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David Adams
2024-09-28 22:56:00 -07:00
parent 64d9b78b3a
commit 1973934e95
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"""Compatibility fixes for older version of python, numpy and scipy
If you add content to this file, please give the version of the package
at which the fix is no longer needed.
"""
# Authors: Emmanuelle Gouillart <emmanuelle.gouillart@normalesup.org>
# Gael Varoquaux <gael.varoquaux@normalesup.org>
# Fabian Pedregosa <fpedregosa@acm.org>
# Lars Buitinck
#
# License: BSD 3 clause
import platform
import struct
import sys
import numpy as np
import scipy
import scipy.sparse.linalg
import scipy.stats
try:
import pandas as pd
except ImportError:
pd = None
from ..externals._packaging.version import parse as parse_version
from .parallel import _get_threadpool_controller
_IS_PYPY = platform.python_implementation() == "PyPy"
_IS_32BIT = 8 * struct.calcsize("P") == 32
_IS_WASM = platform.machine() in ["wasm32", "wasm64"]
np_version = parse_version(np.__version__)
np_base_version = parse_version(np_version.base_version)
sp_version = parse_version(scipy.__version__)
sp_base_version = parse_version(sp_version.base_version)
# TODO: We can consider removing the containers and importing
# directly from SciPy when sparse matrices will be deprecated.
CSR_CONTAINERS = [scipy.sparse.csr_matrix]
CSC_CONTAINERS = [scipy.sparse.csc_matrix]
COO_CONTAINERS = [scipy.sparse.coo_matrix]
LIL_CONTAINERS = [scipy.sparse.lil_matrix]
DOK_CONTAINERS = [scipy.sparse.dok_matrix]
BSR_CONTAINERS = [scipy.sparse.bsr_matrix]
DIA_CONTAINERS = [scipy.sparse.dia_matrix]
if parse_version(scipy.__version__) >= parse_version("1.8"):
# Sparse Arrays have been added in SciPy 1.8
# TODO: When SciPy 1.8 is the minimum supported version,
# those list can be created directly without this condition.
# See: https://github.com/scikit-learn/scikit-learn/issues/27090
CSR_CONTAINERS.append(scipy.sparse.csr_array)
CSC_CONTAINERS.append(scipy.sparse.csc_array)
COO_CONTAINERS.append(scipy.sparse.coo_array)
LIL_CONTAINERS.append(scipy.sparse.lil_array)
DOK_CONTAINERS.append(scipy.sparse.dok_array)
BSR_CONTAINERS.append(scipy.sparse.bsr_array)
DIA_CONTAINERS.append(scipy.sparse.dia_array)
# Remove when minimum scipy version is 1.11.0
try:
from scipy.sparse import sparray # noqa
SPARRAY_PRESENT = True
except ImportError:
SPARRAY_PRESENT = False
# Remove when minimum scipy version is 1.8
try:
from scipy.sparse import csr_array # noqa
SPARSE_ARRAY_PRESENT = True
except ImportError:
SPARSE_ARRAY_PRESENT = False
try:
from scipy.optimize._linesearch import line_search_wolfe1, line_search_wolfe2
except ImportError: # SciPy < 1.8
from scipy.optimize.linesearch import line_search_wolfe2, line_search_wolfe1 # type: ignore # noqa
def _object_dtype_isnan(X):
return X != X
# Rename the `method` kwarg to `interpolation` for NumPy < 1.22, because
# `interpolation` kwarg was deprecated in favor of `method` in NumPy >= 1.22.
def _percentile(a, q, *, method="linear", **kwargs):
return np.percentile(a, q, interpolation=method, **kwargs)
if np_version < parse_version("1.22"):
percentile = _percentile
else: # >= 1.22
from numpy import percentile # type: ignore # noqa
# TODO: Remove when SciPy 1.11 is the minimum supported version
def _mode(a, axis=0):
if sp_version >= parse_version("1.9.0"):
mode = scipy.stats.mode(a, axis=axis, keepdims=True)
if sp_version >= parse_version("1.10.999"):
# scipy.stats.mode has changed returned array shape with axis=None
# and keepdims=True, see https://github.com/scipy/scipy/pull/17561
if axis is None:
mode = np.ravel(mode)
return mode
return scipy.stats.mode(a, axis=axis)
# TODO: Remove when Scipy 1.12 is the minimum supported version
if sp_base_version >= parse_version("1.12.0"):
_sparse_linalg_cg = scipy.sparse.linalg.cg
else:
def _sparse_linalg_cg(A, b, **kwargs):
if "rtol" in kwargs:
kwargs["tol"] = kwargs.pop("rtol")
if "atol" not in kwargs:
kwargs["atol"] = "legacy"
return scipy.sparse.linalg.cg(A, b, **kwargs)
# TODO: Fuse the modern implementations of _sparse_min_max and _sparse_nan_min_max
# into the public min_max_axis function when Scipy 1.11 is the minimum supported
# version and delete the backport in the else branch below.
if sp_base_version >= parse_version("1.11.0"):
def _sparse_min_max(X, axis):
the_min = X.min(axis=axis)
the_max = X.max(axis=axis)
if axis is not None:
the_min = the_min.toarray().ravel()
the_max = the_max.toarray().ravel()
return the_min, the_max
def _sparse_nan_min_max(X, axis):
the_min = X.nanmin(axis=axis)
the_max = X.nanmax(axis=axis)
if axis is not None:
the_min = the_min.toarray().ravel()
the_max = the_max.toarray().ravel()
return the_min, the_max
else:
# This code is mostly taken from scipy 0.14 and extended to handle nans, see
# https://github.com/scikit-learn/scikit-learn/pull/11196
def _minor_reduce(X, ufunc):
major_index = np.flatnonzero(np.diff(X.indptr))
# reduceat tries casts X.indptr to intp, which errors
# if it is int64 on a 32 bit system.
# Reinitializing prevents this where possible, see #13737
X = type(X)((X.data, X.indices, X.indptr), shape=X.shape)
value = ufunc.reduceat(X.data, X.indptr[major_index])
return major_index, value
def _min_or_max_axis(X, axis, min_or_max):
N = X.shape[axis]
if N == 0:
raise ValueError("zero-size array to reduction operation")
M = X.shape[1 - axis]
mat = X.tocsc() if axis == 0 else X.tocsr()
mat.sum_duplicates()
major_index, value = _minor_reduce(mat, min_or_max)
not_full = np.diff(mat.indptr)[major_index] < N
value[not_full] = min_or_max(value[not_full], 0)
mask = value != 0
major_index = np.compress(mask, major_index)
value = np.compress(mask, value)
if axis == 0:
res = scipy.sparse.coo_matrix(
(value, (np.zeros(len(value)), major_index)),
dtype=X.dtype,
shape=(1, M),
)
else:
res = scipy.sparse.coo_matrix(
(value, (major_index, np.zeros(len(value)))),
dtype=X.dtype,
shape=(M, 1),
)
return res.A.ravel()
def _sparse_min_or_max(X, axis, min_or_max):
if axis is None:
if 0 in X.shape:
raise ValueError("zero-size array to reduction operation")
zero = X.dtype.type(0)
if X.nnz == 0:
return zero
m = min_or_max.reduce(X.data.ravel())
if X.nnz != np.prod(X.shape):
m = min_or_max(zero, m)
return m
if axis < 0:
axis += 2
if (axis == 0) or (axis == 1):
return _min_or_max_axis(X, axis, min_or_max)
else:
raise ValueError("invalid axis, use 0 for rows, or 1 for columns")
def _sparse_min_max(X, axis):
return (
_sparse_min_or_max(X, axis, np.minimum),
_sparse_min_or_max(X, axis, np.maximum),
)
def _sparse_nan_min_max(X, axis):
return (
_sparse_min_or_max(X, axis, np.fmin),
_sparse_min_or_max(X, axis, np.fmax),
)
# For +1.25 NumPy versions exceptions and warnings are being moved
# to a dedicated submodule.
if np_version >= parse_version("1.25.0"):
from numpy.exceptions import ComplexWarning, VisibleDeprecationWarning
else:
from numpy import ComplexWarning, VisibleDeprecationWarning # type: ignore # noqa
# TODO: Remove when Scipy 1.6 is the minimum supported version
try:
from scipy.integrate import trapezoid # type: ignore # noqa
except ImportError:
from scipy.integrate import trapz as trapezoid # type: ignore # noqa
# TODO: Adapt when Pandas > 2.2 is the minimum supported version
def pd_fillna(pd, frame):
pd_version = parse_version(pd.__version__).base_version
if parse_version(pd_version) < parse_version("2.2"):
frame = frame.fillna(value=np.nan)
else:
infer_objects_kwargs = (
{} if parse_version(pd_version) >= parse_version("3") else {"copy": False}
)
with pd.option_context("future.no_silent_downcasting", True):
frame = frame.fillna(value=np.nan).infer_objects(**infer_objects_kwargs)
return frame
# TODO: remove when SciPy 1.12 is the minimum supported version
def _preserve_dia_indices_dtype(
sparse_container, original_container_format, requested_sparse_format
):
"""Preserve indices dtype for SciPy < 1.12 when converting from DIA to CSR/CSC.
For SciPy < 1.12, DIA arrays indices are upcasted to `np.int64` that is
inconsistent with DIA matrices. We downcast the indices dtype to `np.int32` to
be consistent with DIA matrices.
The converted indices arrays are affected back inplace to the sparse container.
Parameters
----------
sparse_container : sparse container
Sparse container to be checked.
requested_sparse_format : str or bool
The type of format of `sparse_container`.
Notes
-----
See https://github.com/scipy/scipy/issues/19245 for more details.
"""
if original_container_format == "dia_array" and requested_sparse_format in (
"csr",
"coo",
):
if requested_sparse_format == "csr":
index_dtype = _smallest_admissible_index_dtype(
arrays=(sparse_container.indptr, sparse_container.indices),
maxval=max(sparse_container.nnz, sparse_container.shape[1]),
check_contents=True,
)
sparse_container.indices = sparse_container.indices.astype(
index_dtype, copy=False
)
sparse_container.indptr = sparse_container.indptr.astype(
index_dtype, copy=False
)
else: # requested_sparse_format == "coo"
index_dtype = _smallest_admissible_index_dtype(
maxval=max(sparse_container.shape)
)
sparse_container.row = sparse_container.row.astype(index_dtype, copy=False)
sparse_container.col = sparse_container.col.astype(index_dtype, copy=False)
# TODO: remove when SciPy 1.12 is the minimum supported version
def _smallest_admissible_index_dtype(arrays=(), maxval=None, check_contents=False):
"""Based on input (integer) arrays `a`, determine a suitable index data
type that can hold the data in the arrays.
This function returns `np.int64` if it either required by `maxval` or based on the
largest precision of the dtype of the arrays passed as argument, or by the their
contents (when `check_contents is True`). If none of the condition requires
`np.int64` then this function returns `np.int32`.
Parameters
----------
arrays : ndarray or tuple of ndarrays, default=()
Input arrays whose types/contents to check.
maxval : float, default=None
Maximum value needed.
check_contents : bool, default=False
Whether to check the values in the arrays and not just their types.
By default, check only the types.
Returns
-------
dtype : {np.int32, np.int64}
Suitable index data type (int32 or int64).
"""
int32min = np.int32(np.iinfo(np.int32).min)
int32max = np.int32(np.iinfo(np.int32).max)
if maxval is not None:
if maxval > np.iinfo(np.int64).max:
raise ValueError(
f"maxval={maxval} is to large to be represented as np.int64."
)
if maxval > int32max:
return np.int64
if isinstance(arrays, np.ndarray):
arrays = (arrays,)
for arr in arrays:
if not isinstance(arr, np.ndarray):
raise TypeError(
f"Arrays should be of type np.ndarray, got {type(arr)} instead."
)
if not np.issubdtype(arr.dtype, np.integer):
raise ValueError(
f"Array dtype {arr.dtype} is not supported for index dtype. We expect "
"integral values."
)
if not np.can_cast(arr.dtype, np.int32):
if not check_contents:
# when `check_contents` is False, we stay on the safe side and return
# np.int64.
return np.int64
if arr.size == 0:
# a bigger type not needed yet, let's look at the next array
continue
else:
maxval = arr.max()
minval = arr.min()
if minval < int32min or maxval > int32max:
# a big index type is actually needed
return np.int64
return np.int32
# TODO: Remove when Scipy 1.12 is the minimum supported version
if sp_version < parse_version("1.12"):
from ..externals._scipy.sparse.csgraph import laplacian # type: ignore # noqa
else:
from scipy.sparse.csgraph import laplacian # type: ignore # noqa # pragma: no cover
# TODO: Remove when we drop support for Python 3.9. Note the filter argument has
# been back-ported in 3.9.17 but we can not assume anything about the micro
# version, see
# https://docs.python.org/3.9/library/tarfile.html#tarfile.TarFile.extractall
# for more details
def tarfile_extractall(tarfile, path):
try:
tarfile.extractall(path, filter="data")
except TypeError:
tarfile.extractall(path)
def _in_unstable_openblas_configuration():
"""Return True if in an unstable configuration for OpenBLAS"""
# Import libraries which might load OpenBLAS.
import numpy # noqa
import scipy # noqa
modules_info = _get_threadpool_controller().info()
open_blas_used = any(info["internal_api"] == "openblas" for info in modules_info)
if not open_blas_used:
return False
# OpenBLAS 0.3.16 fixed instability for arm64, see:
# https://github.com/xianyi/OpenBLAS/blob/1b6db3dbba672b4f8af935bd43a1ff6cff4d20b7/Changelog.txt#L56-L58 # noqa
openblas_arm64_stable_version = parse_version("0.3.16")
for info in modules_info:
if info["internal_api"] != "openblas":
continue
openblas_version = info.get("version")
openblas_architecture = info.get("architecture")
if openblas_version is None or openblas_architecture is None:
# Cannot be sure that OpenBLAS is good enough. Assume unstable:
return True # pragma: no cover
if (
openblas_architecture == "neoversen1"
and parse_version(openblas_version) < openblas_arm64_stable_version
):
# See discussions in https://github.com/numpy/numpy/issues/19411
return True # pragma: no cover
return False
# TODO: remove when pandas >= 1.4 is the minimum supported version
if pd is not None and parse_version(pd.__version__) < parse_version("1.4"):
def _create_pandas_dataframe_from_non_pandas_container(X, *, index, copy):
pl = sys.modules.get("polars")
if pl is None or not isinstance(X, pl.DataFrame):
return pd.DataFrame(X, index=index, copy=copy)
# Bug in pandas<1.4: when constructing a pandas DataFrame from a polars
# DataFrame, the data is transposed ...
return pd.DataFrame(X.to_numpy(), index=index, copy=copy)
else:
def _create_pandas_dataframe_from_non_pandas_container(X, *, index, copy):
return pd.DataFrame(X, index=index, copy=copy)