Metadata-Version: 2.1
Name: commonnexus
Version: 0.1.0
Summary: A nexus (phylogenetics) file reader and writer (.nex, .trees)
Home-page: https://github.com/dlce-eva/commonnexus
Author: Robert Forkel
Author-email: robert_forkel@eva.mpg.de
License: Apache 2.0
Project-URL: Bug Tracker, https://github.com/dlce-eva/commonnexus/issues
Keywords: phylogenetics nexus newick paup splitstree
Platform: any
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Python :: Implementation :: PyPy
Classifier: License :: OSI Approved :: BSD License
Requires-Python: >=3.7
Description-Content-Type: text/markdown
Provides-Extra: dev
Provides-Extra: test
Provides-Extra: docs
License-File: LICENSE

# commonnexus

This package provides functionality to read and write the Nexus file format as specified in

> Maddison, Swofford, and Maddison (1997). "NEXUS: An extensible file format for systematic information". Systematic Biology. 46 (4): 590–621. [doi:10.1093/sysbio/46.4.590](https://doi.org/10.1093/sysbio/46.4.590)

Rather than trying to rip out relevant portions of a Nexus file as quickly as possible, the implementation
in `commonnexus` tries to do "the right thing" according to the specification, i.e. parse a file token by
token. Thus, we sacrifice speed for correctness and the ability to support weird edge cases like

> Comments do not break tokens. Thus, `AssuMP[comment]TiONS` is processed as `ASSUMPTIONS`.

