Showing 120 of 341 total issues
Avoid deeply nested control flow statements. Open
if cplx_species.compartment in conc_per_comp:
conc_per_comp[cplx_species.compartment] += stoic * \
cplx_species.distribution_init_concentration.mean
else:
conc_per_comp[cplx_species.compartment] = stoic * \Avoid deeply nested control flow statements. Open
if subunit_id not in gvar.transcript_ntp_usage:
seq = subunit.species_type.get_seq()
gvar.transcript_ntp_usage[subunit.species_type.id] = {
'A': seq.upper().count('A'),
'C': seq.upper().count('C'),Avoid deeply nested control flow statements. Open
if species.distribution_init_concentration:
if species.distribution_init_concentration.mean:
param.value = beta * species.distribution_init_concentration.mean \
/ Avogadro.value / species.compartment.init_volume.mean
param.comments = 'The value was assumed to be {} times the concentration of {} in {}'.format(Avoid deeply nested control flow statements. Open
if model_compl_species.distribution_init_concentration:
param.value = self._effective_dissociation_constant['{}[{}]'.format(
complex_st_id, compl_compartment_id)] * model_compl_species.distribution_init_concentration.mean
else:
param.value = self._effective_dissociation_constant['{}[{}]'.format(Avoid deeply nested control flow statements. Open
for part in prot_deg_reaction.participants:
if part.species.id in met_requirement:
met_requirement[part.species.id] += -part.coefficient * prot_concentration * \
doubling_time / prot_half_life
Avoid deeply nested control flow statements. Open
if aa_coefficient:
old_coef = aa_coefficient.coefficient
el_reaction.participants.remove(aa_coefficient)
el_reaction.participants.add(
aa_species.species_coefficients.get_or_create(Function test_metabolite_production has 5 arguments (exceeds 4 allowed). Consider refactoring. Open
def test_metabolite_production(submodel, reaction_bounds, pseudo_reactions=None, Function gen_michaelis_menten_like_rate_law has 5 arguments (exceeds 4 allowed). Consider refactoring. Open
def gen_michaelis_menten_like_rate_law(model, reaction, modifiers=None, modifier_reactants=None, exclude_substrates=None):Function gen_mass_action_rate_law has 5 arguments (exceeds 4 allowed). Consider refactoring. Open
def gen_mass_action_rate_law(model, reaction, model_k, modifiers=None, modifier_reactants=None):Function calibrate_submodel has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def calibrate_submodel(self):
""" Calibrate the submodel using data in the KB """
model = self.model
beta = self.options.get('beta')
- 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 calibrate_submodel has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def calibrate_submodel(self):
""" Calibrate the submodel using data in the KB """
model = self.model
beta = self.options.get('beta')
- 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 conv_for_optim has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def conv_for_optim(self):
""" Convert metabolism reactions into an optimization problem model
Returns:
:obj:`conv_opt.Model`: a conv_opt model for optimization- 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 gen_rate_laws has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def gen_rate_laws(self):
""" Generate rate laws for the reactions in the submodel """
model = self.model
cell = self.knowledge_base.cell
nucleus = model.compartments.get_one(id='n')- 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 gen_michaelis_menten_like_propensity_function has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def gen_michaelis_menten_like_propensity_function(model, reaction, substrates_as_modifiers=None, exclude_substrates=None):
""" Generate a Michaelis-Menten-like propensity function.
For species that are considered 'substrates', the substrate term is formulated as the
multiplication of a Hill equation with a coefficient of 1 for each 'substrate'.
For species that are considered 'modifiers', the modifier term is formulated- 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 calibrate_submodel has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def calibrate_submodel(self):
""" Calibrate the submodel using data in the KB """
model = self.model
beta = self.options.get('beta')
- 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 gen_compartments has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring. Open
def gen_compartments(self):
""" Generate compartments for the model from knowledge base """
kb = self.knowledge_base
model = self.model
- 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 gen_rate_laws has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def gen_rate_laws(self):
""" Generate rate laws for carbohydrate and lipid formation reactions. High
rates are assumed so that the macromolecules are formed as soon as the
components are available.
"""- 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 calc_gtp_per_translate has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def calc_gtp_per_translate(self):
""" Calculates the average GTP needed for a translation reaction """
submodel = self.model.submodels.get_one(id='translation')
gtp_per_translation = []- 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 gen_kb_reactions has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def gen_kb_reactions(self):
""" Generate reactions encoded within KB
TODO: rxn.submodel attribute is removed from KB, so submodel assignement needs to be taken care of here.
Since all rxns explicitly encoded in KB are metabolic ones, it is manually set to be metablism atm, but
not more sophisticated approach- 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 calc_h_per_transcript has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring. Open
def calc_h_per_transcript(self):
""" Calculates the average H needed for a transcription reaction """
submodel = self.model.submodels.get_one(id='transcription')
h_per_transcript = []- 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"