Showing 7 of 11 total issues
Function get_digraph has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring. Open
def get_digraph(self, submodel):
""" Create a NetworkX network representing the reaction network in `submodel`
To leverage the algorithms in NetworkX, map a reaction network on to a NetworkX
directed graph.- Read upRead up
Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
Function get_dead_end_species has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring. Open
def get_dead_end_species(self, submodel, inactive_reactions):
""" Find the dead end species in a reaction network
Given a set of inactive reactions in submodel, determine species that are not consumed by
any reaction, or are not produced by any reaction. Costs :math:`O(n*p)`, where :math:`n` is- Read upRead up
Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
Function unbounded_paths has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring. Open
def unbounded_paths(self, rxn_network, ex_species, obj_fn_species, min_non_finite_ub=1000.0):
""" Find the unbounded paths from an extracellular species to some objective function species
Return all paths in a reaction network that lack a finite flux upper bound
and go from `ex_species` to an objective function component.- Read upRead up
Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
Function run has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring. Open
def run(self):
""" Run multiple analyses
Raises:
:obj:`ValueError`: if the analysis is not supported- Read upRead up
Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"
Further reading
Function __init__ has 6 arguments (exceeds 4 allowed). Consider refactoring. Open
def __init__(self, knowledge_base=None, model=None, sim_results_path=None,Function __init__ has 5 arguments (exceeds 4 allowed). Consider refactoring. Open
def __init__(self, sim_results_path, model=None, knowledge_base=None, out_path=None, options=None):Function get_inactive_rxns has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def get_inactive_rxns(self, submodel, dead_end_species):
""" Find the inactive reactions in a reaction network
Given the dead end species in a reaction network, find the reactions that must eventually
become inactive. Reactions that consume species which are not produced must become inactive.- Read upRead up
Cognitive Complexity
Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.
A method's cognitive complexity is based on a few simple rules:
- Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
- Code is considered more complex for each "break in the linear flow of the code"
- Code is considered more complex when "flow breaking structures are nested"