IMP: 'subsample' action renamed to 'subsample_ids' (#301)

Author: hagenjp

q2_feature_table/__init__.py

@@ -7,7 +7,7 @@
 # ----------------------------------------------------------------------------
 
 from ._normalize import rarefy
-from ._subsample import subsample
+from ._subsample_ids import subsample_ids
 from ._transform import (presence_absence, relative_frequency, transpose)
 from ._summarize import (summarize, tabulate_seqs, tabulate_sample_frequencies,
                          tabulate_feature_frequencies, summarize_plus)
@@ -28,7 +28,7 @@
            'summarize', 'merge', 'merge_seqs', 'filter_samples',
            'filter_features', 'merge_taxa', 'tabulate_seqs', 'overlap_methods',
            'core_features', 'group', 'heatmap', 'heatmap_choices',
-           'filter_seqs', 'subsample', 'rename_ids',
+           'filter_seqs', 'subsample_ids', 'rename_ids',
            'filter_features_conditionally', 'split',
            'tabulate_feature_frequencies', 'tabulate_sample_frequencies',
            'summarize_plus']

q2_feature_table/_subsample.py q2_feature_table/_subsample_ids.pyq2_feature_table/_subsample.py renamed to q2_feature_table/_subsample_ids.py

@@ -9,8 +9,8 @@
 import biom
 
 
-def subsample(table: biom.Table, subsampling_depth: int,
-              axis: str) -> biom.Table:
+def subsample_ids(table: biom.Table, subsampling_depth: int,
+                  axis: str) -> biom.Table:
     if axis == 'feature':
         # we are transposing the table due to biocore/biom-format#759
         table = table.transpose()

q2_feature_table/plugin_setup.py

@@ -58,7 +58,7 @@
 )
 
 plugin.methods.register_function(
-    function=q2_feature_table.subsample,
+    function=q2_feature_table.subsample_ids,
     inputs={'table': FeatureTable[Frequency]},
     parameters={'subsampling_depth': Int % Range(1, None),
                 'axis': Str % Choices(['sample', 'feature'])},

q2_feature_table/tests/test_subsample.py

@@ -12,16 +12,16 @@
 import numpy.testing as npt
 from biom.table import Table
 
-from q2_feature_table import subsample
+from q2_feature_table import subsample_ids
 
 
-class SubsampleTests(TestCase):
+class SubsampleIDsTests(TestCase):
 
     def test_subsample_samples(self):
         t = Table(np.array([[0, 1, 3], [1, 1, 2]]),
                   ['O1', 'O2'],
                   ['S1', 'S2', 'S3'])
-        a = subsample(t, 2, 'sample')
+        a = subsample_ids(t, 2, 'sample')
         self.assertEqual(a.shape, (2, 2))
 
         sample_ids = frozenset(a.ids(axis='sample'))
@@ -38,7 +38,7 @@ def test_subsample_features(self):
         t = Table(np.array([[0, 1, 3], [1, 1, 2]]).T,
                   ['O1', 'O2', 'O3'],
                   ['S1', 'S2'])
-        a = subsample(t, 2, 'feature')
+        a = subsample_ids(t, 2, 'feature')
         self.assertEqual(a.shape, (2, 2))
 
         sample_ids = frozenset(a.ids(axis='observation'))
@@ -56,28 +56,28 @@ def test_subsample_samples_oversample(self):
                   ['O1', 'O2', 'O3'],
                   ['S1', 'S2'])
         with self.assertRaisesRegex(ValueError, "depth exceeds"):
-            subsample(t, 10, 'sample')
+            subsample_ids(t, 10, 'sample')
 
     def test_subsample_features_oversample(self):
         t = Table(np.array([[0, 1, 3], [1, 1, 2]]).T,
                   ['O1', 'O2', 'O3'],
                   ['S1', 'S2'])
         with self.assertRaisesRegex(ValueError, "depth exceeds"):
-            subsample(t, 10, 'feature')
+            subsample_ids(t, 10, 'feature')
 
     def test_subsample_samples_empty(self):
         t = Table(np.array([[0, 0, 0], [0, 0, 0]]).T,
                   ['O1', 'O2', 'O3'],
                   ['S1', 'S2'])
         with self.assertRaisesRegex(ValueError, "contains no"):
-            subsample(t, 2, 'sample')
+            subsample_ids(t, 2, 'sample')
 
     def test_subsample_features_empty(self):
         t = Table(np.array([[0, 0, 0], [0, 0, 0]]).T,
                   ['O1', 'O2', 'O3'],
                   ['S1', 'S2'])
         with self.assertRaisesRegex(ValueError, "contains no"):
-            subsample(t, 2, 'feature')
+            subsample_ids(t, 2, 'feature')
 
 
 if __name__ == "__main__":