Add cx2 methods

• 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.

Better pandas converter

• 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

• Enhancements
  • Added CX2NetworkXFactory under cx2.py module to convert
    CX2Network object to NetworkX Graph
  • Added NetworkXToCX2NetworkFactory under cx2.py module to convert
    NetworkX Graph to CX2Network object
  • Added PandasDataFrameToCX2NetworkFactory under cx2.py module to
    convert Pandas DataFrame to CX2Network object
  • Added CX2NetworkPandasDataFrameFactory under cx2.py module to convert
    CX2Network object to Pandas DataFrame

CX2Newtork

• Enhancements

  • Added CX2Network class under cx2.py module to represent networks CX2 format
  • 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

numpy bug fix

• Bug fixes
  • Fixed bug where ndex2.create_nice_cx_from_networkx() fails with numpy version 1.24
    Issue #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

• 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

  • 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

  • Fixed bug where converting NiceCXNetwork to networkx and back does not handle
    name attribute correctly. Issue #84

  • Fixed bug where @context was lost if it was set as aspect in CX format and loaded
    into NiceCXNetwork object.
    Issue #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

  • 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 get_networksets_for_user_id

• Added offset and limit parameters to Ndex2.get_network_ids_for_user() to enable
  retrieval of all networks for a user. Issue #78

• Switched NiceCXNetwork.upload_to() to named arguments and added client parameter. Issue #80

• Switched NiceCXNetwork.update_to() to named arguments and added client parameter. Issue #81

• Fixed documentation NiceCXNetwork.update_to() to correctly state method returns empty
  string upon success. Issue #82

• 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

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

bug fix

• Fixed bug where NiceCXNetwork.to_networkx() fails with ValueError when installed
  networkx version has X.Y.Z format (example: 2.5.1) Issue #79

Bug fixes

• Fixed bug where NiceCXNetwork.create_node() and .create_edge() overwrote existing nodes/edges. Issue #60

• Fixed bug where enum34 package would be unnecessarily installed on versions of Python 3.4 and newer. Issue #76

• Improved documentation for Ndex2.set_network_properties() method. Issue #77

Added MANIFEST.in

• 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