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[EDIT] FILE: pyflakes.py

"""Plugin built-in to Flake8 to treat pyflakes as a plugin."""
import argparse
import ast
import os
import tokenize
from typing import Any
from typing import Generator
from typing import List
from typing import Tuple
from typing import Type

import pyflakes.checker

from flake8 import utils
from flake8.options.manager import OptionManager

FLAKE8_PYFLAKES_CODES = {
    "UnusedImport": "F401",
    "ImportShadowedByLoopVar": "F402",
    "ImportStarUsed": "F403",
    "LateFutureImport": "F404",
    "ImportStarUsage": "F405",
    "ImportStarNotPermitted": "F406",
    "FutureFeatureNotDefined": "F407",
    "PercentFormatInvalidFormat": "F501",
    "PercentFormatExpectedMapping": "F502",
    "PercentFormatExpectedSequence": "F503",
    "PercentFormatExtraNamedArguments": "F504",
    "PercentFormatMissingArgument": "F505",
    "PercentFormatMixedPositionalAndNamed": "F506",
    "PercentFormatPositionalCountMismatch": "F507",
    "PercentFormatStarRequiresSequence": "F508",
    "PercentFormatUnsupportedFormatCharacter": "F509",
    "StringDotFormatInvalidFormat": "F521",
    "StringDotFormatExtraNamedArguments": "F522",
    "StringDotFormatExtraPositionalArguments": "F523",
    "StringDotFormatMissingArgument": "F524",
    "StringDotFormatMixingAutomatic": "F525",
    "FStringMissingPlaceholders": "F541",
    "MultiValueRepeatedKeyLiteral": "F601",
    "MultiValueRepeatedKeyVariable": "F602",
    "TooManyExpressionsInStarredAssignment": "F621",
    "TwoStarredExpressions": "F622",
    "AssertTuple": "F631",
    "IsLiteral": "F632",
    "InvalidPrintSyntax": "F633",
    "IfTuple": "F634",
    "BreakOutsideLoop": "F701",
    "ContinueOutsideLoop": "F702",
    "ContinueInFinally": "F703",
    "YieldOutsideFunction": "F704",
    "ReturnOutsideFunction": "F706",
    "DefaultExceptNotLast": "F707",
    "DoctestSyntaxError": "F721",
    "ForwardAnnotationSyntaxError": "F722",
    "CommentAnnotationSyntaxError": "F723",
    "RedefinedWhileUnused": "F811",
    "UndefinedName": "F821",
    "UndefinedExport": "F822",
    "UndefinedLocal": "F823",
    "DuplicateArgument": "F831",
    "UnusedVariable": "F841",
    "RaiseNotImplemented": "F901",
}

class FlakesChecker(pyflakes.checker.Checker):
    """Subclass the Pyflakes checker to conform with the flake8 API."""

with_doctest = False
    include_in_doctest: List[str] = []
    exclude_from_doctest: List[str] = []

def __init__(
        self,
        tree: ast.AST,
        file_tokens: List[tokenize.TokenInfo],
        filename: str,
    ) -> None:
        """Initialize the PyFlakes plugin with an AST tree and filename."""
        filename = utils.normalize_path(filename)
        with_doctest = self.with_doctest
        included_by = [
            include
            for include in self.include_in_doctest
            if include != "" and filename.startswith(include)
        ]
        if included_by:
            with_doctest = True

for exclude in self.exclude_from_doctest:
            if exclude != "" and filename.startswith(exclude):
                with_doctest = False
                overlaped_by = [
                    include
                    for include in included_by
                    if include.startswith(exclude)
                ]

if overlaped_by:
                    with_doctest = True

super().__init__(
            tree,
            filename=filename,
            withDoctest=with_doctest,
            file_tokens=file_tokens,
        )

@classmethod
    def add_options(cls, parser: OptionManager) -> None:
        """Register options for PyFlakes on the Flake8 OptionManager."""
        parser.add_option(
            "--builtins",
            parse_from_config=True,
            comma_separated_list=True,
            help="define more built-ins, comma separated",
        )
        parser.add_option(
            "--doctests",
            default=False,
            action="store_true",
            parse_from_config=True,
            help="also check syntax of the doctests",
        )
        parser.add_option(
            "--include-in-doctest",
            default="",
            dest="include_in_doctest",
            parse_from_config=True,
            comma_separated_list=True,
            normalize_paths=True,
            help="Run doctests only on these files",
        )
        parser.add_option(
            "--exclude-from-doctest",
            default="",
            dest="exclude_from_doctest",
            parse_from_config=True,
            comma_separated_list=True,
            normalize_paths=True,
            help="Skip these files when running doctests",
        )

@classmethod
    def parse_options(cls, options: argparse.Namespace) -> None:
        """Parse option values from Flake8's OptionManager."""
        if options.builtins:
            cls.builtIns = cls.builtIns.union(options.builtins)
        cls.with_doctest = options.doctests

included_files = []
        for included_file in options.include_in_doctest:
            if included_file == "":
                continue
            if not included_file.startswith((os.sep, "./", "~/")):
                included_files.append(f"./{included_file}")
            else:
                included_files.append(included_file)
        cls.include_in_doctest = utils.normalize_paths(included_files)

excluded_files = []
        for excluded_file in options.exclude_from_doctest:
            if excluded_file == "":
                continue
            if not excluded_file.startswith((os.sep, "./", "~/")):
                excluded_files.append(f"./{excluded_file}")
            else:
                excluded_files.append(excluded_file)
        cls.exclude_from_doctest = utils.normalize_paths(excluded_files)

inc_exc = set(cls.include_in_doctest).intersection(
            cls.exclude_from_doctest
        )
        if inc_exc:
            raise ValueError(
                f"{inc_exc!r} was specified in both the "
                f"include-in-doctest and exclude-from-doctest "
                f"options. You are not allowed to specify it in "
                f"both for doctesting."
            )

def run(self) -> Generator[Tuple[int, int, str, Type[Any]], None, None]:
        """Run the plugin."""
        for message in self.messages:
            col = getattr(message, "col", 0)
            yield (
                message.lineno,
                col,
                "{} {}".format(
                    FLAKE8_PYFLAKES_CODES.get(type(message).__name__, "F999"),
                    message.message % message.message_args,
                ),
                message.__class__,
            )

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