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import importlib
import inspect
import pkgutil
import re
from inspect import signature
from typing import Optional
import pytest
import imblearn
from imblearn.utils.testing import all_estimators
numpydoc_validation = pytest.importorskip("numpydoc.validate")
# List of whitelisted modules and methods; regexp are supported.
# These docstrings will fail because they are inheriting from scikit-learn
DOCSTRING_WHITELIST = [
"ADASYN$",
"ADASYN.",
"AllKNN$",
"AllKNN.",
"BalancedBaggingClassifier$",
"BalancedBaggingClassifier.",
"BalancedRandomForestClassifier$",
"BalancedRandomForestClassifier.",
"ClusterCentroids$",
"ClusterCentroids.",
"CondensedNearestNeighbour$",
"CondensedNearestNeighbour.",
"EasyEnsembleClassifier$",
"EasyEnsembleClassifier.",
"EditedNearestNeighbours$",
"EditedNearestNeighbours.",
"FunctionSampler$",
"FunctionSampler.",
"InstanceHardnessThreshold$",
"InstanceHardnessThreshold.",
"SMOTE$",
"SMOTE.",
"NearMiss$",
"NearMiss.",
"NeighbourhoodCleaningRule$",
"NeighbourhoodCleaningRule.",
"OneSidedSelection$",
"OneSidedSelection.",
"Pipeline$",
"Pipeline.",
"RUSBoostClassifier$",
"RUSBoostClassifier.",
"RandomOverSampler$",
"RandomOverSampler.",
"RandomUnderSampler$",
"RandomUnderSampler.",
"TomekLinks$",
"TomekLinks",
"ValueDifferenceMetric$",
"ValueDifferenceMetric.",
]
FUNCTION_DOCSTRING_IGNORE_LIST = [
"imblearn.tensorflow._generator.balanced_batch_generator",
]
FUNCTION_DOCSTRING_IGNORE_LIST = set(FUNCTION_DOCSTRING_IGNORE_LIST)
def get_all_methods():
estimators = all_estimators()
for name, Estimator in estimators:
if name.startswith("_"):
# skip private classes
continue
methods = []
for name in dir(Estimator):
if name.startswith("_"):
continue
method_obj = getattr(Estimator, name)
if hasattr(method_obj, "__call__") or isinstance(method_obj, property):
methods.append(name)
methods.append(None)
for method in sorted(methods, key=lambda x: str(x)):
yield Estimator, method
def _is_checked_function(item):
if not inspect.isfunction(item):
return False
if item.__name__.startswith("_"):
return False
mod = item.__module__
if not mod.startswith("imblearn.") or mod.endswith("estimator_checks"):
return False
return True
def get_all_functions_names():
"""Get all public functions define in the imblearn module"""
modules_to_ignore = {
"tests",
"estimator_checks",
}
all_functions_names = set()
for module_finder, module_name, ispkg in pkgutil.walk_packages(
path=imblearn.__path__, prefix="imblearn."
):
module_parts = module_name.split(".")
if (
any(part in modules_to_ignore for part in module_parts)
or "._" in module_name
):
continue
module = importlib.import_module(module_name)
functions = inspect.getmembers(module, _is_checked_function)
for name, func in functions:
full_name = f"{func.__module__}.{func.__name__}"
all_functions_names.add(full_name)
return sorted(all_functions_names)
def filter_errors(errors, method, Estimator=None):
"""
Ignore some errors based on the method type.
These rules are specific for scikit-learn."""
for code, message in errors:
# We ignore following error code,
# - RT02: The first line of the Returns section
# should contain only the type, ..
# (as we may need refer to the name of the returned
# object)
# - GL01: Docstring text (summary) should start in the line
# immediately after the opening quotes (not in the same line,
# or leaving a blank line in between)
# - GL02: If there's a blank line, it should be before the
# first line of the Returns section, not after (it allows to have
# short docstrings for properties).
if code in ["RT02", "GL01", "GL02"]:
continue
# Ignore PR02: Unknown parameters for properties. We sometimes use
# properties for ducktyping, i.e. SGDClassifier.predict_proba
if code == "PR02" and Estimator is not None and method is not None:
method_obj = getattr(Estimator, method)
if isinstance(method_obj, property):
continue
# Following codes are only taken into account for the
# top level class docstrings:
# - ES01: No extended summary found
# - SA01: See Also section not found
# - EX01: No examples section found
if method is not None and code in ["EX01", "SA01", "ES01"]:
continue
yield code, message
def repr_errors(res, estimator=None, method: Optional[str] = None) -> str:
"""Pretty print original docstring and the obtained errors
Parameters
----------
res : dict
result of numpydoc.validate.validate
estimator : {estimator, None}
estimator object or None
method : str
if estimator is not None, either the method name or None.
Returns
-------
str
String representation of the error.
"""
if method is None:
if hasattr(estimator, "__init__"):
method = "__init__"
elif estimator is None:
raise ValueError("At least one of estimator, method should be provided")
else:
raise NotImplementedError
if estimator is not None:
obj = getattr(estimator, method)
try:
obj_signature = signature(obj)
except TypeError:
# In particular we can't parse the signature of properties
obj_signature = (
"\nParsing of the method signature failed, "
"possibly because this is a property."
)
obj_name = estimator.__name__ + "." + method
else:
obj_signature = ""
obj_name = method
msg = "\n\n" + "\n\n".join(
[
str(res["file"]),
obj_name + str(obj_signature),
res["docstring"],
"# Errors",
"\n".join(
" - {}: {}".format(code, message) for code, message in res["errors"]
),
]
)
return msg
@pytest.mark.parametrize("function_name", get_all_functions_names())
def test_function_docstring(function_name, request):
"""Check function docstrings using numpydoc."""
if function_name in FUNCTION_DOCSTRING_IGNORE_LIST:
request.applymarker(
pytest.mark.xfail(run=False, reason="TODO pass numpydoc validation")
)
res = numpydoc_validation.validate(function_name)
res["errors"] = list(filter_errors(res["errors"], method="function"))
if res["errors"]:
msg = repr_errors(res, method=f"Tested function: {function_name}")
raise ValueError(msg)
@pytest.mark.parametrize("Estimator, method", get_all_methods())
def test_docstring(Estimator, method, request):
base_import_path = Estimator.__module__
import_path = [base_import_path, Estimator.__name__]
if method is not None:
import_path.append(method)
import_path = ".".join(import_path)
if not any(re.search(regex, import_path) for regex in DOCSTRING_WHITELIST):
request.applymarker(
pytest.mark.xfail(run=False, reason="TODO pass numpydoc validation")
)
res = numpydoc_validation.validate(import_path)
res["errors"] = list(filter_errors(res["errors"], method))
if res["errors"]:
msg = repr_errors(res, Estimator, method)
raise ValueError(msg)
if __name__ == "__main__":
import argparse
import sys
parser = argparse.ArgumentParser(description="Validate docstring with numpydoc.")
parser.add_argument("import_path", help="Import path to validate")
args = parser.parse_args()
res = numpydoc_validation.validate(args.import_path)
import_path_sections = args.import_path.split(".")
# When applied to classes, detect class method. For functions
# method = None.
# TODO: this detection can be improved. Currently we assume that we have
# class # methods if the second path element before last is in camel case.
if len(import_path_sections) >= 2 and re.match(
r"(?:[A-Z][a-z]*)+", import_path_sections[-2]
):
method = import_path_sections[-1]
else:
method = None
res["errors"] = list(filter_errors(res["errors"], method))
if res["errors"]:
msg = repr_errors(res, method=args.import_path)
print(msg)
sys.exit(1)
else:
print("All docstring checks passed for {}!".format(args.import_path))
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