biotapy 0.0.1__py3-none-any.whl

biotapy/__init__.py

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+from importlib.metadata import version
+
+__all__ = ["__version__"]
+
+__version__ = version("biotapy")

biotapy/_core/__init__.py

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+"""Private kernel shared by biotapy subpackages (contracts/module-boundaries)."""
+
+from ._optional import import_optional
+from ._rng import as_generator
+
+__all__ = ["as_generator", "import_optional"]

biotapy/_core/_optional.py

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+"""Lazy imports for optional extras (decisions/optional-heavy-dependencies)."""
+
+import importlib
+from types import ModuleType
+
+
+def import_optional(name: str, *, extra: str) -> ModuleType:
+    """Import ``name`` or raise an ImportError that names the extra to install."""
+    try:
+        return importlib.import_module(name)
+    except ImportError as err:
+        msg = f"{name} is required here. Install it with: pip install 'biotapy[{extra}]'"
+        raise ImportError(msg) from err

biotapy/_core/_rng.py

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+"""Single entry point for randomness (rules.md R3.4)."""
+
+import numpy as np
+
+
+def as_generator(seed: int | np.random.Generator | None) -> np.random.Generator:
+    """Return a NumPy Generator for ``seed`` without touching global state."""
+    if isinstance(seed, np.random.Generator):
+        return seed
+    if seed is None or isinstance(seed, int | np.integer):
+        return np.random.default_rng(seed)
+    msg = f"seed must be an int, a numpy Generator or None, got {type(seed).__name__}"
+    raise TypeError(msg)

biotapy-0.0.1.dist-info/METADATA

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+Metadata-Version: 2.5
+Name: biotapy
+Version: 0.0.1
+Summary: mia-style microbiome toolkit for Python on AnnData/TreeData
+Project-URL: Documentation, https://biotapy.readthedocs.io/
+Project-URL: Homepage, https://github.com/pedrocr83/biotapy
+Project-URL: Source, https://github.com/pedrocr83/biotapy
+Author: Pedro Ribeiro
+Maintainer-email: Pedro Ribeiro <pedrocasalribeiro@gmail.com>
+License: BSD 3-Clause License
+        
+        Copyright (c) 2026, Pedro Ribeiro
+        All rights reserved.
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        1. Redistributions of source code must retain the above copyright notice, this
+           list of conditions and the following disclaimer.
+        
+        2. Redistributions in binary form must reproduce the above copyright notice,
+           this list of conditions and the following disclaimer in the documentation
+           and/or other materials provided with the distribution.
+        
+        3. Neither the name of the copyright holder nor the names of its
+           contributors may be used to endorse or promote products derived from
+           this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+License-File: LICENSE
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: >=3.12
+Requires-Dist: anndata
+Requires-Dist: numpy
+Requires-Dist: session-info2
+Description-Content-Type: text/markdown
+
+# biotapy
+
+[![Tests][badge-tests]][tests]
+[![Documentation][badge-docs]][documentation]
+
+[badge-tests]: https://img.shields.io/github/actions/workflow/status/pedrocr83/biotapy/test.yaml?branch=master
+[badge-docs]: https://app.readthedocs.org/projects/biotapy/badge/
+
+mia-style microbiome toolkit for Python on AnnData/TreeData
+
+## Getting started
+
+Please refer to the [documentation][],
+in particular, the [API documentation][].
+
+## Installation
+
+You need to have Python 3.12 or newer installed on your system.
+If you don't have Python installed, we recommend installing [uv][].
+
+We recommend managing dependencies in project-specific virtual environments to avoid dependency conflicts.
+This is most convenient using package managers such as [uv][].
+Choose from the options below to install biotapy:
+
+<!--
+1. Add the latest release of `biotapy` from [PyPI][] to your `uv` project:
+
+   ```bash
+   uv add biotapy
+   ```
+
+1. Install the latest release into a [standard virtual environment][venv]:
+
+   ```bash
+   (after activating your venv)
+   pip install biotapy
+   ```
+
+-->
+
+1. Install the latest development version:
+
+   ```bash
+   pip install git+https://github.com/pedrocr83/biotapy.git  # (or `uv add`)
+   ```
+
+## Release notes
+
+See the [changelog][].
+
+## Contact
+
+For questions and help requests, you can reach out in the [scverse discourse][].
+If you found a bug, please use the [issue tracker][].
+
+## Citation
+
+> t.b.a
+
+[uv]: https://github.com/astral-sh/uv
+[scverse discourse]: https://discourse.scverse.org/
+[issue tracker]: https://github.com/pedrocr83/biotapy/issues
+[tests]: https://github.com/pedrocr83/biotapy/actions/workflows/test.yaml
+[documentation]: https://biotapy.readthedocs.io
+[changelog]: https://biotapy.readthedocs.io/page/changelog.html
+[api documentation]: https://biotapy.readthedocs.io/page/api.html
+[pypi]: https://pypi.org/project/biotapy
+[venv]: https://docs.python.org/3/tutorial/venv.html

biotapy-0.0.1.dist-info/RECORD

@@ -0,0 +1,8 @@
+biotapy/__init__.py,sha256=sv3v_rY596sGY91lgpmiocHj9ytl59jLbMlZA-uiiM8,100
+biotapy/_core/__init__.py,sha256=FjkURXkFRoPdm_VBAJaRWiQvfgooN4dVOUnUZnoJZ0c,200
+biotapy/_core/_optional.py,sha256=q8hyi_cMCDBV818a-A-wrsymRMZXGPJfely_AunV0p4,488
+biotapy/_core/_rng.py,sha256=w2uDraKZqpVbmN7vl-7VY_AzKvPn1occA_WoNjlvdBA,519
+biotapy-0.0.1.dist-info/METADATA,sha256=72lgzqUwhiXaTVuIWUSQfbZ4Lvbkip2l6sOMWTzR0Ys,4428
+biotapy-0.0.1.dist-info/WHEEL,sha256=W3fkpkm7-wf9vBI5Z-7s0eWkeM-spu78I8Neb98DeEg,87
+biotapy-0.0.1.dist-info/licenses/LICENSE,sha256=F2WVKna2SRJ0248orGJc81MguhH_TZ8FCS1-HESgetk,1521
+biotapy-0.0.1.dist-info/RECORD,,

biotapy-0.0.1.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: hatchling 1.32.4
+Root-Is-Purelib: true
+Tag: py3-none-any

biotapy-0.0.1.dist-info/licenses/LICENSE

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2026, Pedro Ribeiro
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.