Closed bgyori closed 2 months ago
The issue is with cycle_basis
producing a changed output. I dug into Networkx's code base and checked the diff for networkx/algorithms/cycles.py
between 2.8.8 and 3.3:
More importantly, they've gone from a set to a dict in the algorithm and when the root node is not specified, this makes a difference.
from indra.statements import *
from indra.assemblers.pysb import PysbAssembler
from indra.assemblers.pysb.export import export_cm_network
from indra.assemblers.pysb.kappa_util import get_cm_cycles
from networkx.algorithms.cycles import cycle_basis
stmts = [Complex([Agent('a'), Agent('b')]),
Complex([Agent('a'), Agent('c')]),
Complex([Agent('b'), Agent('c')])]
pa = PysbAssembler(stmts)
pa.make_model()
graph = export_cm_network(pa.model)
cycles = get_cm_cycles(graph)
nodes_set = set(graph.nodes())
nodes_set.pop()
# 0
nodes_set
# {(0, 0), (0, 1), (1, 0), (1, 1), (2, 0), (2, 1), 1, 2}
nodes_dict = dict.fromkeys(graph)
nodes_dict.popitem()[0]
# (2, 1)
nodes_dict
# {0: None,
# (0, 0): None,
# (0, 1): None,
# 1: None,
# (1, 0): None,
# (1, 1): None,
# 2: None,
# (2, 0): None}
If the root node to look for cycles from is provided, the output can be made consistent between versions:
In Networkx 2.8.8
cycle_basis(graph)
# [[(0, 0), (1, 0), 1, (1, 1), (2, 1), 2, (2, 0), (0, 1), 0]]
cycle_basis(graph, 0)
# [[(0, 0), (1, 0), 1, (1, 1), (2, 1), 2, (2, 0), (0, 1), 0]]
In Networkx 3.3
cycle_basis(graph)
# [[(1, 1), 1, (1, 0), (0, 0), 0, (0, 1), (2, 0), 2, (2, 1)]]
cycle_basis(graph, 0)
# [[(0, 0), (1, 0), 1, (1, 1), (2, 1), 2, (2, 0), (0, 1), 0]]
I will update out get_cm_cycles()
in the pysb assembler module to allow for a root node to be provided with None
as default so the output can be predicted when necessary.
I could not find any literal text match of get_cm_cycles
outside of the indra tests or indra/assemblers/pysb/kappa_util.py
. Unless this function is called in some dynamic manner I don't think its used in any code that I have access to.
It would be good to remove the
networkx<=2
constraint but there is at least one test that fails withnetworkx>=3
:It's possible that this is something trivial like the order of nodes in a reported cycle but would have to be investigated.