Merge pull request #1902 from PrincetonUniversity/devel

Devel

.github/actions/cleanup-pip-cache/action.yml

@@ -13,6 +13,6 @@ runs:
         for P in $CACHED; do
           # Remove cached and not installed
           if [ `echo $INSTALLED | grep -o $P | wc -l` == "0" ] ; then
-            pip cache remove -v $P
+            pip cache remove -v $P || true
           fi
         done

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

@@ -3,20 +3,33 @@ name: PsyNeuLink Docs CI
 on: push
 
 jobs:
-  build:
+  docs-build:
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.6, 3.7] # Doesn't work in 3.8 or 3.9
+        python-version: [3.6, 3.7, 3.8]
         python-architecture: ['x64']
         os: [ubuntu-latest, macos-latest, windows-latest]
 
+    outputs:
+      on_master: ${{ steps.on_master.outputs.on_master }}
+
     steps:
     - name: Checkout sources
       uses: actions/checkout@v2
       with:
-        fetch-depth: 10
+        fetch-depth: 0
+
+    - name: Check if on master
+      id: on_master
+      shell: bash
+      run: |
+        git branch -a --contains $GITHUB_REF
+        git describe --always --tags
+        export ON_MASTER=$(git branch -a --contains $GITHUB_REF | grep -q '^  remotes/origin/master$' && echo "master" || echo "")
+        echo "Found out: ${ON_MASTER}"
+        echo ::set-output name=on_master::$ON_MASTER
 
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/[email protected]
@@ -76,3 +89,61 @@ jobs:
         name: Documentation-${{ matrix.os }}-${{ matrix.python-version }}-${{ matrix.python-architecture }}
         retention-days: 1
         path: pnl-html
+
+  docs-deploy:
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.7]
+        os: [ubuntu-latest]
+
+    runs-on: ${{ matrix.os }}
+    needs: [docs-build]
+    if: github.ref == 'refs/heads/master' || github.ref == 'refs/heads/devel' || github.ref == 'refs/heads/docs' || (contains(github.ref, 'tags') && contains(needs.*.outputs.on_master, 'master'))
+
+    steps:
+    - name: Checkout docs
+      uses: actions/checkout@v2
+      with:
+        ref: gh-pages
+
+    - name: Download branch docs
+      uses: actions/download-artifact@v2
+      with:
+        name: Documentation-${{ matrix.os }}-${{ matrix.python-version }}-x64
+        path: _built_docs/${{ github.ref }}
+      if: github.ref == 'refs/heads/master' || github.ref == 'refs/heads/devel' || github.ref == 'refs/heads/docs'
+
+    - name: Update branch docs
+      shell: bash
+      run: |
+        mkdir -p branch
+        rm -rf "branch/${GITHUB_REF##*/}"
+        # Remove '.doctrees' and move to correct location
+        rm -rf "_built_docs/${GITHUB_REF}/.doctrees"
+        mv -f "_built_docs/${GITHUB_REF}" branch/
+      if: github.ref == 'refs/heads/master' || github.ref == 'refs/heads/devel' || github.ref == 'refs/heads/docs'
+
+    - name: Download main docs
+      uses: actions/download-artifact@v2
+      with:
+        name: Documentation-${{ matrix.os }}-${{ matrix.python-version }}-x64
+        # This overwrites files in current directory
+      if: contains(github.ref, 'tags') && contains(needs.*.outputs.on_master, 'master')
+
+    - name: Update main docs
+      shell: bash
+      run: |
+        # Remove '.doctrees'
+        rm -rf ".doctrees"
+      if: contains(github.ref, 'tags') && contains(needs.*.outputs.on_master, 'master')
+
+    - name: Commit docs changes
+      shell: bash
+      run: |
+        # Commit changes to git
+        git add .
+        git config user.name "Documentation Bot"
+        git config user.email "[email protected]"
+        git commit -m "Docs changes for $GITHUB_REF $GITHUB_SHA"
+        git push

.github/workflows/pnl-ci.yml

@@ -21,7 +21,7 @@ jobs:
         os: [ubuntu-latest, macos-latest, windows-latest]
         include:
           # add 32-bit build on windows
-          - python-version: 3.6
+          - python-version: 3.8
             python-architecture: 'x86'
             os: windows-latest
 

Scripts/Examples/LC Control Mechanism Composition.py

@@ -7,7 +7,7 @@
 
 A = TransferMechanism(function=Logistic(gain=user_specified_gain), name='A')
 B = TransferMechanism(function=Logistic(gain=user_specified_gain), name='B')
-# B.output_ports[0].value *= 0.0  # Reset after init | Doesn't matter here b/c default var = zero, no intercept
+# B.output_ports[0].parameters.value.set(0.0, override=True)  # Reset after init | Doesn't matter here b/c default var = zero, no intercept
 
 LC = LCControlMechanism(
     modulated_mechanisms=[A, B],

dev_requirements.txt

@@ -1,7 +1,7 @@
 jupyter<=1.0.0
-pytest<6.2.2
+pytest<6.2.3
 pytest-benchmark<=3.2.3
-pytest-cov<=2.10.1
+pytest-cov<2.11.2
 pytest-helpers-namespace<=2019.1.8
 pytest-profiling<=1.7.0
 pytest-pycodestyle<=2.2.0

docs/source/Preferences.rst

@@ -7,7 +7,8 @@ Standard prefereces:
 
 - paramValidation (bool): enables/disables run-time validation of the execute method of a Function object
 
-- reportOutput (bool): enables/disables reporting of execution of execute method
+- reportOutput ([bool, str]): enables/disables reporting of execution of execute method:
+   True prints input/output, 'params' or 'parameters' includes parameter values
 
 - log (bool): sets LogCondition for a given Component
 

psyneulink/core/components/component.py

@@ -520,7 +520,7 @@
 from psyneulink.core.globals.utilities import \
     ContentAddressableList, convert_all_elements_to_np_array, convert_to_np_array, get_deepcopy_with_shared,\
     is_instance_or_subclass, is_matrix, iscompatible, kwCompatibilityLength, prune_unused_args, \
-    get_all_explicit_arguments, call_with_pruned_args, safe_equals
+    get_all_explicit_arguments, call_with_pruned_args, safe_equals, safe_len
 from psyneulink.core.scheduling.condition import Never
 
 __all__ = [
@@ -650,7 +650,14 @@ def setter(self, value):
                 f' for example, <object>.{param.name}.base = {value}',
                 FutureWarning,
             )
-        getattr(self.parameters, p.name)._set(value, self.most_recent_context)
+        try:
+            getattr(self.parameters, p.name).set(value, self.most_recent_context)
+        except ParameterError as e:
+            if 'Pass override=True to force set.' in str(e):
+                raise ParameterError(
+                    f"Parameter '{p.name}' is read-only. Set at your own risk."
+                    f' Use .parameters.{p.name}.set with override=True to force set.'
+                ) from None
 
     return property(getter).setter(setter)
 
@@ -1002,7 +1009,10 @@ def _validate_variable(self, variable):
             return None
 
         def _parse_modulable(self, param_name, param_value):
-            from psyneulink.core.components.functions.distributionfunctions import DistributionFunction
+            from psyneulink.core.components.mechanisms.modulatory.modulatorymechanism import ModulatoryMechanism_Base
+            from psyneulink.core.components.ports.modulatorysignals import ModulatorySignal
+            from psyneulink.core.components.projections.modulatory.modulatoryprojection import ModulatoryProjection_Base
+
             # assume 2-tuple with class/instance as second item is a proper
             # modulatory spec, can possibly add in a flag on acceptable
             # classes in the future
@@ -1018,14 +1028,10 @@ def _parse_modulable(self, param_name, param_value):
                 )
             ):
                 value = param_value[0]
-            # assume a DistributionFunction is allowed to persist, for noise
             elif (
-                (
-                    is_instance_or_subclass(param_value, Component)
-                    and not is_instance_or_subclass(
-                        param_value,
-                        DistributionFunction
-                    )
+                is_instance_or_subclass(
+                    param_value,
+                    (ModulatoryMechanism_Base, ModulatorySignal, ModulatoryProjection_Base)
                 )
                 or (
                     isinstance(param_value, str)
@@ -1286,9 +1292,9 @@ def _get_compilation_state(self):
         if not hasattr(self, 'ports'):
             blacklist.add("value")
         def _is_compilation_state(p):
-            val = p.get()   # memoize for this function
-            return val is not None and p.name not in blacklist and \
-                   (p.name in whitelist or isinstance(val, Component))
+            #FIXME: This should use defaults instead of 'p.get'
+            return p.name not in blacklist and \
+                   (p.name in whitelist or isinstance(p.get(), Component))
 
         return filter(_is_compilation_state, self.parameters)
 
@@ -2040,8 +2046,9 @@ def _is_user_specified(parameter):
                 if isinstance(val, Function):
                     val.owner = self
 
+                val = p._parse(val)
                 p._validate(val)
-                p.set(val, context=context, skip_history=True, override=True)
+                p._set(val, context=context, skip_history=True, override=True)
 
             if isinstance(p.default_value, Function):
                 p.default_value.owner = p
@@ -2704,7 +2711,7 @@ def _get_param_value_from_tuple(self, param_spec):
 
         return value
 
-    def _validate_function(self, function):
+    def _validate_function(self, function, context=None):
         """Check that either params[FUNCTION] and/or self.execute are implemented
 
         # FROM _validate_params:
@@ -2752,7 +2759,7 @@ def _validate_function(self, function):
             or isinstance(function, types.MethodType)
             or is_instance_or_subclass(function, Function)
         ):
-            self.function = function
+            self.parameters.function._set(function, context)
             return
         # self.function is NOT OK, so raise exception
         else:
@@ -2813,7 +2820,7 @@ def _instantiate_function(self, function, function_params=None, context=None):
         # Specification is a standard python function, so wrap as a UserDefnedFunction
         # Note:  parameter_ports for function's parameters will be created in_instantiate_attributes_after_function
         if isinstance(function, types.FunctionType):
-            self.function = UserDefinedFunction(default_variable=function_variable,
+            function = UserDefinedFunction(default_variable=function_variable,
                                                 custom_function=function,
                                                 owner=self,
                                                 context=context)
@@ -2840,9 +2847,7 @@ def _instantiate_function(self, function, function_params=None, context=None):
             # class default functions should always be copied, otherwise anything this component
             # does with its function will propagate to anything else that wants to use
             # the default
-            if function.owner is None:
-                self.function = function
-            elif function.owner is self:
+            if function.owner is self:
                 try:
                     if function._is_pnl_inherent:
                         # This will most often occur if a Function instance is
@@ -2860,15 +2865,15 @@ def _instantiate_function(self, function, function_params=None, context=None):
                             ' [email protected] or'
                             ' https://github.com/PrincetonUniversity/PsyNeuLink/issues'
                         )
-                        self.function = copy.deepcopy(function)
+                        function = copy.deepcopy(function)
                 except AttributeError:
-                    self.function = function
-            else:
-                self.function = copy.deepcopy(function)
+                    pass
+            elif function.owner is not None:
+                function = copy.deepcopy(function)
 
             # set owner first because needed for is_initializing calls
-            self.function.owner = self
-            self.function._update_default_variable(function_variable, context)
+            function.owner = self
+            function._update_default_variable(function_variable, context)
 
         # Specification is Function class
         # Note:  parameter_ports for function's parameters will be created in_instantiate_attributes_after_function
@@ -2899,11 +2904,13 @@ def _instantiate_function(self, function, function_params=None, context=None):
                         pass
 
             _, kwargs = prune_unused_args(function.__init__, args=[], kwargs=kwargs_to_instantiate)
-            self.function = function(default_variable=function_variable, owner=self, **kwargs)
+            function = function(default_variable=function_variable, owner=self, **kwargs)
 
         else:
             raise ComponentError(f'Unsupported function type: {type(function)}, function={function}.')
 
+        self.parameters.function._set(function, context)
+
         # KAM added 6/14/18 for functions that do not pass their has_initializers status up to their owner via property
         # FIX: need comprehensive solution for has_initializers; need to determine whether ports affect mechanism's
         # has_initializers status
@@ -3155,6 +3162,77 @@ def _get_current_parameter_value(self, parameter, context=None):
 
         return parameter._get(context)
 
+    def _try_execute_param(self, param, var, context=None):
+        def fill_recursively(arr, value, indices=()):
+            if arr.ndim == 0:
+                try:
+                    value = value(context=context)
+                except TypeError:
+                    try:
+                        value = value()
+                    except TypeError:
+                        pass
+                return value
+
+            try:
+                len_value = len(value)
+                len_arr = safe_len(arr)
+
+                if len_value > len_arr:
+                    if len_arr == len_value - 1:
+                        ignored_items_str = f'Item {len_value - 1}'
+                    else:
+                        ignored_items_str = f'The items {len_arr} to {len_value - 1}'
+
+                    warnings.warn(
+                        f'The length of {value} is greater than that of {arr}.'
+                        f'{ignored_items_str} will be ignored for index {indices}'
+                    )
+            except TypeError:
+                # if noise value is not an iterable, ignore shape warnings
+                pass
+
+            for i, _ in enumerate(arr):
+                new_indices = indices + (i,)  # for error reporting
+                try:
+                    arr[i] = fill_recursively(arr[i], value[i], new_indices)
+                except (IndexError, TypeError):
+                    arr[i] = fill_recursively(arr[i], value, new_indices)
+
+            return arr
+
+        var = convert_all_elements_to_np_array(var, cast_from=np.integer, cast_to=float)
+
+        # handle simple wrapping of a Component (e.g. from ParameterPort in
+        # case of set after Component instantiation)
+        if (
+            (isinstance(param, list) and len(param) == 1)
+            or (isinstance(param, np.ndarray) and param.shape == (1,))
+        ):
+            if isinstance(param[0], Component):
+                param = param[0]
+
+        # Currently most noise functions do not return noise in the same
+        # shape as their variable:
+        if isinstance(param, Component):
+            try:
+                if param.defaults.value.shape == var.shape:
+                    return param(context=context)
+            except AttributeError:
+                pass
+
+        # special case where var is shaped same as param, but with extra dims
+        # assign param elements to deepest dim of var (ex: param [1, 2, 3], var [[0, 0, 0]])
+        try:
+            if param.shape != var.shape:
+                if param.shape == np.squeeze(var).shape:
+                    param = param.reshape(var.shape)
+        except AttributeError:
+            pass
+
+        fill_recursively(var, param)
+        return var
+
     def _increment_execution_count(self, count=1):
         self.parameters.execution_count.set(self.execution_count + count, override=True)
         return self.execution_count
@@ -3768,4 +3846,4 @@ def base(self):
 
     @base.setter
     def base(self, value):
-        self._parameter._set(value, self._owner.most_recent_context)
+        self._parameter.set(value, self._owner.most_recent_context)