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Showing 58 of 59 total issues

Function plot has 36 arguments (exceeds 4 allowed). Consider refactoring.
Open

def plot(
Severity: Major
Found in src/taurenmd/plots/plotparams.py - About 4 hrs to fix

    Cyclomatic complexity is too high in function plot. (18)
    Open

    def plot(
        x_data,
        y_data,
        *,
        labels="No label provided",
    Severity: Minor
    Found in src/taurenmd/plots/plotparams.py by radon

    Cyclomatic Complexity

    Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

    Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

    Construct Effect on CC Reasoning
    if +1 An if statement is a single decision.
    elif +1 The elif statement adds another decision.
    else +0 The else statement does not cause a new decision. The decision is at the if.
    for +1 There is a decision at the start of the loop.
    while +1 There is a decision at the while statement.
    except +1 Each except branch adds a new conditional path of execution.
    finally +0 The finally block is unconditionally executed.
    with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
    assert +1 The assert statement internally roughly equals a conditional statement.
    Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
    Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

    Source: http://radon.readthedocs.org/en/latest/intro.html

    Function plot has 21 arguments (exceeds 4 allowed). Consider refactoring.
    Open

    def plot(
    Severity: Major
    Found in src/taurenmd/plots/labeldots.py - About 2 hrs to fix

      Cyclomatic complexity is too high in function main. (14)
      Open

      def main(
        topology,
        trajectories,
        insort=False,
        start=None,
      Severity: Minor
      Found in src/taurenmd/cli_rmsf.py by radon

      Cyclomatic Complexity

      Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

      Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

      Construct Effect on CC Reasoning
      if +1 An if statement is a single decision.
      elif +1 The elif statement adds another decision.
      else +0 The else statement does not cause a new decision. The decision is at the if.
      for +1 There is a decision at the start of the loop.
      while +1 There is a decision at the while statement.
      except +1 Each except branch adds a new conditional path of execution.
      finally +0 The finally block is unconditionally executed.
      with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
      assert +1 The assert statement internally roughly equals a conditional statement.
      Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
      Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

      Source: http://radon.readthedocs.org/en/latest/intro.html

      Cyclomatic complexity is too high in function main. (13)
      Open

      def main(
        topology,
        trajectories,
        insort=False,
        start=None,
      Severity: Minor
      Found in src/taurenmd/cli_trajedit.py by radon

      Cyclomatic Complexity

      Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

      Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

      Construct Effect on CC Reasoning
      if +1 An if statement is a single decision.
      elif +1 The elif statement adds another decision.
      else +0 The else statement does not cause a new decision. The decision is at the if.
      for +1 There is a decision at the start of the loop.
      while +1 There is a decision at the while statement.
      except +1 Each except branch adds a new conditional path of execution.
      finally +0 The finally block is unconditionally executed.
      with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
      assert +1 The assert statement internally roughly equals a conditional statement.
      Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
      Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

      Source: http://radon.readthedocs.org/en/latest/intro.html

      Cyclomatic complexity is too high in function evaluate_to_slice. (13)
      Open

      def evaluate_to_slice(*, value=None, start=None, stop=None, step=None):
    """
    Evaluate to slice.

    If any of ``start``, ``stop`` or ``step`` is given returns
      Severity: Minor
      Found in src/taurenmd/libs/libio.py by radon

      Cyclomatic Complexity

      Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

      Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

      Construct Effect on CC Reasoning
      if +1 An if statement is a single decision.
      elif +1 The elif statement adds another decision.
      else +0 The else statement does not cause a new decision. The decision is at the if.
      for +1 There is a decision at the start of the loop.
      while +1 There is a decision at the while statement.
      except +1 Each except branch adds a new conditional path of execution.
      finally +0 The finally block is unconditionally executed.
      with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
      assert +1 The assert statement internally roughly equals a conditional statement.
      Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
      Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

      Source: http://radon.readthedocs.org/en/latest/intro.html

      Cyclomatic complexity is too high in function main. (13)
      Open

      def main(
        topology,
        trajectories,
        insort=False,
        sel1='all',
      Severity: Minor
      Found in src/taurenmd/cli_distances.py by radon

      Cyclomatic Complexity

      Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

      Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

      Construct Effect on CC Reasoning
      if +1 An if statement is a single decision.
      elif +1 The elif statement adds another decision.
      else +0 The else statement does not cause a new decision. The decision is at the if.
      for +1 There is a decision at the start of the loop.
      while +1 There is a decision at the while statement.
      except +1 Each except branch adds a new conditional path of execution.
      finally +0 The finally block is unconditionally executed.
      with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
      assert +1 The assert statement internally roughly equals a conditional statement.
      Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
      Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

      Source: http://radon.readthedocs.org/en/latest/intro.html

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

      def evaluate_to_slice(*, value=None, start=None, stop=None, step=None):
    """
    Evaluate to slice.

    If any of ``start``, ``stop`` or ``step`` is given returns
      Severity: Minor
      Found in src/taurenmd/libs/libio.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 __call__ has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
      Open

          def __call__(self, parser, namespace, values, option_string=None):
        """Execute."""
        bool_value = {
            'true': True,
            'false': False,
      Severity: Minor
      Found in src/taurenmd/libs/libcli.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 plot has a Cognitive Complexity of 16 (exceeds 5 allowed). Consider refactoring.
      Open

      def plot(
        x_data,
        y_data,
        *,
        labels="No label provided",
      Severity: Minor
      Found in src/taurenmd/plots/plotparams.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

      Cyclomatic complexity is too high in function main. (12)
      Open

      def main(
        topology,
        trajectories,
        plane_selection,
        insort=False,
      Severity: Minor
      Found in src/taurenmd/cli_rotations.py by radon

      Cyclomatic Complexity

      Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

      Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

      Construct Effect on CC Reasoning
      if +1 An if statement is a single decision.
      elif +1 The elif statement adds another decision.
      else +0 The else statement does not cause a new decision. The decision is at the if.
      for +1 There is a decision at the start of the loop.
      while +1 There is a decision at the while statement.
      except +1 Each except branch adds a new conditional path of execution.
      finally +0 The finally block is unconditionally executed.
      with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
      assert +1 The assert statement internally roughly equals a conditional statement.
      Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
      Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

      Source: http://radon.readthedocs.org/en/latest/intro.html

      Cyclomatic complexity is too high in function main. (11)
      Open

      def main(
        topology,
        trajectories,
        plane_selection,
        insort=False,
      Severity: Minor
      Found in src/taurenmd/cli_pangle.py by radon

      Cyclomatic Complexity

      Cyclomatic Complexity corresponds to the number of decisions a block of code contains plus 1. This number (also called McCabe number) is equal to the number of linearly independent paths through the code. This number can be used as a guide when testing conditional logic in blocks.

      Radon analyzes the AST tree of a Python program to compute Cyclomatic Complexity. Statements have the following effects on Cyclomatic Complexity:

      Construct Effect on CC Reasoning
      if +1 An if statement is a single decision.
      elif +1 The elif statement adds another decision.
      else +0 The else statement does not cause a new decision. The decision is at the if.
      for +1 There is a decision at the start of the loop.
      while +1 There is a decision at the while statement.
      except +1 Each except branch adds a new conditional path of execution.
      finally +0 The finally block is unconditionally executed.
      with +1 The with statement roughly corresponds to a try/except block (see PEP 343 for details).
      assert +1 The assert statement internally roughly equals a conditional statement.
      Comprehension +1 A list/set/dict comprehension of generator expression is equivalent to a for loop.
      Boolean Operator +1 Every boolean operator (and, or) adds a decision point.

      Source: http://radon.readthedocs.org/en/latest/intro.html

      Function main has 14 arguments (exceeds 4 allowed). Consider refactoring.
      Open

      def main(
      Severity: Major
      Found in src/taurenmd/cli_trajedit.py - About 1 hr to fix

        Function main has 13 arguments (exceeds 4 allowed). Consider refactoring.
        Open

        def main(
        Severity: Major
        Found in src/taurenmd/cli_rotations.py - About 1 hr to fix

          Function main has 13 arguments (exceeds 4 allowed). Consider refactoring.
          Open

          def main(
          Severity: Major
          Found in src/taurenmd/cli_pangle.py - About 1 hr to fix

            Function main has 12 arguments (exceeds 4 allowed). Consider refactoring.
            Open

            def main(
            Severity: Major
            Found in src/taurenmd/cli_rmsf.py - About 1 hr to fix

              Function main has 12 arguments (exceeds 4 allowed). Consider refactoring.
              Open

              def main(
              Severity: Major
              Found in src/taurenmd/cli_fext.py - About 1 hr to fix

                Function main has 12 arguments (exceeds 4 allowed). Consider refactoring.
                Open

                def main(
                Severity: Major
                Found in src/taurenmd/cli_rmsd.py - About 1 hr to fix

                  Function main has 12 arguments (exceeds 4 allowed). Consider refactoring.
                  Open

                  def main(
                  Severity: Major
                  Found in src/taurenmd/cli_distances.py - About 1 hr to fix

                    Function plot has 34 lines of code (exceeds 25 allowed). Consider refactoring.
                    Open

                    def plot(
        x_data,
        y_data,
        *,
        labels="No label provided",
                    Severity: Minor
                    Found in src/taurenmd/plots/plotparams.py - About 1 hr to fix
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