[Biopython-dev] [Wg-phyloinformatics] BioGeography update/BioPython tree module discussion

[Nick Matzke]

Peter wrote:
> On Mon, Aug 10, 2009 at 9:23 PM, Nick Matzke<matzke at berkeley.edu> wrote:
>> Hi all...updates...
>>
>> Summary: Major focus is getting the GBIF access/search/parse module into
>> "done"/submittable shape.  This primarily requires getting the documentation
>> and testing up to biopython specs.  I have a fair bit of documentation and
>> testing, need advice (see below) for specifics on what it should look like.
>>
>>> - The test code should move to the 'Tests' directory as a set of
>>>  test_Geography* files that we can use for unit testing the code.
>> OK, I will do this.  Should I try and figure out the unittest stuff?  I
>> could use a simple example of what this is supposed to look like.
> 
> You can either go for "unittest" based tests (generally better, but more
> of a learning curve - but useful for any python project), or our own
> Biopython specific "print and compare" tests (basically sample scripts
> with their expected output).
> 
> Read the tests chapter in the Biopython Tutorial if you haven't already.
> (And if you think anything could be clearer, or you spot a typo, let us
> know please - feedback would be great).

Thanks!
Nick

> 
> Peter
> 

-- 
====================================================
Nicholas J. Matzke
Ph.D. Candidate, Graduate Student Researcher
Huelsenbeck Lab
Center for Theoretical Evolutionary Genomics
4151 VLSB (Valley Life Sciences Building)
Department of Integrative Biology
University of California, Berkeley

Lab websites:
http://ib.berkeley.edu/people/lab_detail.php?lab=54
http://fisher.berkeley.edu/cteg/hlab.html
Dept. personal page: 
http://ib.berkeley.edu/people/students/person_detail.php?person=370
Lab personal page: http://fisher.berkeley.edu/cteg/members/matzke.html
Lab phone: 510-643-6299
Dept. fax: 510-643-6264
Cell phone: 510-301-0179
Email: matzke at berkeley.edu

Mailing address:
Department of Integrative Biology
3060 VLSB #3140
Berkeley, CA 94720-3140

-----------------------------------------------------
"[W]hen people thought the earth was flat, they were wrong. When people 
thought the earth was spherical, they were wrong. But if you think that 
thinking the earth is spherical is just as wrong as thinking the earth 
is flat, then your view is wronger than both of them put together."

Isaac Asimov (1989). "The Relativity of Wrong." The Skeptical Inquirer, 
14(1), 35-44. Fall 1989.
http://chem.tufts.edu/AnswersInScience/RelativityofWrong.htm
====================================================