[bip] Bioinformatics software design

[Kevin Teague]

>
> 1. What would you consider to be a good "API"?
>           well-documented, intuitive, best guess works, pythonic,  
> do people have any examples of what they consider a good API/project?

If you are going with a Python API, then the zope.interface and  
zope.schema packages provides a good way of formally describing a  
Python API:

  - http://pypi.python.org/pypi/zope.interface

  - http://pypi.python.org/pypi/zope.schema

If you have a formally described data schema for your applications  
input/ouptut objects used by your API (e.g. input = "Integer named  
'foo' whose value is > 0 and < 10", output = "Float name 'result'"),  
then it's not too hard to automatically map those to a web service  
API or set of HTML views. It's also a convention with these packages  
that those interfaces that are stable are put into a file named  
'interfaces.py', e.g. the new plone4bio interfaces:

http://www.plone4bio.org/trac/browser/plone4bio.base/trunk/plone4bio/ 
base/interfaces.py

Also, if doing the Python API route and using more than just plain  
Python, it's invaluable to have a build tool that can be used to  
compile and configure all of the moving parts of your application.  
You can use this to make it much easier for end users to install the  
software on whatever platform they happen to be running, as well as  
to bring new developers on your team quickly up to speed. As a  
sysadmin it sucks to have a bioinformatician ask for some software to  
be made available on our servers and realize that the project only  
has an error-filled 12 page INSTALL.txt file (even if the INSTALL.txt  
continually re-assures the frustrated sysadmin that "CPAN is great")!

For example, the PrimaGIS guys depend upon *a lot* of stuff, so they  
maintain a "buildout" project that will compile and configure all of  
the parts required to run their system:

http://trac.gispython.org/projects/PrimaGIS/wiki/PrimaGISBuildout

I've used both BuildIt and zc.buildout, both are good products - the  
PrimaGIS project is a good example of complex buildout using BuildIt.  
zc.buildout is a fairly new project, but it's being used by the Zope/ 
Plone folks so there are already a lot of "recipes" that can be used  
to install assorted parts that your app might depend upon:

  - http://agendaless.com/Members/chrism/software/buildit/

  - http://pypi.python.org/pypi/zc.buildout

  - zc.buildout recipes: http://pypi.python.org/ 
pypi?:action=browse&c=512

  - zc.buildout "configure; make; make install" recipe: http:// 
pypi.python.org/pypi/zc.recipe.cmmi/


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