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:
* `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 <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
Changelog
=========
0.6.4 (2024-03-12)
------------------
- fixed a bug in building the documentation with readthedocs `138`, `129`
- tests now run against live GBIF APIs `101`, `128`
- updated caching.py since the ``remove_expired_responses`` method is deprecated. `126`
0.6.3 (2023-05-25)
------------------
- added support for predicates: ``isNull``, ``isNotNull``, ``in`` and ``not`` `92`, `102` and `103`
- added support for nested queries/dictionaries `104`
- deprecated the ``add_predicate`` function and added ``add_pred_dict`` to accomodate for newly supported predicates to ensure that the arguments that are sent are added in the payload function `108`
- added support for multiple download formats `105`
- updated operators and look-up tables `107`
- included documentation on newly supported predicates and dictionaries `106`
0.6.2 (2023-01-24)
------------------
- update to fix requesting GBIF downloads
- minor documentation updates `95` and `99`
0.6.1 (2022-06-23)
------------------
- update to fix broken dependencies `93`
- minor documentation updates
0.6.0 (2021-07-08)
------------------
- Fix for `occurrences.download` when giving `geometry` as a string rather than using `add_geometry`; predicates were being split on whitespace, which doesn't work for WKT `81` `84`
- Moved to using the `logging` module instead of `print()` for giving information on occurrence download methods `78`
- Clarify that `occurrences.count` for length 1 inputs only; see `occurrences.search` for > 1 value `75` `77`
- Improved documentation for `species.name_usage` method, mostly for the `language` parameter `68`
- Gains download method `download_cancel` for cancelling/deleting a download request `59`
0.5.0 (2020-09-29)
------------------
- `occurrences.search` now supports `recordedByID` and `identifiedByID` search parameters `62`
- clean up the Contributing file, thanks @niconoe `64`
- clean up internal imports in the library, thanks @niconoe `65`
- fix usage of `is` and `==`, was using them inappropriately sometimes (via https://realpython.com/python-is-identity-vs-equality/), `69`
- remove redundant parameter in a doc string, thanks @faroit `71`
- make a test for internal fxn `gbif_GET_write` more general to avoid errors if GBIF changes content type response header slightly `72`
0.4.0 (2019-11-20)
------------------
- changed base url to https for all requests; was already https for maps and downloads in previous versions
- occurrences, species, and registry modules gain docstrings with brief summary of each method
- pygbif gains ability to cache http requests. caching is off by default. See `?pygbif.caching` for all the details `52` `56` via @nleguillarme
- made note in docs that if you are trying to get the same behavior as the GBIF website for name searching, `species.name_backbone` is likely what you want `55` thanks @qgroom
- for parameters that expect a `bool`, convert them to lowercase strings internally before doing HTTP requests
0.3.0 (2019-01-25)
------------------
- pygbif is Python 3 only now `19`
- Gains maps module with maps.map method for working with the GBIF maps API `41` `49`
- Gains new module utils with one method `wkt_rewind` `46` thanks @aubreymoore for the inspiration
- Fixed bug in registry.installations: typo in one of the parameters `identifierTyp` instead of `identifierType` `48` thanks @data-biodiversity-aq
- Link to GitHub issues from Changelog 🎉
- Fix a occurrence download test `47`
- Much more thorough docs `25`
0.2.0 (2016-10-18)
------------------
- Download methods much improved `16` `27` thanks @jlegind @stijnvanhoey @peterdesmet !
- MULTIPOLYGON now supported in `geometry` parameter `35`
- Fixed docs for `occurrences.get`, and `occurrences.get_verbatim`, `occurrences.get_fragment` and demo that used occurrence keys that no longer exist in GBIF `39`
- Added `organizations` method to `registry` module `12`
- Added remainder of datasets methods: `registry.dataset_search` (including faceting support `37`) and `registry.dataset_suggest`, for the `/dataset/search` and `/dataset/suggest` routes, respectively `40`
- Added remainder of species methods: `species.name_lookup` (including faceting support `38`) and `species.name_usage`, for the `/species/search` and `/species` routes, respectively `18`
- Added more tests to cover new methods
- Changed `species.name_suggest` to give back data stucture as received from GBIF. We used to parse out the classification data, but for simplicity and speed, that is left up to the user now.
- `start` parameter in `species.name_suggest`, `occurrences.download_list`, `registry.organizations`, `registry.nodes`, `registry.networks`, and `registry.installations`, changed to `offset` to match GBIF API and match usage throughout remainder of `pygbif`
0.1.5.4 (2016-10-01)
--------------------
- Added many new `occurrence.search` parameters, including `repatriated`, `kingdomKey`, `phylumKey`, `classKey`, `orderKey`, `familyKey`, `genusKey`, `subgenusKey`, `establishmentMeans`, `facet`, `facetMincount`, `facetMultiselect`, and support for facet paging via `**kwargs` `30` `34`
- Fixes to `**kwargs` in `occurrence.search` so that facet parameters can be parsed correctly and `requests` GET request options are collected correctly `36`
- Added `spellCheck` parameter to `occurrence.search` that goes along with the `q` parameter to optionally spell check full text searches `31`
0.1.4 (2016-06-04)
------------------
- Added variable types throughout docs
- Changed default `limit` value to 300 for `occurrences.search` method
- `tox` now included, via @xrotwang `20`
- Added more registry methods `11`
- Started occurrence download methods `16`
- Added more names methods `18`
- All requests now send user-agent headers with `requests` and `pygbif` versions `13`
- Bug fix for `occurrences.download_get` `23`
- Fixed bad example for `occurrences.get` `22`
- Fixed wheel to be universal for 2 and 3 `10`
- Improved documentation a lot, autodoc methods now
0.1.1 (2015-11-03)
------------------
- Fixed distribution for pypi
0.1.0 (2015-11-02)
------------------
- First release
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"keywords": "gbif,biodiversity,specimens,API,web-services,occurrences,species,taxonomy",
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"description": "pygbif\r\n======\r\n\r\n|pypi| |docs| |ghactions| |coverage| |black|\r\n\r\nPython client for the `GBIF API <https://www.gbif.org/developer/summary>`_\r\n\r\n`Source on GitHub at gbif/pygbif <https://github.com/gbif/pygbif>`_\r\n\r\nOther GBIF clients:\r\n\r\n* R: `rgbif`, `ropensci/rgbif <https://github.com/ropensci/rgbif>`_\r\n* Ruby: `gbifrb`, `sckott/gbifrb <https://github.com/sckott/gbifrb>`_\r\n* PHP: `php-gbif`, `restelae/php-gbif <https://gitlab.res-telae.cat/restelae/php-gbif>`_\r\n\r\nContributing: `CONTRIBUTING.md <https://github.com/gbif/pygbif/blob/master/.github/CONTRIBUTING.md>`_\r\n\r\nInstallation\r\n============\r\n\r\nStable from pypi\r\n\r\n.. code-block:: console\r\n\r\n pip install pygbif\r\n\r\nDevelopment version\r\n\r\n.. code-block:: console\r\n\r\n [sudo] pip install git+git://github.com/gbif/pygbif.git#egg=pygbif\r\n\r\n\r\n`pygbif` is split up into modules for each of the major groups of API methods.\r\n\r\n* Registry - Datasets, Nodes, Installations, Networks, Organizations\r\n* Species - Taxonomic names\r\n* Occurrences - Occurrence data, including the download API\r\n* Maps - Maps, get raster maps from GBIF as png or mvt\r\n\r\nYou can import the entire library, or each module individually as needed.\r\n\r\nIn addition there is a utils module, currently with one method: `wkt_rewind`, and\r\na `caching` method to manage whether HTTP requests are cached or not. See `?pygbif.caching`.\r\n\r\nRegistry module\r\n===============\r\n\r\nregistry module API:\r\n\r\n* `organizations`\r\n* `nodes`\r\n* `networks`\r\n* `installations`\r\n* `datasets`\r\n* `dataset_metrics`\r\n* `dataset_suggest`\r\n* `dataset_search`\r\n\r\nExample usage:\r\n\r\n.. code-block:: python\r\n\r\n from pygbif import registry\r\n registry.dataset_metrics(uuid='3f8a1297-3259-4700-91fc-acc4170b27ce')\r\n\r\nSpecies module\r\n==============\r\n\r\nspecies module API:\r\n\r\n* `name_backbone`\r\n* `name_suggest`\r\n* `name_usage`\r\n* `name_lookup`\r\n* `name_parser`\r\n\r\nExample usage:\r\n\r\n.. code-block:: python\r\n\r\n from pygbif import species\r\n species.name_suggest(q='Puma concolor')\r\n\r\nOccurrences module\r\n==================\r\n\r\nregistry module API:\r\n\r\n* `search`\r\n* `get`\r\n* `get_verbatim`\r\n* `get_fragment`\r\n* `count`\r\n* `count_basisofrecord`\r\n* `count_year`\r\n* `count_datasets`\r\n* `count_countries`\r\n* `count_schema`\r\n* `count_publishingcountries`\r\n* `download`\r\n* `download_meta`\r\n* `download_list`\r\n* `download_get`\r\n\r\nExample usage:\r\n\r\n.. code-block:: python\r\n\r\n from pygbif import occurrences as occ\r\n occ.search(taxonKey = 3329049)\r\n occ.get(key = 252408386)\r\n occ.count(isGeoreferenced = True)\r\n occ.download('basisOfRecord = PRESERVED_SPECIMEN')\r\n occ.download('taxonKey = 3119195')\r\n occ.download('decimalLatitude > 50')\r\n occ.download_list(user = \"sckott\", limit = 5)\r\n occ.download_meta(key = \"0000099-140929101555934\")\r\n occ.download_get(\"0000066-140928181241064\")\r\n\r\nMaps module\r\n===========\r\n\r\nmaps module API:\r\n\r\n* `map`\r\n\r\nExample usage:\r\n\r\n.. code-block:: python\r\n\r\n from pygbif import maps\r\n out = maps.map(taxonKey = 212, year = 1998, bin = \"hex\",\r\n hexPerTile = 30, style = \"classic-noborder.poly\")\r\n out.response\r\n out.path\r\n out.img\r\n out.plot()\r\n\r\n.. image:: https://github.com/gbif/pygbif/raw/master/gbif_map.png\r\n :width: 25%\r\n :scale: 25%\r\n\r\nutils module\r\n============\r\n\r\nutils module API:\r\n\r\n* `wkt_rewind`\r\n\r\nExample usage:\r\n\r\n.. code-block:: python\r\n\r\n from pygbif import utils\r\n x = 'POLYGON((144.6 13.2, 144.6 13.6, 144.9 13.6, 144.9 13.2, 144.6 13.2))'\r\n utils.wkt_rewind(x)\r\n\r\n\r\n\r\nContributors\r\n============\r\n\r\n* `Scott Chamberlain <https://github.com/sckott>`_\r\n* `Robert Forkel <https://github.com/xrotwang>`_\r\n* `Jan Legind <https://github.com/jlegind>`_\r\n* `Stijn Van Hoey <https://github.com/stijnvanhoey>`_\r\n* `Peter Desmet <https://github.com/peterdesmet>`_\r\n* `Nicolas No\u00e9 <https://github.com/niconoe>`_\r\n\r\nMeta\r\n====\r\n\r\n* License: MIT, see `LICENSE file <LICENSE>`_\r\n* 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.\r\n\r\n.. |pypi| image:: https://img.shields.io/pypi/v/pygbif.svg\r\n :target: https://pypi.python.org/pypi/pygbif\r\n\r\n.. |docs| image:: https://readthedocs.org/projects/pygbif/badge/?version=latest\r\n :target: http://pygbif.rtfd.org/\r\n\r\n.. |ghactions| image:: https://github.com/gbif/pygbif/workflows/Python/badge.svg\r\n :target: https://github.com/gbif/pygbif/actions?query=workflow%3APython\r\n\r\n.. |coverage| image:: https://codecov.io/gh/gbif/pygbif/branch/master/graph/badge.svg?token=frXPREGk1D\r\n :target: https://codecov.io/gh/gbif/pygbif\r\n\r\n.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg\r\n :target: https://github.com/psf/black\r\n\r\n\r\n\r\n\r\nChangelog\r\n=========\r\n0.6.4 (2024-03-12)\r\n------------------\r\n- fixed a bug in building the documentation with readthedocs `138`, `129`\r\n- tests now run against live GBIF APIs `101`, `128` \r\n- updated caching.py since the ``remove_expired_responses`` method is deprecated. `126`\r\n\r\n0.6.3 (2023-05-25)\r\n------------------\r\n- added support for predicates: ``isNull``, ``isNotNull``, ``in`` and ``not`` `92`, `102` and `103` \r\n- added support for nested queries/dictionaries `104`\r\n- deprecated the ``add_predicate`` function and added ``add_pred_dict`` to accomodate for newly supported predicates to ensure that the arguments that are sent are added in the payload function `108`\r\n- added support for multiple download formats `105`\r\n- updated operators and look-up tables `107`\r\n- included documentation on newly supported predicates and dictionaries `106`\r\n\r\n0.6.2 (2023-01-24)\r\n------------------\r\n- update to fix requesting GBIF downloads\r\n- minor documentation updates `95` and `99`\r\n\r\n0.6.1 (2022-06-23)\r\n------------------\r\n- update to fix broken dependencies `93`\r\n- minor documentation updates\r\n\r\n0.6.0 (2021-07-08)\r\n------------------\r\n- Fix for `occurrences.download` when giving `geometry` as a string rather than using `add_geometry`; predicates were being split on whitespace, which doesn't work for WKT `81` `84`\r\n- Moved to using the `logging` module instead of `print()` for giving information on occurrence download methods `78`\r\n- Clarify that `occurrences.count` for length 1 inputs only; see `occurrences.search` for > 1 value `75` `77`\r\n- Improved documentation for `species.name_usage` method, mostly for the `language` parameter `68`\r\n- Gains download method `download_cancel` for cancelling/deleting a download request `59`\r\n\r\n0.5.0 (2020-09-29)\r\n------------------\r\n- `occurrences.search` now supports `recordedByID` and `identifiedByID` search parameters `62`\r\n- clean up the Contributing file, thanks @niconoe `64`\r\n- clean up internal imports in the library, thanks @niconoe `65`\r\n- fix usage of `is` and `==`, was using them inappropriately sometimes (via https://realpython.com/python-is-identity-vs-equality/), `69`\r\n- remove redundant parameter in a doc string, thanks @faroit `71`\r\n- make a test for internal fxn `gbif_GET_write` more general to avoid errors if GBIF changes content type response header slightly `72`\r\n\r\n0.4.0 (2019-11-20)\r\n------------------\r\n- changed base url to https for all requests; was already https for maps and downloads in previous versions\r\n- occurrences, species, and registry modules gain docstrings with brief summary of each method\r\n- pygbif gains ability to cache http requests. caching is off by default. See `?pygbif.caching` for all the details `52` `56` via @nleguillarme\r\n- made note in docs that if you are trying to get the same behavior as the GBIF website for name searching, `species.name_backbone` is likely what you want `55` thanks @qgroom\r\n- for parameters that expect a `bool`, convert them to lowercase strings internally before doing HTTP requests\r\n\r\n0.3.0 (2019-01-25)\r\n------------------\r\n- pygbif is Python 3 only now `19`\r\n- Gains maps module with maps.map method for working with the GBIF maps API `41` `49`\r\n- Gains new module utils with one method `wkt_rewind` `46` thanks @aubreymoore for the inspiration\r\n- Fixed bug in registry.installations: typo in one of the parameters `identifierTyp` instead of `identifierType` `48` thanks @data-biodiversity-aq\r\n- Link to GitHub issues from Changelog \ud83c\udf89\r\n- Fix a occurrence download test `47`\r\n- Much more thorough docs `25`\r\n\r\n0.2.0 (2016-10-18)\r\n------------------\r\n- Download methods much improved `16` `27` thanks @jlegind @stijnvanhoey @peterdesmet !\r\n- MULTIPOLYGON now supported in `geometry` parameter `35`\r\n- Fixed docs for `occurrences.get`, and `occurrences.get_verbatim`, `occurrences.get_fragment` and demo that used occurrence keys that no longer exist in GBIF `39`\r\n- Added `organizations` method to `registry` module `12`\r\n- Added remainder of datasets methods: `registry.dataset_search` (including faceting support `37`) and `registry.dataset_suggest`, for the `/dataset/search` and `/dataset/suggest` routes, respectively `40`\r\n- Added remainder of species methods: `species.name_lookup` (including faceting support `38`) and `species.name_usage`, for the `/species/search` and `/species` routes, respectively `18`\r\n- Added more tests to cover new methods\r\n- Changed `species.name_suggest` to give back data stucture as received from GBIF. We used to parse out the classification data, but for simplicity and speed, that is left up to the user now.\r\n- `start` parameter in `species.name_suggest`, `occurrences.download_list`, `registry.organizations`, `registry.nodes`, `registry.networks`, and `registry.installations`, changed to `offset` to match GBIF API and match usage throughout remainder of `pygbif`\r\n\r\n0.1.5.4 (2016-10-01)\r\n--------------------\r\n- Added many new `occurrence.search` parameters, including `repatriated`, `kingdomKey`, `phylumKey`, `classKey`, `orderKey`, `familyKey`, `genusKey`, `subgenusKey`, `establishmentMeans`, `facet`, `facetMincount`, `facetMultiselect`, and support for facet paging via\t`**kwargs` `30` `34`\r\n- Fixes to `**kwargs` in `occurrence.search` so that facet parameters can be parsed correctly and `requests` GET\trequest options are collected correctly `36`\r\n- Added `spellCheck` parameter to `occurrence.search` that goes along with the `q` parameter to optionally spell check full text searches `31`\r\n\r\n0.1.4 (2016-06-04)\r\n------------------\r\n- Added variable types throughout docs\r\n- Changed default `limit` value to 300 for `occurrences.search` method\r\n- `tox` now included, via @xrotwang `20`\r\n- Added more registry methods `11`\r\n- Started occurrence download methods `16`\r\n- Added more names methods `18`\r\n- All requests now send user-agent headers with `requests` and `pygbif` versions `13`\r\n- Bug fix for `occurrences.download_get` `23`\r\n- Fixed bad example for `occurrences.get` `22`\r\n- Fixed wheel to be universal for 2 and 3 `10`\r\n- Improved documentation a lot, autodoc methods now\r\n\r\n0.1.1 (2015-11-03)\r\n------------------\r\n- Fixed distribution for pypi\r\n\r\n0.1.0 (2015-11-02)\r\n------------------\r\n- First release\r\n",
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