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Contributing

Thanks for your interest in contributing to sequence-foundation-model-tools!

Development Setup

git clone https://github.com/jsdearbo/sequence_to_function_model_tools.git
cd sequence_to_function_model_tools
pip install -e ".[dev]"

Running Tests

pytest tests/ -v

Tests are designed to run without GPU, genome files, or optional dependencies (gReLU, pysam, pyranges). Core module tests use only numpy, pandas, and torch.

Project Structure

seq_tools/       Sequence encoding, intervals, FASTA, labels, variants
training/        Losses, heads, dataset, LoRA fine-tuning
interpret/       Attribution, ISM, TF-MoDISco (requires gReLU)
tests/           Unit tests (pytest)
examples/        Jupyter notebooks demonstrating usage

Guidelines

  • Tests: Add tests for new functionality in tests/. Follow existing naming (test_<module>.py).
  • Dependencies: Keep core modules free of optional dependencies. Use try/except import guards for gReLU, pysam, and pyranges.
  • Style: Follow existing code style. Type hints for public function signatures.
  • Notebooks: Example notebooks in examples/ should work with synthetic data (no external files).

Adding a New Module

  1. Add the source file to the appropriate package (seq_tools/, training/, or interpret/)
  2. Add exports to the package __init__.py
  3. Write tests in tests/test_<module>.py
  4. Update README.md if the module adds a new capability

Reporting Issues

Open a GitHub issue with:

  • What you expected vs what happened
  • Minimal code to reproduce
  • Python/PyTorch version info