One way to fix this would be to not freeze the logging section in the parser:

In luigi/luigi/configuration/toml_parser.py instead of:

        # freeze dict params
        for section, content in self.data.items():
            for key, value in content.items():
                if isinstance(value, dict):
                    self.data[section][key] = recursively_freeze(value)

It would be possible to do:

        # freeze dict params
        for section, content in self.data.items():
            if key.lower() == 'logging':
                 continue
            for key, value in content.items():
                if isinstance(value, dict):
                    self.data[section][key] = recursively_freeze(value)

Another solution, that is probably better, is to let the config parser make a mutable copy. That would however require us to write a more complicated "recursively_unfreeze" function.

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Also experiencing this issue when attempting to configure logging via toml.

I tried editing my toml_parser.py as suggested by @hirolau and can confirm the solution works (I assume you meant section.lower())

# freeze dict params
        for section, content in self.data.items():
            if section.lower() == 'logging':
                 continue
            for key, value in content.items():
                if isinstance(value, dict):
                    self.data[section][key] = recursively_freeze(value)

I'm confused about why this is WONTFIX. I have a fork with the change (and one other change that was blocking toml config processing) that I will send, will they be accepted? I don't see a way to work around this in the toml file (maybe I'm missing something here?)

EDIT: Is the (non-code-change) "solution" to not include the logging section in the main TOML file? If so, the example toml configuration file in the repository should probably be updated- I had issues using that file verbatim