Merge branch 'devel'

* devel: (140 commits)
  Increment version to 0.4.0
  add more input_state spec tests to handle currently known combinations for setting default_variable
  Refactor/mechanism/preprocess variable (#531)
  Docs/state and projections/docstring revs (#529)
  correct bug in _parse_arg_input_states where a non-list argument wouldn't be made into a list before processing
  change behavior of _parse_state_spec to not populate the state dict with a variable if it's a ClassDefault
  Fixed/state/ parse state spec/projection spec (#528)
  Refactor/distance metrics (#526)
  Docs/latex math (#525)
  Docs/intro materials (#524)
  Logo (#523)
  make self.name return unnamed .__class__ in case no name was set
  Docs/input state specs (#522)
  Fix/input state specs (#521)
  Fix/input state specs (#520)
  Fix/input state specs (#519)
  Fix/input state specs (#518)
  using new EULER option on the LCControlMechanism in GilzenratModel in order to match original model
  adding validation requiring integration_method to either be RK4 or EULER
  adding 'integration_method' to LCControlMechanism so that user can switch between euler and rk4 integration for the built-in FHN function
  ...

docs/source/conf.py

@@ -69,9 +69,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'0.3'
+version = u'0.4'
 # The full version, including alpha/beta/rc tags.
-release = u'0.3.2'
+release = u'0.4.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

setup.py

@@ -16,7 +16,7 @@
     # Versions should comply with PEP440.  For a discussion on single-sourcing
     # the version across setup.py and the project code, see
     # https://packaging.python.org/en/latest/single_source_version.html
-    version='0.3.4',
+    version='0.4.0',
 
     description='A block modeling system for cognitive neuroscience',
     long_description=long_description,

tests/mechanisms/test_input_state_spec.py

@@ -4,8 +4,13 @@
 from psyneulink.components.mechanisms.mechanism import MechanismError
 from psyneulink.components.mechanisms.processing.transfermechanism import TransferMechanism
 from psyneulink.components.projections.pathway.mappingprojection import MappingProjection
+from psyneulink.components.states.inputstate import InputState
+from psyneulink.components.states.state import StateError
 from psyneulink.globals.keywords import INPUT_STATES, MECHANISM, NAME, OUTPUT_STATES, PROJECTIONS, VARIABLE
 
+mismatches_default_variable_error_text = 'not compatible with the specified default variable'
+mismatches_size_error_text = 'not compatible with the default variable determined from size parameter'
+
 
 class TestInputStateSpec:
     # ------------------------------------------------------------------------------------------------
@@ -35,11 +40,11 @@ def test_match_with_default_variable(self):
     def test_mismatch_with_default_variable_error(self):
 
         with pytest.raises(MechanismError) as error_text:
-            T = TransferMechanism(
+            TransferMechanism(
                 default_variable=[[0], [0]],
                 input_states=[[32, 24], 'HELLO']
             )
-        assert "not compatible with the specified default variable" in str(error_text.value)
+        assert mismatches_default_variable_error_text in str(error_text.value)
 
     # ------------------------------------------------------------------------------------------------
     # TEST 3
@@ -355,25 +360,25 @@ def test_dict_with_variable_matches_default_multiple_input_states(self):
 
     def test_dict_with_variable_mismatches_default(self):
         with pytest.raises(MechanismError) as error_text:
-            T = TransferMechanism(
+            TransferMechanism(
                 default_variable=[0],
                 input_states=[{NAME: 'FIRST', VARIABLE: [0, 0]}]
             )
-        assert 'not compatible with the specified default variable' in str(error_text.value)
+        assert mismatches_default_variable_error_text in str(error_text.value)
 
     # ------------------------------------------------------------------------------------------------
     # TEST 23
 
     def test_dict_with_variable_mismatches_default_multiple_input_states(self):
         with pytest.raises(MechanismError) as error_text:
-            T = TransferMechanism(
+            TransferMechanism(
                 default_variable=[[0], [0]],
                 input_states=[
                     {NAME: 'FIRST', VARIABLE: [0, 0]},
                     {NAME: 'SECOND', VARIABLE: [0]}
                 ]
             )
-        assert 'not compatible with the specified default variable' in str(error_text.value)
+        assert mismatches_default_variable_error_text in str(error_text.value)
 
     # ------------------------------------------------------------------------------------------------
     # TEST 24
@@ -391,8 +396,136 @@ def test_dict_with_variable_matches_size(self):
 
     def test_dict_with_variable_mismatches_size(self):
         with pytest.raises(MechanismError) as error_text:
-            T = TransferMechanism(
+            TransferMechanism(
                 size=1,
                 input_states=[{NAME: 'FIRST', VARIABLE: [0, 0]}]
             )
-        assert 'not compatible with the default variable determined from size parameter' in str(error_text.value)
+        assert mismatches_size_error_text in str(error_text.value)
+
+    # ------------------------------------------------------------------------------------------------
+    # TEST 26
+
+    def test_params_override(self):
+        T = TransferMechanism(
+            input_states=[[0], [0]],
+            params={INPUT_STATES: [[0, 0], [0]]}
+        )
+        assert T.instance_defaults.variable.shape == np.array([[0, 0], [0]]).shape
+        assert len(T.input_states) == 2
+
+    # ------------------------------------------------------------------------------------------------
+    # TEST 27
+
+    def test_inputstate_object(self):
+        with pytest.raises(StateError) as error_text:
+            m = TransferMechanism(default_variable=[0, 0, 0])
+            i = InputState(owner=m, variable=[0, 0, 0])
+            TransferMechanism(input_states=[i])
+        assert 'that belongs to another Mechanism' in str(error_text.value)
+
+    # ------------------------------------------------------------------------------------------------
+    # TEST 28
+
+    def test_inputstate_class(self):
+        T = TransferMechanism(input_states=[InputState])
+
+        np.testing.assert_array_equal(T.instance_defaults.variable, [InputState.ClassDefaults.variable])
+        assert len(T.input_states) == 1
+
+    # ------------------------------------------------------------------------------------------------
+    # TEST 29
+
+    def test_inputstate_class_with_variable(self):
+        T = TransferMechanism(default_variable=[0, 0], input_states=[InputState])
+
+        np.testing.assert_array_equal(T.instance_defaults.variable, np.array([[0, 0]]))
+        assert len(T.input_states) == 1
+
+    # ------------------------------------------------------------------------------------------------
+    # TEST 30
+
+    def test_InputState_mismatches_default(self):
+        with pytest.raises(MechanismError) as error_text:
+            i = InputState(reference_value=[0, 0, 0])
+            TransferMechanism(default_variable=[0, 0], input_states=[i])
+        assert mismatches_default_variable_error_text in str(error_text.value)
+
+    # ------------------------------------------------------------------------------------------------
+    # TEST 31
+
+    def test_projection_with_matrix_and_sender(self):
+        m = TransferMechanism(size=2)
+        p = MappingProjection(sender=m, matrix=[[0, 0, 0], [0, 0, 0]])
+        T = TransferMechanism(input_states=[p])
+
+        np.testing.assert_array_equal(T.instance_defaults.variable, np.array([[0, 0, 0]]))
+        assert len(T.input_states) == 1
+
+    # ------------------------------------------------------------------------------------------------
+    # TEST 32
+
+    def test_projection_with_matrix_and_sender_mismatches_default(self):
+        with pytest.raises(MechanismError) as error_text:
+            m = TransferMechanism(size=2)
+            p = MappingProjection(sender=m, matrix=[[0, 0, 0], [0, 0, 0]])
+            TransferMechanism(default_variable=[0, 0], input_states=[p])
+        assert mismatches_default_variable_error_text in str(error_text.value)
+
+    # ------------------------------------------------------------------------------------------------
+    # TEST 33
+
+    def test_projection_with_sender_and_default(self):
+        t = TransferMechanism(size=3)
+        p = MappingProjection(sender=t)
+        T = TransferMechanism(default_variable=[0, 0], input_states=[p])
+
+        np.testing.assert_array_equal(T.instance_defaults.variable, np.array([[0, 0]]))
+        assert len(T.input_states) == 1
+
+    # ------------------------------------------------------------------------------------------------
+    # TEST 34
+
+    def test_projection_no_args_projection_spec(self):
+        p = MappingProjection()
+        T = TransferMechanism(input_states=[p])
+
+        np.testing.assert_array_equal(T.instance_defaults.variable, np.array([[0]]))
+        assert len(T.input_states) == 1
+
+    # ------------------------------------------------------------------------------------------------
+    # TEST 35
+
+    def test_projection_no_args_projection_spec_with_default(self):
+        p = MappingProjection()
+        T = TransferMechanism(default_variable=[0, 0], input_states=[p])
+
+        np.testing.assert_array_equal(T.instance_defaults.variable, np.array([[0, 0]]))
+        assert len(T.input_states) == 1
+
+    # ------------------------------------------------------------------------------------------------
+    # TEST 36
+
+    def test_projection_no_args_dict_spec(self):
+        p = MappingProjection()
+        T = TransferMechanism(input_states=[{VARIABLE: [0, 0, 0], PROJECTIONS:[p]}])
+
+        np.testing.assert_array_equal(T.instance_defaults.variable, np.array([[0, 0, 0]]))
+        assert len(T.input_states) == 1
+
+    # ------------------------------------------------------------------------------------------------
+    # TEST 37
+
+    def test_projection_no_args_dict_spec_mismatch_with_default(self):
+        with pytest.raises(MechanismError) as error_text:
+            p = MappingProjection()
+            TransferMechanism(default_variable=[0, 0], input_states=[{VARIABLE: [0, 0, 0], PROJECTIONS: [p]}])
+        assert mismatches_default_variable_error_text in str(error_text.value)
+
+    # ------------------------------------------------------------------------------------------------
+    # TEST 38
+
+    def test_outputstate_(self):
+        with pytest.raises(MechanismError) as error_text:
+            p = MappingProjection()
+            TransferMechanism(default_variable=[0, 0], input_states=[{VARIABLE: [0, 0, 0], PROJECTIONS: [p]}])
+        assert mismatches_default_variable_error_text in str(error_text.value)