KarrLab/conv_opt

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conv_opt/solver/minos.py

Summary

Maintainability
D
2 days
Test Coverage
A
99%

Function load has a Cognitive Complexity of 33 (exceeds 5 allowed). Consider refactoring.
Open

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

        Args:
            conv_opt_model (:obj:`Model`): model
Severity: Minor
Found in conv_opt/solver/minos.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

File minos.py has 289 lines of code (exceeds 250 allowed). Consider refactoring.
Open

""" MINOS module

References:

* `MINOS <https://web.stanford.edu/group/SOL/minos.htm>`_
Severity: Minor
Found in conv_opt/solver/minos.py - About 2 hrs to fix

    Function solve has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
    Open

        def solve(self):
            """ Solve the model
    
            Returns:
                :obj:`Result`: result
    Severity: Minor
    Found in conv_opt/solver/minos.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 load has 31 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

        def load(self, conv_opt_model):
            """ Load a model to MINOS' data structure
    
            Args:
                conv_opt_model (:obj:`Model`): model
    Severity: Minor
    Found in conv_opt/solver/minos.py - About 1 hr to fix

      Function solve has 30 lines of code (exceeds 25 allowed). Consider refactoring.
      Open

          def solve(self):
              """ Solve the model
      
              Returns:
                  :obj:`Result`: result
      Severity: Minor
      Found in conv_opt/solver/minos.py - About 1 hr to fix

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

        def makeME_LP(S, b, c, xl, xu, csense):
        Severity: Minor
        Found in conv_opt/solver/minos.py - About 45 mins to fix

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

                  float_opt_names = numpy.array(
                      numpy.array([c for c in [s.ljust(55) for s in keys]],
          Severity: Major
          Found in conv_opt/solver/minos.py and 1 other location - About 1 hr to fix
          conv_opt/solver/minos.py on lines 246..247

          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 45.

          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

                  int_opt_names = numpy.array(
                      numpy.array([c for c in [s.ljust(55) for s in keys]],
          Severity: Major
          Found in conv_opt/solver/minos.py and 1 other location - About 1 hr to fix
          conv_opt/solver/minos.py on lines 253..254

          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 45.

          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

                      elif constraint.upper_bound is None:
                          constraint_matrix = numpy.concatenate((constraint_matrix, constraint_row))
                          constraint_senses.append('G')
                          rhs.append(constraint.lower_bound)
          Severity: Major
          Found in conv_opt/solver/minos.py and 2 other locations - About 45 mins to fix
          conv_opt/solver/minos.py on lines 151..154
          conv_opt/solver/minos.py on lines 161..164

          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 35.

          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

                      if constraint.lower_bound is None:
                          constraint_matrix = numpy.concatenate((constraint_matrix, constraint_row))
                          constraint_senses.append('L')
                          rhs.append(constraint.upper_bound)
          Severity: Major
          Found in conv_opt/solver/minos.py and 2 other locations - About 45 mins to fix
          conv_opt/solver/minos.py on lines 156..159
          conv_opt/solver/minos.py on lines 161..164

          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 35.

          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

                  'minos': {
                      'sense': 'Maximize',
                      'solution': 'Solution No',
                      'New basis file': 11,
                      'Save frequency': 500000,
          Severity: Minor
          Found in conv_opt/solver/minos.py and 1 other location - About 45 mins to fix
          conv_opt/solver/minos.py on lines 57..73

          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 35.

          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

                  'qminos': {
                      'sense': 'Maximize',
                      'solution': 'Solution No',
                      'New basis file': 11,
                      'Save frequency': 500000,
          Severity: Minor
          Found in conv_opt/solver/minos.py and 1 other location - About 45 mins to fix
          conv_opt/solver/minos.py on lines 39..55

          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 35.

          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

                      elif constraint.lower_bound == constraint.upper_bound:
                          constraint_matrix = numpy.concatenate((constraint_matrix, constraint_row))
                          constraint_senses.append('E')
                          rhs.append(constraint.lower_bound)
          Severity: Major
          Found in conv_opt/solver/minos.py and 2 other locations - About 45 mins to fix
          conv_opt/solver/minos.py on lines 151..154
          conv_opt/solver/minos.py on lines 156..159

          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 35.

          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 5 locations. Consider refactoring.
          Open

                  if self._options.presolve != Presolve.off:
                      raise ConvOptError('Unsupported presolve mode "{}"'.format(self._options.presolve))
          Severity: Major
          Found in conv_opt/solver/minos.py and 4 other locations - About 35 mins to fix
          conv_opt/solver/cvxpy.py on lines 136..137
          conv_opt/solver/mosek.py on lines 167..168
          conv_opt/solver/scipy.py on lines 264..265
          conv_opt/solver/xpress.py on lines 146..162

          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 33.

          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/minos.py and 3 other locations - About 30 mins to fix
          conv_opt/solver/cplex.py on lines 110..111
          conv_opt/solver/scipy.py on lines 207..208
          conv_opt/solver/soplex.py on lines 107..108

          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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