Metadata-Version: 2.1
Name: pytaxize
Version: 0.7.0
Summary: Taxonomic toolbelt for Python
Home-page: https://github.com/sckott/pytaxize
Author: Scott Chamberlain
Author-email: myrmecocystus@gmail.com
License: MIT
Description: 
        
        pytaxize
        ========
        
        |pypi|  |docs| |travis| |coverage| |black|
        
        This is a port of the R package `taxize <https://github.com/ropensci/taxize>`__.  There is a lot going on in the R version of this library, so it will take a while to get all the same functionality over here.
        
        Why?  A significant advantage of a Python version of `taxize` will be for those that are pythonistas at heart. Also, you could use `pytaxize` in a web app, whereas you could with `taxize` (e.g., in a Shiny app), but it wouldn't scale, be very fast, etc.
        
        python 2/3
        ==========
        
        pytaxize is only developed in and tested with Python 3
        
        Installation
        ============
        
        Stable from pypi
        
        .. code-block:: console
        
            pip install pytaxize
        
        Development version
        
        .. code-block:: console
        
            sudo pip install git+git://github.com/sckott/pytaxize.git#egg=pytaxize
        
        
        Taxonomic Ids
        =============
        
        I've started working on a class interface for taxonomic IDs, which will have a bunch of extension methods to do various things with taxon ids. What's available right now is just getting COL ids.
        
        .. code-block:: python
            
            from pytaxize import Ids
            res = Ids('Poa annua')
            res.ncbi()
            res.ids
        
        .. code-block:: python
        
            {'Poa annua': [{'id': '93036',
               'name': 'Poa annua',
               'rank': 'species',
               'uri': 'https://www.ncbi.nlm.nih.gov/taxonomy/93036'}]}
        
        Vascan search
        =============
        
        .. code-block:: python
          
            import pytaxize
            pytaxize.vascan_search(q = ["Helianthus annuus"])
        
        .. code-block:: python
        
            {u'apiVersion': u'0.1',
             u'results': [{u'matches': [{u'canonicalName': u'Helianthus annuus',
                 u'distribution': [{u'establishmentMeans': u'introduced',
                   u'locality': u'NS',
                   u'locationID': u'ISO 3166-2:CA-NS',
                   u'occurrenceStatus': u'introduced'},
                  {u'establishmentMeans': u'',
                   u'locality': u'PE',
                   u'locationID': u'ISO 3166-2:CA-PE',
                   u'occurrenceStatus': u'excluded'},
                  {u'establishmentMeans': u'',
                   u'locality': u'NT',
                   u'locationID': u'ISO 3166-2:CA-NT',
                   u'occurrenceStatus': u'doubtful'},
                  {u'establishmentMeans': u'introduced',
        
        Scrape taxonomic names
        ======================
        
        .. code-block:: python
        
            out = pytaxize.scrapenames(url = 'http://www.mapress.com/zootaxa/2012/f/z03372p265f.pdf')
            out['data'][0:3]
        
        .. code-block:: python
        
            [{'verbatim': '(Hemiptera:',
              'scientificName': 'Hemiptera',
              'offsetStart': 222,
              'offsetEnd': 233},
             {'verbatim': 'Sternorrhyncha:',
              'scientificName': 'Sternorrhyncha',
              'offsetStart': 234,
              'offsetEnd': 249},
             {'verbatim': 'Coccoidea:',
              'scientificName': 'Coccoidea',
              'offsetStart': 250,
              'offsetEnd': 260}]
        
        ITIS low level functions
        ========================
        
        .. code-block:: python
            
            from pytaxize import itis
            itis.accepted_names(504239)
        
            {'acceptedName': 'Dasiphora fruticosa',
               'acceptedTsn': '836659',
               'author': '(L.) Rydb.'}
        
        .. code-block:: python
        
            itis.comment_detail(tsn=180543)
        
            [{'commentDetail': 'Status: CITES - Appendix I as U. arctos (Mexico, Bhutan, China, and Mongolia populations) and U. a. isabellinus; otherwise Appendix II. U. S. ESA - Endangered as U. arctos pruinosus, as U. arctos in Mexico, and as U. a. arctos in Italy. Threatened as U. a. ho...',
              'commentId': '18556',
              'commentTimeStamp': '2007-08-20 15:06:38.0',
              'commentator': 'Wilson & Reeder, eds. (2005)',
              'updateDate': '2014-02-03'},
             {'commentDetail': "Comments: Reviewed by Erdbrink (1953), Couturier (1954), Rausch (1963a), Kurtén (1973), Hall (1984) and Pasitschniak-Arts (1993). Ognev (1931) and Allen (1938) recognized U. pruinosus as distinct; not followed by Ellerman and Morrison-Scott (1951), Gao (1987), and Stroganov (1962). Lönnberg (1923b) believed that differences between pruinosus and arctos warranted subgeneric distinction as (Mylarctos) pruinosus; however, this was not supported by Pocock's (1932b) thorough revision. Synonyms allocated a...",
              'commentId': '18557',
              'commentTimeStamp': '2007-08-20 15:06:38.0',
              'commentator': 'Wilson & Reeder, eds. (2005)',
              'updateDate': '2014-02-03'}]
        
        .. code-block:: python
        
            itis.hierarchy_up(tsn = 36485)
        
            {'author': 'Raf.',
             'parentName': 'Asteraceae',
             'parentTsn': '35420',
             'rankName': 'Genus',
             'taxonName': 'Agoseris',
             'tsn': '36485'}
        
        Catalogue of Life
        =================
        
        .. code-block:: python
          
            from pytaxize import col
            x = col.children(name=["Apis"])
            x[0][0:3]
        
        .. code-block:: python
        
            [{'id': '7a4a38c5095963949d6d6ec917d471de',
              'name': 'Apis andreniformis',
              'rank': 'Species'},
             {'id': '39610a4ceff7e5244e334a3fbc5e47e5',
              'name': 'Apis cerana',
              'rank': 'Species'},
             {'id': 'e1d4cbf3872c6c310b7a1c17ddd00ebc',
              'name': 'Apis dorsata',
              'rank': 'Species'}]
        
        Parse names
        ===========
        
        Parse names using GBIF's parser API
        
        .. code-block:: python
            
            from pytaxize import gbif
            gbif.parse(name=['Arrhenatherum elatius var. elatius',
            	 'Secale cereale subsp. cereale', 'Secale cereale ssp. cereale',
               'Vanessa atalanta (Linnaeus, 1758)'])
        
        .. code-block:: python
        
            [{'scientificName': 'Arrhenatherum elatius var. elatius',
              'type': 'SCIENTIFIC',
              'genusOrAbove': 'Arrhenatherum',
              'specificEpithet': 'elatius',
              'infraSpecificEpithet': 'elatius',
              'parsed': True,
              'parsedPartially': False,
              'canonicalName': 'Arrhenatherum elatius elatius',
              'canonicalNameWithMarker': 'Arrhenatherum elatius var. elatius',
              'canonicalNameComplete': 'Arrhenatherum elatius var. elatius',
              'rankMarker': 'var.'},
             {'scientificName': 'Secale cereale subsp. cereale',
              'type': 'SCIENTIFIC',
              ...
        
        Contributors
        ============
        
        * `Scott Chamberlain <https://github.com/sckott>`__
        * `Colin Talbert <https://github.com/ColinTalbert>`__
        * `akshayah3 <https://github.com/akshayah3>`__
        * `panks <https://github.com/panks>`__
        * `Yanghao Li <https://github.com/lyttonhao>`__
        * `Ben Morris <https://github.com/bendmorris>`__
        * `Bishakh Ghosh <https://github.com/ghoshbishakh>`__
        * `Yoav Ram <https://github.com/yoavram>`__
        
        Meta
        ====
        
        * Please note that this project is released with a `Contributor Code of Conduct <https://github.com/sckott/pytaxize/blob/master/CONDUCT.md>`__. By participating in this project you agree to abide by its terms.
        * License: MIT; see `LICENSE file <https://github.com/sckott/pytaxize/blob/master/LICENSE>`__
        
        .. |pypi| image:: https://img.shields.io/pypi/v/pytaxize.svg
           :target: https://pypi.python.org/pypi/pytaxize
        
        .. |docs| image:: https://readthedocs.org/projects/pytaxize/badge/?version=latest
           :target: http://pytaxize.rtfd.org/
        
        .. |travis| image:: https://travis-ci.org/sckott/pytaxize.svg?branch=master
           :target: https://travis-ci.org/sckott/pytaxize
        
        .. |coverage| image:: https://codecov.io/gh/sckott/pytaxize/branch/master/graph/badge.svg
           :target: https://codecov.io/gh/sckott/pytaxize
        
        .. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
           :target: https://github.com/psf/black
        
        
        Changelog
        =========
        
        0.7.0 (2020-06-15)
        --------------------
        * first release to pypi
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Natural Language :: English
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Provides-Extra: test
Provides-Extra: dataframe
