update docs and examples

Author: chaoming0625

brainpy/dyn/base.py

@@ -54,13 +54,13 @@ class DynamicalSystem(Base):
 
   """Global delay variables. Useful when the same target
      variable is used in multiple mappings."""
-  global_delay_vars: Dict[str, bm.LengthDelay] = dict()
+  global_delay_vars: Dict[str, bm.LengthDelay] = Collector()
 
   def __init__(self, name=None):
     super(DynamicalSystem, self).__init__(name=name)
 
     # local delay variables
-    self.local_delay_vars: Dict[str, bm.LengthDelay] = dict()
+    self.local_delay_vars: Dict[str, bm.LengthDelay] = Collector()
 
   def __repr__(self):
     return f'{self.__class__.__name__}(name={self.name})'
@@ -334,15 +334,17 @@ def reset(self):
 
   @classmethod
   def has(cls, **children_cls):
-    """
+    """The aggressive operation to gather master and children classes.
 
     Parameters
     ----------
     children_cls
+      The children classes.
 
     Returns
     -------
-
+    wrapper: ContainerWrapper
+      A wrapper which has master and its children classes.
     """
     return ContainerWrapper(master=cls, **children_cls)
 

docs/apis/dyn.rst

@@ -13,4 +13,5 @@
     auto/dyn/neurons
     auto/dyn/synapses
     auto/dyn/rates
+    auto/dyn/others
     auto/dyn/runners

docs/auto_generater.py

@@ -255,7 +255,6 @@ def generate_dyn_docs(path='apis/auto/dyn/'):
   module_and_name = [
     ('biological_models', 'Biological Models'),
     ('fractional_models', 'Fractional-order Models'),
-    ('input_models', 'Input Models'),
     ('reduced_models', 'Reduced Models'),
   ]
   write_submodules(module_name='brainpy.dyn.neurons',
@@ -278,14 +277,23 @@ def generate_dyn_docs(path='apis/auto/dyn/'):
   module_and_name = [
     ('populations', 'Population Models'),
     ('couplings', 'Coupling Models'),
-    ('noises', 'Noise Models'),
   ]
   write_submodules(module_name='brainpy.dyn.rates',
                    filename=os.path.join(path, 'rates.rst'),
                    header='Rate Models',
                    submodule_names=[a[0] for a in module_and_name],
                    section_names=[a[1] for a in module_and_name])
 
+  module_and_name = [
+    ('noises', 'Noise Models'),
+    ('inputs', 'Input Models'),
+  ]
+  write_submodules(module_name='brainpy.dyn.others',
+                   filename=os.path.join(path, 'others.rst'),
+                   header='Helper Models',
+                   submodule_names=[a[0] for a in module_and_name],
+                   section_names=[a[1] for a in module_and_name])
+
   write_module(module_name='brainpy.dyn.runners',
                filename=os.path.join(path, 'runners.rst'),
                header='Runners')

docs/index.rst

@@ -59,8 +59,8 @@ The code of BrainPy is open-sourced at GitHub:
 
    tutorial_toolbox/ode_numerical_solvers
    tutorial_toolbox/sde_numerical_solvers
-   tutorial_toolbox/dde_numerical_solvers
    tutorial_toolbox/fde_numerical_solvers
+   tutorial_toolbox/dde_numerical_solvers
    tutorial_toolbox/joint_equations
    tutorial_toolbox/synaptic_connections
    tutorial_toolbox/synaptic_weights

docs/tutorial_toolbox/fde_numerical_solvers.ipynb

@@ -46,7 +46,7 @@
    "source": [
     "Factional differential equations have several definitions. It can be defined in a variety of different ways that do often do not all lead to the same result even for smooth functions. In neuroscience, we usually use the following two definitions:\n",
     "\n",
-    "- Riemann–Liouville fractional derivative\n",
+    "- Grünwald-Letnikov derivative\n",
     "- Caputo fractional derivative\n",
     "\n",
     "See [Fractional calculus - Wikipedia](https://en.wikipedia.org/wiki/Fractional_calculus) for more details."
@@ -421,7 +421,7 @@
   {
    "cell_type": "markdown",
    "source": [
-    "## Methods for Riemann–Liouville FDEs"
+    "## Methods for Grünwald-Letnikov FDEs"
    ],
    "metadata": {
     "collapsed": false,

docs/tutorial_toolbox/initializing_connection_weights.ipynb

@@ -3,6 +3,7 @@
 import brainpy as bp
 import brainpy.math as bm
 
+bp.check.turn_off()
 bm.set_platform('cpu')
 import matplotlib.pyplot as plt