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@@ -33,3 +33,29 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.zip filter=lfs diff=lfs merge=lfs -text
 *.zst filter=lfs diff=lfs merge=lfs -text
 *tfevents* filter=lfs diff=lfs merge=lfs -text
+scipy/fft/_pocketfft/pypocketfft.cp39-win_amd64.pyd filter=lfs diff=lfs merge=lfs -text
+scipy/interpolate/_rbfinterp_pythran.cp39-win_amd64.pyd filter=lfs diff=lfs merge=lfs -text
+scipy/io/_fast_matrix_market/_fmm_core.cp39-win_amd64.pyd filter=lfs diff=lfs merge=lfs -text
+scipy/linalg/_flapack.cp39-win_amd64.pyd filter=lfs diff=lfs merge=lfs -text
+scipy/misc/face.dat filter=lfs diff=lfs merge=lfs -text
+scipy/optimize/_group_columns.cp39-win_amd64.pyd filter=lfs diff=lfs merge=lfs -text
+scipy/optimize/_highs/_highs_wrapper.cp39-win_amd64.pyd filter=lfs diff=lfs merge=lfs -text
+scipy/signal/_max_len_seq_inner.cp39-win_amd64.pyd filter=lfs diff=lfs merge=lfs -text
+scipy/signal/_spectral.cp39-win_amd64.pyd filter=lfs diff=lfs merge=lfs -text
+scipy/sparse/_sparsetools.cp39-win_amd64.pyd filter=lfs diff=lfs merge=lfs -text
+scipy/spatial/_ckdtree.cp39-win_amd64.pyd filter=lfs diff=lfs merge=lfs -text
+scipy/spatial/_distance_pybind.cp39-win_amd64.pyd filter=lfs diff=lfs merge=lfs -text
+scipy/spatial/_qhull.cp39-win_amd64.pyd filter=lfs diff=lfs merge=lfs -text
+scipy/special/_ufuncs.cp39-win_amd64.pyd filter=lfs diff=lfs merge=lfs -text
+scipy/special/_ufuncs_cxx.cp39-win_amd64.pyd filter=lfs diff=lfs merge=lfs -text
+scipy/special/cython_special.cp39-win_amd64.pyd filter=lfs diff=lfs merge=lfs -text
+scipy/stats/_boost/beta_ufunc.cp39-win_amd64.pyd filter=lfs diff=lfs merge=lfs -text
+scipy/stats/_boost/binom_ufunc.cp39-win_amd64.pyd filter=lfs diff=lfs merge=lfs -text
+scipy/stats/_boost/hypergeom_ufunc.cp39-win_amd64.pyd filter=lfs diff=lfs merge=lfs -text
+scipy/stats/_boost/invgauss_ufunc.cp39-win_amd64.pyd filter=lfs diff=lfs merge=lfs -text
+scipy/stats/_boost/nbinom_ufunc.cp39-win_amd64.pyd filter=lfs diff=lfs merge=lfs -text
+scipy/stats/_boost/ncf_ufunc.cp39-win_amd64.pyd filter=lfs diff=lfs merge=lfs -text
+scipy/stats/_boost/nct_ufunc.cp39-win_amd64.pyd filter=lfs diff=lfs merge=lfs -text
+scipy/stats/_boost/ncx2_ufunc.cp39-win_amd64.pyd filter=lfs diff=lfs merge=lfs -text
+scipy/stats/_stats_pythran.cp39-win_amd64.pyd filter=lfs diff=lfs merge=lfs -text
+scipy/stats/_unuran/unuran_wrapper.cp39-win_amd64.pyd filter=lfs diff=lfs merge=lfs -text

scipy/__config__.py

@@ -0,0 +1,161 @@
+# This file is generated by SciPy's build process
+# It contains system_info results at the time of building this package.
+from enum import Enum
+
+__all__ = ["show"]
+_built_with_meson = True
+
+
+class DisplayModes(Enum):
+    stdout = "stdout"
+    dicts = "dicts"
+
+
+def _cleanup(d):
+    """
+    Removes empty values in a `dict` recursively
+    This ensures we remove values that Meson could not provide to CONFIG
+    """
+    if isinstance(d, dict):
+        return { k: _cleanup(v) for k, v in d.items() if v != '' and _cleanup(v) != '' }
+    else:
+        return d
+
+
+CONFIG = _cleanup(
+    {
+        "Compilers": {
+            "c": {
+                "name": "gcc",
+                "linker": "ld.bfd",
+                "version": "10.3.0",
+                "commands": "cc",
+                "args": "",
+                "linker args": "",
+            },
+            "cython": {
+                "name": "cython",
+                "linker": "cython",
+                "version": "3.0.8",
+                "commands": "cython",
+                "args": "",
+                "linker args": "",
+            },
+            "c++": {
+                "name": "gcc",
+                "linker": "ld.bfd",
+                "version": "10.3.0",
+                "commands": "c++",
+                "args": "",
+                "linker args": "",
+            },
+            "fortran": {
+                "name": "gcc",
+                "linker": "ld.bfd",
+                "version": "10.3.0",
+                "commands": "gfortran",
+                "args": "",
+                "linker args": "",
+            },
+            "pythran": {
+                "version": "0.15.0",
+                "include directory": r"C:\Users\runneradmin\AppData\Local\Temp\pip-build-env-rikezz0v\overlay\Lib\site-packages/pythran"
+            },
+        },
+        "Machine Information": {
+            "host": {
+                "cpu": "x86_64",
+                "family": "x86_64",
+                "endian": "little",
+                "system": "windows",
+            },
+            "build": {
+                "cpu": "x86_64",
+                "family": "x86_64",
+                "endian": "little",
+                "system": "windows",
+            },
+            "cross-compiled": bool("False".lower().replace('false', '')),
+        },
+        "Build Dependencies": {
+            "blas": {
+                "name": "openblas",
+                "found": bool("True".lower().replace('false', '')),
+                "version": "0.3.21.dev",
+                "detection method": "pkgconfig",
+                "include directory": r"/c/opt/64/include",
+                "lib directory": r"/c/opt/64/lib",
+                "openblas configuration": "USE_64BITINT= DYNAMIC_ARCH=1 DYNAMIC_OLDER= NO_CBLAS= NO_LAPACK= NO_LAPACKE= NO_AFFINITY=1 USE_OPENMP= SKYLAKEX MAX_THREADS=2",
+                "pc file directory": r"c:/opt/64/lib/pkgconfig",
+            },
+            "lapack": {
+                "name": "openblas",
+                "found": bool("True".lower().replace('false', '')),
+                "version": "0.3.21.dev",
+                "detection method": "pkgconfig",
+                "include directory": r"/c/opt/64/include",
+                "lib directory": r"/c/opt/64/lib",
+                "openblas configuration": "USE_64BITINT= DYNAMIC_ARCH=1 DYNAMIC_OLDER= NO_CBLAS= NO_LAPACK= NO_LAPACKE= NO_AFFINITY=1 USE_OPENMP= SKYLAKEX MAX_THREADS=2",
+                "pc file directory": r"c:/opt/64/lib/pkgconfig",
+            },
+            "pybind11": {
+                "name": "pybind11",
+                "version": "2.11.1",
+                "detection method": "config-tool",
+                "include directory": r"unknown",
+            },
+        },
+        "Python Information": {
+            "path": r"C:\Users\runneradmin\AppData\Local\Temp\cibw-run-ee1litsm\cp39-win_amd64\build\venv\Scripts\python.exe",
+            "version": "3.9",
+        },
+    }
+)
+
+
+def _check_pyyaml():
+    import yaml
+
+    return yaml
+
+
+def show(mode=DisplayModes.stdout.value):
+    """
+    Show libraries and system information on which SciPy was built
+    and is being used
+
+    Parameters
+    ----------
+    mode : {`'stdout'`, `'dicts'`}, optional.
+        Indicates how to display the config information.
+        `'stdout'` prints to console, `'dicts'` returns a dictionary
+        of the configuration.
+
+    Returns
+    -------
+    out : {`dict`, `None`}
+        If mode is `'dicts'`, a dict is returned, else None
+
+    Notes
+    -----
+    1. The `'stdout'` mode will give more readable
+       output if ``pyyaml`` is installed
+
+    """
+    if mode == DisplayModes.stdout.value:
+        try:  # Non-standard library, check import
+            yaml = _check_pyyaml()
+
+            print(yaml.dump(CONFIG))
+        except ModuleNotFoundError:
+            import warnings
+            import json
+
+            warnings.warn("Install `pyyaml` for better output", stacklevel=1)
+            print(json.dumps(CONFIG, indent=2))
+    elif mode == DisplayModes.dicts.value:
+        return CONFIG
+    else:
+        raise AttributeError(
+            f"Invalid `mode`, use one of: {', '.join([e.value for e in DisplayModes])}"
+        )

scipy/__init__.py

@@ -0,0 +1,169 @@
+"""
+SciPy: A scientific computing package for Python
+================================================
+
+Documentation is available in the docstrings and
+online at https://docs.scipy.org.
+
+Subpackages
+-----------
+Using any of these subpackages requires an explicit import. For example,
+``import scipy.cluster``.
+
+::
+
+ cluster                      --- Vector Quantization / Kmeans
+ constants                    --- Physical and mathematical constants and units
+ datasets                     --- Dataset methods
+ fft                          --- Discrete Fourier transforms
+ fftpack                      --- Legacy discrete Fourier transforms
+ integrate                    --- Integration routines
+ interpolate                  --- Interpolation Tools
+ io                           --- Data input and output
+ linalg                       --- Linear algebra routines
+ misc                         --- Utilities that don't have another home.
+ ndimage                      --- N-D image package
+ odr                          --- Orthogonal Distance Regression
+ optimize                     --- Optimization Tools
+ signal                       --- Signal Processing Tools
+ sparse                       --- Sparse Matrices
+ spatial                      --- Spatial data structures and algorithms
+ special                      --- Special functions
+ stats                        --- Statistical Functions
+
+Public API in the main SciPy namespace
+--------------------------------------
+::
+
+ __version__       --- SciPy version string
+ LowLevelCallable  --- Low-level callback function
+ show_config       --- Show scipy build configuration
+ test              --- Run scipy unittests
+
+"""
+
+
+# start delvewheel patch
+def _delvewheel_patch_1_5_2():
+    import ctypes
+    import os
+    import platform
+    import sys
+    libs_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'scipy.libs'))
+    is_conda_cpython = platform.python_implementation() == 'CPython' and (hasattr(ctypes.pythonapi, 'Anaconda_GetVersion') or 'packaged by conda-forge' in sys.version)
+    if sys.version_info[:2] >= (3, 8) and not is_conda_cpython or sys.version_info[:2] >= (3, 10):
+        if os.path.isdir(libs_dir):
+            os.add_dll_directory(libs_dir)
+    else:
+        load_order_filepath = os.path.join(libs_dir, '.load-order-scipy-1.12.0')
+        if os.path.isfile(load_order_filepath):
+            with open(os.path.join(libs_dir, '.load-order-scipy-1.12.0')) as file:
+                load_order = file.read().split()
+            for lib in load_order:
+                lib_path = os.path.join(os.path.join(libs_dir, lib))
+                kernel32 = ctypes.WinDLL('kernel32', use_last_error=True)
+                if os.path.isfile(lib_path) and not kernel32.LoadLibraryExW(ctypes.c_wchar_p(lib_path), None, 0x00000008):
+                    raise OSError('Error loading {}; {}'.format(lib, ctypes.FormatError(ctypes.get_last_error())))
+
+
+_delvewheel_patch_1_5_2()
+del _delvewheel_patch_1_5_2
+# end delvewheel patch
+
+import importlib as _importlib
+
+from numpy import __version__ as __numpy_version__
+
+
+try:
+    from scipy.__config__ import show as show_config
+except ImportError as e:
+    msg = """Error importing SciPy: you cannot import SciPy while
+    being in scipy source directory; please exit the SciPy source
+    tree first and relaunch your Python interpreter."""
+    raise ImportError(msg) from e
+
+
+from scipy.version import version as __version__
+
+
+# Allow distributors to run custom init code
+from . import _distributor_init
+del _distributor_init
+
+
+from scipy._lib import _pep440
+# In maintenance branch, change to np_maxversion N+3 if numpy is at N
+np_minversion = '1.22.4'
+np_maxversion = '1.29.0'
+if (_pep440.parse(__numpy_version__) < _pep440.Version(np_minversion) or
+        _pep440.parse(__numpy_version__) >= _pep440.Version(np_maxversion)):
+    import warnings
+    warnings.warn(f"A NumPy version >={np_minversion} and <{np_maxversion}"
+                  f" is required for this version of SciPy (detected "
+                  f"version {__numpy_version__})",
+                  UserWarning, stacklevel=2)
+del _pep440
+
+
+# This is the first import of an extension module within SciPy. If there's
+# a general issue with the install, such that extension modules are missing
+# or cannot be imported, this is where we'll get a failure - so give an
+# informative error message.
+try:
+    from scipy._lib._ccallback import LowLevelCallable
+except ImportError as e:
+    msg = "The `scipy` install you are using seems to be broken, " + \
+          "(extension modules cannot be imported), " + \
+          "please try reinstalling."
+    raise ImportError(msg) from e
+
+
+from scipy._lib._testutils import PytestTester
+test = PytestTester(__name__)
+del PytestTester
+
+
+submodules = [
+    'cluster',
+    'constants',
+    'datasets',
+    'fft',
+    'fftpack',
+    'integrate',
+    'interpolate',
+    'io',
+    'linalg',
+    'misc',
+    'ndimage',
+    'odr',
+    'optimize',
+    'signal',
+    'sparse',
+    'spatial',
+    'special',
+    'stats'
+]
+
+__all__ = submodules + [
+    'LowLevelCallable',
+    'test',
+    'show_config',
+    '__version__',
+]
+
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    if name in submodules:
+        return _importlib.import_module(f'scipy.{name}')
+    else:
+        try:
+            return globals()[name]
+        except KeyError:
+            raise AttributeError(
+                f"Module 'scipy' has no attribute '{name}'"
+            )

scipy/_distributor_init.py

@@ -0,0 +1,32 @@
+
+'''
+Helper to preload windows dlls to prevent dll not found errors.
+Once a DLL is preloaded, its namespace is made available to any
+subsequent DLL. This file originated in the numpy-wheels repo,
+and is created as part of the scripts that build the wheel.
+'''
+import os
+import glob
+if os.name == 'nt':
+    # convention for storing / loading the DLL from
+    # numpy/.libs/, if present
+    try:
+        from ctypes import WinDLL
+        basedir = os.path.dirname(__file__)
+    except:
+        pass
+    else:
+        libs_dir = os.path.abspath(os.path.join(basedir, '.libs'))
+        DLL_filenames = []
+        if os.path.isdir(libs_dir):
+            for filename in glob.glob(os.path.join(libs_dir,
+                                                   '*openblas*dll')):
+                # NOTE: would it change behavior to load ALL
+                # DLLs at this path vs. the name restriction?
+                WinDLL(os.path.abspath(filename))
+                DLL_filenames.append(filename)
+        if len(DLL_filenames) > 1:
+            import warnings
+            warnings.warn("loaded more than 1 DLL from .libs:"
+                          "\n%s" % "\n".join(DLL_filenames),
+                          stacklevel=1)

scipy/_lib/__init__.py

@@ -0,0 +1,14 @@
+"""
+Module containing private utility functions
+===========================================
+
+The ``scipy._lib`` namespace is empty (for now). Tests for all
+utilities in submodules of ``_lib`` can be run with::
+
+    from scipy import _lib
+    _lib.test()
+
+"""
+from scipy._lib._testutils import PytestTester
+test = PytestTester(__name__)
+del PytestTester

scipy/_lib/_array_api.py

@@ -0,0 +1,353 @@
+"""Utility functions to use Python Array API compatible libraries.
+
+For the context about the Array API see:
+https://data-apis.org/array-api/latest/purpose_and_scope.html
+
+The SciPy use case of the Array API is described on the following page:
+https://data-apis.org/array-api/latest/use_cases.html#use-case-scipy
+"""
+from __future__ import annotations
+
+import os
+import warnings
+
+import numpy as np
+from numpy.testing import assert_
+import scipy._lib.array_api_compat.array_api_compat as array_api_compat
+from scipy._lib.array_api_compat.array_api_compat import size
+import scipy._lib.array_api_compat.array_api_compat.numpy as array_api_compat_numpy
+
+__all__ = ['array_namespace', 'as_xparray', 'size']
+
+
+# To enable array API and strict array-like input validation
+SCIPY_ARRAY_API: str | bool = os.environ.get("SCIPY_ARRAY_API", False)
+# To control the default device - for use in the test suite only
+SCIPY_DEVICE = os.environ.get("SCIPY_DEVICE", "cpu")
+
+_GLOBAL_CONFIG = {
+    "SCIPY_ARRAY_API": SCIPY_ARRAY_API,
+    "SCIPY_DEVICE": SCIPY_DEVICE,
+}
+
+
+def compliance_scipy(arrays):
+    """Raise exceptions on known-bad subclasses.
+
+    The following subclasses are not supported and raise and error:
+    - `numpy.ma.MaskedArray`
+    - `numpy.matrix`
+    - NumPy arrays which do not have a boolean or numerical dtype
+    - Any array-like which is neither array API compatible nor coercible by NumPy
+    - Any array-like which is coerced by NumPy to an unsupported dtype
+    """
+    for i in range(len(arrays)):
+        array = arrays[i]
+        if isinstance(array, np.ma.MaskedArray):
+            raise TypeError("Inputs of type `numpy.ma.MaskedArray` are not supported.")
+        elif isinstance(array, np.matrix):
+            raise TypeError("Inputs of type `numpy.matrix` are not supported.")
+        if isinstance(array, (np.ndarray, np.generic)):
+            dtype = array.dtype
+            if not (np.issubdtype(dtype, np.number) or np.issubdtype(dtype, np.bool_)):
+                raise TypeError(f"An argument has dtype `{dtype!r}`; "
+                                f"only boolean and numerical dtypes are supported.")
+        elif not array_api_compat.is_array_api_obj(array):
+            try:
+                array = np.asanyarray(array)
+            except TypeError:
+                raise TypeError("An argument is neither array API compatible nor "
+                                "coercible by NumPy.")
+            dtype = array.dtype
+            if not (np.issubdtype(dtype, np.number) or np.issubdtype(dtype, np.bool_)):
+                message = (
+                    f"An argument was coerced to an unsupported dtype `{dtype!r}`; "
+                    f"only boolean and numerical dtypes are supported."
+                )
+                raise TypeError(message)
+            arrays[i] = array
+    return arrays
+
+
+def _check_finite(array, xp):
+    """Check for NaNs or Infs."""
+    msg = "array must not contain infs or NaNs"
+    try:
+        if not xp.all(xp.isfinite(array)):
+            raise ValueError(msg)
+    except TypeError:
+        raise ValueError(msg)
+
+
+def array_namespace(*arrays):
+    """Get the array API compatible namespace for the arrays xs.
+
+    Parameters
+    ----------
+    *arrays : sequence of array_like
+        Arrays used to infer the common namespace.
+
+    Returns
+    -------
+    namespace : module
+        Common namespace.
+
+    Notes
+    -----
+    Thin wrapper around `array_api_compat.array_namespace`.
+
+    1. Check for the global switch: SCIPY_ARRAY_API. This can also be accessed
+       dynamically through ``_GLOBAL_CONFIG['SCIPY_ARRAY_API']``.
+    2. `compliance_scipy` raise exceptions on known-bad subclasses. See
+       it's definition for more details.
+
+    When the global switch is False, it defaults to the `numpy` namespace.
+    In that case, there is no compliance check. This is a convenience to
+    ease the adoption. Otherwise, arrays must comply with the new rules.
+    """
+    if not _GLOBAL_CONFIG["SCIPY_ARRAY_API"]:
+        # here we could wrap the namespace if needed
+        return array_api_compat_numpy
+
+    arrays = [array for array in arrays if array is not None]
+
+    arrays = compliance_scipy(arrays)
+
+    return array_api_compat.array_namespace(*arrays)
+
+
+def as_xparray(
+    array, dtype=None, order=None, copy=None, *, xp=None, check_finite=False
+):
+    """SciPy-specific replacement for `np.asarray` with `order` and `check_finite`.
+
+    Memory layout parameter `order` is not exposed in the Array API standard.
+    `order` is only enforced if the input array implementation
+    is NumPy based, otherwise `order` is just silently ignored.
+
+    `check_finite` is also not a keyword in the array API standard; included
+    here for convenience rather than that having to be a separate function
+    call inside SciPy functions.
+    """
+    if xp is None:
+        xp = array_namespace(array)
+    if xp.__name__ in {"numpy", "scipy._lib.array_api_compat.array_api_compat.numpy"}:
+        # Use NumPy API to support order
+        if copy is True:
+            array = np.array(array, order=order, dtype=dtype)
+        else:
+            array = np.asarray(array, order=order, dtype=dtype)
+
+        # At this point array is a NumPy ndarray. We convert it to an array
+        # container that is consistent with the input's namespace.
+        array = xp.asarray(array)
+    else:
+        try:
+            array = xp.asarray(array, dtype=dtype, copy=copy)
+        except TypeError:
+            coerced_xp = array_namespace(xp.asarray(3))
+            array = coerced_xp.asarray(array, dtype=dtype, copy=copy)
+
+    if check_finite:
+        _check_finite(array, xp)
+
+    return array
+
+
+def atleast_nd(x, *, ndim, xp=None):
+    """Recursively expand the dimension to have at least `ndim`."""
+    if xp is None:
+        xp = array_namespace(x)
+    x = xp.asarray(x)
+    if x.ndim < ndim:
+        x = xp.expand_dims(x, axis=0)
+        x = atleast_nd(x, ndim=ndim, xp=xp)
+    return x
+
+
+def copy(x, *, xp=None):
+    """
+    Copies an array.
+
+    Parameters
+    ----------
+    x : array
+
+    xp : array_namespace
+
+    Returns
+    -------
+    copy : array
+        Copied array
+
+    Notes
+    -----
+    This copy function does not offer all the semantics of `np.copy`, i.e. the
+    `subok` and `order` keywords are not used.
+    """
+    # Note: xp.asarray fails if xp is numpy.
+    if xp is None:
+        xp = array_namespace(x)
+
+    return as_xparray(x, copy=True, xp=xp)
+
+
+def is_numpy(xp):
+    return xp.__name__ == 'scipy._lib.array_api_compat.array_api_compat.numpy'
+
+
+def is_cupy(xp):
+    return xp.__name__ == 'scipy._lib.array_api_compat.array_api_compat.cupy'
+
+
+def is_torch(xp):
+    return xp.__name__ == 'scipy._lib.array_api_compat.array_api_compat.torch'
+
+
+def _strict_check(actual, desired, xp,
+                  check_namespace=True, check_dtype=True, check_shape=True):
+    if check_namespace:
+        _assert_matching_namespace(actual, desired)
+
+    desired = xp.asarray(desired)
+
+    if check_dtype:
+        assert_(actual.dtype == desired.dtype,
+                "dtypes do not match.\n"
+                f"Actual: {actual.dtype}\n"
+                f"Desired: {desired.dtype}")
+
+    if check_shape:
+        assert_(actual.shape == desired.shape,
+                "Shapes do not match.\n"
+                f"Actual: {actual.shape}\n"
+                f"Desired: {desired.shape}")
+        _check_scalar(actual, desired, xp)
+
+    desired = xp.broadcast_to(desired, actual.shape)
+    return desired
+
+
+def _assert_matching_namespace(actual, desired):
+    actual = actual if isinstance(actual, tuple) else (actual,)
+    desired_space = array_namespace(desired)
+    for arr in actual:
+        arr_space = array_namespace(arr)
+        assert_(arr_space == desired_space,
+                "Namespaces do not match.\n"
+                f"Actual: {arr_space.__name__}\n"
+                f"Desired: {desired_space.__name__}")
+
+
+def _check_scalar(actual, desired, xp):
+    # Shape check alone is sufficient unless desired.shape == (). Also,
+    # only NumPy distinguishes between scalars and arrays.
+    if desired.shape != () or not is_numpy(xp):
+        return
+    # We want to follow the conventions of the `xp` library. Libraries like
+    # NumPy, for which `np.asarray(0)[()]` returns a scalar, tend to return
+    # a scalar even when a 0D array might be more appropriate:
+    # import numpy as np
+    # np.mean([1, 2, 3])  # scalar, not 0d array
+    # np.asarray(0)*2  # scalar, not 0d array
+    # np.sin(np.asarray(0))  # scalar, not 0d array
+    # Libraries like CuPy, for which `cp.asarray(0)[()]` returns a 0D array,
+    # tend to return a 0D array in scenarios like those above.
+    # Therefore, regardless of whether the developer provides a scalar or 0D
+    # array for `desired`, we would typically want the type of `actual` to be
+    # the type of `desired[()]`. If the developer wants to override this
+    # behavior, they can set `check_shape=False`.
+    desired = desired[()]
+    assert_((xp.isscalar(actual) and xp.isscalar(desired)
+             or (not xp.isscalar(actual) and not xp.isscalar(desired))),
+            "Types do not match:\n"
+            f"Actual: {type(actual)}\n"
+            f"Desired: {type(desired)}")
+
+
+def xp_assert_equal(actual, desired, check_namespace=True, check_dtype=True,
+                    check_shape=True, err_msg='', xp=None):
+    if xp is None:
+        xp = array_namespace(actual)
+    desired = _strict_check(actual, desired, xp, check_namespace=check_namespace,
+                            check_dtype=check_dtype, check_shape=check_shape)
+    if is_cupy(xp):
+        return xp.testing.assert_array_equal(actual, desired, err_msg=err_msg)
+    elif is_torch(xp):
+        # PyTorch recommends using `rtol=0, atol=0` like this
+        # to test for exact equality
+        err_msg = None if err_msg == '' else err_msg
+        return xp.testing.assert_close(actual, desired, rtol=0, atol=0, equal_nan=True,
+                                       check_dtype=False, msg=err_msg)
+    return np.testing.assert_array_equal(actual, desired, err_msg=err_msg)
+
+
+def xp_assert_close(actual, desired, rtol=1e-07, atol=0, check_namespace=True,
+                    check_dtype=True, check_shape=True, err_msg='', xp=None):
+    if xp is None:
+        xp = array_namespace(actual)
+    desired = _strict_check(actual, desired, xp, check_namespace=check_namespace,
+                            check_dtype=check_dtype, check_shape=check_shape)
+    if is_cupy(xp):
+        return xp.testing.assert_allclose(actual, desired, rtol=rtol,
+                                          atol=atol, err_msg=err_msg)
+    elif is_torch(xp):
+        err_msg = None if err_msg == '' else err_msg
+        return xp.testing.assert_close(actual, desired, rtol=rtol, atol=atol,
+                                       equal_nan=True, check_dtype=False, msg=err_msg)
+    return np.testing.assert_allclose(actual, desired, rtol=rtol,
+                                      atol=atol, err_msg=err_msg)
+
+
+def xp_assert_less(actual, desired, check_namespace=True, check_dtype=True,
+                   check_shape=True, err_msg='', verbose=True, xp=None):
+    if xp is None:
+        xp = array_namespace(actual)
+    desired = _strict_check(actual, desired, xp, check_namespace=check_namespace,
+                            check_dtype=check_dtype, check_shape=check_shape)
+    if is_cupy(xp):
+        return xp.testing.assert_array_less(actual, desired,
+                                            err_msg=err_msg, verbose=verbose)
+    elif is_torch(xp):
+        if actual.device.type != 'cpu':
+            actual = actual.cpu()
+        if desired.device.type != 'cpu':
+            desired = desired.cpu()
+    return np.testing.assert_array_less(actual, desired,
+                                        err_msg=err_msg, verbose=verbose)
+
+
+def cov(x, *, xp=None):
+    if xp is None:
+        xp = array_namespace(x)
+
+    X = copy(x, xp=xp)
+    dtype = xp.result_type(X, xp.float64)
+
+    X = atleast_nd(X, ndim=2, xp=xp)
+    X = xp.asarray(X, dtype=dtype)
+
+    avg = xp.mean(X, axis=1)
+    fact = X.shape[1] - 1
+
+    if fact <= 0:
+        warnings.warn("Degrees of freedom <= 0 for slice",
+                      RuntimeWarning, stacklevel=2)
+        fact = 0.0
+
+    X -= avg[:, None]
+    X_T = X.T
+    if xp.isdtype(X_T.dtype, 'complex floating'):
+        X_T = xp.conj(X_T)
+    c = X @ X_T
+    c /= fact
+    axes = tuple(axis for axis, length in enumerate(c.shape) if length == 1)
+    return xp.squeeze(c, axis=axes)
+
+
+def xp_unsupported_param_msg(param):
+    return f'Providing {param!r} is only supported for numpy arrays.'
+
+
+def is_complex(x, xp):
+    return xp.isdtype(x.dtype, 'complex floating')

scipy/_lib/_bunch.py

@@ -0,0 +1,225 @@
+import sys as _sys
+from keyword import iskeyword as _iskeyword
+
+
+def _validate_names(typename, field_names, extra_field_names):
+    """
+    Ensure that all the given names are valid Python identifiers that
+    do not start with '_'.  Also check that there are no duplicates
+    among field_names + extra_field_names.
+    """
+    for name in [typename] + field_names + extra_field_names:
+        if not isinstance(name, str):
+            raise TypeError('typename and all field names must be strings')
+        if not name.isidentifier():
+            raise ValueError('typename and all field names must be valid '
+                             f'identifiers: {name!r}')
+        if _iskeyword(name):
+            raise ValueError('typename and all field names cannot be a '
+                             f'keyword: {name!r}')
+
+    seen = set()
+    for name in field_names + extra_field_names:
+        if name.startswith('_'):
+            raise ValueError('Field names cannot start with an underscore: '
+                             f'{name!r}')
+        if name in seen:
+            raise ValueError(f'Duplicate field name: {name!r}')
+        seen.add(name)
+
+
+# Note: This code is adapted from CPython:Lib/collections/__init__.py
+def _make_tuple_bunch(typename, field_names, extra_field_names=None,
+                      module=None):
+    """
+    Create a namedtuple-like class with additional attributes.
+
+    This function creates a subclass of tuple that acts like a namedtuple
+    and that has additional attributes.
+
+    The additional attributes are listed in `extra_field_names`.  The
+    values assigned to these attributes are not part of the tuple.
+
+    The reason this function exists is to allow functions in SciPy
+    that currently return a tuple or a namedtuple to returned objects
+    that have additional attributes, while maintaining backwards
+    compatibility.
+
+    This should only be used to enhance *existing* functions in SciPy.
+    New functions are free to create objects as return values without
+    having to maintain backwards compatibility with an old tuple or
+    namedtuple return value.
+
+    Parameters
+    ----------
+    typename : str
+        The name of the type.
+    field_names : list of str
+        List of names of the values to be stored in the tuple. These names
+        will also be attributes of instances, so the values in the tuple
+        can be accessed by indexing or as attributes.  At least one name
+        is required.  See the Notes for additional restrictions.
+    extra_field_names : list of str, optional
+        List of names of values that will be stored as attributes of the
+        object.  See the notes for additional restrictions.
+
+    Returns
+    -------
+    cls : type
+        The new class.
+
+    Notes
+    -----
+    There are restrictions on the names that may be used in `field_names`
+    and `extra_field_names`:
+
+    * The names must be unique--no duplicates allowed.
+    * The names must be valid Python identifiers, and must not begin with
+      an underscore.
+    * The names must not be Python keywords (e.g. 'def', 'and', etc., are
+      not allowed).
+
+    Examples
+    --------
+    >>> from scipy._lib._bunch import _make_tuple_bunch
+
+    Create a class that acts like a namedtuple with length 2 (with field
+    names `x` and `y`) that will also have the attributes `w` and `beta`:
+
+    >>> Result = _make_tuple_bunch('Result', ['x', 'y'], ['w', 'beta'])
+
+    `Result` is the new class.  We call it with keyword arguments to create
+    a new instance with given values.
+
+    >>> result1 = Result(x=1, y=2, w=99, beta=0.5)
+    >>> result1
+    Result(x=1, y=2, w=99, beta=0.5)
+
+    `result1` acts like a tuple of length 2:
+
+    >>> len(result1)
+    2
+    >>> result1[:]
+    (1, 2)
+
+    The values assigned when the instance was created are available as
+    attributes:
+
+    >>> result1.y
+    2
+    >>> result1.beta
+    0.5
+    """
+    if len(field_names) == 0:
+        raise ValueError('field_names must contain at least one name')
+
+    if extra_field_names is None:
+        extra_field_names = []
+    _validate_names(typename, field_names, extra_field_names)
+
+    typename = _sys.intern(str(typename))
+    field_names = tuple(map(_sys.intern, field_names))
+    extra_field_names = tuple(map(_sys.intern, extra_field_names))
+
+    all_names = field_names + extra_field_names
+    arg_list = ', '.join(field_names)
+    full_list = ', '.join(all_names)
+    repr_fmt = ''.join(('(',
+                        ', '.join(f'{name}=%({name})r' for name in all_names),
+                        ')'))
+    tuple_new = tuple.__new__
+    _dict, _tuple, _zip = dict, tuple, zip
+
+    # Create all the named tuple methods to be added to the class namespace
+
+    s = f"""\
+def __new__(_cls, {arg_list}, **extra_fields):
+    return _tuple_new(_cls, ({arg_list},))
+
+def __init__(self, {arg_list}, **extra_fields):
+    for key in self._extra_fields:
+        if key not in extra_fields:
+            raise TypeError("missing keyword argument '%s'" % (key,))
+    for key, val in extra_fields.items():
+        if key not in self._extra_fields:
+            raise TypeError("unexpected keyword argument '%s'" % (key,))
+        self.__dict__[key] = val
+
+def __setattr__(self, key, val):
+    if key in {repr(field_names)}:
+        raise AttributeError("can't set attribute %r of class %r"
+                             % (key, self.__class__.__name__))
+    else:
+        self.__dict__[key] = val
+"""
+    del arg_list
+    namespace = {'_tuple_new': tuple_new,
+                 '__builtins__': dict(TypeError=TypeError,
+                                      AttributeError=AttributeError),
+                 '__name__': f'namedtuple_{typename}'}
+    exec(s, namespace)
+    __new__ = namespace['__new__']
+    __new__.__doc__ = f'Create new instance of {typename}({full_list})'
+    __init__ = namespace['__init__']
+    __init__.__doc__ = f'Instantiate instance of {typename}({full_list})'
+    __setattr__ = namespace['__setattr__']
+
+    def __repr__(self):
+        'Return a nicely formatted representation string'
+        return self.__class__.__name__ + repr_fmt % self._asdict()
+
+    def _asdict(self):
+        'Return a new dict which maps field names to their values.'
+        out = _dict(_zip(self._fields, self))
+        out.update(self.__dict__)
+        return out
+
+    def __getnewargs_ex__(self):
+        'Return self as a plain tuple.  Used by copy and pickle.'
+        return _tuple(self), self.__dict__
+
+    # Modify function metadata to help with introspection and debugging
+    for method in (__new__, __repr__, _asdict, __getnewargs_ex__):
+        method.__qualname__ = f'{typename}.{method.__name__}'
+
+    # Build-up the class namespace dictionary
+    # and use type() to build the result class
+    class_namespace = {
+        '__doc__': f'{typename}({full_list})',
+        '_fields': field_names,
+        '__new__': __new__,
+        '__init__': __init__,
+        '__repr__': __repr__,
+        '__setattr__': __setattr__,
+        '_asdict': _asdict,
+        '_extra_fields': extra_field_names,
+        '__getnewargs_ex__': __getnewargs_ex__,
+    }
+    for index, name in enumerate(field_names):
+
+        def _get(self, index=index):
+            return self[index]
+        class_namespace[name] = property(_get)
+    for name in extra_field_names:
+
+        def _get(self, name=name):
+            return self.__dict__[name]
+        class_namespace[name] = property(_get)
+
+    result = type(typename, (tuple,), class_namespace)
+
+    # For pickling to work, the __module__ variable needs to be set to the
+    # frame where the named tuple is created.  Bypass this step in environments
+    # where sys._getframe is not defined (Jython for example) or sys._getframe
+    # is not defined for arguments greater than 0 (IronPython), or where the
+    # user has specified a particular module.
+    if module is None:
+        try:
+            module = _sys._getframe(1).f_globals.get('__name__', '__main__')
+        except (AttributeError, ValueError):
+            pass
+    if module is not None:
+        result.__module__ = module
+        __new__.__module__ = module
+
+    return result

scipy/_lib/_ccallback.py

@@ -0,0 +1,251 @@
+from . import _ccallback_c
+
+import ctypes
+
+PyCFuncPtr = ctypes.CFUNCTYPE(ctypes.c_void_p).__bases__[0]
+
+ffi = None
+
+class CData:
+    pass
+
+def _import_cffi():
+    global ffi, CData
+
+    if ffi is not None:
+        return
+
+    try:
+        import cffi
+        ffi = cffi.FFI()
+        CData = ffi.CData
+    except ImportError:
+        ffi = False
+
+
+class LowLevelCallable(tuple):
+    """
+    Low-level callback function.
+
+    Some functions in SciPy take as arguments callback functions, which
+    can either be python callables or low-level compiled functions. Using
+    compiled callback functions can improve performance somewhat by
+    avoiding wrapping data in Python objects.
+
+    Such low-level functions in SciPy are wrapped in `LowLevelCallable`
+    objects, which can be constructed from function pointers obtained from
+    ctypes, cffi, Cython, or contained in Python `PyCapsule` objects.
+
+    .. seealso::
+
+       Functions accepting low-level callables:
+
+       `scipy.integrate.quad`, `scipy.ndimage.generic_filter`,
+       `scipy.ndimage.generic_filter1d`, `scipy.ndimage.geometric_transform`
+
+       Usage examples:
+
+       :ref:`ndimage-ccallbacks`, :ref:`quad-callbacks`
+
+    Parameters
+    ----------
+    function : {PyCapsule, ctypes function pointer, cffi function pointer}
+        Low-level callback function.
+    user_data : {PyCapsule, ctypes void pointer, cffi void pointer}
+        User data to pass on to the callback function.
+    signature : str, optional
+        Signature of the function. If omitted, determined from *function*,
+        if possible.
+
+    Attributes
+    ----------
+    function
+        Callback function given.
+    user_data
+        User data given.
+    signature
+        Signature of the function.
+
+    Methods
+    -------
+    from_cython
+        Class method for constructing callables from Cython C-exported
+        functions.
+
+    Notes
+    -----
+    The argument ``function`` can be one of:
+
+    - PyCapsule, whose name contains the C function signature
+    - ctypes function pointer
+    - cffi function pointer
+
+    The signature of the low-level callback must match one of those expected
+    by the routine it is passed to.
+
+    If constructing low-level functions from a PyCapsule, the name of the
+    capsule must be the corresponding signature, in the format::
+
+        return_type (arg1_type, arg2_type, ...)
+
+    For example::
+
+        "void (double)"
+        "double (double, int *, void *)"
+
+    The context of a PyCapsule passed in as ``function`` is used as ``user_data``,
+    if an explicit value for ``user_data`` was not given.
+
+    """
+
+    # Make the class immutable
+    __slots__ = ()
+
+    def __new__(cls, function, user_data=None, signature=None):
+        # We need to hold a reference to the function & user data,
+        # to prevent them going out of scope
+        item = cls._parse_callback(function, user_data, signature)
+        return tuple.__new__(cls, (item, function, user_data))
+
+    def __repr__(self):
+        return f"LowLevelCallable({self.function!r}, {self.user_data!r})"
+
+    @property
+    def function(self):
+        return tuple.__getitem__(self, 1)
+
+    @property
+    def user_data(self):
+        return tuple.__getitem__(self, 2)
+
+    @property
+    def signature(self):
+        return _ccallback_c.get_capsule_signature(tuple.__getitem__(self, 0))
+
+    def __getitem__(self, idx):
+        raise ValueError()
+
+    @classmethod
+    def from_cython(cls, module, name, user_data=None, signature=None):
+        """
+        Create a low-level callback function from an exported Cython function.
+
+        Parameters
+        ----------
+        module : module
+            Cython module where the exported function resides
+        name : str
+            Name of the exported function
+        user_data : {PyCapsule, ctypes void pointer, cffi void pointer}, optional
+            User data to pass on to the callback function.
+        signature : str, optional
+            Signature of the function. If omitted, determined from *function*.
+
+        """
+        try:
+            function = module.__pyx_capi__[name]
+        except AttributeError as e:
+            message = "Given module is not a Cython module with __pyx_capi__ attribute"
+            raise ValueError(message) from e
+        except KeyError as e:
+            message = f"No function {name!r} found in __pyx_capi__ of the module"
+            raise ValueError(message) from e
+        return cls(function, user_data, signature)
+
+    @classmethod
+    def _parse_callback(cls, obj, user_data=None, signature=None):
+        _import_cffi()
+
+        if isinstance(obj, LowLevelCallable):
+            func = tuple.__getitem__(obj, 0)
+        elif isinstance(obj, PyCFuncPtr):
+            func, signature = _get_ctypes_func(obj, signature)
+        elif isinstance(obj, CData):
+            func, signature = _get_cffi_func(obj, signature)
+        elif _ccallback_c.check_capsule(obj):
+            func = obj
+        else:
+            raise ValueError("Given input is not a callable or a "
+                             "low-level callable (pycapsule/ctypes/cffi)")
+
+        if isinstance(user_data, ctypes.c_void_p):
+            context = _get_ctypes_data(user_data)
+        elif isinstance(user_data, CData):
+            context = _get_cffi_data(user_data)
+        elif user_data is None:
+            context = 0
+        elif _ccallback_c.check_capsule(user_data):
+            context = user_data
+        else:
+            raise ValueError("Given user data is not a valid "
+                             "low-level void* pointer (pycapsule/ctypes/cffi)")
+
+        return _ccallback_c.get_raw_capsule(func, signature, context)
+
+
+#
+# ctypes helpers
+#
+
+def _get_ctypes_func(func, signature=None):
+    # Get function pointer
+    func_ptr = ctypes.cast(func, ctypes.c_void_p).value
+
+    # Construct function signature
+    if signature is None:
+        signature = _typename_from_ctypes(func.restype) + " ("
+        for j, arg in enumerate(func.argtypes):
+            if j == 0:
+                signature += _typename_from_ctypes(arg)
+            else:
+                signature += ", " + _typename_from_ctypes(arg)
+        signature += ")"
+
+    return func_ptr, signature
+
+
+def _typename_from_ctypes(item):
+    if item is None:
+        return "void"
+    elif item is ctypes.c_void_p:
+        return "void *"
+
+    name = item.__name__
+
+    pointer_level = 0
+    while name.startswith("LP_"):
+        pointer_level += 1
+        name = name[3:]
+
+    if name.startswith('c_'):
+        name = name[2:]
+
+    if pointer_level > 0:
+        name += " " + "*"*pointer_level
+
+    return name
+
+
+def _get_ctypes_data(data):
+    # Get voidp pointer
+    return ctypes.cast(data, ctypes.c_void_p).value
+
+
+#
+# CFFI helpers
+#
+
+def _get_cffi_func(func, signature=None):
+    # Get function pointer
+    func_ptr = ffi.cast('uintptr_t', func)
+
+    # Get signature
+    if signature is None:
+        signature = ffi.getctype(ffi.typeof(func)).replace('(*)', ' ')
+
+    return func_ptr, signature
+
+
+def _get_cffi_data(data):
+    # Get pointer
+    return ffi.cast('uintptr_t', data)

scipy/_lib/_disjoint_set.py

@@ -0,0 +1,254 @@
+"""
+Disjoint set data structure
+"""
+
+
+class DisjointSet:
+    """ Disjoint set data structure for incremental connectivity queries.
+
+    .. versionadded:: 1.6.0
+
+    Attributes
+    ----------
+    n_subsets : int
+        The number of subsets.
+
+    Methods
+    -------
+    add
+    merge
+    connected
+    subset
+    subset_size
+    subsets
+    __getitem__
+
+    Notes
+    -----
+    This class implements the disjoint set [1]_, also known as the *union-find*
+    or *merge-find* data structure. The *find* operation (implemented in
+    `__getitem__`) implements the *path halving* variant. The *merge* method
+    implements the *merge by size* variant.
+
+    References
+    ----------
+    .. [1] https://en.wikipedia.org/wiki/Disjoint-set_data_structure
+
+    Examples
+    --------
+    >>> from scipy.cluster.hierarchy import DisjointSet
+
+    Initialize a disjoint set:
+
+    >>> disjoint_set = DisjointSet([1, 2, 3, 'a', 'b'])
+
+    Merge some subsets:
+
+    >>> disjoint_set.merge(1, 2)
+    True
+    >>> disjoint_set.merge(3, 'a')
+    True
+    >>> disjoint_set.merge('a', 'b')
+    True
+    >>> disjoint_set.merge('b', 'b')
+    False
+
+    Find root elements:
+
+    >>> disjoint_set[2]
+    1
+    >>> disjoint_set['b']
+    3
+
+    Test connectivity:
+
+    >>> disjoint_set.connected(1, 2)
+    True
+    >>> disjoint_set.connected(1, 'b')
+    False
+
+    List elements in disjoint set:
+
+    >>> list(disjoint_set)
+    [1, 2, 3, 'a', 'b']
+
+    Get the subset containing 'a':
+
+    >>> disjoint_set.subset('a')
+    {'a', 3, 'b'}
+
+    Get the size of the subset containing 'a' (without actually instantiating
+    the subset):
+
+    >>> disjoint_set.subset_size('a')
+    3
+
+    Get all subsets in the disjoint set:
+
+    >>> disjoint_set.subsets()
+    [{1, 2}, {'a', 3, 'b'}]
+    """
+    def __init__(self, elements=None):
+        self.n_subsets = 0
+        self._sizes = {}
+        self._parents = {}
+        # _nbrs is a circular linked list which links connected elements.
+        self._nbrs = {}
+        # _indices tracks the element insertion order in `__iter__`.
+        self._indices = {}
+        if elements is not None:
+            for x in elements:
+                self.add(x)
+
+    def __iter__(self):
+        """Returns an iterator of the elements in the disjoint set.
+
+        Elements are ordered by insertion order.
+        """
+        return iter(self._indices)
+
+    def __len__(self):
+        return len(self._indices)
+
+    def __contains__(self, x):
+        return x in self._indices
+
+    def __getitem__(self, x):
+        """Find the root element of `x`.
+
+        Parameters
+        ----------
+        x : hashable object
+            Input element.
+
+        Returns
+        -------
+        root : hashable object
+            Root element of `x`.
+        """
+        if x not in self._indices:
+            raise KeyError(x)
+
+        # find by "path halving"
+        parents = self._parents
+        while self._indices[x] != self._indices[parents[x]]:
+            parents[x] = parents[parents[x]]
+            x = parents[x]
+        return x
+
+    def add(self, x):
+        """Add element `x` to disjoint set
+        """
+        if x in self._indices:
+            return
+
+        self._sizes[x] = 1
+        self._parents[x] = x
+        self._nbrs[x] = x
+        self._indices[x] = len(self._indices)
+        self.n_subsets += 1
+
+    def merge(self, x, y):
+        """Merge the subsets of `x` and `y`.
+
+        The smaller subset (the child) is merged into the larger subset (the
+        parent). If the subsets are of equal size, the root element which was
+        first inserted into the disjoint set is selected as the parent.
+
+        Parameters
+        ----------
+        x, y : hashable object
+            Elements to merge.
+
+        Returns
+        -------
+        merged : bool
+            True if `x` and `y` were in disjoint sets, False otherwise.
+        """
+        xr = self[x]
+        yr = self[y]
+        if self._indices[xr] == self._indices[yr]:
+            return False
+
+        sizes = self._sizes
+        if (sizes[xr], self._indices[yr]) < (sizes[yr], self._indices[xr]):
+            xr, yr = yr, xr
+        self._parents[yr] = xr
+        self._sizes[xr] += self._sizes[yr]
+        self._nbrs[xr], self._nbrs[yr] = self._nbrs[yr], self._nbrs[xr]
+        self.n_subsets -= 1
+        return True
+
+    def connected(self, x, y):
+        """Test whether `x` and `y` are in the same subset.
+
+        Parameters
+        ----------
+        x, y : hashable object
+            Elements to test.
+
+        Returns
+        -------
+        result : bool
+            True if `x` and `y` are in the same set, False otherwise.
+        """
+        return self._indices[self[x]] == self._indices[self[y]]
+
+    def subset(self, x):
+        """Get the subset containing `x`.
+
+        Parameters
+        ----------
+        x : hashable object
+            Input element.
+
+        Returns
+        -------
+        result : set
+            Subset containing `x`.
+        """
+        if x not in self._indices:
+            raise KeyError(x)
+
+        result = [x]
+        nxt = self._nbrs[x]
+        while self._indices[nxt] != self._indices[x]:
+            result.append(nxt)
+            nxt = self._nbrs[nxt]
+        return set(result)
+
+    def subset_size(self, x):
+        """Get the size of the subset containing `x`.
+
+        Note that this method is faster than ``len(self.subset(x))`` because
+        the size is directly read off an internal field, without the need to
+        instantiate the full subset.
+
+        Parameters
+        ----------
+        x : hashable object
+            Input element.
+
+        Returns
+        -------
+        result : int
+            Size of the subset containing `x`.
+        """
+        return self._sizes[self[x]]
+
+    def subsets(self):
+        """Get all the subsets in the disjoint set.
+
+        Returns
+        -------
+        result : list
+            Subsets in the disjoint set.
+        """
+        result = []
+        visited = set()
+        for x in self:
+            if x not in visited:
+                xset = self.subset(x)
+                visited.update(xset)
+                result.append(xset)
+        return result

scipy/_lib/_docscrape.py

@@ -0,0 +1,679 @@
+"""Extract reference documentation from the NumPy source tree.
+
+"""
+# copied from numpydoc/docscrape.py
+import inspect
+import textwrap
+import re
+import pydoc
+from warnings import warn
+from collections import namedtuple
+from collections.abc import Callable, Mapping
+import copy
+import sys
+
+
+def strip_blank_lines(l):
+    "Remove leading and trailing blank lines from a list of lines"
+    while l and not l[0].strip():
+        del l[0]
+    while l and not l[-1].strip():
+        del l[-1]
+    return l
+
+
+class Reader:
+    """A line-based string reader.
+
+    """
+    def __init__(self, data):
+        """
+        Parameters
+        ----------
+        data : str
+           String with lines separated by '\\n'.
+
+        """
+        if isinstance(data, list):
+            self._str = data
+        else:
+            self._str = data.split('\n')  # store string as list of lines
+
+        self.reset()
+
+    def __getitem__(self, n):
+        return self._str[n]
+
+    def reset(self):
+        self._l = 0  # current line nr
+
+    def read(self):
+        if not self.eof():
+            out = self[self._l]
+            self._l += 1
+            return out
+        else:
+            return ''
+
+    def seek_next_non_empty_line(self):
+        for l in self[self._l:]:
+            if l.strip():
+                break
+            else:
+                self._l += 1
+
+    def eof(self):
+        return self._l >= len(self._str)
+
+    def read_to_condition(self, condition_func):
+        start = self._l
+        for line in self[start:]:
+            if condition_func(line):
+                return self[start:self._l]
+            self._l += 1
+            if self.eof():
+                return self[start:self._l+1]
+        return []
+
+    def read_to_next_empty_line(self):
+        self.seek_next_non_empty_line()
+
+        def is_empty(line):
+            return not line.strip()
+
+        return self.read_to_condition(is_empty)
+
+    def read_to_next_unindented_line(self):
+        def is_unindented(line):
+            return (line.strip() and (len(line.lstrip()) == len(line)))
+        return self.read_to_condition(is_unindented)
+
+    def peek(self, n=0):
+        if self._l + n < len(self._str):
+            return self[self._l + n]
+        else:
+            return ''
+
+    def is_empty(self):
+        return not ''.join(self._str).strip()
+
+
+class ParseError(Exception):
+    def __str__(self):
+        message = self.args[0]
+        if hasattr(self, 'docstring'):
+            message = f"{message} in {self.docstring!r}"
+        return message
+
+
+Parameter = namedtuple('Parameter', ['name', 'type', 'desc'])
+
+
+class NumpyDocString(Mapping):
+    """Parses a numpydoc string to an abstract representation
+
+    Instances define a mapping from section title to structured data.
+
+    """
+
+    sections = {
+        'Signature': '',
+        'Summary': [''],
+        'Extended Summary': [],
+        'Parameters': [],
+        'Returns': [],
+        'Yields': [],
+        'Receives': [],
+        'Raises': [],
+        'Warns': [],
+        'Other Parameters': [],
+        'Attributes': [],
+        'Methods': [],
+        'See Also': [],
+        'Notes': [],
+        'Warnings': [],
+        'References': '',
+        'Examples': '',
+        'index': {}
+    }
+
+    def __init__(self, docstring, config={}):
+        orig_docstring = docstring
+        docstring = textwrap.dedent(docstring).split('\n')
+
+        self._doc = Reader(docstring)
+        self._parsed_data = copy.deepcopy(self.sections)
+
+        try:
+            self._parse()
+        except ParseError as e:
+            e.docstring = orig_docstring
+            raise
+
+    def __getitem__(self, key):
+        return self._parsed_data[key]
+
+    def __setitem__(self, key, val):
+        if key not in self._parsed_data:
+            self._error_location("Unknown section %s" % key, error=False)
+        else:
+            self._parsed_data[key] = val
+
+    def __iter__(self):
+        return iter(self._parsed_data)
+
+    def __len__(self):
+        return len(self._parsed_data)
+
+    def _is_at_section(self):
+        self._doc.seek_next_non_empty_line()
+
+        if self._doc.eof():
+            return False
+
+        l1 = self._doc.peek().strip()  # e.g. Parameters
+
+        if l1.startswith('.. index::'):
+            return True
+
+        l2 = self._doc.peek(1).strip()  # ---------- or ==========
+        return l2.startswith('-'*len(l1)) or l2.startswith('='*len(l1))
+
+    def _strip(self, doc):
+        i = 0
+        j = 0
+        for i, line in enumerate(doc):
+            if line.strip():
+                break
+
+        for j, line in enumerate(doc[::-1]):
+            if line.strip():
+                break
+
+        return doc[i:len(doc)-j]
+
+    def _read_to_next_section(self):
+        section = self._doc.read_to_next_empty_line()
+
+        while not self._is_at_section() and not self._doc.eof():
+            if not self._doc.peek(-1).strip():  # previous line was empty
+                section += ['']
+
+            section += self._doc.read_to_next_empty_line()
+
+        return section
+
+    def _read_sections(self):
+        while not self._doc.eof():
+            data = self._read_to_next_section()
+            name = data[0].strip()
+
+            if name.startswith('..'):  # index section
+                yield name, data[1:]
+            elif len(data) < 2:
+                yield StopIteration
+            else:
+                yield name, self._strip(data[2:])
+
+    def _parse_param_list(self, content, single_element_is_type=False):
+        r = Reader(content)
+        params = []
+        while not r.eof():
+            header = r.read().strip()
+            if ' : ' in header:
+                arg_name, arg_type = header.split(' : ')[:2]
+            else:
+                if single_element_is_type:
+                    arg_name, arg_type = '', header
+                else:
+                    arg_name, arg_type = header, ''
+
+            desc = r.read_to_next_unindented_line()
+            desc = dedent_lines(desc)
+            desc = strip_blank_lines(desc)
+
+            params.append(Parameter(arg_name, arg_type, desc))
+
+        return params
+
+    # See also supports the following formats.
+    #
+    # <FUNCNAME>
+    # <FUNCNAME> SPACE* COLON SPACE+ <DESC> SPACE*
+    # <FUNCNAME> ( COMMA SPACE+ <FUNCNAME>)+ (COMMA | PERIOD)? SPACE*
+    # <FUNCNAME> ( COMMA SPACE+ <FUNCNAME>)* SPACE* COLON SPACE+ <DESC> SPACE*
+
+    # <FUNCNAME> is one of
+    #   <PLAIN_FUNCNAME>
+    #   COLON <ROLE> COLON BACKTICK <PLAIN_FUNCNAME> BACKTICK
+    # where
+    #   <PLAIN_FUNCNAME> is a legal function name, and
+    #   <ROLE> is any nonempty sequence of word characters.
+    # Examples: func_f1  :meth:`func_h1` :obj:`~baz.obj_r` :class:`class_j`
+    # <DESC> is a string describing the function.
+
+    _role = r":(?P<role>\w+):"
+    _funcbacktick = r"`(?P<name>(?:~\w+\.)?[a-zA-Z0-9_\.-]+)`"
+    _funcplain = r"(?P<name2>[a-zA-Z0-9_\.-]+)"
+    _funcname = r"(" + _role + _funcbacktick + r"|" + _funcplain + r")"
+    _funcnamenext = _funcname.replace('role', 'rolenext')
+    _funcnamenext = _funcnamenext.replace('name', 'namenext')
+    _description = r"(?P<description>\s*:(\s+(?P<desc>\S+.*))?)?\s*$"
+    _func_rgx = re.compile(r"^\s*" + _funcname + r"\s*")
+    _line_rgx = re.compile(
+        r"^\s*" +
+        r"(?P<allfuncs>" +        # group for all function names
+        _funcname +
+        r"(?P<morefuncs>([,]\s+" + _funcnamenext + r")*)" +
+        r")" +                     # end of "allfuncs"
+        # Some function lists have a trailing comma (or period)  '\s*'
+        r"(?P<trailing>[,\.])?" +
+        _description)
+
+    # Empty <DESC> elements are replaced with '..'
+    empty_description = '..'
+
+    def _parse_see_also(self, content):
+        """
+        func_name : Descriptive text
+            continued text
+        another_func_name : Descriptive text
+        func_name1, func_name2, :meth:`func_name`, func_name3
+
+        """
+
+        items = []
+
+        def parse_item_name(text):
+            """Match ':role:`name`' or 'name'."""
+            m = self._func_rgx.match(text)
+            if not m:
+                raise ParseError("%s is not a item name" % text)
+            role = m.group('role')
+            name = m.group('name') if role else m.group('name2')
+            return name, role, m.end()
+
+        rest = []
+        for line in content:
+            if not line.strip():
+                continue
+
+            line_match = self._line_rgx.match(line)
+            description = None
+            if line_match:
+                description = line_match.group('desc')
+                if line_match.group('trailing') and description:
+                    self._error_location(
+                        'Unexpected comma or period after function list at '
+                        'index %d of line "%s"' % (line_match.end('trailing'),
+                                                   line),
+                        error=False)
+            if not description and line.startswith(' '):
+                rest.append(line.strip())
+            elif line_match:
+                funcs = []
+                text = line_match.group('allfuncs')
+                while True:
+                    if not text.strip():
+                        break
+                    name, role, match_end = parse_item_name(text)
+                    funcs.append((name, role))
+                    text = text[match_end:].strip()
+                    if text and text[0] == ',':
+                        text = text[1:].strip()
+                rest = list(filter(None, [description]))
+                items.append((funcs, rest))
+            else:
+                raise ParseError("%s is not a item name" % line)
+        return items
+
+    def _parse_index(self, section, content):
+        """
+        .. index:: default
+           :refguide: something, else, and more
+
+        """
+        def strip_each_in(lst):
+            return [s.strip() for s in lst]
+
+        out = {}
+        section = section.split('::')
+        if len(section) > 1:
+            out['default'] = strip_each_in(section[1].split(','))[0]
+        for line in content:
+            line = line.split(':')
+            if len(line) > 2:
+                out[line[1]] = strip_each_in(line[2].split(','))
+        return out
+
+    def _parse_summary(self):
+        """Grab signature (if given) and summary"""
+        if self._is_at_section():
+            return
+
+        # If several signatures present, take the last one
+        while True:
+            summary = self._doc.read_to_next_empty_line()
+            summary_str = " ".join([s.strip() for s in summary]).strip()
+            compiled = re.compile(r'^([\w., ]+=)?\s*[\w\.]+\(.*\)$')
+            if compiled.match(summary_str):
+                self['Signature'] = summary_str
+                if not self._is_at_section():
+                    continue
+            break
+
+        if summary is not None:
+            self['Summary'] = summary
+
+        if not self._is_at_section():
+            self['Extended Summary'] = self._read_to_next_section()
+
+    def _parse(self):
+        self._doc.reset()
+        self._parse_summary()
+
+        sections = list(self._read_sections())
+        section_names = {section for section, content in sections}
+
+        has_returns = 'Returns' in section_names
+        has_yields = 'Yields' in section_names
+        # We could do more tests, but we are not. Arbitrarily.
+        if has_returns and has_yields:
+            msg = 'Docstring contains both a Returns and Yields section.'
+            raise ValueError(msg)
+        if not has_yields and 'Receives' in section_names:
+            msg = 'Docstring contains a Receives section but not Yields.'
+            raise ValueError(msg)
+
+        for (section, content) in sections:
+            if not section.startswith('..'):
+                section = (s.capitalize() for s in section.split(' '))
+                section = ' '.join(section)
+                if self.get(section):
+                    self._error_location("The section %s appears twice"
+                                         % section)
+
+            if section in ('Parameters', 'Other Parameters', 'Attributes',
+                           'Methods'):
+                self[section] = self._parse_param_list(content)
+            elif section in ('Returns', 'Yields', 'Raises', 'Warns',
+                             'Receives'):
+                self[section] = self._parse_param_list(
+                    content, single_element_is_type=True)
+            elif section.startswith('.. index::'):
+                self['index'] = self._parse_index(section, content)
+            elif section == 'See Also':
+                self['See Also'] = self._parse_see_also(content)
+            else:
+                self[section] = content
+
+    def _error_location(self, msg, error=True):
+        if hasattr(self, '_obj'):
+            # we know where the docs came from:
+            try:
+                filename = inspect.getsourcefile(self._obj)
+            except TypeError:
+                filename = None
+            msg = msg + (f" in the docstring of {self._obj} in {filename}.")
+        if error:
+            raise ValueError(msg)
+        else:
+            warn(msg, stacklevel=3)
+
+    # string conversion routines
+
+    def _str_header(self, name, symbol='-'):
+        return [name, len(name)*symbol]
+
+    def _str_indent(self, doc, indent=4):
+        out = []
+        for line in doc:
+            out += [' '*indent + line]
+        return out
+
+    def _str_signature(self):
+        if self['Signature']:
+            return [self['Signature'].replace('*', r'\*')] + ['']
+        else:
+            return ['']
+
+    def _str_summary(self):
+        if self['Summary']:
+            return self['Summary'] + ['']
+        else:
+            return []
+
+    def _str_extended_summary(self):
+        if self['Extended Summary']:
+            return self['Extended Summary'] + ['']
+        else:
+            return []
+
+    def _str_param_list(self, name):
+        out = []
+        if self[name]:
+            out += self._str_header(name)
+            for param in self[name]:
+                parts = []
+                if param.name:
+                    parts.append(param.name)
+                if param.type:
+                    parts.append(param.type)
+                out += [' : '.join(parts)]
+                if param.desc and ''.join(param.desc).strip():
+                    out += self._str_indent(param.desc)
+            out += ['']
+        return out
+
+    def _str_section(self, name):
+        out = []
+        if self[name]:
+            out += self._str_header(name)
+            out += self[name]
+            out += ['']
+        return out
+
+    def _str_see_also(self, func_role):
+        if not self['See Also']:
+            return []
+        out = []
+        out += self._str_header("See Also")
+        out += ['']
+        last_had_desc = True
+        for funcs, desc in self['See Also']:
+            assert isinstance(funcs, list)
+            links = []
+            for func, role in funcs:
+                if role:
+                    link = f':{role}:`{func}`'
+                elif func_role:
+                    link = f':{func_role}:`{func}`'
+                else:
+                    link = "`%s`_" % func
+                links.append(link)
+            link = ', '.join(links)
+            out += [link]
+            if desc:
+                out += self._str_indent([' '.join(desc)])
+                last_had_desc = True
+            else:
+                last_had_desc = False
+                out += self._str_indent([self.empty_description])
+
+        if last_had_desc:
+            out += ['']
+        out += ['']
+        return out
+
+    def _str_index(self):
+        idx = self['index']
+        out = []
+        output_index = False
+        default_index = idx.get('default', '')
+        if default_index:
+            output_index = True
+        out += ['.. index:: %s' % default_index]
+        for section, references in idx.items():
+            if section == 'default':
+                continue
+            output_index = True
+            out += ['   :{}: {}'.format(section, ', '.join(references))]
+        if output_index:
+            return out
+        else:
+            return ''
+
+    def __str__(self, func_role=''):
+        out = []
+        out += self._str_signature()
+        out += self._str_summary()
+        out += self._str_extended_summary()
+        for param_list in ('Parameters', 'Returns', 'Yields', 'Receives',
+                           'Other Parameters', 'Raises', 'Warns'):
+            out += self._str_param_list(param_list)
+        out += self._str_section('Warnings')
+        out += self._str_see_also(func_role)
+        for s in ('Notes', 'References', 'Examples'):
+            out += self._str_section(s)
+        for param_list in ('Attributes', 'Methods'):
+            out += self._str_param_list(param_list)
+        out += self._str_index()
+        return '\n'.join(out)
+
+
+def indent(str, indent=4):
+    indent_str = ' '*indent
+    if str is None:
+        return indent_str
+    lines = str.split('\n')
+    return '\n'.join(indent_str + l for l in lines)
+
+
+def dedent_lines(lines):
+    """Deindent a list of lines maximally"""
+    return textwrap.dedent("\n".join(lines)).split("\n")
+
+
+def header(text, style='-'):
+    return text + '\n' + style*len(text) + '\n'
+
+
+class FunctionDoc(NumpyDocString):
+    def __init__(self, func, role='func', doc=None, config={}):
+        self._f = func
+        self._role = role  # e.g. "func" or "meth"
+
+        if doc is None:
+            if func is None:
+                raise ValueError("No function or docstring given")
+            doc = inspect.getdoc(func) or ''
+        NumpyDocString.__init__(self, doc, config)
+
+    def get_func(self):
+        func_name = getattr(self._f, '__name__', self.__class__.__name__)
+        if inspect.isclass(self._f):
+            func = getattr(self._f, '__call__', self._f.__init__)
+        else:
+            func = self._f
+        return func, func_name
+
+    def __str__(self):
+        out = ''
+
+        func, func_name = self.get_func()
+
+        roles = {'func': 'function',
+                 'meth': 'method'}
+
+        if self._role:
+            if self._role not in roles:
+                print("Warning: invalid role %s" % self._role)
+            out += '.. {}:: {}\n    \n\n'.format(roles.get(self._role, ''),
+                                             func_name)
+
+        out += super().__str__(func_role=self._role)
+        return out
+
+
+class ClassDoc(NumpyDocString):
+
+    extra_public_methods = ['__call__']
+
+    def __init__(self, cls, doc=None, modulename='', func_doc=FunctionDoc,
+                 config={}):
+        if not inspect.isclass(cls) and cls is not None:
+            raise ValueError("Expected a class or None, but got %r" % cls)
+        self._cls = cls
+
+        if 'sphinx' in sys.modules:
+            from sphinx.ext.autodoc import ALL
+        else:
+            ALL = object()
+
+        self.show_inherited_members = config.get(
+                    'show_inherited_class_members', True)
+
+        if modulename and not modulename.endswith('.'):
+            modulename += '.'
+        self._mod = modulename
+
+        if doc is None:
+            if cls is None:
+                raise ValueError("No class or documentation string given")
+            doc = pydoc.getdoc(cls)
+
+        NumpyDocString.__init__(self, doc)
+
+        _members = config.get('members', [])
+        if _members is ALL:
+            _members = None
+        _exclude = config.get('exclude-members', [])
+
+        if config.get('show_class_members', True) and _exclude is not ALL:
+            def splitlines_x(s):
+                if not s:
+                    return []
+                else:
+                    return s.splitlines()
+            for field, items in [('Methods', self.methods),
+                                 ('Attributes', self.properties)]:
+                if not self[field]:
+                    doc_list = []
+                    for name in sorted(items):
+                        if (name in _exclude or
+                                (_members and name not in _members)):
+                            continue
+                        try:
+                            doc_item = pydoc.getdoc(getattr(self._cls, name))
+                            doc_list.append(
+                                Parameter(name, '', splitlines_x(doc_item)))
+                        except AttributeError:
+                            pass  # method doesn't exist
+                    self[field] = doc_list
+
+    @property
+    def methods(self):
+        if self._cls is None:
+            return []
+        return [name for name, func in inspect.getmembers(self._cls)
+                if ((not name.startswith('_')
+                     or name in self.extra_public_methods)
+                    and isinstance(func, Callable)
+                    and self._is_show_member(name))]
+
+    @property
+    def properties(self):
+        if self._cls is None:
+            return []
+        return [name for name, func in inspect.getmembers(self._cls)
+                if (not name.startswith('_') and
+                    (func is None or isinstance(func, property) or
+                     inspect.isdatadescriptor(func))
+                    and self._is_show_member(name))]
+
+    def _is_show_member(self, name):
+        if self.show_inherited_members:
+            return True  # show all class members
+        if name not in self._cls.__dict__:
+            return False  # class member is inherited, we do not show it
+        return True

scipy/_lib/_finite_differences.py

@@ -0,0 +1,145 @@
+from numpy import arange, newaxis, hstack, prod, array
+
+
+def _central_diff_weights(Np, ndiv=1):
+    """
+    Return weights for an Np-point central derivative.
+
+    Assumes equally-spaced function points.
+
+    If weights are in the vector w, then
+    derivative is w[0] * f(x-ho*dx) + ... + w[-1] * f(x+h0*dx)
+
+    Parameters
+    ----------
+    Np : int
+        Number of points for the central derivative.
+    ndiv : int, optional
+        Number of divisions. Default is 1.
+
+    Returns
+    -------
+    w : ndarray
+        Weights for an Np-point central derivative. Its size is `Np`.
+
+    Notes
+    -----
+    Can be inaccurate for a large number of points.
+
+    Examples
+    --------
+    We can calculate a derivative value of a function.
+
+    >>> def f(x):
+    ...     return 2 * x**2 + 3
+    >>> x = 3.0 # derivative point
+    >>> h = 0.1 # differential step
+    >>> Np = 3 # point number for central derivative
+    >>> weights = _central_diff_weights(Np) # weights for first derivative
+    >>> vals = [f(x + (i - Np/2) * h) for i in range(Np)]
+    >>> sum(w * v for (w, v) in zip(weights, vals))/h
+    11.79999999999998
+
+    This value is close to the analytical solution:
+    f'(x) = 4x, so f'(3) = 12
+
+    References
+    ----------
+    .. [1] https://en.wikipedia.org/wiki/Finite_difference
+
+    """
+    if Np < ndiv + 1:
+        raise ValueError(
+            "Number of points must be at least the derivative order + 1."
+        )
+    if Np % 2 == 0:
+        raise ValueError("The number of points must be odd.")
+    from scipy import linalg
+
+    ho = Np >> 1
+    x = arange(-ho, ho + 1.0)
+    x = x[:, newaxis]
+    X = x**0.0
+    for k in range(1, Np):
+        X = hstack([X, x**k])
+    w = prod(arange(1, ndiv + 1), axis=0) * linalg.inv(X)[ndiv]
+    return w
+
+
+def _derivative(func, x0, dx=1.0, n=1, args=(), order=3):
+    """
+    Find the nth derivative of a function at a point.
+
+    Given a function, use a central difference formula with spacing `dx` to
+    compute the nth derivative at `x0`.
+
+    Parameters
+    ----------
+    func : function
+        Input function.
+    x0 : float
+        The point at which the nth derivative is found.
+    dx : float, optional
+        Spacing.
+    n : int, optional
+        Order of the derivative. Default is 1.
+    args : tuple, optional
+        Arguments
+    order : int, optional
+        Number of points to use, must be odd.
+
+    Notes
+    -----
+    Decreasing the step size too small can result in round-off error.
+
+    Examples
+    --------
+    >>> def f(x):
+    ...     return x**3 + x**2
+    >>> _derivative(f, 1.0, dx=1e-6)
+    4.9999999999217337
+
+    """
+    if order < n + 1:
+        raise ValueError(
+            "'order' (the number of points used to compute the derivative), "
+            "must be at least the derivative order 'n' + 1."
+        )
+    if order % 2 == 0:
+        raise ValueError(
+            "'order' (the number of points used to compute the derivative) "
+            "must be odd."
+        )
+    # pre-computed for n=1 and 2 and low-order for speed.
+    if n == 1:
+        if order == 3:
+            weights = array([-1, 0, 1]) / 2.0
+        elif order == 5:
+            weights = array([1, -8, 0, 8, -1]) / 12.0
+        elif order == 7:
+            weights = array([-1, 9, -45, 0, 45, -9, 1]) / 60.0
+        elif order == 9:
+            weights = array([3, -32, 168, -672, 0, 672, -168, 32, -3]) / 840.0
+        else:
+            weights = _central_diff_weights(order, 1)
+    elif n == 2:
+        if order == 3:
+            weights = array([1, -2.0, 1])
+        elif order == 5:
+            weights = array([-1, 16, -30, 16, -1]) / 12.0
+        elif order == 7:
+            weights = array([2, -27, 270, -490, 270, -27, 2]) / 180.0
+        elif order == 9:
+            weights = (
+                array([-9, 128, -1008, 8064, -14350, 8064, -1008, 128, -9])
+                / 5040.0
+            )
+        else:
+            weights = _central_diff_weights(order, 2)
+    else:
+        weights = _central_diff_weights(order, n)
+    val = 0.0
+    ho = order >> 1
+    for k in range(order):
+        val += weights[k] * func(x0 + (k - ho) * dx, *args)
+    return val / prod((dx,) * n, axis=0)

scipy/_lib/_gcutils.py

@@ -0,0 +1,105 @@
+"""
+Module for testing automatic garbage collection of objects
+
+.. autosummary::
+   :toctree: generated/
+
+   set_gc_state - enable or disable garbage collection
+   gc_state - context manager for given state of garbage collector
+   assert_deallocated - context manager to check for circular references on object
+
+"""
+import weakref
+import gc
+
+from contextlib import contextmanager
+from platform import python_implementation
+
+__all__ = ['set_gc_state', 'gc_state', 'assert_deallocated']
+
+
+IS_PYPY = python_implementation() == 'PyPy'
+
+
+class ReferenceError(AssertionError):
+    pass
+
+
+def set_gc_state(state):
+    """ Set status of garbage collector """
+    if gc.isenabled() == state:
+        return
+    if state:
+        gc.enable()
+    else:
+        gc.disable()
+
+
+@contextmanager
+def gc_state(state):
+    """ Context manager to set state of garbage collector to `state`
+
+    Parameters
+    ----------
+    state : bool
+        True for gc enabled, False for disabled
+
+    Examples
+    --------
+    >>> with gc_state(False):
+    ...     assert not gc.isenabled()
+    >>> with gc_state(True):
+    ...     assert gc.isenabled()
+    """
+    orig_state = gc.isenabled()
+    set_gc_state(state)
+    yield
+    set_gc_state(orig_state)
+
+
+@contextmanager
+def assert_deallocated(func, *args, **kwargs):
+    """Context manager to check that object is deallocated
+
+    This is useful for checking that an object can be freed directly by
+    reference counting, without requiring gc to break reference cycles.
+    GC is disabled inside the context manager.
+
+    This check is not available on PyPy.
+
+    Parameters
+    ----------
+    func : callable
+        Callable to create object to check
+    \\*args : sequence
+        positional arguments to `func` in order to create object to check
+    \\*\\*kwargs : dict
+        keyword arguments to `func` in order to create object to check
+
+    Examples
+    --------
+    >>> class C: pass
+    >>> with assert_deallocated(C) as c:
+    ...     # do something
+    ...     del c
+
+    >>> class C:
+    ...     def __init__(self):
+    ...         self._circular = self # Make circular reference
+    >>> with assert_deallocated(C) as c: #doctest: +IGNORE_EXCEPTION_DETAIL
+    ...     # do something
+    ...     del c
+    Traceback (most recent call last):
+        ...
+    ReferenceError: Remaining reference(s) to object
+    """
+    if IS_PYPY:
+        raise RuntimeError("assert_deallocated is unavailable on PyPy")
+
+    with gc_state(False):
+        obj = func(*args, **kwargs)
+        ref = weakref.ref(obj)
+        yield obj
+        del obj
+        if ref() is not None:
+            raise ReferenceError("Remaining reference(s) to object")

scipy/_lib/_pep440.py

@@ -0,0 +1,487 @@
+"""Utility to compare pep440 compatible version strings.
+
+The LooseVersion and StrictVersion classes that distutils provides don't
+work; they don't recognize anything like alpha/beta/rc/dev versions.
+"""
+
+# Copyright (c) Donald Stufft and individual contributors.
+# All rights reserved.
+
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+
+#     1. Redistributions of source code must retain the above copyright notice,
+#        this list of conditions and the following disclaimer.
+
+#     2. Redistributions in binary form must reproduce the above copyright
+#        notice, this list of conditions and the following disclaimer in the
+#        documentation and/or other materials provided with the distribution.
+
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+# POSSIBILITY OF SUCH DAMAGE.
+
+import collections
+import itertools
+import re
+
+
+__all__ = [
+    "parse", "Version", "LegacyVersion", "InvalidVersion", "VERSION_PATTERN",
+]
+
+
+# BEGIN packaging/_structures.py
+
+
+class Infinity:
+    def __repr__(self):
+        return "Infinity"
+
+    def __hash__(self):
+        return hash(repr(self))
+
+    def __lt__(self, other):
+        return False
+
+    def __le__(self, other):
+        return False
+
+    def __eq__(self, other):
+        return isinstance(other, self.__class__)
+
+    def __ne__(self, other):
+        return not isinstance(other, self.__class__)
+
+    def __gt__(self, other):
+        return True
+
+    def __ge__(self, other):
+        return True
+
+    def __neg__(self):
+        return NegativeInfinity
+
+
+Infinity = Infinity()
+
+
+class NegativeInfinity:
+    def __repr__(self):
+        return "-Infinity"
+
+    def __hash__(self):
+        return hash(repr(self))
+
+    def __lt__(self, other):
+        return True
+
+    def __le__(self, other):
+        return True
+
+    def __eq__(self, other):
+        return isinstance(other, self.__class__)
+
+    def __ne__(self, other):
+        return not isinstance(other, self.__class__)
+
+    def __gt__(self, other):
+        return False
+
+    def __ge__(self, other):
+        return False
+
+    def __neg__(self):
+        return Infinity
+
+
+# BEGIN packaging/version.py
+
+
+NegativeInfinity = NegativeInfinity()
+
+_Version = collections.namedtuple(
+    "_Version",
+    ["epoch", "release", "dev", "pre", "post", "local"],
+)
+
+
+def parse(version):
+    """
+    Parse the given version string and return either a :class:`Version` object
+    or a :class:`LegacyVersion` object depending on if the given version is
+    a valid PEP 440 version or a legacy version.
+    """
+    try:
+        return Version(version)
+    except InvalidVersion:
+        return LegacyVersion(version)
+
+
+class InvalidVersion(ValueError):
+    """
+    An invalid version was found, users should refer to PEP 440.
+    """
+
+
+class _BaseVersion:
+
+    def __hash__(self):
+        return hash(self._key)
+
+    def __lt__(self, other):
+        return self._compare(other, lambda s, o: s < o)
+
+    def __le__(self, other):
+        return self._compare(other, lambda s, o: s <= o)
+
+    def __eq__(self, other):
+        return self._compare(other, lambda s, o: s == o)
+
+    def __ge__(self, other):
+        return self._compare(other, lambda s, o: s >= o)
+
+    def __gt__(self, other):
+        return self._compare(other, lambda s, o: s > o)
+
+    def __ne__(self, other):
+        return self._compare(other, lambda s, o: s != o)
+
+    def _compare(self, other, method):
+        if not isinstance(other, _BaseVersion):
+            return NotImplemented
+
+        return method(self._key, other._key)
+
+
+class LegacyVersion(_BaseVersion):
+
+    def __init__(self, version):
+        self._version = str(version)
+        self._key = _legacy_cmpkey(self._version)
+
+    def __str__(self):
+        return self._version
+
+    def __repr__(self):
+        return f"<LegacyVersion({repr(str(self))})>"
+
+    @property
+    def public(self):
+        return self._version
+
+    @property
+    def base_version(self):
+        return self._version
+
+    @property
+    def local(self):
+        return None
+
+    @property
+    def is_prerelease(self):
+        return False
+
+    @property
+    def is_postrelease(self):
+        return False
+
+
+_legacy_version_component_re = re.compile(
+    r"(\d+ | [a-z]+ | \.| -)", re.VERBOSE,
+)
+
+_legacy_version_replacement_map = {
+    "pre": "c", "preview": "c", "-": "final-", "rc": "c", "dev": "@",
+}
+
+
+def _parse_version_parts(s):
+    for part in _legacy_version_component_re.split(s):
+        part = _legacy_version_replacement_map.get(part, part)
+
+        if not part or part == ".":
+            continue
+
+        if part[:1] in "0123456789":
+            # pad for numeric comparison
+            yield part.zfill(8)
+        else:
+            yield "*" + part
+
+    # ensure that alpha/beta/candidate are before final
+    yield "*final"
+
+
+def _legacy_cmpkey(version):
+    # We hardcode an epoch of -1 here. A PEP 440 version can only have an epoch
+    # greater than or equal to 0. This will effectively put the LegacyVersion,
+    # which uses the defacto standard originally implemented by setuptools,
+    # as before all PEP 440 versions.
+    epoch = -1
+
+    # This scheme is taken from pkg_resources.parse_version setuptools prior to
+    # its adoption of the packaging library.
+    parts = []
+    for part in _parse_version_parts(version.lower()):
+        if part.startswith("*"):
+            # remove "-" before a prerelease tag
+            if part < "*final":
+                while parts and parts[-1] == "*final-":
+                    parts.pop()
+
+            # remove trailing zeros from each series of numeric parts
+            while parts and parts[-1] == "00000000":
+                parts.pop()
+
+        parts.append(part)
+    parts = tuple(parts)
+
+    return epoch, parts
+
+
+# Deliberately not anchored to the start and end of the string, to make it
+# easier for 3rd party code to reuse
+VERSION_PATTERN = r"""
+    v?
+    (?:
+        (?:(?P<epoch>[0-9]+)!)?                           # epoch
+        (?P<release>[0-9]+(?:\.[0-9]+)*)                  # release segment
+        (?P<pre>                                          # pre-release
+            [-_\.]?
+            (?P<pre_l>(a|b|c|rc|alpha|beta|pre|preview))
+            [-_\.]?
+            (?P<pre_n>[0-9]+)?
+        )?
+        (?P<post>                                         # post release
+            (?:-(?P<post_n1>[0-9]+))
+            |
+            (?:
+                [-_\.]?
+                (?P<post_l>post|rev|r)
+                [-_\.]?
+                (?P<post_n2>[0-9]+)?
+            )
+        )?
+        (?P<dev>                                          # dev release
+            [-_\.]?
+            (?P<dev_l>dev)
+            [-_\.]?
+            (?P<dev_n>[0-9]+)?
+        )?
+    )
+    (?:\+(?P<local>[a-z0-9]+(?:[-_\.][a-z0-9]+)*))?       # local version
+"""
+
+
+class Version(_BaseVersion):
+
+    _regex = re.compile(
+        r"^\s*" + VERSION_PATTERN + r"\s*$",
+        re.VERBOSE | re.IGNORECASE,
+    )
+
+    def __init__(self, version):
+        # Validate the version and parse it into pieces
+        match = self._regex.search(version)
+        if not match:
+            raise InvalidVersion(f"Invalid version: '{version}'")
+
+        # Store the parsed out pieces of the version
+        self._version = _Version(
+            epoch=int(match.group("epoch")) if match.group("epoch") else 0,
+            release=tuple(int(i) for i in match.group("release").split(".")),
+            pre=_parse_letter_version(
+                match.group("pre_l"),
+                match.group("pre_n"),
+            ),
+            post=_parse_letter_version(
+                match.group("post_l"),
+                match.group("post_n1") or match.group("post_n2"),
+            ),
+            dev=_parse_letter_version(
+                match.group("dev_l"),
+                match.group("dev_n"),
+            ),
+            local=_parse_local_version(match.group("local")),
+        )
+
+        # Generate a key which will be used for sorting
+        self._key = _cmpkey(
+            self._version.epoch,
+            self._version.release,
+            self._version.pre,
+            self._version.post,
+            self._version.dev,
+            self._version.local,
+        )
+
+    def __repr__(self):
+        return f"<Version({repr(str(self))})>"
+
+    def __str__(self):
+        parts = []
+
+        # Epoch
+        if self._version.epoch != 0:
+            parts.append(f"{self._version.epoch}!")
+
+        # Release segment
+        parts.append(".".join(str(x) for x in self._version.release))
+
+        # Pre-release
+        if self._version.pre is not None:
+            parts.append("".join(str(x) for x in self._version.pre))
+
+        # Post-release
+        if self._version.post is not None:
+            parts.append(f".post{self._version.post[1]}")
+
+        # Development release
+        if self._version.dev is not None:
+            parts.append(f".dev{self._version.dev[1]}")
+
+        # Local version segment
+        if self._version.local is not None:
+            parts.append(
+                "+{}".format(".".join(str(x) for x in self._version.local))
+            )
+
+        return "".join(parts)
+
+    @property
+    def public(self):
+        return str(self).split("+", 1)[0]
+
+    @property
+    def base_version(self):
+        parts = []
+
+        # Epoch
+        if self._version.epoch != 0:
+            parts.append(f"{self._version.epoch}!")
+
+        # Release segment
+        parts.append(".".join(str(x) for x in self._version.release))
+
+        return "".join(parts)
+
+    @property
+    def local(self):
+        version_string = str(self)
+        if "+" in version_string:
+            return version_string.split("+", 1)[1]
+
+    @property
+    def is_prerelease(self):
+        return bool(self._version.dev or self._version.pre)
+
+    @property
+    def is_postrelease(self):
+        return bool(self._version.post)
+
+
+def _parse_letter_version(letter, number):
+    if letter:
+        # We assume there is an implicit 0 in a pre-release if there is
+        # no numeral associated with it.
+        if number is None:
+            number = 0
+
+        # We normalize any letters to their lower-case form
+        letter = letter.lower()
+
+        # We consider some words to be alternate spellings of other words and
+        # in those cases we want to normalize the spellings to our preferred
+        # spelling.
+        if letter == "alpha":
+            letter = "a"
+        elif letter == "beta":
+            letter = "b"
+        elif letter in ["c", "pre", "preview"]:
+            letter = "rc"
+        elif letter in ["rev", "r"]:
+            letter = "post"
+
+        return letter, int(number)
+    if not letter and number:
+        # We assume that if we are given a number but not given a letter,
+        # then this is using the implicit post release syntax (e.g., 1.0-1)
+        letter = "post"
+
+        return letter, int(number)
+
+
+_local_version_seperators = re.compile(r"[\._-]")
+
+
+def _parse_local_version(local):
+    """
+    Takes a string like abc.1.twelve and turns it into ("abc", 1, "twelve").
+    """
+    if local is not None:
+        return tuple(
+            part.lower() if not part.isdigit() else int(part)
+            for part in _local_version_seperators.split(local)
+        )
+
+
+def _cmpkey(epoch, release, pre, post, dev, local):
+    # When we compare a release version, we want to compare it with all of the
+    # trailing zeros removed. So we'll use a reverse the list, drop all the now
+    # leading zeros until we come to something non-zero, then take the rest,
+    # re-reverse it back into the correct order, and make it a tuple and use
+    # that for our sorting key.
+    release = tuple(
+        reversed(list(
+            itertools.dropwhile(
+                lambda x: x == 0,
+                reversed(release),
+            )
+        ))
+    )
+
+    # We need to "trick" the sorting algorithm to put 1.0.dev0 before 1.0a0.
+    # We'll do this by abusing the pre-segment, but we _only_ want to do this
+    # if there is no pre- or a post-segment. If we have one of those, then
+    # the normal sorting rules will handle this case correctly.
+    if pre is None and post is None and dev is not None:
+        pre = -Infinity
+    # Versions without a pre-release (except as noted above) should sort after
+    # those with one.
+    elif pre is None:
+        pre = Infinity
+
+    # Versions without a post-segment should sort before those with one.
+    if post is None:
+        post = -Infinity
+
+    # Versions without a development segment should sort after those with one.
+    if dev is None:
+        dev = Infinity
+
+    if local is None:
+        # Versions without a local segment should sort before those with one.
+        local = -Infinity
+    else:
+        # Versions with a local segment need that segment parsed to implement
+        # the sorting rules in PEP440.
+        # - Alphanumeric segments sort before numeric segments
+        # - Alphanumeric segments sort lexicographically
+        # - Numeric segments sort numerically
+        # - Shorter versions sort before longer versions when the prefixes
+        #   match exactly
+        local = tuple(
+            (i, "") if isinstance(i, int) else (-Infinity, i)
+            for i in local
+        )
+
+    return epoch, release, pre, post, dev, local

scipy/_lib/_testutils.py

@@ -0,0 +1,257 @@
+"""
+Generic test utilities.
+
+"""
+
+import os
+import re
+import sys
+import numpy as np
+import inspect
+import sysconfig
+
+
+__all__ = ['PytestTester', 'check_free_memory', '_TestPythranFunc', 'IS_MUSL']
+
+
+IS_MUSL = False
+try:
+    # Note that packaging is not a dependency, hence we need this try-except:
+    from packaging.tags import sys_tags
+    _tags = list(sys_tags())
+    if 'musllinux' in _tags[0].platform:
+        IS_MUSL = True
+except ImportError:
+    # fallback to sysconfig (might be flaky)
+    v = sysconfig.get_config_var('HOST_GNU_TYPE') or ''
+    if 'musl' in v:
+        IS_MUSL = True
+
+
+class FPUModeChangeWarning(RuntimeWarning):
+    """Warning about FPU mode change"""
+    pass
+
+
+class PytestTester:
+    """
+    Run tests for this namespace
+
+    ``scipy.test()`` runs tests for all of SciPy, with the default settings.
+    When used from a submodule (e.g., ``scipy.cluster.test()``, only the tests
+    for that namespace are run.
+
+    Parameters
+    ----------
+    label : {'fast', 'full'}, optional
+        Whether to run only the fast tests, or also those marked as slow.
+        Default is 'fast'.
+    verbose : int, optional
+        Test output verbosity. Default is 1.
+    extra_argv : list, optional
+        Arguments to pass through to Pytest.
+    doctests : bool, optional
+        Whether to run doctests or not. Default is False.
+    coverage : bool, optional
+        Whether to run tests with code coverage measurements enabled.
+        Default is False.
+    tests : list of str, optional
+        List of module names to run tests for. By default, uses the module
+        from which the ``test`` function is called.
+    parallel : int, optional
+        Run tests in parallel with pytest-xdist, if number given is larger than
+        1. Default is 1.
+
+    """
+    def __init__(self, module_name):
+        self.module_name = module_name
+
+    def __call__(self, label="fast", verbose=1, extra_argv=None, doctests=False,
+                 coverage=False, tests=None, parallel=None):
+        import pytest
+
+        module = sys.modules[self.module_name]
+        module_path = os.path.abspath(module.__path__[0])
+
+        pytest_args = ['--showlocals', '--tb=short']
+
+        if doctests:
+            raise ValueError("Doctests not supported")
+
+        if extra_argv:
+            pytest_args += list(extra_argv)
+
+        if verbose and int(verbose) > 1:
+            pytest_args += ["-" + "v"*(int(verbose)-1)]
+
+        if coverage:
+            pytest_args += ["--cov=" + module_path]
+
+        if label == "fast":
+            pytest_args += ["-m", "not slow"]
+        elif label != "full":
+            pytest_args += ["-m", label]
+
+        if tests is None:
+            tests = [self.module_name]
+
+        if parallel is not None and parallel > 1:
+            if _pytest_has_xdist():
+                pytest_args += ['-n', str(parallel)]
+            else:
+                import warnings
+                warnings.warn('Could not run tests in parallel because '
+                              'pytest-xdist plugin is not available.',
+                              stacklevel=2)
+
+        pytest_args += ['--pyargs'] + list(tests)
+
+        try:
+            code = pytest.main(pytest_args)
+        except SystemExit as exc:
+            code = exc.code
+
+        return (code == 0)
+
+
+class _TestPythranFunc:
+    '''
+    These are situations that can be tested in our pythran tests:
+    - A function with multiple array arguments and then
+      other positional and keyword arguments.
+    - A function with array-like keywords (e.g. `def somefunc(x0, x1=None)`.
+    Note: list/tuple input is not yet tested!
+
+    `self.arguments`: A dictionary which key is the index of the argument,
+                      value is tuple(array value, all supported dtypes)
+    `self.partialfunc`: A function used to freeze some non-array argument
+                        that of no interests in the original function
+    '''
+    ALL_INTEGER = [np.int8, np.int16, np.int32, np.int64, np.intc, np.intp]
+    ALL_FLOAT = [np.float32, np.float64]
+    ALL_COMPLEX = [np.complex64, np.complex128]
+
+    def setup_method(self):
+        self.arguments = {}
+        self.partialfunc = None
+        self.expected = None
+
+    def get_optional_args(self, func):
+        # get optional arguments with its default value,
+        # used for testing keywords
+        signature = inspect.signature(func)
+        optional_args = {}
+        for k, v in signature.parameters.items():
+            if v.default is not inspect.Parameter.empty:
+                optional_args[k] = v.default
+        return optional_args
+
+    def get_max_dtype_list_length(self):
+        # get the max supported dtypes list length in all arguments
+        max_len = 0
+        for arg_idx in self.arguments:
+            cur_len = len(self.arguments[arg_idx][1])
+            if cur_len > max_len:
+                max_len = cur_len
+        return max_len
+
+    def get_dtype(self, dtype_list, dtype_idx):
+        # get the dtype from dtype_list via index
+        # if the index is out of range, then return the last dtype
+        if dtype_idx > len(dtype_list)-1:
+            return dtype_list[-1]
+        else:
+            return dtype_list[dtype_idx]
+
+    def test_all_dtypes(self):
+        for type_idx in range(self.get_max_dtype_list_length()):
+            args_array = []
+            for arg_idx in self.arguments:
+                new_dtype = self.get_dtype(self.arguments[arg_idx][1],
+                                           type_idx)
+                args_array.append(self.arguments[arg_idx][0].astype(new_dtype))
+            self.pythranfunc(*args_array)
+
+    def test_views(self):
+        args_array = []
+        for arg_idx in self.arguments:
+            args_array.append(self.arguments[arg_idx][0][::-1][::-1])
+        self.pythranfunc(*args_array)
+
+    def test_strided(self):
+        args_array = []
+        for arg_idx in self.arguments:
+            args_array.append(np.repeat(self.arguments[arg_idx][0],
+                                        2, axis=0)[::2])
+        self.pythranfunc(*args_array)
+
+
+def _pytest_has_xdist():
+    """
+    Check if the pytest-xdist plugin is installed, providing parallel tests
+    """
+    # Check xdist exists without importing, otherwise pytests emits warnings
+    from importlib.util import find_spec
+    return find_spec('xdist') is not None
+
+
+def check_free_memory(free_mb):
+    """
+    Check *free_mb* of memory is available, otherwise do pytest.skip
+    """
+    import pytest
+
+    try:
+        mem_free = _parse_size(os.environ['SCIPY_AVAILABLE_MEM'])
+        msg = '{} MB memory required, but environment SCIPY_AVAILABLE_MEM={}'.format(
+            free_mb, os.environ['SCIPY_AVAILABLE_MEM'])
+    except KeyError:
+        mem_free = _get_mem_available()
+        if mem_free is None:
+            pytest.skip("Could not determine available memory; set SCIPY_AVAILABLE_MEM "
+                        "variable to free memory in MB to run the test.")
+        msg = f'{free_mb} MB memory required, but {mem_free/1e6} MB available'
+
+    if mem_free < free_mb * 1e6:
+        pytest.skip(msg)
+
+
+def _parse_size(size_str):
+    suffixes = {'': 1e6,
+                'b': 1.0,
+                'k': 1e3, 'M': 1e6, 'G': 1e9, 'T': 1e12,
+                'kb': 1e3, 'Mb': 1e6, 'Gb': 1e9, 'Tb': 1e12,
+                'kib': 1024.0, 'Mib': 1024.0**2, 'Gib': 1024.0**3, 'Tib': 1024.0**4}
+    m = re.match(r'^\s*(\d+)\s*({})\s*$'.format('|'.join(suffixes.keys())),
+                 size_str,
+                 re.I)
+    if not m or m.group(2) not in suffixes:
+        raise ValueError("Invalid size string")
+
+    return float(m.group(1)) * suffixes[m.group(2)]
+
+
+def _get_mem_available():
+    """
+    Get information about memory available, not counting swap.
+    """
+    try:
+        import psutil
+        return psutil.virtual_memory().available
+    except (ImportError, AttributeError):
+        pass
+
+    if sys.platform.startswith('linux'):
+        info = {}
+        with open('/proc/meminfo') as f:
+            for line in f:
+                p = line.split()
+                info[p[0].strip(':').lower()] = float(p[1]) * 1e3
+
+        if 'memavailable' in info:
+            # Linux >= 3.14
+            return info['memavailable']
+        else:
+            return info['memfree'] + info['cached']
+
+    return None

scipy/_lib/_threadsafety.py

@@ -0,0 +1,58 @@
+import threading
+
+import scipy._lib.decorator
+
+
+__all__ = ['ReentrancyError', 'ReentrancyLock', 'non_reentrant']
+
+
+class ReentrancyError(RuntimeError):
+    pass
+
+
+class ReentrancyLock:
+    """
+    Threading lock that raises an exception for reentrant calls.
+
+    Calls from different threads are serialized, and nested calls from the
+    same thread result to an error.
+
+    The object can be used as a context manager or to decorate functions
+    via the decorate() method.
+
+    """
+
+    def __init__(self, err_msg):
+        self._rlock = threading.RLock()
+        self._entered = False
+        self._err_msg = err_msg
+
+    def __enter__(self):
+        self._rlock.acquire()
+        if self._entered:
+            self._rlock.release()
+            raise ReentrancyError(self._err_msg)
+        self._entered = True
+
+    def __exit__(self, type, value, traceback):
+        self._entered = False
+        self._rlock.release()
+
+    def decorate(self, func):
+        def caller(func, *a, **kw):
+            with self:
+                return func(*a, **kw)
+        return scipy._lib.decorator.decorate(func, caller)
+
+
+def non_reentrant(err_msg=None):
+    """
+    Decorate a function with a threading lock and prevent reentrant calls.
+    """
+    def decorator(func):
+        msg = err_msg
+        if msg is None:
+            msg = "%s is not re-entrant" % func.__name__
+        lock = ReentrancyLock(msg)
+        return lock.decorate(func)
+    return decorator

scipy/_lib/_tmpdirs.py

@@ -0,0 +1,86 @@
+''' Contexts for *with* statement providing temporary directories
+'''
+import os
+from contextlib import contextmanager
+from shutil import rmtree
+from tempfile import mkdtemp
+
+
+@contextmanager
+def tempdir():
+    """Create and return a temporary directory. This has the same
+    behavior as mkdtemp but can be used as a context manager.
+
+    Upon exiting the context, the directory and everything contained
+    in it are removed.
+
+    Examples
+    --------
+    >>> import os
+    >>> with tempdir() as tmpdir:
+    ...     fname = os.path.join(tmpdir, 'example_file.txt')
+    ...     with open(fname, 'wt') as fobj:
+    ...         _ = fobj.write('a string\\n')
+    >>> os.path.exists(tmpdir)
+    False
+    """
+    d = mkdtemp()
+    yield d
+    rmtree(d)
+
+
+@contextmanager
+def in_tempdir():
+    ''' Create, return, and change directory to a temporary directory
+
+    Examples
+    --------
+    >>> import os
+    >>> my_cwd = os.getcwd()
+    >>> with in_tempdir() as tmpdir:
+    ...     _ = open('test.txt', 'wt').write('some text')
+    ...     assert os.path.isfile('test.txt')
+    ...     assert os.path.isfile(os.path.join(tmpdir, 'test.txt'))
+    >>> os.path.exists(tmpdir)
+    False
+    >>> os.getcwd() == my_cwd
+    True
+    '''
+    pwd = os.getcwd()
+    d = mkdtemp()
+    os.chdir(d)
+    yield d
+    os.chdir(pwd)
+    rmtree(d)
+
+
+@contextmanager
+def in_dir(dir=None):
+    """ Change directory to given directory for duration of ``with`` block
+
+    Useful when you want to use `in_tempdir` for the final test, but
+    you are still debugging. For example, you may want to do this in the end:
+
+    >>> with in_tempdir() as tmpdir:
+    ...     # do something complicated which might break
+    ...     pass
+
+    But, indeed, the complicated thing does break, and meanwhile, the
+    ``in_tempdir`` context manager wiped out the directory with the
+    temporary files that you wanted for debugging. So, while debugging, you
+    replace with something like:
+
+    >>> with in_dir() as tmpdir: # Use working directory by default
+    ...     # do something complicated which might break
+    ...     pass
+
+    You can then look at the temporary file outputs to debug what is happening,
+    fix, and finally replace ``in_dir`` with ``in_tempdir`` again.
+    """
+    cwd = os.getcwd()
+    if dir is None:
+        yield cwd
+        return
+    os.chdir(dir)
+    yield dir
+    os.chdir(cwd)

scipy/_lib/_uarray/LICENSE

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2018, Quansight-Labs
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

scipy/_lib/_uarray/__init__.py

@@ -0,0 +1,116 @@
+"""
+.. note:
+    If you are looking for overrides for NumPy-specific methods, see the
+    documentation for :obj:`unumpy`. This page explains how to write
+    back-ends and multimethods.
+
+``uarray`` is built around a back-end protocol, and overridable multimethods.
+It is necessary to define multimethods for back-ends to be able to override them.
+See the documentation of :obj:`generate_multimethod` on how to write multimethods.
+
+
+
+Let's start with the simplest:
+
+``__ua_domain__`` defines the back-end *domain*. The domain consists of period-
+separated string consisting of the modules you extend plus the submodule. For
+example, if a submodule ``module2.submodule`` extends ``module1``
+(i.e., it exposes dispatchables marked as types available in ``module1``),
+then the domain string should be ``"module1.module2.submodule"``.
+
+
+For the purpose of this demonstration, we'll be creating an object and setting
+its attributes directly. However, note that you can use a module or your own type
+as a backend as well.
+
+>>> class Backend: pass
+>>> be = Backend()
+>>> be.__ua_domain__ = "ua_examples"
+
+It might be useful at this point to sidetrack to the documentation of
+:obj:`generate_multimethod` to find out how to generate a multimethod
+overridable by :obj:`uarray`. Needless to say, writing a backend and
+creating multimethods are mostly orthogonal activities, and knowing
+one doesn't necessarily require knowledge of the other, although it
+is certainly helpful. We expect core API designers/specifiers to write the
+multimethods, and implementors to override them. But, as is often the case,
+similar people write both.
+
+Without further ado, here's an example multimethod:
+
+>>> import uarray as ua
+>>> from uarray import Dispatchable
+>>> def override_me(a, b):
+...   return Dispatchable(a, int),
+>>> def override_replacer(args, kwargs, dispatchables):
+...     return (dispatchables[0], args[1]), {}
+>>> overridden_me = ua.generate_multimethod(
+...     override_me, override_replacer, "ua_examples"
+... )
+
+Next comes the part about overriding the multimethod. This requires
+the ``__ua_function__`` protocol, and the ``__ua_convert__``
+protocol. The ``__ua_function__`` protocol has the signature
+``(method, args, kwargs)`` where ``method`` is the passed
+multimethod, ``args``/``kwargs`` specify the arguments and ``dispatchables``
+is the list of converted dispatchables passed in.
+
+>>> def __ua_function__(method, args, kwargs):
+...     return method.__name__, args, kwargs
+>>> be.__ua_function__ = __ua_function__
+
+The other protocol of interest is the ``__ua_convert__`` protocol. It has the
+signature ``(dispatchables, coerce)``. When ``coerce`` is ``False``, conversion
+between the formats should ideally be an ``O(1)`` operation, but it means that
+no memory copying should be involved, only views of the existing data.
+
+>>> def __ua_convert__(dispatchables, coerce):
+...     for d in dispatchables:
+...         if d.type is int:
+...             if coerce and d.coercible:
+...                 yield str(d.value)
+...             else:
+...                 yield d.value
+>>> be.__ua_convert__ = __ua_convert__
+
+Now that we have defined the backend, the next thing to do is to call the multimethod.
+
+>>> with ua.set_backend(be):
+...      overridden_me(1, "2")
+('override_me', (1, '2'), {})
+
+Note that the marked type has no effect on the actual type of the passed object.
+We can also coerce the type of the input.
+
+>>> with ua.set_backend(be, coerce=True):
+...     overridden_me(1, "2")
+...     overridden_me(1.0, "2")
+('override_me', ('1', '2'), {})
+('override_me', ('1.0', '2'), {})
+
+Another feature is that if you remove ``__ua_convert__``, the arguments are not
+converted at all and it's up to the backend to handle that.
+
+>>> del be.__ua_convert__
+>>> with ua.set_backend(be):
+...     overridden_me(1, "2")
+('override_me', (1, '2'), {})
+
+You also have the option to return ``NotImplemented``, in which case processing moves on
+to the next back-end, which in this case, doesn't exist. The same applies to
+``__ua_convert__``.
+
+>>> be.__ua_function__ = lambda *a, **kw: NotImplemented
+>>> with ua.set_backend(be):
+...     overridden_me(1, "2")
+Traceback (most recent call last):
+    ...
+uarray.BackendNotImplementedError: ...
+
+The last possibility is if we don't have ``__ua_convert__``, in which case the job is
+left up to ``__ua_function__``, but putting things back into arrays after conversion
+will not be possible.
+"""
+
+from ._backend import *
+__version__ = '0.8.8.dev0+aa94c5a4.scipy'