jax_ldsc

Project Intent (Reframed 2026-02-11)

This project started as a clean-room port of LDSC workflows from reference/ldsc into a JAX/Equinox/Lineax + Polars implementation.

The primary objective is now broader: use this repository as a realistic benchmark to harden Codex development skills, especially:

• JAX/Equinox numerics implementation and debugging quality.
• Ed3d/Codex Port context-file and directive-writing quality.

This JAX-based LDSC port remains critical because it provides a non-trivial, testable workload for that hardening effort. This is NOT to be taken as a reference implementation or substitution for either the original LDSC or its Python3 implementation.

Status Against The Original Port Plan

docs/ldsc_port_plan.md remains the baseline plan and now includes a dated reassessment.

Current status:

• CLI workflows implemented: munge, h2, rg, h2-cts, l2.
• Regression, IO, and CLI paths are covered by tests in tests/.
• Verification snapshot (2026-02-11): pytest -q -> 66 passed (1 non-blocking deprecation warning from Polars).

Development Setup

pip install -e ".[test]"
pytest -q
python -m jax_ldsc.cli --help

Repository Layout

• src/jax_ldsc/ - runtime package (cli, io, munge, regression, ldscore, results)
• tests/ - behavior and parity-oriented test coverage
• docs/ - planning and licensing context
• reference/ldsc/ - upstream GPL reference for behavior comparison only

License Boundary

jax_ldsc project code is MIT-licensed, while reference/ldsc remains external GPLv3 reference material.

Runtime code in src/jax_ldsc must not import from or copy source text from reference/ldsc.

See docs/licensing.md for policy details.

License

MIT