Metadata-Version: 2.4
Name: smckit
Version: 0.0.1b2
Summary: Unified framework for Sequentially Markovian Coalescent methods
Project-URL: Homepage, https://github.com/kevinkorfmann/smckit
Project-URL: Repository, https://github.com/kevinkorfmann/smckit
Project-URL: Issues, https://github.com/kevinkorfmann/smckit/issues
Author: Kevin Korfmann
License: MIT License
        
        Copyright (c) 2026 Kevin Korfmann
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
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License-File: LICENSE
Keywords: MSMC,PSMC,SMC,coalescent,demographic-inference,population-genetics
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.10
Requires-Dist: matplotlib>=3.7
Requires-Dist: msprime>=1.3
Requires-Dist: numba>=0.59
Requires-Dist: numpy>=1.24
Requires-Dist: scipy>=1.10
Provides-Extra: all-models
Requires-Dist: asmc-asmc>=1.4.0; (platform_system != 'Windows') and extra == 'all-models'
Provides-Extra: asmc
Requires-Dist: asmc-asmc>=1.4.0; (platform_system != 'Windows') and extra == 'asmc'
Provides-Extra: dev
Requires-Dist: build>=1.2; extra == 'dev'
Requires-Dist: hatchling>=1.27; extra == 'dev'
Requires-Dist: pytest>=7.0; extra == 'dev'
Requires-Dist: ruff>=0.4; extra == 'dev'
Provides-Extra: dical2
Provides-Extra: docs
Requires-Dist: myst-parser; extra == 'docs'
Requires-Dist: sphinx; extra == 'docs'
Requires-Dist: sphinx-rtd-theme; extra == 'docs'
Provides-Extra: esmc2
Provides-Extra: jax
Requires-Dist: jax>=0.4.20; extra == 'jax'
Requires-Dist: jaxlib>=0.4.20; extra == 'jax'
Requires-Dist: optax>=0.2.0; extra == 'jax'
Provides-Extra: msmc-im
Provides-Extra: msmc2
Provides-Extra: psmc
Provides-Extra: smcpp
Description-Content-Type: text/markdown

# smckit

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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

```bash
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:

```bash
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:

```bash
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:

```bash
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](LICENSE).
