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.

0.4.1 - 2026-07-26¶

Added the public ResolvedFingerprintProfile contract and resolve_fingerprint_profile() API for resolving effective fingerprint profiles, widths, and canonical profile hashes without encoding SMILES.
Exposed FingerprintType and FINGERPRINT_TYPES through the top-level package API.

Centralized fingerprint-profile validation and canonical hash resolution so profile inspection and fingerprint encoding use the same scientific metadata source.
Made resolved profiles read-only while preserving FingerprintEncodingResult.profile as a standard dictionary for backward compatibility.
Expanded regression coverage to preserve all seven v0.4.0 default-profile hashes and fingerprint outputs.

Added unified support for Morgan, Feature Morgan, Atom Pair, RDKit topological, Topological Torsion, Layered, and MACCS fingerprints.
Added fingerprint selection through the CLI --fingerprint option and the Python fingerprint_type configuration.
Added fixed, serializable effective profiles for non-Morgan fingerprints while preserving configurable Morgan settings.
Added focused coverage for fingerprint dispatch, profiles, CLI selection, output dimensions, configuration validation, and removed module routes.

Replaced the Morgan-only scientific implementation with the unified molraptor/fingerprints.py core.
Kept Morgan as the default fingerprint and preserved compatibility with the existing positional MorganFingerprintProfile contract.
Renamed the CSV/TXT and artifact-writing implementation from fingerprint.py to workflow.py.
Standardized one fingerprint type per execution with binary numpy.uint8 matrices and natural fingerprint widths.
Made Morgan-only CLI and configuration settings fail explicitly when supplied for another fingerprint type.
Updated the project identity to MOLRAPTOR: Molecular Fingerprint Rapid Generator.
Updated the README, API reference, usage guide, documentation homepage, citation metadata, and package description for multi-fingerprint support.

Added a SMILES-only file workflow for CSV and UTF-8 TXT inputs.
Added direct CLI configuration through --input, --smiles-column, --output-dir, --radius, --fp-size, and --include-chirality.
Added the stable output artifact set: fingerprints.npy, fingerprints.csv, input_statuses.csv, and encoding_metadata.json.
Added per-input validation status with explicit mapping between original input_index values and valid fingerprint matrix rows.
Added workflow metadata for source format, source filename, effective Morgan profile, matrix shape and dtype, runtime versions, and deterministic ordered input and profile hashes.
Added CLI coverage and expanded tests for CSV/TXT parsing, output publication, invalid-input isolation, metadata, and the public API.

Reoriented MOLRAPTOR as a SMILES-first scientific library and command-line tool for reproducible Morgan fingerprint generation.
Unified the command-line interface and file workflow around the public in-memory encode_fingerprints scientific core.
Preserved exact input order and duplicates while allowing invalid individual SMILES to be excluded without discarding valid fingerprint rows.
Standardized binary fingerprint matrices as numpy.uint8 with shape (N_valid, fp_size).
Updated the default Morgan profile to radius 2, 2048 bits, and chirality disabled unless explicitly requested.
Updated the NumPy requirement to numpy>=2.4.
Rewrote the README and MkDocs documentation for the v0.3.0 architecture, CLI, public API, input contract, outputs, failure handling, and scientific boundary.
Updated public API docstrings and release metadata for v0.3.0.

Removed PubChem retrieval and CID-driven workflows.
Removed YAML configuration and the legacy fetch, curate, integrity, result-management, and multi-stage pipeline components.
Removed activity-label handling and legacy outputs such as labels.npy, morgan_fp.csv, morgan_db_*.npy, and summary.txt.
Removed rdkit_canonical_smiles from the public and internal status contracts.
Removed deleted legacy modules including fetch.py, pubchem.py, curate.py, fp_integrity.py, and result_manager.py.

Replaced the obsolete CLI pipeline import path with the current SMILES-only workflow, resolving the startup failure reported in issue #2.

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.

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.

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.

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).