Networkx 3 compatibility

indra/assemblers/pysb/kappa_util.py

@@ -109,21 +109,24 @@ def cm_json_to_networkx(cm_json):
     return graph
 
 
-def get_cm_cycles(cm_graph):
+def get_cm_cycles(cm_graph, root_node=None):
     """Return cycles from a model's Kappa contact map graph representation.
 
     Parameters
     ----------
     cm_graph : networkx.Graph
         A networkx graph produced by cm_json_to_networkx.
+    root_node : Optional[str]
+        The root node of the graph. If None, the root node will be determined
+        by networkx.cycle_basis.
 
     Returns
     -------
     list
         A list of base cycles found in the contact map graph. Each cycle
         is represented as a list of strings of the form Monomer(site).
     """
-    cycles = cycle_basis(cm_graph)
+    cycles = cycle_basis(cm_graph, root_node)
     processed_cycles = []
     for cycle in cycles:
         processed_cycle = []

indra/pipeline/pipeline.py

@@ -320,7 +320,7 @@ def run_function(self, func_dict, statements=None, **kwargs):
             new_kwargs['statements'] = statements
         if kwargs:
             for k, v in kwargs.items():
-                if k not in new_kwargs and k in inspect.getargspec(func).args:
+                if k not in new_kwargs and k in inspect.getfullargspec(func).args:
                     new_kwargs[k] = v
         return self.run_simple_function(func, *new_args, **new_kwargs)
 

indra/tests/test_pysb_assembler.py

@@ -1272,7 +1272,9 @@ def test_contact_map_cycles_1():
     assert len(graph.nodes()) == 9, len(graph.nodes)
     assert len(graph.edges()) == 9, len(graph.edges)
 
-    cycles = get_cm_cycles(graph)
+    # Specify the root node to be 0 - corresponding to Agent 'a' - to
+    # ensure that the order of the output cycles is predictable
+    cycles = get_cm_cycles(graph, root_node=0)
     assert len(cycles) == 1, cycles
     assert cycles[0] == ['a(b)', 'b(a)', 'b(c)', 'c(b)', 'c(a)', 'a(c)']
 

setup.py

@@ -11,7 +11,7 @@
 def main():
     install_list = ['pysb>=1.3.0', 'objectpath',
                     'requests>=2.11', 'lxml', 'ipython', 'future',
-                    'networkx>=2,<3', 'pandas', 'ndex2==2.0.1', 'jinja2',
+                    'networkx>=3', 'pandas>=2', 'ndex2==2.0.1', 'jinja2',
                     'protmapper>=0.0.29', 'obonet',
                     'tqdm', 'pybiopax>=0.0.5']
 
@@ -38,7 +38,9 @@ def main():
                       'api': ['flask<2.0', 'flask_restx<0.4', 'flask_cors',
                               'docstring-parser', 'gunicorn',
                               'markupsafe<2.1.0'],
-                      'sklearn_belief': ['scikit-learn'],
+                      # scikit-learn 1.5.0 breaks DisambManager.run_adeft_disambiguation
+                      # see: https://github.com/gyorilab/adeft/issues/80
+                      'sklearn_belief': ['scikit-learn<1.5.0'],
                       'owl': ['pronto'],
                       'tests':
                         ['pytest',