Metadata-Version: 2.4
Name: phylogenetic
Version: 0.1.0
Summary: Compatibility alias package for the canonical native phylogenetics runtime.
Project-URL: Documentation, https://bijux.io/bijux-phylogenetics/01-bijux-phylogenetics/
Project-URL: Native Workflows, https://bijux.io/bijux-phylogenetics/01-bijux-phylogenetics/operations/
Project-URL: Evidence Book, https://bijux.io/bijux-phylogenetics/02-bijux-phylogenetics-evidence-book/
Project-URL: Benchmarks, https://bijux.io/bijux-phylogenetics/01-bijux-phylogenetics/operations/native-benchmark-review/
Project-URL: Interface Guide, https://bijux.io/bijux-phylogenetics/01-bijux-phylogenetics/interfaces/surface-selection/
Project-URL: Artifact Guide, https://bijux.io/bijux-phylogenetics/01-bijux-phylogenetics/interfaces/artifact-consumption-guide/
Project-URL: Release Guide, https://bijux.io/bijux-phylogenetics/01-bijux-phylogenetics/quality/release-review-workflow/
Project-URL: Repository, https://github.com/bijux/bijux-phylogenetics
Project-URL: Issues, https://github.com/bijux/bijux-phylogenetics/issues
Project-URL: Changelog, https://github.com/bijux/bijux-phylogenetics/blob/main/packages/phylogenetic/CHANGELOG.md
Project-URL: Security, https://github.com/bijux/bijux-phylogenetics/blob/main/SECURITY.md
Author-email: Bijan Mousavi <bijan@bijux.io>
License: Apache-2.0
Keywords: bayesian-inference,bioinformatics,comparative-biology,evolution,maximum-likelihood,phylogenetics
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.11
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.11
Requires-Dist: bijux-phylogenetics<1.0,>=0.1.0
Provides-Extra: dev
Requires-Dist: bandit<2.0,>=1.8.6; extra == 'dev'
Requires-Dist: build<2.0,>=1.3.0; extra == 'dev'
Requires-Dist: codespell<3.0,>=2.4.1; extra == 'dev'
Requires-Dist: deptry<1.0,>=0.24.0; extra == 'dev'
Requires-Dist: hatch<2.0,>=1.14.0; extra == 'dev'
Requires-Dist: mypy<3.0,>=1.18.2; extra == 'dev'
Requires-Dist: pip-audit<3.0,>=2.9.0; extra == 'dev'
Requires-Dist: pydantic<3.0,>=2.12; extra == 'dev'
Requires-Dist: pydocstyle<7.0,>=6.3.0; extra == 'dev'
Requires-Dist: pytest-asyncio<2.0,>=1.0.0; extra == 'dev'
Requires-Dist: pytest-cov<8.0,>=6.2.1; extra == 'dev'
Requires-Dist: pytest-timeout<3.0,>=2.4.0; extra == 'dev'
Requires-Dist: pytest-xdist<4.0,>=3.8.0; extra == 'dev'
Requires-Dist: pytest<10.0,>=9.0.3; extra == 'dev'
Requires-Dist: radon<7.0,>=6.0.1; extra == 'dev'
Requires-Dist: ruff<1.0,>=0.13.0; extra == 'dev'
Requires-Dist: twine<7.0,>=6.2.0; extra == 'dev'
Requires-Dist: vulture<3.0,>=2.14; extra == 'dev'
Description-Content-Type: text/markdown

# phylogenetic

<!-- bijux-phylogenetics-badges:generated:start -->
[![Python 3.11+](https://img.shields.io/badge/python-3.11%2B-3776AB?logo=python&logoColor=white)](https://pypi.org/project/phylogenetic/)
[![License: Apache-2.0](https://img.shields.io/badge/license-Apache--2.0-0F766E)](https://github.com/bijux/bijux-phylogenetics/blob/main/LICENSE)
[![Verify](https://github.com/bijux/bijux-phylogenetics/actions/workflows/verify.yml/badge.svg?branch=main)](https://github.com/bijux/bijux-phylogenetics/actions/workflows/verify.yml?query=branch%3Amain)
[![Release PyPI](https://img.shields.io/badge/release-pypi%20workflow-2563EB?logo=githubactions&logoColor=white)](https://github.com/bijux/bijux-phylogenetics/actions/workflows/release-pypi.yml)
[![Release GHCR](https://img.shields.io/badge/release-ghcr%20workflow-2563EB?logo=githubactions&logoColor=white)](https://github.com/bijux/bijux-phylogenetics/actions/workflows/release-ghcr.yml)
[![Release GitHub](https://img.shields.io/badge/release-github%20workflow-2563EB?logo=githubactions&logoColor=white)](https://github.com/bijux/bijux-phylogenetics/actions/workflows/release-github.yml)
[![Docs](https://github.com/bijux/bijux-phylogenetics/actions/workflows/deploy-docs.yml/badge.svg)](https://github.com/bijux/bijux-phylogenetics/actions/workflows/deploy-docs.yml)

[![phylogenetic](https://img.shields.io/pypi/v/phylogenetic?label=phylogenetic&logo=pypi)](https://pypi.org/project/phylogenetic/)
[![bijux-phylogenetics](https://img.shields.io/pypi/v/bijux-phylogenetics?label=bijux--phylogenetics&logo=pypi)](https://pypi.org/project/bijux-phylogenetics/)

[![phylogenetic](https://img.shields.io/badge/phylogenetic-ghcr-181717?logo=github)](https://github.com/bijux/bijux-phylogenetics/pkgs/container/bijux-phylogenetics%2Fphylogenetic)
[![bijux-phylogenetics](https://img.shields.io/badge/bijux--phylogenetics-ghcr-181717?logo=github)](https://github.com/bijux/bijux-phylogenetics/pkgs/container/bijux-phylogenetics%2Fbijux-phylogenetics)

[![phylogenetic docs](https://img.shields.io/badge/docs-phylogenetic-2563EB?logo=materialformkdocs&logoColor=white)](https://bijux.io/bijux-phylogenetics/01-bijux-phylogenetics/)
[![bijux-phylogenetics docs](https://img.shields.io/badge/docs-bijux--phylogenetics-2563EB?logo=materialformkdocs&logoColor=white)](https://bijux.io/bijux-phylogenetics/01-bijux-phylogenetics/)
<!-- bijux-phylogenetics-badges:generated:end -->

Compatibility alias package for `bijux-phylogenetics`.

This distribution installs the canonical phylogenetics runtime under the
shorter `phylogenetic` package and CLI names. It is not a reduced runtime and
it is not a fork. It points at the same benchmark, workflow, and reporting
surfaces that the canonical package publishes.

```mermaid
flowchart LR
    A[phylogenetic] --> B[Shorter install name]
    A --> C[Shorter CLI name]
    A --> D[Same canonical runtime behavior]
```

## Install

`phylogenetic` supports Python 3.11 and newer.

```bash
python3.11 -m pip install phylogenetic
phylogenetic --help
```

## What You Still Get

Installing the alias package still gives you access to the same documented
runtime depth:

| Capability family | What carries through the alias |
| --- | --- |
| Trees and alignments | inspection, validation, comparison, and preparation workflows |
| Native runtime | native likelihood and native inference surfaces |
| Comparative analysis | comparative and ancestral workflows |
| Reporting | benchmark, workflow, and reporting surfaces |
| External engines | governed wrapper-backed external-engine workflows |

## What The Alias Does Not Change

- it does not remove native inference surfaces
- it does not remove comparative, ancestral, or parsimony families
- it does not change the evidence-book or quality reading model
- it does not publish a smaller scientific contract than the canonical package

Choose this package when you want the shorter install and command names while
keeping the same public runtime contract.

Choose the canonical `bijux-phylogenetics` package instead when you want the
most explicit package name for notebooks, papers, release notes, or downstream
documentation.

## Read This Next

- [Runtime product guide](https://bijux.io/bijux-phylogenetics/01-bijux-phylogenetics/)
- [Runtime architecture](https://bijux.io/bijux-phylogenetics/01-bijux-phylogenetics/architecture/)
- [Surface selection guide](https://bijux.io/bijux-phylogenetics/01-bijux-phylogenetics/interfaces/surface-selection/)
- [Artifact consumption guide](https://bijux.io/bijux-phylogenetics/01-bijux-phylogenetics/interfaces/artifact-consumption-guide/)
- [Native Inference And Benchmark Surfaces](https://bijux.io/bijux-phylogenetics/01-bijux-phylogenetics/interfaces/native-inference-and-benchmarks/)
- [Native maximum-likelihood workflows](https://bijux.io/bijux-phylogenetics/01-bijux-phylogenetics/operations/native-maximum-likelihood-workflows/)
- [Native Bayesian workflows](https://bijux.io/bijux-phylogenetics/01-bijux-phylogenetics/operations/native-bayesian-workflows/)
- [Native benchmark review](https://bijux.io/bijux-phylogenetics/01-bijux-phylogenetics/operations/native-benchmark-review/)
- [Release review workflow](https://bijux.io/bijux-phylogenetics/01-bijux-phylogenetics/quality/release-review-workflow/)
- [Evidence-book guide](https://bijux.io/bijux-phylogenetics/02-bijux-phylogenetics-evidence-book/)
- [Canonical runtime package on GitHub](https://github.com/bijux/bijux-phylogenetics/tree/main/packages/bijux-phylogenetics)
