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https://github.com/gbif/pygbif

GBIF Python client
https://github.com/gbif/pygbif

api biodiversity data ecology gbif

Last synced: 3 months ago
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GBIF Python client

Host: GitHub
URL: https://github.com/gbif/pygbif
Owner: gbif
License: mit
Created: 2014-12-31T05:36:27.000Z (about 10 years ago)
Default Branch: master
Last Pushed: 2024-10-04T09:56:42.000Z (4 months ago)
Last Synced: 2024-10-17T19:26:31.101Z (3 months ago)
Topics: api, biodiversity, data, ecology, gbif
Language: Python
Homepage: https://pygbif.readthedocs.io/en/latest/
Size: 20.5 MB
Stars: 111
Watchers: 19
Forks: 28
Open Issues: 30
Metadata Files:
- Readme: README.rst
- Changelog: Changelog.rst
- Contributing: .github/CONTRIBUTING.md
- License: LICENSE

Awesome Lists containing this project

open-sustainable-technology - pygbif - Making the data of the Global Biodiversity Information Facility API accessible via Python. (Biosphere / Biodiversity Data Access and Management)

README

        pygbif

======

|pypi| |docs| |ghactions| |coverage| |black|

Python client for the `GBIF API `_

`Source on GitHub at gbif/pygbif `_

Other GBIF clients:

* R: `rgbif`, `ropensci/rgbif `_

* Ruby: `gbifrb`, `sckott/gbifrb `_

* PHP: `php-gbif`, `restelae/php-gbif `_

Contributing: `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:

* `organizations`

* `nodes`

* `networks`

* `installations`

* `datasets`

* `dataset_metrics`

* `dataset_suggest`

* `dataset_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_backbone`

* `name_suggest`

* `name_usage`

* `name_lookup`

* `name_parser`

Example usage:

.. code-block:: python

    from pygbif import species

    species.name_suggest(q='Puma concolor')

Occurrences module

==================

registry module API:

* `search`

* `get`

* `get_verbatim`

* `get_fragment`

* `count`

* `count_basisofrecord`

* `count_year`

* `count_datasets`

* `count_countries`

* `count_schema`

* `count_publishingcountries`

* `download`

* `download_meta`

* `download_list`

* `download_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 `_

* `Robert Forkel `_

* `Jan Legind `_

* `Stijn Van Hoey `_

* `Peter Desmet `_

* `Nicolas Noé `_

Meta

====

* License: MIT, see `LICENSE file `_

* Please note that this project is released with a `Contributor Code of Conduct `_. 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