Merge back release nudge to main (sync to v3.0.1) (#130)

* Minor nudge to v3.0.1 (#129)

* minor edit to math in hh-lesson doc

* Fix workflow, numpy install, and pytest bug in github action workflows (#117)

* Update pyproject.toml

* Update python-package-conda.yml

* Update python-package-conda.yml

* Update python-package-conda.yml

* Update python-package-conda.yml

* Update python-package-conda.yml

* Update python-package-conda.yml

* Update python-package-conda.yml

* minor nudge/cleanup to minor patched version 2.0.1

* minor nudge/cleanup to minor patched version 2.0.3

* Merged back minor doc fix back to main (for syncing purposes) (#119)

* Nudge of release to minor patched version 2.0.3 (#118)

* nudge of doc to 2.0.2 (#115)

Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu>

* minor edit to math in hh-lesson doc

* Fix workflow, numpy install, and pytest bug in github action workflows (#117)

* Update pyproject.toml

* Update python-package-conda.yml

* Update python-package-conda.yml

* Update python-package-conda.yml

* Update python-package-conda.yml

* Update python-package-conda.yml

* Update python-package-conda.yml

* Update python-package-conda.yml

* minor nudge/cleanup to minor patched version 2.0.1

* minor nudge/cleanup to minor patched version 2.0.3

---------

Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu>
Co-authored-by: Viet Dung Nguyen <60036798+rxng8@users.noreply.github.com>

* fixed typo/error in doc evolving_synapses.md

---------

Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu>
Co-authored-by: Viet Dung Nguyen <60036798+rxng8@users.noreply.github.com>

* minor clean-up in model_basics docs

* minor fixes/cleanup of docs

* fixed typo in integration tutorial doc

* updated papers/talk page for ngclearn

* Merging over v3 to main (for roll-out of v3 upgrade) (#125)

* Working v3

* Undid fixed compartemts

Undid the fixed compartments to work with new global constant tracking

* Fixed an execution bug

* ported over quad-lif to v3 - needs testing

* ported over IF/quadLIF cells, minor revision to LIF cell

* Start util cleanup

* refactored/ported RAFCell to v3

* ported over/refactored WTASCell for v3

* wrote successful unit-test of WTASCell

* put back in init-structure/pointers

* fixed minor error in LIFCell, got unit-test for LIFCell to run

* quad-lif test sketched

* sketch of ifcell test

* fixed minor bugs and tests locally pass for if, quad-lif, and lif-cells now, with minor patches to help fun and doc-strings

* refactored raf-cell and test passed

* refactored adex/test passed; minor cleanup in lif, raf, and wtas cells

* refactored fn-cell and test passed

* cleaned up lif, raf, wtas, fn, and quad-lif cells repr method

* refactored and tests passed for izh and h-h cells

* JaxProcess update

* cleaned up dunder repr method, moved to JaxComponent parent; fixed __init__ pointer to tensorstats

* refactored alpha and exp-synapses, tests passed; minor edit to __init__ for synapses

* refactored short-term syn, tests passed - including stp-dense-syn and minor cleanup/edit to synapse __init__

* refactored bcm-syn and test passed

* refactored exp-stdp-syn and passed tests for exp-stdp-syn and trace-stdp-syn

* refactored event-stdp-syn and test passed

* refactored mstdpet-syn and test passed

* refactored stdp-conv-syn/conv-syn and test passed

* refactored and passed test for deconv/stdp-deconv-syn and other minor cleanup for conv/deconv support

* Refactoring neuronal and synaptic components (#123) - merge from fork to v3

* refactoring graded cells

* update refactored models

* update sLIF cell

---------

Co-authored-by: Alex Ororbia <agocse109@gmail.com>

* commented out deprecator in hebb-syn and exp-kernel

* update hebbian synapse

* update hebbian synapse

* working reinforce synapse

* minor edits to exp-kernel/wtas-cell

* update requirements

* refactored conv/deconv-hebb-syn and tests passed

* update hebbian synapse reset bug

* update reset methods

* update patched synapse reset

* add `not self.inputs.targeted and ` to required components. Fixing general `__repr__` bug in `jaxcomponent`

* minor edit to lif/modulated-syn init file

* fixed some minor bugs in rate-coded cells/hebb-syn

* update code

* minor patches to components, including hebb-syn/conv/deconv and reward-cell

* minor patches to components, including hebb-syn/conv/deconv and reward-cell

* update testing for graded neurons and input encoders

* update phasor cell

* update test bernoulli cell and poisson cell

* update components and their related test cases

* fixed monitor bugs from v2, tweaked unit-tests for input-encoders/latency-cell

* update test case for test_sLIFCell.py

* some cleanup

* made revisions to components/clean-up; added back in deprecators

* removed lava sub-module, and removed monitor/base-monitor legacy components

* minor cleanup of inits

* refactored regression module to be compliant with v3

* adjusted sphinx-docs w.r.t. new v3 refactoring

* minor revision to double-exp syn pointing, mods to modeling docs

* updated adex tutorial doc to v3

* revised adex and error-cell neurocog tutorials

* fixed minor issues in input-encoders, further revisions to docs for v3

* revised dyn/chem-syn neurocog doc, cleaned up dynamic syn

* revised fn and hh-cell neurocog docs, added some refs to distribution generator

* revised integration and izh-cell neurocog docs

* revised izh-cell, cleaned-up fn-cell, and revised lif neurocog docs

* revised metrics/plotting neurocog docs

* revised mod/reward-stdp neurocog doc

* revised stp-syn neurocog doc and updated stp-syn to use proper initializer

* revised elements of utils to comply with docs

* revised stdp neurocog doc to v3

* revised traces neurocog tutorial to v3

* cleaned up utils.optim and wrote compliant NAG optim

* cleaned up utils.optim and wrote compliant NAG optim

* cleanup of components, added leaky-noise-cell, minor edits

* revised leaky-noise-cell, wrote its unit test, test-passed

* some revisions/updates to toc/pointer/general tutorial docs

* minor revisions to pyproject/req files

* update reinforce synapse

* update test cases

* implemented in-house gmm, in-built to ngclearn; tested on gaussian mode data

* wrote gmm density estimator tutorial

* patched some tests/syn/neuron components, added sketch of bmm density

* fixed test_laplacianErrorCell and laplace-cell bug

* fixed test_laplacianErrorCell and laplace-cell bug

* made patches to bmm

* updated density tutorial/neurocog doc

* minor edit to gmm/bmm docs

* minor edit to gmm/bmm docs

* cleaned up density structure, use parent mixture class to organize model variations

* cleaned up density structure, use parent mixture class to organize model variations

* added basic exp-mixture to utils.density

* minor edits to emm

* cleaned up mixtures and finished debugging EMM/works on example

* removed old weight_distribution.py, other cleanup/revisions throughout

* minor edit to data-loader

* revised tests to no longer use weight_distribution/revisions throughout

* minor edit to emm doc

* added bic calculation to metric_utils

* fix ratecell  ug of passing unrelated kwargs to parent class

* added calc_update() co-routine to hebbian-syn component

* fix weight init

* integrated rbm/harmonium model-exhibit

* Update __init__.py

Added the config/logging back to the init

* placed pointer to rao-ballard1999 exhibit; updates to docs

* updates to docs/revisions

* removed flag from bernoulli/latency-cells for now; minor edit to doc

* updates to theory doc

* updated history log

* minor clean-up of ngclearn.utils.viz.dim_reduce

* Update jaxComponent.py

Added support for turning off autosave

* update hebbian synapse saving

* update saving and loading utils, making hebbian synapse use these utils for custom optimizer params saving and loading

* minor revisions/polish

* modded docs to include v3 foundations

* updates to init for logging

* Updates to lessons

* final cleanup/polish/update to docs for v3 nudge

* updates to museum doc for v3

* nudged citation file

* minor nudge to docs/files to point to v3

---------

Co-authored-by: Will Gebhardt <will@gebhardts.net>
Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu>
Co-authored-by: Viet Dung Nguyen <60036798+rxng8@users.noreply.github.com>
Co-authored-by: Viet Nguyen <alexvn.edu@gmail.com>
Co-authored-by: Viet Dung Nguyen <vietdungnguyen233@gmail.com>

* update to rbm/harmonium doc

* updated leaky-noise-cell to maintain temporal derivative of state

* minor revisons/updates to hebb/dense syn, metric utils

* cleaned-up/revised leaky-noise-cell

* cleaned-up/revised leaky-noise-cell

---------

Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu>
Co-authored-by: Viet Dung Nguyen <60036798+rxng8@users.noreply.github.com>
Co-authored-by: Will Gebhardt <will@gebhardts.net>
Co-authored-by: Viet Nguyen <alexvn.edu@gmail.com>
Co-authored-by: Viet Dung Nguyen <vietdungnguyen233@gmail.com>

* nudge release to v3.0.1

---------

Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu>
Co-authored-by: Viet Dung Nguyen <60036798+rxng8@users.noreply.github.com>
Co-authored-by: Will Gebhardt <will@gebhardts.net>
Co-authored-by: Viet Nguyen <alexvn.edu@gmail.com>
Co-authored-by: Viet Dung Nguyen <vietdungnguyen233@gmail.com>

Author: 4 people

README.md

@@ -122,7 +122,7 @@ $ python install -e .
 </pre>
 
 **Version:**<br>
-3.0.0 <!--1.2.3-Beta--> <!-- -Alpha -->
+3.0.1 <!--1.2.3-Beta--> <!-- -Alpha -->
 
 Author:
 Alexander G. Ororbia II<br>

docs/installation.md

@@ -51,7 +51,7 @@ Python 3.11.4 (main, MONTH  DAY YEAR, TIME) [GCC XX.X.X] on linux
 Type "help", "copyright", "credits" or "license" for more information.
 >>> import ngclearn
 >>> ngclearn.__version__
-'3.0.0'
+'3.0.1'
 ```
 
 <!--

pyproject.toml

@@ -8,7 +8,7 @@ build-backend = "setuptools.build_meta" # using setuptool building engine
 
 [project]
 name = "ngclearn"
-version = "3.0.0"
+version = "3.0.1"
 description = "Simulation software for building and analyzing computational neuroscience models, brain-inspired computing systems, and NeuroAI agents."
 authors = [
   {name = "Alexander Ororbia", email = "ago@cs.rit.edu"},