[Biopython] ERROR: test_doctests

[Peter Cock]

Hi Michal,

Thanks for running that - I had been expected something unusual
on your machine, but the actual problem is more mundane.

On Sat, Apr 9, 2011 at 7:39 AM, Michal <mictadlo at gmail.com> wrote:
> $ python test_Tutorial.py
> Runing Tutorial doctests...
> **********************************************************************
> ...

The important bits are this (three times):

IOError: [Errno 2] No such file or directory: 'ls_orchid.gbk'

and this (also by coincidence three times):

IOError: [Errno 2] No such file or directory: 'PF05371_seed.sth'

There are a bunch of NameError exceptions which are direct
side effects of these missing files not being loaded.

You can see the files here:

https://github.com/biopython/biopython/tree/master/Doc/examples
http://biopython.open-bio.org/SRC/biopython/Doc/examples/

However, they were not being included in the source code
bundles for each release. This should be fixed now:
https://github.com/biopython/biopython/commit/35bd34383d6333f1a0499a581aa1d7235d8d7cfb

For your installation, you don't need to worry about this test
failure. If you want see all the tests pass, just download the
two missing files manually.

Sorry about this - it should have been caught during the
release build, but this isn't fully automated.

Thank you for reporting this :)

Peter