Metadata-Version: 2.2
Name: wags_tails
Version: 0.3.1
Summary: Data acquisition tools for Wagnerds
Author: Kori Kuzma, James S Stevenson, Alex H Wagner
License: MIT License
        
        Copyright (c) 2023-2024 The Wagner/Chaudhari Laboratories at the Institute for Genomic Medicine
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
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        The above copyright notice and this permission notice shall be included in all
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Project-URL: Homepage, https://github.com/GenomicMedLab/wags-tails/
Project-URL: Documentation, https://wags-tails.readthedocs.io/
Project-URL: Changelog, https://github.com/GenomicMedLab/wags-tails/releases
Project-URL: Source, https://github.com/GenomicMedLab/wags-tails/
Project-URL: Bug Tracker, https://github.com/GenomicMedLab/wags-tails/issues
Classifier: Development Status :: 3 - Alpha
Classifier: Framework :: Pydantic
Classifier: Framework :: Pydantic :: 2
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Requires-Python: >=3.11
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: requests
Requires-Dist: tqdm
Requires-Dist: click
Provides-Extra: tests
Requires-Dist: pytest>=6.0; extra == "tests"
Requires-Dist: pytest-cov; extra == "tests"
Requires-Dist: requests-mock; extra == "tests"
Provides-Extra: dev
Requires-Dist: pre-commit>=4.0.1; extra == "dev"
Requires-Dist: ruff==0.8.6; extra == "dev"
Provides-Extra: docs
Requires-Dist: sphinx==6.1.3; extra == "docs"
Requires-Dist: sphinx-autodoc-typehints==1.22.0; extra == "docs"
Requires-Dist: sphinx-autobuild==2021.3.14; extra == "docs"
Requires-Dist: sphinx-copybutton==0.5.2; extra == "docs"
Requires-Dist: sphinxext-opengraph==0.8.2; extra == "docs"
Requires-Dist: furo==2023.3.27; extra == "docs"
Requires-Dist: sphinx-click==5.0.1; extra == "docs"
Requires-Dist: sphinx-github-changelog==1.2.1; extra == "docs"

# Wags-TAILS

*Technology-Assisted Information Loading and Structure (TAILS) for Wagnerds.*

[![image](https://img.shields.io/pypi/v/wags-tails.svg)](https://pypi.python.org/pypi/wags-tails)
[![image](https://img.shields.io/pypi/l/wags-tails.svg)](https://pypi.python.org/pypi/wags-tails)
[![image](https://img.shields.io/pypi/pyversions/wags-tails.svg)](https://pypi.python.org/pypi/wags-tails)
[![Actions status](https://github.com/genomicmedlab/wags-tails/actions/workflows/checks.yaml/badge.svg)](https://github.com/genomicmedlab/wags-tails/actions/workflows/checks.yaml)

<!-- description -->
This tool provides data acquisition and access utilities for several projects developed by the [Wagner Lab](https://www.nationwidechildrens.org/specialties/institute-for-genomic-medicine/research-labs/wagner-lab). It designates a storage location in user-space where external data files can be saved, and provides methods to download and update them when available.
<!-- /description -->

It is currently used in:

* [Thera-Py](https://github.com/cancervariants/therapy-normalization)
* [Gene Normalizer](https://github.com/cancervariants/gene-normalization)
* [Disease Normalizer](https://github.com/cancervariants/disease-normalization)
* and more!

---

**[Documentation](https://wags-tails.readthedocs.io/stable/)** · [Installation](https://wags-tails.readthedocs.io/stable/install.html) · [Usage](https://wags-tails.readthedocs.io/stable/usage.html) · [API reference](https://wags-tails.readthedocs.io/stable/reference/index.html)

---

## Installation

Install from PyPI:

```shell
python3 -m pip install wags_tails
```

---

## Overview

Data source classes provide a `get_latest()` method that acquires the most recent available data file and returns a pathlib.Path object with its location:

```pycon
>>> from wags_tails.mondo import MondoData
>>> m = MondoData()
>>> m.get_latest(force_refresh=True)
Downloading mondo.obo: 100%|█████████████████| 171M/171M [00:28<00:00, 6.23MB/s]
PosixPath('/Users/genomicmedlab/.local/share/wags_tails/mondo/mondo_20241105.obo'), '20241105'
```

This method is also available as a shell command for ease of use and for interoperability with other runtimes:

```console
% wags-tails get-latest mondo
/Users/genomicmedlab/.local/share/wags_tails/mondo/mondo_20241105.obo
```

---

## Configuration

All data is stored within source-specific subdirectories of a designated WagsTails data directory. By default, this location is `~/.local/share/wags_tails/`, but it can be configured by passing a Path directly to a data class on initialization, via the `$WAGS_TAILS_DIR` environment variable, or via [XDG data environment variables](https://specifications.freedesktop.org/basedir-spec/basedir-spec-0.6.html).

---

## Feedback and contributing

We welcome bug reports, feature requests, and code contributions from users and interested collaborators. The [documentation](https://wags-tails.readthedocs.io/latest/contributing.html) contains guidance for submitting feedback and contributing new code.
