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GeorgWa
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Mar 9, 2026
| with open(path, "w") as f: | ||
| json.dump(self.data, f) | ||
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| def __getitem__(self, key: str): |
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Is this recursive?
or is there any assumption about the data structure only having two levels?
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good catch, (how) should we handle this for now?
leave this half-baked solution (and add a comment)?
or revert this part of the PR and do it properly later?
alphadia/workflow/config.py
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| ConfigKeys.QUANT_DIRECTORY, | ||
| ConfigKeys.RAW_PATHS, | ||
| ConfigKeys.FASTA_PATHS, | ||
| ("library_prediction", "peptdeep_model_path"), |
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Should we also move them to constants?
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There's two options for nesting these constants, cf. the diff here:
the downside of the first (= left side of diff):
- unintuitive access
config[ConfigKeys.GENERAL][ConfigKeys.General.SAVE_FIGURES], less cohesion in the definitions
downside of the second:
- IDE does not offer autocompletion on
ConfigKeys.GENERAL. ...
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psm.parquet/fragment.parquetand reported failed search although all was fine