Vivi-tran/PepKit: Prepare release 0.0.5

# Changelog This page summarizes user-visible changes between releases. ## Version 0.0.5 ### Highlights - **Chem** - FASTA/sequence ⇄ SMILES conversion - parsing, validation, standardization - descriptor generation for ML workflows - **Query** - fetch PDB entries from RCSB - online constraint-based filtering (e.g. quality, release date, residue/ligand checks) - **Modelling** - AlphaFold(-Multimer) post-processing pipeline - rescoring with `pDockQ` and `pDockQ2` ### Documentation - Added full documentation on Read the Docs: https://pepkit.readthedocs.io/en/latest/ ### Packaging & dependencies - Split optional dependencies to keep the core package lightweight. - Install core: ```bash pip install pepkit ``` - Install modelling + PDB-heavy extras: ```bash pip install pepkit[modelling] ``` - Install everything: ```bash pip install pepkit[all] ``` ### CLI - Exposed a top-level CLI for common workflows. - Query and post-processing can now be run directly from the command line. - See the docs for examples and usage details.