Fix surrogate gradient function and numpy 2.0 compatibility (#679)

* fix surrogate batching * fix numpy 2.0 compatible issue * fix numpy 2.0 compatible issue * updates * fix numpy2.0 compatible issue * Skip the operators tests for GitHub action server * Update * Update * Update * Update test_taichi_based.py * Update test_get_weight_matrix.py --------- Co-authored-by: He Sichao <[email protected]>
brainpy · Jun 18, 2024 · 5f33a66 · 5f33a66
1 parent b9461eb
commit 5f33a66
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Showing 19 changed files with 124 additions and 88 deletions.
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -51,7 +51,7 @@ jobs:
       - name: Test with pytest
         run: |
           cd brainpy
-          pytest _src/
+          export IS_GITHUB_ACTIONS=1 && pytest _src/
 
 
   test_macos:
@@ -82,7 +82,7 @@ jobs:
       - name: Test with pytest
         run: |
           cd brainpy
-          pytest _src/
+          export IS_GITHUB_ACTIONS=1 && pytest _src/
 
 
   test_windows:
@@ -113,4 +113,4 @@ jobs:
       - name: Test with pytest
         run: |
           cd brainpy
-          pytest _src/ -p no:faulthandler
+          set IS_GITHUB_ACTIONS=1 && pytest _src/
diff --git a/brainpy/_src/losses/comparison.py b/brainpy/_src/losses/comparison.py
@@ -376,7 +376,8 @@ def update(self, input, target):
 
 
 def nll_loss(input, target, reduction: str = 'mean'):
-  r"""The negative log likelihood loss.
+  r"""
+  The negative log likelihood loss.
 
   The negative log likelihood loss. It is useful to train a classification
   problem with `C` classes.

diff --git a/brainpy/_src/math/compat_numpy.py b/brainpy/_src/math/compat_numpy.py
@@ -10,7 +10,6 @@
 from .interoperability import *
 from .ndarray import Array
 
-
 __all__ = [
   'full', 'full_like', 'eye', 'identity', 'diag', 'tri', 'tril', 'triu',
   'empty', 'empty_like', 'ones', 'ones_like', 'zeros', 'zeros_like',
@@ -92,9 +91,8 @@
   'ravel_multi_index', 'result_type', 'sort_complex', 'unpackbits', 'delete',
 
   # unique
-  'add_docstring', 'add_newdoc', 'add_newdoc_ufunc', 'array2string', 'asanyarray',
-  'ascontiguousarray', 'asfarray', 'asscalar', 'common_type', 'disp', 'genfromtxt',
-  'loadtxt', 'info', 'issubclass_', 'place', 'polydiv', 'put', 'putmask', 'safe_eval',
+  'asanyarray', 'ascontiguousarray', 'asfarray', 'asscalar', 'common_type', 'genfromtxt',
+  'loadtxt', 'info', 'place', 'polydiv', 'put', 'putmask', 'safe_eval',
   'savetxt', 'savez_compressed', 'show_config', 'typename', 'copyto', 'matrix', 'asmatrix', 'mat',
 
 ]
@@ -204,11 +202,12 @@ def ascontiguousarray(a, dtype=None, order=None):
   return asarray(a, dtype=dtype, order=order)
 
 
-def asfarray(a, dtype=np.float_):
+def asfarray(a, dtype=None):
   if not np.issubdtype(dtype, np.inexact):
-    dtype = np.float_
+    dtype = np.float64
   return asarray(a, dtype=dtype)
 
+
 def in1d(ar1, ar2, assume_unique: bool = False, invert: bool = False) -> Array:
   del assume_unique
   ar1_flat = ravel(ar1)
@@ -227,6 +226,7 @@ def in1d(ar1, ar2, assume_unique: bool = False, invert: bool = False) -> Array:
   else:
     return asarray((ar1_flat[:, None] == ar2_flat[None, :]).any(-1))
 
+
 # Others
 # ------
 meshgrid = _compatible_with_brainpy_array(jnp.meshgrid)
@@ -454,7 +454,6 @@ def msort(a):
 sometrue = any
 
 
-
 def shape(a):
   """
   Return the shape of an array.
@@ -648,7 +647,6 @@ def size(a, axis=None):
 finfo = jnp.finfo
 iinfo = jnp.iinfo
 
-
 can_cast = _compatible_with_brainpy_array(jnp.can_cast)
 choose = _compatible_with_brainpy_array(jnp.choose)
 copy = _compatible_with_brainpy_array(jnp.copy)
@@ -678,23 +676,6 @@ def size(a, axis=None):
 # Unique APIs
 # -----------
 
-add_docstring = np.add_docstring
-add_newdoc = np.add_newdoc
-add_newdoc_ufunc = np.add_newdoc_ufunc
-
-
-def array2string(a, max_line_width=None, precision=None,
-                 suppress_small=None, separator=' ', prefix="",
-                 style=np._NoValue, formatter=None, threshold=None,
-                 edgeitems=None, sign=None, floatmode=None, suffix="",
-                 legacy=None):
-  a = as_numpy(a)
-  return array2string(a, max_line_width=max_line_width, precision=precision,
-                      suppress_small=suppress_small, separator=separator, prefix=prefix,
-                      style=style, formatter=formatter, threshold=threshold,
-                      edgeitems=edgeitems, sign=sign, floatmode=floatmode, suffix=suffix,
-                      legacy=legacy)
-
 
 def asscalar(a):
   return a.item()
@@ -731,13 +712,9 @@ def common_type(*arrays):
     return array_type[0][precision]
 
 
-disp = np.disp
-
 genfromtxt = lambda *args, **kwargs: asarray(np.genfromtxt(*args, **kwargs))
 loadtxt = lambda *args, **kwargs: asarray(np.loadtxt(*args, **kwargs))
-
 info = np.info
-issubclass_ = np.issubclass_
 
 
 def place(arr, mask, vals):

diff --git a/brainpy/_src/math/event/tests/test_event_csrmm.py b/brainpy/_src/math/event/tests/test_event_csrmm.py
@@ -1,15 +1,27 @@
 # -*- coding: utf-8 -*-
-
+import os
 from functools import partial
 
 import jax
+import pytest
 from absl.testing import parameterized
 
 import brainpy as bp
 import brainpy.math as bm
 
 # bm.set_platform('gpu')
 
+import platform
+force_test = False  # turn on to force test on windows locally
+if platform.system() == 'Windows' and not force_test:
+  pytest.skip('skip windows', allow_module_level=True)
+
+
+# Skip the test in Github Actions
+IS_GITHUB_ACTIONS = os.getenv('IS_GITHUB_ACTIONS', '0')
+if IS_GITHUB_ACTIONS == '1':
+  pytest.skip('Skip the test in Github Actions', allow_module_level=True)
+
 seed = 1234
 
 

diff --git a/brainpy/_src/math/event/tests/test_event_csrmv.py b/brainpy/_src/math/event/tests/test_event_csrmv.py
@@ -1,6 +1,5 @@
 # -*- coding: utf-8 -*-
-
-
+import os
 from functools import partial
 
 import jax
@@ -19,6 +18,10 @@
 if platform.system() == 'Windows' and not force_test:
   pytest.skip('skip windows', allow_module_level=True)
 
+# Skip the test in Github Actions
+IS_GITHUB_ACTIONS = os.getenv('IS_GITHUB_ACTIONS', '0')
+if IS_GITHUB_ACTIONS == '1':
+  pytest.skip('Skip the test in Github Actions', allow_module_level=True)
 
 seed = 1234
 

diff --git a/brainpy/_src/math/jitconn/tests/test_event_matvec.py b/brainpy/_src/math/jitconn/tests/test_event_matvec.py
@@ -1,4 +1,5 @@
 # -*- coding: utf-8 -*-
+import os
 
 import jax
 import jax.numpy as jnp
@@ -16,6 +17,10 @@
 if platform.system() == 'Windows' and not force_test:
   pytest.skip('skip windows', allow_module_level=True)
 
+# Skip the test in Github Actions
+IS_GITHUB_ACTIONS = os.getenv('IS_GITHUB_ACTIONS', '0')
+if IS_GITHUB_ACTIONS == '1':
+  pytest.skip('Skip the test in Github Actions', allow_module_level=True)
 
 shapes = [(100, 200), (1000, 10)]
 

diff --git a/brainpy/_src/math/jitconn/tests/test_get_weight_matrix.py b/brainpy/_src/math/jitconn/tests/test_get_weight_matrix.py
@@ -1,4 +1,6 @@
 # -*- coding: utf-8 -*-
+import os
+
 import jax.numpy as jnp
 import pytest
 from absl.testing import parameterized
@@ -12,8 +14,14 @@
 import platform
 
 force_test = False  # turn on to force test on windows locally
-# if platform.system() == 'Windows' and not force_test:
-#   pytest.skip('skip windows', allow_module_level=True)
+if platform.system() == 'Windows' and not force_test:
+  pytest.skip('skip windows', allow_module_level=True)
+
+# Skip the test in Github Actions
+IS_GITHUB_ACTIONS = os.getenv('IS_GITHUB_ACTIONS', '0')
+if IS_GITHUB_ACTIONS == '1':
+  pytest.skip('Skip the test in Github Actions', allow_module_level=True)
+
 
 shapes = [
   (2, 2),

diff --git a/brainpy/_src/math/jitconn/tests/test_matvec.py b/brainpy/_src/math/jitconn/tests/test_matvec.py
@@ -1,4 +1,5 @@
 # -*- coding: utf-8 -*-
+import os
 
 import jax
 import jax.numpy as jnp
@@ -16,6 +17,10 @@
 if platform.system() == 'Windows' and not force_test:
   pytest.skip('skip windows', allow_module_level=True)
 
+# Skip the test in Github Actions
+IS_GITHUB_ACTIONS = os.getenv('IS_GITHUB_ACTIONS', '0')
+if IS_GITHUB_ACTIONS == '1':
+  pytest.skip('Skip the test in Github Actions', allow_module_level=True)
 
 shapes = [(100, 200), (1000, 10)]
 

diff --git a/brainpy/_src/math/op_register/tests/test_taichi_based.py b/brainpy/_src/math/op_register/tests/test_taichi_based.py
@@ -5,6 +5,11 @@
 import brainpy.math as bm
 from brainpy._src.dependency_check import import_taichi
 
+import platform
+force_test = False  # turn on to force test on windows locally
+if platform.system() == 'Windows' and not force_test:
+  pytest.skip('skip windows', allow_module_level=True)
+
 ti = import_taichi(error_if_not_found=False)
 if ti is None:
   pytest.skip('no taichi', allow_module_level=True)

diff --git a/brainpy/_src/math/sparse/tests/test_csrmm.py b/brainpy/_src/math/sparse/tests/test_csrmm.py
@@ -1,15 +1,28 @@
 # -*- coding: utf-8 -*-
 
+
+import os
 from functools import partial
 
 import jax
+import pytest
 from absl.testing import parameterized
 
 import brainpy as bp
 import brainpy.math as bm
 
 # bm.set_platform('gpu')
 
+import platform
+force_test = False  # turn on to force test on windows locally
+if platform.system() == 'Windows' and not force_test:
+  pytest.skip('skip windows', allow_module_level=True)
+
+# Skip the test in Github Actions
+IS_GITHUB_ACTIONS = os.getenv('IS_GITHUB_ACTIONS', '0')
+if IS_GITHUB_ACTIONS == '1':
+  pytest.skip('Skip the test in Github Actions', allow_module_level=True)
+
 seed = 1234
 
 
@@ -133,7 +146,8 @@ def test_homo_grad(self, transpose, shape, homo_data):
                         argnums=0)
     r1 = dense_f1(homo_data)
     r2 = jax.grad(sum_op(bm.sparse.csrmm))(
-      bm.asarray([homo_data]), indices, indptr, matrix, shape=(shape[1], shape[0]) if transpose else (shape[0], shape[1]),
+      bm.asarray([homo_data]), indices, indptr, matrix,
+      shape=(shape[1], shape[0]) if transpose else (shape[0], shape[1]),
       transpose=transpose)
 
     self.assertTrue(bm.allclose(r1, r2))

diff --git a/brainpy/_src/math/sparse/tests/test_csrmv.py b/brainpy/_src/math/sparse/tests/test_csrmv.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-
+import os
 from functools import partial
 
 import jax
@@ -17,6 +17,10 @@
 if platform.system() == 'Windows' and not force_test:
   pytest.skip('skip windows', allow_module_level=True)
 
+# Skip the test in Github Actions
+IS_GITHUB_ACTIONS = os.getenv('IS_GITHUB_ACTIONS', '0')
+if IS_GITHUB_ACTIONS == '1':
+  pytest.skip('Skip the test in Github Actions', allow_module_level=True)
 
 seed = 1234
 

diff --git a/brainpy/_src/math/surrogate/__init__.py b/brainpy/_src/math/surrogate/__init__.py
@@ -1,6 +1,5 @@
 # -*- coding: utf-8 -*-
 
 
-from .base import *
 from ._one_input_new import *
 from ._two_inputs import *
diff --git a/brainpy/_src/math/surrogate/_one_input.py b/brainpy/_src/math/surrogate/_one_input.py
@@ -8,7 +8,6 @@
 
 from brainpy._src.math.interoperability import as_jax
 from brainpy._src.math.ndarray import Array
-from .base import Surrogate
 
 __all__ = [
   'sigmoid',
@@ -32,6 +31,16 @@
 ]
 
 
+class Surrogate(object):
+  """The base surrograte gradient function."""
+
+  def __call__(self, *args, **kwargs):
+    raise NotImplementedError
+
+  def __repr__(self):
+    return f'{self.__class__.__name__}()'
+
+
 class _OneInpSurrogate(Surrogate):
   def __init__(self, forward_use_surrogate=False):
     self.forward_use_surrogate = forward_use_surrogate

diff --git a/brainpy/_src/math/surrogate/_one_input_new.py b/brainpy/_src/math/surrogate/_one_input_new.py
@@ -12,6 +12,7 @@
 from brainpy._src.math.ndarray import Array
 
 __all__ = [
+  'Surrogate',
   'Sigmoid',
   'sigmoid',
   'PiecewiseQuadratic',
@@ -61,7 +62,7 @@ def _heaviside_imp(x, dx):
 
 
 def _heaviside_batching(args, axes):
-  return heaviside_p.bind(*args), axes
+  return heaviside_p.bind(*args), [axes[0]]
 
 
 def _heaviside_jvp(primals, tangents):

diff --git a/brainpy/_src/math/surrogate/base.py b/brainpy/_src/math/surrogate/base.py
diff --git a/brainpy/math/compat_numpy.py b/brainpy/math/compat_numpy.py
@@ -327,20 +327,14 @@
   sort_complex as sort_complex,
   unpackbits as unpackbits,
   delete as delete,
-  add_docstring as add_docstring,
-  add_newdoc as add_newdoc,
-  add_newdoc_ufunc as add_newdoc_ufunc,
-  array2string as array2string,
   asanyarray as asanyarray,
   ascontiguousarray as ascontiguousarray,
   asfarray as asfarray,
   asscalar as asscalar,
   common_type as common_type,
-  disp as disp,
   genfromtxt as genfromtxt,
   loadtxt as loadtxt,
   info as info,
-  issubclass_ as issubclass_,
   place as place,
   polydiv as polydiv,
   put as put,