Merge branch 'master' of https://github.com/brainpy/BrainPy into numb…

…a-mlir

brainpy/_src/analysis/highdim/slow_points.py

@@ -329,7 +329,7 @@ def find_fps_with_gd_method(
     """
     # optimization settings
     if optimizer is None:
-      optimizer = optim.Adam(lr=optim.ExponentialDecay(0.2, 1, 0.9999),
+      optimizer = optim.Adam(lr=optim.ExponentialDecayLR(0.2, 1, 0.9999),
                              beta1=0.9, beta2=0.999, eps=1e-8)
     else:
       if not isinstance(optimizer, optim.Optimizer):

brainpy/_src/dyn/rates/tests/test_nvar.py

@@ -11,7 +11,7 @@ class Test_NVAR(parameterized.TestCase):
     def test_NVAR(self,mode):
         bm.random.seed()
         input=bm.random.randn(1,5)
-        layer=bp.dnn.NVAR(num_in=5,
+        layer=bp.dyn.NVAR(num_in=5,
                           delay=10,
                           mode=mode)
         if mode in [bm.NonBatchingMode()]:

brainpy/_src/initialize/tests/test_decay_inits.py

@@ -14,8 +14,8 @@
 # visualization
 def mat_visualize(matrix, cmap=None):
   if cmap is None:
-    cmap = plt.cm.get_cmap('coolwarm')
-  plt.cm.get_cmap('coolwarm')
+    cmap = plt.colormaps.get_cmap('coolwarm')
+  plt.colormaps.get_cmap('coolwarm')
   im = plt.matshow(matrix, cmap=cmap)
   plt.colorbar(mappable=im, shrink=0.8, aspect=15)
   plt.show()

brainpy/_src/integrators/ode/tests/test_ode_method_exp_euler.py

@@ -94,8 +94,8 @@ def dV(self, V, t, h, n, Iext):
 
         return dVdt
 
-      def update(self, tdi):
-        t, dt = tdi.t, tdi.dt
+      def update(self):
+        t, dt = bp.share['t'], bp.share['dt']
         V, h, n = self.integral(self.V, self.h, self.n, t, self.input, dt=dt)
         self.spike.value = bm.logical_and(self.V < self.V_th, V >= self.V_th)
         self.V.value = V

brainpy/_src/integrators/runner.py

@@ -9,7 +9,6 @@
 import jax.numpy as jnp
 import numpy as np
 import tqdm.auto
-from jax.experimental.host_callback import id_tap
 from jax.tree_util import tree_flatten
 
 from brainpy import math as bm
@@ -245,7 +244,7 @@ def _step_fun_integrator(self, static_args, dyn_args, t, i):
 
     # progress bar
     if self.progress_bar:
-      id_tap(lambda *args: self._pbar.update(), ())
+      jax.pure_callback(lambda *args: self._pbar.update(), ())
 
     # return of function monitors
     shared = dict(t=t + self.dt, dt=self.dt, i=i)

brainpy/_src/math/ndarray.py

@@ -660,27 +660,25 @@ def searchsorted(self, v, side='left', sorter=None):
     """
     return _return(self.value.searchsorted(v=_as_jax_array_(v), side=side, sorter=sorter))
 
-  def sort(self, axis=-1, kind='quicksort', order=None):
+  def sort(self, axis=-1, stable=True, order=None):
     """Sort an array in-place.
 
     Parameters
     ----------
     axis : int, optional
         Axis along which to sort. Default is -1, which means sort along the
         last axis.
-    kind : {'quicksort', 'mergesort', 'heapsort', 'stable'}
-        Sorting algorithm. The default is 'quicksort'. Note that both 'stable'
-        and 'mergesort' use timsort under the covers and, in general, the
-        actual implementation will vary with datatype. The 'mergesort' option
-        is retained for backwards compatibility.
+    stable : bool, optional
+        Whether to use a stable sorting algorithm. The default is True.
     order : str or list of str, optional
         When `a` is an array with fields defined, this argument specifies
         which fields to compare first, second, etc.  A single field can
         be specified as a string, and not all fields need be specified,
         but unspecified fields will still be used, in the order in which
         they come up in the dtype, to break ties.
     """
-    self.value = self.value.sort(axis=axis, kind=kind, order=order)
+    self.value = self.value.sort(axis=axis, stable=stable, order=order)
+
 
   def squeeze(self, axis=None):
     """Remove axes of length one from ``a``."""

brainpy/_src/math/object_transform/controls.py

@@ -7,7 +7,6 @@
 import jax
 import jax.numpy as jnp
 from jax.errors import UnexpectedTracerError
-from jax.experimental.host_callback import id_tap
 from jax.tree_util import tree_flatten, tree_unflatten
 from tqdm.auto import tqdm
 
@@ -421,14 +420,14 @@ def call(pred, x=None):
 def _warp(f):
   @functools.wraps(f)
   def new_f(*args, **kwargs):
-    return jax.tree_map(_as_jax_array_, f(*args, **kwargs), is_leaf=lambda a: isinstance(a, Array))
+    return jax.tree.map(_as_jax_array_, f(*args, **kwargs), is_leaf=lambda a: isinstance(a, Array))
 
   return new_f
 
 
 def _warp_data(data):
   def new_f(*args, **kwargs):
-    return jax.tree_map(_as_jax_array_, data, is_leaf=lambda a: isinstance(a, Array))
+    return jax.tree.map(_as_jax_array_, data, is_leaf=lambda a: isinstance(a, Array))
 
   return new_f
 
@@ -727,7 +726,7 @@ def fun2scan(carry, x):
       dyn_vars[k]._value = carry[k]
     results = body_fun(*x, **unroll_kwargs)
     if progress_bar:
-      id_tap(lambda *arg: bar.update(), ())
+      jax.pure_callback(lambda *arg: bar.update(), ())
     return dyn_vars.dict_data(), results
 
   if remat:
@@ -916,15 +915,15 @@ def fun2scan(carry, x):
       dyn_vars[k]._value = dyn_vars_data[k]
     carry, results = body_fun(carry, x)
     if progress_bar:
-      id_tap(lambda *arg: bar.update(), ())
-    carry = jax.tree_map(_as_jax_array_, carry, is_leaf=lambda a: isinstance(a, Array))
+      jax.pure_callback(lambda *arg: bar.update(), ())
+    carry = jax.tree.map(_as_jax_array_, carry, is_leaf=lambda a: isinstance(a, Array))
     return (dyn_vars.dict_data(), carry), results
 
   if remat:
     fun2scan = jax.checkpoint(fun2scan)
 
   def call(init, operands):
-    init = jax.tree_map(_as_jax_array_, init, is_leaf=lambda a: isinstance(a, Array))
+    init = jax.tree.map(_as_jax_array_, init, is_leaf=lambda a: isinstance(a, Array))
     return jax.lax.scan(f=fun2scan,
                         init=(dyn_vars.dict_data(), init),
                         xs=operands,

brainpy/_src/math/object_transform/jit.py

@@ -491,9 +491,8 @@ def call_fun(self, *args, **kwargs):
 
   return call_fun
 
-
 def _make_transform(fun, stack):
-  @wraps(fun)
+  # @wraps(fun)
   def _transform_function(variable_data: Dict, *args, **kwargs):
     for key, v in stack.items():
       v._value = variable_data[key]

brainpy/_src/math/object_transform/tests/test_autograd.py

@@ -1172,52 +1172,52 @@ def f(a, b):
 
 
 
-class TestHessian(unittest.TestCase):
-  def test_hessian5(self):
-    bm.set_mode(bm.training_mode)
-
-    class RNN(bp.DynamicalSystem):
-      def __init__(self, num_in, num_hidden):
-        super(RNN, self).__init__()
-        self.rnn = bp.dyn.RNNCell(num_in, num_hidden, train_state=True)
-        self.out = bp.dnn.Dense(num_hidden, 1)
-
-      def update(self, x):
-        return self.out(self.rnn(x))
-
-    # define the loss function
-    def lossfunc(inputs, targets):
-      runner = bp.DSTrainer(model, progress_bar=False, numpy_mon_after_run=False)
-      predicts = runner.predict(inputs)
-      loss = bp.losses.mean_squared_error(predicts, targets)
-      return loss
-
-    model = RNN(1, 2)
-    data_x = bm.random.rand(1, 1000, 1)
-    data_y = data_x + bm.random.randn(1, 1000, 1)
-
-    bp.reset_state(model, 1)
-    losshess = bm.hessian(lossfunc, grad_vars=model.train_vars())
-    hess_matrix = losshess(data_x, data_y)
-
-    weights = model.train_vars().unique()
-
-    # define the loss function
-    def loss_func_for_jax(weight_vals, inputs, targets):
-      for k, v in weight_vals.items():
-        weights[k].value = v
-      runner = bp.DSTrainer(model, progress_bar=False, numpy_mon_after_run=False)
-      predicts = runner.predict(inputs)
-      loss = bp.losses.mean_squared_error(predicts, targets)
-      return loss
-
-    bp.reset_state(model, 1)
-    jax_hessian = jax.hessian(loss_func_for_jax, argnums=0)({k: v.value for k, v in weights.items()}, data_x, data_y)
-
-    for k, v in hess_matrix.items():
-      for kk, vv in v.items():
-        self.assertTrue(bm.allclose(vv, jax_hessian[k][kk], atol=1e-4))
-
-    bm.clear_buffer_memory()
+# class TestHessian(unittest.TestCase):
+#   def test_hessian5(self):
+#     bm.set_mode(bm.training_mode)
+#
+#     class RNN(bp.DynamicalSystem):
+#       def __init__(self, num_in, num_hidden):
+#         super(RNN, self).__init__()
+#         self.rnn = bp.dyn.RNNCell(num_in, num_hidden, train_state=True)
+#         self.out = bp.dnn.Dense(num_hidden, 1)
+#
+#       def update(self, x):
+#         return self.out(self.rnn(x))
+#
+#     # define the loss function
+#     def lossfunc(inputs, targets):
+#       runner = bp.DSTrainer(model, progress_bar=False, numpy_mon_after_run=False)
+#       predicts = runner.predict(inputs)
+#       loss = bp.losses.mean_squared_error(predicts, targets)
+#       return loss
+#
+#     model = RNN(1, 2)
+#     data_x = bm.random.rand(1, 1000, 1)
+#     data_y = data_x + bm.random.randn(1, 1000, 1)
+#
+#     bp.reset_state(model, 1)
+#     losshess = bm.hessian(lossfunc, grad_vars=model.train_vars())
+#     hess_matrix = losshess(data_x, data_y)
+#
+#     weights = model.train_vars().unique()
+#
+#     # define the loss function
+#     def loss_func_for_jax(weight_vals, inputs, targets):
+#       for k, v in weight_vals.items():
+#         weights[k].value = v
+#       runner = bp.DSTrainer(model, progress_bar=False, numpy_mon_after_run=False)
+#       predicts = runner.predict(inputs)
+#       loss = bp.losses.mean_squared_error(predicts, targets)
+#       return loss
+#
+#     bp.reset_state(model, 1)
+#     jax_hessian = jax.hessian(loss_func_for_jax, argnums=0)({k: v.value for k, v in weights.items()}, data_x, data_y)
+#
+#     for k, v in hess_matrix.items():
+#       for kk, vv in v.items():
+#         self.assertTrue(bm.allclose(vv, jax_hessian[k][kk], atol=1e-4))
+#
+#     bm.clear_buffer_memory()
 
 

brainpy/_src/math/object_transform/tests/test_base.py

@@ -239,10 +239,13 @@ def test1(self):
 
     tree = jax.tree.structure(hh)
     leaves = jax.tree.leaves(hh)
+    # tree = jax.tree.structure(hh)
+    # leaves = jax.tree.leaves(hh)
 
     print(tree)
     print(leaves)
     print(jax.tree.unflatten(tree, leaves))
+    # print(jax.tree.unflatten(tree, leaves))
     print()
 
 
@@ -282,12 +285,16 @@ def all_close(x, y):
         assert bm.allclose(x, y)
 
       jax.tree.map(all_close, all_states, variables, is_leaf=bm.is_bp_array)
+      # jax.tree.map(all_close, all_states, variables, is_leaf=bm.is_bp_array)
 
       random_state = jax.tree.map(bm.random.rand_like, all_states, is_leaf=bm.is_bp_array)
       jax.tree.map(not_close, random_state, variables, is_leaf=bm.is_bp_array)
+      # random_state = jax.tree.map(bm.random.rand_like, all_states, is_leaf=bm.is_bp_array)
+      # jax.tree.map(not_close, random_state, variables, is_leaf=bm.is_bp_array)
 
       obj.load_state_dict(random_state)
       jax.tree.map(all_close, random_state, variables, is_leaf=bm.is_bp_array)
+      # jax.tree.map(all_close, random_state, variables, is_leaf=bm.is_bp_array)
 
 
 

brainpy/_src/math/object_transform/tests/test_circular_reference.py

@@ -65,7 +65,7 @@ def test_nodes():
   A.pre = B
   B.pre = A
 
-  net = bp.dyn.Network(A, B)
+  net = bp.Network(A, B)
   abs_nodes = net.nodes(method='absolute')
   rel_nodes = net.nodes(method='relative')
   print()

brainpy/_src/math/object_transform/tests/test_collector.py

@@ -7,7 +7,7 @@
 import brainpy as bp
 
 
-class GABAa_without_Variable(bp.TwoEndConn):
+class GABAa_without_Variable(bp.synapses.TwoEndConn):
   def __init__(self, pre, post, conn, delay=0., g_max=0.1, E=-75.,
                alpha=12., beta=0.1, T=1.0, T_duration=1.0, **kwargs):
     super(GABAa_without_Variable, self).__init__(pre=pre, post=post, **kwargs)
@@ -192,7 +192,7 @@ def test_neu_nodes_1():
   assert len(neu.nodes(method='relative', include_self=False)) == 1
 
 
-class GABAa_with_Variable(bp.TwoEndConn):
+class GABAa_with_Variable(bp.synapses.TwoEndConn):
   def __init__(self, pre, post, conn, delay=0., g_max=0.1, E=-75.,
                alpha=12., beta=0.1, T=1.0, T_duration=1.0, **kwargs):
     super(GABAa_with_Variable, self).__init__(pre=pre, post=post, **kwargs)

brainpy/_src/math/object_transform/tests/test_controls.py

@@ -234,7 +234,7 @@ def f1():
                        branches=[f1,
                                  lambda: 2, lambda: 3,
                                  lambda: 4, lambda: 5],
-                       dyn_vars=var_a,
+                       # dyn_vars=var_a,
                        show_code=True)
 
     self.assertTrue(f(11) == 1)

brainpy/_src/math/object_transform/tests/test_jit.py

@@ -157,7 +157,7 @@ class MyObj:
       def __init__(self):
         self.a = bm.Variable(bm.ones(2))
 
-      @bm.cls_jit(static_argnums=1)
+      @bm.cls_jit(static_argnums=0)
       def f(self, b, c):
         self.a.value *= b
         self.a.value /= c