr9zra2iiv-bash-4.3.39/bin/bash
export 
PYTHONPATH="/gnu/store/bjd27hqk0wnh28nzmawjymdh3gfk98pn-seqmagick-0.6.1/lib/python2.7/site-packages:/gnu/store/qlf4k2b81wms6avlyny7hix175asg8kg-python-2.7.10/lib/python2.7/site-packages:/gnu/store/zmhk5r3lmc3s8ivdx9vv6m5vzn6fqim5-python2-setuptools-12.1/lib/python2.7/site-packages:/gnu/store/20s2vvslsapynhmbfsa3q2iyv9dzjzr2-python2-nose-1.3.4/lib/python2.7/site-packages:/gnu/store/c7navsrzibg2rjgs1fzqry711wch5f3p-python2-biopython-1.65/lib/python2.7/site-packages:/gnu/store/bjd27hqk0wnh28nzmawjymdh3gfk98pn-seqmagick-0.6.1/lib/python2.7/site-packages/${PYTHONPATH:+:}$PYTHONPATH"
exec -a "$0" 
"/gnu/store/bjd27hqk0wnh28nzmawjymdh3gfk98pn-seqmagick-0.6.1/bin/.seqmagick-real" 
"$@"

>> +    (native-inputs
>> +     `(("python-nose" ,python2-nose)))
>> +    (home-page "http://github.com/fhcrc/seqmagick")
>> +    (synopsis
>> +     "Tools for converting and modifying sequence files from the command-line")
> The synopsis is a bit long.  You could shave off two words like this:
>
>    “Command-line tools for converting and modifying sequence files”
>
> but that’s not really much better.  I’m open to suggestions.
"Tools for converting and modifying sequence files"
>> +    (description
>> +     "Bioinformaticians often have to convert sequence files between formats
>> +and do little manipulations on them, and it's not worth writing scripts for
>> +that.  Seqmagick is a utility to expose the file format conversion in
>> +BioPython in a convenient way.  Instead of having a big mess of scripts, there
>> +is one that takes arguments.")
>> +    (license license:gpl3)))
>> +
> I’m not sure if it’s really “GPLv3 only” or “GPLv3 or later” as there
> are no license headers anywhere.  Maybe others could comment what’s the
> proper declaration here.
 From the readme:
 >|seqmagick| is free software under the GPL v3.

Is that not straightforward enough?

Thanks,
ben