INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.
I've done with a deeper investigation of upgrading to networkx3. For the downstream repositories listed below I checked any usage of networkx and cross checked any function calls with the full repository diff between 2.0.0 and 3.3 to see if any update might be needed, tested the code in some cases where it wasn't clear if the update would disrupt its implementation and ran the tests for the repository with networkx 3.3 installed.
Investigated repositories:
trialsynth
indra_network_search
indra_world
indra_reading
protmapper
emmaa
indra_db
indra_cogex
No issues related to removing the networkx<3 constraint were found in the investigation.
I've done with a deeper investigation of upgrading to networkx3. For the downstream repositories listed below I checked any usage of networkx and cross checked any function calls with the full repository diff between 2.0.0 and 3.3 to see if any update might be needed, tested the code in some cases where it wasn't clear if the update would disrupt its implementation and ran the tests for the repository with networkx 3.3 installed.
Investigated repositories:
No issues related to removing the networkx<3 constraint were found in the investigation.
Resolves #1442 and #1445.