+1 to Emily's

On Apr 23, 2014, at 9:36 AM, teravest <notifications@github.com> wrote:

> In tests/test_commands/test_table_validator.py:
> 
> > +                   "rows":[
> > +{"id":"GG_OTU_1", "metadata":{"taxonomy":["k__Bacteria", "p__Proteobacteria",\
> > + "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae",\
> > +  "g__Escherichia", "s__"]}},
> > +{"id":"GG_OTU_2", "metadata":{"taxonomy":["k__Bacteria", "p__Cyanobacteria", \
> > +"c__Nostocophycideae", "o__Nostocales", "f__Nostocaceae", "g__Dolichospermum",\
> > +"s__"]}},
> > +{"id":"GG_OTU_3", "metadata":{"taxonomy":["k__Archaea", "p__Euryarchaeota",\
> > +"c__Methanomicrobia", "o__Methanosarcinales", "f__Methanosarcinaceae",\
> > +"g__Methanosarcina", "s__"]}},
> > +{"id":"GG_OTU_4", "metadata":{"taxonomy":["k__Bacteria", "p__Firmicutes",\
> > +"c__Clostridia", "o__Halanaerobiales", "f__Halanaerobiaceae",\
> > +"g__Halanaerobium", "s__Halanaerobiumsaccharolyticum"]}},
> > +{"id":"GG_OTU_5", "metadata":{"taxonomy":["k__Bacteria",\
> > +"p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales",\
> > +"f__Enterobacteriaceae", "g__Escherichia", "s__"]}}
> I think this would be better
> 
>                     "generated_by": "QIIME revision XYZ",
>                     "date": "2011-12-19T19:00:00",
>                     "rows":[
>                         {"id":"GG_OTU_1",
>                          "metadata":{"taxonomy":["k__Bacteria",
>                                                  "p__Proteobacteria",
>                                                  "c__Gammaproteobacteria",
>                                                  "o__Enterobacteriales",
>                                                  "f__Enterobacteriaceae",
>                                                  "g__Escherichia", "s__"]}},
>                         {"id":"GG_OTU_2", 
>                             "metadata":{"taxonomy":["k__Bacteria",
>                                                     "p__Cyanobacteria",
>                                                     "c__Nostocophycideae",
>                                                     "o__Nostocales",
>                                                     "f__Nostocaceae",
>                                                     "g__Dolichospermum",
>                                                     "s__"]}},
>                         {"id":"GG_OTU_3", 
>                             "metadata":{"taxonomy":["k__Archaea",
>                                                     "p__Euryarchaeota",
>                                                     "c__Methanomicrobia",
>                                                     "o__Methanosarcinales",
>                                                     "f__Methanosarcinaceae",
>                                                     "g__Methanosarcina",
>                                                     "s__"]}},
>                         {"id":"GG_OTU_4", 
>                          "metadata":{"taxonomy":["k__Bacteria",
>                                                  "p__Firmicutes",
>                                                  "c__Clostridia",
>                                                  "o__Halanaerobiales",
>                                                  "f__Halanaerobiaceae",
>                                                  "g__Halanaerobium",
>                                                  ("s__Halanaerobiumsa"
>                                                   "ccharolyticum")]}},
>                         {"id":"GG_OTU_5", 
>                          "metadata":{"taxonomy":["k__Bacteria",
>                                                  "p__Proteobacteria",
>                                                  "c__Gammaproteobacteria",
>                                                  "o__Enterobacteriales",
>                                                  "f__Enterobacteriaceae",
>                                                  "g__Escherichia", "s__"]}}
>                         ],
> It is much clearer what goes in each category, it is pep8 (but my linter is complaining about
> 
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