Rollback

.gitignore

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

README.md

@@ -17,8 +17,8 @@
 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. 
 
 - **Source**: https://github.com/brainpy/BrainPy
-- **Documentation (brainpy v3.0)**: https://brainpy.readthedocs.io/
-- **Documentation (brainpy v2.0)**: https://brainpy-v2.readthedocs.io/
+- **Documentation**: https://brainpy.readthedocs.io/
+- **Documentation (state-based)**: https://brainpy-state.readthedocs.io/
 - **Bug reports**: https://github.com/brainpy/BrainPy/issues
 - **Ecosystem**: https://brainmodeling.readthedocs.io/
 

brainpy/__init__.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 # Copyright 2025 BrainX Ecosystem Limited. All Rights Reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -13,87 +14,172 @@
 # limitations under the License.
 # ==============================================================================
 
-__version__ = "3.0.0"
-__version_info__ = (3, 0, 0)
-
-from . import mixin
-from . import version2
-from ._base import *
-from ._base import __all__ as base_all
-from ._errors import *
-from ._errors import __all__ as errors_all
-from ._exponential import *
-from ._exponential import __all__ as exp_all
-from ._inputs import *
-from ._inputs import __all__ as inputs_all
-from ._lif import *
-from ._lif import __all__ as neuron_all
-from ._projection import *
-from ._projection import __all__ as proj_all
-from ._readout import *
-from ._readout import __all__ as readout_all
-from ._stp import *
-from ._stp import __all__ as stp_all
-from ._synapse import *
-from ._synapse import __all__ as synapse_all
-from ._synaptic_projection import *
-from ._synaptic_projection import __all__ as synproj_all
-from ._synouts import *
-from ._synouts import __all__ as synout_all
-
-__main__ = ['version2', 'mixin'] + errors_all + inputs_all + neuron_all + readout_all + stp_all + synapse_all
-__main__ = __main__ + synout_all + base_all + exp_all + proj_all + synproj_all
-del errors_all, inputs_all, neuron_all, readout_all, stp_all, synapse_all, synout_all, base_all
-del exp_all, proj_all, synproj_all
-
-
-# Deprecation warnings for brainpy.xxx -> brainpy.version2.xxx
-def __getattr__(name):
-    """Provide deprecation warnings for moved modules."""
-    import warnings
-
-    if hasattr(version2, name):
-        warnings.warn(
-            f"Accessing 'brainpy.{name}' is deprecated. "
-            f"Please use 'brainpy.version2.{name}' instead.",
-            DeprecationWarning,
-            stacklevel=2
-        )
-        return getattr(version2, name)
-
-    raise AttributeError(f"'brainpy' has no attribute '{name}'")
-
-
-def __dir__():
-    """Return list of attributes including deprecated ones for tab completion."""
-    # Get the default attributes
-    default_attrs = list(globals().keys())
-
-    # Add all public attributes from version2 for discoverability
-    version2_attrs = [attr for attr in dir(version2) if not attr.startswith('_')]
-
-    # Combine and return unique attributes
-    return sorted(set(default_attrs + version2_attrs))
-
-
-# Register deprecated modules in sys.modules to support "import brainpy.xxx" syntax
-import sys as _sys
-
-_deprecated_modules = [
-    'math', 'check', 'tools', 'connect', 'initialize', 'init', 'conn',
-    'optim', 'losses', 'measure', 'inputs', 'encoding', 'checkpoints',
-    'algorithms', 'integrators', 'ode', 'sde', 'fde',
-    'dnn', 'layers', 'dyn', 'running', 'train', 'analysis',
-    'channels', 'neurons', 'rates', 'synapses', 'synouts', 'synplast',
-    'visualization', 'visualize', 'types', 'modes', 'context',
-    'helpers', 'delay', 'dynsys', 'runners', 'transform', 'dynold'
-]
-
-# Create wrapper modules that show deprecation warnings
-for _mod_name in _deprecated_modules:
-    if hasattr(version2, _mod_name):
-        _sys.modules[f'brainpy.{_mod_name}'] = getattr(version2, _mod_name)
-
-del _sys, _mod_name, _deprecated_modules
-
-version2.__version__ = __version__
+__version__ = "3.0.1"
+__version_info__ = (3, 0, 1)
+
+
+from brainpy import _errors as errors
+from brainpy import mixin
+# fundamental supporting modules
+from brainpy import check, tools
+#  Part: Math Foundation  #
+# ----------------------- #
+# math foundation
+from brainpy import math
+#  Part: Toolbox  #
+# --------------- #
+# modules of toolbox
+from . import (
+    connect,  # synaptic connection
+    initialize,  # weight initialization
+    optim,  # gradient descent optimizers
+    losses,  # loss functions
+    measure,  # methods for data analysis
+    inputs,  # methods for generating input currents
+    encoding,  # encoding schema
+    checkpoints,  # checkpoints
+    check,  # error checking
+    algorithms,  # online or offline training algorithms
+)
+from .math import BrainPyObject
+
+# convenient alias
+conn = connect
+init = initialize
+
+# numerical integrators
+from brainpy import integrators
+from brainpy.integrators import ode, sde, fde
+from brainpy.integrators.base import (Integrator as Integrator)
+from brainpy.integrators.joint_eq import (JointEq as JointEq)
+from brainpy.integrators.runner import (IntegratorRunner as IntegratorRunner)
+from brainpy.integrators.ode.generic import (odeint as odeint)
+from brainpy.integrators.sde.generic import (sdeint as sdeint)
+from brainpy.integrators.fde.generic import (fdeint as fdeint)
+
+#  Part: Models  #
+# -------------- #
+
+# base classes
+from brainpy.dynsys import (
+    DynamicalSystem as DynamicalSystem,
+    DynSysGroup as DynSysGroup,  # collectors
+    Sequential as Sequential,
+    Dynamic as Dynamic,  # category
+    Projection as Projection,
+    receive_update_input,  # decorators
+    receive_update_output,
+    not_receive_update_input,
+    not_receive_update_output,
+)
+
+DynamicalSystemNS = DynamicalSystem
+Network = DynSysGroup
+# delays
+from brainpy.delay import (
+    VarDelay as VarDelay,
+)
+
+# building blocks
+from brainpy import (
+    dnn, layers,  # module for dnn layers
+    dyn,  # module for modeling dynamics
+)
+
+NeuGroup = NeuGroupNS = dyn.NeuDyn
+dyn.DynamicalSystem = DynamicalSystem
+
+# common tools
+from brainpy.context import (share as share)
+from brainpy.helpers import (
+    reset_level as reset_level,
+    reset_state as reset_state,
+    save_state as save_state,
+    load_state as load_state,
+    clear_input as clear_input
+)
+
+#  Part: Running  #
+# --------------- #
+from brainpy.runners import (DSRunner as DSRunner)
+from brainpy.transform import (LoopOverTime as LoopOverTime, )
+from brainpy import (running as running)
+
+#  Part: Training  #
+# ---------------- #
+from brainpy.train.base import (DSTrainer as DSTrainer, )
+from brainpy.train.back_propagation import (BPTT as BPTT,
+                                                     BPFF as BPFF, )
+from brainpy.train.online import (OnlineTrainer as OnlineTrainer,
+                                           ForceTrainer as ForceTrainer, )
+from brainpy.train.offline import (OfflineTrainer as OfflineTrainer,
+                                            RidgeTrainer as RidgeTrainer, )
+
+#  Part: Analysis  #
+# ---------------- #
+from brainpy import (analysis as analysis)
+
+#  Part: Others    #
+# ---------------- #
+import brainpy.visualization as visualize
+
+#  Part: Deprecations  #
+# -------------------- #
+from brainpy import train
+from brainpy import (
+    channels,  # channel models
+    neurons,  # neuron groups
+    synapses,  # synapses
+    rates,  # rate models
+    synouts,  # synaptic output
+    synplast,  # synaptic plasticity
+)
+from brainpy.math.object_transform.base import (
+    Base as Base,
+)
+
+from brainpy.math.object_transform.collectors import (
+    ArrayCollector as ArrayCollector,
+    Collector as Collector,
+)
+
+
+from brainpy.deprecations import deprecation_getattr
+
+optimizers = optim
+
+
+
+if __name__ == '__main__':
+    connect
+    initialize,  # weight initialization
+    optim,  # gradient descent optimizers
+    losses,  # loss functions
+    measure,  # methods for data analysis
+    inputs,  # methods for generating input currents
+    encoding,  # encoding schema
+    checkpoints,  # checkpoints
+    check,  # error checking
+    mixin,  # mixin classes
+    algorithms,  # online or offline training algorithms
+    check, tools, errors, math
+    BrainPyObject,
+    integrators, ode, sde, fde
+    Integrator, JointEq, IntegratorRunner, odeint, sdeint, fdeint
+    DynamicalSystem, DynSysGroup, Sequential, Dynamic, Projection
+    receive_update_input, receive_update_output, not_receive_update_input, not_receive_update_output
+    VarDelay
+    dnn, layers, dyn
+    NeuGroup, NeuGroupNS
+    share
+    reset_level, reset_state, save_state, load_state, clear_input
+    DSRunner, LoopOverTime, running
+    DSTrainer, BPTT, BPFF, OnlineTrainer, ForceTrainer,
+    OfflineTrainer, RidgeTrainer
+    analysis
+    visualize
+    train
+    channels, neurons, synapses, rates, state_based, synouts, synplast
+    modes
+    Base
+    ArrayCollector, Collector, errors

brainpy/version2/algorithms/offline.py → brainpy/algorithms/offline.py

@@ -19,9 +19,9 @@
 import numpy as np
 from jax.lax import while_loop
 
-import brainpy.version2.math as bm
-from brainpy.version2.math.object_transform.base import BrainPyObject
-from brainpy.version2.types import ArrayType
+import brainpy.math as bm
+from brainpy.math.object_transform.base import BrainPyObject
+from brainpy.types import ArrayType
 from .utils import (Sigmoid,
                     Regularization,
                     L1Regularization,

brainpy/version2/algorithms/online.py → brainpy/algorithms/online.py

@@ -17,8 +17,8 @@
 import jax.numpy as jnp
 from jax import vmap
 
-import brainpy.version2.math as bm
-from brainpy.version2.math.object_transform.base import BrainPyObject
+import brainpy.math as bm
+from brainpy.math.object_transform.base import BrainPyObject
 
 __all__ = [
     # brainpy_object class

brainpy/version2/algorithms/utils.py → brainpy/algorithms/utils.py

@@ -15,7 +15,7 @@
 # ==============================================================================
 from itertools import combinations_with_replacement
 
-import brainpy.version2.math as bm
+import brainpy.math as bm
 
 __all__ = [
     'Sigmoid',

brainpy/version2/analysis/highdim/slow_points.py → brainpy/analysis/highdim/slow_points.py

@@ -24,16 +24,16 @@
 import numpy as np
 from jax.scipy.optimize import minimize
 
-import brainpy.version2.math as bm
+import brainpy.math as bm
 from brainpy._errors import AnalyzerError, UnsupportedError
-from brainpy.version2 import optim, losses
-from brainpy.version2.analysis import utils, base, constants
-from brainpy.version2.context import share
-from brainpy.version2.deprecations import _input_deprecate_msg
-from brainpy.version2.dynsys import DynamicalSystem
-from brainpy.version2.helpers import clear_input
-from brainpy.version2.runners import check_and_format_inputs, _f_ops
-from brainpy.version2.types import ArrayType
+from brainpy import optim, losses
+from brainpy.analysis import utils, base, constants
+from brainpy.context import share
+from brainpy.deprecations import _input_deprecate_msg
+from brainpy.dynsys import DynamicalSystem
+from brainpy.helpers import clear_input
+from brainpy.runners import check_and_format_inputs, _f_ops
+from brainpy.types import ArrayType
 
 __all__ = [
     'SlowPointFinder',
@@ -87,7 +87,7 @@ class SlowPointFinder(base.DSAnalyzer):
     dt: float
       Parameter for ``f_cell`` is instance of :py:class:`~.DynamicalSystem`.
       The numerical integration step, which can be used when .
-      The default is given by `brainpy.version2.math.get_dt()`.
+      The default is given by `brainpy.math.get_dt()`.
 
       .. versionadded:: 2.2.0
     inputs: sequence, callable
@@ -595,7 +595,7 @@ def compute_jacobians(
         # visualization
         if plot:
             import matplotlib.pyplot as plt
-            from brainpy.version2 import visualize
+            from brainpy import visualize
             jacobian = bm.as_numpy(jacobian)
 
             num_col = min(num_col, num_point)

brainpy/version2/analysis/highdim/tests/test_slow_points.py → brainpy/analysis/highdim/tests/test_slow_points.py

@@ -15,8 +15,8 @@
 # ==============================================================================
 import unittest
 
-import brainpy.version2 as bp
-import brainpy.version2.math as bm
+import brainpy as bp
+import brainpy.math as bm
 
 
 class HH(bp.dyn.NeuDyn):

brainpy/version2/analysis/lowdim/lowdim_analyzer.py → brainpy/analysis/lowdim/lowdim_analyzer.py

@@ -23,11 +23,11 @@
 from jax.scipy.optimize import minimize
 
 import brainpy._errors as errors
-import brainpy.version2.math as bm
-from brainpy.version2 import tools
-from brainpy.version2.analysis import constants as C, utils
-from brainpy.version2.analysis.base import DSAnalyzer
-from brainpy.version2.math.object_transform.collectors import Collector
+import brainpy.math as bm
+from brainpy import tools
+from brainpy.analysis import constants as C, utils
+from brainpy.analysis.base import DSAnalyzer
+from brainpy.math.object_transform.collectors import Collector
 
 pyplot = None