scipy 1.15.3__cp313-cp313-macosx_14_0_arm64.whl → 1.16.0rc1__cp313-cp313-macosx_14_0_arm64.whl

scipy/special/tests/test_support_alternative_backends.py

@@ -1,107 +1,242 @@
+from functools import partial
+import pickle
+
 import pytest
+from hypothesis import given, strategies
+import hypothesis.extra.numpy as npst
+from packaging import version
 
-from scipy.special._support_alternative_backends import (get_array_special_func,
-                                                         array_special_func_map)
-from scipy.conftest import array_api_compatible
 from scipy import special
+from scipy.special._support_alternative_backends import _special_funcs
 from scipy._lib._array_api_no_0d import xp_assert_close
-from scipy._lib._array_api import is_jax, is_torch, SCIPY_DEVICE
+from scipy._lib._array_api import (is_cupy, is_dask, is_jax, is_torch,
+                                   make_xp_pytest_param, make_xp_test_case,
+                                   xp_default_dtype)
 from scipy._lib.array_api_compat import numpy as np
 
-try:
-    import array_api_strict
-    HAVE_ARRAY_API_STRICT = True
-except ImportError:
-    HAVE_ARRAY_API_STRICT = False
-
+# Run all tests in this module in the Array API CI, including those without
+# the xp fixture
+pytestmark = pytest.mark.array_api_backends
 
-@pytest.mark.skipif(not HAVE_ARRAY_API_STRICT,
-                    reason="`array_api_strict` not installed")
-def test_dispatch_to_unrecognize_library():
-    xp = array_api_strict
-    f = get_array_special_func('ndtr', xp=xp, n_array_args=1)
-    x = [1, 2, 3]
-    res = f(xp.asarray(x))
-    ref = xp.asarray(special.ndtr(np.asarray(x)))
-    xp_assert_close(res, ref, xp=xp)
+lazy_xp_modules = [special]
 
 
-@pytest.mark.parametrize('dtype', ['float32', 'float64', 'int64'])
-@pytest.mark.skipif(not HAVE_ARRAY_API_STRICT,
-                    reason="`array_api_strict` not installed")
-def test_rel_entr_generic(dtype):
-    xp = array_api_strict
-    f = get_array_special_func('rel_entr', xp=xp, n_array_args=2)
-    dtype_np = getattr(np, dtype)
-    dtype_xp = getattr(xp, dtype)
-    x, y = [-1, 0, 0, 1], [1, 0, 2, 3]
+def _skip_or_tweak_alternative_backends(xp, f_name, dtypes):
+    """Skip tests for specific intersections of scipy.special functions 
+    vs. backends vs. dtypes vs. devices.
+    Also suggest bespoke tweaks.
 
-    x_xp, y_xp = xp.asarray(x, dtype=dtype_xp), xp.asarray(y, dtype=dtype_xp)
-    res = f(x_xp, y_xp)
+    Returns
+    -------
+    positive_only : bool
+        Whether you should exclusively test positive inputs.
+    dtypes_np_ref : list[str]
+        The dtypes to use for the reference NumPy arrays.
+    """
+    if ((is_jax(xp) and f_name == 'gammaincc')  # google/jax#20699
+        # gh-20972
+        or ((is_cupy(xp) or is_jax(xp) or is_torch(xp)) and f_name == 'chdtrc')):
+        positive_only = True
+    else:
+        positive_only = False
 
-    x_np, y_np = np.asarray(x, dtype=dtype_np), np.asarray(y, dtype=dtype_np)
-    ref = special.rel_entr(x_np[-1], y_np[-1])
-    ref = np.asarray([np.inf, 0, 0, ref], dtype=ref.dtype)
+    if not any('int' in dtype for dtype in dtypes):
+        return positive_only, dtypes
 
-    xp_assert_close(res, xp.asarray(ref), xp=xp)
+    # Integer-specific issues from this point onwards
 
+    if ((is_torch(xp) and f_name in {'gammainc', 'gammaincc'})
+        or (is_cupy(xp) and f_name in {'stdtr', 'i0e', 'i1e'})
+        or (is_jax(xp) and f_name in {'stdtr', 'ndtr', 'ndtri', 'log_ndtr'})
+    ):
+        pytest.skip(f"`{f_name}` does not support integer types")
 
-@pytest.mark.fail_slow(5)
-@array_api_compatible
-# @pytest.mark.skip_xp_backends('numpy', reason='skip while debugging')
-# @pytest.mark.usefixtures("skip_xp_backends")
-# `reversed` is for developer convenience: test new function first = less waiting
-@pytest.mark.parametrize('f_name_n_args', reversed(array_special_func_map.items()))
-@pytest.mark.parametrize('dtype', ['float32', 'float64'])
-@pytest.mark.parametrize('shapes', [[(0,)]*4, [tuple()]*4, [(10,)]*4,
-                                    [(10,), (11, 1), (12, 1, 1), (13, 1, 1, 1)]])
-def test_support_alternative_backends(xp, f_name_n_args, dtype, shapes):
-    f_name, n_args = f_name_n_args
+    # int/float mismatched args support is sketchy
+    if (any('float' in dtype for dtype in dtypes)
+        and ((is_torch(xp) and f_name in ('rel_entr', 'xlogy'))
+             or (is_jax(xp) and f_name in ('gammainc', 'gammaincc',
+                                           'rel_entr', 'xlogy')))
+    ):
+        pytest.xfail("dtypes do not match")
 
-    if (SCIPY_DEVICE != 'cpu'
-        and is_torch(xp)
-        and f_name in {'stdtr', 'betaincc', 'betainc'}
+    dtypes_np_ref = dtypes
+    if (is_torch(xp) and xp_default_dtype(xp) == xp.float32
+        and f_name not in {'betainc', 'betaincc', 'stdtr', 'stdtrit'}
     ):
-        pytest.skip(f"`{f_name}` does not have an array-agnostic implementation "
-                    f"and cannot delegate to PyTorch.")
+        # On PyTorch with float32 default dtype, sometimes ints are promoted
+        # to float32, and sometimes to float64.
+        # When they are promoted to float32, explicitly convert the reference
+        # numpy arrays to float32 to prevent them from being automatically promoted
+        # to float64 instead.
+        dtypes_np_ref = ['float32' if 'int' in dtype else dtype for dtype in dtypes]
 
-    shapes = shapes[:n_args]
-    f = getattr(special, f_name)
+    return positive_only, dtypes_np_ref
 
+
+@pytest.mark.filterwarnings("ignore:invalid value encountered:RuntimeWarning:dask")
+@pytest.mark.parametrize('shapes', [[(0,)]*4, [tuple()]*4, [(10,)]*4,
+                                    [(10,), (11, 1), (12, 1, 1), (13, 1, 1, 1)]])
+@pytest.mark.parametrize('dtype', ['float32', 'float64', 'int64'])
+@pytest.mark.parametrize(
+    'func,nfo', [make_xp_pytest_param(i.wrapper, i) for i in _special_funcs])
+def test_support_alternative_backends(xp, func, nfo, dtype, shapes):
+    positive_only, [dtype_np_ref] = _skip_or_tweak_alternative_backends(
+        xp, nfo.name, [dtype])
     dtype_np = getattr(np, dtype)
     dtype_xp = getattr(xp, dtype)
 
-    # # To test the robustness of the alternative backend's implementation,
-    # # use Hypothesis to generate arguments
-    # from hypothesis import given, strategies, reproduce_failure, assume
-    # import hypothesis.extra.numpy as npst
-    # @given(data=strategies.data())
-    # mbs = npst.mutually_broadcastable_shapes(num_shapes=n_args)
-    # shapes, final_shape = data.draw(mbs)
-    # elements = dict(allow_subnormal=False)  # consider min_value, max_value
-    # args_np = [np.asarray(data.draw(npst.arrays(dtype_np, shape, elements=elements)),
-    #                       dtype=dtype_np)
-    #            for shape in shapes]
-
-    # For CI, be a little more forgiving; just generate normally distributed arguments
+    shapes = shapes[:nfo.n_args]
+    rng = np.random.default_rng(984254252920492019)
+    if 'int' in dtype:
+        iinfo = np.iinfo(dtype_np)
+        rand = partial(rng.integers, iinfo.min, iinfo.max + 1)
+    else:
+        rand = rng.standard_normal
+    args_np = [rand(size=shape, dtype=dtype_np) for shape in shapes]
+    if positive_only:
+        args_np = [np.abs(arg) for arg in args_np]
+
+    args_xp = [xp.asarray(arg, dtype=dtype_xp) for arg in args_np]
+    args_np = [np.asarray(arg, dtype=dtype_np_ref) for arg in args_np]
+
+    if is_dask(xp):
+        # We're using map_blocks to dispatch the function to Dask.
+        # This is the correct thing to do IF all tested functions are elementwise;
+        # otherwise the output would change depending on chunking.
+        # Try to trigger bugs related to having multiple chunks.
+        args_xp = [arg.rechunk(5) for arg in args_xp]
+
+    res = nfo.wrapper(*args_xp)  # Also wrapped by lazy_xp_function
+    ref = nfo.func(*args_np)  # Unwrapped ufunc
+
+    # When dtype_np is integer, the output dtype can be float
+    atol = 0 if ref.dtype.kind in 'iu' else 10 * np.finfo(ref.dtype).eps
+    xp_assert_close(res, xp.asarray(ref), atol=atol)
+
+
+@pytest.mark.parametrize(
+    'func, nfo',
+    [make_xp_pytest_param(i.wrapper, i) for i in _special_funcs if i.n_args >= 2])
+@pytest.mark.filterwarnings("ignore:invalid value encountered:RuntimeWarning:dask")
+def test_support_alternative_backends_mismatched_dtypes(xp, func, nfo):
+    """Test mix-n-match of int and float arguments"""
+    dtypes = ['int64', 'float32', 'float64'][:nfo.n_args]
+    dtypes_xp = [xp.int64, xp.float32, xp.float64][:nfo.n_args]
+    positive_only, dtypes_np_ref = _skip_or_tweak_alternative_backends(
+        xp, nfo.name, dtypes)
+
     rng = np.random.default_rng(984254252920492019)
-    args_np = [rng.standard_normal(size=shape, dtype=dtype_np) for shape in shapes]
+    iinfo = np.iinfo(np.int64)
+    randint = partial(rng.integers, iinfo.min, iinfo.max + 1)
+    args_np = [
+        randint(size=1, dtype=np.int64),
+        rng.standard_normal(size=1, dtype=np.float32),
+        rng.standard_normal(size=1, dtype=np.float64),
+    ][:nfo.n_args]
+    if positive_only:
+        args_np = [np.abs(arg) for arg in args_np]
+
+    args_xp = [xp.asarray(arg, dtype=dtype_xp)
+               for arg, dtype_xp in zip(args_np, dtypes_xp)]
+    args_np = [np.asarray(arg, dtype=dtype_np_ref)
+               for arg, dtype_np_ref in zip(args_np, dtypes_np_ref)]
+
+    res = nfo.wrapper(*args_xp)  # Also wrapped by lazy_xp_function
+    ref = nfo.func(*args_np)  # Unwrapped ufunc
+
+    atol = 10 * np.finfo(ref.dtype).eps
+    xp_assert_close(res, xp.asarray(ref), atol=atol)
+
+
+@pytest.mark.xslow
+@given(data=strategies.data())
+@pytest.mark.fail_slow(5)
+@pytest.mark.parametrize(
+    'func,nfo', [make_xp_pytest_param(nfo.wrapper, nfo) for nfo in _special_funcs])
+@pytest.mark.filterwarnings("ignore:invalid value encountered:RuntimeWarning:dask")
+@pytest.mark.filterwarnings("ignore:divide by zero encountered:RuntimeWarning:dask")
+@pytest.mark.filterwarnings("ignore:overflow encountered:RuntimeWarning:dask")
+@pytest.mark.filterwarnings(
+    "ignore:overflow encountered:RuntimeWarning:array_api_strict"
+)
+def test_support_alternative_backends_hypothesis(xp, func, nfo, data):
+    dtype = data.draw(strategies.sampled_from(['float32', 'float64', 'int64']))
+    positive_only, [dtype_np_ref] = _skip_or_tweak_alternative_backends(
+        xp, nfo.name, [dtype])
+    dtype_np = getattr(np, dtype)
+    dtype_xp = getattr(xp, dtype)
+
+    elements = {'allow_subnormal': False}
+    # Most failures are due to NaN or infinity; uncomment to suppress them
+    # elements['allow_infinity'] = False
+    # elements['allow_nan'] = False
+    if positive_only:
+        elements['min_value'] = 0
+
+    shapes, _ = data.draw(
+        npst.mutually_broadcastable_shapes(num_shapes=nfo.n_args))
+    args_np = [data.draw(npst.arrays(dtype_np, shape, elements=elements))
+               for shape in shapes]
+
+    args_xp = [xp.asarray(arg, dtype=dtype_xp) for arg in args_np]
+    args_np = [np.asarray(arg, dtype=dtype_np_ref) for arg in args_np]
+
+    res = nfo.wrapper(*args_xp)  # Also wrapped by lazy_xp_function
+    ref = nfo.func(*args_np)  # Unwrapped ufunc
+
+    # When dtype_np is integer, the output dtype can be float
+    atol = 0 if ref.dtype.kind in 'iu' else 10 * np.finfo(ref.dtype).eps
+    xp_assert_close(res, xp.asarray(ref), atol=atol)
+
+
+@pytest.mark.parametrize("func", [nfo.wrapper for nfo in _special_funcs])
+def test_pickle(func):
+    roundtrip = pickle.loads(pickle.dumps(func))
+    assert roundtrip is func
+
+
+@pytest.mark.parametrize("func", [nfo.wrapper for nfo in _special_funcs])
+def test_repr(func):
+    assert func.__name__ in repr(func)
+    assert "locals" not in repr(func)
+
+
+@pytest.mark.skipif(
+    version.parse(np.__version__) < version.parse("2.2"),
+    reason="Can't update ufunc __doc__ when SciPy is compiled vs. NumPy < 2.2")
+@pytest.mark.parametrize('func', [nfo.wrapper for nfo in _special_funcs])
+def test_doc(func):
+    """xp_capabilities updates the docstring in place. 
+    Make sure it does so exactly once, including when SCIPY_ARRAY_API is not set.
+    """
+    match = "has experimental support for Python Array API"
+    assert func.__doc__.count(match) == 1
+
 
-    if (is_jax(xp) and f_name == 'gammaincc'  # google/jax#20699
-            or f_name == 'chdtrc'):  # gh-20972
-        args_np[0] = np.abs(args_np[0])
-        args_np[1] = np.abs(args_np[1])
+@pytest.mark.parametrize('func,n_args',
+                         [(nfo.wrapper, nfo.n_args) for nfo in _special_funcs])
+def test_ufunc_kwargs(func, n_args):
+    """Test that numpy-specific out= and dtype= keyword arguments
+    of ufuncs still work when SCIPY_ARRAY_API is set.
+    """
+    # out=
+    args = [np.asarray([.1, .2])] * n_args
+    out = np.empty(2)
+    y = func(*args, out=out)
+    xp_assert_close(y, out)
 
-    args_xp = [xp.asarray(arg[()], dtype=dtype_xp) for arg in args_np]
+    # out= with out.dtype != args.dtype
+    out = np.empty(2, dtype=np.float32)
+    y = func(*args, out=out)
+    xp_assert_close(y, out)
 
-    res = f(*args_xp)
-    ref = xp.asarray(f(*args_np), dtype=dtype_xp)
+    # dtype=
+    y = func(*args, dtype=np.float32)
+    assert y.dtype == np.float32
 
-    eps = np.finfo(dtype_np).eps
-    xp_assert_close(res, ref, atol=10*eps)
 
 
-@array_api_compatible
+@make_xp_test_case(special.chdtr)
 def test_chdtr_gh21311(xp):
     # the edge case behavior of generic chdtr was not right; see gh-21311
     # be sure to test at least these cases

scipy/stats/__init__.py

@@ -280,6 +280,7 @@ Frequency statistics
    :toctree: generated/
 
    cumfreq
+   quantile
    percentileofscore
    scoreatpercentile
    relfreq
@@ -471,6 +472,7 @@ Random Variables
    make_distribution
    Normal
    Uniform
+   Binomial
    Mixture
    order_statistic
    truncate
@@ -649,9 +651,10 @@ from ._survival import *
 from ._distribution_infrastructure import (
     make_distribution, Mixture, order_statistic, truncate, exp, log, abs
 )
-from ._new_distributions import Normal, Uniform
+from ._new_distributions import Normal, Uniform, Binomial
 from ._mgc import multiscale_graphcorr
 from ._correlation import chatterjeexi
+from ._quantile import quantile
 
 
 # Deprecated namespaces, to be removed in v2.0.0

scipy/stats/_axis_nan_policy.py

@@ -42,6 +42,7 @@ def _broadcast_arrays(arrays, axis=None, xp=None):
     """
     Broadcast shapes of arrays, ignoring incompatibility of specified axes
     """
+    arrays = tuple(arrays)
     if not arrays:
         return arrays
     xp = array_namespace(*arrays) if xp is None else xp
@@ -554,11 +555,11 @@ def _axis_nan_policy_factory(tuple_to_result, default_axis=0,
             if np.all(ndims <= 1):
                 # Addresses nan_policy == "raise"
                 if nan_policy != 'propagate' or override['nan_propagation']:
-                    contains_nan = [_contains_nan(sample, nan_policy)[0]
+                    contains_nan = [_contains_nan(sample, nan_policy)
                                     for sample in samples]
                 else:
                     # Behave as though there are no NaNs (even if there are)
-                    contains_nan = [False]*len(samples)
+                    contains_nan = [False] * len(samples)
 
                 # Addresses nan_policy == "propagate"
                 if any(contains_nan) and (nan_policy == 'propagate'
@@ -610,7 +611,7 @@ def _axis_nan_policy_factory(tuple_to_result, default_axis=0,
 
             # Addresses nan_policy == "raise"
             if nan_policy != 'propagate' or override['nan_propagation']:
-                contains_nan, _ = _contains_nan(x, nan_policy)
+                contains_nan = _contains_nan(x, nan_policy)
             else:
                 contains_nan = False  # behave like there are no NaNs