Yes, some logging system that you could initialize and have the output of all your commands post to would be amazing

On Feb 20, 2013, at 3:40 PM, Greg Caporaso <notifications@github.com> wrote:

> In doc/developer/coding_guidelines.rst:
> 
> >  
> >   * if you have been passing dest= to parser.add_option, note that you do not need to do this -- dest will be generated from the long format option (e.g., the value passed to --input_file will be stored in input_file)
> >   
> >   * Your usage string should be defined in a variable called ``usage_str`` as a multiline string outside of the function that is using it. This makes the code look neater, and will help automated documentation tools find that text (eventually). 
> >  
> > + * Scripts that process a metadata mapping file and a data file (biom-formatted otu table, distance matrix, principal coordinates file, etc.) within QIIME, should execute faultlessly in the case where sample identifiers exist only in the mapping file but not in the data files.
> We haven't been doing that to-date (e.g., in make_3d_plots.py). I agree that it would be good, but might require a centralized logging system (something I'd really like to get in place - more on that at the strategic directions call) to do efficiently.
> 
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