[Biopython-dev] Progress with ticket 3336

[Nate Sutton]

I appreciate your review of the code, the feedback helps me become better!  I made the pull request here: https://github.com/biopython/biopython/pull/189 .  

I have worked on fixing all the things you commented on and added comments describing the edits to the new file version at: https://github.com/nmsutton/biopython/commit/893a6508ad18278b9d5cdb10d3c81c823125c90f
and 2 minor changes at:
https://github.com/nmsutton/biopython/commit/c8215edba1bd796684722372cec3c94bffdafc91

-Nate

P.S.  To acknowledge assistance I got from a friend I added a co-authored-by line in the commit due to reading that can be helpful for authors who want to include that they were helped with their code.  If you or anyone else knows a better way to let others get recognized for providing assistance on someone's code let me know.


________________________________
 From: Eric Talevich <eric.talevich at gmail.com>
To: Nate Sutton <natemsutton at yahoo.com> 
Cc: "biopython-dev at lists.open-bio.org" <biopython-dev at lists.open-bio.org> 
Sent: Sunday, June 16, 2013 10:15 AM
Subject: Re: [Biopython-dev] Progress with ticket 3336
 


On Tue, May 7, 2013 at 5:12 PM, Nate Sutton <natemsutton at yahoo.com> wrote:

Hi,
>
>Here is a progress follow up to http://lists.open-bio.org/pipermail/biopython-dev/2013-April/010548.html .  I have added a commit to the github branch that adds an option to create claude branch lines using linecollection.  The linecollection objects are stored in a tuple before adding them to the plot.  It’s in Bio/Phylo/_utils.py.  Is this what the last bullet point was requesting in https://redmine.open-bio.org/issues/3336 ?  
>
>Thanks!
>
>Nate
>
>P. S.  I used a tuple to store the linecollection objects instead of a list because that was mentioned in the ticket but if that looks like it should be different let me know.  Also, I got some global variables to work with the code but I was only able to do that after declaring them as globals twice.  If there are suggestions on how to code that differently let me know.
>
 


Hi Nate,

I left some comments on your commits in your branch on GitHub. When you're done, would you mind rebasing to the current master branch and doing a pull request?

Regarding
 the global variables, I think you might have to declare them as such in
 every new scope where they're used, or not at all, and in this case, 
you don't need to declare them as global at all.

Thanks,
Eric