[Biopython-dev] Deprecating Bio.PDB.Dice

[Peter Cock]

What none of us noticed till recently was that the extract function from
Bio.PDB.Dice is also exposed as Bio.PDB.extract - so people may
be using the Dice code unwittingly.

We have two options, undo the deprecation, or extend it to cover
the function via Bio.PDB.extract as well (with a minor code change
to make that a lazy import to avoid giving the deprecation warning
when import just PDB).

Peter



On Tue, Apr 25, 2017 at 5:40 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> Applied to master.
>
> Peter
>
> On Tue, Apr 18, 2017 at 1:36 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>> Pull request to do this is here:
>>
>> https://github.com/biopython/biopython/pull/1166
>>
>> Issue to reuse the code is here:
>>
>> https://github.com/biopython/biopython/issues/1167
>>
>> On Tue, Apr 18, 2017 at 1:29 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>>> Hello all,
>>>
>>> This came up in discussion on GitHub issue #820 [*] about turning
>>> existing self-tests into proper unit tests for user under TravisCI etc.
>>>
>>> Bio/PDB/Dice.py is essentially an example of how to write your
>>> own selector for use with PDBIO to write a subset of a PDB file.
>>>
>>> We are proposing to formally deprecate Bio.PDB.Dice (and later
>>> remove it [**]), and ideally reuse this as an example script and/or
>>> test case.
>>>
>>> If anyone is using the Dice module, please let us know.
>>>
>>> Thank you,
>>>
>>> Peter
>>>
>>> [*] https://github.com/biopython/biopython/issues/820
>>> [**] http://biopython.org/wiki/Deprecation_policy