ndex2 3.11.0
Nice CX Python includes a client and a data model.
License: BSD
Keywords: network analysis biology

**NDEx2 Python Client**
=========================

.. _NDEx: http://ndexbio.org
.. _NDEx REST Server API: http://home.ndexbio.org/using-the-ndex-server-api

.. image:: https://app.travis-ci.com/ndexbio/ndex2-client.svg?branch=master
        :target: https://app.travis-ci.com/ndexbio/ndex2-client

.. image:: https://img.shields.io/pypi/v/ndex2.svg
        :target: https://pypi.python.org/pypi/ndex2

.. image:: https://coveralls.io/repos/github/ndexbio/ndex2-client/badge.svg?branch=master
        :target: https://coveralls.io/github/ndexbio/ndex2-client?branch=master

.. image:: https://readthedocs.org/projects/ndex2/badge/?version=latest
        :target: https://ndex2.readthedocs.io/en/latest/?badge=latest
        :alt: Documentation Status


**Overview**
--------------

The NDEx2 Python Client provides methods to access NDEx_ via
the `NDEx REST Server API`_. As well as methods for common operations on
networks via the NiceCXNetwork class.

**Dependencies**
---------------------

* `six <https://pypi.org/project/six>`__
* `ijson <https://pypi.org/project/ijson>`__
* `requests <https://pypi.org/project/requests>`__
* `requests_toolbelt <https://pypi.org/project/requests_toolbelt>`__
* `networkx <https://pypi.org/project/networkx>`__
* `urllib3 <https://pypi.org/project/urllib3>`__
* `pandas <https://pypi.org/project/pandas>`__
* `enum34 <https://pypi.org/project/enum34>`__ (Python < 3.4)
* `numpy <https://pypi.org/project/numpy>`__
* `enum <https://pypi.org/project/enum>`__ (Python 2.6 & 2.7)

**Compatibility**
-----------------------

Python 3.5+

.. note::

    Python < 3.5 may have some issues

**Installation**
--------------------------------------

The NDEx2 Python Client module can be installed from the Python Package
Index (PyPI) repository using PIP:

::

    pip install ndex2

If you already have an older version of the ndex2 module installed, you
can use this command instead:

::

    pip install --upgrade ndex2


**Resources**
--------------------------------------

* The NDEx2 Python Client `documentation <https://ndex2.readthedocs.io/en/latest/>`_ is available on Read the Docs.
* Please refer to our `Jupyter Notebook Tutorials <https://github.com/ndexbio/ndex-jupyter-notebooks>`_ GitHub repository for code examples to work with networks using the NDEx2 Python Client and NiceCX object class. 


**License**
--------------------------------------

See `LICENSE.txt <https://github.com/ndexbio/ndex2-client/blob/master/LICENSE.txt>`_




=======
History
=======

3.11.0 (2025-07-22)
-------------------

* Enhancements
    * Added `CX2Network.rename_attribute` method to rename attributes in the network.

3.10.0 (2025-01-14)
-------------------

* Enhancements
    * Added ``store_layout_in_pos`` argument in ``get_graph`` method of ``CX2NetworkXFactory`` that saves layout
      coordinates in G.pos (x and y) and G.zpos (z).
    * Added ``get_layout_from_pos`` argument in ``get_cx2network`` method of ``NetworkXToCX2NetworkFactory`` that
      determines the source of the layout coordinates. If True, the layout is derived from G.pos (x and y) and G.zpos.
      If False, the layout uses the (x, y, z) values specified as the node attributes.
    * Added ``interaction_col`` argument in ``get_cx2network`` of ``PandasDataFrameToCX2NetworkFactory`` that allows to
      specify the name of the column with edge interactions

* Bug fixes
    * Fix for string IDs in NetworkX networks - cast to integer if possible or add as name attribute.
    * Fix for DataFrames without column names



3.9.0 (2024-06-18)
-------------------

* 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.


3.8.0 (2024-02-07)
-------------------

* 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.

3.7.0 (2024-01-03)
-------------------

* 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>`__



3.6.0 (2023-11-14)
-------------------

* 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>`__

3.5.1 (2023-04-11)
-------------------

* 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

3.5.0 (2022-06-28)
-------------------

* 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()``


3.4.0 (2021-05-06)
-------------------

* 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.

3.3.3 (2021-04-22)
-------------------

* 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>`_

3.3.2 (2021-04-13)
-------------------

* 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>`_

3.3.1 (2019-09-23)
-------------------

* 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`

3.3.0 (2019-09-11)
------------------

* 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>`_


3.2.0 (2019-04-23)
------------------

* Verify consistent conversion of CX for networkx 1.11 and 2.0+
  `Issue #30 <https://github.com/ndexbio/ndex2-client/issues/30>`_

* `NiceCXNetwork.get_nodes()`, `NiceCXNetwork.get_edges()`, `NiceCXNetwork.get_metadata()` needs to make correct iterator call in Python 2
  `Issue #44 <https://github.com/ndexbio/ndex2-client/issues/44>`_

* Add `NiceCXNetwork.get_network_attribute_names()` function enhancement
  `Issue #45 <https://github.com/ndexbio/ndex2-client/issues/45>`_

* `NiceCXNetwork.create_edge()` fails to correctly create edge when node dict passed in
  `Issue #46 <https://github.com/ndexbio/ndex2-client/issues/46>`_

3.1.0a1 (2019-03-20)
--------------------

* Add method to ndex2 python client to apply style from one NiceCXNetwork 
  to another NiceCXNetwork
  `Issue #43 <https://github.com/ndexbio/ndex2-client/issues/43>`_

3.0.0a1 (2019-02-11)
--------------------

* In NiceCXNetwork class ability to add to User-Agent for calls to NDEx service
  `Issue #36 <https://github.com/ndexbio/ndex2-client/issues/36>`_

* Methods in `ndex2/client.py` should raise an NDExError for invalid credentials
  `Issue #39 <https://github.com/ndexbio/ndex2-client/issues/39>`_

* Add timeout flag to all web request calls
  `Issue #33 <https://github.com/ndexbio/ndex2-client/issues/33>`_

* Update `User-Agent` to reflect actual version of software
  `Issue #35 <https://github.com/ndexbio/ndex2-client/issues/35>`_

* `NiceCXNetwork.set_node_attribute()` incorrectly handles duplicate attributes
  `Issue #41 <https://github.com/ndexbio/ndex2-client/issues/41>`_

* `NiceCXNetwork.set_node_attribute()` fails if node object passed to it
  `Issue #42 <https://github.com/ndexbio/ndex2-client/issues/42>`_

* Passing None to user_agent parameterin `Ndex2()` constructor raises TypeError
  `Issue #34 <https://github.com/ndexbio/ndex2-client/issues/34>`_

* `Ndex2()` constructor does not properly handle invalid json from server
  `Issue #28 <https://github.com/ndexbio/ndex2-client/issues/28>`_

* Eliminate circular import between ndex2 and ndex2cx/nice_cx_builder.py
  `Issue #31 <https://github.com/ndexbio/ndex2-client/issues/31>`_

* Replace print statements with logging calls in `ndex2/client.py`
  `Issue #32 <https://github.com/ndexbio/ndex2-client/issues/32>`_


2.0.1 (2019-01-03)
------------------

* Fixed bug where logs directory is created within
  the package installation directory. 
  `Issue #26 <https://github.com/ndexbio/ndex2-client/issues/26>`_