ndex2 3.3.1

Nice CX Python includes a client and a data model.

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.

Jupyter Notebook Tutorials

• Basic Use of the NDEx2 Python Client: NDEx2 Client v2.0 Tutorial

• Working with the NiceCX Network Class: NiceCX v2.0 Tutorial

To use these tutorials or if Github isn’t showing the above notebooks in the browser, clone the ndex-jupyter-notebooks repository to your local machine and start Jupyter Notebooks in the project directory.

For information on installing and using Jupyter Notebooks, go to jupyter.org

Requirements

The NDEx2 Python Client module works best with Python 3.6+ and the latest version of the PIP Python package manager for installation. Click here to download the PIP Python package.

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

License

See LICENSE.txt

History

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

• 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

• Fixed bug in NiceCXNetwork.add_network_attribute() method where type not properly reset when adding duplicate attribute Issue #50

• Added delete_networksets() method to Ndex2 client to allow deletion of networksets Issue #59

3.2.0 (2019-04-23)

• Verify consistent conversion of cx for networkx 1.11 and 2.0+ Issue #30

• NiceCXNetwork.get_nodes(), NiceCXNetwork.get_edges(), NiceCXNetwork.get_metadata() needs to make correct iterator call in Python 2 Issue #44

• Add NiceCXNetwork.get_network_attribute_names() function enhancement Issue #45

• NiceCXNetwork.create_edge fails to correctly create edge when node dict passed in Issue #46

3.1.0a1 (2019-03-20)

• Add method to ndex2 python client to apply style from one NiceCXNetwork to another NiceCXNetwork Issue #43

3.0.0a1 (2019-02-11)

• In NiceCXNetwork class ability to add to User-Agent for calls to NDEx service Issue #36

• Methods in ndex2/client.py should raise an NDExError for invalid credentials Issue #39

• Add timeout flag to all web request calls Issue #33

• Update User-Agent to reflect actual version of software Issue #35

• NiceCXNetwork.set_node_attribute() incorrectly handles duplicate attributes Issue #41

• NiceCXNetwork.set_node_attribute() fails if node object passed to it Issue #42

• Passing None to user_agent parameterin Ndex2() constructor raises TypeError Issue #34

• Ndex2() constructor does not properly handle invalid json from server Issue #28

• Eliminate circular import between ndex2 and ndex2cx/nice_cx_builder.py Issue #31

• Replace print statements with logging calls in ndex2/client.py Issue #32

2.0.1 (2019-01-03)

• Fixed bug where logs directory is created within the package installation directory. Issue #26