patched docs to reflect revisions/refactor

Alexander Ororbia · Alexander Ororbia · commit d536e3337b8a · 2025-04-02T19:17:13.000-04:00
diff --git a/docs/conf.py b/docs/conf.py
@@ -117,7 +117,7 @@
 html_logo = "images/ngc-learn-logo.png"
 html_theme_options = {
     'logo_only': True,
-    'display_version': True,
+    #'display_version': True,
 }
 
 # def setup(app):
diff --git a/docs/museum/index.rst b/docs/museum/index.rst
@@ -17,3 +17,4 @@ relevant, referenced publicly available ngc-learn simulation code.
   sparse_coding
   snn_dc
   snn_bfa
+  sindy
diff --git a/docs/museum/sindy.md b/docs/museum/sindy.md
@@ -436,7 +436,7 @@ $\mathbf{ẏ} = -2.0\mathbf{x} - 0.1\mathbf{y}$
 ẋ =  2.000  𝑦 -0.100  𝑥 
 ẏ = -0.100  𝑦 -2.000  𝑥
 
-$[𝑦, 𝑦^2, 𝑥, 𝑥𝑦, 𝑥^2]$
+[𝑦, 𝑦^2, 𝑥, 𝑥𝑦, 𝑥^2]
 [[ 1.999  0. -0.100  0.  0.]
  [-0.099  0. -1.999  0.  0.]]
 ```
diff --git a/docs/source/ngclearn.components.input_encoders.rst b/docs/source/ngclearn.components.input_encoders.rst
@@ -20,6 +20,14 @@ ngclearn.components.input\_encoders.latencyCell module
    :undoc-members:
    :show-inheritance:
 
+ngclearn.components.input\_encoders.phasorCell module
+-----------------------------------------------------
+
+.. automodule:: ngclearn.components.input_encoders.phasorCell
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 ngclearn.components.input\_encoders.poissonCell module
 ------------------------------------------------------
 
diff --git a/docs/source/ngclearn.components.neurons.graded.rst b/docs/source/ngclearn.components.neurons.graded.rst
@@ -4,6 +4,14 @@ ngclearn.components.neurons.graded package
 Submodules
 ----------
 
+ngclearn.components.neurons.graded.bernoulliErrorCell module
+------------------------------------------------------------
+
+.. automodule:: ngclearn.components.neurons.graded.bernoulliErrorCell
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 ngclearn.components.neurons.graded.gaussianErrorCell module
 -----------------------------------------------------------
 
diff --git a/docs/source/ngclearn.components.neurons.spiking.rst b/docs/source/ngclearn.components.neurons.spiking.rst
@@ -4,6 +4,14 @@ ngclearn.components.neurons.spiking package
 Submodules
 ----------
 
+ngclearn.components.neurons.spiking.IFCell module
+-------------------------------------------------
+
+.. automodule:: ngclearn.components.neurons.spiking.IFCell
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 ngclearn.components.neurons.spiking.LIFCell module
 --------------------------------------------------
 
@@ -12,6 +20,14 @@ ngclearn.components.neurons.spiking.LIFCell module
    :undoc-members:
    :show-inheritance:
 
+ngclearn.components.neurons.spiking.RAFCell module
+--------------------------------------------------
+
+.. automodule:: ngclearn.components.neurons.spiking.RAFCell
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 ngclearn.components.neurons.spiking.WTASCell module
 ---------------------------------------------------
 
@@ -36,6 +52,14 @@ ngclearn.components.neurons.spiking.fitzhughNagumoCell module
    :undoc-members:
    :show-inheritance:
 
+ngclearn.components.neurons.spiking.hodgkinHuxleyCell module
+------------------------------------------------------------
+
+.. automodule:: ngclearn.components.neurons.spiking.hodgkinHuxleyCell
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 ngclearn.components.neurons.spiking.izhikevichCell module
 ---------------------------------------------------------
 
diff --git a/docs/source/ngclearn.components.synapses.hebbian.rst b/docs/source/ngclearn.components.synapses.hebbian.rst
@@ -12,14 +12,6 @@ ngclearn.components.synapses.hebbian.BCMSynapse module
    :undoc-members:
    :show-inheritance:
 
-ngclearn.components.synapses.hebbian.STDPSynapse module
--------------------------------------------------------
-
-.. automodule:: ngclearn.components.synapses.hebbian.STDPSynapse
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 ngclearn.components.synapses.hebbian.eventSTDPSynapse module
 ------------------------------------------------------------
 
diff --git a/docs/source/ngclearn.components.synapses.modulated.rst b/docs/source/ngclearn.components.synapses.modulated.rst
@@ -4,22 +4,6 @@ ngclearn.components.synapses.modulated package
 Submodules
 ----------
 
-ngclearn.components.synapses.modulated.MSTDPETConvSynapse module
-----------------------------------------------------------------
-
-.. automodule:: ngclearn.components.synapses.modulated.MSTDPETConvSynapse
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-ngclearn.components.synapses.modulated.MSTDPETDeconvSynapse module
-------------------------------------------------------------------
-
-.. automodule:: ngclearn.components.synapses.modulated.MSTDPETDeconvSynapse
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 ngclearn.components.synapses.modulated.MSTDPETSynapse module
 ------------------------------------------------------------
 
@@ -28,14 +12,6 @@ ngclearn.components.synapses.modulated.MSTDPETSynapse module
    :undoc-members:
    :show-inheritance:
 
-ngclearn.components.synapses.modulated.eligibilityTrace module
---------------------------------------------------------------
-
-.. automodule:: ngclearn.components.synapses.modulated.eligibilityTrace
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
 Module contents
 ---------------
 
diff --git a/docs/source/ngclearn.components.synapses.patched.rst b/docs/source/ngclearn.components.synapses.patched.rst
@@ -0,0 +1,37 @@
+ngclearn.components.synapses.patched package
+============================================
+
+Submodules
+----------
+
+ngclearn.components.synapses.patched.hebbianPatchedSynapse module
+-----------------------------------------------------------------
+
+.. automodule:: ngclearn.components.synapses.patched.hebbianPatchedSynapse
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ngclearn.components.synapses.patched.patchedSynapse module
+----------------------------------------------------------
+
+.. automodule:: ngclearn.components.synapses.patched.patchedSynapse
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ngclearn.components.synapses.patched.staticPatchedSynapse module
+----------------------------------------------------------------
+
+.. automodule:: ngclearn.components.synapses.patched.staticPatchedSynapse
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: ngclearn.components.synapses.patched
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/ngclearn.components.synapses.rst b/docs/source/ngclearn.components.synapses.rst
@@ -10,6 +10,7 @@ Subpackages
    ngclearn.components.synapses.convolution
    ngclearn.components.synapses.hebbian
    ngclearn.components.synapses.modulated
+   ngclearn.components.synapses.patched
 
 Submodules
 ----------
diff --git a/docs/source/ngclearn.modules.regression.rst b/docs/source/ngclearn.modules.regression.rst
@@ -0,0 +1,37 @@
+ngclearn.modules.regression package
+===================================
+
+Submodules
+----------
+
+ngclearn.modules.regression.elastic\_net module
+-----------------------------------------------
+
+.. automodule:: ngclearn.modules.regression.elastic_net
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ngclearn.modules.regression.lasso module
+----------------------------------------
+
+.. automodule:: ngclearn.modules.regression.lasso
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ngclearn.modules.regression.ridge module
+----------------------------------------
+
+.. automodule:: ngclearn.modules.regression.ridge
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: ngclearn.modules.regression
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/ngclearn.modules.rst b/docs/source/ngclearn.modules.rst
@@ -0,0 +1,18 @@
+ngclearn.modules package
+========================
+
+Subpackages
+-----------
+
+.. toctree::
+   :maxdepth: 4
+
+   ngclearn.modules.regression
+
+Module contents
+---------------
+
+.. automodule:: ngclearn.modules
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/ngclearn.rst b/docs/source/ngclearn.rst
@@ -9,6 +9,7 @@ Subpackages
 
    ngclearn.commands
    ngclearn.components
+   ngclearn.modules
    ngclearn.operations
    ngclearn.utils
 
diff --git a/docs/source/ngclearn.utils.analysis.rst b/docs/source/ngclearn.utils.analysis.rst
@@ -0,0 +1,37 @@
+ngclearn.utils.analysis package
+===============================
+
+Submodules
+----------
+
+ngclearn.utils.analysis.attentive\_probe module
+-----------------------------------------------
+
+.. automodule:: ngclearn.utils.analysis.attentive_probe
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ngclearn.utils.analysis.linear\_probe module
+--------------------------------------------
+
+.. automodule:: ngclearn.utils.analysis.linear_probe
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ngclearn.utils.analysis.probe module
+------------------------------------
+
+.. automodule:: ngclearn.utils.analysis.probe
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: ngclearn.utils.analysis
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/ngclearn.utils.diffeq.rst b/docs/source/ngclearn.utils.diffeq.rst
@@ -12,6 +12,14 @@ ngclearn.utils.diffeq.ode\_utils module
    :undoc-members:
    :show-inheritance:
 
+ngclearn.utils.diffeq.odes module
+---------------------------------
+
+.. automodule:: ngclearn.utils.diffeq.odes
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 Module contents
 ---------------
 
diff --git a/docs/source/ngclearn.utils.rst b/docs/source/ngclearn.utils.rst
@@ -7,6 +7,7 @@ Subpackages
 .. toctree::
    :maxdepth: 4
 
+   ngclearn.utils.analysis
    ngclearn.utils.density
    ngclearn.utils.diffeq
    ngclearn.utils.optim
diff --git a/ngclearn/utils/diffeq/odes.py b/ngclearn/utils/diffeq/odes.py

Original file line number	Diff line number	Diff line change
`@@ -117,7 +117,7 @@`
`117`	`117`	`html_logo = "images/ngc-learn-logo.png"`
`118`	`118`	`html_theme_options = {`
`119`	`119`	`'logo_only': True,`
`120`		`- 'display_version': True,`
	`120`	`+ #'display_version': True,`
`121`	`121`	`}`
`122`	`122`
`123`	`123`	`# def setup(app):`
-Original file line number
+Diff line change
   sparse_coding
   snn_dc
   snn_bfa
 +  sindy