why? if 'clarity' is not the metric then what metric are we using to
exclude this kind of method? i did a cursory search to look for performance
information and found nothing. if it's a performance issue that seems
totally reasonable, but absent that it seems arbitrary.


On Wed, Dec 4, 2013 at 10:48 AM, Jose Carlos Clemente Litran <
notifications@github.com> wrote:

> In qiime/otu_significance.py:
>
> > +    taxonomy_md = biom_taxonomy_formatter(bt, md_key)
> > +    if taxonomy_md is not None:
> > +        for i in range(num_lines):
> > +            lines[i+1]=lines[i+1]+'\t'+taxonomy_md[i] #skip header line in lines
> > +    return lines
> > +
> > +# Functions for gradient correlation testing
> > +
> > +def grouped_correlation_row_
> generator(bt, pmf, category, gc_to_samples):
> > +    '''Create generator for grouped correlation tests.
> > +
> > +    '''
> > +    data = array([bt.observationData(i) for i in bt.ObservationIds])
> > +    category_values = gc_to_samples.keys()
> > +    samples = gc_to_samples.values()
> > +    sample_inds = [[bt.getSampleIndex(i) for i in group] for group in samples]
>
> Although this one is clear, I think we should just not allow nested list
> comprehensions for clarity and make this part of our guidelines.
> @gregcaporaso <https://github.com/gregcaporaso> @jrrideout<https://github.com/jrrideout>
> @antgonza <https://github.com/antgonza> @ElDeveloper<https://github.com/ElDeveloper>
> @adamrp <https://github.com/adamrp> @walterst<https://github.com/walterst>what do you think?
>
> —
> Reply to this email directly or view it on GitHub<https://github.com/qiime/qiime/pull/1091/files#r8103175>
> .
>