diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 4dd94bba..0513b670 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -48,6 +48,8 @@ jobs: if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi pip install -e . - name: Test with pytest + env: + MPLBACKEND: Agg # Use non-interactive backend for matplotlib run: | pytest brainpy/ @@ -77,6 +79,8 @@ jobs: if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi pip install -e . - name: Test with pytest + env: + MPLBACKEND: Agg # Use non-interactive backend for matplotlib run: | pytest brainpy/ @@ -106,5 +110,7 @@ jobs: python -m pip install -r requirements-dev.txt pip install -e . - name: Test with pytest + env: + MPLBACKEND: Agg # Use non-interactive backend for matplotlib run: | pytest brainpy/ diff --git a/brainpy/math/object_transform/__init__.py b/brainpy/math/object_transform/__init__.py index 4002250a..b6fbdd53 100644 --- a/brainpy/math/object_transform/__init__.py +++ b/brainpy/math/object_transform/__init__.py @@ -29,6 +29,8 @@ Details please see the following. """ +from brainstate.transform import ProgressBar + from .autograd import * from .base import * from .collectors import * diff --git a/brainpy/math/object_transform/controls.py b/brainpy/math/object_transform/controls.py index 65131067..c1c75b05 100644 --- a/brainpy/math/object_transform/controls.py +++ b/brainpy/math/object_transform/controls.py @@ -16,6 +16,7 @@ import numbers from typing import Union, Sequence, Any, Dict, Callable, Optional +import jax import jax.numpy as jnp import brainstate @@ -31,6 +32,42 @@ ] +def _convert_progress_bar_to_pbar( + progress_bar: Union[bool, brainstate.transform.ProgressBar, int, None] +) -> Optional[brainstate.transform.ProgressBar]: + """Convert progress_bar parameter to brainstate pbar format. + + Parameters + ---------- + progress_bar : bool, ProgressBar, int, None + The progress_bar parameter value. + + Returns + ------- + pbar : ProgressBar or None + The converted ProgressBar instance or None. + + Raises + ------ + TypeError + If progress_bar is not a valid type. + """ + if progress_bar is False or progress_bar is None: + return None + elif progress_bar is True: + return brainstate.transform.ProgressBar() + elif isinstance(progress_bar, int): + # Support brainstate convention: int means freq parameter + return brainstate.transform.ProgressBar(freq=progress_bar) + elif isinstance(progress_bar, brainstate.transform.ProgressBar): + return progress_bar + else: + raise TypeError( + f"progress_bar must be bool, int, or ProgressBar instance, " + f"got {type(progress_bar).__name__}" + ) + + def cond( pred: bool, true_fun: Union[Callable, jnp.ndarray, Array, numbers.Number], @@ -205,10 +242,8 @@ def for_loop( operands: Any, reverse: bool = False, unroll: int = 1, - remat: bool = False, jit: Optional[bool] = None, - progress_bar: bool = False, - unroll_kwargs: Optional[Dict] = None, + progress_bar: Union[bool, brainstate.transform.ProgressBar, int] = False, ): """``for-loop`` control flow with :py:class:`~.Variable`. @@ -266,10 +301,6 @@ def for_loop( If body function `body_func` receives multiple arguments, `operands` should be a tuple/list whose length is equal to the number of arguments. - remat: bool - Make ``fun`` recompute internal linearization points when differentiated. - jit: bool - Whether to just-in-time compile the function. reverse: bool Optional boolean specifying whether to run the scan iteration forward (the default) or in reverse, equivalent to reversing the leading @@ -278,10 +309,37 @@ def for_loop( Optional positive int specifying, in the underlying operation of the scan primitive, how many scan iterations to unroll within a single iteration of a loop. - progress_bar: bool - Whether we use the progress bar to report the running progress. + jit: bool + Whether to just-in-time compile the function. Set to ``False`` to disable JIT compilation. + progress_bar: bool, ProgressBar, int + Whether and how to display a progress bar during execution: + + - ``False`` (default): No progress bar + - ``True``: Display progress bar with default settings + - ``ProgressBar`` instance: Display progress bar with custom settings + - ``int``: Display progress bar updating every N iterations (treated as freq parameter) + + For advanced customization, create a :py:class:`brainpy.math.ProgressBar` instance: + + >>> import brainpy.math as bm + >>> # Custom update frequency + >>> pbar = bm.ProgressBar(freq=10) + >>> result = bm.for_loop(body_fun, operands, progress_bar=pbar) + >>> + >>> # Custom description + >>> pbar = bm.ProgressBar(desc="Processing data") + >>> result = bm.for_loop(body_fun, operands, progress_bar=pbar) + >>> + >>> # Update exactly 20 times during execution + >>> pbar = bm.ProgressBar(count=20) + >>> result = bm.for_loop(body_fun, operands, progress_bar=pbar) + >>> + >>> # Integer shorthand (equivalent to ProgressBar(freq=10)) + >>> result = bm.for_loop(body_fun, operands, progress_bar=10) .. versionadded:: 2.4.2 + .. versionchanged:: 2.7.3 + Now accepts ProgressBar instances and integers for advanced customization. dyn_vars: Variable, sequence of Variable, dict The instances of :py:class:`~.Variable`. @@ -296,8 +354,6 @@ def for_loop( .. deprecated:: 2.4.0 No longer need to provide ``child_objs``. This function is capable of automatically collecting the children objects used in the target ``func``. - unroll_kwargs: dict - The keyword arguments without unrolling. Returns:: @@ -306,11 +362,45 @@ def for_loop( """ if not isinstance(operands, (tuple, list)): operands = (operands,) - return brainstate.transform.for_loop( - warp_to_no_state_input_output(body_fun), - *operands, reverse=reverse, unroll=unroll, - pbar=brainstate.transform.ProgressBar() if progress_bar else None, - ) + + # Convert progress_bar to pbar format + pbar = _convert_progress_bar_to_pbar(progress_bar) + + # Handle jit parameter + # Note: JAX's scan doesn't support zero-length inputs in disable_jit mode. + # For zero-length inputs, we need to use JIT mode even when jit=False. + should_disable_jit = False + if jit is False: + # Check if any operand has zero length + first_operand = operands[0] + is_zero_length = False + if hasattr(first_operand, 'shape') and len(first_operand.shape) > 0: + is_zero_length = (first_operand.shape[0] == 0) + + if is_zero_length: + # Use JIT mode for zero-length inputs to avoid JAX limitation + import warnings + warnings.warn( + "for_loop with jit=False and zero-length input detected. " + "Using JIT mode to avoid JAX's disable_jit limitation with zero-length scans.", + UserWarning + ) + else: + should_disable_jit = True + + if should_disable_jit: + with jax.disable_jit(): + return brainstate.transform.for_loop( + warp_to_no_state_input_output(body_fun), + *operands, reverse=reverse, unroll=unroll, + pbar=pbar, + ) + else: + return brainstate.transform.for_loop( + warp_to_no_state_input_output(body_fun), + *operands, reverse=reverse, unroll=unroll, + pbar=pbar, + ) def scan( @@ -320,7 +410,7 @@ def scan( reverse: bool = False, unroll: int = 1, remat: bool = False, - progress_bar: bool = False, + progress_bar: Union[bool, brainstate.transform.ProgressBar, int] = False, ): """``scan`` control flow with :py:class:`~.Variable`. @@ -359,23 +449,35 @@ def scan( Optional positive int specifying, in the underlying operation of the scan primitive, how many scan iterations to unroll within a single iteration of a loop. - progress_bar: bool - Whether we use the progress bar to report the running progress. + progress_bar: bool, ProgressBar, int + Whether and how to display a progress bar during execution: + + - ``False`` (default): No progress bar + - ``True``: Display progress bar with default settings + - ``ProgressBar`` instance: Display progress bar with custom settings + - ``int``: Display progress bar updating every N iterations (treated as freq parameter) + + See :py:func:`for_loop` for detailed examples of ProgressBar usage. .. versionadded:: 2.4.2 + .. versionchanged:: 2.7.3 + Now accepts ProgressBar instances and integers for advanced customization. Returns:: outs: Any The stacked outputs of ``body_fun`` when scanned over the leading axis of the inputs. """ + # Convert progress_bar to pbar format + pbar = _convert_progress_bar_to_pbar(progress_bar) + return brainstate.transform.scan( warp_to_no_state_input_output(body_fun), init=init, xs=operands, reverse=reverse, unroll=unroll, - pbar=brainstate.transform.ProgressBar() if progress_bar else None, + pbar=pbar, ) diff --git a/brainpy/math/object_transform/tests/test_controls.py b/brainpy/math/object_transform/tests/test_controls.py index 7920d1a7..ba1f86ec 100644 --- a/brainpy/math/object_transform/tests/test_controls.py +++ b/brainpy/math/object_transform/tests/test_controls.py @@ -63,6 +63,72 @@ def test_for_loop_progress_bar(self): ys = bm.for_loop(lambda a: a, xs, progress_bar=True) self.assertTrue(bm.allclose(xs, ys)) + def test_for_loop_progress_bar_custom(self): + """Test for_loop with custom ProgressBar instances""" + xs = bm.arange(100) + + # Test 1: ProgressBar with custom frequency + pbar = bm.ProgressBar(freq=10) + ys = bm.for_loop(lambda a: a, xs, progress_bar=pbar) + self.assertTrue(bm.allclose(xs, ys)) + + # Test 2: ProgressBar with custom description + pbar = bm.ProgressBar(desc="Custom progress") + ys = bm.for_loop(lambda a: a, xs, progress_bar=pbar) + self.assertTrue(bm.allclose(xs, ys)) + + # Test 3: ProgressBar with count parameter + pbar = bm.ProgressBar(count=5) + ys = bm.for_loop(lambda a: a, xs, progress_bar=pbar) + self.assertTrue(bm.allclose(xs, ys)) + + def test_for_loop_progress_bar_int(self): + """Test for_loop with int as progress_bar (freq shorthand)""" + xs = bm.arange(50) + + # Int should be treated as freq parameter + ys = bm.for_loop(lambda a: a, xs, progress_bar=10) + self.assertTrue(bm.allclose(xs, ys)) + + def test_for_loop_progress_bar_backward_compat(self): + """Ensure backward compatibility with bool parameter""" + xs = bm.arange(20) + + # Test False (default) + ys = bm.for_loop(lambda a: a, xs, progress_bar=False) + self.assertTrue(bm.allclose(xs, ys)) + + # Test True + ys = bm.for_loop(lambda a: a, xs, progress_bar=True) + self.assertTrue(bm.allclose(xs, ys)) + + def test_for_loop_progress_bar_invalid_type(self): + """Test that invalid progress_bar types raise TypeError""" + xs = bm.arange(10) + + # Should raise TypeError for string + with self.assertRaises(TypeError) as cm: + bm.for_loop(lambda a: a, xs, progress_bar="invalid") + self.assertIn("progress_bar must be bool, int, or ProgressBar", str(cm.exception)) + + # Should raise TypeError for dict + with self.assertRaises(TypeError) as cm: + bm.for_loop(lambda a: a, xs, progress_bar={}) + self.assertIn("progress_bar must be bool, int, or ProgressBar", str(cm.exception)) + + def test_for_loop_progress_bar_with_jit_false(self): + """Test progress_bar works with jit=False""" + xs = bm.arange(20) + + # Test with ProgressBar instance and jit=False + pbar = bm.ProgressBar(freq=5) + ys = bm.for_loop(lambda a: a, xs, progress_bar=pbar, jit=False) + self.assertTrue(bm.allclose(xs, ys)) + + # Test with bool and jit=False + ys = bm.for_loop(lambda a: a, xs, progress_bar=True, jit=False) + self.assertTrue(bm.allclose(xs, ys)) + def test_for_loop2(self): class MyClass(bp.DynamicalSystem): def __init__(self): @@ -77,6 +143,61 @@ def update(self): bm.for_loop(cls.step_run, indices) self.assertTrue(bm.allclose(cls.a, 10.)) + def test_for_loop_jit_false(self): + """Test that jit=False disables JIT compilation""" + a = bm.Variable(bm.zeros(1)) + call_count = {'count': 0} + + def body(x): + # This side effect should be visible when jit=False + call_count['count'] += 1 + a.value += x + return a.value + + # Test with jit=False - should execute eagerly + a.value = bm.zeros(1) + call_count['count'] = 0 + result = bm.for_loop(body, operands=bm.arange(3), jit=False) + # With jit=False, the function should be called 3 times + self.assertEqual(call_count['count'], 3) + self.assertTrue(bm.allclose(a.value, 3.)) + + def test_for_loop_jit_default(self): + """Test that default behavior (jit=None) allows JIT compilation""" + a = bm.Variable(bm.zeros(1)) + + def body(x): + a.value += x + return a.value + + # Test with default jit (None) - should work normally + result = bm.for_loop(body, operands=bm.arange(3)) + self.assertTrue(bm.allclose(a.value, 3.)) + self.assertTrue(bm.allclose(result, bm.array([[0.], [1.], [3.]]))) + + def test_for_loop_jit_false_zero_length(self): + """Test that jit=False handles zero-length inputs gracefully""" + a = bm.Variable(bm.zeros(1)) + + def body(x): + a.value += x + return a.value + + # Test with zero-length input and jit=False + # Should automatically fall back to JIT mode and issue a warning + import warnings + with warnings.catch_warnings(record=True) as w: + warnings.simplefilter("always") + result = bm.for_loop(body, operands=bm.arange(0), jit=False) + # Check that our specific warning was issued + zero_length_warnings = [warning for warning in w + if "zero-length input" in str(warning.message)] + self.assertGreaterEqual(len(zero_length_warnings), 1, + "Expected at least one zero-length input warning") + + # Variable should not have changed + self.assertTrue(bm.allclose(a.value, 0.)) + class TestScan(unittest.TestCase): def test1(self): @@ -138,6 +259,64 @@ def cumsum(res, el): with jax.disable_jit(): final, result = bm.scan(cumsum, result_init, b) + def test_scan_progress_bar_custom(self): + """Test scan with custom ProgressBar instances""" + a = bm.Variable(1) + + def f(carry, x): + carry += x + a.value += 1. + return carry, a.value + + # Test with custom ProgressBar + pbar = bm.ProgressBar(freq=2) + carry, outs = bm.scan(f, bm.zeros(2), bm.arange(10), progress_bar=pbar) + self.assertTrue(bm.allclose(carry, 45.)) + expected = bm.arange(1, 11).astype(outs.dtype) + expected = bm.expand_dims(expected, axis=-1) + self.assertTrue(bm.allclose(outs, expected)) + + def test_scan_progress_bar_int(self): + """Test scan with int as progress_bar (freq shorthand)""" + a = bm.Variable(1) + + def f(carry, x): + carry += x + a.value += 1. + return carry, a.value + + # Int should be treated as freq parameter + carry, outs = bm.scan(f, bm.zeros(2), bm.arange(10), progress_bar=5) + self.assertTrue(bm.allclose(carry, 45.)) + + def test_scan_progress_bar_backward_compat(self): + """Ensure backward compatibility with bool parameter""" + a = bm.Variable(1) + + def f(carry, x): + carry += x + a.value += 1. + return carry, a.value + + # Test with True + carry, outs = bm.scan(f, bm.zeros(2), bm.arange(10), progress_bar=True) + self.assertTrue(bm.allclose(carry, 45.)) + + # Test with False - reset variable properly + a.value = bm.asarray([1.]) + carry, outs = bm.scan(f, bm.zeros(2), bm.arange(10), progress_bar=False) + self.assertTrue(bm.allclose(carry, 45.)) + + def test_scan_progress_bar_invalid_type(self): + """Test that invalid progress_bar types raise TypeError""" + def f(carry, x): + return carry + x, carry + + # Should raise TypeError for invalid types + with self.assertRaises(TypeError) as cm: + bm.scan(f, 0, bm.arange(10), progress_bar=[1, 2, 3]) + self.assertIn("progress_bar must be bool, int, or ProgressBar", str(cm.exception)) + class TestCond(unittest.TestCase): def test1(self): diff --git a/brainpy/runners.py b/brainpy/runners.py index 2e7d2bdd..b0c98658 100644 --- a/brainpy/runners.py +++ b/brainpy/runners.py @@ -13,6 +13,7 @@ # See the License for the specific language governing permissions and # limitations under the License. # ============================================================================== +import functools import inspect import time import warnings @@ -662,8 +663,7 @@ def _fun_predict(self, indices, *inputs, shared_args=None): return outs, None else: - return bm.for_loop(self._step_func_predict, + return bm.for_loop(functools.partial(self._step_func_predict, shared_args=shared_args), (indices, *inputs), jit=self.jit['predict'], - unroll_kwargs={'shared_args': shared_args}, progress_bar=self.progress_bar) diff --git a/brainpy/transform.py b/brainpy/transform.py index b42ed276..00d83464 100644 --- a/brainpy/transform.py +++ b/brainpy/transform.py @@ -142,9 +142,20 @@ def __init__( data_first_axis: str = 'T', name: str = None, jit: bool = True, - remat: bool = False, + remat: bool = False, # Deprecated parameter, kept for backward compatibility ): super().__init__(name=name) + + # Warn about deprecated remat parameter + if remat: + import warnings + warnings.warn( + "The 'remat' parameter is deprecated and no longer has any effect. " + "It will be removed in a future version.", + DeprecationWarning, + stacklevel=2 + ) + assert data_first_axis in ['B', 'T'] is_integer(i0, 'i0', allow_none=True) is_float(t0, 't0', allow_none=True) @@ -162,7 +173,7 @@ def __init__( self.i0 = None if i0 is None else bm.Variable(bm.as_jax(i0)) self.jit = jit - self.remat = remat + # self.remat = remat # Removed - no longer used self.shared_arg = shared_arg self.data_first_axis = data_first_axis self.target = target @@ -279,8 +290,7 @@ def __call__( xs = jax.tree.map(lambda x: x.value if isinstance(x, bm.Variable) else x, xs, is_leaf=lambda x: isinstance(x, bm.Variable)) results = bm.for_loop(functools.partial(self._run, self.shared_arg), (shared, xs), - jit=self.jit, - remat=self.remat) + jit=self.jit) if self.i0 is not None: self.i0 += length[0] if self.t0 is not None: diff --git a/docs_classic/apis/brainpy.math.oo_transform.rst b/docs_classic/apis/brainpy.math.oo_transform.rst index 9ed9cf46..cd4d2fa4 100644 --- a/docs_classic/apis/brainpy.math.oo_transform.rst +++ b/docs_classic/apis/brainpy.math.oo_transform.rst @@ -65,6 +65,7 @@ Object-oriented Transformations cls_jit to_object function + ProgressBar Helpers for Object-oriented Transformations diff --git a/uv.lock b/uv.lock new file mode 100644 index 00000000..a9fe7838 --- /dev/null +++ b/uv.lock @@ -0,0 +1,1961 @@ +version = 1 +revision = 2 +requires-python = ">=3.10" +resolution-markers = [ + "python_full_version >= '3.13'", + "python_full_version == '3.12.*'", + "python_full_version == '3.11.*'", + "python_full_version < '3.11'", +] + +[[package]] +name = "absl-py" +version = "2.3.1" +source = { registry = "https://pypi.org/simple" } +sdist = { url = "https://files.pythonhosted.org/packages/10/2a/c93173ffa1b39c1d0395b7e842bbdc62e556ca9d8d3b5572926f3e4ca752/absl_py-2.3.1.tar.gz", hash = "sha256:a97820526f7fbfd2ec1bce83f3f25e3a14840dac0d8e02a0b71cd75db3f77fc9", size = 116588, upload-time = "2025-07-03T09:31:44.05Z" } +wheels = [ + { url = 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upload-time = "2025-08-07T02:55:09.365Z" }, +] + +[[package]] +name = "brainpy" +source = { editable = "." } +dependencies = [ + { name = "brainevent" }, + { name = "brainstate" }, + { name = "braintools" }, + { name = "brainunit" }, + { name = "jax", version = "0.6.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" }, + { name = "jax", version = "0.8.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" }, + { name = "numpy", version = "2.2.6", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" }, + { name = "numpy", version = "2.3.5", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" }, + { name = "tqdm" }, +] + +[package.optional-dependencies] +cpu = [ + { name = "brainevent" }, + { name = "brainstate" }, + { name = "braintools" }, + { name = "brainunit" }, + { name = "jax", version = "0.6.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" }, + { name = "jax", version = "0.8.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.11'" }, +] +cuda12 = [ + { name = "brainevent" }, + { name = "brainstate" }, + { name = "braintools" }, + { name = "brainunit" }, + { name = "jax", version = "0.6.2", source = { registry = "https://pypi.org/simple" }, extra = ["cuda12"], marker = "python_full_version < '3.11'" }, + { name = "jax", version = "0.8.1", source = { registry = "https://pypi.org/simple" }, extra = ["cuda12"], marker = "python_full_version >= '3.11'" }, +] +cuda13 = [ + { name = "brainevent" }, + { name = "brainstate" }, + { name = "braintools" }, + { name = "brainunit" }, + { name = "jax", version = "0.6.2", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.11'" }, + { name = "jax", version = "0.8.1", source = { registry = "https://pypi.org/simple" }, extra = ["cuda13"], marker = 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