Psyneulink

* Tests/projections/maskedmappingprojection (779)
* Fix/docs/maskedmappingprojection (778)
* handling array of DistributionFunctions case for new noise._execute rule
* adding replacing noise with noise._execute in function validation (to allow for noise=DistributionFunction())
* removing use of noise=DistributionFunction().function from constructors in pytests
* swapping .function with ._execute in noise validation to comply with the standard that functions are always executed through ._execute

* README: fix formatting to appear properly on PyPI
* Feat/projections/masked mapping projection (775)
* adding exceptions to get_current_function_param and get_current_mechanism_param - not intended for looking up 'variable'
* Feat/projections/masked mapping projection (771)
* LCA (770)
* LCA (769)
* Refactor/mechanism/transfermechanism (768)
* Fix default_variable bug (767)
* Feat/inputstate/combine (766)
* Refactor/context/source (765)
* Defaults: ensure that function attr appears when examining Defaults
* Rewrite Function instantiation:
* Component: create fewer instances during init when function arg is a class
* LinearMatrix: make keyword method static to reflect how it is used
* refactor/rename _variable_not_specified to be more generic, using enum
* Defaults: add enum to denote flexibility of assignments
* Component: add class method to get new param class defaults
* Defaults: add ClassDefaults.function to several classes, and use it as fallback
* utilities: add function to detect if obj is an instance or a subclass of a class
* Component: override __deepcopy__ method to use shared items
* parsing: add method to parse function variable from variable
* imports: pycharm-optimize to avoid unnecessary circularities
* Params: copy dict/ROODs nested in params arguments to avoid side effects
* Refactor/context/set and test (762)
* fixing bug in looking up target values for learning which caused first target value to be repeated
* LinearCombination, Reduce: handle negative exponents during init (avoid zero division)
* Functions: simplify noise validation
* adding a note to the ddm plot() documentation to clarify that the plot does not correspond to the actual results of the mechanism
* fixing drift diffusion integrator bug - returned threshold even when it crossed the negative threshold
* Fix/misc/misc (759)
* PredictionErrorMechanism: correct infinite recursion in _execute
* Docs/context/context (757)
* Mechanism (756)
* Refactor/mechanisms/ execute (754)
* LearningAuxilliary: rename to LearningAuxiliary (correct double l typo)
* scheduling: decouple Scheduler and Condition, allow multiple execution_ids
* utilites: get method to prune unused args from a function from composition branch
* Feat/mechanism/input target lable dicts (752)
* testing: Resolve leftover merge conflicts, fixes 747
* testing: correct pytest setup ovewrite, losing some settings
* Feat/mechanism/input target label dicts (751)
* Scheduling: fix bug where termination conditions persisted across calls to run
* tests,function/LinearCombination: Add tests with absent parameters
* test,function/LinearCombination: Rename second test function to prevent overwriting results
* Context (746)
* Refactor/context/deprecate init status (745)
* Refactor/context/structured (744)
* Fix/function/stability (743)
* IntegratorMechanism (742)

* documentation typos
* documenting reinitialize on mechanism
* continuing to add tests and docs for reinitialize
* fixing bugs that prevented initialize method on system from ever executing, and adding pytests for it now that it works
* revising outdated TransferMechanism docs for reinitialize
* continuing to add tests to highlight differences between calling reinitialize on a mechanisms and on a function
* adding nparray_dictionary to docs and revising nparray to use the same helper methods as nparray_dictionary
* Time: fix bug where RUN counter would not be incremented on new runs
* fixing (temporarily) time_step bug in nparray_dictionary; reorganzing nparray_dictionary into methods that can be reused by nparray
* refactoring log to have a dictionary option and writing tests for it
* beginning to add a dictionary alternative to the options for whats returned by the log
* more calls to _dealias_owner_name required in order to create log.nparray
* fixing bug in log: needed to switch between 'value' and mechanism name in several loops in order to assemble log.nparray
* adding more pytests for reinitialize and fixing reinitialize bugs; beginning to update documentation
* adding pytests for reinitializing at both function and mechanism level; cleaning up mistakes in reinitialize() methods along the way
* adding a reinitialize method on mechanisms, which calls reinitialize on its function or integrator_function, then updates the mechanism's value and output states
* beginning to refactor reinitialize as a method on integrator functions

* (561)
* Fix/component/default naming (558)
* remove Scratch Pad
* clean up DDM examples with verified parameters from matlab
* skip NavarroAndFuss doctest because build server cannot access matlab
* update NavarroAndFuss to use the correct version of the MATLAB simulation
* convert DDM return_value for NavarroAndFuss function to be floats to allow NaN assignment
* fix bug in using the matlab engine to run a script outside of the current dir
* adding validation on NormalDist function in the case where some numpy versions throw an error
* • System (556)
* Feat/system/show graph (555)
* Fix/modulatory specifications (554)
* clean imports in function.py
* cleanup Scheduler doc examples
* add parsing handler for Scheduler termination_conditions
* move static .svg files from docs build directory to source dir
* update docs to show 0.0.x versions instead of just 0.x (we use the former frequently)
* fix broken package link for AutoAssociativeMechanism that caused sphinx automodule to fail
* removing references to 'inhibition' and 'decay' in LCA docs
* removing gilzenrat transfer mechanism from the repo
* updating gilzenrat unit tests to use LCA mechanism in place of GilzenratTransferMechanism
* ...

RecurrentTransferMechanism Learning

* Core and Subsystems directories added
* Control mechanism refactored
* LC and AGT mechanisms implemented
* Show graph method repaired
* Bugs fixed in tutorial