phylogenetic 0.1.0__py3-none-any.whl

phylogenetic/__init__.py

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+"""Compatibility alias module for bijux-phylogenetics."""
+
+from __future__ import annotations
+
+from importlib import import_module, metadata
+from typing import Any
+
+from bijux_phylogenetics.comparative.common import (
+    ComparativeDataset as ComparativeDataset,
+)
+
+from .runtime_alias import install_runtime_aliases
+
+_ALIAS_PACKAGE = "phylogenetic"
+_RUNTIME_PACKAGE = "bijux_phylogenetics"
+_LOCAL_SUBMODULES = frozenset({"__main__", "cli", "runtime_alias"})
+_runtime_module = import_module(_RUNTIME_PACKAGE)
+
+install_runtime_aliases(
+    alias_package=_ALIAS_PACKAGE,
+    runtime_package=_RUNTIME_PACKAGE,
+    local_submodules=_LOCAL_SUBMODULES,
+)
+
+for _name in getattr(_runtime_module, "__all__", ()):
+    if _name == "__version__":
+        continue
+    globals()[_name] = getattr(_runtime_module, _name)
+
+try:
+    __version__ = metadata.version(_ALIAS_PACKAGE)
+except metadata.PackageNotFoundError:
+    __version__ = "0.1.0"
+
+__all__ = list(getattr(_runtime_module, "__all__", ()))
+if "ComparativeDataset" not in __all__:
+    __all__.append("ComparativeDataset")
+
+
+def __getattr__(name: str) -> Any:
+    """Forward top-level compatibility lookups to the canonical runtime package."""
+    return getattr(_runtime_module, name)
+
+
+def __dir__() -> list[str]:
+    """Expose the canonical runtime attributes in interactive discovery."""
+    return sorted(set(globals()) | set(dir(_runtime_module)))

phylogenetic/__main__.py

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+"""Module entrypoint for the `phylogenetic` compatibility CLI."""
+
+from __future__ import annotations
+
+from .cli import main
+
+if __name__ == "__main__":
+    raise SystemExit(main())

phylogenetic/cli.py

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+"""Compatibility CLI entrypoint for the `phylogenetic` distribution."""
+
+from __future__ import annotations
+
+import argparse
+from collections.abc import Sequence
+from typing import Any
+
+from bijux_phylogenetics.cli import build_parser as build_runtime_parser
+from bijux_phylogenetics.cli import run_command as dispatch_runtime_command
+
+__all__ = ["build_parser", "main", "run_command"]
+
+
+def build_parser() -> argparse.ArgumentParser:
+    """Build the canonical command-line parser for the alias package."""
+    parser = build_runtime_parser()
+    parser.prog = "phylogenetic"
+    return parser
+
+
+def run_command(
+    args: Any,
+    *,
+    parser: argparse.ArgumentParser | None = None,
+) -> int:
+    """Dispatch parsed command-line arguments through runtime handlers."""
+    if parser is None:
+        parser = build_parser()
+    return dispatch_runtime_command(args, parser=parser)
+
+
+def main(argv: Sequence[str] | None = None) -> int:
+    """CLI entry point."""
+    parser = build_parser()
+    args = parser.parse_args(argv)
+    return run_command(args, parser=parser)
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())

phylogenetic/py.typed

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+

phylogenetic/runtime_alias.py

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+"""Route compatibility-package submodules to the canonical runtime package."""
+
+from __future__ import annotations
+
+from collections.abc import Collection
+from importlib import import_module
+from importlib.abc import Loader, MetaPathFinder
+from importlib.machinery import ModuleSpec
+from importlib.util import find_spec
+import sys
+from types import ModuleType
+
+
+class _RuntimeAliasLoader(Loader):
+    """Load the canonical runtime module for an alias-package submodule."""
+
+    def __init__(self, alias_name: str, runtime_name: str) -> None:
+        """Remember the alias and runtime module names for one import."""
+        self._alias_name = alias_name
+        self._runtime_name = runtime_name
+
+    def create_module(self, spec: ModuleSpec) -> ModuleType:
+        """Import the canonical runtime module and register the alias name."""
+        module = import_module(self._runtime_name)
+        sys.modules[self._alias_name] = module
+        return module
+
+    def exec_module(self, module: ModuleType) -> None:
+        """Keep the alias name bound to the already imported runtime module."""
+        sys.modules.setdefault(self._alias_name, module)
+
+
+class _RuntimeAliasFinder(MetaPathFinder):
+    """Resolve alias-package submodules through the canonical runtime package."""
+
+    def __init__(
+        self,
+        *,
+        alias_package: str,
+        runtime_package: str,
+        local_submodules: Collection[str],
+    ) -> None:
+        """Configure one alias-package namespace bridge."""
+        self.alias_package = alias_package
+        self.runtime_package = runtime_package
+        self.local_submodules = frozenset(local_submodules)
+        self._alias_prefix = f"{alias_package}."
+
+    def find_spec(
+        self,
+        fullname: str,
+        path: object | None = None,
+        target: ModuleType | None = None,
+    ) -> ModuleSpec | None:
+        """Return an alias-module spec when the runtime module exists."""
+        del path, target
+        if not fullname.startswith(self._alias_prefix):
+            return None
+        module_suffix = fullname.removeprefix(self._alias_prefix)
+        if module_suffix.partition(".")[0] in self.local_submodules:
+            return None
+        runtime_name = f"{self.runtime_package}.{module_suffix}"
+        runtime_spec = find_spec(runtime_name)
+        if runtime_spec is None:
+            return None
+        alias_spec = ModuleSpec(
+            name=fullname,
+            loader=_RuntimeAliasLoader(fullname, runtime_name),
+            origin=runtime_spec.origin,
+            is_package=runtime_spec.submodule_search_locations is not None,
+        )
+        if runtime_spec.submodule_search_locations is not None:
+            alias_spec.submodule_search_locations = list(
+                runtime_spec.submodule_search_locations
+            )
+        return alias_spec
+
+
+def install_runtime_aliases(
+    *,
+    alias_package: str,
+    runtime_package: str,
+    local_submodules: Collection[str],
+) -> None:
+    """Install a finder that maps alias-package submodules onto runtime modules."""
+    for finder in sys.meta_path:
+        if not isinstance(finder, _RuntimeAliasFinder):
+            continue
+        if (
+            finder.alias_package == alias_package
+            and finder.runtime_package == runtime_package
+        ):
+            return
+    sys.meta_path.insert(
+        0,
+        _RuntimeAliasFinder(
+            alias_package=alias_package,
+            runtime_package=runtime_package,
+            local_submodules=local_submodules,
+        ),
+    )

phylogenetic-0.1.0.dist-info/METADATA

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+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)

phylogenetic-0.1.0.dist-info/RECORD

@@ -0,0 +1,9 @@
+phylogenetic/__init__.py,sha256=0IPjTw1RjCQn2TfssxZxF0Qj2C_IrBCryiLz3WkwgaE,1398
+phylogenetic/__main__.py,sha256=PlcZ--oVLN93-DXCckDZU0SbTLxO_G_J8oqnZoJdjGs,182
+phylogenetic/cli.py,sha256=fVIIk3vVhxH4-TpVjqMmEh-dx20yYGMIN6biAOyffCs,1130
+phylogenetic/py.typed,sha256=AbpHGcgLb-kRsJGnwFEktk7uzpZOCcBY74-YBdrKVGs,1
+phylogenetic/runtime_alias.py,sha256=-LJzUHr2b_vUGbym_gxrsmER73vuCfrUMKyleWRVgLc,3533
+phylogenetic-0.1.0.dist-info/METADATA,sha256=CGxlAhZTgJ47zgyOQ1Eg4OMlfmh9ZjV7yJhMDEBC4Vw,8345
+phylogenetic-0.1.0.dist-info/WHEEL,sha256=mffPy8wBnZQn2VnJUU5jE99KsxaSfiyMHV9Yt0aLVxs,87
+phylogenetic-0.1.0.dist-info/entry_points.txt,sha256=Qkm7N5I4WeJIF7d9t7-5KF2ktLmZmCB5rF-_xewsNEU,55
+phylogenetic-0.1.0.dist-info/RECORD,,

phylogenetic-0.1.0.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: hatchling 1.30.1
+Root-Is-Purelib: true
+Tag: py3-none-any

phylogenetic-0.1.0.dist-info/entry_points.txt

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+[console_scripts]
+phylogenetic = phylogenetic.cli:main