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
==================
occurrences 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`
* `download_citation`
* `download_describe`
* `download_sql`
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")
occ.download_citation("0002526-241107131044228")
occ.download_describe("simpleCsv")
occ.download_sql("SELECT gbifid,countryCode FROM occurrence WHERE genusKey = 2435098")
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%
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
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:target: http://pygbif.rtfd.org/
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: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
=========
0.6.5 (2024-10-28)
------------------
- added support for `occurrences.download_citation` `158`
- added support for `occurrences.download_sql` `157`
- added support for `occurrences.download_describe` `142`
- added support for `literature.search` `149`
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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"description": "pygbif\n======\n\n|pypi| |docs| |ghactions| |coverage| |black|\n\nPython client for the `GBIF API <https://www.gbif.org/developer/summary>`_\n\n`Source on GitHub at gbif/pygbif <https://github.com/gbif/pygbif>`_\n\nOther GBIF clients:\n\n* R: `rgbif`, `ropensci/rgbif <https://github.com/ropensci/rgbif>`_\n* Ruby: `gbifrb`, `sckott/gbifrb <https://github.com/sckott/gbifrb>`_\n* PHP: `php-gbif`, `restelae/php-gbif <https://gitlab.res-telae.cat/restelae/php-gbif>`_\n\nContributing: `CONTRIBUTING.md <https://github.com/gbif/pygbif/blob/master/.github/CONTRIBUTING.md>`_\n\nInstallation\n============\n\nStable from pypi\n\n.. code-block:: console\n\n pip install pygbif\n\nDevelopment version\n\n.. code-block:: console\n\n [sudo] pip install git+git://github.com/gbif/pygbif.git#egg=pygbif\n\n\n`pygbif` is split up into modules for each of the major groups of API methods.\n\n* Registry - Datasets, Nodes, Installations, Networks, Organizations\n* Species - Taxonomic names\n* Occurrences - Occurrence data, including the download API\n* Maps - Maps, get raster maps from GBIF as png or mvt\n\nYou can import the entire library, or each module individually as needed.\n\nIn addition there is a utils module, currently with one method: `wkt_rewind`, and\na `caching` method to manage whether HTTP requests are cached or not. See `?pygbif.caching`.\n\nRegistry module\n===============\n\nregistry module API:\n\n* `organizations`\n* `nodes`\n* `networks`\n* `installations`\n* `datasets`\n* `dataset_metrics`\n* `dataset_suggest`\n* `dataset_search`\n\nExample usage:\n\n.. code-block:: python\n\n from pygbif import registry\n registry.dataset_metrics(uuid='3f8a1297-3259-4700-91fc-acc4170b27ce')\n\nSpecies module\n==============\n\nspecies module API:\n\n* `name_backbone`\n* `name_suggest`\n* `name_usage`\n* `name_lookup`\n* `name_parser`\n\nExample usage:\n\n.. code-block:: python\n\n from pygbif import species\n species.name_suggest(q='Puma concolor')\n\nOccurrences module\n==================\n\noccurrences module API:\n\n* `search`\n* `get`\n* `get_verbatim`\n* `get_fragment`\n* `count`\n* `count_basisofrecord`\n* `count_year`\n* `count_datasets`\n* `count_countries`\n* `count_schema`\n* `count_publishingcountries`\n* `download`\n* `download_meta`\n* `download_list`\n* `download_get`\n* `download_citation`\n* `download_describe`\n* `download_sql`\n\nExample usage:\n\n.. code-block:: python\n\n from pygbif import occurrences as occ\n occ.search(taxonKey = 3329049)\n occ.get(key = 252408386)\n occ.count(isGeoreferenced = True)\n occ.download('basisOfRecord = PRESERVED_SPECIMEN')\n occ.download('taxonKey = 3119195')\n occ.download('decimalLatitude > 50')\n occ.download_list(user = \"sckott\", limit = 5)\n occ.download_meta(key = \"0000099-140929101555934\")\n occ.download_get(\"0000066-140928181241064\")\n occ.download_citation(\"0002526-241107131044228\")\n occ.download_describe(\"simpleCsv\")\n occ.download_sql(\"SELECT gbifid,countryCode FROM occurrence WHERE genusKey = 2435098\")\n\nMaps module\n===========\n\nmaps module API:\n\n* `map`\n\nExample usage:\n\n.. code-block:: python\n\n from pygbif import maps\n out = maps.map(taxonKey = 212, year = 1998, bin = \"hex\",\n hexPerTile = 30, style = \"classic-noborder.poly\")\n out.response\n out.path\n out.img\n out.plot()\n\n.. image:: https://github.com/gbif/pygbif/raw/master/gbif_map.png\n :width: 25%\n\nutils module\n============\n\nutils module API:\n\n* `wkt_rewind`\n\nExample usage:\n\n.. code-block:: python\n\n from pygbif import utils\n x = 'POLYGON((144.6 13.2, 144.6 13.6, 144.9 13.6, 144.9 13.2, 144.6 13.2))'\n utils.wkt_rewind(x)\n\n\n\nContributors\n============\n\n* `Scott Chamberlain <https://github.com/sckott>`_\n* `Robert Forkel <https://github.com/xrotwang>`_\n* `Jan Legind <https://github.com/jlegind>`_\n* `Stijn Van Hoey <https://github.com/stijnvanhoey>`_\n* `Peter Desmet <https://github.com/peterdesmet>`_\n* `Nicolas No\u00e9 <https://github.com/niconoe>`_\n\nMeta\n====\n\n* License: MIT, see `LICENSE file <LICENSE>`_\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.\n\n.. |pypi| image:: https://img.shields.io/pypi/v/pygbif.svg\n :target: https://pypi.python.org/pypi/pygbif\n\n.. |docs| image:: https://readthedocs.org/projects/pygbif/badge/?version=latest\n :target: http://pygbif.rtfd.org/\n\n.. |ghactions| image:: https://github.com/gbif/pygbif/workflows/Python/badge.svg\n :target: https://github.com/gbif/pygbif/actions?query=workflow%3APython\n\n.. |coverage| image:: https://codecov.io/gh/gbif/pygbif/branch/master/graph/badge.svg?token=frXPREGk1D\n :target: https://codecov.io/gh/gbif/pygbif\n\n.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg\n :target: https://github.com/psf/black\n\n\n\n\nChangelog\n=========\n0.6.5 (2024-10-28)\n------------------\n- added support for `occurrences.download_citation` `158`\n- added support for `occurrences.download_sql` `157`\n- added support for `occurrences.download_describe` `142`\n- added support for `literature.search` `149`\n\n0.6.4 (2024-03-12)\n------------------\n- fixed a bug in building the documentation with readthedocs `138`, `129`\n- tests now run against live GBIF APIs `101`, `128` \n- updated caching.py since the ``remove_expired_responses`` method is deprecated. `126`\n\n0.6.3 (2023-05-25)\n------------------\n- added support for predicates: ``isNull``, ``isNotNull``, ``in`` and ``not`` `92`, `102` and `103` \n- added support for nested queries/dictionaries `104`\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`\n- added support for multiple download formats `105`\n- updated operators and look-up tables `107`\n- included documentation on newly supported predicates and dictionaries `106`\n\n0.6.2 (2023-01-24)\n------------------\n- update to fix requesting GBIF downloads\n- minor documentation updates `95` and `99`\n\n0.6.1 (2022-06-23)\n------------------\n- update to fix broken dependencies `93`\n- minor documentation updates\n\n0.6.0 (2021-07-08)\n------------------\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`\n- Moved to using the `logging` module instead of `print()` for giving information on occurrence download methods `78`\n- Clarify that `occurrences.count` for length 1 inputs only; see `occurrences.search` for > 1 value `75` `77`\n- Improved documentation for `species.name_usage` method, mostly for the `language` parameter `68`\n- Gains download method `download_cancel` for cancelling/deleting a download request `59`\n\n0.5.0 (2020-09-29)\n------------------\n- `occurrences.search` now supports `recordedByID` and `identifiedByID` search parameters `62`\n- clean up the Contributing file, thanks @niconoe `64`\n- clean up internal imports in the library, thanks @niconoe `65`\n- fix usage of `is` and `==`, was using them inappropriately sometimes (via https://realpython.com/python-is-identity-vs-equality/), `69`\n- remove redundant parameter in a doc string, thanks @faroit `71`\n- make a test for internal fxn `gbif_GET_write` more general to avoid errors if GBIF changes content type response header slightly `72`\n\n0.4.0 (2019-11-20)\n------------------\n- changed base url to https for all requests; was already https for maps and downloads in previous versions\n- occurrences, species, and registry modules gain docstrings with brief summary of each method\n- pygbif gains ability to cache http requests. caching is off by default. See `?pygbif.caching` for all the details `52` `56` via @nleguillarme\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\n- for parameters that expect a `bool`, convert them to lowercase strings internally before doing HTTP requests\n\n0.3.0 (2019-01-25)\n------------------\n- pygbif is Python 3 only now `19`\n- Gains maps module with maps.map method for working with the GBIF maps API `41` `49`\n- Gains new module utils with one method `wkt_rewind` `46` thanks @aubreymoore for the inspiration\n- Fixed bug in registry.installations: typo in one of the parameters `identifierTyp` instead of `identifierType` `48` thanks @data-biodiversity-aq\n- Link to GitHub issues from Changelog \ud83c\udf89\n- Fix a occurrence download test `47`\n- Much more thorough docs `25`\n\n0.2.0 (2016-10-18)\n------------------\n- Download methods much improved `16` `27` thanks @jlegind @stijnvanhoey @peterdesmet !\n- MULTIPOLYGON now supported in `geometry` parameter `35`\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`\n- Added `organizations` method to `registry` module `12`\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`\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`\n- Added more tests to cover new methods\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.\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`\n\n0.1.5.4 (2016-10-01)\n--------------------\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`\n- Fixes to `**kwargs` in `occurrence.search` so that facet parameters can be parsed correctly and `requests` GET\trequest options are collected correctly `36`\n- Added `spellCheck` parameter to `occurrence.search` that goes along with the `q` parameter to optionally spell check full text searches `31`\n\n0.1.4 (2016-06-04)\n------------------\n- Added variable types throughout docs\n- Changed default `limit` value to 300 for `occurrences.search` method\n- `tox` now included, via @xrotwang `20`\n- Added more registry methods `11`\n- Started occurrence download methods `16`\n- Added more names methods `18`\n- All requests now send user-agent headers with `requests` and `pygbif` versions `13`\n- Bug fix for `occurrences.download_get` `23`\n- Fixed bad example for `occurrences.get` `22`\n- Fixed wheel to be universal for 2 and 3 `10`\n- Improved documentation a lot, autodoc methods now\n\n0.1.1 (2015-11-03)\n------------------\n- Fixed distribution for pypi\n\n0.1.0 (2015-11-02)\n------------------\n- First release\n",
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