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Fixed some bugs, see description#3

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Flo3141 wants to merge 25 commits intodieterich-lab:mainfrom
Flo3141:main
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Fixed some bugs, see description#3
Flo3141 wants to merge 25 commits intodieterich-lab:mainfrom
Flo3141:main

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@Flo3141
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@Flo3141 Flo3141 commented Dec 13, 2025

Fixed bug in biolm.py:

  • The call to the test() function in the main() function did not have a model parameter, although it is required. So I changed the test function and made it so, that it is None by default, because then a model is created in the function.
  • Added the "predict" and "interpret" scenarios in the _validate_split_exclusivity() function so that the splitpos spliration must be defined error does not occur.
  • Fixed a bug with the regex when reading a line from the sequence TXT file. Now only the FIRST occurence of the regex gets stripped an not multiple, which can lead to the sequence column to be deleted.
  • I changed the tokenizer_config_file path when doing the predict function, because right now when using the biolm with the saluki repository, the variable pretraining_required is always set to False. So the config file of the tokenizer is never loaded during the predict option. Please take a look at this, because I do not know if my changes break anything else.

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phiwi commented Dec 28, 2025

Thank you Flo! Can you somehow merge your PR to a single commit (or up to 5). It's difficult to sinpect the changes as some of the commits offset each other.

@phiwi phiwi assigned phiwi and Flo3141 and unassigned phiwi Dec 28, 2025
@phiwi phiwi added the bug Something isn't working label Dec 28, 2025
@Flo3141 Flo3141 closed this by deleting the head repository Mar 13, 2026
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