Showing 84 of 109 total issues
File core.py
has 4288 lines of code (exceeds 250 allowed). Consider refactoring. Open
""" Data model to represent composite, multi-algorithmic biochemical models.
This module defines classes that represent the schema and provenance of a biochemical model:
* :obj:`Model`
File util.py
has 876 lines of code (exceeds 250 allowed). Consider refactoring. Open
""" Utilities for writing/reading a `wc_lang` model to/from SBML
* Higher level functions for creating, getting, and setting SBML objects
* Utilities for wrapping libSBML calls
Function run
has a Cognitive Complexity of 96 (exceeds 5 allowed). Consider refactoring. Open
def run(self, model):
""" Split reversible reactions in submodels into separate forward and backward reactions
Args:
model (:obj:`Model`): model definition
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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 66 (exceeds 5 allowed). Consider refactoring. Open
def run(self, model):
""" Merge groups of algorithmically-like submodels into individual submodels
* dFBA objectives are merged by summing
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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 transform
has a Cognitive Complexity of 52 (exceeds 5 allowed). Consider refactoring. Open
def transform(filename):
# read
wb = openpyxl.load_workbook(filename=filename)
# TOC
- 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_authors_annotation
has a Cognitive Complexity of 40 (exceeds 5 allowed). Consider refactoring. Open
def get_authors_annotation(cls, model, sbml_model, model_objs):
""" Import the SBML annotation of the authors of a model to a model
Args:
model (:obj:`wc_lang.core.Model`): model
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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 validate
has a Cognitive Complexity of 36 (exceeds 5 allowed). Consider refactoring. Open
def validate(self, obj, value, tolerance=1E-10):
""" Determine if `value` is a valid value of the attribute
Args:
obj (:obj:`Reaction`): object being validated
- 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 transform
has a Cognitive Complexity of 33 (exceeds 5 allowed). Consider refactoring. Open
def transform(filename):
# read
wb = openpyxl.load_workbook(filename=filename)
for ws in wb:
- 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 32 (exceeds 5 allowed). Consider refactoring. Open
def run(self, path, models=None,
ignore_missing_models=None, ignore_extra_models=None, ignore_sheet_order=None,
include_all_attributes=False, ignore_missing_attributes=None, ignore_extra_attributes=None,
ignore_attribute_order=None, validate=None):
""" Read a list of model objects from file(s) and, optionally, validate them
- 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
LibSbmlInterface
has 35 functions (exceeds 20 allowed). Consider refactoring. Open
class LibSbmlInterface(object):
''' Methods for compactly using libSBML to create SBML objects.
The libSBML method calls provide narrow interfaces, typically exchanging one
value per call, which creates verbose code. The methods below aggregate multiple
Function get_products
has a Cognitive Complexity of 30 (exceeds 5 allowed). Consider refactoring. Open
def get_products(self, __type=None, **kwargs):
""" Get the species produced by this objective function
Args:
__type (:obj:`types.TypeType` or :obj:`tuple` of :obj:`types.TypeType`): subclass(es) of :obj:`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 call_libsbml
has a Cognitive Complexity of 29 (exceeds 5 allowed). Consider refactoring. Open
def call_libsbml(cls, method, *args, returns_int=False, debug=False):
""" Call a libSBML method and handle any errors.
Unfortunately, libSBML methods that do not return data usually report errors via return codes,
instead of exceptions, and the generic return codes contain virtually no information.
- 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
Model
has 31 functions (exceeds 20 allowed). Consider refactoring. Open
class Model(obj_tables.Model, SbmlModelMixin):
""" Model
Attributes:
id (:obj:`str`): unique identifier
File __main__.py
has 325 lines of code (exceeds 250 allowed). Consider refactoring. Open
""" Command line programs for manipulating model definitions
:Author: Jonathan Karr <karr@mssm.edu>
:Author: Arthur Goldberg <Arthur.Goldberg@mssm.edu>
:Date: 2016-12-07
Function run
has a Cognitive Complexity of 26 (exceeds 5 allowed). Consider refactoring. Open
def run(self, model):
""" Transform model
Args:
model (:obj:`Model`): 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 run
has a Cognitive Complexity of 25 (exceeds 5 allowed). Consider refactoring. Open
def run(self, model):
""" Create implicit exchange reactions for dFBA submodels
Args:
model (:obj:`Model`): 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 _get_cyclic_deps
has a Cognitive Complexity of 25 (exceeds 5 allowed). Consider refactoring. Open
def _get_cyclic_deps(self):
""" Verify that the networks of depencencies for observables and functions are acyclic
Returns:
:obj:`dict`: dictionary of dictionary of lists of objects with cyclic dependencies,
- 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 import_from_sbml
has a Cognitive Complexity of 22 (exceeds 5 allowed). Consider refactoring. Open
def import_from_sbml(self, sbml_rxn):
""" Load from SBML reaction
Args:
sbml (:obj:`libsbml.Reaction`): SBML reaction
- 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 validate
has a Cognitive Complexity of 22 (exceeds 5 allowed). Consider refactoring. Open
def validate(self):
""" Check that the structure is valid
* Format provided when structure is not None
* Value provided when format is not None
- 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 transform
has a Cognitive Complexity of 20 (exceeds 5 allowed). Consider refactoring. Open
def transform(filename):
# read
wb = openpyxl.load_workbook(filename=filename)
for ws in wb:
- 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"