Validation and refactoring of differential expression analysis #388
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This reverts commit 804f2ac.
… and check the correct one is raised.
mschwoer
reviewed
Dec 20, 2024
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| for parameter in kwargs: | ||
| if parameter not in self._allowed_parameters(): | ||
| raise TypeError( | ||
| f"Parameter {parameter} should not be provided for this analysis. Accepted keyword arguments to perform are {', '.join(self._allowed_parameters())}." | ||
| ) | ||
|
|
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| def _allowed_parameters(self) -> List[str]: | ||
| """Method returning a list of allowed parameters for the analysis to avoid calling tests with additional parameters.""" | ||
| perform_signature = inspect.signature(self._perform) | ||
| parameters = list(perform_signature.parameters.keys()) | ||
| return [parameter for parameter in parameters if parameter != "kwargs"] |
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can be removed, python does that for you :-)
(from for parameter in kwargs: ... to return return [para..
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Not if I pass kwargs to _perform though, right? Which I need to do to match the signature of the abstract method? The idea was that by adding this here I enforce kwargs to be empty without relying on every implementation of _perform to contain that check.
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| **valid_parameter_input_two_groups, | ||
| **{ | ||
| DeaParameters.TEST_TYPE: DeaTestTypes.INDEPENDENT, | ||
| DeaParameters.FDR_METHOD: "fdr_bh", | ||
| DeaParameters.ISLOG2TRANSFORMED: False, | ||
| }, |
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could we pass those parameters explicitly?
mschwoer
approved these changes
Dec 20, 2024
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This is a base branch for a major effort to refactor the differential expression analysis.
Currently this covers a skeleton for a new 3-tier class system for all differential expression analysis:
If you review at this stage, please check in particular if
Checklist to do before branching off:
Branches that can then be based on this: