peyotl 0.1.2

Instructions

virtualenv pey
. pey/bin/activate
pip install -r requirements.txt
python setup.py develop
python setup.py test

performs the basic installation and test. For full(er) documentation, check out the wiki.

Thanks

Thanks to NSF and HITS for funding support.

peyotl is primarily written by Mark Holder, Emily Jane McTavish, and Jim Allman, but see the CONTRIBUTORS file for a more complete list of people who have contributed code.

The fabulous Karl Gude created the logo.

Several parts of the setup.py, logging, documentation, and test suite were based on Jeet Sukumraran’s work in the DendroPy package.

The sortattr.xslt stylesheet (which is only used in round-trip testing) is from

http://stackoverflow.com/questions/1429991/using-xsl-to-sort-attributes

The peyotl.phylesystem.git_actions (and the tests) were a part of the api.opentreeoflife.org

repo which was primarily the work of Duke Leto (at that time).

Jim Allman, Karen Cranston, Cody Hinchliff, Mark Holder, Peter Midford, and Jonathon Rees all participated in the discussions that led to the NexSON mapping.

The peyotl/test/data/nexson/phenoscape/nexml test file is from

https://raw.github.com/phenoscape/phenoscape-data/master/Curation%20Files/completed-phenex-files/Characiformes/Buckup_1998.xml Phenoscape file (download), NESCent [Feb 16, 2014] The citation for the data is in the nexml doc itself.

Etymology: According to Wikipedia, peyotl is the Nahuatl word for Lophophora williamsii.