Major release update merge to main (sync up) (#101)

* add initial patch mask features

* minor edit to bern-cell

* fixed bernoulli error cell

* example rate cell test

* made some corrections to bern err-cell and heb syn

* made some corrections to bern err-cell and heb syn

* cleaned up bern-cell, hebb-syn

* minor mod to model-utils

* attempted rewrite of bernoulli-cell

* got bernoulli-cell rewritten and unit-tested

* edit to bern-cell

* bernoulli and poisson cells revised, unit-tested

* latency-cell refactored and unit-tested

* refactored Rate Cell

* minor revisions to input-encoders, revised phasor-cell w/ unit-test

* revised and add unit-test for varTrace

* revised and added unit-test for exp-kernel

* revised and added unit-test for exp-kernel

* revised slif cell w/ unit-test; needed mod to diffeq

* revised slif-cell w/ unit-test; cleaned up ode_utils to play nicer w/ new sim-lib

* revised lif-cell w/ unit-test

* revised unit-tests to pass globally; some minor patches to phasor-cell and lif

* minor cleanup of unit-test for phasor

* revised if-cell w/ unit-test

* revised if-cell w/ unit-test

* revised quad-lif w/ unit-test

* revised adex-cell w/ unit test, minor cleanup of quad-lif

* minor edit to adex unit-test

* refactor bernoulli, laplacian, and rewarderror cells

* revised raf-cell w/ unit test; fixed typos/mistakes in all spiking cells

* revised wtas-cell w/ unit test

* revised fh-cell w/ unit test

* revised izh-cell w/ unit test

* patched ode_utils backend wrt jax, cleaned up unit-tests, added disable flag for phasor-cell

* update rate cell

* fix test rate cell

* update test for bernoulli cell

* update refactoring for gaussian error cell

* update unit testing for all graded neurons

* wrote+unit-test of hodgkin-huxley spike cell, minor tweaks/clean-up elsewhere

* added rk2 support for H-H cell

* update rate cell and fix bug of passing a tuple of (jax Array -- not hashable)  to jax jit functions. Basically, simplify the codebase by using a hashmap of functions

* update test rate cell

* refactored dense and trace-stdp syn w/ unit-test

* refactored exp-stdp syn w/ unit-test

* refactored event-stdp w/ unit-test

* cleanup of stdp-syn

* refactored bcm syn w/ unit-test

* refactored stp-syn with unit-test

* cleaned up modulated

* refactored mstdp-et syn w/ unit-test

* refactored lava components to new sim-lib

* refactored conv/hebb-conv syn w/ unit-test

* refactored/revised hebb-deconv syn w/ unit-test

* revised/refactored hebb/stdp conv/deconv syn w/ unit-tests

* updated modeling doc to point to hodgkin-huxley cell

* updated modeling docs

* fixed typo in adex-cell tutorial doc

* revised tutorials to reflect new sim-lib config/syntax

* revised tutorials to reflect new sim-lib config/syntax

* patched docs to reflect revisions/refactor

* tweaked requirements in prep for major release

* cleaned up a few unit tests to use deterministic syn init vals

* mod to requirements

* nudge toml to upcoming 2.0.0

* update to support docs in prep for 2.0.0

* update patched synapses and their test cases

* cleaned up syn modeling doc

* push hebbian synapse

* push reinforce synapse

* push np seed

* patched minor prior None arg issue in hebb-syn

* moved reinforce-syn to right spot

* update reinforce synapse and testing

* tweaked trace-stdp and mstdpet

* patched mstdpet unit-test

* update reinforce synapse and test cases

* add reinforce synapse fix

* minor mod to mstdpet

* update test code for more than 1 steps

* Updated monitors

* patched tests to use process naming

* Added wrapper for reset and advance_state

* Added a JaxProcess

Added Jax Process to allow for scanning over the process.

* update the old rate cell

* update old hebbian synapse

* minor edit to if-cell

* ported over adex tutorial to new ngclearn format

* hh-cell supports rk4 integration

* clean up and integrated hodgkin-huxley mini lesson in neurocog tutorials

* Update jaxProcess.py

Updated the jax process to allow for more configurations of inputs.

* update working reinforce synapse

* update correct reinforce and testing

* update documentation

* update features, documentation, and testing

* update testing for REINFORCE cell

* update code and test

* update code

* add clipping gradient to model utils

* update reinforce cell to the new model utils clip

* major cleanup in prep for merge over to main/prep for major release

* update test cases

* update to require file in docs

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Co-authored-by: Viet Dung Nguyen <vietdungnguyen233@gmail.com>
Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu>
Co-authored-by: Will Gebhardt <will@gebhardts.net>

Author: 4 people