expand unit tests, fixes #11

caporaso-lab · Jul 2, 2024 · 65b652c · 65b652c
1 parent cbc0a24
commit 65b652c
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Showing 2 changed files with 34 additions and 8 deletions.
diff --git a/q2_boots/_normalize.py b/q2_boots/_normalize.py
@@ -13,14 +13,9 @@
 def _bootstrap_iteration(table: biom.Table, sampling_depth: int) -> biom.Table:
     table = table.filter(lambda v, i, m: v.sum() >= sampling_depth,
                          inplace=False, axis='sample')
-
     table = table.subsample(sampling_depth, axis='sample', by_id=False,
                             with_replacement=True)
 
-    if table.is_empty():
-        return ValueError('The output table contains no samples or features.'
-                          'Verify your table is valid and that you provided a '
-                          'shallow enough samplign depth')
 
     return table
 

diff --git a/q2_boots/tests/test_normalize.py b/q2_boots/tests/test_normalize.py
@@ -16,12 +16,43 @@
 
 class TestBootstrapIteration(TestCase):
 
-    def test_bootstrap_iteration(self):
+    def test_bootstrap_iteration_filters_samples(self):
         t = Table(np.array([[0, 1, 3], [1, 1, 2]]),
                   ['O1', 'O2'],
                   ['S1', 'S2', 'S3'])
-        a = _bootstrap_iteration(t, 2)
-        self.assertEqual(a.shape, (2, 2))
+
+        observed = _bootstrap_iteration(t, 6)
+        self.assertTrue(observed.is_empty())
+
+        observed = _bootstrap_iteration(t, 5)
+        self.assertEqual(list(observed.ids(axis='sample')), ['S3'])
+
+        observed = _bootstrap_iteration(t, 2)
+        self.assertEqual(list(observed.ids(axis='sample')), ['S2', 'S3'])
+
+        observed = _bootstrap_iteration(t, 1)
+        self.assertEqual(list(observed.ids(axis='sample')), ['S1', 'S2', 'S3'])
+
+    def test_bootstrap_iteration_obtains_expected_counts(self):
+        t = Table(np.array([[0, 10, 30], [1, 10, 20]]),
+                  ['O1', 'O2'],
+                  ['S1', 'S2', 'S3'])
+
+        observed = _bootstrap_iteration(t, 1)
+        self.assertEqual(list(observed.sum(axis="sample")), [1., 1., 1.])
+
+        observed = _bootstrap_iteration(t, 10)
+        self.assertEqual(list(observed.sum(axis="sample")), [10., 10.])
+
+        observed = _bootstrap_iteration(t, 19)
+        self.assertEqual(list(observed.sum(axis="sample")), [19., 19.])
+
+        observed = _bootstrap_iteration(t, 25)
+        self.assertEqual(list(observed.sum(axis="sample")), [25.])
+
+        observed = _bootstrap_iteration(t, 49)
+        self.assertEqual(list(observed.sum(axis="sample")), [49.])
+
 
 
 if __name__ == "__main__":