[Biopython] problem with Bio.Align _aligns.c

[Peter Cock]

OK, so this seems to affect all the C code on the master branch
(which is currently what I would like to release as Biopython 1.72).

Can you work out what has changed on your system to trigger
this? Is it specific to using a virtual environment?

On the bright side, it looks like my last attempt to fix the wheels
worked - making a copy of the test folder to ensure an isolated
test environment, rather than a symlink:

https://travis-ci.org/biopython/biopython-wheels/builds/396456761

Peter

On Tue, Jun 26, 2018 at 3:35 PM, Francesco Gastaldello (Staff)
<f.gastaldello at dundee.ac.uk> wrote:
> I'm running the test via Pycharm and it is connected to my origin and
> upstream branches on GitHub.
>
>
> I've done a quick test of the other modules that use C and I can confirm
> that the same problem is visible.
>
> I've run some tests even on the master branch, which I consider to be stable
> environment.
>
>
> Francesco
>
> ________________________________
> From: Peter Cock <p.j.a.cock at googlemail.com>
> Sent: 26 June 2018 15:29:39
> To: Francesco Gastaldello (Staff)
> Cc: biopython at mailman.open-bio.org
> Subject: Re: [Biopython] problem with Bio.Align _aligns.c
>
> You must be running from Git, perhaps even the
> provisional tag for Biopython 1.72?
>
> The error is worryingly similar to what I am getting
> with the automated wheels for Linux and macOS
> under TravisCI - they seem to build fine, but when
> running the tests, the compiled code can't be found.
>
> This is holding up the Biopython 1.72 release, see also:
> http://mailman.open-bio.org/pipermail/biopython/2018-June/016474.html
>
> Do you see this with other C code as well, e.g.
> Bio.Cluster, or cpairwise2, or KDTree?
>
> Perhaps this is a problem with the current code in
> GitHub, not just something strange with the multi-
> wheel setup as I had been assuming?
>
> Peter
>
> On Tue, Jun 26, 2018 at 12:26 PM, Francesco Gastaldello (Staff)
> <f.gastaldello at dundee.ac.uk> wrote:
>> Hi all,
>>
>>
>> I have a virtual environment with python 2.7.15rc1 and I get this error
>> when
>> I run some commands:
>>
>>
>> ////
>>
>> Python 2.7.15rc1 (default, Apr 15 2018, 21:51:34)
>> [GCC 7.3.0] on linux2
>> Type "help", "copyright", "credits" or "license" for more information.
>>>>> from Bio import SeqIO
>> Traceback (most recent call last):
>>   File "<stdin>", line 1, in <module>
>>   File "Bio/SeqIO/__init__.py", line 375, in <module>
>>     from Bio.Align import MultipleSeqAlignment
>>   File "Bio/Align/__init__.py", line 22, in <module>
>>     from Bio.Align import _aligners
>> ImportError: cannot import name _aligners
>>
>> ////
>>
>>
>> I've made sure to run "python setup.py build" before trying anything but
>> that did not solve the problem.
>>
>> I'm on Ububtu 18.04 on a virtual machine.
>>
>>
>> Thanks,
>>
>> Francesco
>>
>>
>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>
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