Doc for brainpylib>=0.3.0 (#645)

* update docs * update changelogs * add `noise` option to neurons in `brainpy.dyn`
brainpy · Mar 3, 2024 · 5e54107 · 5e54107
1 parent a8377cb
commit 5e54107
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Showing 14 changed files with 2,939 additions and 1,210 deletions.
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
diff --git a/brainpy-changelog.md b/brainpy-changelog.md
diff --git a/brainpy/_src/dyn/neurons/hh.py b/brainpy/_src/dyn/neurons/hh.py
@@ -315,6 +315,9 @@ def __init__(
       m_initializer: Optional[Union[Callable, ArrayType]] = None,
       h_initializer: Optional[Union[Callable, ArrayType]] = None,
       n_initializer: Optional[Union[Callable, ArrayType]] = None,
+
+      # noise
+      noise: Union[float, ArrayType, Callable] = None,
   ):
     # initialization
     super().__init__(size=size,
@@ -340,8 +343,14 @@ def __init__(
     self._n_initializer = is_initializer(n_initializer, allow_none=True)
     self._V_initializer = is_initializer(V_initializer)
 
+    # noise
+    self.noise = init_noise(noise, self.varshape, num_vars=4)
+
     # integral
-    self.integral = odeint(method=method, f=self.derivative)
+    if self.noise is None:
+      self.integral = odeint(method=method, f=self.derivative)
+    else:
+      self.integral = sdeint(method=self.method, f=self.derivative, g=self.noise)
 
     # model
     if init_var:
@@ -622,6 +631,9 @@ def __init__(
       V_th: Union[float, ArrayType, Callable] = 10.,
       W_initializer: Union[Callable, ArrayType] = OneInit(0.02),
       V_initializer: Union[Callable, ArrayType] = Uniform(-70., -60.),
+
+      # noise
+      noise: Union[float, ArrayType, Callable] = None,
   ):
     # initialization
     super().__init__(size=size,
@@ -650,8 +662,13 @@ def __init__(
     self._W_initializer = is_initializer(W_initializer)
     self._V_initializer = is_initializer(V_initializer)
 
+    # noise
+    self.noise = init_noise(noise, self.varshape, num_vars=2)
     # integral
-    self.integral = odeint(method=method, f=self.derivative)
+    if self.noise is not None:
+      self.integral = sdeint(method=self.method, f=self.derivative, g=self.noise)
+    else:
+      self.integral = odeint(method=method, f=self.derivative)
 
     # model
     if init_var:
@@ -895,6 +912,9 @@ def __init__(
       V_initializer: Union[Callable, ArrayType] = OneInit(-65.),
       h_initializer: Union[Callable, ArrayType] = OneInit(0.6),
       n_initializer: Union[Callable, ArrayType] = OneInit(0.32),
+
+      # noise
+      noise: Union[float, ArrayType, Callable] = None,
   ):
     # initialization
     super().__init__(size=size,
@@ -920,8 +940,13 @@ def __init__(
     self._n_initializer = is_initializer(n_initializer)
     self._V_initializer = is_initializer(V_initializer)
 
+    # noise
+    self.noise = init_noise(noise, self.varshape, num_vars=3)
     # integral
-    self.integral = odeint(method=method, f=self.derivative)
+    if self.noise is not None:
+      self.integral = sdeint(method=self.method, f=self.derivative, g=self.noise)
+    else:
+      self.integral = odeint(method=method, f=self.derivative)
 
     # model
     if init_var: