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@coleslaw481 coleslaw481 released this 28 Jun 18:00
· 182 commits to master since this release
v3.5.0
b0679a9

  • 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()

Assets 4