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Changelog

All notable changes to MOLRAPTOR will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[0.2.0] - 2026-07-16

Added

  • Added a public, in-memory API for generating binary Morgan fingerprints from ordered SMILES.
  • Added MorganFingerprintProfile, FingerprintEncodingResult, FingerprintInputStatus, and encode_fingerprints to the public API.
  • Added explicit profile serialization, deterministic input and profile hashes, RDKit and MOLRAPTOR version metadata, and traceable valid/invalid input status.
  • Added focused tests for in-memory fingerprint encoding and the file-based fingerprint step.

Changed

  • Refactored the file-based fingerprint pipeline to reuse the public Morgan encoder instead of maintaining a separate implementation.
  • Preserved CSV and NPY outputs for valid datasets.
  • Made the file-based pipeline reject invalid SMILES before writing fingerprint or label artifacts.
  • Documented the distinction between the in-memory library API and the file-based pipeline.
  • Updated CI public-API checks for the new exported symbols.

[0.1.1] - 2026-05-28

Added

  • CITATION.cff for software citation metadata.
  • CHANGELOG.md to track project history.

Changed

  • License changed from MIT to GNU LGPL v3 or later (LGPL-3.0-or-later).
  • pyproject.toml: version updated to 0.1.0 and Python requirement lowered to >=3.11.

[0.1.0] - 2025-06-12

Added

  • Initial pre-release of MOLRAPTOR (formerly tagged as v1.0.0).
  • Modular pipeline architecture: fetch → curate → fingerprint → validate.
  • PubChem REST API integration via PubChemService.
  • Morgan fingerprint generation using RDKit (GetMorganGenerator).
  • YAML-based configuration schema via Pydantic v2 (MolraptorConfig).
  • CLI entry point via Typer (molraptor run, molraptor version).
  • Abstract base class BaseStep for pipeline step contract.
  • Utility modules: chunks, log_print, validators, reporter, result_manager.
  • Initial configs/default.yaml with PPARγ dataset configuration.
  • MIT License (superseded in v0.1.1).