bijux-proteomics-core 0.3.0__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.
- bijux_proteomics_core-0.3.0/.gitignore +155 -0
- bijux_proteomics_core-0.3.0/CHANGELOG.md +24 -0
- bijux_proteomics_core-0.3.0/PKG-INFO +77 -0
- bijux_proteomics_core-0.3.0/README.md +45 -0
- bijux_proteomics_core-0.3.0/docs/maintainer/pypi.md +14 -0
- bijux_proteomics_core-0.3.0/pyproject.toml +64 -0
- bijux_proteomics_core-0.3.0/src/bijux_proteomics/py.typed +1 -0
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# Changelog
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All notable changes for `bijux-proteomics-core` are recorded here.
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## 0.3.0 - 2026-04-06
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### Added
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- Package maintainer and ownership docs were added in canonical package-doc
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format.
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### Changed
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- Package metadata and release links now follow unified `bijux-proteomics`
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repository standards.
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## 0.1.0 - 2026-04-06
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### Added
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- Program domain models for targets, assays, review gates, and lifecycle
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transitions.
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- Domain invariant validation and identifier-contract checks.
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- Runtime adapter and CLI boundaries for package-level integration.
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Metadata-Version: 2.4
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Name: bijux-proteomics-core
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Version: 0.3.0
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Summary: Program models and execution adapters for Bijux Proteomics
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Project-URL: Homepage, https://bijux.io/bijux-proteomics/
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Project-URL: Documentation, https://bijux.io/bijux-proteomics/
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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/bijux-proteomics-core/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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Keywords: bioinformatics,domain-contracts,lifecycle,program-modeling,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: >=3.11
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Requires-Dist: bijux-proteomics-foundation>=0.3.0
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Requires-Dist: click>=8.1
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Requires-Dist: pydantic>=2.0.2
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Description-Content-Type: text/markdown
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# bijux-proteomics-core
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[](https://pypi.org/project/bijux-proteomics-core/)
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[-0A7BBB)](https://pypi.org/project/bijux-proteomics-core/)
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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/ci-bijux-proteomics-core.yml)
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[](https://github.com/bijux/bijux-proteomics)
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`bijux-proteomics-core` defines protein program entities, lifecycle transitions,
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review gates, assay requirements, and execution adapters used by the platform.
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If you need to understand what a program is, when it can advance, and which
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review constraints must hold before progression, this is the package boundary.
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## What this package owns
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- program, target, assay, and review domain models
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- lifecycle transition and stage eligibility logic
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- invariant validation for identifiers, gating, and scientific consistency
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- runtime adapter interfaces and CLI entrypoints for program workflows
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## What this package does not own
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- evidence bundle conflict resolution and trust scoring
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- candidate ranking and scenario evaluation policies
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- lab scheduling, outcome promotion, and rerun policies
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## Source map
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- [`src/bijux_proteomics/program_spec.py`](https://github.com/bijux/bijux-proteomics/blob/main/packages/bijux-proteomics-core/src/bijux_proteomics/program_spec.py) for core program entities
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- [`src/bijux_proteomics/repositories.py`](https://github.com/bijux/bijux-proteomics/blob/main/packages/bijux-proteomics-core/src/bijux_proteomics/repositories.py) for decision and gate repository protocols
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- [`src/bijux_proteomics/validation.py`](https://github.com/bijux/bijux-proteomics/blob/main/packages/bijux-proteomics-core/src/bijux_proteomics/validation.py) for domain invariant checks
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- [`src/bijux_proteomics/interfaces`](https://github.com/bijux/bijux-proteomics/tree/main/packages/bijux-proteomics-core/src/bijux_proteomics/interfaces) for package-facing CLI boundaries
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- [`tests`](https://github.com/bijux/bijux-proteomics/tree/main/packages/bijux-proteomics-core/tests) for executable package expectations
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## Read this next
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- [Architecture](https://github.com/bijux/bijux-proteomics/blob/main/packages/bijux-proteomics-core/docs/ARCHITECTURE.md)
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- [Boundaries](https://github.com/bijux/bijux-proteomics/blob/main/packages/bijux-proteomics-core/docs/BOUNDARIES.md)
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- [Contracts](https://github.com/bijux/bijux-proteomics/blob/main/packages/bijux-proteomics-core/docs/CONTRACTS.md)
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- [PyPI maintainer notes](https://github.com/bijux/bijux-proteomics/blob/main/packages/bijux-proteomics-core/docs/maintainer/pypi.md)
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## Primary entrypoint
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- console script: `bijux-proteomics`
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# bijux-proteomics-core
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[](https://pypi.org/project/bijux-proteomics-core/)
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[-0A7BBB)](https://pypi.org/project/bijux-proteomics-core/)
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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/ci-bijux-proteomics-core.yml)
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[](https://github.com/bijux/bijux-proteomics)
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`bijux-proteomics-core` defines protein program entities, lifecycle transitions,
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review gates, assay requirements, and execution adapters used by the platform.
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If you need to understand what a program is, when it can advance, and which
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review constraints must hold before progression, this is the package boundary.
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## What this package owns
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- program, target, assay, and review domain models
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- lifecycle transition and stage eligibility logic
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- invariant validation for identifiers, gating, and scientific consistency
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- runtime adapter interfaces and CLI entrypoints for program workflows
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## What this package does not own
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- evidence bundle conflict resolution and trust scoring
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- candidate ranking and scenario evaluation policies
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- lab scheduling, outcome promotion, and rerun policies
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## Source map
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- [`src/bijux_proteomics/program_spec.py`](https://github.com/bijux/bijux-proteomics/blob/main/packages/bijux-proteomics-core/src/bijux_proteomics/program_spec.py) for core program entities
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- [`src/bijux_proteomics/repositories.py`](https://github.com/bijux/bijux-proteomics/blob/main/packages/bijux-proteomics-core/src/bijux_proteomics/repositories.py) for decision and gate repository protocols
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- [`src/bijux_proteomics/validation.py`](https://github.com/bijux/bijux-proteomics/blob/main/packages/bijux-proteomics-core/src/bijux_proteomics/validation.py) for domain invariant checks
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- [`src/bijux_proteomics/interfaces`](https://github.com/bijux/bijux-proteomics/tree/main/packages/bijux-proteomics-core/src/bijux_proteomics/interfaces) for package-facing CLI boundaries
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- [`tests`](https://github.com/bijux/bijux-proteomics/tree/main/packages/bijux-proteomics-core/tests) for executable package expectations
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## Read this next
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- [Architecture](https://github.com/bijux/bijux-proteomics/blob/main/packages/bijux-proteomics-core/docs/ARCHITECTURE.md)
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- [Boundaries](https://github.com/bijux/bijux-proteomics/blob/main/packages/bijux-proteomics-core/docs/BOUNDARIES.md)
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- [Contracts](https://github.com/bijux/bijux-proteomics/blob/main/packages/bijux-proteomics-core/docs/CONTRACTS.md)
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- [PyPI maintainer notes](https://github.com/bijux/bijux-proteomics/blob/main/packages/bijux-proteomics-core/docs/maintainer/pypi.md)
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## Primary entrypoint
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- console script: `bijux-proteomics`
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# PyPI Maintainer Notes
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- package: `bijux-proteomics-core`
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- owner: Bijan Mousavi (`bijan@bijux.io`)
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- repository: `bijux/bijux-proteomics`
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Release checklist:
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1. Validate `README.md` and package docs describe current domain ownership.
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2. Confirm compatibility-sensitive model changes are reflected in tests.
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3. Run `make lint test quality security` from repository root.
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4. Verify `.github/workflows/publish-bijux-proteomics-core.yml` is configured for tag-triggered publish (`v*`) with trusted publishing permissions.
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5. Create and push the release tag (`vX.Y.Z`) after changelog and metadata are final.
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6. Confirm the publish workflow uploaded and released both wheel and sdist artifacts.
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@@ -0,0 +1,64 @@
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[build-system]
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requires = ["hatchling>=1.27.0,<1.28"]
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build-backend = "hatchling.build"
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[project]
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name = "bijux-proteomics-core"
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version = "0.3.0"
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description = "Program models and execution adapters for Bijux Proteomics"
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readme = "README.md"
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license = { text = "Apache-2.0" }
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requires-python = ">=3.11"
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authors = [{ name = "Bijan Mousavi", email = "bijan@bijux.io" }]
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maintainers = [{ name = "Bijan Mousavi", email = "bijan@bijux.io" }]
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keywords = [
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"proteomics",
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"program-modeling",
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"lifecycle",
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"bioinformatics",
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"domain-contracts",
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]
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classifiers = [
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"Development Status :: 3 - Alpha",
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"Intended Audience :: Science/Research",
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"Intended Audience :: Developers",
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"License :: OSI Approved :: Apache Software License",
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"Operating System :: OS Independent",
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"Programming Language :: Python :: 3",
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"Programming Language :: Python :: 3 :: Only",
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"Programming Language :: Python :: 3.11",
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"Programming Language :: Python :: 3.12",
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"Programming Language :: Python :: 3.13",
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"Programming Language :: Python :: 3.14",
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"Typing :: Typed",
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]
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dependencies = [
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"click>=8.1",
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"pydantic>=2.0.2",
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"bijux-proteomics-foundation>=0.3.0",
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]
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+
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[project.urls]
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Homepage = "https://bijux.io/bijux-proteomics/"
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Documentation = "https://bijux.io/bijux-proteomics/"
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Repository = "https://github.com/bijux/bijux-proteomics"
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Issues = "https://github.com/bijux/bijux-proteomics/issues"
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+
Changelog = "https://github.com/bijux/bijux-proteomics/blob/main/packages/bijux-proteomics-core/CHANGELOG.md"
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Security = "https://github.com/bijux/bijux-proteomics/blob/main/SECURITY.md"
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+
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[project.scripts]
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bijux-proteomics = "bijux_proteomics.interfaces.cli:cli"
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+
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[tool.hatch.build]
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include = [
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"README.md",
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"CHANGELOG.md",
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"docs/maintainer/pypi.md",
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"src/bijux_proteomics/py.typed",
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]
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[tool.hatch.build.targets.wheel]
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packages = ["src/bijux_proteomics"]
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+
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|
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[tool.hatch.build.targets.wheel.package-data]
|
|
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|
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"bijux_proteomics" = ["py.typed"]
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@@ -0,0 +1 @@
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1
|
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|