Merge pull request #570 from GavinHuttley/develop

BUG: catch additional case in casting to array from string

src/cogent3/util/table.py

@@ -210,7 +210,7 @@ def cast_str_to_array(values, static_type=False):
         try:
             v = eval(v)
             all_fail = False
-        except (NameError, SyntaxError):
+        except (TypeError, NameError, SyntaxError):
             # syntax error from empty strings
             pass
         result.append(v)

tests/test_util/test_table.py

@@ -14,7 +14,12 @@
 from numpy.testing import assert_equal
 
 from cogent3 import load_table, make_table
-from cogent3.util.table import Table, cast_to_array, formatted_array
+from cogent3.util.table import (
+    Table,
+    cast_str_to_array,
+    cast_to_array,
+    formatted_array,
+)
 
 
 try:
@@ -1053,6 +1058,17 @@ def test_load_table(self):
         table = load_table(path)
         self.assertEqual(table.shape, (10, 3))
 
+    def test_cast_str_to_array(self):
+        """handle processing string series"""
+        d = [".123|.345", "123"]
+        r = cast_str_to_array(d, static_type=True)
+        self.assertTrue("str" in r.dtype.name)
+        r = cast_str_to_array(d, static_type=False)
+        self.assertEqual(r.dtype.name, "object")
+        d = [".123|.345", "123", "()"]
+        r = cast_str_to_array(d, static_type=False)
+        self.assertEqual(r[-1], ())
+
 
 if __name__ == "__main__":
     main()