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chaoming0625oujago
chaoming0625
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oujago
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Rollback (#789)
* remove version2 * remove .version2 import * fix: create static directory and remove version-specific announcements from conf.py * refactor: rename experimental directories and update imports to state-based * refactor: update imports to use brainpy.state_based and clean up code structure * refactor: update imports to use brainpy.state_based and remove deprecated version notes * refactor: update documentation to reflect module renaming from version2 to main namespace --------- Co-authored-by: oujago <[email protected]>
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‎.gitignore‎

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@@ -233,8 +233,8 @@ cython_debug/
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/docs/_static/logos/
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/docs/_build/
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/docs/changelog.md
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/docs_version3/_build/
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/docs_version3/_static/logos/
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/docs_version3/changelog.md
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/docs_state_based/_build/
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/docs_state_based/_static/logos/
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/docs_state_based/changelog.md
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/examples_version2/dynamics_training/data/
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/docs/

‎README.md‎

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BrainPy is a flexible, efficient, and extensible framework for computational neuroscience and brain-inspired computation based on the Just-In-Time (JIT) compilation. It provides an integrative ecosystem for brain dynamics programming, including brain dynamics **building**, **simulation**, **training**, **analysis**, etc.
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- **Source**: https://github.com/brainpy/BrainPy
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- **Documentation (brainpy v3.0)**: https://brainpy.readthedocs.io/
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- **Documentation (brainpy v2.0)**: https://brainpy-v2.readthedocs.io/
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- **Documentation**: https://brainpy.readthedocs.io/
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- **Documentation (state-based)**: https://brainpy-state.readthedocs.io/
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- **Bug reports**: https://github.com/brainpy/BrainPy/issues
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- **Ecosystem**: https://brainmodeling.readthedocs.io/
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‎brainpy/__init__.py‎

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# -*- coding: utf-8 -*-
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# Copyright 2025 BrainX Ecosystem Limited. All Rights Reserved.
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# limitations under the License.
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# ==============================================================================
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__version__ = "3.0.0"
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__version_info__ = (3, 0, 0)
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from . import mixin
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from . import version2
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from ._base import *
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from ._base import __all__ as base_all
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from ._errors import *
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from ._errors import __all__ as errors_all
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from ._exponential import *
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from ._exponential import __all__ as exp_all
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from ._inputs import *
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from ._inputs import __all__ as inputs_all
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from ._lif import *
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from ._lif import __all__ as neuron_all
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from ._projection import *
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from ._projection import __all__ as proj_all
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from ._readout import *
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from ._readout import __all__ as readout_all
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from ._stp import *
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from ._stp import __all__ as stp_all
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from ._synapse import *
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from ._synapse import __all__ as synapse_all
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from ._synaptic_projection import *
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from ._synaptic_projection import __all__ as synproj_all
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from ._synouts import *
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from ._synouts import __all__ as synout_all
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__main__ = ['version2', 'mixin'] + errors_all + inputs_all + neuron_all + readout_all + stp_all + synapse_all
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__main__ = __main__ + synout_all + base_all + exp_all + proj_all + synproj_all
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del errors_all, inputs_all, neuron_all, readout_all, stp_all, synapse_all, synout_all, base_all
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del exp_all, proj_all, synproj_all
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# Deprecation warnings for brainpy.xxx -> brainpy.version2.xxx
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def __getattr__(name):
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"""Provide deprecation warnings for moved modules."""
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import warnings
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if hasattr(version2, name):
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warnings.warn(
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f"Accessing 'brainpy.{name}' is deprecated. "
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f"Please use 'brainpy.version2.{name}' instead.",
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DeprecationWarning,
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stacklevel=2
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)
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return getattr(version2, name)
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raise AttributeError(f"'brainpy' has no attribute '{name}'")
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def __dir__():
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"""Return list of attributes including deprecated ones for tab completion."""
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# Get the default attributes
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default_attrs = list(globals().keys())
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# Add all public attributes from version2 for discoverability
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version2_attrs = [attr for attr in dir(version2) if not attr.startswith('_')]
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# Combine and return unique attributes
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return sorted(set(default_attrs + version2_attrs))
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# Register deprecated modules in sys.modules to support "import brainpy.xxx" syntax
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import sys as _sys
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_deprecated_modules = [
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'math', 'check', 'tools', 'connect', 'initialize', 'init', 'conn',
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'optim', 'losses', 'measure', 'inputs', 'encoding', 'checkpoints',
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'algorithms', 'integrators', 'ode', 'sde', 'fde',
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'dnn', 'layers', 'dyn', 'running', 'train', 'analysis',
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'channels', 'neurons', 'rates', 'synapses', 'synouts', 'synplast',
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'visualization', 'visualize', 'types', 'modes', 'context',
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'helpers', 'delay', 'dynsys', 'runners', 'transform', 'dynold'
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]
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# Create wrapper modules that show deprecation warnings
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for _mod_name in _deprecated_modules:
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if hasattr(version2, _mod_name):
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_sys.modules[f'brainpy.{_mod_name}'] = getattr(version2, _mod_name)
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del _sys, _mod_name, _deprecated_modules
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version2.__version__ = __version__
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__version__ = "3.0.1"
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__version_info__ = (3, 0, 1)
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from brainpy import _errors as errors
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from brainpy import mixin
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# fundamental supporting modules
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from brainpy import check, tools
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# Part: Math Foundation #
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# ----------------------- #
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# math foundation
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from brainpy import math
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# Part: Toolbox #
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# --------------- #
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# modules of toolbox
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from . import (
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connect, # synaptic connection
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initialize, # weight initialization
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optim, # gradient descent optimizers
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losses, # loss functions
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measure, # methods for data analysis
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inputs, # methods for generating input currents
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encoding, # encoding schema
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checkpoints, # checkpoints
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check, # error checking
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algorithms, # online or offline training algorithms
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)
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from .math import BrainPyObject
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# convenient alias
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conn = connect
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init = initialize
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# numerical integrators
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from brainpy import integrators
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from brainpy.integrators import ode, sde, fde
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from brainpy.integrators.base import (Integrator as Integrator)
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from brainpy.integrators.joint_eq import (JointEq as JointEq)
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from brainpy.integrators.runner import (IntegratorRunner as IntegratorRunner)
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from brainpy.integrators.ode.generic import (odeint as odeint)
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from brainpy.integrators.sde.generic import (sdeint as sdeint)
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from brainpy.integrators.fde.generic import (fdeint as fdeint)
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# Part: Models #
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# -------------- #
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# base classes
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from brainpy.dynsys import (
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DynamicalSystem as DynamicalSystem,
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DynSysGroup as DynSysGroup, # collectors
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Sequential as Sequential,
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Dynamic as Dynamic, # category
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Projection as Projection,
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receive_update_input, # decorators
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receive_update_output,
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not_receive_update_input,
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not_receive_update_output,
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)
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DynamicalSystemNS = DynamicalSystem
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Network = DynSysGroup
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# delays
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from brainpy.delay import (
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VarDelay as VarDelay,
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)
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# building blocks
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from brainpy import (
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dnn, layers, # module for dnn layers
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dyn, # module for modeling dynamics
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)
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NeuGroup = NeuGroupNS = dyn.NeuDyn
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dyn.DynamicalSystem = DynamicalSystem
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# common tools
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from brainpy.context import (share as share)
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from brainpy.helpers import (
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reset_level as reset_level,
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reset_state as reset_state,
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save_state as save_state,
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load_state as load_state,
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clear_input as clear_input
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)
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# Part: Running #
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# --------------- #
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from brainpy.runners import (DSRunner as DSRunner)
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from brainpy.transform import (LoopOverTime as LoopOverTime, )
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from brainpy import (running as running)
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# Part: Training #
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# ---------------- #
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from brainpy.train.base import (DSTrainer as DSTrainer, )
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from brainpy.train.back_propagation import (BPTT as BPTT,
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BPFF as BPFF, )
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from brainpy.train.online import (OnlineTrainer as OnlineTrainer,
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ForceTrainer as ForceTrainer, )
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from brainpy.train.offline import (OfflineTrainer as OfflineTrainer,
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RidgeTrainer as RidgeTrainer, )
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# Part: Analysis #
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# ---------------- #
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from brainpy import (analysis as analysis)
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# Part: Others #
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# ---------------- #
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import brainpy.visualization as visualize
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# Part: Deprecations #
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# -------------------- #
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from brainpy import train
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from brainpy import (
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channels, # channel models
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neurons, # neuron groups
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synapses, # synapses
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rates, # rate models
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synouts, # synaptic output
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synplast, # synaptic plasticity
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)
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from brainpy.math.object_transform.base import (
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Base as Base,
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)
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from brainpy.math.object_transform.collectors import (
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ArrayCollector as ArrayCollector,
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Collector as Collector,
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)
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from brainpy.deprecations import deprecation_getattr
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optimizers = optim
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if __name__ == '__main__':
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connect
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initialize, # weight initialization
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optim, # gradient descent optimizers
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losses, # loss functions
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measure, # methods for data analysis
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inputs, # methods for generating input currents
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encoding, # encoding schema
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checkpoints, # checkpoints
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check, # error checking
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mixin, # mixin classes
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algorithms, # online or offline training algorithms
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check, tools, errors, math
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BrainPyObject,
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integrators, ode, sde, fde
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Integrator, JointEq, IntegratorRunner, odeint, sdeint, fdeint
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DynamicalSystem, DynSysGroup, Sequential, Dynamic, Projection
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receive_update_input, receive_update_output, not_receive_update_input, not_receive_update_output
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VarDelay
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dnn, layers, dyn
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NeuGroup, NeuGroupNS
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share
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reset_level, reset_state, save_state, load_state, clear_input
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DSRunner, LoopOverTime, running
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DSTrainer, BPTT, BPFF, OnlineTrainer, ForceTrainer,
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OfflineTrainer, RidgeTrainer
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analysis
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visualize
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train
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channels, neurons, synapses, rates, state_based, synouts, synplast
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modes
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Base
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ArrayCollector, Collector, errors

‎brainpy/version2/algorithms/__init__.py‎ renamed to ‎brainpy/algorithms/__init__.py‎

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‎brainpy/version2/algorithms/offline.py‎ renamed to ‎brainpy/algorithms/offline.py‎

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import numpy as np
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from jax.lax import while_loop
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import brainpy.version2.math as bm
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from brainpy.version2.math.object_transform.base import BrainPyObject
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from brainpy.version2.types import ArrayType
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import brainpy.math as bm
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from brainpy.math.object_transform.base import BrainPyObject
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from brainpy.types import ArrayType
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from .utils import (Sigmoid,
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Regularization,
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L1Regularization,

‎brainpy/version2/algorithms/online.py‎ renamed to ‎brainpy/algorithms/online.py‎

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import jax.numpy as jnp
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from jax import vmap
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import brainpy.version2.math as bm
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from brainpy.version2.math.object_transform.base import BrainPyObject
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import brainpy.math as bm
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from brainpy.math.object_transform.base import BrainPyObject
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__all__ = [
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# brainpy_object class

‎brainpy/version2/algorithms/utils.py‎ renamed to ‎brainpy/algorithms/utils.py‎

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# ==============================================================================
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from itertools import combinations_with_replacement
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import brainpy.version2.math as bm
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import brainpy.math as bm
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__all__ = [
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'Sigmoid',

‎brainpy/version2/analysis/__init__.py‎ renamed to ‎brainpy/analysis/__init__.py‎

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‎brainpy/version2/analysis/base.py‎ renamed to ‎brainpy/analysis/base.py‎

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‎brainpy/version2/analysis/constants.py‎ renamed to ‎brainpy/analysis/constants.py‎

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