peyotl
python library for interacting with Open Tree of Life resources
Science Score: 26.0%
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○CITATION.cff file
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✓codemeta.json file
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✓.zenodo.json file
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○DOI references
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○Academic publication links
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○Scientific vocabulary similarity
Low similarity (13.4%) to scientific vocabulary
Repository
python library for interacting with Open Tree of Life resources
Basic Info
- Host: GitHub
- Owner: OpenTreeOfLife
- License: bsd-2-clause
- Language: Jupyter Notebook
- Default Branch: master
- Size: 10.4 MB
Statistics
- Stars: 11
- Watchers: 16
- Forks: 7
- Open Issues: 29
- Releases: 1
Metadata Files
README.md
peyotl is a python package written to make it easier to
interact with the software produced by the Open Tree of Life project.
Specifically, to:
interact with a local version of the phylesystem repository of curated phylogenetic studies ;
call web services associated with the studies (served by web app running the phylesystem-api code);
call web services associated with taxonomic resolution services (running taxomachine );
call web services associated with Open Tree of Life's "synthetic" estimate of the tree of life (running treemachine);
call web services associated with an annotation database (that we have not built yet)
Currently peyotl is used to implement most of the functionality in the phylesystem-api backend of the study curation tool.
Instructions
You probably want to be using a virtualenv. Then you can:
$ pip install -r requirements.txt
$ python setup.py develop
For full(er) documentation, check out our http://opentreeoflife.github.io/peyotl/ documentation site.
Testing
Use:
python setup.py test
to trigger the unittests. The testing page of the documentation site describes the other tests scripts.
Thanks
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 Sukumaran's work in the DendroPy package.
The tree/node iteration functions in peyotl.phylo.tree are also adapted from DendroPy.
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 Jonathan 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 PhenoscapeKB, [U.S. National Evolutionary Synthesis Center], http://kb.phenoscape.org; [Feb 16, 2014] The citation for the data is in the nexml doc itself.
peyotl includes the ez_setup.py tool from setuptools
To satisfy the Python Software Foundation license we note here that peyotl does not
alter the python sourcee code itself. By installing the package you enable the python
interpreter to find the code included in this package for interacting with open tree of life
data and web services.
Etymology: According to Wikipedia, peyotl is the Nahuatl word for Lophophora williamsii.
Owner
- Name: OpenTreeOfLife
- Login: OpenTreeOfLife
- Kind: organization
- Website: http://opentreeoflife.github.io/
- Repositories: 62
- Profile: https://github.com/OpenTreeOfLife
GitHub Events
Total
- Push event: 2
Last Year
- Push event: 2
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Mark T. Holder | m****r@g****m | 979 |
| Jim Allman | j****m@i****m | 219 |
| Emily Jane McTavish | e****h@g****m | 112 |
| Benjamin Redelings | b****s@g****m | 18 |
| Karen Cranston | k****n@g****m | 11 |
| Jonathan A Rees | j****8@m****t | 6 |
| Joseph W. Brown | p****b@g****m | 4 |
| Cody Hinchliff | c****f@g****m | 2 |
| Rutger Vos | r****o@g****m | 1 |
| OpenTree API | a****i@o****g | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 39
- Total pull requests: 64
- Average time to close issues: 6 months
- Average time to close pull requests: 9 days
- Total issue authors: 6
- Total pull request authors: 9
- Average comments per issue: 1.74
- Average comments per pull request: 0.89
- Merged pull requests: 58
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- jar398 (12)
- mtholder (11)
- jimallman (8)
- kcranston (6)
- snacktavish (1)
- pmidford (1)
Pull Request Authors
- mtholder (35)
- jimallman (12)
- snacktavish (5)
- kcranston (5)
- josephwb (2)
- jar398 (2)
- bredelings (1)
- rvosa (1)
- chinchliff (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- pypi 5 last-month
- Total dependent packages: 0
- Total dependent repositories: 4
- Total versions: 1
- Total maintainers: 1
pypi.org: peyotl
Library for interacting with Open Tree of Life resources
- Homepage: https://github.com/OpenTreeOfLife/peyotl
- Documentation: https://peyotl.readthedocs.io/
- License: BSD
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Latest release: 0.1.2
published over 11 years ago
Rankings
Maintainers (1)
Dependencies
- anyjson *
- argcomplete *
- coverage *
- enum34 *
- locket >=0.1.1
- python-dateutil *
- redis *
- requests >=2.2.1
- setuptools <58
- sh >=1.08
- anyjson *
- argcomplete *
- coverage *
- enum34 *
- locket >=0.1.1
- python-dateutil *
- redis *
- requests >=2.2.1
- setuptools *
- sh >=1.08