CLAUDE.md

Clodius

A Python library and CLI tool for aggregating large genomic datasets into tile-based formats for display at multiple resolutions (used by HiGlass).

Project Structure

• clodius/ — main package
  • cli/ — Click-based CLI commands (aggregate.py, convert.py)
  • tiles/ — tile generation modules per file type (bigwig, cooler, bed, etc.)
  • models/ — Pydantic data models
• test/ — pytest tests mirroring the source layout
• test/sample_data/ — small sample files used by tests

Development Setup

pip install -e ".[dev]"

Common Commands

Run all tests:

pytest

Run a specific test:

pytest test/cli_test.py::test_clodius_aggregate_bedgraph

Lint:

flake8 clodius

Key Conventions

• Linting: flake8 (configured via pyproject.toml)
• Tests: pytest with coverage (pytest --cov=clodius)
• Build: hatchling
• Main branch: develop (use this as the base for PRs)
• Python packaging: pyproject.toml (no setup.py)