proteomics-foundation 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_foundation-0.3.8/.gitignore +62 -0
- proteomics_foundation-0.3.8/CHANGELOG.md +22 -0
- proteomics_foundation-0.3.8/LICENSE +1 -0
- proteomics_foundation-0.3.8/NOTICE +1 -0
- proteomics_foundation-0.3.8/PKG-INFO +205 -0
- proteomics_foundation-0.3.8/README.md +173 -0
- proteomics_foundation-0.3.8/pyproject.toml +59 -0
- proteomics_foundation-0.3.8/src/proteomics_foundation/py.typed +1 -0
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# Bijux shared
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# Changelog
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All notable changes for `proteomics-foundation` 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-foundation` distribution as the short install and
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import alias for `bijux-proteomics-foundation`.
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- Added alias-package contract and README guidance that points short-name
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users back to the canonical foundation owner and its handbook.
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### Changed
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- Aligned the fallback version and canonical dependency floor 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 stays a forwarding layer instead of a
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second foundation surface.
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../../LICENSE
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../../NOTICE
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Metadata-Version: 2.4
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Name: proteomics-foundation
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Version: 0.3.8
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Summary: Install and import alias package for bijux-proteomics-foundation.
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Project-URL: Homepage, https://bijux.io/bijux-proteomics/
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Project-URL: Documentation, https://bijux.io/bijux-proteomics/03-bijux-proteomics-foundation/
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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-foundation/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,foundation,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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Description-Content-Type: text/markdown
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# proteomics-foundation
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<!-- bijux-proteomics-badges:generated:start -->
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[](https://pypi.org/project/proteomics-foundation/)
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[-0A7BBB)](https://pypi.org/project/proteomics-foundation/)
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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-foundation/)
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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/03-bijux-proteomics-foundation/)
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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-foundation` is the compatibility alias for the canonical foundation
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owner `bijux-proteomics-foundation`.
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It is the install and import alias for bijux-proteomics-foundation.
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Use this package when you want a shorter distribution and import name for the
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serialization, schema, and compatibility kernel without creating a second
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foundation owner.
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## Alias at a glance
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- Use `proteomics-foundation` when you want a shorter package name for the
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shared kernel without changing who owns the contracts.
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- Start with the
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[canonical foundation package docs](https://bijux.io/bijux-proteomics/03-bijux-proteomics-foundation/)
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because this package only forwards into that owner surface.
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- Route all schema, serialization, and compatibility behavior to
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`bijux-proteomics-foundation`; keep this package focused on compatibility
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naming.
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## 0.3.8 Release Highlights
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- The alias now routes readers to the current foundation handbook instead of
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reading like a second kernel surface.
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- Compatibility prose now makes the canonical ownership and forwarding-only
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contract explicit in the first screen.
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## Installation
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```bash
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pip install proteomics-foundation
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```
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## Public APIs
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The alias forwards the canonical foundation exports through
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`proteomics_foundation`:
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```python
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from proteomics_foundation import DocumentSchema, hash_payload, to_canonical_json
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schema = DocumentSchema(
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created_by="proteomics-foundation",
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document_kind="readme_example",
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package_name="proteomics-foundation",
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)
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payload = {
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"document_kind": schema.document_kind,
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"schema_version": schema.schema_version,
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}
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rendered = to_canonical_json(payload)
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digest = hash_payload(payload)
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assert '"readme_example"' in rendered
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assert digest
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```
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## Package identity
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- Distribution name: `proteomics-foundation`
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- Import root: `proteomics_foundation`
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- Canonical owner package: `bijux-proteomics-foundation`
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- Canonical owner import root: `bijux_proteomics_foundation`
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## Package boundaries
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- this package owns compatibility naming for the foundation surface
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- schema, serialization, compatibility, and outcome contracts remain owned by
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`bijux-proteomics-foundation`
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- new behavior must land in the canonical owner before alias exports change
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## What this package must not do
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- define a second foundation kernel
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- drift away from canonical serialization or compatibility behavior
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- become a separate owner for outcome or schema policy
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## Contract checkpoints
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- alias exports must forward to the canonical foundation package cleanly
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- docs must name the canonical owner explicitly
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- compatibility updates must stay covered by alias-package tests
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## Choose this package when
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- you want a shorter import and distribution name for foundation contracts
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- migration or ergonomics favor `proteomics_foundation`
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- compatibility packaging work needs a named alias for the foundation owner
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## Route elsewhere when
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- the change alters schema, serialization, compatibility, or outcome behavior
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- the work introduces exports that are not already owned by foundation
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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 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 foundation 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 a naming alias only
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- is the canonical foundation 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 kernel behavior changes to `bijux-proteomics-foundation`
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- stop and review alias boundaries when package-local semantics start appearing
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- escalate before release when import or metadata drift could confuse ownership
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## Consumer impact signals
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- import-path or package-name changes are high-impact because downstream code
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may depend on them directly
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- alias documentation changes should still be reviewed against the canonical
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foundation owner
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- wording-only clarifications carry lower release risk than routing or metadata
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changes
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## Explicit non-goals
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- this package does not own scientific workflow or evidence semantics
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- this package does not define runtime, intelligence, knowledge, or lab policy
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- this package does not replace the canonical foundation 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 foundation 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 foundation package docs](https://bijux.io/bijux-proteomics/03-bijux-proteomics-foundation/)
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- [Changelog](CHANGELOG.md)
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# proteomics-foundation
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<!-- bijux-proteomics-badges:generated:start -->
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[](https://pypi.org/project/proteomics-foundation/)
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[-0A7BBB)](https://pypi.org/project/proteomics-foundation/)
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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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9
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+
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[](https://pypi.org/project/proteomics-foundation/)
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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/03-bijux-proteomics-foundation/)
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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-foundation` is the compatibility alias for the canonical foundation
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owner `bijux-proteomics-foundation`.
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It is the install and import alias for bijux-proteomics-foundation.
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Use this package when you want a shorter distribution and import name for the
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serialization, schema, and compatibility kernel without creating a second
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foundation owner.
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## Alias at a glance
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- Use `proteomics-foundation` when you want a shorter package name for the
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shared kernel without changing who owns the contracts.
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- Start with the
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[canonical foundation package docs](https://bijux.io/bijux-proteomics/03-bijux-proteomics-foundation/)
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because this package only forwards into that owner surface.
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- Route all schema, serialization, and compatibility behavior to
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`bijux-proteomics-foundation`; keep this package focused on compatibility
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naming.
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## 0.3.8 Release Highlights
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- The alias now routes readers to the current foundation handbook instead of
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reading like a second kernel surface.
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- Compatibility prose now makes the canonical ownership and forwarding-only
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contract explicit in the first screen.
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## Installation
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```bash
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pip install proteomics-foundation
|
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```
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## Public APIs
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The alias forwards the canonical foundation exports through
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`proteomics_foundation`:
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```python
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from proteomics_foundation import DocumentSchema, hash_payload, to_canonical_json
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schema = DocumentSchema(
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created_by="proteomics-foundation",
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document_kind="readme_example",
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package_name="proteomics-foundation",
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)
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payload = {
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"document_kind": schema.document_kind,
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"schema_version": schema.schema_version,
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}
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rendered = to_canonical_json(payload)
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+
digest = hash_payload(payload)
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+
|
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+
assert '"readme_example"' in rendered
|
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+
assert digest
|
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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-foundation`
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+
- Import root: `proteomics_foundation`
|
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+
- Canonical owner package: `bijux-proteomics-foundation`
|
|
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+
- Canonical owner import root: `bijux_proteomics_foundation`
|
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+
|
|
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+
## Package boundaries
|
|
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|
+
|
|
101
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+
- this package owns compatibility naming for the foundation surface
|
|
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|
+
- schema, serialization, compatibility, and outcome contracts remain owned by
|
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|
+
`bijux-proteomics-foundation`
|
|
104
|
+
- new behavior must land in the canonical owner before alias exports change
|
|
105
|
+
|
|
106
|
+
## What this package must not do
|
|
107
|
+
|
|
108
|
+
- define a second foundation kernel
|
|
109
|
+
- drift away from canonical serialization or compatibility behavior
|
|
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|
+
- become a separate owner for outcome or schema policy
|
|
111
|
+
|
|
112
|
+
## Contract checkpoints
|
|
113
|
+
|
|
114
|
+
- alias exports must forward to the canonical foundation package cleanly
|
|
115
|
+
- docs must name the canonical owner explicitly
|
|
116
|
+
- compatibility updates must stay covered by alias-package tests
|
|
117
|
+
|
|
118
|
+
## Choose this package when
|
|
119
|
+
|
|
120
|
+
- you want a shorter import and distribution name for foundation contracts
|
|
121
|
+
- migration or ergonomics favor `proteomics_foundation`
|
|
122
|
+
- compatibility packaging work needs a named alias for the foundation owner
|
|
123
|
+
|
|
124
|
+
## Route elsewhere when
|
|
125
|
+
|
|
126
|
+
- the change alters schema, serialization, compatibility, or outcome behavior
|
|
127
|
+
- the work introduces exports that are not already owned by foundation
|
|
128
|
+
- the alias would stop being forwarding-only
|
|
129
|
+
|
|
130
|
+
## Verification route
|
|
131
|
+
|
|
132
|
+
- run alias compatibility tests before changing imports or metadata
|
|
133
|
+
- review `docs/ARCHITECTURE.md`, `docs/BOUNDARIES.md`, and `docs/CONTRACTS.md`
|
|
134
|
+
when alias claims or routing language change
|
|
135
|
+
- validate the canonical foundation README and tests when behavior changes are
|
|
136
|
+
proposed
|
|
137
|
+
|
|
138
|
+
## Review questions
|
|
139
|
+
|
|
140
|
+
- does the change preserve this package as a naming alias only
|
|
141
|
+
- is the canonical foundation owner still explicit in docs and behavior
|
|
142
|
+
- would the same outcome remain correct if consumers imported the canonical
|
|
143
|
+
package directly
|
|
144
|
+
|
|
145
|
+
## Escalation route
|
|
146
|
+
|
|
147
|
+
- route kernel behavior changes to `bijux-proteomics-foundation`
|
|
148
|
+
- stop and review alias boundaries when package-local semantics start appearing
|
|
149
|
+
- escalate before release when import or metadata drift could confuse ownership
|
|
150
|
+
|
|
151
|
+
## Consumer impact signals
|
|
152
|
+
|
|
153
|
+
- import-path or package-name changes are high-impact because downstream code
|
|
154
|
+
may depend on them directly
|
|
155
|
+
- alias documentation changes should still be reviewed against the canonical
|
|
156
|
+
foundation owner
|
|
157
|
+
- wording-only clarifications carry lower release risk than routing or metadata
|
|
158
|
+
changes
|
|
159
|
+
|
|
160
|
+
## Explicit non-goals
|
|
161
|
+
|
|
162
|
+
- this package does not own scientific workflow or evidence semantics
|
|
163
|
+
- this package does not define runtime, intelligence, knowledge, or lab policy
|
|
164
|
+
- this package does not replace the canonical foundation release surface
|
|
165
|
+
|
|
166
|
+
## Documentation
|
|
167
|
+
|
|
168
|
+
- Release guidance lives in this `README.md`, this package `CHANGELOG.md`, and
|
|
169
|
+
package `docs/*.md` under the canonical foundation owner surface.
|
|
170
|
+
- [Product architecture](https://bijux.io/bijux-proteomics/01-bijux-proteomics/foundation/product-architecture/)
|
|
171
|
+
- [Cross-package ownership](https://bijux.io/bijux-proteomics/01-bijux-proteomics/foundation/cross-package-ownership/)
|
|
172
|
+
- [Canonical foundation package docs](https://bijux.io/bijux-proteomics/03-bijux-proteomics-foundation/)
|
|
173
|
+
- [Changelog](CHANGELOG.md)
|
|
@@ -0,0 +1,59 @@
|
|
|
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-foundation"
|
|
7
|
+
dynamic = ["version"]
|
|
8
|
+
description = "Install and import alias package for bijux-proteomics-foundation."
|
|
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", "foundation", "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
|
+
]
|
|
32
|
+
|
|
33
|
+
[project.urls]
|
|
34
|
+
Homepage = "https://bijux.io/bijux-proteomics/"
|
|
35
|
+
Documentation = "https://bijux.io/bijux-proteomics/03-bijux-proteomics-foundation/"
|
|
36
|
+
Repository = "https://github.com/bijux/bijux-proteomics"
|
|
37
|
+
Issues = "https://github.com/bijux/bijux-proteomics/issues"
|
|
38
|
+
Changelog = "https://github.com/bijux/bijux-proteomics/blob/main/packages/proteomics-foundation/CHANGELOG.md"
|
|
39
|
+
Security = "https://github.com/bijux/bijux-proteomics/blob/main/SECURITY.md"
|
|
40
|
+
|
|
41
|
+
[tool.hatch.version]
|
|
42
|
+
source = "vcs"
|
|
43
|
+
tag-pattern = "^v(?P<version>.*)$"
|
|
44
|
+
fallback-version = "0.3.8"
|
|
45
|
+
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 }
|
|
46
|
+
|
|
47
|
+
[tool.hatch.build]
|
|
48
|
+
include = [
|
|
49
|
+
"README.md",
|
|
50
|
+
"CHANGELOG.md",
|
|
51
|
+
"src/proteomics_foundation/py.typed",
|
|
52
|
+
]
|
|
53
|
+
force-include = { "LICENSE" = "LICENSE", "NOTICE" = "NOTICE" }
|
|
54
|
+
|
|
55
|
+
[tool.hatch.build.targets.wheel]
|
|
56
|
+
packages = ["src/proteomics_foundation"]
|
|
57
|
+
|
|
58
|
+
[tool.hatch.build.targets.wheel.package-data]
|
|
59
|
+
"proteomics_foundation" = ["py.typed"]
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
|