ENH: adds citations (#177)

q2_types/citations.bib

@@ -0,0 +1,20 @@
+@article{mcdonald2012biological,
+  title={The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome},
+  author={McDonald, Daniel and Clemente, Jose C and Kuczynski, Justin and Rideout, Jai Ram and Stombaugh, Jesse and Wendel, Doug and Wilke, Andreas and Huse, Susan and Hufnagle, John and Meyer, Folker and Knight, Rob and Caporaso, J Gregory},
+  journal={GigaScience},
+  volume={1},
+  number={1},
+  pages={7},
+  year={2012},
+  publisher={BioMed Central},
+  doi={10.1186/2047-217X-1-7}
+}
+
+@InProceedings{ mckinney-proc-scipy-2010,
+  author    = { Wes McKinney },
+  title     = { Data Structures for Statistical Computing in Python },
+  booktitle = { Proceedings of the 9th Python in Science Conference },
+  pages     = { 51 -- 56 },
+  year      = { 2010 },
+  editor    = { St{\'e}fan van der Walt and Jarrod Millman }
+}

q2_types/feature_table/_format.py

@@ -7,10 +7,11 @@
 # ----------------------------------------------------------------------------
 import ijson
 import h5py
+import biom
 
 import qiime2.plugin.model as model
 
-from ..plugin_setup import plugin
+from ..plugin_setup import plugin, citations
 
 
 class BIOMV100Format(model.TextFileFormat):
@@ -91,6 +92,6 @@ def sniff(self):
                                                  'feature-table.biom',
                                                  BIOMV210Format)
 
-plugin.register_formats(
-    BIOMV100Format, BIOMV210Format, BIOMV100DirFmt, BIOMV210DirFmt
-)
+plugin.register_views(BIOMV100Format, BIOMV210Format, BIOMV100DirFmt,
+                      BIOMV210DirFmt, biom.Table,
+                      citations=[citations['mcdonald2012biological']])

q2_types/plugin_setup.py

@@ -8,12 +8,13 @@
 
 import importlib
 
+import pandas as pd
 import qiime2.plugin
 import qiime2.sdk
 
 from q2_types import __version__
 
-
+citations = qiime2.plugin.Citations.load('citations.bib', package='q2_types')
 plugin = qiime2.plugin.Plugin(
     name='types',
     version=__version__,
@@ -24,6 +25,9 @@
     short_description='Plugin defining types for microbiome analysis.'
 )
 
+plugin.register_views(pd.Series, pd.DataFrame,
+                      citations=[citations['mckinney-proc-scipy-2010']])
+
 importlib.import_module('q2_types.feature_table')
 importlib.import_module('q2_types.distance_matrix')
 importlib.import_module('q2_types.tree')

setup.py

@@ -25,6 +25,7 @@
         ['q2-types=q2_types.plugin_setup:plugin']
     },
     package_data={
+        'q2_types': ['citations.bib'],
         'q2_types.tests': ['data/*'],
         'q2_types.distance_matrix.tests': ['data/*'],
         'q2_types.feature_data.tests': ['data/*', 'data/taxonomy/*'],