Utilities for hierarchy creation and comparision plus fixes

• Add HierarchyDiff class with compare_hierarchies method to compare two hierarchies in CX2 format, and output
  a hierarchy with robustness score of each system.

• Add version bounds for required packages.

• Add convert_hierarchical_network_to_hcx (utility function that aids convertion of a hierarchical network in CX2 to
  HCX) and add_hcx_members_annotation (adds 'HCX::members' attribute to nodes) to hcx_utils

• Fixes in IF and APMS tools

Added converters for DDOT and HiDeF

• Add HiDeFToHierarchyConverter, a class to convert a edge list and node list
  in HiDeF format to hierarchy in HCX.
• Add InteractomeToDDOTConverter and DDOTToInteractomeConverter, classes to convert network in
  CX2 format to DDOT format and vice versa, HierarchyToDDOTConverter and DDOTToHierarchyConverter,
  classes to convert hierarchy network in HCX format to DDOT and vice versa.

Enhance converters support and add utils for handling hierarchies

• Updated provenance utils, added checks in for missing data in input RO-Crate,
  and allowing to continue but logging errors in the process

• Add HierarchyToHiDeFConverter, a class to convert a hierarchy network
  (in CX2 format) to a HiDeF format nodes and edges lists.

• Add NDExHierarchyUploader, a class for uploading hierarchy and
  its parent network to NDEx.

• Updated cellmaps_utilscmd.py apmsconverter, ifconverter,
  crisprconverter to support tissue as well as output
  data_info.json file to resulting RO-Crate so subsequent tools can
  more easily get provenance information

• Updated cellmaps_utilscmd.py crisprconverter to consume .h5ad
  files and updated readme.txt file

FAIRSCAPE-CLI upgrade

• Bumped fairscape-cli dependency to 0.2.0

Schema support in fairscape

• Bumped fairscape-cli dependency to 0.1.14 to support schemas

• Added support for schema to data_dict parameter in ProvenanceUtil.register_dataset()

• Added --release flag to cellmaps_utilscmd.py rocratetable and
  in output table renamed "Name of Computation" to "Name" as well as
  added "Type", "Cell Line", "Treatment", "Gene set", and "Version" to
  table output

• Set default logging level to ERROR for cellmaps_utilscmd.py command

First release

• First release