[Biopython-dev] Deprecating Bio.ParserSupport, Bio.Blast.NCBIStandalone

[Michiel de Hoon]

Hi Peter,

--- On Wed, 1/30/13, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> However for anything like the following convenient
> alternatives to work and run the doctests, you need
> some path magic:
> ~/biopython $ emacs Bio/SeqRecord.py
> ~/biopython $ python Bio/SeqRecord.py

Here I agree.
> Or,
> 
> ~/biopython/Bio $ emacs SeqRecord.py
> ~/biopython/Bio $ python SeqRecord.py
> 
Well I was thinking that the doctests in SeqRecord.py could use a relative path to the Tests directory, e.g. ../Tests/Quality/solexa_faked.fastq.
But I agree that this will fail again for any script in submodules.

Still I would think that there is a better way to do this, and I doubt that we are the first ones who want to access test files with doctests. I can write a short message to comp.lang.python to see have anybody has any suggestions.

Best,
-Michiel.