feat(state): make brainpy.state in-tree code

Move the state-based models into brainpy/state/: neurons, synapses,
synaptic outputs, STP, projections, readouts and inputs, plus the
Dynamics/Neuron/Synapse bases and their tests. brainpy.state was a
re-export of the external brainpy_state package; it now has an explicit
__all__. The source is brainpy-state main @ 0f2e3ab.

- Drop the brainpy_state dependency; raise brainevent to >=0.2.1.
- Host the brainpy.state tutorials, how-to guides, concept chapters,
  gallery and API reference in docs/state/ and docs/apis/state.rst, and
  move the example scripts to examples/state/.
- Point readthedocs links at https://brainpy.readthedocs.io/ (no /en/latest/).
- Version 2.9.0.

Author: chaoming0625

CONTRIBUTING.md

@@ -215,7 +215,7 @@ pytest --cov=brainpy tests/
 - Keep the API reference up to date
 - Fix typos and improve clarity
 
-For comprehensive contribution guidelines, see our [detailed documentation](https://brainpy.readthedocs.io/en/latest/tutorial_advanced/contributing.html).
+For comprehensive contribution guidelines, see our [detailed documentation](https://brainpy.readthedocs.io/tutorial_advanced/contributing.html).
 
 ## Community
 

README.md

@@ -7,7 +7,7 @@
 <p align="center">
 	<a href="https://pypi.org/project/brainpy/"><img alt="Supported Python Version" src="https://img.shields.io/pypi/pyversions/brainpy"></a>
 	<a href="https://github.com/brainpy/BrainPy"><img alt="LICENSE" src="https://img.shields.io/badge/license-%20%20GNU%20GPLv3%20-green?style=plastic"></a>
-  	<a href="https://brainpy.readthedocs.io/en/latest/?badge=latest"><img alt="Documentation" src="https://readthedocs.org/projects/brainpy/badge/?version=latest"></a>
+  	<a href="https://brainpy.readthedocs.io/?badge=latest"><img alt="Documentation" src="https://readthedocs.org/projects/brainpy/badge/?version=latest"></a>
   	<a href="https://badge.fury.io/py/brainpy"><img alt="PyPI version" src="https://badge.fury.io/py/brainpy.svg"></a>
     <a href="https://github.com/brainpy/BrainPy/actions/workflows/CI.yml"><img alt="Continuous Integration" src="https://github.com/brainpy/BrainPy/actions/workflows/CI.yml/badge.svg"></a>
     <a href="https://codecov.io/gh/brainpy/BrainPy"><img alt="Test Coverage" src="https://codecov.io/gh/brainpy/BrainPy/branch/main/graph/badge.svg"></a>
@@ -19,7 +19,7 @@ BrainPy is a flexible, efficient, and extensible framework for computational neu
 - **Source**: https://github.com/brainpy/BrainPy
 - **Bug reports**: https://github.com/brainpy/BrainPy/issues
 - **Documentation**: https://brainpy.readthedocs.io/
-- **Documentation (state-based)**: https://brainx.chaobrain.com/brainpy-state
+- **Documentation (state-based)**: https://brainpy.readthedocs.io/state/index.html
 - **Ecosystem**: https://brainx.chaobrain.com
 - **BrainPy and BrainX**: https://brainx.chaobrain.com/summ/brainpy-to-brainx.html
 
@@ -64,7 +64,6 @@ We provide a Binder environment for BrainPy. You can use the following button to
 
 - **[brain modeling ecosystem](https://brainmodeling.readthedocs.io/)**: A collection of tools and libraries for brain modeling and simulation.
 - **[brainpy-examples](https://github.com/brainpy/examples)**: Comprehensive examples of BrainPy computation. 
-- **[brainpy-state](https://github.com/chaobrain/brainpy.state)**: Moderize BrainPy simulation with `brainstate` syntax.
 - **[BrainPy to BrainX](https://brainx.chaobrain.com/summ/brainpy-to-brainx.html)**: How `brainpy` relates to the BrainX packages, and [migration notes](https://brainx.chaobrain.com/summ/brainpy-migration-notes.html) for moving a project across.
 - [《神经计算建模实战》 (Neural Modeling in Action)](https://github.com/c-xy17/NeuralModeling)
 - [第一届神经计算建模与编程培训班 (First Training Course on Neural Modeling and Programming)](https://github.com/brainpy/1st-neural-modeling-and-programming-course)

brainpy/_version.py

@@ -14,5 +14,5 @@
 # limitations under the License.
 # ==============================================================================
 
-__version__ = "2.8.2"
+__version__ = "2.9.0"
 __version_info__ = tuple(map(int, __version__.split(".")))

brainpy/dynsys.py

@@ -283,7 +283,7 @@ def reset(self, *args, **kwargs):
 
         ``reset()`` function is a collective behavior which resets all states in this model.
 
-        See https://brainpy.readthedocs.io/en/latest/tutorial_toolbox/state_resetting.html for details.
+        See https://brainpy.readthedocs.io/tutorial_toolbox/state_resetting.html for details.
         """
         global reset_state
         if reset_state is None:
@@ -297,7 +297,7 @@ def reset_state(self, *args, **kwargs):
         Simply speaking, this function should implement the logic of resetting of
         local variables in this node.
 
-        See https://brainpy.readthedocs.io/en/latest/tutorial_toolbox/state_resetting.html for details.
+        See https://brainpy.readthedocs.io/tutorial_toolbox/state_resetting.html for details.
         """
         pass
 
@@ -511,7 +511,7 @@ def _compatible_reset_state(self, *args, **kwargs):
                 self.reset(*args, **kwargs)
                 warnings.warn(
                     '''
-                From version >= 2.4.6, the policy of ``.reset_state()`` has been changed. See https://brainpy.readthedocs.io/en/latest/tutorial_toolbox/state_saving_and_loading.html for details.
+                From version >= 2.4.6, the policy of ``.reset_state()`` has been changed. See https://brainpy.readthedocs.io/tutorial_toolbox/state_saving_and_loading.html for details.
           
                 1. If you are resetting all states in a network by calling "net.reset_state(*args, **kwargs)", please use
                    "bp.reset_state(net, *args, **kwargs)" function, or "net.reset(*args, **kwargs)". 

brainpy/helpers.py

@@ -58,7 +58,7 @@ def wrap(fun: Callable):
 def reset_state(target: DynamicalSystem, *args, **kwargs):
     """Reset states of all children nodes in the given target.
 
-    See https://brainpy.readthedocs.io/en/latest/tutorial_toolbox/state_resetting.html for details.
+    See https://brainpy.readthedocs.io/tutorial_toolbox/state_resetting.html for details.
 
     Parameters
     ----------

brainpy/state/README.md

@@ -2,11 +2,13 @@
 
 ## Overview
 
-The `brainpy.state` module provides a state-based programming interface for brain dynamics modeling in BrainPy. This module is maintained as a separate package [`brainpy_state`](https://github.com/chaobrain/brainpy.state) and re-exported through BrainPy for seamless integration.
+The `brainpy.state` module provides a state-based programming interface for brain dynamics modeling in BrainPy, built on [`brainstate`](https://github.com/chaobrain/brainstate).
+
+Its motivation is compatibility with the [BrainX ecosystem](https://brainx.chaobrain.com): `brainpy.state` models carry physical units through [`brainunit`](https://github.com/chaobrain/brainunit), compose with `brainstate` transformations, and can be trained online with [`braintrace`](https://github.com/chaobrain/braintrace).
 
 State-based programming offers an alternative paradigm for defining and managing neural models, emphasizing explicit state management and transformations for building complex brain dynamics systems.
 
-`brainpy.state` is the recommended starting point for new `State`-based, differentiable models; the classic `DynamicalSystem`-based `brainpy` API (`brainpy.dyn`, `brainpy.math`, `brainpy.integrators`) is unchanged and fully supported. The two paradigms coexist — see the [relationship declaration](https://brainx.chaobrain.com/brainpy-state/project/relationship.html) for how they relate.
+`brainpy.state` is the recommended starting point for new `State`-based, differentiable models; the classic `DynamicalSystem`-based `brainpy` API (`brainpy.dyn`, `brainpy.math`, `brainpy.integrators`) is unchanged and fully supported.
 
 ## Features
 
@@ -17,19 +19,11 @@ State-based programming offers an alternative paradigm for defining and managing
 
 ## Documentation
 
-For comprehensive documentation on state-based programming in BrainPy, please visit:
-
-- **State-based Documentation**: https://brainx.chaobrain.com/brainpy-state/
-- **Main BrainPy Documentation**: https://brainpy.readthedocs.io/
+- **State-based Documentation**: https://brainpy.readthedocs.io/state/index.html
+- **API Reference**: https://brainpy.readthedocs.io/apis/state.html
 - **BrainPy and BrainX**: https://brainx.chaobrain.com/summ/brainpy-to-brainx.html
 - **Migration notes**: https://brainx.chaobrain.com/summ/brainpy-migration-notes.html
 
-## Source Repository
-
-This module is maintained in a separate repository:
-
-- **GitHub**: https://github.com/chaobrain/brainpy.state
-
 ## Installation
 
 The `brainpy.state` module is included when you install BrainPy:
@@ -38,28 +32,17 @@ The `brainpy.state` module is included when you install BrainPy:
 pip install brainpy -U
 ```
 
-For development or to install the state module separately:
-
-```bash
-pip install brainpy.state -U
-```
-
 ## Usage
 
-Import the state module from BrainPy:
-
 ```python
-import brainpy as bp
-from brainpy import state
+import brainpy
 
-# Use state-based components
-# (See documentation for detailed examples)
+neuron = brainpy.state.LIF(100)
 ```
 
 ## Support
 
 - **Bug Reports**: Please report issues at https://github.com/brainpy/BrainPy/issues
-- **State Module Issues**: For state-specific issues, see https://github.com/chaobrain/brainpy.state/issues
 
 ## License
 

brainpy/state/__init__.py

@@ -13,9 +13,81 @@
 # limitations under the License.
 # ==============================================================================
 
-from brainpy_state import *
-from brainpy_state import __all__
+r"""
+State-based brain dynamics models built on ``brainstate``.
 
-if __name__ == '__main__':
-    print(LIF)  # type: ignore[name-defined]  # provided by `from brainpy_state import *`
-    print(__all__)
+This module provides composable neuron, synapse, projection, readout, and
+input models with explicit ``State`` objects, so they compose with
+``brainstate`` transformations (``jit``, ``grad``, ``vmap``, ``for_loop``).
+"""
+
+from brainpy.state._base import Dynamics, Neuron, Synapse
+from brainpy.state.exponential import Expon, DualExpon
+from brainpy.state.hh import HH, MorrisLecar, WangBuzsakiHH
+from brainpy.state.inputs import SpikeTime, PoissonSpike, PoissonEncoder, PoissonInput, poisson_input
+from brainpy.state.inputs import (SectionInput, ConstantInput, StepInput, RampInput,
+                                  SinusoidalInput, OUProcessInput, WienerProcessInput)
+from brainpy.state.izhikevich import Izhikevich, IzhikevichRef
+from brainpy.state.lif import (
+    IF, LIF, LIFRef, ALIF,
+    ExpIF, ExpIFRef,
+    AdExIF, AdExIFRef,
+    QuaIF, AdQuaIF, AdQuaIFRef,
+    Gif, GifRef,
+    CubaLIF, CobaLIF,
+)
+from brainpy.state.projection import (
+    Projection, AlignPostProj, DeltaProj, CurrentProj,
+    align_pre_projection, align_post_projection,
+)
+from brainpy.state.readout import LeakyRateReadout
+from brainpy.state.reduced import FitzHughNagumo, HindmarshRose
+from brainpy.state.stp import STP, STD
+from brainpy.state.synapse import Alpha, AMPA, GABAa, BioNMDA
+from brainpy.state.synaptic_projection import SymmetryGapJunction, AsymmetryGapJunction
+from brainpy.state.synouts import SynOut, COBA, CUBA, MgBlock
+
+__all__ = [
+    # Base models
+    'Dynamics', 'Neuron', 'Synapse',
+
+    # Neuron models - LIF family
+    'IF', 'LIF', 'LIFRef', 'ALIF',
+    'ExpIF', 'ExpIFRef',
+    'AdExIF', 'AdExIFRef',
+    'QuaIF', 'AdQuaIF', 'AdQuaIFRef',
+    'Gif', 'GifRef',
+    'CubaLIF', 'CobaLIF',
+
+    # Neuron models - Hodgkin-Huxley family
+    'HH', 'MorrisLecar', 'WangBuzsakiHH',
+
+    # Neuron models - Izhikevich family
+    'Izhikevich', 'IzhikevichRef',
+
+    # Neuron models - reduced (FitzHugh-Nagumo, Hindmarsh-Rose)
+    'FitzHughNagumo', 'HindmarshRose',
+
+    # Synapse models
+    'Expon', 'DualExpon',
+    'Alpha', 'AMPA', 'GABAa', 'BioNMDA',
+
+    # Synaptic outputs
+    'SynOut', 'COBA', 'CUBA', 'MgBlock',
+
+    # Short-term plasticity
+    'STP', 'STD',
+
+    # Projections
+    'Projection', 'AlignPostProj', 'DeltaProj', 'CurrentProj',
+    'align_pre_projection', 'align_post_projection',
+    'SymmetryGapJunction', 'AsymmetryGapJunction',
+
+    # Readouts
+    'LeakyRateReadout',
+
+    # Input generators
+    'SpikeTime', 'PoissonSpike', 'PoissonEncoder', 'PoissonInput', 'poisson_input',
+    'SectionInput', 'ConstantInput', 'StepInput', 'RampInput',
+    'SinusoidalInput', 'OUProcessInput', 'WienerProcessInput',
+]