Release 3.0.0

3.0.0 (2025-01-31)

Feat

• predict: predict call from CLI now always outputs something
• 2.enumeration_results: notebook to perform the molecule enumeration
• 1.enumeration_create_alphabets: notebook to create alphabets
• notebooks: add notebook
• configure: add interface for simple configuration
• predict: add interface for predicting (without evaluation)
• model: fully batch-vectorized version for beam search
• predict: test for equality of canonic SMILES
• predict: decode beam in parallel

Fix

• predict: convert python objects to strings
• predict: dataclass attribute poorly tested
• predict: remove pickle writing
• evaluate: add output file handling to write results
• evaluate: correctly deal with the max number of rows
• evaluate: include chirality in ECFP
• predict: stop crashing when beam size > vocab size
• predict: allow selection of the accelerator device
• predict: column indexes

Refactor

• predict: update default arg values
• predict: update result refinements
• configure: add default output path to None
• config: remove unused method
• imports: refine
• add empty data folder
• notebooks: merge cells
• notebooks: rename nb
• notebooks: rename notebook for fig 2
• utils: move utilities functions
• evaluate: remove file
• predict: make col names more explicit
• evaluate: sweep code
• utils: sweep code
• predict: refine outputs
• predict: remove unused args
• utils: additional shared functions
• predict: delagate results refining to subsequent code
• predict: allow calls from other script
• predict: better print
• predict: improve imports
• predict: print result to stdout on request
• predict: print default values