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KarrLab/conv_opt

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conv_opt/solver/soplex.py

Summary

Maintainability
D
1 day
Test Coverage
A
100%

Function load has a Cognitive Complexity of 50 (exceeds 5 allowed). Consider refactoring.
Open

    def load(self, conv_opt_model):
        """ Load a model to SoPlex's data structure

        Args:
            conv_opt_model (:obj:`Model`): model
Severity: Minor
Found in conv_opt/solver/soplex.py - About 7 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

Avoid deeply nested control flow statements.
Open

                        if range_constraint:
                            cobra_model.reactions[i_reaction]._metabolites[met2] += term.coefficient
                    else:
Severity: Major
Found in conv_opt/solver/soplex.py - About 45 mins to fix

    Avoid deeply nested control flow statements.
    Open

                            if range_constraint:
                            cobra_model.reactions[i_reaction]._metabolites[met2] = term.coefficient
                else:
    Severity: Major
    Found in conv_opt/solver/soplex.py - About 45 mins to fix

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

              if conv_opt_model.objective_direction in [ObjectiveDirection.max, ObjectiveDirection.maximize]:
            objective_sense = 'maximize'
        elif conv_opt_model.objective_direction in [ObjectiveDirection.min, ObjectiveDirection.minimize]:
            objective_sense = 'minimize'
        else:
      Severity: Major
      Found in conv_opt/solver/soplex.py and 1 other location - About 3 hrs to fix
      conv_opt/solver/optlang.py on lines 59..64

      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 65.

      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 4 locations. Consider refactoring.
      Open

                  if constraint.lower_bound is None and constraint.upper_bound is None:
                raise ConvOptError('Constraints must have at least one bound')
      Severity: Major
      Found in conv_opt/solver/soplex.py and 3 other locations - About 30 mins to fix
      conv_opt/solver/cplex.py on lines 110..111
      conv_opt/solver/minos.py on lines 148..149
      conv_opt/solver/scipy.py on lines 207..208

      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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