proteomics-intelligence 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_intelligence-0.3.8/.gitignore +62 -0
- proteomics_intelligence-0.3.8/CHANGELOG.md +21 -0
- proteomics_intelligence-0.3.8/LICENSE +1 -0
- proteomics_intelligence-0.3.8/NOTICE +1 -0
- proteomics_intelligence-0.3.8/PKG-INFO +216 -0
- proteomics_intelligence-0.3.8/README.md +183 -0
- proteomics_intelligence-0.3.8/pyproject.toml +60 -0
- proteomics_intelligence-0.3.8/src/proteomics_intelligence/py.typed +1 -0
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# Bijux shared
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# Changelog
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All notable changes for `proteomics-intelligence` 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-intelligence` distribution as the short install and
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import alias for `bijux-proteomics-intelligence`.
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- Added alias-package contract and README guidance that points short-name
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users to the canonical recommendation and interpretation 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 does not become a second public owner.
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../../LICENSE
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../../NOTICE
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Metadata-Version: 2.4
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Name: proteomics-intelligence
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Version: 0.3.8
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Summary: Install and import alias package for bijux-proteomics-intelligence.
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Project-URL: Homepage, https://bijux.io/bijux-proteomics/
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Project-URL: Documentation, https://bijux.io/bijux-proteomics/05-bijux-proteomics-intelligence/
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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-intelligence/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,intelligence,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-intelligence<0.4.0,>=0.3.8
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Description-Content-Type: text/markdown
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# proteomics-intelligence
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<!-- bijux-proteomics-badges:generated:start -->
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[](https://pypi.org/project/proteomics-intelligence/)
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[-0A7BBB)](https://pypi.org/project/proteomics-intelligence/)
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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-intelligence/)
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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/05-bijux-proteomics-intelligence/)
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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-intelligence` is the compatibility alias for the canonical
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intelligence owner `bijux-proteomics-intelligence`.
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It is the install and import alias for bijux-proteomics-intelligence.
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Use this package when you want a shorter distribution and import name for the
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recommendation and review layer without creating a second owner.
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## Alias at a glance
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- Use `proteomics-intelligence` when a shorter name is useful for the
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recommendation and review surface, but canonical ownership must stay the
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same.
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- Start with the
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[canonical intelligence package docs](https://bijux.io/bijux-proteomics/05-bijux-proteomics-intelligence/)
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because this package only forwards into that owner surface.
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- Route recommendation behavior to `bijux-proteomics-intelligence`; keep this
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package focused on compatibility naming and import forwarding.
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## 0.3.8 Release Highlights
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- The alias now routes readers to the current intelligence handbook instead of
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sounding like a second analytical owner.
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- Documentation and release guidance now state the forwarding contract in
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direct, audit-friendly language.
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## Installation
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```bash
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pip install proteomics-intelligence
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```
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## Public APIs
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The alias forwards the canonical intelligence review surface through
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`proteomics_intelligence`:
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```python
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from proteomics_intelligence import falsifiers
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from proteomics_knowledge import EvidenceClaim
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claim = EvidenceClaim(
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claim_id="protein-claim:p11111",
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target_id="protein:p11111",
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statement="Protein PTM1 increased after treatment.",
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subject="P11111",
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relation="protein_abundance_change",
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object="up",
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direction="up",
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claim_type="biomarker",
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evidence_ids=["evidence:1"],
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status="supported",
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polarity="supporting",
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resolution_state="open",
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evidence_state="supported",
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)
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items = falsifiers.generate_falsifiers(claim)
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assert items.summary.claim_count == 1
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assert items.entries[0].claim_id == claim.claim_id
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```
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## Package identity
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- Distribution name: `proteomics-intelligence`
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- Import root: `proteomics_intelligence`
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- Canonical owner package: `bijux-proteomics-intelligence`
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- Canonical owner import root: `bijux_proteomics_intelligence`
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## Package boundaries
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- this package owns compatibility naming for the intelligence surface
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- recommendation logic, scientific support, and claim review remain owned by
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`bijux-proteomics-intelligence`
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- new review 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 recommendation or review-policy owner
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- drift away from canonical intelligence semantics
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- become an independent release surface for intelligence behavior
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## Contract checkpoints
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- alias exports must keep forwarding to canonical intelligence behavior
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- docs must keep the canonical intelligence 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 intelligence entrypoints
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- migration constraints prefer `proteomics_intelligence`
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- packaging or compatibility work needs a named alias for the intelligence
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owner
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## Route elsewhere when
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- the change alters recommendation, falsifier, or review semantics
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- the work adds behavior that is 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 intelligence imports or
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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 intelligence README and tests when behavior changes
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are 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 intelligence 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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intelligence package directly
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## Escalation route
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- route intelligence behavior changes to `bijux-proteomics-intelligence`
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- stop and review boundaries when package-local review 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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intelligence owner
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## Consumer impact signals
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- import-path or package-name changes are high-impact because downstream review
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code may depend on them directly
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- alias documentation changes should still be reviewed against the canonical
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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 knowledge curation, runtime delivery, or lab policy
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- this package does not create a second recommendation engine
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- this package does not replace the canonical intelligence 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 intelligence 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 intelligence package docs](https://bijux.io/bijux-proteomics/05-bijux-proteomics-intelligence/)
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- [Changelog](CHANGELOG.md)
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# proteomics-intelligence
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<!-- bijux-proteomics-badges:generated:start -->
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[](https://pypi.org/project/proteomics-intelligence/)
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[-0A7BBB)](https://pypi.org/project/proteomics-intelligence/)
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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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+
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[](https://pypi.org/project/proteomics-intelligence/)
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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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+
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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/05-bijux-proteomics-intelligence/)
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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-intelligence` is the compatibility alias for the canonical
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intelligence owner `bijux-proteomics-intelligence`.
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It is the install and import alias for bijux-proteomics-intelligence.
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Use this package when you want a shorter distribution and import name for the
|
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+
recommendation and review layer without creating a second owner.
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## Alias at a glance
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- Use `proteomics-intelligence` when a shorter name is useful for the
|
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recommendation and review surface, but canonical ownership must stay the
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+
same.
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- Start with the
|
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+
[canonical intelligence package docs](https://bijux.io/bijux-proteomics/05-bijux-proteomics-intelligence/)
|
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because this package only forwards into that owner surface.
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- Route recommendation behavior to `bijux-proteomics-intelligence`; keep this
|
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package focused on compatibility naming and import forwarding.
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## 0.3.8 Release Highlights
|
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- The alias now routes readers to the current intelligence handbook instead of
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sounding like a second analytical owner.
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- Documentation and release guidance now state the forwarding contract in
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direct, audit-friendly language.
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## Installation
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```bash
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pip install proteomics-intelligence
|
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```
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## Public APIs
|
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The alias forwards the canonical intelligence review surface through
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`proteomics_intelligence`:
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```python
|
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from proteomics_intelligence import falsifiers
|
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from proteomics_knowledge import EvidenceClaim
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claim = EvidenceClaim(
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claim_id="protein-claim:p11111",
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target_id="protein:p11111",
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statement="Protein PTM1 increased after treatment.",
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subject="P11111",
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relation="protein_abundance_change",
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object="up",
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direction="up",
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claim_type="biomarker",
|
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evidence_ids=["evidence:1"],
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status="supported",
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polarity="supporting",
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resolution_state="open",
|
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evidence_state="supported",
|
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+
)
|
|
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|
+
items = falsifiers.generate_falsifiers(claim)
|
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|
+
|
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|
+
assert items.summary.claim_count == 1
|
|
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|
+
assert items.entries[0].claim_id == claim.claim_id
|
|
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|
+
```
|
|
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|
+
|
|
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|
+
## Package identity
|
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+
|
|
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+
- Distribution name: `proteomics-intelligence`
|
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- Import root: `proteomics_intelligence`
|
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- Canonical owner package: `bijux-proteomics-intelligence`
|
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- Canonical owner import root: `bijux_proteomics_intelligence`
|
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|
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+
## Package boundaries
|
|
105
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+
|
|
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|
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- this package owns compatibility naming for the intelligence surface
|
|
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+
- recommendation logic, scientific support, and claim review remain owned by
|
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|
+
`bijux-proteomics-intelligence`
|
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+
- new review behavior must land in the canonical owner before alias exports
|
|
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+
change
|
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+
|
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|
+
## What this package must not do
|
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|
|
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|
+
- define a second recommendation or review-policy owner
|
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|
+
- drift away from canonical intelligence semantics
|
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|
+
- become an independent release surface for intelligence behavior
|
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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 intelligence behavior
|
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+
- docs must keep the canonical intelligence owner explicit
|
|
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|
+
- compatibility changes must stay covered by alias-package tests
|
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+
|
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124
|
+
## Choose this package when
|
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|
+
|
|
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+
- you need a shorter import and distribution name for intelligence entrypoints
|
|
127
|
+
- migration constraints prefer `proteomics_intelligence`
|
|
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|
+
- packaging or compatibility work needs a named alias for the intelligence
|
|
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|
+
owner
|
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|
+
|
|
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|
+
## Route elsewhere when
|
|
132
|
+
|
|
133
|
+
- the change alters recommendation, falsifier, or review semantics
|
|
134
|
+
- the work adds behavior that is not already owned by the canonical package
|
|
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|
+
- the alias would stop being forwarding-only
|
|
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|
+
|
|
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|
+
## Verification route
|
|
138
|
+
|
|
139
|
+
- run alias compatibility tests before changing intelligence imports or
|
|
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|
+
metadata
|
|
141
|
+
- review `docs/ARCHITECTURE.md`, `docs/BOUNDARIES.md`, and `docs/CONTRACTS.md`
|
|
142
|
+
when alias claims or routing language change
|
|
143
|
+
- validate the canonical intelligence README and tests when behavior changes
|
|
144
|
+
are proposed
|
|
145
|
+
|
|
146
|
+
## Review questions
|
|
147
|
+
|
|
148
|
+
- does the change preserve this package as an alias only
|
|
149
|
+
- is the canonical intelligence owner still explicit in docs and behavior
|
|
150
|
+
- would the same outcome remain correct if consumers imported the canonical
|
|
151
|
+
intelligence package directly
|
|
152
|
+
|
|
153
|
+
## Escalation route
|
|
154
|
+
|
|
155
|
+
- route intelligence behavior changes to `bijux-proteomics-intelligence`
|
|
156
|
+
- stop and review boundaries when package-local review semantics start
|
|
157
|
+
appearing
|
|
158
|
+
- escalate before release when routing or metadata drift could confuse the
|
|
159
|
+
intelligence owner
|
|
160
|
+
|
|
161
|
+
## Consumer impact signals
|
|
162
|
+
|
|
163
|
+
- import-path or package-name changes are high-impact because downstream review
|
|
164
|
+
code may depend on them directly
|
|
165
|
+
- alias documentation changes should still be reviewed against the canonical
|
|
166
|
+
intelligence owner
|
|
167
|
+
- wording-only clarifications carry lower release risk than routing or behavior
|
|
168
|
+
changes
|
|
169
|
+
|
|
170
|
+
## Explicit non-goals
|
|
171
|
+
|
|
172
|
+
- this package does not own knowledge curation, runtime delivery, or lab policy
|
|
173
|
+
- this package does not create a second recommendation engine
|
|
174
|
+
- this package does not replace the canonical intelligence release surface
|
|
175
|
+
|
|
176
|
+
## Documentation
|
|
177
|
+
|
|
178
|
+
- Release guidance lives in this `README.md`, this package `CHANGELOG.md`, and
|
|
179
|
+
package `docs/*.md` under the canonical intelligence owner surface.
|
|
180
|
+
- [Product architecture](https://bijux.io/bijux-proteomics/01-bijux-proteomics/foundation/product-architecture/)
|
|
181
|
+
- [Cross-package ownership](https://bijux.io/bijux-proteomics/01-bijux-proteomics/foundation/cross-package-ownership/)
|
|
182
|
+
- [Canonical intelligence package docs](https://bijux.io/bijux-proteomics/05-bijux-proteomics-intelligence/)
|
|
183
|
+
- [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-intelligence"
|
|
7
|
+
dynamic = ["version"]
|
|
8
|
+
description = "Install and import alias package for bijux-proteomics-intelligence."
|
|
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", "intelligence", "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-intelligence>=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/05-bijux-proteomics-intelligence/"
|
|
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-intelligence/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_intelligence/py.typed",
|
|
53
|
+
]
|
|
54
|
+
force-include = { "LICENSE" = "LICENSE", "NOTICE" = "NOTICE" }
|
|
55
|
+
|
|
56
|
+
[tool.hatch.build.targets.wheel]
|
|
57
|
+
packages = ["src/proteomics_intelligence"]
|
|
58
|
+
|
|
59
|
+
[tool.hatch.build.targets.wheel.package-data]
|
|
60
|
+
"proteomics_intelligence" = ["py.typed"]
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
|