Re: Adding python3-biopython

[Peter Cock <p.j.a.cock@googlemail.com>]

On Wed, Mar 5, 2014 at 12:28 PM, Andreas Tille <andreas@an3as.eu> wrote:
>
> Hi again,
>
> when running biopython test suite I detected a wrong error message in
> Tests/test_Cluster.py
>
>
> ...
>
> import unittest
>
> try:
>     from Bio import Cluster
> except ImportError:
>     from Bio import MissingPythonDependencyError
>     raise MissingPythonDependencyError("If you want to use Bio.Cluster, "
>                                        "install NumPy first and then "
>                                        "reinstall Biopython")
>
> try:
>     import numpy
> except ImportError:
>     from Bio import MissingPythonDependencyError
>     raise MissingPythonDependencyError(
>         "Install NumPy if you want to use Bio.Cluster")
>
> ...
>
>
> The first error message is misleading since the problem is not the
> missing NumPy but rather Bio.Cluster seems to be broken.
>
> Is it OK if I send this kind of reports to you or should I rather use
> the bug tracker or any mailing list.  Sorry, I have not maintained the
> package before and thus do  not know the prefered way of communication.
>
> Kind regards
>
>         Andreas.


Hi Andreas,

Apologies for the later reply, I missed this email.

I agree the import checks are in the wrong order, fixed on the
master branch (which will be in the forthcoming Biopython 1.64):

https://github.com/biopython/biopython/commit/3e0f34a2adc83a80864348f74cb034da58af905e

Thanks,

Peter