Ndex2

-------------------

* Enhancements
* Added ``set_name()``, ``remove_node_attribute()``, ``remove_edge_attribute``,
``get_opaque_aspect()``, and ``set_opaque_aspect()`` to ``CX2Network`` class.

* Bug fixes
* Fixed bug in type conversion. Datatypes in shorter form such as 'str', 'int' etc. are accepted.

-------------------

* Enhancements
* Added ``add_network_attribute()``, ``add_node_attribute()``, ``add_edge_attribute()``, ``lookup_node_id_by_name()`` to ``CX2Network`` class.
* Added new parameters to ``get_cx2network`` in ``PandasDataFrameToCX2NetworkFactory`` to make it easier to convert Pandas Dataframe.
* Added ``get_nodelist_table()`` to ``CX2NetworkPandasDataFrameFactory`` class.

-------------------

* Enhancements
* Added ``CX2NetworkXFactory`` under ``cx2.py`` module to convert
``CX2Network`` object to `NetworkX Graph <https://networkx.org>`__
* Added ``NetworkXToCX2NetworkFactory`` under ``cx2.py`` module to convert
`NetworkX Graph <https://networkx.org>`__ to ``CX2Network`` object
* Added ``PandasDataFrameToCX2NetworkFactory`` under ``cx2.py`` module to
convert `Pandas DataFrame <https://pandas.org>`__ to ``CX2Network`` object
* Added ``CX2NetworkPandasDataFrameFactory`` under ``cx2.py`` module to convert
``CX2Network`` object to `Pandas DataFrame <https://pandas.org>`__

-------------------

* Enhancements
* Added ``CX2Network`` class under ``cx2.py`` module to represent networks `CX2 format <https://cytoscape.org/cx/cx2/specification/cytoscape-exchange-format-specification-(version-2)/>`__
* Added ``RawCX2NetworkFactory`` class under ``cx2.py`` to create ``CX2Network`` objects
* Added ``NoStyleCXToCX2NetworkFactory`` class under ``cx2.py`` to convert ``NiceCXNetwork`` to ``CX2Network``

* Bug fixes
* Fixed SyntaxWarnings `Issue 92 <https://github.com/ndexbio/ndex2-client/issues/92>`__

-------------------

* Bug fixes
* Fixed bug where ``ndex2.create_nice_cx_from_networkx()`` fails with numpy version 1.24
`Issue 96 <https://github.com/ndexbio/ndex2-client/issues/96>`__
* Updated post and put calls in ``client.py`` to only pass credentials if they are
set. This change is to accommodate changes in upcoming version 3 of requests library

-------------------

* Enhancements
* Added **skip_version_check** parameter to ``Ndex2()`` constructor to let caller
optionally bypass NDEx server call to see if **v2** endpoint is supported

* Added the following *CX2* methods to ``Ndex2()`` client:
``get_network_as_cx2_stream()``, ``get_network_aspect_as_cx2_stream()``,
``save_cx2_stream_as_new_network()``,
``save_new_cx2_network()``, and ``update_cx2_network()``
`Issue 87 <https://github.com/ndexbio/ndex2-client/issues/87>`__

* In ``Ndex2()`` client, methods that raise ``NDExError`` exceptions from calls
to NDEx server will now raise the more specific ``NDExUnauthorizedError``
subclass when the response from NDEx server is a 401 aka unauthorized.

* Added new parameters **dataconverter** and **include_attributes** to ``NiceCXNetwork.to_pandas_dataframe()``.
**dataconverter** parameter specifies data type conversion and **include_attributes** parameter lets
caller specify whether all node/edge attributes are added to the resulting DataFrame

* Added new parameter to ``ndex2.create_nice_cx_from_server()`` named **ndex_client**
that lets caller specify ``NDex2()`` client object to use.

* Passing ``None`` for the **server** positional parameter into ``ndex2.create_nice_cx_from_server(None, uuid='XXXX')`` will default to the production
NDEx server

* Bug fixes
* Fixed bug where creation of `NiceCXNetwork` from networkx via ``ndex2.create_nice_cx_from_networkx()``
incorrectly set the data type for boolean values to integer.
Issue `83 <https://github.com/ndexbio/ndex2-client/issues/83>`__

* Fixed bug where converting `NiceCXNetwork` to networkx and back does not handle
name attribute correctly. `Issue 84 <https://github.com/ndexbio/ndex2-client/issues/84>`__

* Fixed bug where `context` was lost if it was set as aspect in CX format and loaded
into NiceCXNetwork object.
`Issue 88 <https://github.com/ndexbio/ndex2-client/issues/88>`__

* Fixed bug where creation of `NiceCXNetwork` from networkx via ``ndex2.create_nice_cx_from_networkx()``
incorrectly set the data type for empty list to string.
Issue `90 <https://github.com/ndexbio/ndex2-client/issues/90>`__

* Fixed bug where Y coordinates of nodes would be inverted when converting to/from
networkx from `NiceCXNetwork`. This was due to differences in coordinate systems
between networkx and `NiceCXNetwork`

* `DefaultNetworkXFactory` networkx converter (used by ``NiceCXNetwork.to_networkx(mode='default')``)
no longer converts edge attributes that are of type list into strings delimited by
commas

* Fixed bug where ``ndex2.create_nice_cx_from_server()`` failed on networks
with `provenanceHistory` aspect

* Removals
* Removed unused test methods from internal class `NiceCXBuilder`:
``load_aspect()``, ``stream_aspect()``, ``stream_aspect_raw()``

* Removed the following deprecated methods from `NiceCXNetwork`:
``add_node()``, ``add_edge()``, ``get_edge_attribute_object()``,
``get_node_attribute_objects()``, ``get_edge_attribute_objects()``,
``add_metadata()``, ``get_provenance()``, ``set_provenance()``,
``__merge_node_attributes()``, ``create_from_pandas()``,
``create_from_networkx()``, ``create_from_server()``, ``upload_new_network_stream()``, &
``create_from_cx()``