Metadata-Version: 2.4
Name: bijux-proteomics-core
Version: 0.3.0
Summary: Program models and execution adapters for Bijux Proteomics
Project-URL: Homepage, https://bijux.io/bijux-proteomics/
Project-URL: Documentation, https://bijux.io/bijux-proteomics/
Project-URL: Repository, https://github.com/bijux/bijux-proteomics
Project-URL: Issues, https://github.com/bijux/bijux-proteomics/issues
Project-URL: Changelog, https://github.com/bijux/bijux-proteomics/blob/main/packages/bijux-proteomics-core/CHANGELOG.md
Project-URL: Security, https://github.com/bijux/bijux-proteomics/blob/main/SECURITY.md
Author-email: Bijan Mousavi <bijan@bijux.io>
Maintainer-email: Bijan Mousavi <bijan@bijux.io>
License: Apache-2.0
Keywords: bioinformatics,domain-contracts,lifecycle,program-modeling,proteomics
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Classifier: Typing :: Typed
Requires-Python: >=3.11
Requires-Dist: bijux-proteomics-foundation>=0.3.0
Requires-Dist: click>=8.1
Requires-Dist: pydantic>=2.0.2
Description-Content-Type: text/markdown

# bijux-proteomics-core

[![Python 3.11+](https://img.shields.io/badge/python-3.11%2B-3776AB?logo=python&logoColor=white)](https://pypi.org/project/bijux-proteomics-core/)
[![Typing: typed](https://img.shields.io/badge/typing-typed%20(PEP%20561)-0A7BBB)](https://pypi.org/project/bijux-proteomics-core/)
[![License: Apache-2.0](https://img.shields.io/badge/license-Apache--2.0-0F766E)](https://github.com/bijux/bijux-proteomics/blob/main/LICENSE)
[![CI Status](https://github.com/bijux/bijux-proteomics/actions/workflows/ci-bijux-proteomics-core.yml/badge.svg)](https://github.com/bijux/bijux-proteomics/actions/workflows/ci-bijux-proteomics-core.yml)
[![GitHub Repository](https://img.shields.io/badge/github-bijux%2Fbijux--proteomics-181717?logo=github)](https://github.com/bijux/bijux-proteomics)

`bijux-proteomics-core` defines protein program entities, lifecycle transitions,
review gates, assay requirements, and execution adapters used by the platform.

If you need to understand what a program is, when it can advance, and which
review constraints must hold before progression, this is the package boundary.

## What this package owns

- program, target, assay, and review domain models
- lifecycle transition and stage eligibility logic
- invariant validation for identifiers, gating, and scientific consistency
- runtime adapter interfaces and CLI entrypoints for program workflows

## What this package does not own

- evidence bundle conflict resolution and trust scoring
- candidate ranking and scenario evaluation policies
- lab scheduling, outcome promotion, and rerun policies

## Source map

- [`src/bijux_proteomics/program_spec.py`](https://github.com/bijux/bijux-proteomics/blob/main/packages/bijux-proteomics-core/src/bijux_proteomics/program_spec.py) for core program entities
- [`src/bijux_proteomics/repositories.py`](https://github.com/bijux/bijux-proteomics/blob/main/packages/bijux-proteomics-core/src/bijux_proteomics/repositories.py) for decision and gate repository protocols
- [`src/bijux_proteomics/validation.py`](https://github.com/bijux/bijux-proteomics/blob/main/packages/bijux-proteomics-core/src/bijux_proteomics/validation.py) for domain invariant checks
- [`src/bijux_proteomics/interfaces`](https://github.com/bijux/bijux-proteomics/tree/main/packages/bijux-proteomics-core/src/bijux_proteomics/interfaces) for package-facing CLI boundaries
- [`tests`](https://github.com/bijux/bijux-proteomics/tree/main/packages/bijux-proteomics-core/tests) for executable package expectations

## Read this next

- [Architecture](https://github.com/bijux/bijux-proteomics/blob/main/packages/bijux-proteomics-core/docs/ARCHITECTURE.md)
- [Boundaries](https://github.com/bijux/bijux-proteomics/blob/main/packages/bijux-proteomics-core/docs/BOUNDARIES.md)
- [Contracts](https://github.com/bijux/bijux-proteomics/blob/main/packages/bijux-proteomics-core/docs/CONTRACTS.md)
- [PyPI maintainer notes](https://github.com/bijux/bijux-proteomics/blob/main/packages/bijux-proteomics-core/docs/maintainer/pypi.md)

## Primary entrypoint

- console script: `bijux-proteomics`
