Merge pull request #1915 from PrincetonUniversity/devel

Devel

Author: kmantel

.github/workflows/pnl-ci-docs.yml

@@ -46,7 +46,7 @@ jobs:
         echo ::set-output name=pip_cache_dir::$(python -m pip cache dir)
 
     - name: Wheels cache
-      uses: actions/cache@v2.1.3
+      uses: actions/cache@v2.1.4
       with:
         path: ${{ steps.pip_cache.outputs.pip_cache_dir }}/wheels
         key: ${{ runner.os }}-python-${{ matrix.python-version }}-${{ matrix.python-architecture }}-pip-wheels-v2-${{ github.sha }}

.github/workflows/pnl-ci.yml

@@ -46,7 +46,7 @@ jobs:
         echo ::set-output name=pip_cache_dir::$(python -m pip cache dir)
 
     - name: Wheels cache
-      uses: actions/cache@v2.1.3
+      uses: actions/cache@v2.1.4
       with:
         path: ${{ steps.pip_cache.outputs.pip_cache_dir }}/wheels
         key: ${{ runner.os }}-python-${{ matrix.python-version }}-${{ matrix.python-architecture }}-pip-wheels-v2-${{ github.sha }}

Scripts/Debug/Hebbian_Simon.py

@@ -0,0 +1,64 @@
+import psyneulink as pnl
+import numpy as np
+import matplotlib.pyplot as plt
+#sample Hebb
+
+FeatureNames=['small','medium','large','red','yellow','blue','circle','rectangle','triangle']
+
+# create a variable that corresponds to the size of our feature space
+sizeF = len(FeatureNames)
+small_red_circle = [1,0,0,1,0,0,1,0,0]
+src = small_red_circle
+
+
+Hebb_comp = pnl.Composition()
+
+Hebb_mech=pnl.RecurrentTransferMechanism(
+    size=sizeF,
+    function=pnl.Linear,
+    #integrator_mode = True,
+    #integration_rate = 0.5,
+    enable_learning = True,
+    learning_rate = .1,
+    name='Hebb_mech',
+    #matrix=pnl.AutoAssociativeProjection,
+    auto=0,
+    hetero=0
+    )
+
+Hebb_comp.add_node(Hebb_mech)
+
+Hebb_comp.execution_id = 1
+
+# Use print_info to show numerical values and vis_info to show graphs of the changing values
+
+def print_info():
+    print('\nWeight matrix:\n', Hebb_mech.matrix.base, '\nActivity: ', Hebb_mech.value)
+
+
+def vis_info():
+  ub=1#np.amax(np.amax(np.abs(Hebb_mech.matrix.modulated)))
+  lb=-ub
+  plt.figure()
+  plt.imshow(Hebb_mech.matrix.modulated,cmap='RdBu_r',vmin=lb,vmax=ub)
+  plt.title('PNL Hebbian Matrix')
+  plt.xticks(np.arange(0,sizeF),FeatureNames,rotation=35)
+  plt.yticks(np.arange(0,sizeF),FeatureNames,rotation=35)
+
+  plt.colorbar()
+  plt.show()
+
+  plt.figure()
+  plt.stem(Hebb_mech.value[0])
+  plt.title('Activation from Stimulus with PNL Hebbian Matrix')
+  plt.xticks(np.arange(0,sizeF),FeatureNames,rotation=35)
+  plt.xlabel('Feature')
+  plt.ylabel('Activation')
+  plt.show()
+
+inputs_dict = {Hebb_mech:np.array(src)}
+out=Hebb_comp.learn(num_trials=5,
+      # call_after_trial=vis_info,
+      inputs=inputs_dict)
+
+print_info()

docs/source/Core.rst

@@ -12,9 +12,10 @@ Core
    - `CompositionFunctionApproximator`
 
 * `Services`
-   - `Visualization`
-   - `Log`
    - `Registry`
    - `Preferences`
-   - `json`
+   - `Visualization`
+   - `Scheduling`
    - `Compilation`
+   - `Log`
+   - `json`

docs/source/Mechanisms.rst

@@ -1,10 +1,11 @@
 Mechanisms
 ==========
 
-.. toctree::
-   :maxdepth: 3
-
 .. container:: subclasses
-   *Subclasses*
-   ProcessingMechanisms
-   ModulatoryMechanisms
+
+   .. toctree::
+      :maxdepth: 3
+
+      *Subclasses:*
+      ProcessingMechanisms
+      ModulatoryMechanisms

docs/source/Preferences.rst

@@ -7,8 +7,12 @@ Standard prefereces:
 
 - paramValidation (bool): enables/disables run-time validation of the execute method of a Function object
 
-- reportOutput ([bool, str]): enables/disables reporting of execution of execute method:
-   True prints input/output, 'params' or 'parameters' includes parameter values
+- reportOutput ([bool, str]): enables/disables reporting execution of `Component`\'s `execute <Component_Execution>`
+  method to console:
+    - ``True``: prints record of execution, including the input and output of the Component;
+    - 'params' or 'parameters': includes report of the Component's `parameter <Parameters>` values.
+    - 'terse': (Composition only) restricts output to just a listing of `trials <TimeScale.TRIAL>`, `time_steps
+      <TimeScale.TIME_STEP>` and `nodes <Composition_Nodes>` executed.
 
 - log (bool): sets LogCondition for a given Component
 

psyneulink/__init__.py

@@ -31,6 +31,9 @@
 from .core import *
 from .library import *
 
+# from rich import print, box
+# print("Initializing...")
+
 _pnl_global_names = [
     'primary_registries', 'System', 'Process'
 ]

psyneulink/core/components/component.py

@@ -338,7 +338,8 @@
 Execution
 ---------
 
-A Component is executed when its `execute` method is called, which in turn calls its `function <Component_Function>`.
+A Component is executed when its `execute <Component.execute>` method is called, which in turn calls its `function
+<Component_Function>`.
 
 .. _Component_Lazy_Updating:
 
@@ -486,7 +487,6 @@
 import itertools
 import logging
 import numbers
-import toposort
 import types
 import warnings
 
@@ -2024,7 +2024,7 @@ def _is_user_specified(parameter):
                 else:
                     param_defaults[p.source.name] = param_defaults[p.name]
 
-        for p in filter(lambda x: not isinstance(x, (ParameterAlias, SharedParameter)), self.parameters):
+        for p in filter(lambda x: not isinstance(x, (ParameterAlias, SharedParameter)), self.parameters._in_dependency_order):
             # copy spec so it is not overwritten later
             # TODO: check if this is necessary
             p.spec = copy_parameter_value(p.spec)
@@ -2085,19 +2085,8 @@ def _instantiate_parameter_classes(self, context=None):
         """
         from psyneulink.core.components.shellclasses import Function
 
-        parameter_function_ordering = list(toposort.toposort({
-            p.name: p.dependencies for p in self.parameters if p.dependencies is not None
-        }))
-        parameter_function_ordering = list(itertools.chain.from_iterable(parameter_function_ordering))
-
-        def ordering(p):
-            try:
-                return parameter_function_ordering.index(p.name)
-            except ValueError:
-                return -1
-
         # (this originally occurred in _validate_params)
-        for p in sorted(self.parameters, key=ordering):
+        for p in self.parameters._in_dependency_order:
             if p.getter is None:
                 val = p._get(context)
                 if (
@@ -2188,7 +2177,7 @@ def _create_justified_line(k, v, error_line_len=110):
         self._override_unspecified_shared_parameters(context)
 
     def _override_unspecified_shared_parameters(self, context):
-        for param_name, param in self.parameters.values(show_all=True).items():
+        for param in self.parameters._in_dependency_order:
             if (
                 isinstance(param, SharedParameter)
                 and not isinstance(param.source, ParameterAlias)
@@ -2984,7 +2973,7 @@ def _update_default_variable(self, new_default_variable, context=None):
         )
         self._instantiate_value(context)
 
-        for p in self.parameters:
+        for p in self.parameters._in_dependency_order:
             val = p._get(context)
             if (
                 not p.reference
@@ -3028,6 +3017,9 @@ def reset(self, *args, context=None, **kwargs):
 
     @handle_external_context()
     def execute(self, variable=None, context=None, runtime_params=None):
+        """Executes Component's `function <Component_Function>`.  See Component-specific execute method for details.
+        """
+
         if context is None:
             try:
                 context = self.owner.most_recent_context
@@ -3102,7 +3094,7 @@ def _execute(self, variable=None, context=None, runtime_params=None, **kwargs):
 
     def is_finished(self, context=None):
         """
-            set by a Component to signal completion of its `execution <Component_Execution>` in a `TRIAL
+            Set by a Component to signal completion of its `execution <Component_Execution>` in a `TRIAL
             <TimeScale.TRIAL>`; used by `Component-based Conditions <Conditions_Component_Based>` to predicate the
             execution of one or more other Components on a Component.
         """

psyneulink/core/components/functions/optimizationfunctions.py

@@ -1459,7 +1459,7 @@ def _gen_llvm_select_min_function(self, *, ctx:pnlvm.LLVMBuilderContext, tags:fr
 
         # KDM 8/22/19: nonstateful direction here - OK?
         direction = "<" if self.direction == MINIMIZE else ">"
-        replace_ptr = builder.alloca(pnlvm.ir.IntType(1))
+        replace_ptr = builder.alloca(ctx.bool_ty)
 
         # Check the value against current min
         with pnlvm.helpers.for_loop_zero_inc(builder, count, "compare_loop") as (b, idx):

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

@@ -780,7 +780,7 @@ def _gen_llvm_function_body(self, ctx, builder, params, state, arg_in, arg_out,
         out_val_ptr = builder.gep(arg_out, [ctx.int32_ty(0), ctx.int32_ty(1)])
 
         # Check retrieval probability
-        retr_ptr = builder.alloca(pnlvm.ir.IntType(1))
+        retr_ptr = builder.alloca(ctx.bool_ty)
         builder.store(retr_ptr.type.pointee(1), retr_ptr)
         retr_prob_ptr = pnlvm.helpers.get_param_ptr(builder, self, params, RETRIEVAL_PROB)
 
@@ -844,7 +844,7 @@ def _gen_llvm_function_body(self, ctx, builder, params, state, arg_in, arg_out,
             builder.store(selected_val, out_val_ptr)
 
         # Check storage probability
-        store_ptr = builder.alloca(pnlvm.ir.IntType(1))
+        store_ptr = builder.alloca(ctx.bool_ty)
         builder.store(store_ptr.type.pointee(1), store_ptr)
         store_prob_ptr = pnlvm.helpers.get_param_ptr(builder, self, params, STORAGE_PROB)
 
@@ -866,14 +866,14 @@ def _gen_llvm_function_body(self, ctx, builder, params, state, arg_in, arg_out,
         with builder.if_then(store, likely=True):
 
             # Check if such key already exists
-            is_new_key_ptr = builder.alloca(pnlvm.ir.IntType(1))
+            is_new_key_ptr = builder.alloca(ctx.bool_ty)
             builder.store(is_new_key_ptr.type.pointee(1), is_new_key_ptr)
             with pnlvm.helpers.for_loop_zero_inc(builder, entries, "distance_loop") as (b,idx):
                 cmp_key_ptr = b.gep(keys_ptr, [ctx.int32_ty(0), idx])
 
                 # Vector compare
                 # TODO: move this to helpers
-                key_differs_ptr = b.alloca(pnlvm.ir.IntType(1))
+                key_differs_ptr = b.alloca(ctx.bool_ty)
                 b.store(key_differs_ptr.type.pointee(0), key_differs_ptr)
                 with pnlvm.helpers.array_ptr_loop(b, cmp_key_ptr, "key_compare") as (b2, idx2):
                     var_key_element = b2.gep(var_key_ptr, [ctx.int32_ty(0), idx2])

psyneulink/core/components/mechanisms/mechanism.py

@@ -2532,13 +2532,18 @@ def execute(self,
             if not self.parameters.execute_until_finished._get(context):
                 break
 
-        # REPORT EXECUTION
-        if self.prefs.reportOutputPref and (context.execution_phase & ContextFlags.PROCESSING | ContextFlags.LEARNING):
-            self._report_mechanism_execution(
-                self.get_input_values(context),
-                output=self.output_port.parameters.value._get(context),
-                context=context
-            )
+        # REPORT EXECUTION if called from command line
+        #  If called by a Composition, it handles reporting.
+        if context.source == ContextFlags.COMMAND_LINE:
+            if self.prefs.reportOutputPref and (context.execution_phase & ContextFlags.PROCESSING | ContextFlags.LEARNING):
+                from psyneulink.core.compositions.composition import _report_node_execution
+                from rich import print
+                print(
+                    _report_node_execution(self,
+                                           input_val=self.get_input_values(context),
+                                           output_val=self.output_port.parameters.value._get(context),
+                                           context=context)
+                )
 
         return value
 
@@ -2965,7 +2970,7 @@ def _gen_llvm_invoke_function(self, ctx, builder, function, params, state, varia
         return fun_out, builder
 
     def _gen_llvm_is_finished_cond(self, ctx, builder, params, state):
-        return pnlvm.ir.IntType(1)(1)
+        return ctx.bool_ty(1)
 
     def _gen_llvm_mechanism_functions(self, ctx, builder, params, state, arg_in,
                                       ip_output, *, tags:frozenset):
@@ -3043,8 +3048,7 @@ def _gen_llvm_function(self, *, extra_args=[], ctx:pnlvm.LLVMBuilderContext, tag
                 ctx.get_input_struct_type(self).as_pointer(),
                 ctx.get_output_struct_type(self).as_pointer()]
 
-        builder = ctx.create_llvm_function(args, self,
-                                           return_type=pnlvm.ir.IntType(1),
+        builder = ctx.create_llvm_function(args, self, return_type=ctx.bool_ty,
                                            tags=tags)
         params, state = builder.function.args[:2]
         finished = self._gen_llvm_is_finished_cond(ctx, builder, params, state)
@@ -3083,7 +3087,7 @@ def _gen_llvm_function_body(self, ctx, builder, params, state, arg_in, arg_out,
         args_t = [a.type for a in builder.function.args]
         internal_builder = ctx.create_llvm_function(args_t, self,
                                                     name=builder.function.name + "_internal",
-                                                    return_type=pnlvm.ir.IntType(1))
+                                                    return_type=ctx.bool_ty)
         iparams, istate, iin, iout = internal_builder.function.args[:4]
         internal_builder, is_finished = self._gen_llvm_function_internal(ctx, internal_builder,
                                                                          iparams, istate, iin, iout, tags=tags)
@@ -3131,74 +3135,6 @@ def _gen_llvm_function_body(self, ctx, builder, params, state, arg_in, arg_out,
 
         return builder
 
-    def _report_mechanism_execution(self, input_val=None, params=None, output=None, context=None):
-
-        if input_val is None:
-            input_val = self.get_input_values(context)
-        if output is None:
-            output = self.output_port.parameters.value._get(context)
-        params = params or {p.name: p._get(context) for p in self.parameters}
-
-        if 'mechanism' in self.name or 'Mechanism' in self.name:
-            mechanism_string = ' '
-        else:
-            mechanism_string = ' mechanism'
-
-        # FIX: kmantel: previous version would fail on anything but iterables of things that can be cast to floats
-        #      if you want more specific output, you can add conditional tests here
-        try:
-            input_string = [float("{:0.3}".format(float(i))) for i in input_val].__str__().strip("[]")
-        except TypeError:
-            input_string = input_val
-
-        print("\n\'{}\'{} executed:\n- input:  {}".format(self.name, mechanism_string, input_string))
-
-        try:
-            include_params = re.match('param(eter)?s?', self.reportOutputPref, flags=re.IGNORECASE)
-        except TypeError:
-            include_params = False
-
-        if include_params:
-            print("- params:")
-            # Sort for consistency of output
-            params_keys_sorted = sorted(params.keys())
-            for param_name in params_keys_sorted:
-                # No need to report:
-                #    function_params here, as they will be reported for the function itself below;
-                #    input_ports or output_ports, as these are inherent in the structure
-                if param_name in {FUNCTION_PARAMS, INPUT_PORTS, OUTPUT_PORTS}:
-                    continue
-                param_is_function = False
-                param_value = params[param_name]
-                if isinstance(param_value, Function):
-                    param = param_value.name
-                    param_is_function = True
-                elif isinstance(param_value, type(Function)):
-                    param = param_value.__name__
-                    param_is_function = True
-                elif isinstance(param_value, (types.FunctionType, types.MethodType)):
-                    param = param_value.__self__.__class__.__name__
-                    param_is_function = True
-                else:
-                    param = param_value
-                print("\t{}: {}".format(param_name, str(param).__str__().strip("[]")))
-                if param_is_function:
-                    # Sort for consistency of output
-                    func_params_keys_sorted = sorted(self.function.parameters.names())
-                    for fct_param_name in func_params_keys_sorted:
-                        print("\t\t{}: {}".
-                              format(fct_param_name,
-                                     str(getattr(self.function.parameters, fct_param_name)._get(context)).__str__().strip("[]")))
-
-        # FIX: kmantel: previous version would fail on anything but iterables of things that can be cast to floats
-        #   if you want more specific output, you can add conditional tests here
-        try:
-            output_string = re.sub(r'[\[,\],\n]', '', str([float("{:0.3}".format(float(i))) for i in output]))
-        except TypeError:
-            output_string = output
-
-        print("- output: {}".format(output_string))
-
     @tc.typecheck
     def _show_structure(self,
                         show_functions:bool=False,