biosustain/optlang

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Container has 26 functions (exceeds 20 allowed). Consider refactoring.
Open

class Container(object):
    '''
    A container for objects that have a name attribute.
    Items in the Container can be accessed by index like a list or by key (the name attribute of the item).
    For convenience, an item can also be accessed as an attribute with the same name as the name attribute of the item.
Severity: Minor
Found in src/optlang/container.py - About 3 hrs to fix

    Function inheritdocstring has a Cognitive Complexity of 21 (exceeds 5 allowed). Consider refactoring.
    Open

    def inheritdocstring(name, bases, attrs):
        """
        Use as metaclass to inherit class and method docstrings from parent.
        Adapted from http://stackoverflow.com/questions/13937500/inherit-a-parent-class-docstring-as-doc-attribute
        Use this on classes defined in solver-specific interfaces to inherit docstrings from the high-level interface.
    Severity: Minor
    Found in src/optlang/util.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

    Variable has 24 functions (exceeds 20 allowed). Consider refactoring.
    Open

    class Variable(symbolics.Symbol):
        """Optimization variables.
    
        Variable objects are used to represents each variable of the optimization problem. When the optimization is
        performed, the combination of variable values that optimizes the objective function, while not violating any
    Severity: Minor
    Found in src/optlang/interface.py - About 2 hrs to fix

      Model has 24 functions (exceeds 20 allowed). Consider refactoring.
      Open

      class Model(interface.Model):
          def _initialize_problem(self):
              self.problem = glp_create_prob()
              glp_create_index(self.problem)
              if self.name is not None:
      Severity: Minor
      Found in src/optlang/glpk_interface.py - About 2 hrs to fix

        Function git_versions_from_keywords has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.
        Open

        def git_versions_from_keywords(
            keywords: Dict[str, str],
            tag_prefix: str,
            verbose: bool,
        ) -> Dict[str, Any]:
        Severity: Minor
        Found in src/optlang/_version.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 git_versions_from_keywords has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.
        Open

        def git_versions_from_keywords(
            keywords: Dict[str, str],
            tag_prefix: str,
            verbose: bool,
        ) -> Dict[str, Any]:
        Severity: Minor
        Found in versioneer.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 get_versions has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.
        Open

        def get_versions(verbose: bool = False) -> Dict[str, Any]:
            """Get the project version from whatever source is available.
        
            Returns dict with two keys: 'version' and 'full'.
            """
        Severity: Minor
        Found in versioneer.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 _initialize_model_from_problem has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.
        Open

            def _initialize_model_from_problem(self, problem):
                try:
                    self.problem = problem
                    glp_create_index(self.problem)
                except TypeError:
        Severity: Minor
        Found in src/optlang/glpk_interface.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 run_command has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.
        Open

        def run_command(
            commands: List[str],
            args: List[str],
            cwd: Optional[str] = None,
            verbose: bool = False,
        Severity: Minor
        Found in src/optlang/_version.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 run_command has a Cognitive Complexity of 18 (exceeds 5 allowed). Consider refactoring.
        Open

        def run_command(
            commands: List[str],
            args: List[str],
            cwd: Optional[str] = None,
            verbose: bool = False,
        Severity: Minor
        Found in versioneer.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

        Model has 22 functions (exceeds 20 allowed). Consider refactoring.
        Open

        class Model(interface.Model):
            def _initialize_problem(self):
                self.problem = cplex.Cplex()
        
            def _initialize_model_from_problem(self, problem):
        Severity: Minor
        Found in src/optlang/cplex_interface.py - About 2 hrs to fix

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

          def git_get_keywords(versionfile_abs: str) -> Dict[str, str]:
              """Extract version information from the given file."""
              # the code embedded in _version.py can just fetch the value of these
              # keywords. When used from setup.py, we don't want to import _version.py,
              # so we do it with a regexp instead. This function is not used from
          Severity: Minor
          Found in src/optlang/_version.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 git_get_keywords has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
          Open

          def git_get_keywords(versionfile_abs: str) -> Dict[str, str]:
              """Extract version information from the given file."""
              # the code embedded in _version.py can just fetch the value of these
              # keywords. When used from setup.py, we don't want to import _version.py,
              # so we do it with a regexp instead. This function is not used from
          Severity: Minor
          Found in versioneer.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

          Model has 21 functions (exceeds 20 allowed). Consider refactoring.
          Open

          class Model(interface.Model):
              ProblemClass = MatrixProblem
              status_map = _STATUS_MAP
          
              def _initialize_problem(self):
          Severity: Minor
          Found in src/optlang/matrix_interface.py - About 2 hrs to fix

            Configuration has 21 functions (exceeds 20 allowed). Consider refactoring.
            Open

            class Configuration(interface.MathematicalProgrammingConfiguration):
                lp_methods = _LP_METHODS
                qp_methods = _QP_METHODS
            
                def __init__(
            Severity: Minor
            Found in src/optlang/matrix_interface.py - About 2 hrs to fix

              Model has 21 functions (exceeds 20 allowed). Consider refactoring.
              Open

              class Model(interface.Model):
              
                  def _initialize_problem(self):
                      self.problem = gurobipy.Model()
                      self.problem.params.OutputFlag = 0
              Severity: Minor
              Found in src/optlang/gurobi_interface.py - About 2 hrs to fix

                Function _add_constraints has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
                Open

                    def _add_constraints(self, constraints, sloppy=False):
                        for constraint in constraints:
                            constraint_id = constraint.name
                            if sloppy is False:
                                variables = constraint.variables
                Severity: Minor
                Found in src/optlang/interface.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

                File inspyred_interface.py has 252 lines of code (exceeds 250 allowed). Consider refactoring.
                Open

                # Copyright 2013 Novo Nordisk Foundation Center for Biosustainability,
                # Technical University of Denmark.
                #
                # Licensed under the Apache License, Version 2.0 (the "License");
                # you may not use this file except in compliance with the License.
                Severity: Minor
                Found in src/optlang/inspyred_interface.py - About 2 hrs to fix

                  Function _parse_linear_expression has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.
                  Open

                  def _parse_linear_expression(expression, expanded=False, **kwargs):
                      """
                      Parse the coefficients of a linear expression (linearity is assumed).
                  
                      Returns a dictionary of variable: coefficient pairs.
                  Severity: Minor
                  Found in src/optlang/expression_parsing.py - About 1 hr 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 do_vcs_install has a Cognitive Complexity of 15 (exceeds 5 allowed). Consider refactoring.
                  Open

                  def do_vcs_install(versionfile_source: str, ipy: Optional[str]) -> None:
                      """Git-specific installation logic for Versioneer.
                  
                      For Git, this means creating/changing .gitattributes to mark _version.py
                      for export-subst keyword substitution.
                  Severity: Minor
                  Found in versioneer.py - About 1 hr 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

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