peacock-data-public-datasets-idc-cronscript
/
venv
/lib
/python3.10
/site-packages
/sklearn
/utils
/_testing.py
"""Testing utilities.""" | |
# Copyright (c) 2011, 2012 | |
# Authors: Pietro Berkes, | |
# Andreas Muller | |
# Mathieu Blondel | |
# Olivier Grisel | |
# Arnaud Joly | |
# Denis Engemann | |
# Giorgio Patrini | |
# Thierry Guillemot | |
# License: BSD 3 clause | |
import atexit | |
import contextlib | |
import functools | |
import importlib | |
import inspect | |
import os | |
import os.path as op | |
import re | |
import shutil | |
import sys | |
import tempfile | |
import unittest | |
import warnings | |
from collections.abc import Iterable | |
from dataclasses import dataclass | |
from functools import wraps | |
from inspect import signature | |
from subprocess import STDOUT, CalledProcessError, TimeoutExpired, check_output | |
from unittest import TestCase | |
import joblib | |
import numpy as np | |
import scipy as sp | |
from numpy.testing import assert_allclose as np_assert_allclose | |
from numpy.testing import ( | |
assert_almost_equal, | |
assert_approx_equal, | |
assert_array_almost_equal, | |
assert_array_equal, | |
assert_array_less, | |
assert_no_warnings, | |
) | |
import sklearn | |
from sklearn.utils import ( | |
_IS_32BIT, | |
IS_PYPY, | |
_in_unstable_openblas_configuration, | |
) | |
from sklearn.utils._array_api import _check_array_api_dispatch | |
from sklearn.utils.fixes import VisibleDeprecationWarning, parse_version, sp_version | |
from sklearn.utils.multiclass import check_classification_targets | |
from sklearn.utils.validation import ( | |
check_array, | |
check_is_fitted, | |
check_X_y, | |
) | |
__all__ = [ | |
"assert_raises", | |
"assert_raises_regexp", | |
"assert_array_equal", | |
"assert_almost_equal", | |
"assert_array_almost_equal", | |
"assert_array_less", | |
"assert_approx_equal", | |
"assert_allclose", | |
"assert_run_python_script_without_output", | |
"assert_no_warnings", | |
"SkipTest", | |
] | |
_dummy = TestCase("__init__") | |
assert_raises = _dummy.assertRaises | |
SkipTest = unittest.case.SkipTest | |
assert_dict_equal = _dummy.assertDictEqual | |
assert_raises_regex = _dummy.assertRaisesRegex | |
# assert_raises_regexp is deprecated in Python 3.4 in favor of | |
# assert_raises_regex but lets keep the backward compat in scikit-learn with | |
# the old name for now | |
assert_raises_regexp = assert_raises_regex | |
def ignore_warnings(obj=None, category=Warning): | |
"""Context manager and decorator to ignore warnings. | |
Note: Using this (in both variants) will clear all warnings | |
from all python modules loaded. In case you need to test | |
cross-module-warning-logging, this is not your tool of choice. | |
Parameters | |
---------- | |
obj : callable, default=None | |
callable where you want to ignore the warnings. | |
category : warning class, default=Warning | |
The category to filter. If Warning, all categories will be muted. | |
Examples | |
-------- | |
>>> import warnings | |
>>> from sklearn.utils._testing import ignore_warnings | |
>>> with ignore_warnings(): | |
... warnings.warn('buhuhuhu') | |
>>> def nasty_warn(): | |
... warnings.warn('buhuhuhu') | |
... print(42) | |
>>> ignore_warnings(nasty_warn)() | |
42 | |
""" | |
if isinstance(obj, type) and issubclass(obj, Warning): | |
# Avoid common pitfall of passing category as the first positional | |
# argument which result in the test not being run | |
warning_name = obj.__name__ | |
raise ValueError( | |
"'obj' should be a callable where you want to ignore warnings. " | |
"You passed a warning class instead: 'obj={warning_name}'. " | |
"If you want to pass a warning class to ignore_warnings, " | |
"you should use 'category={warning_name}'".format(warning_name=warning_name) | |
) | |
elif callable(obj): | |
return _IgnoreWarnings(category=category)(obj) | |
else: | |
return _IgnoreWarnings(category=category) | |
class _IgnoreWarnings: | |
"""Improved and simplified Python warnings context manager and decorator. | |
This class allows the user to ignore the warnings raised by a function. | |
Copied from Python 2.7.5 and modified as required. | |
Parameters | |
---------- | |
category : tuple of warning class, default=Warning | |
The category to filter. By default, all the categories will be muted. | |
""" | |
def __init__(self, category): | |
self._record = True | |
self._module = sys.modules["warnings"] | |
self._entered = False | |
self.log = [] | |
self.category = category | |
def __call__(self, fn): | |
"""Decorator to catch and hide warnings without visual nesting.""" | |
def wrapper(*args, **kwargs): | |
with warnings.catch_warnings(): | |
warnings.simplefilter("ignore", self.category) | |
return fn(*args, **kwargs) | |
return wrapper | |
def __repr__(self): | |
args = [] | |
if self._record: | |
args.append("record=True") | |
if self._module is not sys.modules["warnings"]: | |
args.append("module=%r" % self._module) | |
name = type(self).__name__ | |
return "%s(%s)" % (name, ", ".join(args)) | |
def __enter__(self): | |
if self._entered: | |
raise RuntimeError("Cannot enter %r twice" % self) | |
self._entered = True | |
self._filters = self._module.filters | |
self._module.filters = self._filters[:] | |
self._showwarning = self._module.showwarning | |
warnings.simplefilter("ignore", self.category) | |
def __exit__(self, *exc_info): | |
if not self._entered: | |
raise RuntimeError("Cannot exit %r without entering first" % self) | |
self._module.filters = self._filters | |
self._module.showwarning = self._showwarning | |
self.log[:] = [] | |
def assert_raise_message(exceptions, message, function, *args, **kwargs): | |
"""Helper function to test the message raised in an exception. | |
Given an exception, a callable to raise the exception, and | |
a message string, tests that the correct exception is raised and | |
that the message is a substring of the error thrown. Used to test | |
that the specific message thrown during an exception is correct. | |
Parameters | |
---------- | |
exceptions : exception or tuple of exception | |
An Exception object. | |
message : str | |
The error message or a substring of the error message. | |
function : callable | |
Callable object to raise error. | |
*args : the positional arguments to `function`. | |
**kwargs : the keyword arguments to `function`. | |
""" | |
try: | |
function(*args, **kwargs) | |
except exceptions as e: | |
error_message = str(e) | |
if message not in error_message: | |
raise AssertionError( | |
"Error message does not include the expected" | |
" string: %r. Observed error message: %r" % (message, error_message) | |
) | |
else: | |
# concatenate exception names | |
if isinstance(exceptions, tuple): | |
names = " or ".join(e.__name__ for e in exceptions) | |
else: | |
names = exceptions.__name__ | |
raise AssertionError("%s not raised by %s" % (names, function.__name__)) | |
def assert_allclose( | |
actual, desired, rtol=None, atol=0.0, equal_nan=True, err_msg="", verbose=True | |
): | |
"""dtype-aware variant of numpy.testing.assert_allclose | |
This variant introspects the least precise floating point dtype | |
in the input argument and automatically sets the relative tolerance | |
parameter to 1e-4 float32 and use 1e-7 otherwise (typically float64 | |
in scikit-learn). | |
`atol` is always left to 0. by default. It should be adjusted manually | |
to an assertion-specific value in case there are null values expected | |
in `desired`. | |
The aggregate tolerance is `atol + rtol * abs(desired)`. | |
Parameters | |
---------- | |
actual : array_like | |
Array obtained. | |
desired : array_like | |
Array desired. | |
rtol : float, optional, default=None | |
Relative tolerance. | |
If None, it is set based on the provided arrays' dtypes. | |
atol : float, optional, default=0. | |
Absolute tolerance. | |
equal_nan : bool, optional, default=True | |
If True, NaNs will compare equal. | |
err_msg : str, optional, default='' | |
The error message to be printed in case of failure. | |
verbose : bool, optional, default=True | |
If True, the conflicting values are appended to the error message. | |
Raises | |
------ | |
AssertionError | |
If actual and desired are not equal up to specified precision. | |
See Also | |
-------- | |
numpy.testing.assert_allclose | |
Examples | |
-------- | |
>>> import numpy as np | |
>>> from sklearn.utils._testing import assert_allclose | |
>>> x = [1e-5, 1e-3, 1e-1] | |
>>> y = np.arccos(np.cos(x)) | |
>>> assert_allclose(x, y, rtol=1e-5, atol=0) | |
>>> a = np.full(shape=10, fill_value=1e-5, dtype=np.float32) | |
>>> assert_allclose(a, 1e-5) | |
""" | |
dtypes = [] | |
actual, desired = np.asanyarray(actual), np.asanyarray(desired) | |
dtypes = [actual.dtype, desired.dtype] | |
if rtol is None: | |
rtols = [1e-4 if dtype == np.float32 else 1e-7 for dtype in dtypes] | |
rtol = max(rtols) | |
np_assert_allclose( | |
actual, | |
desired, | |
rtol=rtol, | |
atol=atol, | |
equal_nan=equal_nan, | |
err_msg=err_msg, | |
verbose=verbose, | |
) | |
def assert_allclose_dense_sparse(x, y, rtol=1e-07, atol=1e-9, err_msg=""): | |
"""Assert allclose for sparse and dense data. | |
Both x and y need to be either sparse or dense, they | |
can't be mixed. | |
Parameters | |
---------- | |
x : {array-like, sparse matrix} | |
First array to compare. | |
y : {array-like, sparse matrix} | |
Second array to compare. | |
rtol : float, default=1e-07 | |
relative tolerance; see numpy.allclose. | |
atol : float, default=1e-9 | |
absolute tolerance; see numpy.allclose. Note that the default here is | |
more tolerant than the default for numpy.testing.assert_allclose, where | |
atol=0. | |
err_msg : str, default='' | |
Error message to raise. | |
""" | |
if sp.sparse.issparse(x) and sp.sparse.issparse(y): | |
x = x.tocsr() | |
y = y.tocsr() | |
x.sum_duplicates() | |
y.sum_duplicates() | |
assert_array_equal(x.indices, y.indices, err_msg=err_msg) | |
assert_array_equal(x.indptr, y.indptr, err_msg=err_msg) | |
assert_allclose(x.data, y.data, rtol=rtol, atol=atol, err_msg=err_msg) | |
elif not sp.sparse.issparse(x) and not sp.sparse.issparse(y): | |
# both dense | |
assert_allclose(x, y, rtol=rtol, atol=atol, err_msg=err_msg) | |
else: | |
raise ValueError( | |
"Can only compare two sparse matrices, not a sparse matrix and an array." | |
) | |
def set_random_state(estimator, random_state=0): | |
"""Set random state of an estimator if it has the `random_state` param. | |
Parameters | |
---------- | |
estimator : object | |
The estimator. | |
random_state : int, RandomState instance or None, default=0 | |
Pseudo random number generator state. | |
Pass an int for reproducible results across multiple function calls. | |
See :term:`Glossary <random_state>`. | |
""" | |
if "random_state" in estimator.get_params(): | |
estimator.set_params(random_state=random_state) | |
try: | |
_check_array_api_dispatch(True) | |
ARRAY_API_COMPAT_FUNCTIONAL = True | |
except ImportError: | |
ARRAY_API_COMPAT_FUNCTIONAL = False | |
try: | |
import pytest | |
skip_if_32bit = pytest.mark.skipif(_IS_32BIT, reason="skipped on 32bit platforms") | |
fails_if_pypy = pytest.mark.xfail(IS_PYPY, reason="not compatible with PyPy") | |
fails_if_unstable_openblas = pytest.mark.xfail( | |
_in_unstable_openblas_configuration(), | |
reason="OpenBLAS is unstable for this configuration", | |
) | |
skip_if_no_parallel = pytest.mark.skipif( | |
not joblib.parallel.mp, reason="joblib is in serial mode" | |
) | |
skip_if_array_api_compat_not_configured = pytest.mark.skipif( | |
not ARRAY_API_COMPAT_FUNCTIONAL, | |
reason="requires array_api_compat installed and a new enough version of NumPy", | |
) | |
# Decorator for tests involving both BLAS calls and multiprocessing. | |
# | |
# Under POSIX (e.g. Linux or OSX), using multiprocessing in conjunction | |
# with some implementation of BLAS (or other libraries that manage an | |
# internal posix thread pool) can cause a crash or a freeze of the Python | |
# process. | |
# | |
# In practice all known packaged distributions (from Linux distros or | |
# Anaconda) of BLAS under Linux seems to be safe. So we this problem seems | |
# to only impact OSX users. | |
# | |
# This wrapper makes it possible to skip tests that can possibly cause | |
# this crash under OS X with. | |
# | |
# Under Python 3.4+ it is possible to use the `forkserver` start method | |
# for multiprocessing to avoid this issue. However it can cause pickling | |
# errors on interactively defined functions. It therefore not enabled by | |
# default. | |
if_safe_multiprocessing_with_blas = pytest.mark.skipif( | |
sys.platform == "darwin", reason="Possible multi-process bug with some BLAS" | |
) | |
except ImportError: | |
pass | |
def check_skip_network(): | |
if int(os.environ.get("SKLEARN_SKIP_NETWORK_TESTS", 0)): | |
raise SkipTest("Text tutorial requires large dataset download") | |
def _delete_folder(folder_path, warn=False): | |
"""Utility function to cleanup a temporary folder if still existing. | |
Copy from joblib.pool (for independence). | |
""" | |
try: | |
if os.path.exists(folder_path): | |
# This can fail under windows, | |
# but will succeed when called by atexit | |
shutil.rmtree(folder_path) | |
except OSError: | |
if warn: | |
warnings.warn("Could not delete temporary folder %s" % folder_path) | |
class TempMemmap: | |
""" | |
Parameters | |
---------- | |
data | |
mmap_mode : str, default='r' | |
""" | |
def __init__(self, data, mmap_mode="r"): | |
self.mmap_mode = mmap_mode | |
self.data = data | |
def __enter__(self): | |
data_read_only, self.temp_folder = create_memmap_backed_data( | |
self.data, mmap_mode=self.mmap_mode, return_folder=True | |
) | |
return data_read_only | |
def __exit__(self, exc_type, exc_val, exc_tb): | |
_delete_folder(self.temp_folder) | |
def create_memmap_backed_data(data, mmap_mode="r", return_folder=False): | |
""" | |
Parameters | |
---------- | |
data | |
mmap_mode : str, default='r' | |
return_folder : bool, default=False | |
""" | |
temp_folder = tempfile.mkdtemp(prefix="sklearn_testing_") | |
atexit.register(functools.partial(_delete_folder, temp_folder, warn=True)) | |
filename = op.join(temp_folder, "data.pkl") | |
joblib.dump(data, filename) | |
memmap_backed_data = joblib.load(filename, mmap_mode=mmap_mode) | |
result = ( | |
memmap_backed_data if not return_folder else (memmap_backed_data, temp_folder) | |
) | |
return result | |
# Utils to test docstrings | |
def _get_args(function, varargs=False): | |
"""Helper to get function arguments.""" | |
try: | |
params = signature(function).parameters | |
except ValueError: | |
# Error on builtin C function | |
return [] | |
args = [ | |
key | |
for key, param in params.items() | |
if param.kind not in (param.VAR_POSITIONAL, param.VAR_KEYWORD) | |
] | |
if varargs: | |
varargs = [ | |
param.name | |
for param in params.values() | |
if param.kind == param.VAR_POSITIONAL | |
] | |
if len(varargs) == 0: | |
varargs = None | |
return args, varargs | |
else: | |
return args | |
def _get_func_name(func): | |
"""Get function full name. | |
Parameters | |
---------- | |
func : callable | |
The function object. | |
Returns | |
------- | |
name : str | |
The function name. | |
""" | |
parts = [] | |
module = inspect.getmodule(func) | |
if module: | |
parts.append(module.__name__) | |
qualname = func.__qualname__ | |
if qualname != func.__name__: | |
parts.append(qualname[: qualname.find(".")]) | |
parts.append(func.__name__) | |
return ".".join(parts) | |
def check_docstring_parameters(func, doc=None, ignore=None): | |
"""Helper to check docstring. | |
Parameters | |
---------- | |
func : callable | |
The function object to test. | |
doc : str, default=None | |
Docstring if it is passed manually to the test. | |
ignore : list, default=None | |
Parameters to ignore. | |
Returns | |
------- | |
incorrect : list | |
A list of string describing the incorrect results. | |
""" | |
from numpydoc import docscrape | |
incorrect = [] | |
ignore = [] if ignore is None else ignore | |
func_name = _get_func_name(func) | |
if not func_name.startswith("sklearn.") or func_name.startswith( | |
"sklearn.externals" | |
): | |
return incorrect | |
# Don't check docstring for property-functions | |
if inspect.isdatadescriptor(func): | |
return incorrect | |
# Don't check docstring for setup / teardown pytest functions | |
if func_name.split(".")[-1] in ("setup_module", "teardown_module"): | |
return incorrect | |
# Dont check estimator_checks module | |
if func_name.split(".")[2] == "estimator_checks": | |
return incorrect | |
# Get the arguments from the function signature | |
param_signature = list(filter(lambda x: x not in ignore, _get_args(func))) | |
# drop self | |
if len(param_signature) > 0 and param_signature[0] == "self": | |
param_signature.remove("self") | |
# Analyze function's docstring | |
if doc is None: | |
records = [] | |
with warnings.catch_warnings(record=True): | |
warnings.simplefilter("error", UserWarning) | |
try: | |
doc = docscrape.FunctionDoc(func) | |
except UserWarning as exp: | |
if "potentially wrong underline length" in str(exp): | |
# Catch warning raised as of numpydoc 1.2 when | |
# the underline length for a section of a docstring | |
# is not consistent. | |
message = str(exp).split("\n")[:3] | |
incorrect += [f"In function: {func_name}"] + message | |
return incorrect | |
records.append(str(exp)) | |
except Exception as exp: | |
incorrect += [func_name + " parsing error: " + str(exp)] | |
return incorrect | |
if len(records): | |
raise RuntimeError("Error for %s:\n%s" % (func_name, records[0])) | |
param_docs = [] | |
for name, type_definition, param_doc in doc["Parameters"]: | |
# Type hints are empty only if parameter name ended with : | |
if not type_definition.strip(): | |
if ":" in name and name[: name.index(":")][-1:].strip(): | |
incorrect += [ | |
func_name | |
+ " There was no space between the param name and colon (%r)" % name | |
] | |
elif name.rstrip().endswith(":"): | |
incorrect += [ | |
func_name | |
+ " Parameter %r has an empty type spec. Remove the colon" | |
% (name.lstrip()) | |
] | |
# Create a list of parameters to compare with the parameters gotten | |
# from the func signature | |
if "*" not in name: | |
param_docs.append(name.split(":")[0].strip("` ")) | |
# If one of the docstring's parameters had an error then return that | |
# incorrect message | |
if len(incorrect) > 0: | |
return incorrect | |
# Remove the parameters that should be ignored from list | |
param_docs = list(filter(lambda x: x not in ignore, param_docs)) | |
# The following is derived from pytest, Copyright (c) 2004-2017 Holger | |
# Krekel and others, Licensed under MIT License. See | |
# https://github.com/pytest-dev/pytest | |
message = [] | |
for i in range(min(len(param_docs), len(param_signature))): | |
if param_signature[i] != param_docs[i]: | |
message += [ | |
"There's a parameter name mismatch in function" | |
" docstring w.r.t. function signature, at index %s" | |
" diff: %r != %r" % (i, param_signature[i], param_docs[i]) | |
] | |
break | |
if len(param_signature) > len(param_docs): | |
message += [ | |
"Parameters in function docstring have less items w.r.t." | |
" function signature, first missing item: %s" | |
% param_signature[len(param_docs)] | |
] | |
elif len(param_signature) < len(param_docs): | |
message += [ | |
"Parameters in function docstring have more items w.r.t." | |
" function signature, first extra item: %s" | |
% param_docs[len(param_signature)] | |
] | |
# If there wasn't any difference in the parameters themselves between | |
# docstring and signature including having the same length then return | |
# empty list | |
if len(message) == 0: | |
return [] | |
import difflib | |
import pprint | |
param_docs_formatted = pprint.pformat(param_docs).splitlines() | |
param_signature_formatted = pprint.pformat(param_signature).splitlines() | |
message += ["Full diff:"] | |
message.extend( | |
line.strip() | |
for line in difflib.ndiff(param_signature_formatted, param_docs_formatted) | |
) | |
incorrect.extend(message) | |
# Prepend function name | |
incorrect = ["In function: " + func_name] + incorrect | |
return incorrect | |
def assert_run_python_script_without_output(source_code, pattern=".+", timeout=60): | |
"""Utility to check assertions in an independent Python subprocess. | |
The script provided in the source code should return 0 and the stdtout + | |
stderr should not match the pattern `pattern`. | |
This is a port from cloudpickle https://github.com/cloudpipe/cloudpickle | |
Parameters | |
---------- | |
source_code : str | |
The Python source code to execute. | |
pattern : str | |
Pattern that the stdout + stderr should not match. By default, unless | |
stdout + stderr are both empty, an error will be raised. | |
timeout : int, default=60 | |
Time in seconds before timeout. | |
""" | |
fd, source_file = tempfile.mkstemp(suffix="_src_test_sklearn.py") | |
os.close(fd) | |
try: | |
with open(source_file, "wb") as f: | |
f.write(source_code.encode("utf-8")) | |
cmd = [sys.executable, source_file] | |
cwd = op.normpath(op.join(op.dirname(sklearn.__file__), "..")) | |
env = os.environ.copy() | |
try: | |
env["PYTHONPATH"] = os.pathsep.join([cwd, env["PYTHONPATH"]]) | |
except KeyError: | |
env["PYTHONPATH"] = cwd | |
kwargs = {"cwd": cwd, "stderr": STDOUT, "env": env} | |
# If coverage is running, pass the config file to the subprocess | |
coverage_rc = os.environ.get("COVERAGE_PROCESS_START") | |
if coverage_rc: | |
kwargs["env"]["COVERAGE_PROCESS_START"] = coverage_rc | |
kwargs["timeout"] = timeout | |
try: | |
try: | |
out = check_output(cmd, **kwargs) | |
except CalledProcessError as e: | |
raise RuntimeError( | |
"script errored with output:\n%s" % e.output.decode("utf-8") | |
) | |
out = out.decode("utf-8") | |
if re.search(pattern, out): | |
if pattern == ".+": | |
expectation = "Expected no output" | |
else: | |
expectation = f"The output was not supposed to match {pattern!r}" | |
message = f"{expectation}, got the following output instead: {out!r}" | |
raise AssertionError(message) | |
except TimeoutExpired as e: | |
raise RuntimeError( | |
"script timeout, output so far:\n%s" % e.output.decode("utf-8") | |
) | |
finally: | |
os.unlink(source_file) | |
def _convert_container( | |
container, | |
constructor_name, | |
columns_name=None, | |
dtype=None, | |
minversion=None, | |
categorical_feature_names=None, | |
): | |
"""Convert a given container to a specific array-like with a dtype. | |
Parameters | |
---------- | |
container : array-like | |
The container to convert. | |
constructor_name : {"list", "tuple", "array", "sparse", "dataframe", \ | |
"series", "index", "slice", "sparse_csr", "sparse_csc"} | |
The type of the returned container. | |
columns_name : index or array-like, default=None | |
For pandas container supporting `columns_names`, it will affect | |
specific names. | |
dtype : dtype, default=None | |
Force the dtype of the container. Does not apply to `"slice"` | |
container. | |
minversion : str, default=None | |
Minimum version for package to install. | |
categorical_feature_names : list of str, default=None | |
List of column names to cast to categorical dtype. | |
Returns | |
------- | |
converted_container | |
""" | |
if constructor_name == "list": | |
if dtype is None: | |
return list(container) | |
else: | |
return np.asarray(container, dtype=dtype).tolist() | |
elif constructor_name == "tuple": | |
if dtype is None: | |
return tuple(container) | |
else: | |
return tuple(np.asarray(container, dtype=dtype).tolist()) | |
elif constructor_name == "array": | |
return np.asarray(container, dtype=dtype) | |
elif constructor_name in ("pandas", "dataframe"): | |
pd = pytest.importorskip("pandas", minversion=minversion) | |
result = pd.DataFrame(container, columns=columns_name, dtype=dtype, copy=False) | |
if categorical_feature_names is not None: | |
for col_name in categorical_feature_names: | |
result[col_name] = result[col_name].astype("category") | |
return result | |
elif constructor_name == "pyarrow": | |
pa = pytest.importorskip("pyarrow", minversion=minversion) | |
array = np.asarray(container) | |
if columns_name is None: | |
columns_name = [f"col{i}" for i in range(array.shape[1])] | |
data = {name: array[:, i] for i, name in enumerate(columns_name)} | |
result = pa.Table.from_pydict(data) | |
if categorical_feature_names is not None: | |
for col_idx, col_name in enumerate(result.column_names): | |
if col_name in categorical_feature_names: | |
result = result.set_column( | |
col_idx, col_name, result.column(col_name).dictionary_encode() | |
) | |
return result | |
elif constructor_name == "polars": | |
pl = pytest.importorskip("polars", minversion=minversion) | |
result = pl.DataFrame(container, schema=columns_name, orient="row") | |
if categorical_feature_names is not None: | |
for col_name in categorical_feature_names: | |
result = result.with_columns(pl.col(col_name).cast(pl.Categorical)) | |
return result | |
elif constructor_name == "series": | |
pd = pytest.importorskip("pandas", minversion=minversion) | |
return pd.Series(container, dtype=dtype) | |
elif constructor_name == "index": | |
pd = pytest.importorskip("pandas", minversion=minversion) | |
return pd.Index(container, dtype=dtype) | |
elif constructor_name == "slice": | |
return slice(container[0], container[1]) | |
elif "sparse" in constructor_name: | |
if not sp.sparse.issparse(container): | |
# For scipy >= 1.13, sparse array constructed from 1d array may be | |
# 1d or raise an exception. To avoid this, we make sure that the | |
# input container is 2d. For more details, see | |
# https://github.com/scipy/scipy/pull/18530#issuecomment-1878005149 | |
container = np.atleast_2d(container) | |
if "array" in constructor_name and sp_version < parse_version("1.8"): | |
raise ValueError( | |
f"{constructor_name} is only available with scipy>=1.8.0, got " | |
f"{sp_version}" | |
) | |
if constructor_name in ("sparse", "sparse_csr"): | |
# sparse and sparse_csr are equivalent for legacy reasons | |
return sp.sparse.csr_matrix(container, dtype=dtype) | |
elif constructor_name == "sparse_csr_array": | |
return sp.sparse.csr_array(container, dtype=dtype) | |
elif constructor_name == "sparse_csc": | |
return sp.sparse.csc_matrix(container, dtype=dtype) | |
elif constructor_name == "sparse_csc_array": | |
return sp.sparse.csc_array(container, dtype=dtype) | |
def raises(expected_exc_type, match=None, may_pass=False, err_msg=None): | |
"""Context manager to ensure exceptions are raised within a code block. | |
This is similar to and inspired from pytest.raises, but supports a few | |
other cases. | |
This is only intended to be used in estimator_checks.py where we don't | |
want to use pytest. In the rest of the code base, just use pytest.raises | |
instead. | |
Parameters | |
---------- | |
excepted_exc_type : Exception or list of Exception | |
The exception that should be raised by the block. If a list, the block | |
should raise one of the exceptions. | |
match : str or list of str, default=None | |
A regex that the exception message should match. If a list, one of | |
the entries must match. If None, match isn't enforced. | |
may_pass : bool, default=False | |
If True, the block is allowed to not raise an exception. Useful in | |
cases where some estimators may support a feature but others must | |
fail with an appropriate error message. By default, the context | |
manager will raise an exception if the block does not raise an | |
exception. | |
err_msg : str, default=None | |
If the context manager fails (e.g. the block fails to raise the | |
proper exception, or fails to match), then an AssertionError is | |
raised with this message. By default, an AssertionError is raised | |
with a default error message (depends on the kind of failure). Use | |
this to indicate how users should fix their estimators to pass the | |
checks. | |
Attributes | |
---------- | |
raised_and_matched : bool | |
True if an exception was raised and a match was found, False otherwise. | |
""" | |
return _Raises(expected_exc_type, match, may_pass, err_msg) | |
class _Raises(contextlib.AbstractContextManager): | |
# see raises() for parameters | |
def __init__(self, expected_exc_type, match, may_pass, err_msg): | |
self.expected_exc_types = ( | |
expected_exc_type | |
if isinstance(expected_exc_type, Iterable) | |
else [expected_exc_type] | |
) | |
self.matches = [match] if isinstance(match, str) else match | |
self.may_pass = may_pass | |
self.err_msg = err_msg | |
self.raised_and_matched = False | |
def __exit__(self, exc_type, exc_value, _): | |
# see | |
# https://docs.python.org/2.5/whatsnew/pep-343.html#SECTION000910000000000000000 | |
if exc_type is None: # No exception was raised in the block | |
if self.may_pass: | |
return True # CM is happy | |
else: | |
err_msg = self.err_msg or f"Did not raise: {self.expected_exc_types}" | |
raise AssertionError(err_msg) | |
if not any( | |
issubclass(exc_type, expected_type) | |
for expected_type in self.expected_exc_types | |
): | |
if self.err_msg is not None: | |
raise AssertionError(self.err_msg) from exc_value | |
else: | |
return False # will re-raise the original exception | |
if self.matches is not None: | |
err_msg = self.err_msg or ( | |
"The error message should contain one of the following " | |
"patterns:\n{}\nGot {}".format("\n".join(self.matches), str(exc_value)) | |
) | |
if not any(re.search(match, str(exc_value)) for match in self.matches): | |
raise AssertionError(err_msg) from exc_value | |
self.raised_and_matched = True | |
return True | |
class MinimalClassifier: | |
"""Minimal classifier implementation with inheriting from BaseEstimator. | |
This estimator should be tested with: | |
* `check_estimator` in `test_estimator_checks.py`; | |
* within a `Pipeline` in `test_pipeline.py`; | |
* within a `SearchCV` in `test_search.py`. | |
""" | |
_estimator_type = "classifier" | |
def __init__(self, param=None): | |
self.param = param | |
def get_params(self, deep=True): | |
return {"param": self.param} | |
def set_params(self, **params): | |
for key, value in params.items(): | |
setattr(self, key, value) | |
return self | |
def fit(self, X, y): | |
X, y = check_X_y(X, y) | |
check_classification_targets(y) | |
self.classes_, counts = np.unique(y, return_counts=True) | |
self._most_frequent_class_idx = counts.argmax() | |
return self | |
def predict_proba(self, X): | |
check_is_fitted(self) | |
X = check_array(X) | |
proba_shape = (X.shape[0], self.classes_.size) | |
y_proba = np.zeros(shape=proba_shape, dtype=np.float64) | |
y_proba[:, self._most_frequent_class_idx] = 1.0 | |
return y_proba | |
def predict(self, X): | |
y_proba = self.predict_proba(X) | |
y_pred = y_proba.argmax(axis=1) | |
return self.classes_[y_pred] | |
def score(self, X, y): | |
from sklearn.metrics import accuracy_score | |
return accuracy_score(y, self.predict(X)) | |
class MinimalRegressor: | |
"""Minimal regressor implementation with inheriting from BaseEstimator. | |
This estimator should be tested with: | |
* `check_estimator` in `test_estimator_checks.py`; | |
* within a `Pipeline` in `test_pipeline.py`; | |
* within a `SearchCV` in `test_search.py`. | |
""" | |
_estimator_type = "regressor" | |
def __init__(self, param=None): | |
self.param = param | |
def get_params(self, deep=True): | |
return {"param": self.param} | |
def set_params(self, **params): | |
for key, value in params.items(): | |
setattr(self, key, value) | |
return self | |
def fit(self, X, y): | |
X, y = check_X_y(X, y) | |
self.is_fitted_ = True | |
self._mean = np.mean(y) | |
return self | |
def predict(self, X): | |
check_is_fitted(self) | |
X = check_array(X) | |
return np.ones(shape=(X.shape[0],)) * self._mean | |
def score(self, X, y): | |
from sklearn.metrics import r2_score | |
return r2_score(y, self.predict(X)) | |
class MinimalTransformer: | |
"""Minimal transformer implementation with inheriting from | |
BaseEstimator. | |
This estimator should be tested with: | |
* `check_estimator` in `test_estimator_checks.py`; | |
* within a `Pipeline` in `test_pipeline.py`; | |
* within a `SearchCV` in `test_search.py`. | |
""" | |
def __init__(self, param=None): | |
self.param = param | |
def get_params(self, deep=True): | |
return {"param": self.param} | |
def set_params(self, **params): | |
for key, value in params.items(): | |
setattr(self, key, value) | |
return self | |
def fit(self, X, y=None): | |
check_array(X) | |
self.is_fitted_ = True | |
return self | |
def transform(self, X, y=None): | |
check_is_fitted(self) | |
X = check_array(X) | |
return X | |
def fit_transform(self, X, y=None): | |
return self.fit(X, y).transform(X, y) | |
def _array_api_for_tests(array_namespace, device): | |
try: | |
if array_namespace == "numpy.array_api": | |
# FIXME: once it is not experimental anymore | |
with ignore_warnings(category=UserWarning): | |
# UserWarning: numpy.array_api submodule is still experimental. | |
array_mod = importlib.import_module(array_namespace) | |
else: | |
array_mod = importlib.import_module(array_namespace) | |
except ModuleNotFoundError: | |
raise SkipTest( | |
f"{array_namespace} is not installed: not checking array_api input" | |
) | |
try: | |
import array_api_compat # noqa | |
except ImportError: | |
raise SkipTest( | |
"array_api_compat is not installed: not checking array_api input" | |
) | |
# First create an array using the chosen array module and then get the | |
# corresponding (compatibility wrapped) array namespace based on it. | |
# This is because `cupy` is not the same as the compatibility wrapped | |
# namespace of a CuPy array. | |
xp = array_api_compat.get_namespace(array_mod.asarray(1)) | |
if ( | |
array_namespace == "torch" | |
and device == "cuda" | |
and not xp.backends.cuda.is_built() | |
): | |
raise SkipTest("PyTorch test requires cuda, which is not available") | |
elif array_namespace == "torch" and device == "mps": | |
if os.getenv("PYTORCH_ENABLE_MPS_FALLBACK") != "1": | |
# For now we need PYTORCH_ENABLE_MPS_FALLBACK=1 for all estimators to work | |
# when using the MPS device. | |
raise SkipTest( | |
"Skipping MPS device test because PYTORCH_ENABLE_MPS_FALLBACK is not " | |
"set." | |
) | |
if not xp.backends.mps.is_built(): | |
raise SkipTest( | |
"MPS is not available because the current PyTorch install was not " | |
"built with MPS enabled." | |
) | |
elif array_namespace in {"cupy", "cupy.array_api"}: # pragma: nocover | |
import cupy | |
if cupy.cuda.runtime.getDeviceCount() == 0: | |
raise SkipTest("CuPy test requires cuda, which is not available") | |
return xp | |
def _get_warnings_filters_info_list(): | |
class WarningInfo: | |
action: "warnings._ActionKind" | |
message: str = "" | |
category: type[Warning] = Warning | |
def to_filterwarning_str(self): | |
if self.category.__module__ == "builtins": | |
category = self.category.__name__ | |
else: | |
category = f"{self.category.__module__}.{self.category.__name__}" | |
return f"{self.action}:{self.message}:{category}" | |
return [ | |
WarningInfo("error", category=DeprecationWarning), | |
WarningInfo("error", category=FutureWarning), | |
WarningInfo("error", category=VisibleDeprecationWarning), | |
# TODO: remove when pyamg > 5.0.1 | |
# Avoid a deprecation warning due pkg_resources usage in pyamg. | |
WarningInfo( | |
"ignore", | |
message="pkg_resources is deprecated as an API", | |
category=DeprecationWarning, | |
), | |
WarningInfo( | |
"ignore", | |
message="Deprecated call to `pkg_resources", | |
category=DeprecationWarning, | |
), | |
# pytest-cov issue https://github.com/pytest-dev/pytest-cov/issues/557 not | |
# fixed although it has been closed. https://github.com/pytest-dev/pytest-cov/pull/623 | |
# would probably fix it. | |
WarningInfo( | |
"ignore", | |
message=( | |
"The --rsyncdir command line argument and rsyncdirs config variable are" | |
" deprecated" | |
), | |
category=DeprecationWarning, | |
), | |
# XXX: Easiest way to ignore pandas Pyarrow DeprecationWarning in the | |
# short-term. See https://github.com/pandas-dev/pandas/issues/54466 for | |
# more details. | |
WarningInfo( | |
"ignore", | |
message=r"\s*Pyarrow will become a required dependency", | |
category=DeprecationWarning, | |
), | |
] | |
def get_pytest_filterwarning_lines(): | |
warning_filters_info_list = _get_warnings_filters_info_list() | |
return [ | |
warning_info.to_filterwarning_str() | |
for warning_info in warning_filters_info_list | |
] | |
def turn_warnings_into_errors(): | |
warnings_filters_info_list = _get_warnings_filters_info_list() | |
for warning_info in warnings_filters_info_list: | |
warnings.filterwarnings( | |
warning_info.action, | |
message=warning_info.message, | |
category=warning_info.category, | |
) | |