update docs (#260)

updates

Author: chaoming0625

brainpy/connect/random_conn.py

@@ -68,7 +68,7 @@ def build_conn(self):
       if posts is not None:
         ind.append(posts)
         count[i] = len(posts)
-    ind = np.concatenate(ind)
+    ind = np.concatenate(ind) if len(ind) > 0 else np.asarray([], dtype=IDX_DTYPE)
     indptr = np.concatenate(([0], count)).cumsum()
 
     return 'csr', (ind, indptr)
@@ -143,7 +143,7 @@ def build_conn(self):
     for i in range(self.post_num):
       pres = self._connect(num_need=num, num_total=self.pre_num, i=i)
       pre_ids.append(pres)
-    pre_ids = np.concatenate(pre_ids)
+    pre_ids = np.concatenate(pre_ids) if len(pre_ids) > 0 else np.asarray([], dtype=IDX_DTYPE)
     post_ids = np.repeat(np.arange(self.post_num), num)
 
     return 'ij', (pre_ids, post_ids)

brainpy/dyn/base.py

@@ -269,9 +269,13 @@ def update_local_delays(self, nodes: Union[Sequence, Dict] = None):
     """
     # update delays
     if nodes is None:
-      nodes = self.nodes(level=1, include_self=False).subset(DynamicalSystem).unique().values()
+      nodes = tuple(self.nodes(level=1, include_self=False).subset(DynamicalSystem).unique().values())
+    elif isinstance(nodes, DynamicalSystem):
+      nodes = (nodes, )
     elif isinstance(nodes, dict):
-      nodes = nodes.values()
+      nodes = tuple(nodes.values())
+    if not isinstance(nodes, (tuple, list)):
+      raise ValueError('Please provide nodes as a list/tuple/dict of DynamicalSystem.')
     for node in nodes:
       for name in node.local_delay_vars:
         delay = self.global_delay_data[name][0]
@@ -554,7 +558,8 @@ def update(self, *args, **kwargs):
     nodes = nodes.unique()
     neuron_groups = nodes.subset(NeuGroup)
     synapse_groups = nodes.subset(SynConn)
-    other_nodes = nodes - neuron_groups - synapse_groups
+    ds_views = nodes.subset(DSView)
+    other_nodes = nodes - neuron_groups - synapse_groups - ds_views
 
     # shared arguments
     shared = args[0]
@@ -636,11 +641,11 @@ def __init__(
       if len(size) <= 0:
         raise ModelBuildError(f'size must be int, or a tuple/list of int. '
                               f'But we got {type(size)}')
-      if not isinstance(size[0], int):
+      if not isinstance(size[0], (int, np.integer)):
         raise ModelBuildError('size must be int, or a tuple/list of int.'
                               f'But we got {type(size)}')
       size = tuple(size)
-    elif isinstance(size, int):
+    elif isinstance(size, (int, np.integer)):
       size = (size,)
     else:
       raise ModelBuildError('size must be int, or a tuple/list of int.'
@@ -1318,7 +1323,7 @@ def __setattr__(self, key, value):
     super(DSView, self).__setattr__(key, value)
 
   def update(self, *args, **kwargs):
-    pass
+    raise NoImplementationError(f'DSView {self} cannot be updated. Please update its parent {self.target}')
 
   def reset_state(self, batch_size=None):
     pass

brainpy/math/delayvars.py

@@ -299,6 +299,9 @@ def __init__(
     # initialization
     self.reset(delay_target, delay_len, initial_delay_data, batch_axis)
 
+  def __repr__(self):
+    return f'{self.__class__.__name__}(num_delay_step={self.num_delay_step}, delay_target_shape={self.data.shape[1:]})'
+
   def reset(
       self,
       delay_target,

brainpy/tools/others/others.py

@@ -39,7 +39,7 @@ def feedback(self):
 
 
 def size2num(size):
-  if isinstance(size, int):
+  if isinstance(size, (int, np.integer)):
     return size
   elif isinstance(size, (tuple, list)):
     a = 1
@@ -53,7 +53,7 @@ def size2num(size):
 def to_size(x) -> Optional[Tuple[int]]:
   if isinstance(x, (tuple, list)):
     return tuple(x)
-  if isinstance(x, int):
+  if isinstance(x, (int, np.integer)):
     return (x, )
   if x is None:
     return x

changelog.rst

@@ -10,6 +10,111 @@ tackling the shortcomings of brainpy 2.1.x generation,
 effectively bringing it to research needs and standards.
 
 
+
+
+Version 2.2.1 (2022.09.09)
+==========================
+
+This release fixes bugs found in the codebase and improves the usability and functions of BrainPy.
+
+Bug fixes
+~~~~~~~~~~~~~~
+
+
+#. Fix the bug of operator customization in ``brainpy.math.XLACustomOp`` and ``brainpy.math.register_op``. Now, it supports operator customization by using NumPy and Numba interface. For instance,
+
+.. code-block:: python
+
+   import brainpy.math as bm
+
+   def abs_eval(events, indices, indptr, post_val, values):
+         return post_val
+
+   def con_compute(outs, ins):
+         post_val = outs
+         events, indices, indptr, _, values = ins
+         for i in range(events.size):
+           if events[i]:
+             for j in range(indptr[i], indptr[i + 1]):
+               index = indices[j]
+               old_value = post_val[index]
+               post_val[index] = values + old_value
+
+   event_sum = bm.XLACustomOp(eval_shape=abs_eval, con_compute=con_compute)
+
+
+#. Fix the bug of ``brainpy.tools.DotDict``. Now, it is compatible with the transformations of JAX. For instance,
+
+.. code-block:: python
+
+   import brainpy as bp
+   from jax import vmap
+
+   @vmap
+   def multiple_run(I):
+     hh = bp.neurons.HH(1)
+     runner = bp.dyn.DSRunner(hh, inputs=('input', I), numpy_mon_after_run=False)
+     runner.run(100.)
+     return runner.mon
+
+   mon = multiple_run(bp.math.arange(2, 10, 2))
+
+New features
+~~~~~~~~~~~~~~
+
+
+#. Add numpy operators ``brainpy.math.mat``\ , ``brainpy.math.matrix``\ , ``brainpy.math.asmatrix``.
+#. Improve translation rules of brainpylib operators, improve its running speeds.
+#. Support ``DSView`` of ``DynamicalSystem`` instance. Now, it supports defining models with a slice view of a DS instance. For example,
+
+.. code-block:: python
+
+   import brainpy as bp
+   import brainpy.math as bm
+
+
+   class EINet_V2(bp.dyn.Network):
+     def __init__(self, scale=1.0, method='exp_auto'):
+       super(EINet_V2, self).__init__()
+
+       # network size
+       num_exc = int(3200 * scale)
+       num_inh = int(800 * scale)
+
+       # neurons
+       self.N = bp.neurons.LIF(num_exc + num_inh,
+                               V_rest=-60., V_th=-50., V_reset=-60., tau=20., tau_ref=5.,
+                               method=method, V_initializer=bp.initialize.Normal(-55., 2.))
+
+       # synapses
+       we = 0.6 / scale  # excitatory synaptic weight (voltage)
+       wi = 6.7 / scale  # inhibitory synaptic weight
+       self.Esyn = bp.synapses.Exponential(pre=self.N[:num_exc], post=self.N,
+                                           conn=bp.connect.FixedProb(0.02),
+                                           g_max=we, tau=5.,
+                                           output=bp.synouts.COBA(E=0.),
+                                           method=method)
+       self.Isyn = bp.synapses.Exponential(pre=self.N[num_exc:], post=self.N,
+                                           conn=bp.connect.FixedProb(0.02),
+                                           g_max=wi, tau=10.,
+                                           output=bp.synouts.COBA(E=-80.),
+                                           method=method)
+
+   net = EINet_V2(scale=1., method='exp_auto')
+   # simulation
+   runner = bp.dyn.DSRunner(
+       net,
+       monitors={'spikes': net.N.spike},
+       inputs=[(net.N.input, 20.)]
+     )
+   runner.run(100.)
+
+   # visualization
+   bp.visualize.raster_plot(runner.mon.ts, runner.mon['spikes'], show=True)
+
+
+
+
 Version 2.2.0 (2022.08.12)
 ==========================
 

docs/index.rst

@@ -72,6 +72,7 @@ The code of BrainPy is open-sourced at GitHub:
    tutorial_toolbox/synaptic_weights
    tutorial_toolbox/optimizers
    tutorial_toolbox/saving_and_loading
+   tutorial_toolbox/inputs
 
 
 .. toctree::