Merge pull request #108 from HIIT/wrapper_fix

Wrapper fix

elfi/__init__.py

@@ -6,6 +6,7 @@
 from elfi.storage import *
 from elfi.visualization import *
 from elfi.inference_task import InferenceTask
+from elfi.wrapper import *
 from elfi.env import client, inference_task, new_inference_task
 from elfi import tools
 

elfi/methods.py

@@ -16,6 +16,7 @@
 from elfi.bo.acquisition import LCBAcquisition, SecondDerivativeNoiseMixin, RbfAtPendingPointsMixin
 
 logger = logging.getLogger(__name__)
+logger.setLevel(logging.INFO)
 
 """Implementations of some ABC algorithms.
 

elfi/wrapper.py

@@ -5,7 +5,8 @@
 class Wrapper():
     """ Wraps an external command to work as a callable operation for a node.
 
-        Currently only supports sequential operations (not vectorized).
+        Currently only supports sequential operations (not vectorized). This should be
+        enforced in ELFI by setting batch_size=1 in the ABC method.
 
         Parameters
         ----------
@@ -26,28 +27,31 @@ def __init__(self, command_template="", post=None, pre=None):
 
     @staticmethod
     def process_elfi_internals(command_template, args, kwargs):
-        """ Replace 'prng' in kwargs with a seed from the generator if present in template """
+        """ Replace 'random_state' in kwargs with a seed from the generator if present in template """
         proc_args = list()
         for a in args:
             if isinstance(a, np.ndarray):
-                if a.shape == (1,):
+                if a.shape == (1, 1):
                     # take single values out of array
-                    proc_args.append(a[0])
+                    proc_args.append(a.item())
                 else:
                     raise NotImplementedError("Wrapper does not yet support array arguments")
             else:
                 proc_args.append(a)
-        if "prng" in kwargs.keys():
+        if "random_state" in kwargs.keys():
             if "{seed}" in command_template:
-                if isinstance(kwargs["prng"], np.random.RandomState):
-                    kwargs["seed"] = str(kwargs["prng"].randint(np.iinfo(np.uint32).max))
-            del kwargs["prng"]
+                if isinstance(kwargs["random_state"], np.random.RandomState):
+                    kwargs["seed"] = str(kwargs["random_state"].randint(np.iinfo(np.uint32).max))
+            del kwargs["random_state"]
         return command_template, proc_args, kwargs
 
     @staticmethod
     def read_nparray(stdout):
-        """ Interpret the stdout as a space-separated numpy array """
-        return np.fromstring(stdout, sep=" ")
+        """ Interpret the stdout as a space-separated numpy array.
+        """
+        arr = np.fromstring(stdout, sep=" ")
+        arr = arr[None, :]  # for compatibility with core
+        return arr
 
     def __call__(self, *args, **kwargs):
         """ Executes the wrapped command, with additional arguments and keyword arguments.
@@ -65,4 +69,3 @@ def __call__(self, *args, **kwargs):
         argv = command.split(" ")
         stdout = check_output(argv, universal_newlines=True)
         return self.post(stdout)
-

tests/unit/test_wrapper.py

@@ -43,9 +43,9 @@ def test_echo_non_string_args(self):
         ret = wrapper(1)
         assert ret == 1
 
-    def test_echo_1d_array_args(self):
+    def test_echo_2d_array_args(self):
         command = "echo {0}"
         wrapper = Wrapper(command, post=int)
-        ret = wrapper(np.array([1]))
+        ret = wrapper(np.array([[1]]))
         assert ret == 1