Fix. Resolving merge conflicts

.gitignore

@@ -20,6 +20,6 @@
 test.py
 tests.sh
 .gitpod.yml
-.vscode
-.pytest_cache
-Function_Changes.md
+EXAMPLES.md
+Function_Changes.md
+.vscode

README.rst

@@ -6,7 +6,7 @@ pyobis
 Python client for the `OBIS API
 <https://api.obis.org/>`__.
 
-`Source on GitHub at iobis/pyobis <https://github.com/iobis/pyobis>`__
+`Source Code here  <https://github.com/iobis/pyobis>`__
 
 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>`__
+* 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/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

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

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