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        "author": "Roderick Bovee & One Codex <roderick@onecodex.com>",
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        "description": "# Taxonomy\n\n[![PyPI version](https://badge.fury.io/py/taxonomy.svg)](https://pypi.org/project/taxonomy/)\n[![Crates version](https://img.shields.io/crates/v/taxonomy.svg)](https://crates.io/crates/taxonomy)\n[![CircleCI](https://circleci.com/gh/onecodex/taxonomy.svg?style=shield)](https://circleci.com/gh/onecodex/taxonomy)\n\nThis is a Rust library for reading, writing, and editing biological taxonomies. There are associated Python bindings for accessing most of the functionality from Python.\n\nThis library was developed initially as a component in One Codex's metagenomic classification pipeline before being refactored out, expanded, and open-sourced. It is designed such that it can be used *as is* with a number of taxonomic formats *or* the Taxonomy trait it provides can be used to add last common ancestor, traversal, etc. methods to a downstream package's taxonomy implementation.\n\nThe library ships with a number of features:\n - [X] Common support for taxonomy handling across Rust and Python\n - [X] Fast and low(er) memory usage\n - [X] NCBI taxonomy, JSON (\"tree\" and \"node_link_data\" formats), Newick, and PhyloXML support\n - [X] Easily extensible (in Rust) to support other formats and operations\n\n\n# Python Usage\n\nThe Python taxonomy API can open and manipulate all of the formats from the Rust library:\n\n```python\nfrom taxonomy import Taxonomy\n\ntax = Taxonomy.from_newick('(A,(B,C)D)E;')\nassert tax.parent('A') == 'E'\nassert tax.parent('B') == 'D'\n```\n\nIf you have the NCBI taxonomy locally ([found on their FTP](ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz)), you can use that too:\n\n```python\nncbi_tax = Taxonomy.from_ncbi('./nodes.dmp', './names.dmp')\nassert tax.name('562') == 'Escherichia coli'\nassert tax.rank('562') == 'species'\n```\n\nNote that Taxonomy IDs in NCBI format are integers, but they're converted to strings on import. We find working with \"string taxonomy IDs\" greatly simplifies interoperation between different taxonomy systems.\n\n\n# Installation\n\n## Rust\nThis library can be added to an existing Cargo.toml file and installed straight from crates.io.\n\n## Python\nYou can install the Python bindings directly from PyPI (binaries are only built for select architextures) with:\n```bash\npip install taxonomy\n```\n\n\n# Development\n\n## Rust\nThere is a test suite runable with `cargo test`.\n\n## Python\nTo work on the Python library on a Mac OS X/Unix system (requires Python 3):\n```bash\n# you need the nightly version of Rust installed\ncurl https://sh.rustup.rs -sSf | sh\nrustup default nightly\n\n# finally, install the library\n./setup.py install  # (or ./setup.py develop)\n```\n\n### Building binary wheels and pushing to PyPI\n\n```\n# For each supported Python version and architecture combination...\n## On a Mac\npython setup.py install\npython setup.py bdist_wheel\ntwine upload dist/*\n\n## On Linux\n# I built the 0.3.1 wheels with a forked version of pyo3-pack; we should reevaluate the next time\n# we build wheels if we can just get this to work with rust-python.\ngit clone https://github.com/onecodex/pyo3-pack\ndocker run -it --rm --entrypoint /bin/bash -v .../pyo3-pack:/pyo3pack -v .../taxonomy/:/mnt konstin2/pyo3-pack\ncd /pyo3pack\ncargo install --path . --force\ncd /mnt\nrustup default nightly\npyo3-pack build --python-feature-gate python\n```\n\n# Other Taxonomy Libraries\n\nThere are taxonomic toolkits for other programming languages that offer different features and provided some inspiration for this library:\n\n*ETE Toolkit (http://etetoolkit.org/)* A Python taxonomy library\n\n*Taxize (https://ropensci.github.io/taxize-book/)* An R toolkit for working with taxonomic data\n\n",
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