History

0.6.0 (2025-02-05)

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

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.

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

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