Re: [PATCH] Add python2-seqmagick.

[Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>]

Ben Woodcroft <b.woodcroft@uq.edu.au> writes:

>>> +       ("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?

I’m sorry to have confused you here.  “biopython” should *not* be a
propagated input here, because “seqmagick” provides an executable, not a
library.  I was not aware of the fact that the executables are
automatically wrapped here (although the PYTHONPATH is a little too
broad as you also noted).

> 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?

Good question.  I think it’s because the wrapping phase just wraps the
scripts in “$out/bin” with whatever the PYTHONPATH variable contains.
It doesn’t construct a minimally sufficient PYTHONPATH.  Maybe that’s
worth changing in the python-build-system?

>>> +    (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"

That’s okay.

>>> +    (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?

I’m still not sure, but the explicit mention of “v3” is enough for me to
not write “gpl3+” here.

I’ll push your latest patch with minor modifications (undoing the
“propagated-inputs” confusion I caused and moving the synopsis on one
line).

Thanks again!

~~ Ricardo