Merge pull request #356 from chaoming0625/master

fix `Array` transform bug

Author: chaoming0625

brainpy/_src/math/ndarray.py

@@ -1655,12 +1655,11 @@ def update(self, value):
 
 def _jaxarray_unflatten(aux_data, flat_contents):
   r = Array(*flat_contents)
-  r._transform_context = aux_data[0]
   return r
 
 
 register_pytree_node(Array,
-                     lambda t: ((t.value,), (t._transform_context,)),
+                     lambda t: ((t.value,), None),
                      _jaxarray_unflatten)
 
 register_pytree_node(Variable,

brainpy/_src/tools/package.py

@@ -23,6 +23,8 @@
   'SUPPORT_NUMBA',
 ]
 
+_minimal_brainpylib_version = '0.1.7'
+
 
 def import_numba():
   if numba is None:
@@ -35,6 +37,8 @@ def import_brainpylib():
   if brainpylib is None:
     raise ModuleNotFoundError('brainpylib is needed. Please install brainpylib through:\n'
                               '> pip install brainpylib\n\n')
+  if brainpylib.__version__ < _minimal_brainpylib_version:
+    raise SystemError(f'This version of brainpy needs brainpylib >= {_minimal_brainpylib_version}.')
   return brainpylib
 
 

changes.md

@@ -1,155 +1,19 @@
 # Change from Version 2.3.4 to Version 2.3.5
 
 
-This release (under the branch of ``brainpy=2.3.x``) continues to add supports for brain-inspired computation.
+This release continues to add supports for improving the usability of BrainPy.
 
 
 ## New Features
 
 
-### 1. ``brainpy.share`` for sharing data across submodules
+1. New data structures for object-oriented transformations. 
+   - ``NodeList`` and ``NodeDict`` for a list/tuple/dict of ``BrainPyObject`` instances.
+   - ``ListVar`` and ``DictVar`` for a list/tuple/dict of brainpy data.
+2. `Clip` transformation for brainpy initializers.
+3. All ``brainpylib`` operators are accessible in ``brainpy.math`` module.
+4. Enable monitoring GPU models on CPU when setting ``DSRunner(..., memory_efficient=True)``. This setting can usually reduce so much memory usage.   
+5. ``brainpylib`` wheels on the linux platform support the GPU operators. Users can install gpu version of ``brainpylib`` (require ``brainpylib>=0.1.7``) directly by ``pip install brainpylib``.
 
-In this release, we abstract the shared data as a ``brainpy.share`` object. 
 
-This object together with ``brainpy.Delay`` we will introduce below 
-constitute the support that enable to define SNN models like ANN ones.
-
-
-### 2. ``brainpy.Delay`` for delay processing
-
-``Delay`` is abstracted as a dynamical system, which can be updated / retrieved by users. 
-
-```python
-import brainpy as bp
-
-class EINet(bp.DynamicalSystemNS):
-  def __init__(self, scale=1.0, e_input=20., i_input=20., delay=None):
-    super().__init__()
-
-    self.bg_exc = e_input
-    self.bg_inh = i_input
-
-    # network size
-    num_exc = int(3200 * scale)
-    num_inh = int(800 * scale)
-
-    # neurons
-    pars = dict(V_rest=-60., V_th=-50., V_reset=-60., tau=20., tau_ref=5.,
-                V_initializer=bp.init.Normal(-55., 2.), input_var=False)
-    self.E = bp.neurons.LIF(num_exc, **pars)
-    self.I = bp.neurons.LIF(num_inh, **pars)
-
-    # synapses
-    we = 0.6 / scale  # excitatory synaptic weight (voltage)
-    wi = 6.7 / scale  # inhibitory synaptic weight
-    self.E2E = bp.experimental.Exponential(
-      bp.conn.FixedProb(0.02, pre=self.E.size, post=self.E.size),
-      g_max=we, tau=5., out=bp.experimental.COBA(E=0.)
-    )
-    self.E2I = bp.experimental.Exponential(
-      bp.conn.FixedProb(0.02, pre=self.E.size, post=self.I.size, ),
-      g_max=we, tau=5., out=bp.experimental.COBA(E=0.)
-    )
-    self.I2E = bp.experimental.Exponential(
-      bp.conn.FixedProb(0.02, pre=self.I.size, post=self.E.size),
-      g_max=wi, tau=10., out=bp.experimental.COBA(E=-80.)
-    )
-    self.I2I = bp.experimental.Exponential(
-      bp.conn.FixedProb(0.02, pre=self.I.size, post=self.I.size),
-      g_max=wi, tau=10., out=bp.experimental.COBA(E=-80.)
-    )
-    self.delayE = bp.Delay(self.E.spike, entries={'E': delay})
-    self.delayI = bp.Delay(self.I.spike, entries={'I': delay})
-
-  def update(self):
-    e_spike = self.delayE.at('E')
-    i_spike = self.delayI.at('I')
-    e_inp = self.E2E(e_spike, self.E.V) + self.I2E(i_spike, self.E.V) + self.bg_exc
-    i_inp = self.I2I(i_spike, self.I.V) + self.E2I(e_spike, self.I.V) + self.bg_inh
-    self.delayE(self.E(e_inp))
-    self.delayI(self.I(i_inp))
-
-```
-
-
-
-### 3.  ``brainpy.checkpoints.save_pytree`` and ``brainpy.checkpoints.load_pytree`` for saving/loading target from the filename
-
-Now we can directly use ``brainpy.checkpoints.save_pytree`` to save a 
-network state into the filepath we specified. 
-
-Similarly, we can use ``brainpy.checkpoints.load_pytree`` to load 
-states from the given file path.
-
-
-### 4. More ANN layers
-
-
-- brainpy.layers.ConvTranspose1d
-- brainpy.layers.ConvTranspose2d
-- brainpy.layers.ConvTranspose3d
-- brainpy.layers.Conv1dLSTMCell
-- brainpy.layers.Conv2dLSTMCell
-- brainpy.layers.Conv3dLSTMCell
-
-
-### 5. More compatible dense operators
-
-PyTorch operators:
-
-- brainpy.math.Tensor
-- brainpy.math.flatten
-- brainpy.math.cat
-- brainpy.math.abs
-- brainpy.math.absolute
-- brainpy.math.acos
-- brainpy.math.arccos
-- brainpy.math.acosh
-- brainpy.math.arccosh
-- brainpy.math.add
-- brainpy.math.addcdiv
-- brainpy.math.addcmul
-- brainpy.math.angle
-- brainpy.math.asin
-- brainpy.math.arcsin
-- brainpy.math.asinh
-- brainpy.math.arcsin
-- brainpy.math.atan
-- brainpy.math.arctan
-- brainpy.math.atan2
-- brainpy.math.atanh
-
-
-TensorFlow operators:
-
-- brainpy.math.concat
-- brainpy.math.reduce_sum
-- brainpy.math.reduce_max
-- brainpy.math.reduce_min
-- brainpy.math.reduce_mean
-- brainpy.math.reduce_all
-- brainpy.math.reduce_any
-- brainpy.math.reduce_logsumexp
-- brainpy.math.reduce_prod
-- brainpy.math.reduce_std
-- brainpy.math.reduce_variance
-- brainpy.math.reduce_euclidean_norm
-- brainpy.math.unsorted_segment_sqrt_n
-- brainpy.math.segment_mean
-- brainpy.math.unsorted_segment_sum
-- brainpy.math.unsorted_segment_prod
-- brainpy.math.unsorted_segment_max
-- brainpy.math.unsorted_segment_min
-- brainpy.math.unsorted_segment_mean
-- brainpy.math.segment_sum
-- brainpy.math.segment_prod
-- brainpy.math.segment_max
-- brainpy.math.segment_min
-- brainpy.math.clip_by_value
-- brainpy.math.cast
-
-
-### Others
-
-- Remove the hard requirements of ``brainpylib`` and ``numba``.