[Biopython-dev] Use of depreciated string functions

[Bruce Southey]

Peter wrote:
> On Fri, Nov 21, 2008 at 3:19 PM, Bruce Southey <bsouthey at gmail.com> wrote:
>   
>> Hi,
>> There are a number of files in Bio that import string. Many of these use
>> depreciated functions (since Version 2) that are now string methods mainly
>>  string.atof(), string.atoi()  and string.join(). The only real advantage of
>> modifying these is to remove an import statement because these will not be
>> removed until Python 3.
>>
>> Perhaps the one exception is in HotRand.py: hex_digit =
>> string.hexdigits.find( letter )
>>
>> There are about 23 unique files that I identified via grep and many have
>> more than one usage. While changing these is busy work, please let me know
>> if you would like me to create patches for the next version of Biopython (ie
>> 1.50) or just ignore this.
>>     
>
> As you say, there isn't much benefit from doing this other than
> removing an import and making another small step towards Python 3.0
> compatibility.  We have gradually been phasing out "import string"
> already, usually when working on a module which used it.
>
> Once I've dealt with Biopython 1.49, I'd be happy to look at a patch
> to remove more "import string" usage from non-obsolete, non-deprecated
> code.  It would be a little risky doing this to modules without unit
> tests, but that's another area you've shown some interest in anyway...
>
> Thanks,
>
> Peter
>
>   
Hi,
I was planning to get started on with these depending on what time I 
have available. So just a quick question:
Do you want one bug report per patch per file?

Or just let me know if there is another way.

Thanks
Bruce