Sync up of main with release (#131)

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Viet Dung Nguyen <[email protected]>

* fixed typo/error in doc evolving_synapses.md

---------

Co-authored-by: Alexander Ororbia <[email protected]>
Co-authored-by: Viet Dung Nguyen <[email protected]>

* 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 <[email protected]>

* 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 <[email protected]>
Co-authored-by: Alexander Ororbia <[email protected]>
Co-authored-by: Viet Dung Nguyen <[email protected]>
Co-authored-by: Viet Nguyen <[email protected]>
Co-authored-by: Viet Dung Nguyen <[email protected]>

* 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 <[email protected]>
Co-authored-by: Viet Dung Nguyen <[email protected]>
Co-authored-by: Will Gebhardt <[email protected]>
Co-authored-by: Viet Nguyen <[email protected]>
Co-authored-by: Viet Dung Nguyen <[email protected]>

* nudge release to v3.0.1

* minor revision of leaky-noise-cell

---------

Co-authored-by: Alexander Ororbia <[email protected]>
Co-authored-by: Viet Dung Nguyen <[email protected]>
Co-authored-by: Will Gebhardt <[email protected]>
Co-authored-by: Viet Nguyen <[email protected]>
Co-authored-by: Viet Dung Nguyen <[email protected]>

Author: 4 people

ngclearn/components/neurons/graded/leakyNoiseCell.py

@@ -71,7 +71,6 @@ def __init__(
     ):
         super().__init__(name, **kwargs)
 
-
         self.tau_x = tau_x
         self.sigma_pre = sigma_pre ## a pre-rectification scaling factor
         self.sigma_post = sigma_post ## a post-rectification scaling factor
@@ -110,7 +109,6 @@ def advance_state(self, t, dt):
         key, skey = random.split(self.key.get(), 2)
         eps_post = random.normal(skey, shape=self.x.get().shape)  ## post-rectifier distributional noise
 
-        #x = _run_cell(dt, self.j_input.get(), self.j_recurrent.get(), self.x.get(), eps, self.tau_x, self.sigma_rec, integType=self.intgFlag)
         _step_fns = {
             0: step_euler,
             1: step_rk2,
@@ -152,13 +150,16 @@ def help(cls): ## component help function
             "states":
                 {"x": "Update to continuous noisy, leaky dynamics; value at time t"},
             "outputs":
-                {"r": "A linear rectifier applied to rate-coded dynamics; f(z)"},
+                {"r": "A linear rectifier applied to rate-coded dynamics; f(z)",
+                 "r_prime": "Temporal derivative applied to rate-coded dynamics; f'(z)"},
         }
         hyperparams = {
             "n_units": "Number of neuronal cells to model in this layer",
             "batch_size": "Batch size dimension of this component",
             "tau_x": "State time constant",
-            "sigma_pre": "The non-zero degree/scale of (pre-rectification) noise to inject into this neuron"
+            "act_fx": "Type of rectification function to use",
+            "sigma_pre": "The non-zero degree/scale of pre-rectification noise to inject into this neuron",
+            "sigma_post": "The non-zero degree/scale of post-rectification noise to inject into this neuron"
         }
         info = {cls.__name__: properties,
                 "compartments": compartment_props,