v0.4.7.1

• 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

v0.4.7.0

• 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)

v0.4.4.0

• 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

v0.4.0rc1

• (#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
• ...

v0.3.4-alpha: Merge pull request #481 from PrincetonUniversity/devel

RecurrentTransferMechanism Learning

v0.3.3-alpha: Merge pull request #474 from PrincetonUniversity/temp/merge-devel

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