BUG: fixes #717

ChangeLog.md

@@ -19,7 +19,9 @@ New Features:
 * `Table.sort_order` was performing an implicit cast to dense, and not leveraging fancy indexing. A substantial performance gain was acheived. See [PR #720](https://github.com/biocore/biom-format/pull/720)
 
 Bug fixes:
+
 * ``-o`` is now a required parameter of ``biom from-uc``. This was not the case previously, which resulted in a cryptic error message if ``-o`` was not provided. See [issue #683](https://github.com/biocore/biom-format/issues/683).
+* Matrices are now cast to csr on `Table` construction if the data evaluate as `isspmatrix`. This fixes [#717](https://github.com/biocore/biom-format/issues/717) where some API methods assumed the data were csc or csr.
 
 biom 2.1.5
 ----------

tests/test_table.py

@@ -19,6 +19,7 @@
 import numpy.testing as npt
 import numpy as np
 from scipy.sparse import lil_matrix, csr_matrix, csc_matrix
+import scipy.sparse
 
 from biom import example_table
 from biom.exception import (UnknownAxisError, UnknownIDError, TableException,
@@ -1711,6 +1712,15 @@ def test_update_ids_cache_bug(self):
         exp_index = {'x': 0, 'y': 1}
         self.assertEqual(obs._sample_index, exp_index)
 
+    def test_other_spmatrix_type(self):
+        # I dont actually remember what bug stemmed from this...
+        ss = scipy.sparse
+        for c in [ss.lil_matrix, ss.bsr_matrix, ss.coo_matrix, ss.dia_matrix,
+                  ss.dok_matrix, ss.csc_matrix, ss.csr_matrix]:
+            mat = c((2, 2))
+            t = Table(mat, ['a', 'b'], [1, 2])
+            self.assertTrue(isinstance(t.matrix_data, (csr_matrix, csc_matrix)))
+
     def test_sort_order(self):
         """sorts tables by arbitrary order"""
         # sort by observations arbitrary order