[Biopython-dev] Deprecating Bio.PDB.Dice

[Peter Cock]

I've opted for the simple change and reverted the deprecation
done in https://github.com/biopython/biopython/pull/1166

See:

https://github.com/biopython/biopython/commit/3b7f121371e2a0f30177a7643acf9ac521996ffd

Peter

On Mon, May 8, 2017 at 3:30 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 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