Metadata-Version: 2.5
Name: altar
Version: 0.1.0
Summary: Public contracts, orchestration primitives, and conformance suites for genomic variant analysis
Project-URL: Documentation, https://kundajelab.github.io/altar/
Project-URL: Issues, https://github.com/kundajelab/altar/issues
Project-URL: Repository, https://github.com/kundajelab/altar
Author: Riya Sinha
License-Expression: MIT
License-File: LICENSE
Keywords: bioinformatics,genomics,machine-learning,variant-annotation,variant-effect-prediction
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Typing :: Typed
Requires-Python: >=3.12
Requires-Dist: altar-identity==0.1.0
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Requires-Dist: numpy>=1.26
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Requires-Dist: pydantic>=2
Requires-Dist: pyfaidx>=0.6.1
Requires-Dist: pysam>=0.22.1
Requires-Dist: pytest>=8
Provides-Extra: agent
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Provides-Extra: bigquery
Requires-Dist: google-cloud-bigquery[pandas]>=3; extra == 'bigquery'
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Description-Content-Type: text/markdown

# Altar

Altar is an extensible Python framework for analyses that combine genomic variants, executable model scores,
and precomputed biological evidence.

The package provides:

- canonical VCF/TSV variant ingestion and validation;
- model-binding interfaces for container and hosted-API scoring;
- portable execution-task and storage interfaces;
- score, annotation, and variant–gene relation sources;
- attributable per-variant result assembly;
- conformance suites for third-party extensions.

Install the framework and the bindings you need from PyPI:

```bash
pip install altar
pip install altar-chrombpnet altar-alphamissense
```

`altar-chrombpnet`, `altar-cherimoya`, `altar-alphamissense`, and `altar-opentargets-e2g` are on PyPI. The
other bindings install from a source checkout of the repository.

Cloud providers, hosted-model SDKs, and the experimental investigation agent are optional extras, such as
`pip install "altar[bigquery]"`. Model frameworks and weights stay in separately locked runtime images. See
[installation](https://kundajelab.github.io/altar/getting-started/installation/) for every binding and extra,
and for installing from a source checkout.

## Documentation

The full site is published at **<https://kundajelab.github.io/altar/>**.

- [Start with Altar](https://kundajelab.github.io/altar/getting-started/)
- [Real scoring tutorial](https://kundajelab.github.io/altar/quickstart/)
- [Scientific guide](https://kundajelab.github.io/altar/science/)
- [Integration catalog](https://kundajelab.github.io/altar/integrations/)
- [Extension guide](https://kundajelab.github.io/altar/extend/)
- [Public API policy](https://kundajelab.github.io/altar/public-api/)

External packages should import only the compatibility-controlled façade modules: `altar.models`,
`altar.execution`, `altar.results`, `altar.sources`, `altar.predicates`, `altar.registry`, `altar.access`,
`altar.scoring`, `altar.testing`, and `altar.variants`. The authentication (`altar.access`) and job-queue
names are provisional: importable, but outside the compatibility commitment until they have a public adapter
and consumer.

Plugin discovery and Python imports both use the canonical `altar.*` namespace. See the
[plugin packaging guide](https://kundajelab.github.io/altar/concepts/plugins/) for the nine entry-point groups, two
of them provisional, and validation rules.

## License

Altar is copyright 2026 Riya Sinha and released under the MIT License. See the repository's `LICENSE` and
`CITATION.cff` files for license and citation metadata.
