Release v0.3.0 - SQLite Threading Fix, Professional CLI, Genome Build Corrections

What's Changed

Critical Fixes

• SQLite Threading Fix: Resolved parallel processing failures by restructuring resolver to avoid connection sharing across threads

CLI Enhancements

• Professional Output Design: Replaced emoji-based format with structured box-drawing tables
• Color-Coded Results: Added ANSI colors (green for success, yellow for ambiguous, red for failed)
• Dynamic Width: Implemented content-based box sizing to prevent overflow issues
• Improved User Experience: Clean, professional CLI output suitable for production environments

Performance & Reliability

• Thread-Safe Operations: Parallel processing now works reliably without SQLite threading errors

Installation

pip install gene-id-resolver==0.3.0

Quick Start

# One-time setup
gene-resolver init

# Convert genes (with professional colored output)
gene-resolver convert TP53 BRCA1 EGFR --to-type ensembl

Example Output

┌─ Conversion Results ───────────────────────────────────┐
│ Genome: GRCh38     │ Strategy: primary  │
├───────────────────────────────────────────────────────────┤
│ ✓ Successful: 3 │ ⚠ Ambiguous: 0 │ ✗ Failed: 0 │
└───────────────────────────────────────────────────────────┘

[SUCCESSFUL CONVERSIONS]
   TP53 → ENSG00000141510
   BRCA1 → ENSG00000012048
   EGFR → ENSG00000146648

Links

• PyPI Package: https://pypi.org/project/gene-id-resolver/0.3.0/
• Full Changelog: v0.2.0...v0.3.0
• Documentation: https://github.com/tahagill/gene-id-resolver#readme

Citation

If you use this tool in your research, please cite:

@software{ahmad_2025_gene_id_resolver,
  author       = {Ahmad, Taha},
  title        = {gene-id-resolver: Production-grade gene ID conversion with deprecated gene support},
  year         = 2025,
  publisher    = {Zenodo},
  version      = {0.3.0},
  doi          = {10.5281/zenodo.17547077},
  url          = {https://github.com/tahagill/gene-id-resolver}
}