[Biopython-dev] Bio.Motif._Motif has_instances, has_counts

[Peter Cock]

On Fri, Aug 10, 2012 at 9:33 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Thu, Aug 9, 2012 at 5:00 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
>> OK, done. Thanks!
>> -Michiel.
>
> You'll also need to update the example in the Tutorial, quote:
>
>     The arnt and srf motifs can both do the same things for us,
>     but they use different internal representations of the motif.
>     We can tell that by inspecting the \verb|has_counts| and
>     has_instances properties:
>
>     >>> arnt.has_instances
>    True
>     >>> srf.has_instances
>     False
>     >>> srf.has_counts
>     True
>
> This means test_Tutorial.py is failing (across all platforms).
> Presumably we would suggest switching these to somethinglike:
>
>     >>> arnt.instances is None
>     False

Fixed:
https://github.com/biopython/biopython/commit/b866e74dc9b6162517588ea4c0e4d1ecde5ed87c

> etc? In fact given the old methods were documents like
> this, I would be happier if we could phase them out with
> a deprecation warning via a read only property method,
>
>     @property
>     def has_instances(self):
>         """"Does this motif have instances (DEPRECATED)."""
>         import warnings
>         from Bio import BiopythonDeprecationWarning
>         warnings.warn("Check if motif.instance is None or not instead",
>             BiopythonDeprecationWarning)
>         return self.instances is not None
>
> (untested, but something like that)

Done:
https://github.com/biopython/biopython/commit/fd2223d118227c921524e070c803b97bc979a70f

Although since that won't work on old Biopython either (you'd
get an AttributeError), perhaps we should label these new
backwards compatible properties as obsolete with a pending
deprecation warning for the next release (delay the deprecation)?

Peter