[Biopython-dev] Pending deprecations

[Frank Kauff]

On 12/21/2010 07:21 PM, Peter wrote:
> On Tue, Dec 21, 2010 at 3:15 PM, Michiel de Hoon<mjldehoon at yahoo.com>  wrote:
>> --- On Sat, 12/18/10, Peter<biopython at maubp.freeserve.co.uk>  wrote:
>>>> Bio.Nexus.Nexus._kill_comments_and_break_lines
>>> That's a private method so we can just remove it.
>>>
>> Well, looking at this code it seems that this method is still needed if
>> cnexus (C module) is not available, for example in case of Jython.
>> So I think we should remove the PendingDeprecationWarning for
>> this function because we cannot remove it.
Yep, that's what it's for. Not needed if cnexus code is available. 
However, if it is needed, the method takes a prohibitive amount of time 
for larger nexus files anyway. We could still remove it and make cnexus 
mandatory, I don't see any reason why cnexus could not be available.

Frank
> I haven't checked, but that sounds sensible.
>
> Peter
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