v3 #84
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v3 #84
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- Change package structure - Implement psm_utils - Re-implement MS²PIP feature generator
- Write PSM file if no rescoring engines configured - Clean up CLI help - Clean up logging - Remove broken 'keep lower ranks' code in mokapot integration - Remove unused code
…ema docs, add tutorial notebook...) - Use tomllib/tomli instead of tomlkit - Improve robustness of report generation - GUI tweaks (add fasta config, relocate psm file type dropdown, add more citations, tweak colors for light mode - Fix GUI setting for DeepLC transfer learning (was always on due to wrong argument name) - Disable DeepLC retrain by default - ...
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This PR merges all ongoing work for the fully reworked v3 of MS²Rescore into the main branch.