Config values from `tool.flakeheaven.base` are not being overridden when configuring specific plugins

Issue

The changes introduced in #115 break overriding of config values when using the tool.flakeheaven.base option.

For example, if a project’s pyproject.toml previously disabled pylint from a base config like so:

[tool.flakeheaven]
base = "https://raw.githubusercontent.com/flakeheaven/flakeheaven/master/pyproject.toml"
...
[tool.flakeheaven.plugins]
...
pylint = ["-*"]

in 2.0.0 that override is ignored and the value from the base pyproject.toml is used, as below:

https://github.com/flakeheaven/flakeheaven/blob/24f3ba08b9fc4d798d61c3a10b6a07a6a70e4817/pyproject.toml#L135

Fix

Instead of manually deep updating specific parts of the config dict, it might be better to add a deep update function and use that to build the dict. This resolves the issue and has the added benefit of not needing to be updated if more entries which require deep updating are added in the future.

def _deep_update(old_dict, new_dict) -> Dict[str, Any]:
    for key, value in new_dict.items():
        if isinstance(value, collections.abc.Mapping):
            old_dict[key] = _deep_update(old_dict.get(key, {}), value)
        else:
            old_dict[key] = value
    return old_dict


def _merge_configs(*configs) -> Dict[str, Any]:
    config: Dict[str, Any] = defaultdict(dict)
    for subconfig in configs:
        _deep_update(config, subconfig)

    return dict(config)

[rwwiv]

@pwoolvett I’ve corrected the issue, this is specifically when using tool.flakeheaven.base

You can reproduce this by slightly modifying the script you provided:

import difflib
import sys
import tempfile
from pathlib import Path

import toml
from flakeheaven.commands._lint import NAME, VERSION, FlakeHeavenApplication

TOML = """\
[tool.flakeheaven]
base = "https://raw.githubusercontent.com/flakeheaven/flakeheaven/master/pyproject.toml"
[tool.flakeheaven.plugins]
pylint = ["-*"]
"""


def check(argv):
    app = FlakeHeavenApplication(program=NAME, version=VERSION)
    app.initialize(argv)
    config = vars(app.options)["plugins"]
    print(config)


with tempfile.NamedTemporaryFile(mode="w", suffix=".toml") as pyproject:
    pyproject.write(TOML)
    pyproject.flush()
    check(["--config", pyproject.name])

check([])

which produces this output: (EDITED for output when run outside of project context)

{'pylint': ['+F*', '+E*', '-E0611', '-E1101', '-E0401', '-E1102', '-E1123'], 'pycodestyle': ['+*'], 'pyflakes': ['+*'], 'flake8-commas': ['+*'], 'flake8-quotes': ['+*']}
{'pyflakes': ['+*'], 'pycodestyle': ['+*']}

[gone]

I think I"m able to replicate this - pylint runs always regardless of config on 2 but respects configuration on 1.0.2