Merge branch 'master' into master

brainpy · Sep 11, 2023 · 36f4585 · 36f4585
2 parents c6548b2 + 7b1faf2
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diff --git a/.gitignore b/.gitignore
@@ -225,3 +225,4 @@ cython_debug/
 /docs/tutorial_advanced/data/
 /my_tests/
 /examples/dynamics_simulation/Joglekar_2018_data/
+/docs/apis/deprecated/generated/
diff --git a/ACKNOWLEDGMENTS.md b/ACKNOWLEDGMENTS.md
@@ -0,0 +1,13 @@
+# Acknowledgments
+
+The development of BrainPy is being or has been supported by many organizations, programs, and individuals since 2020. 
+The following list of support received is therefore necessarily incomplete.
+
+
+This project has received funding from Science and Technology Innovation 2030 (China Brain Project):
+
+- Brain Science and Brain-inspired Intelligence Project (No. 2021ZD0200204).
+
+Additionally, BrainPy gratefully acknowledges the support and funding received from:
+
+- Beijing Academy of Artificial Intelligence. 
diff --git a/README.md b/README.md
@@ -40,16 +40,13 @@ For detailed installation instructions, please refer to the documentation: [Quic
 - **[brainpy-examples](https://github.com/brainpy/examples)**: Comprehensive examples of BrainPy computation. 
 - **[brainpy-datasets](https://github.com/brainpy/datasets)**: Neuromorphic and Cognitive Datasets for Brain Dynamics Modeling.
 
-## Citing and Funding
-
-If you are using ``brainpy``, please consider citing [the corresponding papers](https://brainpy.readthedocs.io/en/latest/tutorial_FAQs/citing_and_publication.html). 
+## Citing 
 
 BrainPy is developed by a team in Neural Information Processing Lab at Peking University, China. 
 Our team is committed to the long-term maintenance and development of the project. 
 
-Moreover, the development of BrainPy is being or has been supported by Science and Technology 
-Innovation 2030 - Brain Science and Brain-inspired Intelligence Project (China Brain Project), 
-and Beijing Academy of Artificial Intelligence. 
+If you are using ``brainpy``, please consider citing [the corresponding papers](https://brainpy.readthedocs.io/en/latest/tutorial_FAQs/citing_and_publication.html). 
+
 
 
 ## Ongoing development plans

diff --git a/brainpy/_src/dnn/linear.py b/brainpy/_src/dnn/linear.py
@@ -10,13 +10,12 @@
 from brainpy import math as bm
 from brainpy._src import connect, initialize as init
 from brainpy._src.context import share
-from brainpy.algorithms import OnlineAlgorithm, OfflineAlgorithm
 from brainpy.check import is_initializer
 from brainpy.errors import MathError
 from brainpy.initialize import XavierNormal, ZeroInit, Initializer, parameter
 from brainpy.types import ArrayType, Sharding
 from brainpy._src.dnn.base import Layer
-from brainpy._src.mixin import SupportSTDP
+from brainpy._src.mixin import SupportOnline, SupportOffline, SupportSTDP
 
 __all__ = [
   'Dense', 'Linear',
@@ -30,7 +29,7 @@
 ]
 
 
-class Dense(Layer, SupportSTDP):
+class Dense(Layer, SupportOnline, SupportOffline, SupportSTDP):
   r"""A linear transformation applied over the last dimension of the input.
 
   Mathematically, this node can be defined as:
@@ -53,12 +52,6 @@ class Dense(Layer, SupportSTDP):
     Enable training this node or not. (default True)
   """
 
-  online_fit_by: Optional[OnlineAlgorithm]
-  '''Online fitting method.'''
-
-  offline_fit_by: Optional[OfflineAlgorithm]
-  '''Offline fitting method.'''
-
   def __init__(
       self,
       num_in: int,
@@ -96,8 +89,8 @@ def __init__(
     self.b = b
 
     # fitting parameters
-    self.online_fit_by = None
-    self.offline_fit_by = None
+    self.online_fit_by = None  # support online training
+    self.offline_fit_by = None  # support offline training
     self.fit_record = dict()
 
   def __repr__(self):

diff --git a/brainpy/_src/dyn/base.py b/brainpy/_src/dyn/base.py
@@ -1,19 +1,19 @@
 # -*- coding: utf-8 -*-
 
 from brainpy._src.dynsys import Dynamic
-from brainpy._src.mixin import AutoDelaySupp, ParamDesc
+from brainpy._src.mixin import SupportAutoDelay, ParamDesc
 
 __all__ = [
   'NeuDyn', 'SynDyn', 'IonChaDyn',
 ]
 
 
-class NeuDyn(Dynamic, AutoDelaySupp):
+class NeuDyn(Dynamic, SupportAutoDelay):
   """Neuronal Dynamics."""
   pass
 
 
-class SynDyn(Dynamic, AutoDelaySupp, ParamDesc):
+class SynDyn(Dynamic, SupportAutoDelay, ParamDesc):
   """Synaptic Dynamics."""
   pass
 

diff --git a/brainpy/_src/dyn/projections/aligns.py b/brainpy/_src/dyn/projections/aligns.py
@@ -4,7 +4,7 @@
 from brainpy._src.delay import Delay, DelayAccess, delay_identifier, init_delay_by_return
 from brainpy._src.dynsys import DynamicalSystem, Projection
 from brainpy._src.mixin import (JointType, ParamDescInit, ReturnInfo,
-                                AutoDelaySupp, BindCondData, AlignPost)
+                                SupportAutoDelay, BindCondData, AlignPost)
 
 __all__ = [
   'VanillaProj',
@@ -297,7 +297,7 @@ def update(self, inp):
 
   def __init__(
       self,
-      pre: JointType[DynamicalSystem, AutoDelaySupp],
+      pre: JointType[DynamicalSystem, SupportAutoDelay],
       delay: Union[None, int, float],
       comm: DynamicalSystem,
       syn: ParamDescInit[JointType[DynamicalSystem, AlignPost]],
@@ -310,7 +310,7 @@ def __init__(
     super().__init__(name=name, mode=mode)
 
     # synaptic models
-    check.is_instance(pre, JointType[DynamicalSystem, AutoDelaySupp])
+    check.is_instance(pre, JointType[DynamicalSystem, SupportAutoDelay])
     check.is_instance(comm, DynamicalSystem)
     check.is_instance(syn, ParamDescInit[JointType[DynamicalSystem, AlignPost]])
     check.is_instance(out, ParamDescInit[JointType[DynamicalSystem, BindCondData]])
@@ -507,7 +507,7 @@ def update(self, inp):
 
   def __init__(
       self,
-      pre: JointType[DynamicalSystem, AutoDelaySupp],
+      pre: JointType[DynamicalSystem, SupportAutoDelay],
       delay: Union[None, int, float],
       comm: DynamicalSystem,
       syn: JointType[DynamicalSystem, AlignPost],
@@ -520,7 +520,7 @@ def __init__(
     super().__init__(name=name, mode=mode)
 
     # synaptic models
-    check.is_instance(pre, JointType[DynamicalSystem, AutoDelaySupp])
+    check.is_instance(pre, JointType[DynamicalSystem, SupportAutoDelay])
     check.is_instance(comm, DynamicalSystem)
     check.is_instance(syn, JointType[DynamicalSystem, AlignPost])
     check.is_instance(out, JointType[DynamicalSystem, BindCondData])
@@ -631,7 +631,7 @@ def update(self, inp):
   def __init__(
       self,
       pre: DynamicalSystem,
-      syn: ParamDescInit[JointType[DynamicalSystem, AutoDelaySupp]],
+      syn: ParamDescInit[JointType[DynamicalSystem, SupportAutoDelay]],
       delay: Union[None, int, float],
       comm: DynamicalSystem,
       out: JointType[DynamicalSystem, BindCondData],
@@ -644,7 +644,7 @@ def __init__(
 
     # synaptic models
     check.is_instance(pre, DynamicalSystem)
-    check.is_instance(syn, ParamDescInit[JointType[DynamicalSystem, AutoDelaySupp]])
+    check.is_instance(syn, ParamDescInit[JointType[DynamicalSystem, SupportAutoDelay]])
     check.is_instance(comm, DynamicalSystem)
     check.is_instance(out, JointType[DynamicalSystem, BindCondData])
     check.is_instance(post, DynamicalSystem)
@@ -654,7 +654,7 @@ def __init__(
     self._syn_id = f'{syn.identifier} // Delay'
     if not pre.has_aft_update(self._syn_id):
       # "syn_cls" needs an instance of "ProjAutoDelay"
-      syn_cls: AutoDelaySupp = syn()
+      syn_cls: SupportAutoDelay = syn()
       delay_cls = init_delay_by_return(syn_cls.return_info())
       # add to "after_updates"
       pre.add_aft_update(self._syn_id, _AlignPre(syn_cls, delay_cls))
@@ -755,7 +755,7 @@ def update(self, inp):
 
   def __init__(
       self,
-      pre: JointType[DynamicalSystem, AutoDelaySupp],
+      pre: JointType[DynamicalSystem, SupportAutoDelay],
       delay: Union[None, int, float],
       syn: ParamDescInit[DynamicalSystem],
       comm: DynamicalSystem,
@@ -768,7 +768,7 @@ def __init__(
     super().__init__(name=name, mode=mode)
 
     # synaptic models
-    check.is_instance(pre, JointType[DynamicalSystem, AutoDelaySupp])
+    check.is_instance(pre, JointType[DynamicalSystem, SupportAutoDelay])
     check.is_instance(syn, ParamDescInit[DynamicalSystem])
     check.is_instance(comm, DynamicalSystem)
     check.is_instance(out, JointType[DynamicalSystem, BindCondData])
@@ -884,7 +884,7 @@ def update(self, inp):
   def __init__(
       self,
       pre: DynamicalSystem,
-      syn: JointType[DynamicalSystem, AutoDelaySupp],
+      syn: JointType[DynamicalSystem, SupportAutoDelay],
       delay: Union[None, int, float],
       comm: DynamicalSystem,
       out: JointType[DynamicalSystem, BindCondData],
@@ -897,7 +897,7 @@ def __init__(
 
     # synaptic models
     check.is_instance(pre, DynamicalSystem)
-    check.is_instance(syn, JointType[DynamicalSystem, AutoDelaySupp])
+    check.is_instance(syn, JointType[DynamicalSystem, SupportAutoDelay])
     check.is_instance(comm, DynamicalSystem)
     check.is_instance(out, JointType[DynamicalSystem, BindCondData])
     check.is_instance(post, DynamicalSystem)
@@ -1002,7 +1002,7 @@ def update(self, inp):
 
   def __init__(
       self,
-      pre: JointType[DynamicalSystem, AutoDelaySupp],
+      pre: JointType[DynamicalSystem, SupportAutoDelay],
       delay: Union[None, int, float],
       syn: DynamicalSystem,
       comm: DynamicalSystem,
@@ -1015,7 +1015,7 @@ def __init__(
     super().__init__(name=name, mode=mode)
 
     # synaptic models
-    check.is_instance(pre, JointType[DynamicalSystem, AutoDelaySupp])
+    check.is_instance(pre, JointType[DynamicalSystem, SupportAutoDelay])
     check.is_instance(syn, DynamicalSystem)
     check.is_instance(comm, DynamicalSystem)
     check.is_instance(out, JointType[DynamicalSystem, BindCondData])

diff --git a/brainpy/_src/dynold/synapses/base.py b/brainpy/_src/dynold/synapses/base.py
@@ -11,7 +11,7 @@
 from brainpy._src.dynsys import DynamicalSystem
 from brainpy._src.initialize import parameter
 from brainpy._src.mixin import (ParamDesc, JointType,
-                                AutoDelaySupp, BindCondData, ReturnInfo)
+                                SupportAutoDelay, BindCondData, ReturnInfo)
 from brainpy.errors import UnsupportedError
 from brainpy.types import ArrayType
 
@@ -109,7 +109,7 @@ def update(self):
     pass
 
 
-class _SynSTP(_SynapseComponent, ParamDesc, AutoDelaySupp):
+class _SynSTP(_SynapseComponent, ParamDesc, SupportAutoDelay):
   """Base class for synaptic short-term plasticity."""
 
   def update(self, pre_spike):

diff --git a/brainpy/_src/dynsys.py b/brainpy/_src/dynsys.py
@@ -10,7 +10,7 @@
 
 from brainpy import tools, math as bm
 from brainpy._src.initialize import parameter, variable_
-from brainpy._src.mixin import AutoDelaySupp, Container, ReceiveInputProj, DelayRegister, global_delay_data
+from brainpy._src.mixin import SupportAutoDelay, Container, ReceiveInputProj, DelayRegister, global_delay_data
 from brainpy.errors import NoImplementationError, UnsupportedError
 from brainpy.types import ArrayType, Shape
 from brainpy._src.deprecations import _update_deprecate_msg
@@ -487,7 +487,7 @@ class Network(DynSysGroup):
   pass
 
 
-class Sequential(DynamicalSystem, AutoDelaySupp, Container):
+class Sequential(DynamicalSystem, SupportAutoDelay, Container):
   """A sequential `input-output` module.
 
   Modules will be added to it in the order they are passed in the
@@ -557,9 +557,9 @@ def update(self, x):
 
   def return_info(self):
     last = self[-1]
-    if not isinstance(last, AutoDelaySupp):
+    if not isinstance(last, SupportAutoDelay):
       raise UnsupportedError(f'Does not support "return_info()" because the last node is '
-                             f'not instance of {AutoDelaySupp.__name__}')
+                             f'not instance of {SupportAutoDelay.__name__}')
     return last.return_info()
 
   def __getitem__(self, key: Union[int, slice, str]):