pygbif
pygbif copied to clipboard
gbif
GBIF Python client
pygbif
|pypi| |docs| |ghactions| |coverage| |black|
Python client for the GBIF API <https://www.gbif.org/developer/summary>_
Source on GitHub at gbif/pygbif <https://github.com/gbif/pygbif>_
Other GBIF clients:
- R:
rgbif,ropensci/rgbif <https://github.com/ropensci/rgbif>_ - Ruby:
gbifrb,sckott/gbifrb <https://github.com/sckott/gbifrb>_ - PHP:
php-gbif,restelae/php-gbif <https://gitlab.res-telae.cat/restelae/php-gbif>_
Contributing: CONTRIBUTING.md <https://github.com/gbif/pygbif/blob/master/.github/CONTRIBUTING.md>_
Installation
Stable from pypi
.. code-block:: console
pip install pygbif
Development version
.. code-block:: console
[sudo] pip install git+git://github.com/gbif/pygbif.git#egg=pygbif
pygbif is split up into modules for each of the major groups of API methods.
- Registry - Datasets, Nodes, Installations, Networks, Organizations
- Species - Taxonomic names
- Occurrences - Occurrence data, including the download API
- Maps - Maps, get raster maps from GBIF as png or mvt
You can import the entire library, or each module individually as needed.
In addition there is a utils module, currently with one method: wkt_rewind, and
a caching method to manage whether HTTP requests are cached or not. See ?pygbif.caching.
Registry module
registry module API:
organizationsnodesnetworksinstallationsdatasetsdataset_metricsdataset_suggestdataset_search
Example usage:
.. code-block:: python
from pygbif import registry
registry.dataset_metrics(uuid='3f8a1297-3259-4700-91fc-acc4170b27ce')
Species module
species module API:
name_backbonename_suggestname_usagename_lookupname_parser
Example usage:
.. code-block:: python
from pygbif import species
species.name_suggest(q='Puma concolor')
Occurrences module
registry module API:
searchgetget_verbatimget_fragmentcountcount_basisofrecordcount_yearcount_datasetscount_countriescount_schemacount_publishingcountriesdownloaddownload_metadownload_listdownload_get
Example usage:
.. code-block:: python
from pygbif import occurrences as occ
occ.search(taxonKey = 3329049)
occ.get(key = 252408386)
occ.count(isGeoreferenced = True)
occ.download('basisOfRecord = PRESERVED_SPECIMEN')
occ.download('taxonKey = 3119195')
occ.download('decimalLatitude > 50')
occ.download_list(user = "sckott", limit = 5)
occ.download_meta(key = "0000099-140929101555934")
occ.download_get("0000066-140928181241064")
Maps module
maps module API:
map
Example usage:
.. code-block:: python
from pygbif import maps
out = maps.map(taxonKey = 212, year = 1998, bin = "hex",
hexPerTile = 30, style = "classic-noborder.poly")
out.response
out.path
out.img
out.plot()
.. image:: https://github.com/gbif/pygbif/raw/master/gbif_map.png :width: 25% :scale: 25%
utils module
utils module API:
wkt_rewind
Example usage:
.. code-block:: python
from pygbif import utils
x = 'POLYGON((144.6 13.2, 144.6 13.6, 144.9 13.6, 144.9 13.2, 144.6 13.2))'
utils.wkt_rewind(x)
Contributors
Scott Chamberlain <https://github.com/sckott>_Robert Forkel <https://github.com/xrotwang>_Jan Legind <https://github.com/jlegind>_Stijn Van Hoey <https://github.com/stijnvanhoey>_Peter Desmet <https://github.com/peterdesmet>_Nicolas Noé <https://github.com/niconoe>_
Meta
- License: MIT, see
LICENSE file <LICENSE>_ - Please note that this project is released with a
Contributor Code of Conduct <CONDUCT.md>_. By participating in this project you agree to abide by its terms.
.. |pypi| image:: https://img.shields.io/pypi/v/pygbif.svg :target: https://pypi.python.org/pypi/pygbif
.. |docs| image:: https://readthedocs.org/projects/pygbif/badge/?version=latest :target: http://pygbif.rtfd.org/
.. |ghactions| image:: https://github.com/gbif/pygbif/workflows/Python/badge.svg :target: https://github.com/gbif/pygbif/actions?query=workflow%3APython
.. |coverage| image:: https://codecov.io/gh/gbif/pygbif/branch/master/graph/badge.svg?token=frXPREGk1D :target: https://codecov.io/gh/gbif/pygbif
.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg :target: https://github.com/psf/black
gbif