Metadata-Version: 2.4
Name: proteomics
Version: 0.3.8
Summary: Install, import, and CLI alias package for bijux-proteomics-core.
Project-URL: Homepage, https://bijux.io/bijux-proteomics/
Project-URL: Documentation, https://bijux.io/bijux-proteomics/04-bijux-proteomics-core/
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/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: bioinformatics,compatibility,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-core<0.4.0,>=0.3.8
Requires-Dist: bijux-proteomics-foundation<0.4.0,>=0.3.8
Description-Content-Type: text/markdown

# proteomics

<!-- 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/)
[![Typing: typed](https://img.shields.io/badge/typing-typed%20(PEP%20561)-0A7BBB)](https://pypi.org/project/proteomics/)
[![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](https://img.shields.io/pypi/v/proteomics?label=proteomics&logo=pypi)](https://pypi.org/project/proteomics/)
[![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 docs](https://img.shields.io/badge/docs-proteomics-2563EB?logo=materialformkdocs&logoColor=white)](https://bijux.io/bijux-proteomics/04-bijux-proteomics-core/)
[![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` is the short-name compatibility alias for the canonical core owner
`bijux-proteomics-core`.
It is the install and import alias for bijux-proteomics-core.

Use this package when you want the shortest public distribution and import name
for the core scientific surface without creating a second owner.

## Alias at a glance

- Use `proteomics` when the shortest install and import name matters more than
  the canonical owner package spelling.
- Start behavior discovery from the
  [canonical core package docs](https://bijux.io/bijux-proteomics/04-bijux-proteomics-core/)
  because this package is only a short-name forwarding layer.
- Route all scientific behavior to `bijux-proteomics-core`; keep this package
  focused on compatibility naming and short-form ergonomics.

## 0.3.8 Release Highlights

- The short-name alias now points readers straight at the current core docs
  and shipped scientific examples instead of reading like a second owner.
- Compatibility wording, package boundaries, and release guidance now state
  directly that `bijux-proteomics-core` owns all real behavior.

## Installation

```bash
pip install proteomics
```

## Public APIs

The alias forwards to the canonical core surface through the short import root:

```python
from proteomics import parse_fasta_document

report = parse_fasta_document(">sp|P11111|PTM1 Protein 1\nMPEPTIDEK\n")

assert report.total_records == 1
assert len(report.accepted_records) == 1
assert report.accepted_records[0].canonical_accession == "P11111"
```

## Package identity

- Distribution name: `proteomics`
- Import root: `proteomics`
- Canonical owner package: `bijux-proteomics-core`
- Canonical owner import root: `bijux_proteomics`

## Package boundaries

- this package owns compatibility naming for installs, imports, and the short
  CLI surface
- all scientific behavior remains owned by `bijux-proteomics-core`
- new features must land in the canonical owner before alias exports change

## What this package must not do

- define independent scientific or workflow behavior
- diverge from canonical core exports
- become a second place where core release policy is decided

## Contract checkpoints

- the short import surface must keep forwarding to canonical core behavior
- docs must continue to name `bijux-proteomics-core` as the owner
- compatibility updates must stay covered by alias-package tests

## Choose this package when

- you need the shortest import and install name for the core surface
- migration or user ergonomics favor `proteomics` over the canonical package
  name
- compatibility packaging work needs a clear short-name alias

## Route elsewhere when

- the change alters core scientific logic or workflow semantics
- the work adds a feature that is not already owned by core
- the proposal would make the alias more than a forwarding layer

## Verification route

- run alias compatibility tests before changing imports or console-script
  expectations
- review `docs/ARCHITECTURE.md`, `docs/BOUNDARIES.md`, and `docs/CONTRACTS.md`
  when alias claims or routing language change
- validate the canonical core README and tests when the proposal changes
  user-facing scientific behavior

## Review questions

- does the change preserve this package as a short-name alias only
- is the canonical owner explicit in behavior and documentation
- would the same behavior remain valid if core were imported directly

## Escalation route

- route scientific behavior changes to `bijux-proteomics-core`
- stop and review alias boundaries when the proposal introduces package-local
  semantics
- escalate before release when packaging or command-name drift could confuse
  consumers

## Consumer impact signals

- short-name install or import changes are high-impact because downstream code
  may rely on them directly
- alias documentation changes should still be reviewed against the core owner
- wording-only or documentation-only clarifications carry lower release risk

## Explicit non-goals

- this package does not own assay-processing or workflow semantics
- this package does not define runtime, intelligence, knowledge, or lab policy
- this package does not replace the canonical core release surface

## Documentation

- Release guidance lives in this `README.md`, this package `CHANGELOG.md`, and
  package `docs/*.md` under the canonical core 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 core package docs](https://bijux.io/bijux-proteomics/04-bijux-proteomics-core/)
- [Changelog](CHANGELOG.md)
