option_manager.add_option ignores action when reading from config

how did you install flake8?

pip install flake8

also when cloned from github master

unmodified output of flake8 --bug-report

{
  "platform": {
    "python_implementation": "CPython",
    "python_version": "3.10.8",
    "system": "Linux"
  },
  "plugins": [
    {
      "plugin": "mccabe",
      "version": "0.7.0"
    },
    {
      "plugin": "pycodestyle",
      "version": "2.10.0"
    },
    {
      "plugin": "pyflakes",
      "version": "3.0.1"
    }
  ],
  "version": "6.0.0"
}

describe the problem

what I expected to happen

my argparse.Action to be called regardless of if the parameter is specified on the command line or in the config

sample code

I implemented a test that reproduces the error. The first one passes, the second one doesn't.

from collections.abc import Sequence
from flake8.options import config

# always sets the value to bar regardless of what `values` is
class MyAction(argparse.Action):
    def __call__(
        self,
        parser: argparse.ArgumentParser,
        namespace: argparse.Namespace,
        values: Sequence[str] | None,
        option_string: str | None = None,
    ) -> None:
        setattr(namespace, self.dest, "bar")


def test_action_cmdline(optmanager):
    optmanager.add_option(
        "--my-option",
        parse_from_config=True,
        required=False,
        action=MyAction,
    )
    options = optmanager.parse_args(["--my-option", "foo"])
    assert options.my_option == 'bar'

def test_action_config(tmpdir):
    tmpdir.join("setup.cfg").write("[flake8]\nmy-option=foo\n")

    with tmpdir.as_cwd():
        cfg, cfg_dir = config.load_config(None, [], isolated=False)

    assert cfg.get("flake8", "my-option") == "bar"

commands ran

$ pytest -k test_action_ 
===================================== test session starts =====================================
platform linux -- Python 3.10.8, pytest-7.2.0, pluggy-1.0.0
rootdir: /home/h/Git/flake8, configfile: pytest.ini
collected 465 items / 463 deselected / 2 selected                                             

tests/unit/test_option_manager.py .F                                                    [100%]

========================================== FAILURES ===========================================
_____________________________________ test_action_config ______________________________________

tmpdir = local('/tmp/pytest-of-h/pytest-62/test_action_config0')

    def test_action_config(tmpdir):
        tmpdir.join("setup.cfg").write("[flake8]\nmy-option=foo\n")
    
        with tmpdir.as_cwd():
            cfg, cfg_dir = config.load_config(None, [], isolated=False)
    
>       assert cfg.get("flake8", "my-option") == "bar"
E       AssertionError: assert 'foo' == 'bar'
E         - bar
E         + foo

tests/unit/test_option_manager.py:243: AssertionError
========================= 1 failed, 1 passed, 463 deselected in 0.26s =========================

The value is foo, which it would be if there's no action specified, but it completely sidesteps calling the action completely.

Start with tests/unit/test_option_manager.py, especially test_action_cmdline and test_action_config, and trace how option_manager.add_option handles parse_from_config through config.load_config. Done means the configured value invokes the argparse.Action just like the command-line value and the regression test passes.