def _all_estimators(self):
"""Retrieve list of all estimator classes of type self.estimator_type_filter."""
return all_estimators(
estimator_types=getattr(self, "estimator_type_filter", None),
return_names=False,
exclude_estimators=EXCLUDE_ESTIMATORS,
)
def test_all_estimators_return_tags(return_tags, return_names):
"""Test ability to return estimator value of passed tags."""
estimators = all_estimators(
return_tags=return_tags,
return_names=return_names,
)
# Helps us keep track of estimator index within the tuple:
ESTIMATOR_INDEX = 1 if return_names else 0
TAG_START_INDEX = ESTIMATOR_INDEX + 1
assert isinstance(estimators[0], tuple)
# check length of tuple is what we expect:
if isinstance(return_tags, str):
assert len(estimators[0]) == TAG_START_INDEX + 1
else:
assert len(estimators[0]) == len(return_tags) + TAG_START_INDEX
# check that for each estimator the value for that tag is correct:
for est_tuple in estimators:
est = est_tuple[ESTIMATOR_INDEX]
if isinstance(return_tags, str):
assert est.get_class_tag(return_tags) == est_tuple[TAG_START_INDEX]
else:
for tag_index, tag in enumerate(return_tags):
assert est.get_class_tag(tag) == est_tuple[TAG_START_INDEX +
tag_index]
def test_all_estimators_exclude_estimators(exclude_estimators):
estimators = all_estimators(return_names=True,
exclude_estimators=exclude_estimators)
assert isinstance(estimators, list)
assert len(estimators) > 0
names, estimators = list(zip(*estimators))
if not isinstance(exclude_estimators, list):
exclude_estimators = [exclude_estimators]
for estimator in exclude_estimators:
assert estimator not in names
def test_all_estimators_filter_estimator_types(estimator_type):
estimators = all_estimators(estimator_types=estimator_type,
return_names=False)
assert isinstance(estimators, list)
# assert len(estimators) > 0
if isinstance(estimator_type, str):
estimator_type = VALID_ESTIMATOR_BASE_TYPE_LOOKUP[estimator_type]
assert all(
[issubclass(estimator, estimator_type) for estimator in estimators])
def test_all_estimators_return_names(return_names):
estimators = all_estimators(return_names=return_names)
assert isinstance(estimators, list)
assert len(estimators) > 0
if return_names:
assert all([isinstance(estimator, tuple) for estimator in estimators])
names, estimators = list(zip(*estimators))
assert all([isinstance(name, str) for name in names])
assert all([
name == estimator.__name__
for name, estimator in zip(names, estimators)
])
assert all([isinstance(estimator, type) for estimator in estimators])
def test_all_estimators_by_scitype(estimator_scitype, return_names):
"""Check that all_estimators return argument has correct type."""
estimators = all_estimators(
estimator_types=estimator_scitype,
return_names=return_names,
)
estimator_classes = _get_type_tuple(estimator_scitype)
assert isinstance(estimators, list)
# there should be at least one estimator returned
assert len(estimators) > 0
# checks return type specification (see docstring)
if return_names:
for estimator in estimators:
assert isinstance(estimator, tuple) and len(estimator) == 2
assert isinstance(estimator[0], str)
assert issubclass(estimator[1], estimator_classes)
assert estimator[0] == estimator[1].__name__
else:
for estimator in estimators:
assert issubclass(estimator, estimator_classes)
# -*- coding: utf-8 -*-
"""Tests for pairwise transformer."""
import numpy as np
import pytest
from sktime.registry import all_estimators
from sktime.utils._testing.panel import make_transformer_problem
PAIRWISE_TRANSFORMERS = all_estimators(estimator_types="transformer-pairwise",
return_names=False)
PAIRWISE_TRANSFORMERS_PANEL = all_estimators(
estimator_types="transformer-pairwise-panel", return_names=False)
EXPECTED_SHAPE = (4, 5)
X1_tab = make_transformer_problem(
n_instances=4,
n_columns=4,
n_timepoints=5,
random_state=1,
return_numpy=True,
panel=False,
)
X2_tab = make_transformer_problem(
n_instances=5,
n_columns=5,
n_timepoints=5,
random_state=2,
return_numpy=True,
panel=False,
from sktime.registry import all_estimators
# List of columns in the table
df_columns = [
"Classifier Category",
"Classifier Name",
"multivariate",
"unequal_length",
"missing_values",
"train_estimate",
"contractable",
]
# creates dataframe as df
df = pd.DataFrame([], columns=df_columns)
# Loop through all the classifiers
for classiName, classiClass in all_estimators(estimator_types="classifier"):
category = str(classiClass).split(".")[2]
try:
# capabilites of each of the classifier classifier
cap_dict = classiClass.capabilities
multivariate = str(cap_dict["multivariate"])
unequal_length = str(cap_dict["unequal_length"])
missing_values = str(cap_dict["missing_values"])
train_estimate = str(cap_dict["train_estimate"])
contractable = str(cap_dict["contractable"])
# Adding capabilites for each classifier in the table
df = df.append(
{
"Classifier Category": category,
"Classifier Name": classiName,
"multivariate": multivariate,
# -*- coding: utf-8 -*-
# copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
"""Tests for BaseAligner API points."""
__author__ = ["fkiraly"]
import pandas as pd
import pytest
from sktime.datatypes._check import check_raise
from sktime.registry import all_estimators
from sktime.utils._testing.series import _make_series
# get all aligners
ALIGNERS = all_estimators(estimator_types="aligner", return_names=False)
INVALID_X_INPUT_TYPES = [list(), tuple()]
INVALID_y_INPUT_TYPES = [list(), tuple()]
@pytest.mark.parametrize("Aligner", ALIGNERS)
def test_get_alignment(Aligner):
"""Test that get_alignment returns an alignment (iloc)."""
f = Aligner.create_test_instance()
X = [_make_series(n_columns=2), _make_series(n_columns=2)]
align = f.fit(X).get_alignment()
check_raise(align, mtype="alignment", scitype="Alignment")
@pytest.mark.parametrize("Aligner", ALIGNERS)
#!/usr/bin/env python3 -u
# -*- coding: utf-8 -*-
# copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
__author__ = ["Markus Löning"]
__all__ = ["test_estimator"]
import pytest
from sktime.tests._config import EXCLUDE_ESTIMATORS
from sktime.tests._config import EXCLUDED_TESTS
from sktime.registry import all_estimators
from sktime.utils._testing.estimator_checks import check_estimator
ALL_ESTIMATORS = all_estimators(return_names=False,
exclude_estimators=EXCLUDE_ESTIMATORS)
@pytest.mark.parametrize("Estimator", ALL_ESTIMATORS)
def test_estimator(Estimator):
# We run a number of basic checks on all estimators to ensure correct
# implementation of our framework and compatibility with scikit-learn.
check_estimator(Estimator, EXCLUDED_TESTS.get(Estimator.__name__, []))
from sktime.tests._config import VALID_TRANSFORMER_TYPES
from sktime.transformations.base import (
BaseTransformer,
_PanelToPanelTransformer,
_PanelToTabularTransformer,
_SeriesToPrimitivesTransformer,
_SeriesToSeriesTransformer,
)
from sktime.utils._testing.estimator_checks import (
_assert_array_almost_equal,
_construct_instance,
_has_capability,
_make_args,
)
ALL_TRANSFORMERS = all_estimators(estimator_types="transformer",
return_names=False)
@pytest.mark.parametrize("Estimator", ALL_TRANSFORMERS)
def test_all_transformers(Estimator):
check_transformer(Estimator)
def check_transformer(Estimator):
for check in _yield_transformer_checks(Estimator):
check(Estimator)
def _construct_fit_transform(Estimator, **kwargs):
estimator = _construct_instance(Estimator)
# -*- coding: utf-8 -*-
import numpy as np
from sktime.dists_kernels.compose_tab_to_panel import AggrDist
from sktime.dists_kernels.scipy_dist import ScipyDist
from sktime.utils._testing.panel import make_transformer_problem
from sktime.registry import all_estimators
PAIRWISE_TRANSFORMERS_TAB = all_estimators(
estimator_types="transformer-pairwise", return_names=False
)
AGGFUNCS = [
np.mean,
np.std,
np.var,
np.sum,
np.prod,
np.min,
np.max,
np.argmin,
np.argmax,
np.any,
]
X1_num_pan = make_transformer_problem(
n_instances=4, n_columns=4, n_timepoints=5, random_state=1, return_numpy=True
)
X2_num_pan = make_transformer_problem(
n_instances=5, n_columns=5, n_timepoints=5, random_state=2, return_numpy=True
)
]
import numpy as np
import pytest
from sktime.registry import all_estimators
from sktime.series_as_features.tests._config import ACCEPTED_OUTPUT_TYPES
from sktime.tests._config import EXCLUDE_ESTIMATORS, NON_STATE_CHANGING_METHODS
from sktime.transformations.base import (
_PanelToPanelTransformer,
_PanelToTabularTransformer,
)
from sktime.utils._testing.estimator_checks import _construct_instance, _make_args
CLASSIFIERS = all_estimators("classifier",
return_names=False,
exclude_estimators=EXCLUDE_ESTIMATORS)
REGRESSORS = all_estimators("regressor",
return_names=False,
exclude_estimators=EXCLUDE_ESTIMATORS)
PANEL_TRANSFORMERS = all_estimators(
estimator_types=[_PanelToPanelTransformer, _PanelToTabularTransformer],
return_names=False,
exclude_estimators=EXCLUDE_ESTIMATORS,
)
PANEL_ESTIMATORS = CLASSIFIERS + REGRESSORS + PANEL_TRANSFORMERS
# We here only check the ouput for a single number of classes
N_CLASSES = 3
# -*- coding: utf-8 -*-
import pandas as pd
import pytest
from sktime.utils._testing.estimator_checks import _construct_instance, _make_args
from sktime.registry import all_estimators
ALL_ANNOTATORS = all_estimators(estimator_types="series-annotator", return_names=False)
@pytest.mark.parametrize("Estimator", ALL_ANNOTATORS)
def test_output_type(Estimator):
estimator = _construct_instance(Estimator)
args = _make_args(estimator, "fit")
estimator.fit(*args)
args = _make_args(estimator, "predict")
y_pred = estimator.predict(*args)
assert isinstance(y_pred, pd.Series)
__all__ = [
"test_regressor_output",
"test_multivariate_input",
"test_3d_numpy_input",
]
import numpy as np
import pandas as pd
import pytest
from sktime.registry import all_estimators
from sktime.tests._config import EXCLUDE_ESTIMATORS, NON_STATE_CHANGING_METHODS
from sktime.utils._testing.estimator_checks import _has_capability, _make_args
REGRESSORS = all_estimators("regressor",
return_names=False,
exclude_estimators=EXCLUDE_ESTIMATORS)
ACCEPTED_OUTPUT_TYPES = (np.ndarray, pd.Series)
# We here only check the ouput for a single number of classes
N_CLASSES = 3
@pytest.mark.parametrize("Estimator", REGRESSORS)
def test_3d_numpy_input(Estimator):
"""Test classifiers handle 3D numpy input correctly."""
estimator = Estimator.create_test_instance()
fit_args = _make_args(estimator, "fit", return_numpy=True)
estimator.fit(*fit_args)
"test_3d_numpy_input",
]
import pytest
from sktime.registry import all_estimators
from sktime.tests._config import EXCLUDE_ESTIMATORS, NON_STATE_CHANGING_METHODS
from sktime.transformations.base import (
_PanelToPanelTransformer,
_PanelToTabularTransformer,
)
from sktime.utils._testing.estimator_checks import _has_capability, _make_args
PANEL_TRANSFORMERS = all_estimators(
estimator_types=[_PanelToPanelTransformer, _PanelToTabularTransformer],
return_names=False,
exclude_estimators=EXCLUDE_ESTIMATORS,
)
PANEL_ESTIMATORS = PANEL_TRANSFORMERS
# We here only check the ouput for a single number of classes
N_CLASSES = 3
@pytest.mark.parametrize("Estimator", PANEL_TRANSFORMERS)
def test_3d_numpy_input(Estimator):
"""Test classifiers handle 3D numpy input correctly."""
estimator = Estimator.create_test_instance()
fit_args = _make_args(estimator, "fit", return_numpy=True)
estimator.fit(*fit_args)
)
from sktime.performance_metrics.forecasting import mean_absolute_percentage_error
from sktime.registry import all_estimators
from sktime.utils._testing.estimator_checks import _construct_instance
from sktime.utils._testing.forecasting import (
_assert_correct_pred_time_index,
_get_expected_index_for_update_predict,
_get_n_columns,
_make_fh,
make_forecasting_problem,
)
from sktime.utils._testing.series import _make_series
from sktime.utils.validation.forecasting import check_fh
# get all forecasters
FORECASTERS = all_estimators(estimator_types="forecaster", return_names=False)
FH0 = 1
INVALID_X_INPUT_TYPES = [list(), tuple()]
INVALID_y_INPUT_TYPES = [list(), tuple()]
# testing data
y = make_forecasting_problem()
y_train, y_test = temporal_train_test_split(y, train_size=0.75)
@pytest.mark.parametrize("Forecaster", FORECASTERS)
def test_get_fitted_params(Forecaster):
"""Test get_fitted_params."""
f = _construct_instance(Forecaster)
columns = _get_n_columns(f.get_tag("scitype:y"))
for n_columns in columns:
__author__ = ["mloning"]
import numpy as np
import pytest
from sktime.forecasting.base._sktime import _BaseWindowForecaster
from sktime.forecasting.model_selection import temporal_train_test_split
from sktime.registry import all_estimators
from sktime.utils._testing.forecasting import _get_n_columns, make_forecasting_problem
from sktime.utils._testing.series import _make_series
FH0 = 1
WINDOW_FORECASTERS = [
forecaster
for (name, forecaster) in all_estimators(estimator_types="forecaster")
if issubclass(forecaster, _BaseWindowForecaster)
]
# testing data
y = make_forecasting_problem()
y_train, y_test = temporal_train_test_split(y, train_size=0.75)
@pytest.mark.parametrize("Forecaster", WINDOW_FORECASTERS)
def test_last_window(Forecaster):
"""Test window forecaster common API points."""
f = Forecaster.create_test_instance()
n_columns_list = _get_n_columns(f.get_tag("scitype:y"))
for n_columns in n_columns_list:
def test_all_estimators_return_tags_bad_arg(return_tags):
"""Test ability to catch bad arguments of return_tags."""
with pytest.raises(TypeError):
_ = all_estimators(return_tags=return_tags)
def _make_estimator_overview(app):
"""Make estimator overview table."""
import pandas as pd
from sktime.registry import all_estimators
def _process_author_info(author_info):
"""
Process author information from source code files.
Parameters
----------
author_info : str
Author information string from source code files.
Returns
-------
author_info : str
Preprocessed author information.
Notes
-----
A list of author names is turned into a string.
Multiple author names will be separated by a comma,
with the final name always preceded by "&".
"""
if isinstance(author_info, list):
if len(author_info) > 1:
return ", ".join(author_info[:-1]) + " & " + author_info[-1]
else:
return author_info[0]
else:
return author_info
def _does_not_start_with_underscore(input_string):
return not input_string.startswith("_")
# creates dataframe as df
COLNAMES = ["Class Name", "Estimator Type", "Authors"]
df = pd.DataFrame([], columns=COLNAMES)
for modname, modclass in all_estimators():
algorithm_type = "::".join(str(modclass).split(".")[1:-2])
try:
author_info = _process_author_info(modclass.__author__)
except AttributeError:
try:
author_info = _process_author_info(
import_module(modclass.__module__).__author__)
except AttributeError:
author_info = "no author info"
# includes part of class string
modpath = str(modclass)[8:-2]
path_parts = modpath.split(".")
# joins strings excluding starting with '_'
clean_path = ".".join(
list(filter(_does_not_start_with_underscore, path_parts)))
# adds html link reference
modname = str(
'<a href="https://www.sktime.org/en/latest/api_reference' +
"/auto_generated/" + clean_path + '.html">' + modname + "</a>")
df = df.append(
pd.Series([modname, algorithm_type, author_info], index=COLNAMES),
ignore_index=True,
)
with open("estimator_overview_table.md", "w") as file:
df.to_markdown(file, index=False)
__author__ = ["mloning", "TonyBagnall"]
__all__ = [
"test_classifier_output",
"test_multivariate_input",
"test_3d_numpy_input",
]
import numpy as np
import pytest
from sktime.registry import all_estimators
from sktime.tests._config import EXCLUDE_ESTIMATORS, NON_STATE_CHANGING_METHODS
from sktime.utils._testing.estimator_checks import _has_capability, _make_args
CLASSIFIERS = all_estimators("classifier",
return_names=False,
exclude_estimators=EXCLUDE_ESTIMATORS)
N_CLASSES = 3
@pytest.mark.parametrize("Estimator", CLASSIFIERS)
def test_3d_numpy_input(Estimator):
"""Test classifiers handle 3D numpy input correctly."""
estimator = Estimator.create_test_instance()
fit_args = _make_args(estimator, "fit", return_numpy=True)
estimator.fit(*fit_args)
for method in NON_STATE_CHANGING_METHODS:
if _has_capability(estimator, method):
# try if methods can handle 3d numpy input data
