Ndex2

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

* 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()``

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

* Added **offset** and **limit** parameters to `Ndex2.get_network_ids_for_user()` to enable
retrieval of all networks for a user.
`Issue 78 <https://github.com/ndexbio/ndex2-client/issues/78>`__

* Switched `NiceCXNetwork.upload_to()` to named arguments and added **client** parameter.
`Issue 80 <https://github.com/ndexbio/ndex2-client/issues/80>`__

* Switched `NiceCXNetwork.update_to()` to named arguments and added **client** parameter.
`Issue 81 <https://github.com/ndexbio/ndex2-client/issues/81>`__

* Fixed documentation `NiceCXNetwork.update_to()` to correctly state method returns empty
string upon success.
`Issue 82 <https://github.com/ndexbio/ndex2-client/issues/82>`__

* Fixed bug in `NiceCXNetwork.set_opaque_aspect()` where passing `None` in the **aspect_elements**
parameter raised an error instead of removing the aspect

* Added `Ndex2.get_user_by_id()` method to get user information by NDEx user Id.

* Added `Ndex2.get_id_for_user()` method to get NDEx user Id by username.

* Added `Ndex2.get_networksets_for_user_id()` to get Network Sets for a given user Id.
`Issue 61 <https://github.com/ndexbio/ndex2-client/issues/61>`__

* Improved documentation by adding intersphinx to provide links to python documentation for
python objects.

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

* Fixed bug where `NiceCXNetwork.to_networkx()` fails with `ValueError` when installed
networkx version has X.Y.Z format (example: 2.5.1)
`Issue 79 <https://github.com/ndexbio/ndex2-client/issues/79>`_

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

* Fixed bug where `NiceCXNetwork.create_node()` and `.create_edge()` overwrote existing nodes/edges.
`Issue 60 <https://github.com/ndexbio/ndex2-client/issues/60>`_

* Fixed bug where `enum34` package would be unnecessarily installed on versions of Python 3.4 and newer.
`Issue 76 <https://github.com/ndexbio/ndex2-client/issues/76>`_

* Improved documentation for `Ndex2.set_network_properties()` method.
`Issue 77 <https://github.com/ndexbio/ndex2-client/issues/77>`_

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

* Added `MANIFEST.in` file to include `README.rst, HISTORY.rst, and LICENSE.txt` files as well as documentation and tests so `python setup.py install` will work properly on distribution of this client on PyPI. Thanks to Ben G. for catching this. `Issue 62 <https://github.com/ndexbio/ndex2-client/pull/62>`_

* Minor updates to `README.rst`

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

* Fixed bug where if server version is not 2.0 exactly then `Ndex2()` object incorrectly falls back to version of 1.3 of REST calls
`Issue 40 <https://github.com/ndexbio/ndex2-client/issues/40>`_

* Fixed bug in `NiceCXNetwork.add_network_attribute()` method where type not properly reset when adding duplicate attribute
`Issue 50 <https://github.com/ndexbio/ndex2-client/issues/50>`_

* Added `delete_networksets()` method to Ndex2 client to allow deletion of networksets `Issue 59 <https://github.com/ndexbio/ndex2-client/issues/59>`_