Migration to Hugging Face datasets #35
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* new file structure * skeleton rt dataset * [Testing] abstraction + intensity + alphabet updates * pprint args dict * modified seq utils not to add empty n-c terms * parallel and batch processing - faster pipeline * removed datasets_sql and pyteomics parser from base class * Added a working version of time delta and updated prosit model * minor fixes * minor fix + added tf prob dep * refactoring, improvements, feature extraction * Added different PTM features * Added dict in pkl file * refactoring * updated .gitignore * refactored ptm handling workflow with naive and unmod schemes * updated feature tables from wassim * refactored tests to new hf datasets style * package restructure for clean install + minor fixes * updates to package dir in gitignore, makefile, docs conf * clean-up of unnecessary files and code * unified parsed column names + cleaner user messages * minor user message edits * docs system improvements * refactored vocab to alphabet and minor fixed * updates to runscripts and notebooks + minor fixes * example intensity data in parquet to lists as strings in csv * [WIP]: adding tests * model tests and run files for features and ptms * added docstrings --------- Co-authored-by: WassimG <[email protected]>
* Added reduced smiles feature extractor and pkl file * splitting logic refactored + comments for lookup features --------- Co-authored-by: victorgiurcoiu <[email protected]>
* improvements to prosit intensity + dataset caching + others * removed extra notebook * cleaned up print statements * dev install command fix * added flag for tf dataset cache + notebook minor updates * remove wandb from report init + notebook updates * uncommented notebook pip install
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