proteomics-runtime 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_runtime-0.3.8/.gitignore +62 -0
- proteomics_runtime-0.3.8/CHANGELOG.md +21 -0
- proteomics_runtime-0.3.8/LICENSE +1 -0
- proteomics_runtime-0.3.8/NOTICE +1 -0
- proteomics_runtime-0.3.8/PKG-INFO +203 -0
- proteomics_runtime-0.3.8/README.md +170 -0
- proteomics_runtime-0.3.8/pyproject.toml +63 -0
- proteomics_runtime-0.3.8/src/proteomics_runtime/py.typed +1 -0
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# Changelog
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All notable changes for `proteomics-runtime` 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-runtime` distribution as the short install and import
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alias for `bijux-proteomics-runtime`.
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- Added alias-package contract and README guidance that points runtime users to
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the canonical execution owner, rerun docs, and compatibility expectations.
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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, lazy imports, and
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clean-checkout runtime verification instead of implicit shim behavior.
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../../LICENSE
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../../NOTICE
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Metadata-Version: 2.4
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Name: proteomics-runtime
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Version: 0.3.8
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Summary: Install and import alias package for bijux-proteomics-runtime.
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Project-URL: Homepage, https://bijux.io/bijux-proteomics/
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Project-URL: Documentation, https://bijux.io/bijux-proteomics/09-bijux-proteomics-runtime/
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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-runtime/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,packaging,proteomics,runtime
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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-runtime<0.4.0,>=0.3.8
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Description-Content-Type: text/markdown
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# proteomics-runtime
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<!-- bijux-proteomics-badges:generated:start -->
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[](https://pypi.org/project/proteomics-runtime/)
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[-0A7BBB)](https://pypi.org/project/proteomics-runtime/)
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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-runtime/)
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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/09-bijux-proteomics-runtime/)
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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-runtime` is the compatibility alias for the canonical runtime owner
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`bijux-proteomics-runtime`.
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It is the install and import alias for bijux-proteomics-runtime.
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Use this package when you want a shorter runtime distribution and import name
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without creating a second execution owner.
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## Alias at a glance
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- Use `proteomics-runtime` when you want a shorter install or import name for
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canonical runtime entrypoints.
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- Start with the
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[canonical runtime package docs](https://bijux.io/bijux-proteomics/09-bijux-proteomics-runtime/)
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because this package only forwards into that execution owner.
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- Route all runtime behavior to `bijux-proteomics-runtime`; keep this package
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focused on compatibility naming and CLI/import forwarding.
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## 0.3.8 Release Highlights
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- The alias now sends readers straight to the live runtime handbook and CLI
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contract instead of looking like a second execution product.
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- Release guidance and boundary language now make the forwarding-only contract
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easier to review before publishing.
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## Installation
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```bash
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pip install proteomics-runtime
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```
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## Public APIs
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The alias forwards the canonical runtime execution surface through
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`proteomics_runtime`:
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```python
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from pathlib import Path
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from proteomics_runtime import AppConfig, create_app
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base_dir = Path("artifacts/readme-runtime-alias-app")
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app = create_app(AppConfig(base_dir=base_dir, docs_enabled=False))
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assert app.state.base_dir == base_dir
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assert app.docs_url is None
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```
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## Package identity
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- Distribution name: `proteomics-runtime`
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- Import root: `proteomics_runtime`
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- Canonical owner package: `bijux-proteomics-runtime`
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- Canonical owner import root: `bijux_proteomics_runtime`
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## Package boundaries
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- this package owns compatibility naming for runtime installs, imports, and CLI
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routing
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- execution planning, providers, state, and workflow delivery remain owned by
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`bijux-proteomics-runtime`
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- new runtime 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 runtime execution owner
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- fork provider, run-manager, or API behavior from the canonical runtime
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- become an independent migration target for runtime semantics
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## Contract checkpoints
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- alias exports must keep forwarding to canonical runtime behavior
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- docs must keep the canonical runtime 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 runtime entrypoints
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- migration constraints prefer `proteomics_runtime`
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- packaging or compatibility work needs a short runtime alias
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## Route elsewhere when
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- the change alters execution planning, providers, workflow delivery, or API
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semantics
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- the work introduces runtime behavior that is not already owned by the
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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 runtime imports or metadata
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- review `docs/ARCHITECTURE.md`, `docs/BOUNDARIES.md`, and `docs/CONTRACTS.md`
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when alias routing or claims change
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- validate the canonical runtime 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 runtime alias only
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- is the canonical runtime 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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runtime directly
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## Escalation route
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- route runtime behavior changes to `bijux-proteomics-runtime`
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- stop and review boundaries when the alias starts gaining package-local
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execution semantics
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- escalate before release when routing or metadata drift could confuse runtime
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ownership
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## Consumer impact signals
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- import-path, command-name, or package-name changes are high-impact because
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runtime automation 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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## Explicit non-goals
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- this package does not own scientific workflow semantics
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- this package does not define a second provider or execution policy layer
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- this package does not replace the canonical runtime 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 runtime 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 runtime package docs](https://bijux.io/bijux-proteomics/09-bijux-proteomics-runtime/)
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- [Changelog](CHANGELOG.md)
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# proteomics-runtime
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<!-- bijux-proteomics-badges:generated:start -->
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[](https://pypi.org/project/proteomics-runtime/)
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[-0A7BBB)](https://pypi.org/project/proteomics-runtime/)
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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-runtime/)
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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/09-bijux-proteomics-runtime/)
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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-runtime` is the compatibility alias for the canonical runtime owner
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`bijux-proteomics-runtime`.
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It is the install and import alias for bijux-proteomics-runtime.
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Use this package when you want a shorter runtime distribution and import name
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without creating a second execution owner.
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## Alias at a glance
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- Use `proteomics-runtime` when you want a shorter install or import name for
|
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canonical runtime entrypoints.
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- Start with the
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[canonical runtime package docs](https://bijux.io/bijux-proteomics/09-bijux-proteomics-runtime/)
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because this package only forwards into that execution owner.
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- Route all runtime behavior to `bijux-proteomics-runtime`; keep this package
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focused on compatibility naming and CLI/import forwarding.
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## 0.3.8 Release Highlights
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- The alias now sends readers straight to the live runtime handbook and CLI
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contract instead of looking like a second execution product.
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- Release guidance and boundary language now make the forwarding-only contract
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easier to review before publishing.
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## Installation
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```bash
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pip install proteomics-runtime
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```
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## Public APIs
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The alias forwards the canonical runtime execution surface through
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`proteomics_runtime`:
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```python
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from pathlib import Path
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from proteomics_runtime import AppConfig, create_app
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base_dir = Path("artifacts/readme-runtime-alias-app")
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app = create_app(AppConfig(base_dir=base_dir, docs_enabled=False))
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assert app.state.base_dir == base_dir
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assert app.docs_url is None
|
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```
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## Package identity
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+
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- Distribution name: `proteomics-runtime`
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- Import root: `proteomics_runtime`
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- Canonical owner package: `bijux-proteomics-runtime`
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- Canonical owner import root: `bijux_proteomics_runtime`
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+
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## Package boundaries
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+
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- this package owns compatibility naming for runtime installs, imports, and CLI
|
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+
routing
|
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+
- execution planning, providers, state, and workflow delivery remain owned by
|
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+
`bijux-proteomics-runtime`
|
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96
|
+
- new runtime 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 runtime execution owner
|
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+
- fork provider, run-manager, or API behavior from the canonical runtime
|
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|
+
- become an independent migration target for runtime semantics
|
|
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|
+
|
|
105
|
+
## Contract checkpoints
|
|
106
|
+
|
|
107
|
+
- alias exports must keep forwarding to canonical runtime behavior
|
|
108
|
+
- docs must keep the canonical runtime owner explicit
|
|
109
|
+
- compatibility changes must stay covered by alias-package tests
|
|
110
|
+
|
|
111
|
+
## Choose this package when
|
|
112
|
+
|
|
113
|
+
- you need a shorter import and distribution name for runtime entrypoints
|
|
114
|
+
- migration constraints prefer `proteomics_runtime`
|
|
115
|
+
- packaging or compatibility work needs a short runtime alias
|
|
116
|
+
|
|
117
|
+
## Route elsewhere when
|
|
118
|
+
|
|
119
|
+
- the change alters execution planning, providers, workflow delivery, or API
|
|
120
|
+
semantics
|
|
121
|
+
- the work introduces runtime behavior that is not already owned by the
|
|
122
|
+
canonical package
|
|
123
|
+
- the alias would stop being forwarding-only
|
|
124
|
+
|
|
125
|
+
## Verification route
|
|
126
|
+
|
|
127
|
+
- run alias compatibility tests before changing runtime imports or metadata
|
|
128
|
+
- review `docs/ARCHITECTURE.md`, `docs/BOUNDARIES.md`, and `docs/CONTRACTS.md`
|
|
129
|
+
when alias routing or claims change
|
|
130
|
+
- validate the canonical runtime README and tests when behavior changes are
|
|
131
|
+
proposed
|
|
132
|
+
|
|
133
|
+
## Review questions
|
|
134
|
+
|
|
135
|
+
- does the change preserve this package as a runtime alias only
|
|
136
|
+
- is the canonical runtime owner still explicit in docs and behavior
|
|
137
|
+
- would the same outcome remain correct if consumers imported the canonical
|
|
138
|
+
runtime directly
|
|
139
|
+
|
|
140
|
+
## Escalation route
|
|
141
|
+
|
|
142
|
+
- route runtime behavior changes to `bijux-proteomics-runtime`
|
|
143
|
+
- stop and review boundaries when the alias starts gaining package-local
|
|
144
|
+
execution semantics
|
|
145
|
+
- escalate before release when routing or metadata drift could confuse runtime
|
|
146
|
+
ownership
|
|
147
|
+
|
|
148
|
+
## Consumer impact signals
|
|
149
|
+
|
|
150
|
+
- import-path, command-name, or package-name changes are high-impact because
|
|
151
|
+
runtime automation may depend on them directly
|
|
152
|
+
- alias documentation changes should still be reviewed against the canonical
|
|
153
|
+
runtime owner
|
|
154
|
+
- wording-only clarifications carry lower release risk than routing or behavior
|
|
155
|
+
changes
|
|
156
|
+
|
|
157
|
+
## Explicit non-goals
|
|
158
|
+
|
|
159
|
+
- this package does not own scientific workflow semantics
|
|
160
|
+
- this package does not define a second provider or execution policy layer
|
|
161
|
+
- this package does not replace the canonical runtime release surface
|
|
162
|
+
|
|
163
|
+
## Documentation
|
|
164
|
+
|
|
165
|
+
- Release guidance lives in this `README.md`, this package `CHANGELOG.md`, and
|
|
166
|
+
package `docs/*.md` under the canonical runtime owner surface.
|
|
167
|
+
- [Product architecture](https://bijux.io/bijux-proteomics/01-bijux-proteomics/foundation/product-architecture/)
|
|
168
|
+
- [Cross-package ownership](https://bijux.io/bijux-proteomics/01-bijux-proteomics/foundation/cross-package-ownership/)
|
|
169
|
+
- [Canonical runtime package docs](https://bijux.io/bijux-proteomics/09-bijux-proteomics-runtime/)
|
|
170
|
+
- [Changelog](CHANGELOG.md)
|
|
@@ -0,0 +1,63 @@
|
|
|
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-runtime"
|
|
7
|
+
dynamic = ["version"]
|
|
8
|
+
description = "Install and import alias package for bijux-proteomics-runtime."
|
|
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", "runtime", "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-runtime>=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/09-bijux-proteomics-runtime/"
|
|
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-runtime/CHANGELOG.md"
|
|
40
|
+
Security = "https://github.com/bijux/bijux-proteomics/blob/main/SECURITY.md"
|
|
41
|
+
|
|
42
|
+
[project.scripts]
|
|
43
|
+
proteomics-runtime = "proteomics_runtime.cli:main"
|
|
44
|
+
|
|
45
|
+
[tool.hatch.version]
|
|
46
|
+
source = "vcs"
|
|
47
|
+
tag-pattern = "^v(?P<version>.*)$"
|
|
48
|
+
fallback-version = "0.3.8"
|
|
49
|
+
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 }
|
|
50
|
+
|
|
51
|
+
[tool.hatch.build]
|
|
52
|
+
include = [
|
|
53
|
+
"README.md",
|
|
54
|
+
"CHANGELOG.md",
|
|
55
|
+
"src/proteomics_runtime/py.typed",
|
|
56
|
+
]
|
|
57
|
+
force-include = { "LICENSE" = "LICENSE", "NOTICE" = "NOTICE" }
|
|
58
|
+
|
|
59
|
+
[tool.hatch.build.targets.wheel]
|
|
60
|
+
packages = ["src/proteomics_runtime"]
|
|
61
|
+
|
|
62
|
+
[tool.hatch.build.targets.wheel.package-data]
|
|
63
|
+
"proteomics_runtime" = ["py.typed"]
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
|