Showing 140 of 219 total issues
Function ferguson_to_mu0 has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring. Open
def ferguson_to_mu0(
field,
Tvals,
DNAvals,
dataset,- 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 __getitem__ has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring. Open
def __getitem__(self, i):
"""Save indices of accessed items."""
if isinstance(i, slice):
result = self.__class__(self.data[i])
for ind in range(i.start, i.stop, i.step or 1):- 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 __getitem__ has a Cognitive Complexity of 13 (exceeds 5 allowed). Consider refactoring. Open
def __getitem__(self, sl):
"""Returns a subsequence. This method is used by the slice notation"""
if not self.circular:
x = len(self.crick) - self.ovhg - len(self.watson)- 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 pcr has a Cognitive Complexity of 12 (exceeds 5 allowed). Consider refactoring. Open
def pcr(*args, **kwargs):
"""pcr is a convenience function for the Anneal class to simplify its
usage, especially from the command line. If more than one or no PCR
product is formed, a ValueError is raised.
- 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 11 arguments (exceeds 4 allowed). Consider refactoring. Open
def __init__(Function __init__ has 32 lines of code (exceeds 25 allowed). Consider refactoring. Open
def __init__(
self,
samples, # list of lists of Dseqrecords
names=None,
percentgel=Q_(1.0, "(g/(100 mL))*100"), # agar/bufferFunction __add__ has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring. Open
def __add__(self, other):
if hasattr(other, "seq") and hasattr(other.seq, "watson"):
other = _copy.deepcopy(other)
other_five_prime = other.seq.five_prime_end()
if other_five_prime[0] == "5'":- 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 10 arguments (exceeds 4 allowed). Consider refactoring. Open
def __init__(Function open has a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring. Open
def open(self, seq_to_open):
"""Open a sequence for editing in an external (DNA) editor.
Parameters
----------- 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 a Cognitive Complexity of 11 (exceeds 5 allowed). Consider refactoring. Open
def __init__(self, primers, template, limit=13, **kwargs):
r"""The Anneal class has to be initiated with at least an iterable of
primers and a template.
- 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 _findDNAConcentrations has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring. Open
def _findDNAConcentrations(self, background):
"""Determines where in the concentration of DNA in every part of the gel"""
length = len(self.lanes[0])
- 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 _findDNAConcentrations has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring. Open
def _findDNAConcentrations(self, background):
"""Determines where in the concentration of DNA in every part of the gel"""
length = len(self.lanes[0])
- 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 vWBRfit has 8 arguments (exceeds 4 allowed). Consider refactoring. Open
def vWBRfit(Function ferguson_to_mu0 has 8 arguments (exceeds 4 allowed). Consider refactoring. Open
def ferguson_to_mu0(Function wrapstring has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring. Open
def wrapstring(str_, rowstart, rowend, padfirst=True):
"""
wraps the provided string in lines of length rowend-rowstart
and padded on the left by rowstart.
-> if padfirst is false the first line is not padded- 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 _to_units has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring. Open
def _to_units(quantity, units, var_name=None):
"""Asserts that the quantity has the proper dimensions
(inferred from the default units) if the quantity is an instance of
pint.unit.Quantity or assigns the default units if it's not.
"""- 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 __contains__ has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring. Open
def __contains__(self, other):
if other.lower() in str(self.seq).lower():
return True
else:
s = self.seq.watson.replace(" ", "")- 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 lcs has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring. Open
def lcs(self, other, *args, limit=25, **kwargs):
"""Return the longest common substring between the sequence.
and another sequence (other). The other sequence can be a string,
Seq, SeqRecord, Dseq or DseqRecord.- 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 wrapstring has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring. Open
def wrapstring(str_, rowstart, rowend, padfirst=True):
"""
wraps the provided string in lines of length rowend-rowstart
and padded on the left by rowstart.
-> if padfirst is false the first line is not padded- 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 add_feature has 7 arguments (exceeds 4 allowed). Consider refactoring. Open
def add_feature(self, x=None, y=None, seq=None, type_="misc", strand=1, *args, **kwargs):