[Biopython-dev] Code review request for phyloxml branch

[Peter]

On Mon, Jan 11, 2010 at 4:43 PM, Eric Talevich <eric.talevich at gmail.com> wrote:
> On Mon, Jan 11, 2010 at 11:17 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
>> Or (if the functions are reasonably complex) keep the
>> input/output code in a separate file, but make it explicit
>> that it is not a public interface - e.g. use Bio/Phylo/_IO.py?
>
> Something like this?
>
> Phylo/
>    BaseTree.py
>    Newick.py
>    PhyloXML.py
>    _IO.py
>    _Utils.py
>    PhyloXMLIO.py
>    NewickIO.py
>    NexusIO.py
>
> This plays well with the expected import styles:
>
> from Bio import Phylo  # most common
> from Bio.Phylo import PhyloXML  # access the defined types
> from Bio.Phylo import PhyloXMLIO  # special parsing

I'd forgotten Bio/Phylo/IO was a directory, and that the users may
want to access PhyloXMLIO directly. That suggested structure
looks reasonable... what do you think Michiel?

Peter