Refactor/pec

docs/source/Composition.rst

@@ -10,6 +10,8 @@ Composition
 
        AutodiffComposition
        CompositionFunctionApproximator
+       ParameterEstimationComposition
+
     |
 
 .. container:: related

docs/source/Compositions.rst

@@ -8,4 +8,5 @@ Subclasses of `Core` `Composition` that implement specialized operations.
 
    AutodiffComposition
    CompositionFunctionApproximator
+   ParameterEstimationComposition
 

docs/source/Core.rst

@@ -3,13 +3,87 @@ Core
 
 * `Component`
    - `Mechanism`
+
+      - `ProcessingMechanism`
+
+        - `TransferMechanism`
+
+        - `IntegratorMechanism`
+
+        - `ObjectiveMechanism`
+
+
+      - `ModulatoryMechanism`
+
+        - `ControlMechanism`
+
+        - `LearningMechanism`
+
    - `Projection`
+
+      - `PathwayProjection`
+
+        - `MappingProjection`
+
+        - `MaskedMappingProjection`
+
+        - `AutoAssociativeProjection`
+
+      - `ModulatoryProjection`
+
+        - `LearningProjection`
+
+        - `ControlProjection`
+
+        - `GatingProjection`
+
    - `Port`
+
+      - `InputPort`
+
+      - `ParameterPort`
+
+      - `OutputPort`
+
+      - `ModulatorySignal`
+
+        - `LearningSignal`
+
+        - `ControlSignal`
+
+        - `GatingSignal`
+
    - `Function`
 
+      - `NonStatefulFunctions`
+
+            - `CombinationFunctions`
+
+            - `DistributionFunctions`
+
+            - `LearningFunctions`
+
+            - `ObjectiveFunctions`
+
+            - `OptimizationFunctions`
+
+            - `SelectionFunctions`
+
+            - `TransferFunctions`
+
+      - `StatefulFunctions`
+
+            - `IntegratorFunctions`
+
+            - `MemoryFunctions`
+
+      - `UserDefinedFunction`
+
+
 * `Composition`
    - `AutodiffComposition`
    - `CompositionFunctionApproximator`
+   - `ParameterEstimationComposition`
 
 * `Services`
    - `Registry`

docs/source/LearningMechanism.rst

@@ -1,5 +1,5 @@
-Learning Mechanism
-==================
+LearningMechanism
+=================
 
 .. automodule:: psyneulink.core.components.mechanisms.modulatory.learning.learningmechanism
    :members:

docs/source/ParameterEstimationComposition.rst

@@ -0,0 +1,10 @@
+ParameterEstimationComposition
+==============================
+
+.. toctree::
+   :maxdepth: 2
+
+.. automodule:: psyneulink.core.compositions.parameterestimationcomposition
+   :members:
+   :private-members:
+   :exclude-members: _validate_params, run, evaluate

freeze.txt

@@ -0,0 +1,131 @@
+aenum==2.2.3
+alabaster==0.7.12
+apipkg==1.5
+appnope==0.1.0
+attrs==19.3.0
+autograd==1.3
+Babel==2.8.0
+backcall==0.1.0
+beautifulsoup4==4.9.3
+bleach==3.1.1
+bokeh==2.2.3
+certifi==2019.11.28
+chardet==3.0.4
+colorama==0.4.4
+commonmark==0.9.1
+coverage==5.4
+cycler==0.10.0
+decorator==4.4.2
+defusedxml==0.6.0
+dill==0.3.1.1
+docutils==0.16
+elfi==0.7.5
+entrypoints==0.3
+execnet==1.7.1
+future==0.18.2
+google==3.0.0
+gprof2dot==2019.11.30
+GPy==1.9.9
+graph-scheduler==1.0.0
+graphviz==0.13.2
+grpcio==1.33.2
+grpcio-tools==1.33.2
+idna==2.9
+imagesize==1.2.0
+importlib-metadata==1.5.0
+iniconfig==1.1.1
+ipykernel==5.1.4
+ipyparallel==6.2.4
+ipython==7.13.0
+ipython-genutils==0.2.0
+ipywidgets==7.5.1
+jedi==0.16.0
+Jinja2==2.11.1
+joblib==0.14.1
+jsonschema==3.2.0
+jupyter==1.0.0
+jupyter-client==6.0.0
+jupyter-console==6.1.0
+jupyter-core==4.6.3
+kiwisolver==1.1.0
+leabra-psyneulink==0.3.2
+llvmlite==0.31.0
+MarkupSafe==1.1.1
+matplotlib==3.3.3
+mistune==0.8.4
+more-itertools==8.2.0
+nbconvert==5.6.1
+nbformat==5.0.4
+networkx==1.11
+notebook==6.0.3
+numpy==1.18.1
+packaging==20.3
+pandas==1.2.3
+pandocfilters==1.4.2
+paramz==0.9.5
+parso==0.6.2
+pexpect==4.8.0
+pickleshare==0.7.5
+Pillow==7.0.0
+Pint==0.17
+pluggy==0.13.1
+prometheus-client==0.7.1
+prompt-toolkit==3.0.4
+protobuf==3.14.0
+psyneulink==0.7.5.4
+psyneulink-sphinx-theme==1.1.3.0
+ptyprocess==0.6.0
+py==1.10.0
+py-cpuinfo==5.0.0
+pycodestyle==2.5.0
+pydocstyle==5.0.2
+Pygments==2.6.1
+pyparsing==2.4.6
+pyrsistent==0.15.7
+pytest==6.2.2
+pytest-benchmark==3.2.3
+pytest-cov==2.11.1
+pytest-forked==1.1.3
+pytest-helpers-namespace==2019.1.8
+pytest-profiling==1.7.0
+pytest-pycharm==0.6.0
+pytest-pycodestyle==2.2.0
+pytest-pydocstyle==2.2.0
+pytest-xdist==2.2.1
+python-dateutil==2.8.1
+pytz==2019.3
+PyYAML==5.4.1
+pyzmq==19.0.0
+qtconsole==4.7.1
+QtPy==1.9.0
+requests==2.23.0
+rich==10.1.0
+scikit-learn==0.22.2.post1
+scipy==1.4.1
+Send2Trash==1.5.0
+six==1.14.0
+snowballstemmer==2.0.0
+soupsieve==2.0.1
+Sphinx==3.5.4
+sphinx-autodoc-typehints==1.10.3
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==1.0.3
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.4
+terminado==0.8.3
+testpath==0.4.4
+toml==0.10.2
+toolz==0.10.0
+toposort==1.4
+torch==1.4.0
+tornado==6.0.4
+traitlets==4.3.3
+typecheck-decorator==1.2
+typing-extensions==3.7.4.3
+urllib3==1.25.8
+wcwidth==0.1.8
+webencodings==0.5.1
+widgetsnbextension==3.5.1
+zipp==3.1.0

psyneulink/core/components/component.py

@@ -1445,6 +1445,7 @@ def _get_values(p):
                 return (param,)
             elif p.name == 'num_estimates':
                 return 0 if param is None else param
+            # FIX: ADD num_trials_per_estimate HERE  11/3/21
             elif p.name == 'matrix': # Flatten matrix
                 return tuple(np.asfarray(param).flatten())
             return _convert(param)

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

@@ -111,10 +111,10 @@ class Concatenate(CombinationFunction):  # -------------------------------------
 
     .. _Concatenate:
 
-    Concatenates items in outer dimension (axis 0) of of `variable <Concatenate.variable>` into a single array,
+    Concatenates items in outer dimension (axis 0) of `variable <Concatenate.variable>` into a single array,
     optionally scaling and/or adding an offset to the result after concatenating.
 
-    `function <Concatenate.function>` returns a 1d array with lenght equal to the sum of the lengths of the items
+    `function <Concatenate.function>` returns a 1d array with length equal to the sum of the lengths of the items
     in `variable <Concatenate.variable>`.
 
     Arguments