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intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py

Summary

Maintainability
F
5 days
Test Coverage
A
100%

File model.py has 671 lines of code (exceeds 250 allowed). Consider refactoring.
Open

'''
Reads models specified in Excel into a Python object

@author Jonathan Karr, karr@mssm.edu
@date 3/22/2016
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py - About 1 day to fix

    Function getModelFromExcel has a Cognitive Complexity of 44 (exceeds 5 allowed). Consider refactoring.
    Open

    def getModelFromExcel(filename):
    # Reads model from Excel file into a Python object

    with warnings.catch_warnings():
        warnings.filterwarnings("ignore", "Discarded range with reserved name", UserWarning)
    Severity: Minor
    Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py - About 6 hrs to fix

    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 setupSimulation has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.
    Open

        def setupSimulation(self):
        '''setup reaction participant, enzyme counts matrices'''
        Submodel.setupSimulation(self)

        '''Setup FBA'''
    Severity: Minor
    Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py - About 2 hrs to fix

    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__(self, id='', name='', submodel='', reversible=None, participants=[],
    Severity: Major
    Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py - About 1 hr to fix

      Function __init__ has 10 arguments (exceeds 4 allowed). Consider refactoring.
      Open

          def __init__(self, id='', name='', structure='', empiricalFormula='', molecularWeight=None,
      Severity: Major
      Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py - About 1 hr to fix

        Function __init__ has 6 arguments (exceeds 4 allowed). Consider refactoring.
        Open

            def __init__(self, id='', name='', submodel='', value=None, units='', comments=''):
        Severity: Minor
        Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py - About 45 mins to fix

          Function __init__ has 6 arguments (exceeds 4 allowed). Consider refactoring.
          Open

              def __init__(self, submodels=None, compartments=None, species=None, reactions=None, parameters=None, references=None):
          Severity: Minor
          Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py - About 45 mins to fix

            Function calcMass has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
            Open

                def calcMass(self):
        for comp in self.compartments:
            if comp.id == 'c':
                iCellComp = comp.index
            Severity: Minor
            Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py - About 25 mins to fix

            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 6 (exceeds 5 allowed). Consider refactoring.
            Open

                def __init__(self, submodels=None, compartments=None, species=None, reactions=None, parameters=None, references=None):
        if submodels is None:
            submodels = []
        if compartments is None:
            compartments = []
            Severity: Minor
            Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py - About 25 mins to fix

            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 setComponentIndices has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
            Open

                def setComponentIndices(self):
        for index, obj in enumerate(self.submodels):
            obj.index = index
        for index, obj in enumerate(self.compartments):
            obj.index = index
            Severity: Minor
            Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py - About 25 mins to fix

            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 getModifiers has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
            Open

                def getModifiers(self, species, compartments):
        # get modifiers of rate law
        modifiers = []
        for spec in species:
            for comp in compartments:
            Severity: Minor
            Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py - About 25 mins to fix

            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

            Identical blocks of code found in 2 locations. Consider refactoring.
            Open

                def calcIdName(self):
        self.id = '%s[%s]' % (self.species.id, self.compartment.id)
        self.name = '%s (%s)' % (self.species.name, self.compartment.name)
            Severity: Major
            Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py and 1 other location - About 2 hrs to fix
            intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py on lines 574..576

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 54.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Identical blocks of code found in 2 locations. Consider refactoring.
            Open

                def calcIdName(self):
        self.id = '%s[%s]' % (self.species.id, self.compartment.id)
        self.name = '%s (%s)' % (self.species.name, self.compartment.name)
            Severity: Major
            Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py and 1 other location - About 2 hrs to fix
            intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py on lines 605..607

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 54.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 2 locations. Consider refactoring.
            Open

                    upperBounds = util.nanminimum(upperBounds, self.dryWeight / 3600 * N_AVOGADRO * 1e-3 * self.exchangeRateBounds['upper'])
            Severity: Major
            Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py and 1 other location - About 1 hr to fix
            intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py on lines 402..402

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 46.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 2 locations. Consider refactoring.
            Open

                    lowerBounds = util.nanmaximum(lowerBounds, self.dryWeight / 3600 * N_AVOGADRO * 1e-3 * self.exchangeRateBounds['lower'])
            Severity: Major
            Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py and 1 other location - About 1 hr to fix
            intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py on lines 403..403

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 46.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 3 locations. Consider refactoring.
            Open

                    model.reactions.append(Reaction(
            id=str(ws.cell(row=iRow, column=1).value),
            name=ws.cell(row=iRow, column=2).value,
            submodel=ws.cell(row=iRow, column=3).value,
            reversible=stoichiometry['reversible'],
            Severity: Major
            Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py and 2 other locations - About 1 hr to fix
            intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py on lines 698..713
            intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py on lines 765..771

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 40.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 3 locations. Consider refactoring.
            Open

                    model.references.append(Reference(
            id=str(ws.cell(row=iRow, column=1).value),
            name=ws.cell(row=iRow, column=2).value,
            crossRefs=[
                Identifier(
            Severity: Major
            Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py and 2 other locations - About 1 hr to fix
            intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py on lines 698..713
            intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py on lines 731..744

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 40.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 3 locations. Consider refactoring.
            Open

                    model.species.append(Species(
            id=str(ws.cell(row=iRow, column=1).value),
            name=ws.cell(row=iRow, column=2).value,
            structure=ws.cell(row=iRow, column=3).value,
            empiricalFormula=ws.cell(row=iRow, column=4).value,
            Severity: Major
            Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py and 2 other locations - About 1 hr to fix
            intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py on lines 731..744
            intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py on lines 765..771

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 40.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 2 locations. Consider refactoring.
            Open

            class Concentration(object):
    # Represents a concentration in a compartment

    compartment = ''
    value = None
            Severity: Major
            Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py and 1 other location - About 1 hr to fix
            intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py on lines 579..587

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 39.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 2 locations. Consider refactoring.
            Open

            class ExchangedSpecies(object):
    # Represents an external

    id = ''
    reactionIndex = None
            Severity: Major
            Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py and 1 other location - About 1 hr to fix
            intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py on lines 548..556

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 39.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 2 locations. Consider refactoring.
            Open

                            Concentration(compartment='e', value=float(ws.cell(row=iRow, column=9).value or 0)),
            Severity: Minor
            Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py and 1 other location - About 30 mins to fix
            intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py on lines 707..707

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 32.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

            Similar blocks of code found in 2 locations. Consider refactoring.
            Open

                            Concentration(compartment='c', value=float(ws.cell(row=iRow, column=8).value or 0)),
            Severity: Minor
            Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py and 1 other location - About 30 mins to fix
            intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/model.py on lines 708..708

            Duplicated Code

            Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

            Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

            When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

            Tuning

            This issue has a mass of 32.

            We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

            The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

            If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

            See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

            Refactorings

            Further Reading

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