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Similar blocks of code found in 3 locations. Consider refactoring.
Open

for i in range(len(fes_muscle_models)):
    fes_muscle_models[i].alpha_a = fes_muscle_models[i].alpha_a * alpha_a_proportion_list[i]
    fes_muscle_models[i].a_scale = fes_muscle_models[i].a_scale * a_scale_proportion_list[i]
Severity: Major
Found in cocofest/examples/dynamics/reaching_task/reaching_task_pulse_duration_optimization.py and 2 other locations - About 4 hrs to fix
cocofest/examples/dynamics/reaching_task/reaching_task_frequency_optimization.py on lines 60..62
cocofest/examples/dynamics/reaching_task/reaching_task_intensity_optimization.py on lines 60..62

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 80.

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

for i in range(len(fes_muscle_models)):
    fes_muscle_models[i].alpha_a = fes_muscle_models[i].alpha_a * alpha_a_proportion_list[i]
    fes_muscle_models[i].a_rest = fes_muscle_models[i].a_rest * a_rest_proportion_list[i]
Severity: Major
Found in cocofest/examples/dynamics/reaching_task/reaching_task_intensity_optimization.py and 2 other locations - About 4 hrs to fix
cocofest/examples/dynamics/reaching_task/reaching_task_frequency_optimization.py on lines 60..62
cocofest/examples/dynamics/reaching_task/reaching_task_pulse_duration_optimization.py on lines 60..62

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 80.

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

for i in range(len(fes_muscle_models)):
    fes_muscle_models[i].alpha_a = fes_muscle_models[i].alpha_a * alpha_a_proportion_list[i]
    fes_muscle_models[i].a_rest = fes_muscle_models[i].a_rest * a_rest_proportion_list[i]
Severity: Major
Found in cocofest/examples/dynamics/reaching_task/reaching_task_frequency_optimization.py and 2 other locations - About 4 hrs to fix
cocofest/examples/dynamics/reaching_task/reaching_task_intensity_optimization.py on lines 60..62
cocofest/examples/dynamics/reaching_task/reaching_task_pulse_duration_optimization.py on lines 60..62

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 80.

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 fes_identification_ocp.py has 344 lines of code (exceeds 250 allowed). Consider refactoring.
Open

import numpy as np

from bioptim import (
    BoundsList,
    ConstraintList,
Severity: Minor
Found in cocofest/optimization/fes_identification_ocp.py - About 4 hrs to fix

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

            model_time_data = (
            data["time"]
            if data["stim_time"][0] == 0
            else [[(time - data["stim_time"][0]) for time in row] for row in data["time"]]
    Severity: Major
    Found in cocofest/identification/identification_method.py and 1 other location - About 4 hrs to fix
    cocofest/identification/identification_method.py on lines 37..40

    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 75.

    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

            model_time_data = (
            data["time"]
            if data["stim_time"][0] == 0
            else [[(time - data["stim_time"][0]) for time in row] for row in data["time"]]
    Severity: Major
    Found in cocofest/identification/identification_method.py and 1 other location - About 4 hrs to fix
    cocofest/identification/identification_method.py on lines 112..115

    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 75.

    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 force_from_c3d.py has 326 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    import numpy as np
import matplotlib.pyplot as plt
from scipy.signal import find_peaks
from copy import deepcopy
import heapq
    Severity: Minor
    Found in data_process/force_from_c3d.py - About 3 hrs to fix

      Similar blocks of code found in 3 locations. Consider refactoring.
      Open

              b11
        * exp(
            (-0.5 * ((norm_length - b21) * (norm_length - b21)))
            / ((b31 + b41 * norm_length) * (b31 + b41 * norm_length))
        )
      Severity: Major
      Found in cocofest/models/hill_coefficients.py and 2 other locations - About 3 hrs to fix
      cocofest/models/hill_coefficients.py on lines 49..52
      cocofest/models/hill_coefficients.py on lines 39..42

      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 71.

      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

              + b13
        * exp(
            (-0.5 * ((norm_length - b23) * (norm_length - b23)))
            / ((b33 + b43 * norm_length) * (b33 + b43 * norm_length))
      Severity: Major
      Found in cocofest/models/hill_coefficients.py and 2 other locations - About 3 hrs to fix
      cocofest/models/hill_coefficients.py on lines 39..47
      cocofest/models/hill_coefficients.py on lines 39..42

      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 71.

      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 hmed2018.py has 322 lines of code (exceeds 250 allowed). Consider refactoring.
      Open

      from typing import Callable

from casadi import MX, vertcat, tanh
import numpy as np
      Severity: Minor
      Found in cocofest/models/hmed2018.py - About 3 hrs to fix

        File fes_ocp_nmpc_cyclic.py has 318 lines of code (exceeds 250 allowed). Consider refactoring.
        Open

        import math

import numpy as np
from bioptim import (
    SolutionMerge,
        Severity: Minor
        Found in cocofest/optimization/fes_ocp_nmpc_cyclic.py - About 3 hrs to fix

          File hmed2018_force_parameter_identification.py has 310 lines of code (exceeds 250 allowed). Consider refactoring.
          Open

          import time as time_package
import numpy as np

from bioptim import Solver, Objective, OdeSolver
from ..models.hmed2018 import DingModelIntensityFrequency
          Severity: Minor
          Found in cocofest/identification/hmed2018_force_parameter_identification.py - About 3 hrs to fix

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

                        an = (2.0 / self.p) * spi.trapezoid(y * np.cos(2 * np.pi * i * x / self.p), x)
            Severity: Major
            Found in cocofest/fourier_approx.py and 1 other location - About 3 hrs to fix
            cocofest/fourier_approx.py on lines 16..16

            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 66.

            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

                        bn = (2.0 / self.p) * spi.trapezoid(y * np.sin(2 * np.pi * i * x / self.p), x)
            Severity: Major
            Found in cocofest/fourier_approx.py and 1 other location - About 3 hrs to fix
            cocofest/fourier_approx.py on lines 15..15

            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 66.

            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 average_data_extraction has a Cognitive Complexity of 23 (exceeds 5 allowed). Consider refactoring.
            Open

            def average_data_extraction(model_data_path):
    """
    Extracts average data from the provided path.

    Parameters
            Severity: Minor
            Found in cocofest/identification/identification_method.py - About 3 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

                objective_functions.add(
        ObjectiveFcn.Mayer.MINIMIZE_STATE,
        key="qdot",
        index=[0, 1],
        node=Node.ALL,
            Severity: Major
            Found in cocofest/examples/dynamics/intensity_optimization_hold_position_multi_muscle.py and 1 other location - About 3 hrs to fix
            cocofest/examples/dynamics/intensity_optimization_hold_position_multi_muscle.py on lines 24..29

            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

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

                objective_functions.add(
        ObjectiveFcn.Mayer.MINIMIZE_STATE,
        key="q",
        index=[0, 1],
        node=Node.ALL,
            Severity: Major
            Found in cocofest/examples/dynamics/intensity_optimization_hold_position_multi_muscle.py and 1 other location - About 3 hrs to fix
            cocofest/examples/dynamics/intensity_optimization_hold_position_multi_muscle.py on lines 34..39

            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

            File ding2007_force_parameter_identification.py has 297 lines of code (exceeds 250 allowed). Consider refactoring.
            Open

            import time as time_package
import numpy as np

from bioptim import Solver, Objective, OdeSolver
from ..models.ding2007 import DingModelPulseDurationFrequency
            Severity: Minor
            Found in cocofest/identification/ding2007_force_parameter_identification.py - About 3 hrs to fix

              Similar blocks of code found in 3 locations. Consider refactoring.
              Open

                          if parameter_list[i][counter] == [1, 1]:
                a_ocp_time = [single_ocp_time][i][counter]
                a_integration_time = [single_computations_time][i][counter]
              Severity: Major
              Found in cocofest/examples/sensitivity/truncation/summation_truncation_graph.py and 2 other locations - About 3 hrs to fix
              cocofest/examples/sensitivity/truncation/summation_truncation_graph.py on lines 99..101
              cocofest/examples/sensitivity/truncation/summation_truncation_graph.py on lines 103..105

              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 63.

              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

                  objective_functions.add(
        ObjectiveFcn.Mayer.MINIMIZE_STATE,
        key="qdot",
        index=[0],
        node=Node.ALL,
              Severity: Major
              Found in cocofest/examples/dynamics/intensity_optimization_hold_position.py and 1 other location - About 3 hrs to fix
              cocofest/examples/dynamics/intensity_optimization_hold_position.py on lines 25..30

              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 63.

              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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