Issue 948 (#959)

* TST: regression test for issue #948

* BUG: fixes issue #948

* DOC: changelog mention for issue #948

ChangeLog.md

@@ -22,6 +22,7 @@ Bug fixes:
 * Allow `Table.to_json` to properly handle numpy types in metadata, see issue [#886](https://github.com/biocore/biom-format/issues/886)
 * Do not modify IDs in place in the presence of duplicate relabels, see issue [#892](https://github.com/biocore/biom-format/issues/892)
 * Catch an edge case where a failured ID update in place would actually change IDs, see issue [#892](https://github.com/biocore/biom-format/issues/892)
+* Fixed an edge case on in `align_tree` when a feature was empty, see issue [#948](https://github.com/biocore/biom-format/issues/948)
 
 New features:
 

biom/table.py

@@ -1073,7 +1073,6 @@ def align_tree(self, tree, axis='observation'):
             raise TableException("No common ids between table and tree.")
         _tree = tree.shear(names=common_tips)
         _table = self.filter(common_tips, axis=axis, inplace=False)
-        _table.remove_empty()
         _tree.prune()
         order = [n.name for n in _tree.tips()]
         _table = _table.sort_order(order, axis=axis)

biom/tests/test_table.py

@@ -2013,6 +2013,21 @@ def test_align_to_dataframe_samples_no_common_ids(self):
         with self.assertRaises(TableException):
             table.align_to_dataframe(metadata)
 
+    @pytest.mark.skipif(not HAVE_SKBIO, reason="skbio not installed")
+    def test_align_tree_issue_948(self):
+        table = Table(np.array([[0, 0, 0, 0],
+                                [2, 3, 4, 4],
+                                [5, 5, 3, 3],
+                                [0, 0, 0, 1]]).T,
+                      ['a', 'b', 'c', 'd'],
+                      ['s1', 's2', 's3', 's4'])
+        tree = skbio.TreeNode.read(["(a,b,c,d)r;"])
+        exp_tree = tree
+        exp_table = table.copy()
+        res_table, res_tree = table.align_tree(tree)
+        self.assertEqual(res_table, exp_table)
+        self.assertEqual(str(exp_tree), str(res_tree))
+
     @pytest.mark.skipif(not HAVE_SKBIO, reason="skbio not installed")
     def test_align_tree_intersect_tips(self):
         # there are less tree tips than observations