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

        return (self.gR*self.VmPFK*x[3]*(-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)*(1 + x[3]/self.KmPFKF6P + (-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)/((2 - 8*self.KeqAK)*self.KmPFKATP) + (self.gR*x[3]*(-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5))/((2 - 8*self.KeqAK)*self.KmPFKATP*self.KmPFKF6P)))/((2 - 8*self.KeqAK)*self.KmPFKATP*self.KmPFKF6P*((self.L0*(1 + (self.CPFKF26BP*self.F26BP)/self.KPFKF26BP + (self.CPFKF16BP*x[2])/self.KPFKF16BP)**2*(1 + (2*self.CPFKAMP*self.KeqAK*(self.SUMAXP - (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)**2)/((-1 + 4*self.KeqAK)*self.KPFKAMP*(self.SUMAXP - x[12] + 4*self.KeqAK*x[12] - (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)))**2*(1 + (self.CiPFKATP*(-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5))/((2 - 8*self.KeqAK)*self.KiPFKATP))**2*(1 + (self.CPFKATP*(-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5))/((2 - 8*self.KeqAK)*self.KmPFKATP))**2)/((1 + self.F26BP/self.KPFKF26BP + x[2]/self.KPFKF16BP)**2*(1 + (2*self.KeqAK*(self.SUMAXP - (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)**2)/((-1 + 4*self.KeqAK)*self.KPFKAMP*(self.SUMAXP - x[12] + 4*self.KeqAK*x[12] - (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)))**2*(1 + (-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)/((2 - 8*self.KeqAK)*self.KiPFKATP))**2) + (1 + x[3]/self.KmPFKF6P + (-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)/((2 - 8*self.KeqAK)*self.KmPFKATP) + (self.gR*x[3]*(-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5))/((2 - 8*self.KeqAK)*self.KmPFKATP*self.KmPFKF6P))**2))
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/model_composition.py and 1 other location - About 4 days to fix
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 292..292

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 465.

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

        return (self.VmPGK*((self.KeqPGK*x[1]*(self.SUMAXP - (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5))/(1 - 4*self.KeqAK) - (x[9]*(-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5))/(2 - 8*self.KeqAK)))/(self.KmPGKATP*self.KmPGKP3G*(1 + x[1]/self.KmPGKBPG + x[9]/self.KmPGKP3G)*(1 + (self.SUMAXP - (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)/((1 - 4*self.KeqAK)*self.KmPGKADP) + (-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)/((2 - 8*self.KeqAK)*self.KmPGKATP)))
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/model_composition.py and 1 other location - About 4 days to fix
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 271..272

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 437.

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

        return (self.VmGLK*(-((x[4]*(self.SUMAXP - (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)) /
                              ((1 - 4*self.KeqAK)*self.KeqGLK)) + (x[5]*(-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5))/(2 - 8*self.KeqAK)))/(self.KmGLKATP*self.KmGLKGLCi*(1 + x[4]/self.KmGLKG6P + x[5]/self.KmGLKGLCi)*(1 + (self.SUMAXP - (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)/((1 - 4*self.KeqAK)*self.KmGLKADP) + (-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)/((2 - 8*self.KeqAK)*self.KmGLKATP)))
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/model_composition.py and 1 other location - About 4 days to fix
intro_to_wc_modeling/cell_modeling/model_composition.py on lines 307..307

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 437.

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

File mrna_and_proteins_using_several_methods.py has 743 lines of code (exceeds 250 allowed). Consider refactoring.
Open

""" Stochastic simulation tutorial

:Author: Jonathan Karr <jonrkarr@gmail.com>
:Date: 2017-08-30
:Copyright: 2017, Karr Lab
Severity: Major
Found in intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py - About 1 day to fix

    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

      File model_composition.py has 614 lines of code (exceeds 250 allowed). Consider refactoring.
      Open

      """ Model composition tutorial

- Glycolysis model (Teusink et al., 2000)
- Glycerol synthesis model (Cronwright et al., 2002)
      Severity: Major
      Found in intro_to_wc_modeling/cell_modeling/model_composition.py - About 1 day to fix

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

                return (self.VmPYK*((x[10]*(self.SUMAXP - (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5))/(1 - 4*self.KeqAK) - ((-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)*x[11])/((2 - 8*self.KeqAK)*self.KeqPYK)))/(self.KmPYKADP*self.KmPYKPEP*(1 + (self.SUMAXP - (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)/((1 - 4*self.KeqAK)*self.KmPYKADP) + (-self.SUMAXP + x[12] - 4*self.KeqAK*x[12] + (self.SUMAXP**2 - 2*self.SUMAXP*x[12] + 8*self.KeqAK*self.SUMAXP*x[12] + x[12]**2 - 4*self.KeqAK*x[12]**2)**0.5)/((2 - 8*self.KeqAK)*self.KmPYKATP))*(1 + x[10]/self.KmPYKPEP + x[11]/self.KmPYKPYR))
        Severity: Major
        Found in intro_to_wc_modeling/cell_modeling/model_composition.py and 1 other location - About 1 day to fix
        intro_to_wc_modeling/cell_modeling/model_composition.py on lines 271..271

        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 145.

        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

                    m_percentiles[i, :] = [
                numpy.percentile(m[i, :], 1),
                numpy.percentile(m[i, :], 5),
                numpy.percentile(m[i, :], 33.33),
                numpy.percentile(m[i, :], 50),
        Severity: Major
        Found in intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py and 1 other location - About 1 day to fix
        intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 898..905

        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 134.

        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

                    n_percentiles[i, :] = [
                numpy.percentile(n[i, :], 1),
                numpy.percentile(n[i, :], 5),
                numpy.percentile(n[i, :], 33.33),
                numpy.percentile(n[i, :], 50),
        Severity: Major
        Found in intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py and 1 other location - About 1 day to fix
        intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 889..896

        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 134.

        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

        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

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

        class Specie(Base):
    """ Represents a species

    Attributes:
        name (:obj:`str`): name
        Severity: Major
        Found in intro_to_wc_modeling/concepts_skills/software_engineering/databases/core.py and 1 other location - About 6 hrs to fix
        intro_to_wc_modeling/concepts_skills/software_engineering/databases/core.py on lines 44..58

        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 106.

        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 Compartment(Base):
    """ Represents an compartment

    Attributes:
        name (:obj:`str`): name
        Severity: Major
        Found in intro_to_wc_modeling/concepts_skills/software_engineering/databases/core.py and 1 other location - About 6 hrs to fix
        intro_to_wc_modeling/concepts_skills/software_engineering/databases/core.py on lines 61..74

        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 106.

        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

            def v_2(self, x):
        # Glucose-6-phosphate isomerase
        # G6P <=> F6P
        return (self.VmPGI*(-(x[3]/self.KeqPGI) + x[4]))/(self.KmPGIG6P*(1 + x[3]/self.KmPGIF6P + x[4]/self.KmPGIG6P))
        Severity: Major
        Found in intro_to_wc_modeling/cell_modeling/model_composition.py and 1 other location - About 6 hrs to fix
        intro_to_wc_modeling/cell_modeling/model_composition.py on lines 309..312

        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 102.

        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

            def v_9(self, x):
        # Phosphoglycerate mutase
        # P3G <=> P2G
        return (self.VmPGM*(-(x[8]/self.KeqPGM) + x[9]))/(self.KmPGMP3G*(1 + x[8]/self.KmPGMP2G + x[9]/self.KmPGMP3G))
        Severity: Major
        Found in intro_to_wc_modeling/cell_modeling/model_composition.py and 1 other location - About 6 hrs to fix
        intro_to_wc_modeling/cell_modeling/model_composition.py on lines 274..277

        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 102.

        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 __init__(self, k_m=5, k_n=20, gamma_m=numpy.log(2) * 60 / 3, gamma_n=numpy.log(2) / 10, m_0=1, n_0=98):
        """
        Args:
            k_m (:obj:`float`, optional): mRNA synthesis rate constant (molecules h\ :sup:`-1`)
            k_n (:obj:`float`, optional): protein synthesis rate constant (\ :sup:`-1`\  h\ :sup:`-1`)
        Severity: Major
        Found in intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py and 1 other location - About 5 hrs to fix
        intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 36..51

        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 94.

        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 __init__(self, k_m=5, k_n=20, gamma_m=numpy.log(2) * 60 / 3, gamma_n=numpy.log(2) / 10, m_0=1, n_0=98):
        """
        Args:
            k_m (:obj:`float`, optional): mRNA synthesis rate constant (molecules h\ :sup:`-1`)
            k_n (:obj:`float`, optional): protein synthesis rate constant (\ :sup:`-1`\  h\ :sup:`-1`)
        Severity: Major
        Found in intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py and 1 other location - About 5 hrs to fix
        intro_to_wc_modeling/cell_modeling/simulation/mrna_and_proteins_using_several_methods.py on lines 674..689

        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 94.

        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

        GlycolysisModel has 35 functions (exceeds 20 allowed). Consider refactoring.
        Open

        class GlycolysisModel(object):
    """ Glycolysis model (Teusink et al., 2000)

    Based on the `version from JWS Online <http://jjj.biochem.sun.ac.za/models/teusink/>`_
        Severity: Minor
        Found in intro_to_wc_modeling/cell_modeling/model_composition.py - About 4 hrs to fix

          Function simulate has a Cognitive Complexity of 30 (exceeds 5 allowed). Consider refactoring.
          Open

          def simulate(mdl):
    # simulates model

    # Get metabolism submodel
    submdl = mdl.getComponentById('Metabolism')
          Severity: Minor
          Found in intro_to_wc_modeling/cell_modeling/simulation/multi_algorithm/submodel_simulation.py - About 4 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

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

              def dNAD_dt(self, x):
        return 1.0 * self.v_15(x) + 1.0 * self.v_16(x) - 1.0 * self.v_7(x) - 3.0 * self.v_13(x)
          Severity: Major
          Found in intro_to_wc_modeling/cell_modeling/model_composition.py and 1 other location - About 4 hrs to fix
          intro_to_wc_modeling/cell_modeling/model_composition.py on lines 375..376

          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 76.

          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

              def dNADH_dt(self, x):
        return 1.0 * self.v_7(x) + 3.0 * self.v_13(x) - 1.0 * self.v_15(x) - 1.0 * self.v_16(x)
          Severity: Major
          Found in intro_to_wc_modeling/cell_modeling/model_composition.py and 1 other location - About 4 hrs to fix
          intro_to_wc_modeling/cell_modeling/model_composition.py on lines 372..373

          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 76.

          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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