bijux-proteomics 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.
- bijux_proteomics-0.3.8/.gitignore +62 -0
- bijux_proteomics-0.3.8/CHANGELOG.md +23 -0
- bijux_proteomics-0.3.8/LICENSE +1 -0
- bijux_proteomics-0.3.8/NOTICE +1 -0
- bijux_proteomics-0.3.8/PKG-INFO +206 -0
- bijux_proteomics-0.3.8/README.md +174 -0
- bijux_proteomics-0.3.8/pyproject.toml +62 -0
- bijux_proteomics-0.3.8/src/bijux_proteomics_alias/py.typed +1 -0
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# Bijux shared
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# Changelog
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All notable changes for `bijux-proteomics` 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 `bijux-proteomics` distribution as an install and command alias for
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`bijux-proteomics-core`.
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- Added explicit package-contract and README guidance that points users from
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the top-level alias back to the canonical core owner and the numbered
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handbook routes.
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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 alias imports and command entrypoints through governed compatibility
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helpers with lazy loading and clean-checkout compatibility coverage instead
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of root 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: bijux-proteomics
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Version: 0.3.8
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Summary: Install and command 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/bijux-proteomics/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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Description-Content-Type: text/markdown
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# bijux-proteomics
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<!-- bijux-proteomics-badges:generated:start -->
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[](https://pypi.org/project/bijux-proteomics/)
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[-0A7BBB)](https://pypi.org/project/bijux-proteomics/)
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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/bijux-proteomics/)
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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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`bijux-proteomics` is the distribution-name alias for the canonical core owner
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`bijux-proteomics-core`.
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It is the install and command alias for bijux-proteomics-core, while the
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public Python import surface remains the canonical `bijux_proteomics`
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namespace shipped by core.
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Use this package when you need the flagship install name on PyPI while keeping
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all scientific behavior owned by the canonical core package.
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## Alias at a glance
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- Use `bijux-proteomics` when packaging, documentation, or deployment needs
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the flagship distribution name rather than the canonical owner package name.
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- Start scientific feature discovery from the
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[canonical core package docs](https://bijux.io/bijux-proteomics/04-bijux-proteomics-core/)
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because this package forwards into the core owner surface.
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- Route all new scientific behavior to `bijux-proteomics-core`; keep this
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package focused on install-name compatibility and publication metadata.
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## 0.3.8 Release Highlights
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- The flagship distribution name now routes readers directly to the current
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core scientific surface instead of implying a second owner package.
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- The alias follows the `0.3.8` release line while the canonical
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`bijux-proteomics-core` package continues to own FASTA, digestion, search,
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quantification, PTM, QC, and workflow-planning behavior.
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## Installation
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```bash
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pip install bijux-proteomics
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```
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## Public APIs
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The distribution alias installs the canonical core package, so the public
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Python surface remains `bijux_proteomics`:
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```python
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from bijux_proteomics 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: `bijux-proteomics`
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- Import root: `bijux_proteomics`
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- Private metadata helper: `bijux_proteomics_alias`
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- Canonical owner package: `bijux-proteomics-core`
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- Canonical owner docs: `packages/bijux-proteomics-core/README.md`
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## Package boundaries
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- this package owns distribution-name compatibility and publication metadata
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- scientific parsing, quantification, review, and workflow logic remain owned
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by `bijux-proteomics-core`
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- new behavior must land in the canonical owner before this alias surface
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changes
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## What this package must not do
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- introduce independent scientific semantics or workflow logic
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- fork the canonical `bijux_proteomics` import surface
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- become a second release-policy owner for the core package
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## Contract checkpoints
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- the install alias must continue to resolve to the canonical core owner
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- docs must state clearly that `bijux-proteomics-core` owns the behavior
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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 want the flagship `bijux-proteomics` distribution name on PyPI
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- deployment tooling depends on the canonical install alias rather than the
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owner package name
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- packaging or documentation work needs the install alias without changing core
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behavior
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## Route elsewhere when
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- the change alters scientific parsing, review, workflow, or result semantics
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- the work needs a new Python export that is not already owned by core
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- the change would make this package more than a distribution alias
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## Verification route
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- run the alias compatibility tests before treating install-name changes as
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safe
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- review `docs/ARCHITECTURE.md`, `docs/BOUNDARIES.md`, and `docs/CONTRACTS.md`
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when the alias claims shift
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- check the canonical core README and tests when the proposed change touches
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user-facing scientific behavior
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## Review questions
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- does the change preserve this package as a distribution alias only
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- is the canonical owner still explicit in both docs and behavior
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- would the change still make sense if all scientific logic stayed in core
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## Escalation route
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- route the work to `bijux-proteomics-core` when any scientific behavior needs
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to change
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- stop and review alias boundaries when the proposal starts adding
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- escalate before release when dependency or metadata changes could confuse
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## Consumer impact signals
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- treat install-name, dependency, or metadata changes as high-impact because
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they affect package resolution
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- expect review from core owners when alias docs or expectations shift
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- expect a smaller release burden when the change only clarifies routing or
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compatibility wording
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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 owner surface.
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- [Product overview](https://bijux.io/bijux-proteomics/01-bijux-proteomics/foundation/product-overview/)
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- [Workflow families](https://bijux.io/bijux-proteomics/01-bijux-proteomics/foundation/workflow-families/)
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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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- [Execution overview](https://bijux.io/bijux-proteomics/09-bijux-proteomics-runtime/execution-overview/)
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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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# bijux-proteomics
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<!-- bijux-proteomics-badges:generated:start -->
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[](https://pypi.org/project/bijux-proteomics/)
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[-0A7BBB)](https://pypi.org/project/bijux-proteomics/)
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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/bijux-proteomics/)
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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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`bijux-proteomics` is the distribution-name alias for the canonical core owner
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`bijux-proteomics-core`.
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It is the install and command alias for bijux-proteomics-core, while the
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public Python import surface remains the canonical `bijux_proteomics`
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namespace shipped by core.
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Use this package when you need the flagship install name on PyPI while keeping
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all scientific behavior owned by the canonical core package.
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## Alias at a glance
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- Use `bijux-proteomics` when packaging, documentation, or deployment needs
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the flagship distribution name rather than the canonical owner package name.
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- Start scientific feature discovery from the
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[canonical core package docs](https://bijux.io/bijux-proteomics/04-bijux-proteomics-core/)
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because this package forwards into the core owner surface.
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- Route all new scientific behavior to `bijux-proteomics-core`; keep this
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package focused on install-name compatibility and publication metadata.
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## 0.3.8 Release Highlights
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- The flagship distribution name now routes readers directly to the current
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core scientific surface instead of implying a second owner package.
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- The alias follows the `0.3.8` release line while the canonical
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`bijux-proteomics-core` package continues to own FASTA, digestion, search,
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quantification, PTM, QC, and workflow-planning behavior.
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## Installation
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```bash
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pip install bijux-proteomics
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```
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## Public APIs
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The distribution alias installs the canonical core package, so the public
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Python surface remains `bijux_proteomics`:
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```python
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from bijux_proteomics 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: `bijux-proteomics`
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- Import root: `bijux_proteomics`
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- Private metadata helper: `bijux_proteomics_alias`
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- Canonical owner package: `bijux-proteomics-core`
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- Canonical owner docs: `packages/bijux-proteomics-core/README.md`
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## Package boundaries
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- this package owns distribution-name compatibility and publication metadata
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- scientific parsing, quantification, review, and workflow logic remain owned
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by `bijux-proteomics-core`
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- new behavior must land in the canonical owner before this alias surface
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changes
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## What this package must not do
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- introduce independent scientific semantics or workflow logic
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- fork the canonical `bijux_proteomics` import surface
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- become a second release-policy owner for the core package
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## Contract checkpoints
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- the install alias must continue to resolve to the canonical core owner
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- docs must state clearly that `bijux-proteomics-core` owns the behavior
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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 want the flagship `bijux-proteomics` distribution name on PyPI
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- deployment tooling depends on the canonical install alias rather than the
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owner package name
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- packaging or documentation work needs the install alias without changing core
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behavior
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## Route elsewhere when
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- the change alters scientific parsing, review, workflow, or result semantics
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- the work needs a new Python export that is not already owned by core
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- the change would make this package more than a distribution alias
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## Verification route
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- run the alias compatibility tests before treating install-name changes as
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safe
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- review `docs/ARCHITECTURE.md`, `docs/BOUNDARIES.md`, and `docs/CONTRACTS.md`
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when the alias claims shift
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- check the canonical core README and tests when the proposed change touches
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user-facing scientific behavior
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## Review questions
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- does the change preserve this package as a distribution alias only
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- is the canonical owner still explicit in both docs and behavior
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- would the change still make sense if all scientific logic stayed in core
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## Escalation route
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- route the work to `bijux-proteomics-core` when any scientific behavior needs
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to change
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- stop and review alias boundaries when the proposal starts adding
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package-specific behavior
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- escalate before release when dependency or metadata changes could confuse
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canonical owner selection
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## Consumer impact signals
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- treat install-name, dependency, or metadata changes as high-impact because
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they affect package resolution
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- expect review from core owners when alias docs or expectations shift
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- expect a smaller release burden when the change only clarifies routing or
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compatibility wording
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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 owner surface.
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- [Product overview](https://bijux.io/bijux-proteomics/01-bijux-proteomics/foundation/product-overview/)
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- [Workflow families](https://bijux.io/bijux-proteomics/01-bijux-proteomics/foundation/workflow-families/)
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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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- [Execution overview](https://bijux.io/bijux-proteomics/09-bijux-proteomics-runtime/execution-overview/)
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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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[build-system]
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requires = ["hatchling>=1.27.0,<1.31", "hatch-vcs>=0.4.0,<1.0"]
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build-backend = "hatchling.build"
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[project]
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name = "bijux-proteomics"
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dynamic = ["version"]
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description = "Install and command alias package for bijux-proteomics-core."
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readme = "README.md"
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license = { text = "Apache-2.0" }
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requires-python = ">=3.11,<4"
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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 = ["proteomics", "bioinformatics", "compatibility", "packaging"]
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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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"bijux-proteomics-core>=0.3.8,<0.4.0",
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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/04-bijux-proteomics-core/"
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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/CHANGELOG.md"
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Security = "https://github.com/bijux/bijux-proteomics/blob/main/SECURITY.md"
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[project.scripts]
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bijux-proteomics = "bijux_proteomics.interfaces.cli:cli"
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[tool.hatch.version]
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source = "vcs"
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tag-pattern = "^v(?P<version>.*)$"
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fallback-version = "0.3.8"
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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 }
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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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"src/bijux_proteomics_alias/py.typed",
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]
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force-include = { "LICENSE" = "LICENSE", "NOTICE" = "NOTICE" }
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[tool.hatch.build.targets.wheel]
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packages = ["src/bijux_proteomics_alias"]
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[tool.hatch.build.targets.wheel.package-data]
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"bijux_proteomics_alias" = ["py.typed"]
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