[Biopython] problem with Bio.Align _aligns.c

[Peter Cock]

On Wed, Jun 27, 2018 at 1:05 PM, Francesco Gastaldello (Staff)
<f.gastaldello at dundee.ac.uk> wrote:
>
> The problem with Bio.SeqIO and other related C modules disappear when I’m
> outside the source directory.
>
> What does it mean? I haven’t touched the code for those modules.
>

Python will import local file foo.py or foo/__init__.py over an
installed module foo of the same name. That is likely part
of this?

However, in run_tests.py we try to prioritise the locally built
Biopython over any (older) copy which might already be installed.
It seems that the sys.path manipulation to do that might be
breaking somehow?

https://github.com/biopython/biopython/blob/biopython-172/Tests/run_tests.py#L218

There is a known issue that this trick does not seem to
work for the doctests:

https://github.com/biopython/biopython/issues/531

But the goal is to support this flow:

python setup.py build
python setup.py test
python setup.py install

Note internally, that will change to the Tests/ directory,
and run:

python run_tests.py

Peter