Reduce number of warnings emitted during testing (#2887)

A collection of minor fixes and updates improves the handling of warnings by updating tests to use new interfaces.
The original distribution of warnings when running 4 test jobs was 7299 emitted warnings in 211 locations:
5 DeprecationWarning
9 FutureWarning
1 MatplotlibDeprecationWarning
4 PendingDeprecationWarning
12 PNLCompilerWarning
2 PytestBenchmarkWarning
1 PytestRemovedIn8Warning
1 PytestReturnNotNoneWarning
4 RuntimeWarning
1 SyntaxWarning
171 UserWarning

Changes in this PR reduce this to 5696 emitted warnings in 191 locations:
2 FutureWarning
1 MatplotlibDeprecationWarning
4 PendingDeprecationWarning
12 PNLCompilerWarning
2 RuntimeWarning
170 UserWarning

Individual commits target different warning classes.

psyneulink/core/components/functions/nonstateful/combinationfunctions.py

@@ -1442,7 +1442,8 @@ def _function(self,
         elif operation == CROSS_ENTROPY:
             v1 = variable[0]
             v2 = variable[1]
-            combination = np.where(np.logical_and(v1 == 0, v2 == 0), 0.0, v1 * np.log(v2))
+            both_zero = np.logical_and(v1 == 0, v2 == 0)
+            combination = v1 * np.where(both_zero, 0.0, np.log(v2, where=np.logical_not(both_zero)))
         else:
             raise FunctionError("Unrecognized operator ({0}) for LinearCombination function".
                                 format(operation.self.Operation.SUM))

psyneulink/core/components/functions/nonstateful/objectivefunctions.py

@@ -1207,7 +1207,8 @@ def _function(self,
             # MODIFIED CW 3/20/18: avoid divide by zero error by plugging in two zeros
             # FIX: unsure about desired behavior when v2 = 0 and v1 != 0
             # JDC: returns [inf]; leave, and let it generate a warning or error message for user
-            result = -np.sum(np.where(np.logical_and(v1 == 0, v2 == 0), 0.0, v1 * np.log(v2)))
+            both_zero = np.logical_and(v1 == 0, v2 == 0)
+            result = -np.sum(v1 * np.where(both_zero, 0.0, np.log(v2, where=np.logical_not(both_zero))))
 
         # Energy
         elif self.metric == ENERGY:

psyneulink/core/components/functions/stateful/memoryfunctions.py

@@ -301,7 +301,7 @@ def reset(self, previous_value=None, context=None):
         if previous_value is None:
             previous_value = self._get_current_parameter_value("initializer", context)
 
-        if previous_value is None or previous_value == []:
+        if previous_value is None or np.asarray(previous_value).size == 0:
             self.parameters.previous_value._get(context).clear()
             value = deque([], maxlen=self.parameters.history.get(context))
 
@@ -1752,7 +1752,7 @@ def _get_distance(self, cue:Union[list, np.ndarray],
             field_weights = self._get_current_parameter_value('distance_field_weights', context)
         # Set any items in field_weights to None if they are None or an empty list:
         field_weights = np.atleast_1d([None if
-                                       fw is None or fw == [] or isinstance(fw, np.ndarray) and fw.tolist()==[]
+                                       fw is None or np.asarray(fw).size == 0
                                        else fw
                                        for fw in field_weights])
         if granularity == 'per_field':
@@ -1763,7 +1763,7 @@ def _get_distance(self, cue:Union[list, np.ndarray],
             if len(field_weights)==1:
                 field_weights = np.full(num_fields, field_weights[0])
             for i in range(num_fields):
-                if not any([item is None or item == [] or isinstance(item, np.ndarray) and item.tolist() == []
+                if not any([item is None or np.asarray(item).size == 0
                             for item in [cue[i], candidate[i], field_weights[i]]]):
                     distances_by_field[i] = distance_fct([cue[i], candidate[i]]) * field_weights[i]
             return list(distances_by_field)
@@ -2623,7 +2623,7 @@ def reset(self, previous_value=None, context=None):
         if previous_value is None:
             previous_value = self._get_current_parameter_value("initializer", context)
 
-        if previous_value == []:
+        if np.asarray(previous_value).size == 0:
             value = np.ndarray(shape=(2, 0, len(self.defaults.variable[0])))
             self.parameters.previous_value._set(copy.deepcopy(value), context)
 

psyneulink/core/components/mechanisms/processing/transfermechanism.py

@@ -443,7 +443,7 @@
 **noise** (it must be the same length as the Mechanism's `variable <Mechanism_Base.variable>`), in which case each
 element is applied Hadamard (elementwise) to the result, as shown here::
 
-    >>> my_linear_tm.noise = [1.0,1.2,.9]
+    >>> my_linear_tm.noise.base = [1.0,1.2,.9]
     >>> my_linear_tm.execute([1.0, 1.0, 1.0])
     array([[2. , 2.2, 1.9]])
 

psyneulink/core/components/ports/port.py

@@ -3002,7 +3002,7 @@ def _parse_port_spec(port_type=None,
     port_type_name = port_type.__name__
 
     proj_is_feedback = False
-    if isinstance(port_specification, tuple) and port_specification[1] == FEEDBACK:
+    if isinstance(port_specification, tuple) and str(port_specification[1]) == FEEDBACK:
         port_specification = port_specification[0]
         proj_is_feedback = True
 

setup.cfg

@@ -67,9 +67,9 @@ required_plugins = pytest-benchmark pytest-cov pytest-helpers-namespace pytest-p
 xfail_strict = True
 
 filterwarnings =
+	error::SyntaxWarning
 	error:Creating an ndarray from ragged nested sequences \(which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes\) is deprecated.*:numpy.VisibleDeprecationWarning
 	error:Invalid escape sequence
-	ignore:Multiple ParameterPorts:UserWarning
 
 [pycodestyle]
 # for code explanation see https://pep8.readthedocs.io/en/latest/intro.html#error-codes

tests/composition/test_composition.py

@@ -1185,19 +1185,22 @@ def test_add_processing_pathway_subset_duplicate_warning(self, verbosity):
         C = TransferMechanism()
         comp = Composition()
 
-        comp.add_linear_processing_pathway(pathway=[A,B,C])
+        comp.add_linear_processing_pathway(pathway=[A, B, C])
+        comp.verbosePref = PreferenceEntry(verbosity, PreferenceLevel.INSTANCE)
+
+        with warnings.catch_warnings(record=True) as msgs:
+            comp.add_linear_processing_pathway(pathway=[A, B])
 
-        # Test for warning if verbosePref is set to True
         if verbosity:
-            regexp = f"Pathway specified in 'pathway' arg for add_linear_processing_pathway method of '{comp.name}' " \
-                     f"has a subset of nodes in a Pathway already in '{comp.name}': Pathway-0; the latter will be used."
-            with pytest.warns(UserWarning, match=regexp):
-                comp.verbosePref = PreferenceEntry(True, PreferenceLevel.INSTANCE)
-                comp.add_linear_processing_pathway(pathway=[A,B])
+            # Test for warning if verbosePref is set to True
+            warning = f"Pathway specified in 'pathway' arg for add_linear_processing_pathway method of '{comp.name}' " \
+                      f"has a subset of nodes in a Pathway already in '{comp.name}': Pathway-0; the latter will be used."
+
+            # The above issues 2 warnings, but we only test for one of them here
+            assert any(str(m.message) == warning for m in msgs), list(str(m.message) for m in msgs)
         else:
-            # Test for suppression of warning if verbosePref not set
-            with pytest.warns(None):
-                comp.add_linear_processing_pathway(pathway=[A,B])
+            # Test for suppression of warning if verbosePref is not set
+            assert len(msgs) == 0
 
     def test_add_backpropagation_pathway_exact_duplicate_warning(self):
         A = TransferMechanism()
@@ -1230,19 +1233,24 @@ def test_add_backpropagation_pathway_contiguous_subset_duplicate_warning(self, v
         B = TransferMechanism()
         C = TransferMechanism()
         comp = Composition()
-        comp.add_backpropagation_learning_pathway(pathway=[A,B,C])
+        comp.add_backpropagation_learning_pathway(pathway=[A, B, C])
+
+        comp.verbosePref = PreferenceEntry(verbosity, PreferenceLevel.INSTANCE)
+
+        with warnings.catch_warnings(record=True) as msgs:
+            comp.add_backpropagation_learning_pathway(pathway=[A, B])
 
-        # Test for warning if verbosePref is set to True
         if verbosity:
-            regexp = f"Pathway specified in 'pathway' arg for add_backpropagation_learning_pathway method of '{comp.name}'" \
-                     f" has a subset of nodes in a Pathway already in '{comp.name}':.*; the latter will be used."
-            with pytest.warns(UserWarning, match=regexp):
-                comp.verbosePref = PreferenceEntry(True, PreferenceLevel.INSTANCE)
-                comp.add_backpropagation_learning_pathway(pathway=[A,B])
+            # Test for warning if verbosePref is set to True
+            warning = f"Pathway specified in 'pathway' arg for add_backpropagation_learning_pathway method of '{comp.name}'" \
+                      f" has a subset of nodes in a Pathway already in '{comp.name}': Pathway-0; the latter will be used."
+
+            # The above issues 2 warnings, but we only test for one of them here
+            assert any(str(m.message) == warning for m in msgs), list(str(m.message) for m in msgs)
         else:
             # Test for suppression of warning if verbosePref is not set
-            with pytest.warns(None):
-                comp.add_backpropagation_learning_pathway(pathway=[A,B])
+            assert len(msgs) == 0
+
 
     def test_add_processing_pathway_non_contiguous_subset_is_OK(self):
         A = TransferMechanism()
@@ -3833,7 +3841,10 @@ def test_execute_no_inputs(self, mode):
         inner_comp = Composition(pathways=[m_inner])
         m_outer = ProcessingMechanism(size=2)
         outer_comp = Composition(pathways=[m_outer, inner_comp])
-        result = outer_comp.run(execution_mode=mode)
+
+        with pytest.warns(UserWarning, match="No inputs provided in call"):
+            result = outer_comp.run(execution_mode=mode)
+
         np.testing.assert_allclose(result, [[0.0, 0.0]])
 
     @pytest.mark.composition
@@ -3842,7 +3853,10 @@ def test_run_no_inputs(self, comp_mode):
         inner_comp = Composition(pathways=[m_inner])
         m_outer = ProcessingMechanism(size=2)
         outer_comp = Composition(pathways=[m_outer, inner_comp])
-        result = outer_comp.run(execution_mode=comp_mode)
+
+        with pytest.warns(UserWarning, match="No inputs provided in call"):
+            result = outer_comp.run(execution_mode=comp_mode)
+
         np.testing.assert_allclose(result, [[0.0, 0.0]])
 
     def test_lpp_invalid_matrix_keyword(self):
@@ -4922,7 +4936,7 @@ def test_invalid_projection_deletion_when_nesting_comps(self):
                                                    allocation_samples=pnl.SampleSpec(start=1.0, stop=5.0, num=5))])
         )
         assert not ocomp._check_for_existing_projections(sender=ib, receiver=ocomp_objective_mechanism)
-        return ocomp
+
     # # Does not work yet due to initialize_cycle_values bug that causes first recurrent projection to pass different values
     # # to TranfserMechanism version vs Logistic fn + AdaptiveIntegrator fn version
     # def test_recurrent_transfer_mechanism_composition(self):

tests/composition/test_control.py

@@ -1,5 +1,5 @@
+import contextlib
 import re
-
 import numpy as np
 import pytest
 
@@ -3587,27 +3587,27 @@ def test_model_based_num_estimates(self, num_estimates, rand_var):
                                            intensity_cost_function=pnl.Linear(slope=0.))
 
         objective_mech = pnl.ObjectiveMechanism(monitor=[B])
-        warning_type = None
+        warning_msg = f"'OptimizationControlMechanism-0' has 'num_estimates = {num_estimates}' specified, " \
+                      f"but its 'agent_rep' \\('comp'\\) has no random variables: " \
+                      f"'RANDOMIZATION_CONTROL_SIGNAL' will not be created, and num_estimates set to None."
+
         if num_estimates and not rand_var:
-            warning_type = UserWarning
-        warning_msg = f'"\'OptimizationControlMechanism-0\' has \'num_estimates = {num_estimates}\' specified, ' \
-                      f'but its \'agent_rep\' (\'comp\') has no random variables: ' \
-                      f'\'RANDOMIZATION_CONTROL_SIGNAL\' will not be created, and num_estimates set to None."'
-        with pytest.warns(warning_type) as warnings:
+            warning_context = pytest.warns(UserWarning, match=warning_msg)
+        else:
+            warning_context = contextlib.nullcontext()
+
+        with warning_context:
             ocm = pnl.OptimizationControlMechanism(agent_rep=comp,
                                                    state_features=[A.input_port],
                                                    objective_mechanism=objective_mech,
                                                    function=pnl.GridSearch(),
                                                    num_estimates=num_estimates,
                                                    control_signals=[control_signal])
-            if warning_type:
-                assert any(warning_msg == repr(w.message.args[0]) for w in warnings)
 
         comp.add_controller(ocm)
         inputs = {A: [[[1.0]]]}
 
-        comp.run(inputs=inputs,
-                 num_trials=2)
+        comp.run(inputs=inputs, num_trials=2)
 
         if not num_estimates or not rand_var:
             assert pnl.RANDOMIZATION_CONTROL_SIGNAL not in comp.controller.control_signals # Confirm no estimates
@@ -3710,22 +3710,17 @@ def test_grid_search_random_selection(self, comp_mode, benchmark):
 
         inputs = {A: [[[1.0]]]}
 
-        comp.run(inputs=inputs, num_trials=10, context='outer_comp', execution_mode=comp_mode)
-        np.testing.assert_allclose(comp.results, [[[0.7310585786300049]], [[0.999999694097773]], [[0.999999694097773]], [[0.9999999979388463]], [[0.9999999979388463]], [[0.999999694097773]], [[0.9999999979388463]], [[0.999999999986112]], [[0.999999694097773]], [[0.9999999999999993]]])
+        benchmark(comp.run, inputs=inputs, num_trials=10, context='outer_comp', execution_mode=comp_mode)
+        np.testing.assert_allclose(comp.results[:10],
+                                   [[[0.7310585786300049]], [[0.999999694097773]], [[0.999999694097773]], [[0.9999999979388463]], [[0.9999999979388463]],
+                                    [[0.999999694097773]], [[0.9999999979388463]], [[0.999999999986112]], [[0.999999694097773]], [[0.9999999999999993]]])
 
         # control signal value (mod slope) is chosen randomly from all of the control signal values
         # that correspond to a net outcome of 1
         if comp_mode is pnl.ExecutionMode.Python:
             log_arr = A.log.nparray_dictionary()
             np.testing.assert_allclose([[1.], [15.], [15.], [20.], [20.], [15.], [20.], [25.], [15.], [35.]],
-                               log_arr['outer_comp']['mod_slope'])
-
-        if benchmark.enabled:
-            # Disable logging for the benchmark run
-            A.log.set_log_conditions(items="mod_slope", log_condition=LogCondition.OFF)
-            A.log.clear_entries()
-            benchmark(comp.run, inputs=inputs, num_trials=10, context='bench_outer_comp', execution_mode=comp_mode)
-            assert len(A.log.get_logged_entries()) == 0
+                               log_arr['outer_comp']['mod_slope'][:10])
 
 
     def test_input_CIM_assignment(self, comp_mode):

tests/composition/test_learning.py

@@ -36,8 +36,9 @@ def xor_network():
                                              matrix=np.full((10,1), 0.1),
                                              sender=hidden_layer,
                                              receiver=output_layer)
-    inputs = np.array([[0, 0],[0, 1],[1, 0],[1, 1]])
-    targets = np.array([[0],[1],[1],[0]])
+    inputs = np.array([[0, 0], [0, 1], [1, 0], [1, 1]])
+    targets = np.array([[0], [1], [1], [0]])
+
     def _get_comp_type(comp_type, comp_learning_rate, pathway_learning_rate):
         if comp_type == 'composition':
             xor = Composition(learning_rate=comp_learning_rate)
@@ -65,18 +66,15 @@ def _get_comp_type(comp_type, comp_learning_rate, pathway_learning_rate):
 class TestInputAndTargetSpecs:
 
     @pytest.mark.pytorch
-    @pytest.mark.parametrize('input_type', ['dict', 'func', 'gen', 'gen_func'],
-                             ids=['dict', 'func', 'gen', 'gen_func'])
+    @pytest.mark.parametrize('input_type', ['dict', 'func', 'gen', 'gen_func'])
     @pytest.mark.parametrize('exec_mode', [pnl.ExecutionMode.PyTorch,
                                            pnl.ExecutionMode.LLVMRun,
-                                           pnl.ExecutionMode.Python],
-                             ids=['PyTorch', 'LLVM', 'Python'])
-    @pytest.mark.parametrize('comp_type', ['composition', 'autodiff'],
-                             ids=['composition', 'autodiff'])
-    def node_spec_types(self, xor_network, comp_type, input_type, exec_mode):
+                                           pnl.ExecutionMode.Python])
+    @pytest.mark.parametrize('comp_type', ['composition', 'autodiff'])
+    def test_node_spec_types(self, xor_network, comp_type, input_type, exec_mode):
 
         if comp_type == 'composition' and exec_mode != pnl.ExecutionMode.Python:
-            pytest.skip(f"Execution mode {exec_mode} not relevant for Composition")
+            pytest.skip(f"Execution mode {exec_mode} not relevant for Composition learn")
 
         comp, input_layer, hidden_layer, output_layer, target_mechanism, stims, targets =\
             xor_network(comp_type, 0.001, None)
@@ -113,12 +111,8 @@ def get_inputs_gen():
         else:
             assert False, f"Unrecognized input_type: {input_type}"
 
-        expected_results = [[0.6341436044849351]]
-        if comp_type is 'composition':
-            results = comp.learn(inputs=inputs)
-        else:
-            results = comp.learn(inputs=inputs, execution_mode=exec_mode)
-        np.testing.assert_allclose(results, expected_results)
+        results = comp.learn(inputs=inputs, execution_mode=exec_mode)
+        np.testing.assert_allclose(results, [[0.6341436044849351]])
 
     @pytest.mark.composition
     @pytest.mark.pytorch

tests/functions/test_memory.py

@@ -444,7 +444,7 @@ def test_DictionaryMemory_without_assoc(self):
 
     def test_DictionaryMemory_with_duplicate_entry_in_initializer_warning(self):
 
-        regexp = r'Attempt to initialize memory of DictionaryMemory with an entry \([[1 2 3]'
+        regexp = r'Attempt to initialize memory of DictionaryMemory with an entry \(\[\[1 2 3\]'
         with pytest.warns(UserWarning, match=regexp):
             em = EpisodicMemoryMechanism(
                     name='EPISODIC MEMORY MECH',
@@ -1034,7 +1034,7 @@ def test_ContentAddressableMemory_without_initializer_and_diff_field_sizes(self)
 
     def test_ContentAddressableMemory_with_duplicate_entry_in_initializer_warning(self):
 
-        regexp = r'Attempt to initialize memory of ContentAddressableMemory with an entry \([[1 2 3]'
+        regexp = r'Attempt to initialize memory of ContentAddressableMemory with an entry \(\[\[1 2 3\]'
         with pytest.warns(UserWarning, match=regexp):
             c = ContentAddressableMemory(
                 initializer=np.array([[[1,2,3], [4,5,6]],

tests/mechanisms/test_ddm_mechanism.py

@@ -77,7 +77,7 @@ def test_valid(self):
 
         # reset only decision variable
         D.function.initializer = 1.0
-        D.function.non_decision_time = 0.0
+        D.function.non_decision_time.base = 0.0
         D.reset()
         np.testing.assert_allclose(D.function.value[0], 1.0)
         np.testing.assert_allclose(D.function.parameters.previous_value.get(), 1.0)

tests/mechanisms/test_lca.py

@@ -185,12 +185,14 @@ def test_LCAMechanism_threshold_with_convergence(self, benchmark, comp_mode):
         comp = Composition()
         comp.add_node(lca)
 
-        result = comp.run(inputs={lca:[0,1,2]}, execution_mode=comp_mode)
-        np.testing.assert_allclose(result, [[0.19153799, 0.5, 0.80846201]])
+        def func(*args, **kwargs):
+            res = comp.run(*args, **kwargs)
+            return (res, lca.num_executions_before_finished)
+
+        results = benchmark(func, inputs={lca:[0,1,2]}, execution_mode=comp_mode)
+        np.testing.assert_allclose(results[0], [[0.19153799, 0.5, 0.80846201]])
         if comp_mode is pnl.ExecutionMode.Python:
-            assert lca.num_executions_before_finished == 18
-        if benchmark.enabled:
-            benchmark(comp.run, inputs={lca:[0,1,2]}, execution_mode=comp_mode)
+            assert results[1] == 18
 
     @pytest.mark.composition
     @pytest.mark.lca_mechanism

tests/mechanisms/test_mechanisms.py

@@ -50,7 +50,7 @@ def test_noise_assignment_equivalence(self, noise):
         t2 = pnl.TransferMechanism(name='t2', size=2)
         t2.integrator_function.parameters.noise.set(noise())
 
-        t1.integrator_function.noise.seed = 0
+        t1.integrator_function.noise.seed.base = 0
         t2.integrator_function.noise.base.seed = 0
 
         for _ in range(5):