Allow DictList to be selected with boolean arrays

Allows numpy-like behavior in ArrayBasedModel. For example:
model.reactions[model.lower_bounds > 0]

This commit also includes a unit test for this behavior.

cobra/core/DictList.py

@@ -3,6 +3,11 @@
 from ..external.six import string_types, iteritems
 from itertools import islice
 
+try:
+    from numpy import bool_
+except:
+    bool_ = bool
+
 
 class DictList(list):
     """A combined dict and list
@@ -291,6 +296,14 @@ def __getitem__(self, i):
             selection = self.__class__()
             selection._extend_nocheck(list.__getitem__(self, i))
             return selection
+        elif hasattr(i, "__len__"):
+            if len(i) == len(self) and isinstance(i[0], (bool, bool_)):
+                selection = self.__class__()
+                result = (o for j, o in enumerate(self) if i[j])
+                selection._extend_nocheck(result)
+                return selection
+            else:
+                return self.__class__(list.__getitem__(self, i))
         else:
             return list.__getitem__(self, i)
 

cobra/test/unit_tests.py

@@ -527,6 +527,17 @@ def test_array_based_model_add(self):
             self.assertEqual(model.S[1605, 0], -1)
             self.assertEqual(model.lower_bounds[2546], -3.14)
 
+    def test_array_based_select(self):
+        model = self.model
+        atpm_select = model.reactions[model.lower_bounds > 0]
+        self.assertEqual(len(atpm_select), 1)
+        self.assertEqual(atpm_select[0].id, "ATPM")
+        self.assertEqual(len(model.reactions[model.lower_bounds <= 0]),
+                         len(model.reactions) - 1)
+        # mismatched dimensions should give an error
+        with self.assertRaises(TypeError):
+            model.reactions[[True, False]]
+
 
 # make a test suite to run all of the tests
 loader = TestLoader()