proteomics 0.3.8__py3-none-any.whl
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.
- LICENSE +192 -0
- NOTICE +3 -0
- proteomics/__init__.py +42 -0
- proteomics/__main__.py +8 -0
- proteomics/cli.py +19 -0
- proteomics/py.typed +1 -0
- proteomics-0.3.8.dist-info/METADATA +195 -0
- proteomics-0.3.8.dist-info/RECORD +12 -0
- proteomics-0.3.8.dist-info/WHEEL +4 -0
- proteomics-0.3.8.dist-info/entry_points.txt +2 -0
- proteomics-0.3.8.dist-info/licenses/LICENSE +192 -0
- proteomics-0.3.8.dist-info/licenses/NOTICE +3 -0
LICENSE
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END OF TERMS AND CONDITIONS
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APPENDIX: How to apply the Apache License to your work.
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Copyright 2026 Bijan Mousavi <bijan@bijux.io>
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Licensed under the Apache License, Version 2.0 (the "License");
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See the License for the specific language governing permissions and
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limitations under the License.
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NOTICE
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proteomics/__init__.py
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"""Compatibility alias module for bijux-proteomics-core."""
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from __future__ import annotations
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from importlib import import_module
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from typing import Any
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from bijux_proteomics_foundation._package_aliases import (
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alias_package_version,
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canonical_module_dir,
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install_import_aliases,
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)
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_ALIAS_PACKAGE = "proteomics"
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_CANONICAL_PACKAGE = "bijux_proteomics"
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_LOCAL_SUBMODULES = frozenset({"__main__", "cli"})
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install_import_aliases(
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alias_package=_ALIAS_PACKAGE,
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canonical_package=_CANONICAL_PACKAGE,
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local_submodules=_LOCAL_SUBMODULES,
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)
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__version__ = alias_package_version(_ALIAS_PACKAGE)
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__all__ = ["__version__"]
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def _canonical_module() -> Any:
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return import_module(_CANONICAL_PACKAGE)
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def __getattr__(name: str) -> Any:
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"""Forward top-level compatibility lookups to the canonical core package."""
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return getattr(_canonical_module(), name)
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def __dir__() -> list[str]:
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"""Expose canonical core attributes in interactive discovery."""
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return canonical_module_dir(globals(), _CANONICAL_PACKAGE)
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proteomics/__main__.py
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proteomics/cli.py
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"""Compatibility CLI entrypoint for the `proteomics` distribution."""
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from __future__ import annotations
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from collections.abc import Sequence
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from bijux_proteomics_foundation._package_aliases import dispatch_alias_entrypoint
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__all__ = ["main"]
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def main(argv: Sequence[str] | None = None) -> int:
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"""Run the canonical core CLI with the alias package name."""
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return dispatch_alias_entrypoint(
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canonical_module="bijux_proteomics.interfaces.cli",
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attribute_name="cli",
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prog_name="proteomics",
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argv=argv,
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)
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proteomics/py.typed
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Metadata-Version: 2.4
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Name: proteomics
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Version: 0.3.8
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Summary: Install, import, and CLI 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/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
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<!-- bijux-proteomics-badges:generated:start -->
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[](https://pypi.org/project/proteomics/)
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[-0A7BBB)](https://pypi.org/project/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/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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`proteomics` is the short-name 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 the shortest public distribution and import name
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for the core scientific surface without creating a second owner.
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## Alias at a glance
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[canonical core package docs](https://bijux.io/bijux-proteomics/04-bijux-proteomics-core/)
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because this package is only a short-name forwarding layer.
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focused on compatibility naming and short-form ergonomics.
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## 0.3.8 Release Highlights
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## Installation
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pip install proteomics
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## Public APIs
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from 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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```
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## Package identity
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- Distribution name: `proteomics`
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- Import root: `proteomics`
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## Package boundaries
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CLI surface
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## What this package must not do
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## Choose this package when
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|
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name
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## Route elsewhere when
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## Verification route
|
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|
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|
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expectations
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- review `docs/ARCHITECTURE.md`, `docs/BOUNDARIES.md`, and `docs/CONTRACTS.md`
|
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when alias claims or routing language change
|
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- validate the canonical core README and tests when the proposal changes
|
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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 short-name alias only
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- is the canonical owner explicit in behavior and documentation
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- would the same behavior remain valid if core were imported directly
|
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|
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## Escalation route
|
|
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|
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|
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- route scientific behavior changes to `bijux-proteomics-core`
|
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- stop and review alias boundaries when the proposal introduces package-local
|
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semantics
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- escalate before release when packaging or command-name drift could confuse
|
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consumers
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|
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## Consumer impact signals
|
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|
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- short-name install or import changes are high-impact because downstream code
|
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may rely on them directly
|
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- alias documentation changes should still be reviewed against the core owner
|
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- wording-only or documentation-only clarifications carry lower release risk
|
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|
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## Explicit non-goals
|
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|
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|
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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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|
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|
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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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|
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- [Product architecture](https://bijux.io/bijux-proteomics/01-bijux-proteomics/foundation/product-architecture/)
|
|
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|
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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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|
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- [Changelog](CHANGELOG.md)
|
|
@@ -0,0 +1,12 @@
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proteomics/__init__.py,sha256=XDedw5QOj-7XiEccJmCii-71m-qMMenVITv0P1wBMD8,1051
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proteomics/__main__.py,sha256=nLsscw5hOY37W7FuuLovGn59vctT3bZUWerOsI_Wk7Y,172
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proteomics/cli.py,sha256=qUutgvnqACexStvqL9g8Dc5n52zwTTPZ42NikWyKBCk,553
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proteomics/py.typed,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
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LICENSE,sha256=iajBAJ7hjmqKMNLH08a20tPiniMNzlLDKrDYSKCfbeI,10865
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NOTICE,sha256=wQxicjRQ_-O8q8-3cmGAZ8BTLQyw8Lsuho_SNrZ772A,114
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|
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proteomics-0.3.8.dist-info/METADATA,sha256=o0y35t4P1iE834KCSj4ohzZmO66jx67ttY7M56oM_e4,11088
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|
+
proteomics-0.3.8.dist-info/WHEEL,sha256=mffPy8wBnZQn2VnJUU5jE99KsxaSfiyMHV9Yt0aLVxs,87
|
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9
|
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proteomics-0.3.8.dist-info/entry_points.txt,sha256=zrBwKcyKLllL30ihVfvP7vYSxG79JSYzFq8CYHHBhh4,51
|
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10
|
+
proteomics-0.3.8.dist-info/licenses/LICENSE,sha256=iajBAJ7hjmqKMNLH08a20tPiniMNzlLDKrDYSKCfbeI,10865
|
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proteomics-0.3.8.dist-info/licenses/NOTICE,sha256=wQxicjRQ_-O8q8-3cmGAZ8BTLQyw8Lsuho_SNrZ772A,114
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+
proteomics-0.3.8.dist-info/RECORD,,
|
|
@@ -0,0 +1,192 @@
|
|
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1
|
+
Apache License
|
|
2
|
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Version 2.0, January 2004
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http://www.apache.org/licenses/
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APPENDIX: How to apply the Apache License to your work.
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Copyright 2026 Bijan Mousavi <bijan@bijux.io>
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