proteomics-knowledge 0.3.8__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- proteomics_knowledge-0.3.8/.gitignore +62 -0
- proteomics_knowledge-0.3.8/CHANGELOG.md +21 -0
- proteomics_knowledge-0.3.8/LICENSE +1 -0
- proteomics_knowledge-0.3.8/NOTICE +1 -0
- proteomics_knowledge-0.3.8/PKG-INFO +205 -0
- proteomics_knowledge-0.3.8/README.md +172 -0
- proteomics_knowledge-0.3.8/pyproject.toml +60 -0
- proteomics_knowledge-0.3.8/src/proteomics_knowledge/py.typed +1 -0
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# Changelog
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All notable changes for `proteomics-knowledge` are recorded here.
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## Unreleased
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## 0.3.8 - 2026-07-01
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### Added
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- Added the `proteomics-knowledge` distribution as the short install and
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import alias for `bijux-proteomics-knowledge`.
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- Added alias-package contract and README guidance that sends readers to the
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canonical grounding and scientific-memory owner.
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### Changed
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- Aligned the fallback version and canonical dependency floors with the
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`0.3.8` release line.
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- Routed the alias through governed compatibility helpers and clean-checkout
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verification so the short distribution remains a forwarding surface only.
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../../LICENSE
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../../NOTICE
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Metadata-Version: 2.4
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Name: proteomics-knowledge
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Version: 0.3.8
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Summary: Install and import alias package for bijux-proteomics-knowledge.
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Project-URL: Homepage, https://bijux.io/bijux-proteomics/
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Project-URL: Documentation, https://bijux.io/bijux-proteomics/06-bijux-proteomics-knowledge/
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Project-URL: Repository, https://github.com/bijux/bijux-proteomics
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Project-URL: Issues, https://github.com/bijux/bijux-proteomics/issues
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Project-URL: Changelog, https://github.com/bijux/bijux-proteomics/blob/main/packages/proteomics-knowledge/CHANGELOG.md
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Project-URL: Security, https://github.com/bijux/bijux-proteomics/blob/main/SECURITY.md
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Author-email: Bijan Mousavi <bijan@bijux.io>
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Maintainer-email: Bijan Mousavi <bijan@bijux.io>
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License: Apache-2.0
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License-File: LICENSE
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License-File: NOTICE
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Keywords: compatibility,knowledge,packaging,proteomics
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Classifier: Development Status :: 3 - Alpha
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Classifier: Intended Audience :: Developers
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Classifier: Intended Audience :: Science/Research
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Classifier: License :: OSI Approved :: Apache Software License
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Classifier: Operating System :: OS Independent
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Classifier: Programming Language :: Python :: 3
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Classifier: Programming Language :: Python :: 3 :: Only
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Classifier: Programming Language :: Python :: 3.11
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Classifier: Programming Language :: Python :: 3.12
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Classifier: Programming Language :: Python :: 3.13
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Classifier: Programming Language :: Python :: 3.14
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Classifier: Typing :: Typed
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Requires-Python: <4,>=3.11
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Requires-Dist: bijux-proteomics-foundation<0.4.0,>=0.3.8
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Requires-Dist: bijux-proteomics-knowledge<0.4.0,>=0.3.8
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Description-Content-Type: text/markdown
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# proteomics-knowledge
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<!-- bijux-proteomics-badges:generated:start -->
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[](https://pypi.org/project/proteomics-knowledge/)
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[-0A7BBB)](https://pypi.org/project/proteomics-knowledge/)
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[](https://github.com/bijux/bijux-proteomics/blob/main/LICENSE)
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[](https://github.com/bijux/bijux-proteomics/actions/workflows/verify.yml?query=branch%3Amain)
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[](https://github.com/bijux/bijux-proteomics)
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[](https://pypi.org/project/proteomics-knowledge/)
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[](https://pypi.org/project/agentic-proteins/)
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[](https://pypi.org/project/bijux-proteomics-foundation/)
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[](https://pypi.org/project/bijux-proteomics-core/)
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[](https://pypi.org/project/bijux-proteomics-runtime/)
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[](https://pypi.org/project/bijux-proteomics-intelligence/)
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[](https://pypi.org/project/bijux-proteomics-knowledge/)
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[](https://pypi.org/project/bijux-proteomics-lab/)
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[](https://github.com/bijux/bijux-proteomics/pkgs/container/bijux-proteomics%2Fagentic-proteins)
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[](https://github.com/bijux/bijux-proteomics/pkgs/container/bijux-proteomics%2Fbijux-proteomics-foundation)
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[](https://github.com/bijux/bijux-proteomics/pkgs/container/bijux-proteomics%2Fbijux-proteomics-core)
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[](https://github.com/bijux/bijux-proteomics/pkgs/container/bijux-proteomics%2Fbijux-proteomics-intelligence)
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[](https://github.com/bijux/bijux-proteomics/pkgs/container/bijux-proteomics%2Fbijux-proteomics-knowledge)
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[](https://github.com/bijux/bijux-proteomics/pkgs/container/bijux-proteomics%2Fbijux-proteomics-lab)
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[](https://bijux.io/bijux-proteomics/06-bijux-proteomics-knowledge/)
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[](https://bijux.io/bijux-proteomics/02-agentic-proteins/)
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[](https://bijux.io/bijux-proteomics/03-bijux-proteomics-foundation/)
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[](https://bijux.io/bijux-proteomics/04-bijux-proteomics-core/)
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[](https://bijux.io/bijux-proteomics/09-bijux-proteomics-runtime/)
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[](https://bijux.io/bijux-proteomics/05-bijux-proteomics-intelligence/)
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[](https://bijux.io/bijux-proteomics/06-bijux-proteomics-knowledge/)
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[](https://bijux.io/bijux-proteomics/07-bijux-proteomics-lab/)
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<!-- bijux-proteomics-badges:generated:end -->
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`proteomics-knowledge` is the compatibility alias for the canonical knowledge
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owner `bijux-proteomics-knowledge`.
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It is the install and import alias for bijux-proteomics-knowledge.
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Use this package when you want a shorter distribution and import name for the
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curated scientific memory surface without creating a second owner.
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## Alias at a glance
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- Use `proteomics-knowledge` when you want a shorter package name for curated
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scientific memory without changing who owns the behavior.
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- Start with the
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[canonical knowledge package docs](https://bijux.io/bijux-proteomics/06-bijux-proteomics-knowledge/)
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because this package only forwards into that owner surface.
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- Route curation and grounding behavior to `bijux-proteomics-knowledge`; keep
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this package focused on compatibility naming and import forwarding.
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## 0.3.8 Release Highlights
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- The alias now points readers at the current knowledge handbook instead of
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reading like a second memory owner.
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- Boundaries, release guidance, and compatibility wording now state the
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forwarding-only contract more clearly.
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## Installation
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```bash
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pip install proteomics-knowledge
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```
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## Public APIs
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The alias forwards the canonical knowledge surface through
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`proteomics_knowledge`:
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```python
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from proteomics_foundation import DocumentSchema
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from proteomics_knowledge import evaluate_schema_compatibility
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report = evaluate_schema_compatibility(
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DocumentSchema(
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created_by="proteomics-knowledge",
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document_kind="annotation_pack",
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package_name="proteomics-knowledge",
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)
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)
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assert report.compatible is True
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assert report.profile_id == "knowledge-default-profile"
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```
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## Package identity
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- Distribution name: `proteomics-knowledge`
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- Import root: `proteomics_knowledge`
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- Canonical owner package: `bijux-proteomics-knowledge`
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- Canonical owner import root: `bijux_proteomics_knowledge`
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## Package boundaries
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- this package owns compatibility naming for the knowledge surface
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- reference curation, pathway memory, and evidence grounding remain owned by
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`bijux-proteomics-knowledge`
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- new knowledge behavior must land in the canonical owner before alias exports
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change
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## What this package must not do
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- define a second knowledge graph or grounding owner
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- drift away from canonical curation behavior
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- become an independent release surface for knowledge semantics
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## Contract checkpoints
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- alias exports must keep forwarding to canonical knowledge behavior
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- docs must keep the canonical knowledge owner explicit
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- compatibility changes must stay covered by alias-package tests
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## Choose this package when
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- you need a shorter import and distribution name for knowledge entrypoints
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- migration constraints prefer `proteomics_knowledge`
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- packaging or compatibility work needs a named alias for the knowledge owner
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## Route elsewhere when
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- the change alters curation, grounding, or pathway semantics
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- the work adds behavior not already owned by the canonical package
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- the alias would stop being forwarding-only
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## Verification route
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- run alias compatibility tests before changing knowledge imports or metadata
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- review `docs/ARCHITECTURE.md`, `docs/BOUNDARIES.md`, and `docs/CONTRACTS.md`
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when alias claims or routing language change
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- validate the canonical knowledge README and tests when behavior changes are
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proposed
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## Review questions
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- does the change preserve this package as an alias only
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- is the canonical knowledge owner still explicit in docs and behavior
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- would the same outcome remain correct if consumers imported the canonical
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package directly
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## Escalation route
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- route knowledge behavior changes to `bijux-proteomics-knowledge`
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- stop and review boundaries when package-local curation semantics start
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appearing
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- escalate before release when routing or metadata drift could confuse the
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knowledge owner
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## Consumer impact signals
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- import-path or package-name changes are high-impact because downstream
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grounding code may depend on them directly
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- alias documentation changes should still be reviewed against the canonical
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knowledge owner
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- wording-only clarifications carry lower release risk than routing or behavior
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changes
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## Explicit non-goals
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- this package does not own intelligence scoring, runtime delivery, or lab
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policy
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- this package does not create a second knowledge graph
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- this package does not replace the canonical knowledge release surface
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## Documentation
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- Release guidance lives in this `README.md`, this package `CHANGELOG.md`, and
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package `docs/*.md` under the canonical knowledge owner surface.
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- [Product architecture](https://bijux.io/bijux-proteomics/01-bijux-proteomics/foundation/product-architecture/)
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- [Cross-package ownership](https://bijux.io/bijux-proteomics/01-bijux-proteomics/foundation/cross-package-ownership/)
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- [Canonical knowledge package docs](https://bijux.io/bijux-proteomics/06-bijux-proteomics-knowledge/)
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- [Changelog](CHANGELOG.md)
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# proteomics-knowledge
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<!-- bijux-proteomics-badges:generated:start -->
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[](https://pypi.org/project/proteomics-knowledge/)
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[-0A7BBB)](https://pypi.org/project/proteomics-knowledge/)
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[](https://github.com/bijux/bijux-proteomics/blob/main/LICENSE)
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[](https://github.com/bijux/bijux-proteomics/actions/workflows/verify.yml?query=branch%3Amain)
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[](https://github.com/bijux/bijux-proteomics)
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[](https://pypi.org/project/proteomics-knowledge/)
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[](https://pypi.org/project/agentic-proteins/)
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[](https://pypi.org/project/bijux-proteomics-foundation/)
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[](https://pypi.org/project/bijux-proteomics-core/)
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[](https://pypi.org/project/bijux-proteomics-runtime/)
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[](https://pypi.org/project/bijux-proteomics-intelligence/)
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[](https://pypi.org/project/bijux-proteomics-knowledge/)
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[](https://pypi.org/project/bijux-proteomics-lab/)
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[](https://github.com/bijux/bijux-proteomics/pkgs/container/bijux-proteomics%2Fagentic-proteins)
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[](https://github.com/bijux/bijux-proteomics/pkgs/container/bijux-proteomics%2Fbijux-proteomics-foundation)
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[](https://github.com/bijux/bijux-proteomics/pkgs/container/bijux-proteomics%2Fbijux-proteomics-core)
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[](https://github.com/bijux/bijux-proteomics/pkgs/container/bijux-proteomics%2Fbijux-proteomics-intelligence)
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[](https://github.com/bijux/bijux-proteomics/pkgs/container/bijux-proteomics%2Fbijux-proteomics-knowledge)
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[](https://github.com/bijux/bijux-proteomics/pkgs/container/bijux-proteomics%2Fbijux-proteomics-lab)
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[](https://bijux.io/bijux-proteomics/06-bijux-proteomics-knowledge/)
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[](https://bijux.io/bijux-proteomics/02-agentic-proteins/)
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[](https://bijux.io/bijux-proteomics/03-bijux-proteomics-foundation/)
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[](https://bijux.io/bijux-proteomics/04-bijux-proteomics-core/)
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[](https://bijux.io/bijux-proteomics/09-bijux-proteomics-runtime/)
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[](https://bijux.io/bijux-proteomics/05-bijux-proteomics-intelligence/)
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[](https://bijux.io/bijux-proteomics/06-bijux-proteomics-knowledge/)
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[](https://bijux.io/bijux-proteomics/07-bijux-proteomics-lab/)
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<!-- bijux-proteomics-badges:generated:end -->
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`proteomics-knowledge` is the compatibility alias for the canonical knowledge
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owner `bijux-proteomics-knowledge`.
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It is the install and import alias for bijux-proteomics-knowledge.
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Use this package when you want a shorter distribution and import name for the
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curated scientific memory surface without creating a second owner.
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## Alias at a glance
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- Use `proteomics-knowledge` when you want a shorter package name for curated
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scientific memory without changing who owns the behavior.
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- Start with the
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[canonical knowledge package docs](https://bijux.io/bijux-proteomics/06-bijux-proteomics-knowledge/)
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because this package only forwards into that owner surface.
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- Route curation and grounding behavior to `bijux-proteomics-knowledge`; keep
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this package focused on compatibility naming and import forwarding.
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## 0.3.8 Release Highlights
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- The alias now points readers at the current knowledge handbook instead of
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reading like a second memory owner.
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- Boundaries, release guidance, and compatibility wording now state the
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forwarding-only contract more clearly.
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## Installation
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```bash
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pip install proteomics-knowledge
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```
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## Public APIs
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The alias forwards the canonical knowledge surface through
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`proteomics_knowledge`:
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```python
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from proteomics_foundation import DocumentSchema
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from proteomics_knowledge import evaluate_schema_compatibility
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report = evaluate_schema_compatibility(
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DocumentSchema(
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created_by="proteomics-knowledge",
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document_kind="annotation_pack",
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package_name="proteomics-knowledge",
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)
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)
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assert report.compatible is True
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assert report.profile_id == "knowledge-default-profile"
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```
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## Package identity
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- Distribution name: `proteomics-knowledge`
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- Import root: `proteomics_knowledge`
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- Canonical owner package: `bijux-proteomics-knowledge`
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- Canonical owner import root: `bijux_proteomics_knowledge`
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## Package boundaries
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+
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- this package owns compatibility naming for the knowledge surface
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- reference curation, pathway memory, and evidence grounding remain owned by
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`bijux-proteomics-knowledge`
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- new knowledge behavior must land in the canonical owner before alias exports
|
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change
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## What this package must not do
|
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- define a second knowledge graph or grounding owner
|
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+
- drift away from canonical curation behavior
|
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+
- become an independent release surface for knowledge semantics
|
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+
|
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|
+
## Contract checkpoints
|
|
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|
+
|
|
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|
+
- alias exports must keep forwarding to canonical knowledge behavior
|
|
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|
+
- docs must keep the canonical knowledge owner explicit
|
|
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|
+
- compatibility changes must stay covered by alias-package tests
|
|
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|
+
|
|
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|
+
## Choose this package when
|
|
115
|
+
|
|
116
|
+
- you need a shorter import and distribution name for knowledge entrypoints
|
|
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|
+
- migration constraints prefer `proteomics_knowledge`
|
|
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|
+
- packaging or compatibility work needs a named alias for the knowledge owner
|
|
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|
+
|
|
120
|
+
## Route elsewhere when
|
|
121
|
+
|
|
122
|
+
- the change alters curation, grounding, or pathway semantics
|
|
123
|
+
- the work adds behavior not already owned by the canonical package
|
|
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|
+
- the alias would stop being forwarding-only
|
|
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|
+
|
|
126
|
+
## Verification route
|
|
127
|
+
|
|
128
|
+
- run alias compatibility tests before changing knowledge imports or metadata
|
|
129
|
+
- review `docs/ARCHITECTURE.md`, `docs/BOUNDARIES.md`, and `docs/CONTRACTS.md`
|
|
130
|
+
when alias claims or routing language change
|
|
131
|
+
- validate the canonical knowledge README and tests when behavior changes are
|
|
132
|
+
proposed
|
|
133
|
+
|
|
134
|
+
## Review questions
|
|
135
|
+
|
|
136
|
+
- does the change preserve this package as an alias only
|
|
137
|
+
- is the canonical knowledge owner still explicit in docs and behavior
|
|
138
|
+
- would the same outcome remain correct if consumers imported the canonical
|
|
139
|
+
package directly
|
|
140
|
+
|
|
141
|
+
## Escalation route
|
|
142
|
+
|
|
143
|
+
- route knowledge behavior changes to `bijux-proteomics-knowledge`
|
|
144
|
+
- stop and review boundaries when package-local curation semantics start
|
|
145
|
+
appearing
|
|
146
|
+
- escalate before release when routing or metadata drift could confuse the
|
|
147
|
+
knowledge owner
|
|
148
|
+
|
|
149
|
+
## Consumer impact signals
|
|
150
|
+
|
|
151
|
+
- import-path or package-name changes are high-impact because downstream
|
|
152
|
+
grounding code may depend on them directly
|
|
153
|
+
- alias documentation changes should still be reviewed against the canonical
|
|
154
|
+
knowledge owner
|
|
155
|
+
- wording-only clarifications carry lower release risk than routing or behavior
|
|
156
|
+
changes
|
|
157
|
+
|
|
158
|
+
## Explicit non-goals
|
|
159
|
+
|
|
160
|
+
- this package does not own intelligence scoring, runtime delivery, or lab
|
|
161
|
+
policy
|
|
162
|
+
- this package does not create a second knowledge graph
|
|
163
|
+
- this package does not replace the canonical knowledge release surface
|
|
164
|
+
|
|
165
|
+
## Documentation
|
|
166
|
+
|
|
167
|
+
- Release guidance lives in this `README.md`, this package `CHANGELOG.md`, and
|
|
168
|
+
package `docs/*.md` under the canonical knowledge owner surface.
|
|
169
|
+
- [Product architecture](https://bijux.io/bijux-proteomics/01-bijux-proteomics/foundation/product-architecture/)
|
|
170
|
+
- [Cross-package ownership](https://bijux.io/bijux-proteomics/01-bijux-proteomics/foundation/cross-package-ownership/)
|
|
171
|
+
- [Canonical knowledge package docs](https://bijux.io/bijux-proteomics/06-bijux-proteomics-knowledge/)
|
|
172
|
+
- [Changelog](CHANGELOG.md)
|
|
@@ -0,0 +1,60 @@
|
|
|
1
|
+
[build-system]
|
|
2
|
+
requires = ["hatchling>=1.27.0,<1.31", "hatch-vcs>=0.4.0,<1.0"]
|
|
3
|
+
build-backend = "hatchling.build"
|
|
4
|
+
|
|
5
|
+
[project]
|
|
6
|
+
name = "proteomics-knowledge"
|
|
7
|
+
dynamic = ["version"]
|
|
8
|
+
description = "Install and import alias package for bijux-proteomics-knowledge."
|
|
9
|
+
readme = "README.md"
|
|
10
|
+
license = { text = "Apache-2.0" }
|
|
11
|
+
requires-python = ">=3.11,<4"
|
|
12
|
+
authors = [{ name = "Bijan Mousavi", email = "bijan@bijux.io" }]
|
|
13
|
+
maintainers = [{ name = "Bijan Mousavi", email = "bijan@bijux.io" }]
|
|
14
|
+
keywords = ["proteomics", "knowledge", "compatibility", "packaging"]
|
|
15
|
+
classifiers = [
|
|
16
|
+
"Development Status :: 3 - Alpha",
|
|
17
|
+
"Intended Audience :: Science/Research",
|
|
18
|
+
"Intended Audience :: Developers",
|
|
19
|
+
"License :: OSI Approved :: Apache Software License",
|
|
20
|
+
"Operating System :: OS Independent",
|
|
21
|
+
"Programming Language :: Python :: 3",
|
|
22
|
+
"Programming Language :: Python :: 3 :: Only",
|
|
23
|
+
"Programming Language :: Python :: 3.11",
|
|
24
|
+
"Programming Language :: Python :: 3.12",
|
|
25
|
+
"Programming Language :: Python :: 3.13",
|
|
26
|
+
"Programming Language :: Python :: 3.14",
|
|
27
|
+
"Typing :: Typed",
|
|
28
|
+
]
|
|
29
|
+
dependencies = [
|
|
30
|
+
"bijux-proteomics-foundation>=0.3.8,<0.4.0",
|
|
31
|
+
"bijux-proteomics-knowledge>=0.3.8,<0.4.0",
|
|
32
|
+
]
|
|
33
|
+
|
|
34
|
+
[project.urls]
|
|
35
|
+
Homepage = "https://bijux.io/bijux-proteomics/"
|
|
36
|
+
Documentation = "https://bijux.io/bijux-proteomics/06-bijux-proteomics-knowledge/"
|
|
37
|
+
Repository = "https://github.com/bijux/bijux-proteomics"
|
|
38
|
+
Issues = "https://github.com/bijux/bijux-proteomics/issues"
|
|
39
|
+
Changelog = "https://github.com/bijux/bijux-proteomics/blob/main/packages/proteomics-knowledge/CHANGELOG.md"
|
|
40
|
+
Security = "https://github.com/bijux/bijux-proteomics/blob/main/SECURITY.md"
|
|
41
|
+
|
|
42
|
+
[tool.hatch.version]
|
|
43
|
+
source = "vcs"
|
|
44
|
+
tag-pattern = "^v(?P<version>.*)$"
|
|
45
|
+
fallback-version = "0.3.8"
|
|
46
|
+
raw-options = { git_describe_command = "git describe --dirty --tags --long --match 'v*'", local_scheme = "dirty-tag", version_scheme = "guess-next-dev", root = "../..", search_parent_directories = true }
|
|
47
|
+
|
|
48
|
+
[tool.hatch.build]
|
|
49
|
+
include = [
|
|
50
|
+
"README.md",
|
|
51
|
+
"CHANGELOG.md",
|
|
52
|
+
"src/proteomics_knowledge/py.typed",
|
|
53
|
+
]
|
|
54
|
+
force-include = { "LICENSE" = "LICENSE", "NOTICE" = "NOTICE" }
|
|
55
|
+
|
|
56
|
+
[tool.hatch.build.targets.wheel]
|
|
57
|
+
packages = ["src/proteomics_knowledge"]
|
|
58
|
+
|
|
59
|
+
[tool.hatch.build.targets.wheel.package-data]
|
|
60
|
+
"proteomics_knowledge" = ["py.typed"]
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
|