proteomics-core 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_core-0.3.8/.gitignore +62 -0
- proteomics_core-0.3.8/CHANGELOG.md +22 -0
- proteomics_core-0.3.8/LICENSE +1 -0
- proteomics_core-0.3.8/NOTICE +1 -0
- proteomics_core-0.3.8/PKG-INFO +192 -0
- proteomics_core-0.3.8/README.md +159 -0
- proteomics_core-0.3.8/pyproject.toml +63 -0
- proteomics_core-0.3.8/src/proteomics_core/py.typed +1 -0
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# Changelog
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All notable changes for `proteomics-core` 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-core` distribution as the short install and import
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alias for `bijux-proteomics-core`.
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- Added alias-package contract and architecture docs that explain why the
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short distribution is a forwarding surface rather than a second 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, lazy imports, and
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clean-checkout verification so the short name stays a thin surface over the
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canonical core package.
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../../LICENSE
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../../NOTICE
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Metadata-Version: 2.4
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Name: proteomics-core
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Version: 0.3.8
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Summary: Install and import alias package for bijux-proteomics-core.
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Project-URL: Homepage, https://bijux.io/bijux-proteomics/
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Project-URL: Documentation, https://bijux.io/bijux-proteomics/04-bijux-proteomics-core/
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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-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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License-File: LICENSE
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License-File: NOTICE
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Keywords: bioinformatics,compatibility,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-core<0.4.0,>=0.3.8
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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-core
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<!-- bijux-proteomics-badges:generated:start -->
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[](https://pypi.org/project/proteomics-core/)
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[-0A7BBB)](https://pypi.org/project/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/verify.yml?query=branch%3Amain)
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[](https://github.com/bijux/bijux-proteomics)
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[](https://pypi.org/project/proteomics-core/)
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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/04-bijux-proteomics-core/)
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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-core` is the compatibility alias for the canonical core owner
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`bijux-proteomics-core`.
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It is the install and import alias for bijux-proteomics-core.
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Use this package when you want a shorter distribution and import name while
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keeping the same scientific processing owner and behavior.
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## Alias at a glance
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- Use `proteomics-core` when you need a family-specific short name without
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changing who owns the scientific surface.
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- Start with the
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[canonical core package docs](https://bijux.io/bijux-proteomics/04-bijux-proteomics-core/)
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because every export in this package forwards into that owner surface.
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- Route behavior changes to `bijux-proteomics-core`; keep this package focused
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on compatibility naming and import forwarding.
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## 0.3.8 Release Highlights
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- The alias now points explicitly at the current core handbook and stops
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sounding like an independent scientific package.
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- Release guidance, boundaries, and verification text now make the forwarding
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contract easier to audit before publication.
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## Installation
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```bash
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pip install proteomics-core
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```
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## Public APIs
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The alias forwards core scientific imports through `proteomics_core`:
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```python
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from proteomics_core import parse_fasta_document
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report = parse_fasta_document(">sp|P11111|PTM1 Protein 1\nMPEPTIDEK\n")
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assert report.total_records == 1
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assert len(report.accepted_records) == 1
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assert report.accepted_records[0].canonical_accession == "P11111"
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```
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## Package identity
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- Distribution name: `proteomics-core`
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- Import root: `proteomics_core`
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- Canonical owner package: `bijux-proteomics-core`
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- Canonical owner import root: `bijux_proteomics`
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## Package boundaries
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- this package owns compatibility naming for the core package surface
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- all scientific semantics remain owned by `bijux-proteomics-core`
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- new exports must appear in the canonical owner before they appear here
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## What this package must not do
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- invent independent core behavior or documentation claims
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- fork canonical scientific or workflow semantics
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- become a second release-policy owner for the core surface
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## Contract checkpoints
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- forwarded imports must keep canonical behavior without semantic drift
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- docs must keep the canonical owner explicit
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- alias compatibility tests must stay green when exports or packaging change
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## Choose this package when
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- you need a shorter core-specific distribution name than the canonical owner
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- migration constraints prefer `proteomics_core` imports
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- packaging or compatibility work needs a named alias for the core owner
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## Route elsewhere when
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- the change alters scientific parsing, review, or workflow behavior
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- the work introduces exports that are not already owned by core
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- the package would stop being a forwarding alias
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## Verification route
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- run alias compatibility tests before changing imports or packaging metadata
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- review `docs/ARCHITECTURE.md`, `docs/BOUNDARIES.md`, and `docs/CONTRACTS.md`
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when alias claims or boundaries shift
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- validate the canonical core README and tests when behavior changes are being
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proposed
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## Review questions
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- does the change preserve this package as a compatibility alias only
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- is the canonical owner still named clearly for maintainers and consumers
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- would the same behavior remain correct if consumers imported core directly
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## Escalation route
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- route scientific behavior changes to `bijux-proteomics-core`
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- stop and review boundaries when the alias starts gaining package-local logic
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- escalate before release when package metadata or import routing could confuse
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core 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 import this alias directly
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- alias contract wording changes should still be reviewed against canonical core
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- documentation-only clarifications carry lower release risk than routing or
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metadata changes
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## Explicit non-goals
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- this package does not own assay-processing or workflow 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 core 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 core 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 core package docs](https://bijux.io/bijux-proteomics/04-bijux-proteomics-core/)
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- [Changelog](CHANGELOG.md)
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# proteomics-core
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<!-- bijux-proteomics-badges:generated:start -->
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[](https://pypi.org/project/proteomics-core/)
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[-0A7BBB)](https://pypi.org/project/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/verify.yml?query=branch%3Amain)
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[](https://github.com/bijux/bijux-proteomics)
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[](https://pypi.org/project/proteomics-core/)
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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/04-bijux-proteomics-core/)
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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-core` is the compatibility alias for the canonical core owner
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`bijux-proteomics-core`.
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It is the install and import alias for bijux-proteomics-core.
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Use this package when you want a shorter distribution and import name while
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keeping the same scientific processing owner and behavior.
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## Alias at a glance
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- Use `proteomics-core` when you need a family-specific short name without
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changing who owns the scientific surface.
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- Start with the
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[canonical core package docs](https://bijux.io/bijux-proteomics/04-bijux-proteomics-core/)
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because every export in this package forwards into that owner surface.
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- Route behavior changes to `bijux-proteomics-core`; keep this package focused
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on compatibility naming and import forwarding.
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## 0.3.8 Release Highlights
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- The alias now points explicitly at the current core handbook and stops
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sounding like an independent scientific package.
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- Release guidance, boundaries, and verification text now make the forwarding
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contract easier to audit before publication.
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## Installation
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```bash
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pip install proteomics-core
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```
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## Public APIs
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The alias forwards core scientific imports through `proteomics_core`:
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```python
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from proteomics_core import parse_fasta_document
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report = parse_fasta_document(">sp|P11111|PTM1 Protein 1\nMPEPTIDEK\n")
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assert report.total_records == 1
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assert len(report.accepted_records) == 1
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assert report.accepted_records[0].canonical_accession == "P11111"
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```
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## Package identity
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- Distribution name: `proteomics-core`
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- Import root: `proteomics_core`
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- Canonical owner package: `bijux-proteomics-core`
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- Canonical owner import root: `bijux_proteomics`
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+
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## Package boundaries
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+
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- this package owns compatibility naming for the core package surface
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- all scientific semantics remain owned by `bijux-proteomics-core`
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- new exports must appear in the canonical owner before they appear here
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+
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## What this package must not do
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+
|
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- invent independent core behavior or documentation claims
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+
- fork canonical scientific or workflow semantics
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- become a second release-policy owner for the core surface
|
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+
|
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+
## Contract checkpoints
|
|
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|
+
|
|
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|
+
- forwarded imports must keep canonical behavior without semantic drift
|
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|
+
- docs must keep the canonical owner explicit
|
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|
+
- alias compatibility tests must stay green when exports or packaging change
|
|
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|
+
|
|
105
|
+
## Choose this package when
|
|
106
|
+
|
|
107
|
+
- you need a shorter core-specific distribution name than the canonical owner
|
|
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|
+
- migration constraints prefer `proteomics_core` imports
|
|
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|
+
- packaging or compatibility work needs a named alias for the core owner
|
|
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|
+
|
|
111
|
+
## Route elsewhere when
|
|
112
|
+
|
|
113
|
+
- the change alters scientific parsing, review, or workflow behavior
|
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|
+
- the work introduces exports that are not already owned by core
|
|
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|
+
- the package would stop being a forwarding alias
|
|
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|
+
|
|
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|
+
## Verification route
|
|
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|
+
|
|
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|
+
- run alias compatibility tests before changing imports or packaging metadata
|
|
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|
+
- review `docs/ARCHITECTURE.md`, `docs/BOUNDARIES.md`, and `docs/CONTRACTS.md`
|
|
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|
+
when alias claims or boundaries shift
|
|
122
|
+
- validate the canonical core README and tests when behavior changes are being
|
|
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|
+
proposed
|
|
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|
+
|
|
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|
+
## Review questions
|
|
126
|
+
|
|
127
|
+
- does the change preserve this package as a compatibility alias only
|
|
128
|
+
- is the canonical owner still named clearly for maintainers and consumers
|
|
129
|
+
- would the same behavior remain correct if consumers imported core directly
|
|
130
|
+
|
|
131
|
+
## Escalation route
|
|
132
|
+
|
|
133
|
+
- route scientific behavior changes to `bijux-proteomics-core`
|
|
134
|
+
- stop and review boundaries when the alias starts gaining package-local logic
|
|
135
|
+
- escalate before release when package metadata or import routing could confuse
|
|
136
|
+
core ownership
|
|
137
|
+
|
|
138
|
+
## Consumer impact signals
|
|
139
|
+
|
|
140
|
+
- import-path or package-name changes are high-impact because downstream code
|
|
141
|
+
may import this alias directly
|
|
142
|
+
- alias contract wording changes should still be reviewed against canonical core
|
|
143
|
+
- documentation-only clarifications carry lower release risk than routing or
|
|
144
|
+
metadata changes
|
|
145
|
+
|
|
146
|
+
## Explicit non-goals
|
|
147
|
+
|
|
148
|
+
- this package does not own assay-processing or workflow semantics
|
|
149
|
+
- this package does not define runtime, intelligence, knowledge, or lab policy
|
|
150
|
+
- this package does not replace the canonical core release surface
|
|
151
|
+
|
|
152
|
+
## Documentation
|
|
153
|
+
|
|
154
|
+
- Release guidance lives in this `README.md`, this package `CHANGELOG.md`, and
|
|
155
|
+
package `docs/*.md` under the canonical core owner surface.
|
|
156
|
+
- [Product architecture](https://bijux.io/bijux-proteomics/01-bijux-proteomics/foundation/product-architecture/)
|
|
157
|
+
- [Cross-package ownership](https://bijux.io/bijux-proteomics/01-bijux-proteomics/foundation/cross-package-ownership/)
|
|
158
|
+
- [Canonical core package docs](https://bijux.io/bijux-proteomics/04-bijux-proteomics-core/)
|
|
159
|
+
- [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-core"
|
|
7
|
+
dynamic = ["version"]
|
|
8
|
+
description = "Install and import alias package for bijux-proteomics-core."
|
|
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", "bioinformatics", "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-core>=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/04-bijux-proteomics-core/"
|
|
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-core/CHANGELOG.md"
|
|
40
|
+
Security = "https://github.com/bijux/bijux-proteomics/blob/main/SECURITY.md"
|
|
41
|
+
|
|
42
|
+
[project.scripts]
|
|
43
|
+
proteomics-core = "proteomics_core.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_core/py.typed",
|
|
56
|
+
]
|
|
57
|
+
force-include = { "LICENSE" = "LICENSE", "NOTICE" = "NOTICE" }
|
|
58
|
+
|
|
59
|
+
[tool.hatch.build.targets.wheel]
|
|
60
|
+
packages = ["src/proteomics_core"]
|
|
61
|
+
|
|
62
|
+
[tool.hatch.build.targets.wheel.package-data]
|
|
63
|
+
"proteomics_core" = ["py.typed"]
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
|