smckit 0.0.1b2

Unified framework for Sequentially Markovian Coalescent methods

smckit

Unified framework for Sequentially Markovian Coalescent methods.

PSMC, MSMC/MSMC2, SMC++, diCal2, ASMC, and related workflows in one preservation-first toolkit.

smckit keeps upstream tools runnable from the same repository while building native implementations that do not lose contact with upstream truth.

Why smckit

• Upstream-first: original tools in vendor/ remain the oracle implementation.
• Provenance-aware: results can record which tool ran and how it was bootstrapped.
• One API surface: shared data structures and workflows across multiple SMC methods.
• Native path: performance-oriented in-repo implementations can grow without pretending parity before it is validated.

Installation

pip install smckit

Install contract:

• pip install smckit guarantees the packaged example data and the documented native quickstarts.
• Full implementation="upstream" preservation workflows are a source-checkout feature unless the method page explicitly says otherwise.
• When an upstream runtime is missing, smckit reports platform-specific install commands and, when needed, tells you to switch to a source checkout.

Repo environment:

uv sync --extra dev --extra docs
pixi run test-fast

Use uv for the Python package environment and pixi for the repo-level cross-language task environment.

Model extras:

pip install "smckit[all-models]"
pip install "smckit[asmc]"
pip install "smckit[psmc,msmc2,msmc_im,smcpp,esmc2,dical2]"

These extras describe intent. Today only asmc adds an extra Python runtime; the other upstream-backed methods still need platform runtimes such as Java, R, or a D/C toolchain. When an upstream runtime is missing, smckit now returns platform-specific install commands for macOS, Linux, or Windows.

Development extras:

pip install "smckit[jax]"
pip install "smckit[dev]"
pip install "smckit[docs]"

Philosophy

smckit is upstream-first by design.

• vendor/ holds the original source or release artifacts that act as the oracle.
• implementation="upstream" means "run the original tool" when that bridge is wired and ready.
• implementation="native" means "run the in-repo implementation".
• implementation="auto" should prefer upstream fidelity whenever the upstream path is ready.

The repository exposes smckit.upstream.status() and smckit.upstream.bootstrap() so upstream readiness is inspectable rather than implicit.

Status

smckit is early-stage software. The priority is preserving access to upstream methods, making readiness explicit, and validating native implementations against upstream behavior before claiming equivalence.

Recent parity progress:

• eSMC2 native/upstream interchangeability is now tracked across the public .psmcfa and multihetsep input families, including missing-site, multi-record, multi-pair, multi-file, and skip_ambiguous=True cases.
• The docs landing page and gallery summarize which methods have fixture-only validation and which now have broader public-surface parity gates.

Repository Guide

• Method docs: docs/agents/algorithms.md
• Usage notes: docs/agents/using-smckit.md
• Developer architecture: docs/developer/architecture.md

License

MIT. See LICENSE.