Metadata-Version: 2.4
Name: proteomics-foundation
Version: 0.3.8
Summary: Install and import alias package for bijux-proteomics-foundation.
Project-URL: Homepage, https://bijux.io/bijux-proteomics/
Project-URL: Documentation, https://bijux.io/bijux-proteomics/03-bijux-proteomics-foundation/
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/proteomics-foundation/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
License-File: LICENSE
License-File: NOTICE
Keywords: compatibility,foundation,packaging,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: <4,>=3.11
Requires-Dist: bijux-proteomics-foundation<0.4.0,>=0.3.8
Description-Content-Type: text/markdown

# proteomics-foundation

<!-- bijux-proteomics-badges:generated:start -->
[![Python 3.11+](https://img.shields.io/badge/python-3.11%2B-3776AB?logo=python&logoColor=white)](https://pypi.org/project/proteomics-foundation/)
[![Typing: typed](https://img.shields.io/badge/typing-typed%20(PEP%20561)-0A7BBB)](https://pypi.org/project/proteomics-foundation/)
[![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/verify.yml/badge.svg?branch=main)](https://github.com/bijux/bijux-proteomics/actions/workflows/verify.yml?query=branch%3Amain)
[![GitHub Repository](https://img.shields.io/badge/github-bijux%2Fbijux--proteomics-181717?logo=github)](https://github.com/bijux/bijux-proteomics)

[![proteomics-foundation](https://img.shields.io/pypi/v/proteomics-foundation?label=proteomics--foundation&logo=pypi)](https://pypi.org/project/proteomics-foundation/)
[![agentic-proteins](https://img.shields.io/pypi/v/agentic-proteins?label=agentic--proteins&logo=pypi)](https://pypi.org/project/agentic-proteins/)
[![bijux-proteomics-foundation](https://img.shields.io/pypi/v/bijux-proteomics-foundation?label=foundation&logo=pypi)](https://pypi.org/project/bijux-proteomics-foundation/)
[![bijux-proteomics-core](https://img.shields.io/pypi/v/bijux-proteomics-core?label=core&logo=pypi)](https://pypi.org/project/bijux-proteomics-core/)
[![bijux-proteomics-runtime](https://img.shields.io/pypi/v/bijux-proteomics-runtime?label=runtime&logo=pypi)](https://pypi.org/project/bijux-proteomics-runtime/)
[![bijux-proteomics-intelligence](https://img.shields.io/pypi/v/bijux-proteomics-intelligence?label=intelligence&logo=pypi)](https://pypi.org/project/bijux-proteomics-intelligence/)
[![bijux-proteomics-knowledge](https://img.shields.io/pypi/v/bijux-proteomics-knowledge?label=knowledge&logo=pypi)](https://pypi.org/project/bijux-proteomics-knowledge/)
[![bijux-proteomics-lab](https://img.shields.io/pypi/v/bijux-proteomics-lab?label=lab&logo=pypi)](https://pypi.org/project/bijux-proteomics-lab/)

[![agentic-proteins](https://img.shields.io/badge/agentic--proteins-ghcr-181717?logo=github)](https://github.com/bijux/bijux-proteomics/pkgs/container/bijux-proteomics%2Fagentic-proteins)
[![bijux-proteomics-foundation](https://img.shields.io/badge/foundation-ghcr-181717?logo=github)](https://github.com/bijux/bijux-proteomics/pkgs/container/bijux-proteomics%2Fbijux-proteomics-foundation)
[![bijux-proteomics-core](https://img.shields.io/badge/core-ghcr-181717?logo=github)](https://github.com/bijux/bijux-proteomics/pkgs/container/bijux-proteomics%2Fbijux-proteomics-core)
[![bijux-proteomics-intelligence](https://img.shields.io/badge/intelligence-ghcr-181717?logo=github)](https://github.com/bijux/bijux-proteomics/pkgs/container/bijux-proteomics%2Fbijux-proteomics-intelligence)
[![bijux-proteomics-knowledge](https://img.shields.io/badge/knowledge-ghcr-181717?logo=github)](https://github.com/bijux/bijux-proteomics/pkgs/container/bijux-proteomics%2Fbijux-proteomics-knowledge)
[![bijux-proteomics-lab](https://img.shields.io/badge/lab-ghcr-181717?logo=github)](https://github.com/bijux/bijux-proteomics/pkgs/container/bijux-proteomics%2Fbijux-proteomics-lab)

[![proteomics-foundation docs](https://img.shields.io/badge/docs-proteomics--foundation-2563EB?logo=materialformkdocs&logoColor=white)](https://bijux.io/bijux-proteomics/03-bijux-proteomics-foundation/)
[![agentic-proteins docs](https://img.shields.io/badge/docs-agentic--proteins-2563EB?logo=materialformkdocs&logoColor=white)](https://bijux.io/bijux-proteomics/02-agentic-proteins/)
[![bijux-proteomics-foundation docs](https://img.shields.io/badge/docs-foundation-2563EB?logo=materialformkdocs&logoColor=white)](https://bijux.io/bijux-proteomics/03-bijux-proteomics-foundation/)
[![bijux-proteomics-core docs](https://img.shields.io/badge/docs-core-2563EB?logo=materialformkdocs&logoColor=white)](https://bijux.io/bijux-proteomics/04-bijux-proteomics-core/)
[![bijux-proteomics-runtime docs](https://img.shields.io/badge/docs-runtime-2563EB?logo=materialformkdocs&logoColor=white)](https://bijux.io/bijux-proteomics/09-bijux-proteomics-runtime/)
[![bijux-proteomics-intelligence docs](https://img.shields.io/badge/docs-intelligence-2563EB?logo=materialformkdocs&logoColor=white)](https://bijux.io/bijux-proteomics/05-bijux-proteomics-intelligence/)
[![bijux-proteomics-knowledge docs](https://img.shields.io/badge/docs-knowledge-2563EB?logo=materialformkdocs&logoColor=white)](https://bijux.io/bijux-proteomics/06-bijux-proteomics-knowledge/)
[![bijux-proteomics-lab docs](https://img.shields.io/badge/docs-lab-2563EB?logo=materialformkdocs&logoColor=white)](https://bijux.io/bijux-proteomics/07-bijux-proteomics-lab/)
<!-- bijux-proteomics-badges:generated:end -->

`proteomics-foundation` is the compatibility alias for the canonical foundation
owner `bijux-proteomics-foundation`.
It is the install and import alias for bijux-proteomics-foundation.

Use this package when you want a shorter distribution and import name for the
serialization, schema, and compatibility kernel without creating a second
foundation owner.

## Alias at a glance

- Use `proteomics-foundation` when you want a shorter package name for the
  shared kernel without changing who owns the contracts.
- Start with the
  [canonical foundation package docs](https://bijux.io/bijux-proteomics/03-bijux-proteomics-foundation/)
  because this package only forwards into that owner surface.
- Route all schema, serialization, and compatibility behavior to
  `bijux-proteomics-foundation`; keep this package focused on compatibility
  naming.

## 0.3.8 Release Highlights

- The alias now routes readers to the current foundation handbook instead of
  reading like a second kernel surface.
- Compatibility prose now makes the canonical ownership and forwarding-only
  contract explicit in the first screen.

## Installation

```bash
pip install proteomics-foundation
```

## Public APIs

The alias forwards the canonical foundation exports through
`proteomics_foundation`:

```python
from proteomics_foundation import DocumentSchema, hash_payload, to_canonical_json

schema = DocumentSchema(
    created_by="proteomics-foundation",
    document_kind="readme_example",
    package_name="proteomics-foundation",
)
payload = {
    "document_kind": schema.document_kind,
    "schema_version": schema.schema_version,
}
rendered = to_canonical_json(payload)
digest = hash_payload(payload)

assert '"readme_example"' in rendered
assert digest
```

## Package identity

- Distribution name: `proteomics-foundation`
- Import root: `proteomics_foundation`
- Canonical owner package: `bijux-proteomics-foundation`
- Canonical owner import root: `bijux_proteomics_foundation`

## Package boundaries

- this package owns compatibility naming for the foundation surface
- schema, serialization, compatibility, and outcome contracts remain owned by
  `bijux-proteomics-foundation`
- new behavior must land in the canonical owner before alias exports change

## What this package must not do

- define a second foundation kernel
- drift away from canonical serialization or compatibility behavior
- become a separate owner for outcome or schema policy

## Contract checkpoints

- alias exports must forward to the canonical foundation package cleanly
- docs must name the canonical owner explicitly
- compatibility updates must stay covered by alias-package tests

## Choose this package when

- you want a shorter import and distribution name for foundation contracts
- migration or ergonomics favor `proteomics_foundation`
- compatibility packaging work needs a named alias for the foundation owner

## Route elsewhere when

- the change alters schema, serialization, compatibility, or outcome behavior
- the work introduces exports that are not already owned by foundation
- the alias would stop being forwarding-only

## Verification route

- run alias compatibility tests before changing imports or metadata
- review `docs/ARCHITECTURE.md`, `docs/BOUNDARIES.md`, and `docs/CONTRACTS.md`
  when alias claims or routing language change
- validate the canonical foundation README and tests when behavior changes are
  proposed

## Review questions

- does the change preserve this package as a naming alias only
- is the canonical foundation owner still explicit in docs and behavior
- would the same outcome remain correct if consumers imported the canonical
  package directly

## Escalation route

- route kernel behavior changes to `bijux-proteomics-foundation`
- stop and review alias boundaries when package-local semantics start appearing
- escalate before release when import or metadata drift could confuse ownership

## Consumer impact signals

- import-path or package-name changes are high-impact because downstream code
  may depend on them directly
- alias documentation changes should still be reviewed against the canonical
  foundation owner
- wording-only clarifications carry lower release risk than routing or metadata
  changes

## Explicit non-goals

- this package does not own scientific workflow or evidence semantics
- this package does not define runtime, intelligence, knowledge, or lab policy
- this package does not replace the canonical foundation release surface

## Documentation

- Release guidance lives in this `README.md`, this package `CHANGELOG.md`, and
  package `docs/*.md` under the canonical foundation owner surface.
- [Product architecture](https://bijux.io/bijux-proteomics/01-bijux-proteomics/foundation/product-architecture/)
- [Cross-package ownership](https://bijux.io/bijux-proteomics/01-bijux-proteomics/foundation/cross-package-ownership/)
- [Canonical foundation package docs](https://bijux.io/bijux-proteomics/03-bijux-proteomics-foundation/)
- [Changelog](CHANGELOG.md)
