Updates (#315)

Updates (#315)

.gitignore

@@ -3,7 +3,7 @@ publishment.md
 .vscode
 io_test_tmp*
 
-brainpy/base/tests/io_test_tmp*
+brainpy/math/brainpy_object/tests/io_test_tmp*
 
 development
 
@@ -217,3 +217,7 @@ cython_debug/
 /docs/apis/simulation/generated/
 !/brainpy/dyn/tests/data/
 /examples/dynamics_simulation/data/
+/examples/training_snn_models/logs/T100_b64_lr0.001/
+/examples/training_snn_models/logs/
+/examples/training_snn_models/data/
+/docs/tutorial_advanced/data/

brainpy/__init__.py

@@ -6,22 +6,8 @@
 # fundamental modules
 from . import errors, check, tools
 
-# "base" module
-from . import base
-from .base import (
-  # base class
-  Base,
-  BrainPyObject,
-
-  # collector
-  Collector,
-  ArrayCollector,
-  TensorCollector,
-)
-
 # math foundation
 from . import math
-from . import modes
 
 # toolboxes
 from . import (
@@ -69,7 +55,7 @@
   synouts,  # synaptic output
   synplast,  # synaptic plasticity
 
-  # base classes
+  # brainpy_object classes
   DynamicalSystem,
   Container,
   Sequential,
@@ -113,9 +99,7 @@
 
 # running
 from . import running
-from .running import (
-  Runner
-)
+from .running import (Runner)
 
 # "visualization" module, will be removed soon
 from .visualization import visualize
@@ -124,3 +108,15 @@
 conn = connect
 init = initialize
 optim = optimizers
+
+from . import experimental
+
+
+# deprecated
+from . import base
+# use ``brainpy.math.*`` instead
+from brainpy.math.object_transform.base_object import (Base, BrainPyObject,)
+# use ``brainpy.math.*`` instead
+from brainpy.math.object_transform.collector import (Collector, ArrayCollector, TensorCollector,)
+# use ``brainpy.math.*`` instead
+from . import modes

brainpy/algorithms/offline.py

@@ -6,14 +6,13 @@
 from jax.lax import while_loop
 
 import brainpy.math as bm
-from brainpy.base import BrainPyObject
 from brainpy.types import ArrayType
 from .utils import (Sigmoid,
                     Regularization, L1Regularization, L1L2Regularization, L2Regularization,
                     polynomial_features, normalize)
 
 __all__ = [
-  # base class for offline training algorithm
+  # brainpy_object class for offline training algorithm
   'OfflineAlgorithm',
 
   # training methods
@@ -33,7 +32,7 @@
 name2func = dict()
 
 
-class OfflineAlgorithm(BrainPyObject):
+class OfflineAlgorithm(bm.BrainPyObject):
   """Base class for offline training algorithm."""
 
   def __init__(self, name=None):

brainpy/algorithms/online.py

@@ -1,12 +1,11 @@
 # -*- coding: utf-8 -*-
 
 import brainpy.math as bm
-from brainpy.base import BrainPyObject
 from jax import vmap
 import jax.numpy as jnp
 
 __all__ = [
-  # base class
+  # brainpy_object class
   'OnlineAlgorithm',
 
   # online learning algorithms
@@ -21,7 +20,7 @@
 name2func = dict()
 
 
-class OnlineAlgorithm(BrainPyObject):
+class OnlineAlgorithm(bm.BrainPyObject):
   """Base class for online training algorithm."""
 
   def __init__(self, name=None):

brainpy/analysis/highdim/slow_points.py

@@ -13,7 +13,6 @@
 import brainpy.math as bm
 from brainpy import optimizers as optim, losses
 from brainpy.analysis import utils, base, constants
-from brainpy.base import ArrayCollector
 from brainpy.dyn.base import DynamicalSystem
 from brainpy.dyn.runners import check_and_format_inputs, _f_ops
 from brainpy.errors import AnalyzerError, UnsupportedError
@@ -133,11 +132,11 @@ def __init__(
 
     # update function
     if target_vars is None:
-      self.target_vars = ArrayCollector()
+      self.target_vars = bm.ArrayCollector()
     else:
       if not isinstance(target_vars, dict):
         raise TypeError(f'"target_vars" must be a dict but we got {type(target_vars)}')
-      self.target_vars = ArrayCollector(target_vars)
+      self.target_vars = bm.ArrayCollector(target_vars)
     excluded_vars = () if excluded_vars is None else excluded_vars
     if isinstance(excluded_vars, dict):
       excluded_vars = tuple(excluded_vars.values())

brainpy/analysis/lowdim/lowdim_analyzer.py

@@ -12,7 +12,6 @@
 from brainpy import errors, tools
 from brainpy.analysis import constants as C, utils
 from brainpy.analysis.base import DSAnalyzer
-from brainpy.base.collector import Collector
 
 pyplot = None
 
@@ -91,7 +90,7 @@ def __init__(
     if not isinstance(target_vars, dict):
       raise errors.AnalyzerError('"target_vars" must be a dict, with the format of '
                                  '{"var1": (var1_min, var1_max)}.')
-    self.target_vars = Collector(target_vars)
+    self.target_vars = bm.Collector(target_vars)
     self.target_var_names = list(self.target_vars.keys())  # list of target vars
     for key in self.target_vars.keys():
       if key not in self.model.variables:
@@ -110,7 +109,7 @@ def __init__(
     for key in fixed_vars.keys():
       if key not in self.model.variables:
         raise ValueError(f'{key} is not a dynamical variable in {self.model}.')
-    self.fixed_vars = Collector(fixed_vars)
+    self.fixed_vars = bm.Collector(fixed_vars)
 
     # check duplicate
     for key in self.fixed_vars.keys():
@@ -125,7 +124,7 @@ def __init__(
     if not isinstance(pars_update, dict):
       raise errors.AnalyzerError('"pars_update" must be a dict with the format '
                                  'of {"par1": val1, "par2": val2}.')
-    pars_update = Collector(pars_update)
+    pars_update = bm.Collector(pars_update)
     for key in pars_update.keys():
       if key not in self.model.parameters:
         raise errors.AnalyzerError(f'"{key}" is not a valid parameter in "{self.model}" model.')
@@ -144,7 +143,7 @@ def __init__(
         raise errors.AnalyzerError(
           f'The range of parameter {key} is reversed, which means {value[0]} should be smaller than {value[1]}.')
 
-    self.target_pars = Collector(target_pars)
+    self.target_pars = bm.Collector(target_pars)
     self.target_par_names = list(self.target_pars.keys())  # list of target_pars
 
     # check duplicate

brainpy/base/__init__.py

@@ -1,28 +1,14 @@
 # -*- coding: utf-8 -*-
 
 """
-The ``base`` module for whole BrainPy ecosystem.
-
-- This module provides the most fundamental class ``BrainPyObject``,
-  and its associated helper class ``Collector`` and ``ArrayCollector``.
-- For each instance of "BrainPyObject" class, users can retrieve all
-  the variables (or trainable variables), integrators, and nodes.
-- This module also provides a ``FunAsObject`` class to wrap user-defined
-  functions. In each function, maybe several nodes are used, and
-  users can initialize a ``FunAsObject`` by providing the nodes used
-  in the function. Unfortunately, ``FunAsObject`` class does not have
-  the ability to gather nodes automatically.
-- This module provides ``io`` helper functions to help users save/load
-  model states, or share user's customized model with others.
-- This module provides ``naming`` tools to guarantee the unique nameing
-  for each BrainPyObject object.
-
-Details please see the following.
+This module is deprecated since version 2.3.1.
+Please use ``brainpy.math.*`` instead.
 """
 
-from brainpy.base.base import *
-from brainpy.base.collector import *
-from brainpy.base.function import *
-from brainpy.base.io import *
-from brainpy.base.naming import *
+
+from .base import *
+from .collector import *
+from .function import *
+from .io import *
+from .naming import *