fix: updating of non-dict config values gives error

[padix-key]

Description

This PR addresses an issue in config merging: If a config value that is not a dict (e.g. it is None) is replaced by a dict an exception is raised, as update_config() tries to update the keys of the config, which is not possible (e.g. None has no keys). This PR fixes this problem by just overwriting the original value in this case (e.g. None is replaced by the new dictionary).

QC

• The PR contains a test case for the changes or the changes are already covered by an existing test case.
• The documentation (docs/) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).

[padix-key]

Now the updated tests are included

[johanneskoester]

Seems like a testcase fails because the result is not as expected?

[padix-key]

Hi, The problem was the removal of the inner function: When replacing None with a new dict this is no in-place modification anymore. Hence, without a return value the config does not get updated in this case. I reenabled the inner function with return value to solve this issue and edited the PR description accordingly.

[padix-key]

Conceptually, the function was correct, only formatting changes of the module and the test output file was required in the failed jobs. My changes should hopefully fix this now.

[sonarcloud]

Kudos, SonarCloud Quality Gate passed!   

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