Update core concepts documentation and LIF neuron dynamics (#800)

* Refactor neural network classes and update progress bar parameters for simulations

* Refactor documentation and update synapse initialization for clarity and consistency

Author: chaoming0625

brainpy/state/_lif.py

@@ -248,6 +248,7 @@ def __init__(
         V_reset: ArrayLike = 0. * u.mV,
         V_rest: ArrayLike = 0. * u.mV,
         V_initializer: Callable = braintools.init.Constant(0. * u.mV),
+        noise: ArrayLike = None,
         spk_fun: Callable = braintools.surrogate.ReluGrad(),
         spk_reset: str = 'soft',
         name: str = None,
@@ -279,8 +280,8 @@ def update(self, x=0. * u.mA):
         V_th = self.V_th if self.spk_reset == 'soft' else jax.lax.stop_gradient(last_v)
         V = last_v - (V_th - self.V_reset) * last_spk
         # membrane potential
-        dv = lambda v: (-v + self.V_rest + self.R * self.sum_current_inputs(x, v)) / self.tau
-        V = brainstate.nn.exp_euler_step(dv, V)
+        dv = lambda v, t: (-v + self.V_rest + self.R * self.sum_current_inputs(x, v)) / self.tau
+        V = braintools.quad.ode_expeuler_step(dv, V, None)
         V = self.sum_delta_inputs(V)
         self.V.value = V
         return self.get_spike(V)

docs/conf.py

@@ -28,6 +28,7 @@
             print(f"Error deleting {item}: {e}")
 
 build_version = os.environ.get('CURRENT_VERSION', 'v2')
+build_version = os.environ.get('CURRENT_VERSION', 'v3')
 if build_version == 'v2':
     shutil.copytree(
         os.path.join(os.path.dirname(__file__), '../docs_classic'),

docs_state/README.md

@@ -1,7 +1,7 @@
 API Reference
 =============
 
-Complete API reference for ``brainpy.state``
+Complete API reference for ``brainpy.state``.
 
 .. note::
    ``brainpy.state`` is built on top of `brainstate <https://brainstate.readthedocs.io/>`_,
@@ -49,10 +49,8 @@ The API is organized into the following categories:
 
       Spike and current generators (PoissonSpike, SpikeTime)
 
-Quick Reference
----------------
-
-**Most commonly used classes:**
+Example Reference
+-----------------
 
 Neurons
 ~~~~~~~
@@ -184,6 +182,7 @@ Readout Layers
    brainpy.state.LeakySpikeReadout(in_size=100, tau=5*u.ms, V_th=1*u.mV)
 
 .. toctree::
+   :hidden:
    :maxdepth: 2
 
    neurons
@@ -192,4 +191,4 @@ Readout Layers
    synouts
    stp
    readouts
-   inputs
+   inputs

docs_state/api/index.rst

@@ -142,9 +142,6 @@ Series of models exploring different gamma generation mechanisms:
       - Excitatory-inhibitory interaction
 
 
-**Combined**: `Susin_Destexhe_2021_gamma_oscillation.py <https://github.com/brainpy/BrainPy/tree/master/examples_state/Susin_Destexhe_2021_gamma_oscillation.py>`_ - All mechanisms
-
-**Key Concepts**: Gamma mechanisms, network states, oscillation generation
 
 Spiking Neural Network Training
 --------------------------------

docs_state/apis.rst

@@ -112,7 +112,7 @@ Learn more
 
       .. card:: :material-regular:`data_exploration;2em` ``brainpy`` APIs
          :class-card: sd-text-black sd-bg-light
-         :link: https://brainpy.readthedocs.io/
+         :link: https://brainpy.readthedocs.io
 
 
 ----
@@ -131,7 +131,6 @@ See also the ecosystem
    :caption: Tutorials
 
    quickstart/index.rst
-   tutorials/index.rst
    examples/gallery.rst