diff --git a/.gitignore b/.gitignore
index d79ee0a9..f82fec7f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -20,6 +20,6 @@
test.py
tests.sh
.gitpod.yml
-.vscode
-.pytest_cache
-Function_Changes.md
\ No newline at end of file
+EXAMPLES.md
+Function_Changes.md
+.vscode
\ No newline at end of file
diff --git a/README.rst b/README.rst
index 2b1c818f..72d72f97 100644
--- a/README.rst
+++ b/README.rst
@@ -6,7 +6,7 @@ pyobis
Python client for the `OBIS API
`__.
-`Source on GitHub at iobis/pyobis `__
+`Source Code here `__
Other OBIS clients:
@@ -28,7 +28,7 @@ dev version
pip install git+git://github.com/sckott/pyobis.git#egg=pyobis
-library API
+Library API
===========
`pyobis` is split up into modules for each of the groups of API methods.
@@ -39,6 +39,11 @@ library API
* `nodes` - Nodes
* `checklist` - Checklist
+
+
+Usage
+===========
+
You can import the entire library, or each module individually as needed.
Taxa module
@@ -83,7 +88,7 @@ Dataset module
from pyobis import dataset
dataset.search(scientificname = ['Mola', 'Abra', 'Lanice', 'Pectinaria'])
- dataset.get(id = 'ec9df3b9-3b2b-4d83-881b-27bcbcd57b95')
+ dataset.get(id = 2126)
Nodes module
===========
@@ -104,7 +109,7 @@ Checklist module
Meta
====
-* License: MIT, see `LICENSE file `__
+* 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/pyobis.svg
@@ -113,8 +118,8 @@ Meta
.. |docs| image:: https://readthedocs.org/projects/pyobis/badge/?version=latest
:target: http://pyobis.readthedocs.org/en/latest/?badge=latest
-.. |tests| image:: https://github.com/ayushanand18/pyobis/actions/workflows/tests.yml/badge.svg
- :target: https://github.com/ayushanand18/pyobis/actions/workflows/tests.yml
+.. |tests| image:: https://github.com/iobis/pyobis/actions/workflows/tests.yml/badge.svg
+ :target: https://github.com/iobis/pyobis/actions/workflows/tests.yml
.. |coverage| image:: https://coveralls.io/repos/sckott/pyobis/badge.svg?branch=master&service=github
- :target: https://coveralls.io/github/sckott/pyobis?branch=gsoc2022
+ :target: https://coveralls.io/github/sckott/pyobis?branch=master
\ No newline at end of file
diff --git a/pyobis/__init__.py b/pyobis/__init__.py
index b9818fc2..376f99f7 100644
--- a/pyobis/__init__.py
+++ b/pyobis/__init__.py
@@ -5,8 +5,11 @@
'''
pyobis library
~~~~~~~~~~~~~~~~~~~~~
+
pyobis is a Python client for OBIS.
+
Example usage:
+
# Import entire library
import pyobis
# or import modules as needed
@@ -18,6 +21,7 @@
from pyobis import dataset
## checklist
from pyobis import checklist
+
## use advanced logging
### setup first
import requests
@@ -40,7 +44,7 @@
__license__ = 'MIT'
from .occurrences import search, get, grid, getpoints, point, tile, centroid, download, ObisDownload
-from .taxa import search, taxon, annotations
+from .taxa import search, taxon, annotations, common, taxon_search
from .nodes import search, activities
from .dataset import get, search
from .checklist import list, redlist, newest
\ No newline at end of file
diff --git a/pyobis/taxa/taxa.py b/pyobis/taxa/taxa.py
index 4c9556f4..4368c123 100644
--- a/pyobis/taxa/taxa.py
+++ b/pyobis/taxa/taxa.py
@@ -5,7 +5,7 @@ def search(scientificname=None, **kwargs):
Get taxon records.
:param scientificname: [String,Array] One or more scientific names from the OBIS backbone. All included and synonym taxa
are included in the search.
-
+
:return: A dictionary
Usage::
@@ -41,18 +41,61 @@ def taxon(id, **kwargs):
out = obis_GET(url, {}, 'application/json; charset=utf-8', **kwargs)
return out
-def annotations(scientificname=None, **kwargs):
+def annotations(scientificname, **kwargs):
'''
Get scientific name annotations by the WoRMS team.
:param scientificname: [String] Scientific name. Leave empty to include all taxa.
-
:return: A dictionary
Usage::
from pyobis import taxa
- taxa.annotations('Abra')
+ taxa.annotations(Abra)
'''
url = obis_baseurl + 'taxon/annotations'
scientificname = handle_arrstr(scientificname)
out = obis_GET(url, {'scientificname':scientificname}, 'application/json; charset=utf-8', **kwargs)
return out
+
+def taxon_search(scientificname=None, aphiaid=None, obisid=None, **kwargs):
+ '''
+ This function has become obsolete.
+
+ :param id: [Fixnum] An OBIS taxon identifier
+
+ :return: A dictionary
+
+ Usage::
+
+ from pyobis import taxa
+ taxa.taxon_search(scientificname = 'Mola mola')
+ taxa.taxon_search(scientificname = 'Mola')
+ taxa.taxon_search(aphiaid = 127405)
+ taxa.taxon_search(obisid = 472375)
+ '''
+ url = obis_baseurl + 'taxon/' + handle_arrstr(scientificname)
+ out = obis_GET(url, {'aphiaid': aphiaid, 'obisid': obisid,
+ 'scientificname': scientificname}, 'application/json; charset=utf-8', **kwargs)
+ return out
+
+def common(id, **kwargs):
+ '''
+ This function has become obsolete.
+
+ Get common names for a taxon by ID
+
+ :param id: [Fixnum] An OBIS taxon identifier. Required
+
+ :return: A dictionary
+
+ Usage::
+
+ from pyobis import taxa
+ # have common names
+ taxa.common(402913)
+ taxa.common(406296)
+ # no common names
+ taxa.common(415282)
+ '''
+ url = obis_baseurl + 'taxon/' + str(id) + '/common'
+ out = obis_GET(url, {}, 'application/json; charset=utf-8', **kwargs)
+ return out
\ No newline at end of file