[Biopython-dev] Features of the GSOC branch ready to be merged

[Peter]

2010/12/16 Eric Talevich <eric.talevich at gmail.com>:
> On Thu, Dec 9, 2010 at 2:03 PM, Eric Talevich <eric.talevich at gmail.com>wrote:
>
>> On Tue, Nov 30, 2010 at 10:45 AM, João Rodrigues <anaryin at gmail.com>wrote:
>>
>>> Hello all,
>>>
>>> I've been looking at the code I wrote for the GSOC to see what is ready to
>>> be merged in the main branch. I have to thank Kristian and whoever
>>> participated in the Python & Friends for the input.
>>>
>>>
>> Hi João,
>>
>> It sounds like everyone is happy with this branch:
>> https://github.com/JoaoRodrigues/biopython/tree/atom-element
>>
>> So I will try to fetch your branch, correct the spelling of the
>> IUPACData.atom_weights references (unless you beat me to it), test, rebase
>> onto biopython/biopython/master, and merge it this weekend.
>>
>
>
> I just did this and pushed it to biopython/biopython/master. The Biopython
> network graph on GitHub looks reasonable and the tests pass, so I think it
> all went OK.
> https://github.com/biopython/biopython/commits/master

Hi Eric,

Yeah, it looks OK. For future reference (and I'm trying to be constructive
rather than critical), there were a few things like these commits which
could have been omitted:

https://github.com/biopython/biopython/commit/06008c298c14a2178bebf1f9795c0740f02937b1
https://github.com/biopython/biopython/commit/f4568562a914d31f04a55148b9aa927e849b101d
https://github.com/biopython/biopython/commit/6c7ef358e5f93599ca165ce8e7b46261106e2b06
https://github.com/biopython/biopython/commit/9a4a3a5b968e8918fd6ca02b436382c1e3c5d604

Also there appears to have been a net change to Tests/PDB/1A8O.pdb
(just white space so probably harmless).

In this particular case I would have been tempted to have collapsed
it all into just one or two commits - it is actually quite a small
change overall, and much easier to follow. As it stands we see
several iterations of the code (e.g. adding them removing the
hetatm arg, removing then restoring elements in one of the test
files). In some respects this is more a matter of taste, the end
result is the same. What are your thoughts on this Eric (et al)?

Regards,

Peter