refactor(docs): clean up import statements and improve code formatting

Author: oujago

brainpy/__init__.py

@@ -82,7 +82,7 @@ def __dir__():
 _deprecated_modules = [
     'math', 'check', 'tools', 'connect', 'initialize', 'init', 'conn',
     'optim', 'losses', 'measure', 'inputs', 'encoding', 'checkpoints',
-    'mixin', 'algorithms', 'integrators', 'ode', 'sde', 'fde',
+    'algorithms', 'integrators', 'ode', 'sde', 'fde',
     'dnn', 'layers', 'dyn', 'running', 'train', 'analysis',
     'channels', 'neurons', 'rates', 'synapses', 'synouts', 'synplast',
     'visualization', 'visualize', 'types', 'modes', 'context',

brainpy/_stp.py

@@ -209,7 +209,6 @@ def __init__(
         self,
         in_size: Size,
         name: Optional[str] = None,
-        # synapse parameters
         tau: ArrayLike = 200. * u.ms,
         U: ArrayLike = 0.07,
     ):
@@ -220,7 +219,9 @@ def __init__(
         self.U = braintools.init.param(U, self.varshape)
 
     def init_state(self, batch_size: int = None, **kwargs):
-        self.x = brainstate.HiddenState(braintools.init.param(braintools.init.Constant(1.), self.varshape, batch_size))
+        self.x = brainstate.HiddenState(
+            braintools.init.param(braintools.init.Constant(1.), self.varshape, batch_size)
+        )
 
     def reset_state(self, batch_size: int = None, **kwargs):
         self.x.value = braintools.init.param(braintools.init.Constant(1.), self.varshape, batch_size)

docs/apis.rst

@@ -0,0 +1,102 @@
+API Reference
+=============
+
+This page provides a comprehensive reference for all BrainPy APIs.
+
+.. currentmodule:: brainpy
+.. automodule:: brainpy
+
+
+
+Neuron Models
+-------------
+
+.. autosummary::
+   :toctree: generated/
+   :nosignatures:
+
+   Neuron
+   LIF
+   LIFRef
+   ALIF
+   Izhikevich
+   IF
+   ExpIF
+   AdExIF
+
+
+Synapse Models
+--------------
+
+.. autosummary::
+   :toctree: generated/
+   :nosignatures:
+
+   Synapse
+   Delta
+   Exponential
+   DualExponential
+   Alpha
+   NMDA
+   AMPA
+   GABAa
+
+
+Short-Term Plasticity
+---------------------
+
+.. autosummary::
+   :toctree: generated/
+   :nosignatures:
+
+   STP
+   STD
+   STF
+
+
+Synaptic Output
+---------------
+
+.. autosummary::
+   :toctree: generated/
+   :nosignatures:
+
+   CUBA
+   COBA
+   MgBlock
+
+
+Projection
+----------
+
+.. autosummary::
+   :toctree: generated/
+   :nosignatures:
+
+   Projection
+   FullProjDelta
+   FullProjAlignPostDelta
+
+
+Readout
+-------
+
+.. autosummary::
+   :toctree: generated/
+   :nosignatures:
+
+   Readout
+   Dense
+   Linear
+
+
+Input Generators
+----------------
+
+.. autosummary::
+   :toctree: generated/
+   :nosignatures:
+
+   spike_input
+   latency_input
+

docs/conf.py

@@ -17,10 +17,11 @@
 
 sys.path.insert(0, os.path.abspath('./'))
 sys.path.insert(0, os.path.abspath('../'))
+sys.path.insert(0, r'D:\codes\projects\brainstate')
 
 import brainpy
-
 shutil.copytree('../images/', './_static/logos/', dirs_exist_ok=True)
+shutil.copyfile('../changelog.md', './changelog.md')
 
 # -- Project information -----------------------------------------------------
 

docs/index.rst

@@ -1,49 +1,10 @@
 ``brainpy`` documentation
 =========================
 
-`brainpy <https://github.com/brainpy/BrainPy>`_
+`brainpy <https://github.com/brainpy/BrainPy>`_ provides a powerful and flexible framework
+for building, simulating, and training spiking neural networks.
 
 
-----
-
-Features
-^^^^^^^^^
-
-.. grid::
-
-
-
-   .. grid-item::
-      :columns: 12 12 12 6
-
-      .. card:: Program Compilation
-         :class-card: sd-border-0
-         :shadow: none
-         :class-title: sd-fs-6
-
-         .. div:: sd-font-normal
-
-            ``BrainState`` supports `program compilation <./apis/compile.html>`__ (such as just-in-time compilation) with its `state-based <./apis/brainstate.html>`__ IR construction.
-
-
-
-   .. grid-item::
-      :columns: 12 12 12 6
-
-      .. card:: Program Augmentation
-         :class-card: sd-border-0
-         :shadow: none
-         :class-title: sd-fs-6
-
-         .. div:: sd-font-normal
-
-            ``BrainState`` supports program `functionality augmentation <./apis/augment.html>`__ (such batching) with its `graph-based <./apis/graph.html>`__ Python objects.
-
-
-
-
-----
-
 
 Installation
 ^^^^^^^^^^^^
@@ -79,6 +40,8 @@ See also the ecosystem
 ``brainpy`` is one part of our `brain simulation ecosystem <https://brainmodeling.readthedocs.io/>`_.
 
 
+
+
 .. toctree::
    :hidden:
    :maxdepth: 1
@@ -97,14 +60,5 @@ See also the ecosystem
    :caption: API Reference
 
    changelog.md
-   apis/brainstate.rst
-   apis/graph.rst
-   apis/transform.rst
-   apis/nn.rst
-   apis/random.rst
-   apis/util.rst
-   apis/surrogate.rst
-   apis/typing.rst
-   apis/mixin.rst
-   apis/environ.rst
+   apis.rst
 

docs_version2/index.rst

@@ -10,6 +10,27 @@ general-purpose Brain Dynamics Programming (BDP).
 
 
 
+.. note::
+
+    From September 2025, BrainPy has been upgraded to version 3.x.
+    To compatible apis within version 2.x. Please change your code:
+
+    .. code-block:: python
+
+       # Old version (v2.x)
+       import brainpy as bp
+       import brainpy.math as bm
+
+    to the new version:
+
+
+    .. code-block:: python
+
+       # New version (v3.x)
+       import brainpy.version2 as bp
+       import brainpy.version2.math as bm
+
+
 
 ----
 

examples/110_Susin_Destexhe_2021_gamma_oscillation_AI.py

@@ -23,12 +23,12 @@
 #  Asynchronous Network
 
 
+import braintools
 import brainunit as u
 import matplotlib.pyplot as plt
 
 import brainpy
 import brainstate
-import braintools
 from Susin_Destexhe_2021_gamma_oscillation import (
     get_inputs, visualize_simulation_results,
     RS_par, FS_par, Ch_par, AdEx
@@ -164,7 +164,8 @@ def simulate_ai_net():
         # simulation
         times = u.math.arange(0. * u.ms, duration, brainstate.environ.get_dt())
         indices = u.math.arange(0, len(times))
-        returns = brainstate.transform.for_loop(net.update, indices, times, varied_rates, pbar=brainstate.transform.ProgressBar(100))
+        returns = brainstate.transform.for_loop(net.update, indices, times, varied_rates,
+                                                pbar=brainstate.transform.ProgressBar(100))
 
         # # spike raster plot
         # spikes = returns['FS.spike']

examples/111_Susin_Destexhe_2021_gamma_oscillation_CHING.py

@@ -182,7 +182,7 @@ def simulate_ching_net():
         times = u.math.arange(0. * u.ms, duration, brainstate.environ.get_dt())
         indices = u.math.arange(0, len(times))
         returns = brainstate.transform.for_loop(net.update, indices, times, varied_rates,
-                                              pbar=brainstate.transform.ProgressBar(100))
+                                                pbar=brainstate.transform.ProgressBar(100))
 
         # visualization
         visualize_simulation_results(

examples/112_Susin_Destexhe_2021_gamma_oscillation_ING.py

@@ -179,7 +179,7 @@ def simulate_ing_net():
         times = u.math.arange(0. * u.ms, duration, brainstate.environ.get_dt())
         indices = u.math.arange(0, len(times))
         returns = brainstate.transform.for_loop(net.update, indices, times, varied_rates,
-                                              pbar=brainstate.transform.ProgressBar(100))
+                                                pbar=brainstate.transform.ProgressBar(100))
 
         # visualization
         visualize_simulation_results(

examples/113_Susin_Destexhe_2021_gamma_oscillation_PING.py

@@ -128,7 +128,7 @@ def simulate_ping_net():
         times = u.math.arange(0. * u.ms, duration, brainstate.environ.get_dt())
         indices = u.math.arange(0, len(times))
         returns = brainstate.transform.for_loop(net.update, indices, times, varied_rates,
-                                              pbar=brainstate.transform.ProgressBar(100))
+                                                pbar=brainstate.transform.ProgressBar(100))
 
         # visualization
         visualize_simulation_results(