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Function main has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

def main():
    """Main"""
    import matplotlib.pyplot as plt

    for deterministic in [True, False]:
Severity: Minor
Found in examples/stochkv/stochkvcell.py - About 35 mins 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 find_icomp has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def find_icomp(self, sim, iseclist):
        """Find the index of the compartment based on a list of isec
           and a distance"""
        icomp = None
Severity: Minor
Found in bluepyopt/ephys/locations.py - About 35 mins 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 generate_reinitrng_hoc_block has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def generate_reinitrng_hoc_block(self):
        """"Create re_init_rng code blocks for this channel"""

        reinitrng_hoc_block = ''
Severity: Minor
Found in bluepyopt/ephys/mechanisms.py - About 35 mins 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_individual_params has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

def plot_individual_params(
        opt,
        ax,
        params,
        marker,
Severity: Minor
Found in examples/l5pc/l5pc_analysis.py - About 35 mins 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 __str__ has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def __str__(self):
        """Return string representation"""

        content = "%s:\n" % self.name
Severity: Minor
Found in bluepyopt/ephys/models.py - About 35 mins 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 scale has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def scale(self, values, segment, sim=None):
        """Scale a value based on a segment"""

        # find section
        target_sec = None
Severity: Minor
Found in bluepyopt/ephys/parameterscalers/parameterscalers.py - About 35 mins 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 __init__ has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def __init__(
        self,
        name,
        morph=None,
        mechs=None,
Severity: Minor
Found in bluepyopt/ephys/models.py - About 35 mins 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 create_acc has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def create_acc(self, param_values,
                   ignored_globals=(), template='acc/*_template.jinja2',
                   disable_banner=False,
                   template_dir=None,
                   ext_catalogues=None,
Severity: Minor
Found in bluepyopt/ephys/models.py - About 35 mins 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 _generate_channels_by_location has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

def _generate_channels_by_location(mechs, location_order, loc_desc):
    """Create a OrderedDictionary of all channel mechs for hoc template."""
    channels = OrderedDict((location, []) for location in location_order)
    point_channels = OrderedDict((location, []) for location in location_order)
    for mech in mechs:
Severity: Minor
Found in bluepyopt/ephys/create_hoc.py - About 35 mins 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 _deserializer has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def _deserializer(value):
        """_deserializer"""
        if (isinstance(value, list) and value and
           isinstance(value[0], dict) and SENTINAL in value[0]):
            return [instantiator(v) for v in value]
Severity: Minor
Found in bluepyopt/ephys/serializer.py - About 35 mins 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 __init__ has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def __init__(
            self,
            name=None,
            distribution=None,
            comment='',
Severity: Minor
Found in bluepyopt/ephys/parameterscalers/parameterscalers.py - About 35 mins 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 __init__ has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def __init__(
        self,
        name,
        electrode=None,
        morph=None,
Severity: Minor
Found in bluepyopt/ephys/models.py - About 35 mins 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 __str__ has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
Open

    def __str__(self):
        """Return string representation"""

        content = '%s:\n' % self.name
Severity: Minor
Found in bluepyopt/ephys/models.py - About 35 mins 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

    def calculate_values(self, responses):
        """Calculator the value of each objective"""

        return {objective.name: objective.calculate_value(responses)
                for objective in self.objectives}
Severity: Minor
Found in bluepyopt/ephys/objectivescalculators.py and 1 other location - About 35 mins to fix
bluepyopt/ephys/objectivescalculators.py on lines 38..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 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

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

    def calculate_scores(self, responses):
        """Calculator the score for every objective"""

        return {objective.name: objective.calculate_score(responses)
                for objective in self.objectives}
Severity: Minor
Found in bluepyopt/ephys/objectivescalculators.py and 1 other location - About 35 mins to fix
bluepyopt/ephys/objectivescalculators.py on lines 44..48

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

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

param_cortical = {
    'tau_ca': 22.6936e-3,  # [s]
    'C_pre': 0.5617539,
    'C_post': 1.23964,
    'theta_d': 1.0,
Severity: Minor
Found in examples/graupnerbrunelstdp/stdputil.py and 1 other location - About 35 mins to fix
examples/graupnerbrunelstdp/stdputil.py on lines 65..78

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 2 locations. Consider refactoring.
Open

    def calculate_score(self, responses):
        """Objective score"""

        return self.calculate_feature_scores(responses)[0] * self.weight
Severity: Minor
Found in bluepyopt/ephys/objectives.py and 1 other location - About 35 mins to fix
examples/thalamocortical-cell/CellEvalSetup/evaluator.py on lines 304..307

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 2 locations. Consider refactoring.
Open

    def calculate_score(self, responses):
        """Objective score"""

        return self.calculate_feature_scores(responses)[0] * self.weight
Severity: Minor
Found in examples/thalamocortical-cell/CellEvalSetup/evaluator.py and 1 other location - About 35 mins to fix
bluepyopt/ephys/objectives.py on lines 105..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 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 2 locations. Consider refactoring.
Open

    refs = set([r.strip() for r in refnames.strip("()").split(",")])
Severity: Minor
Found in versioneer.py and 1 other location - About 35 mins to fix
bluepyopt/_version.py on lines 180..180

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

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

param_hippocampal = {
    'tau_ca': 48.8373e-3,  # [s]
    'C_pre': 1.0,
    'C_post': 0.275865,
    'theta_d': 1.0,
Severity: Minor
Found in examples/graupnerbrunelstdp/stdputil.py and 1 other location - About 35 mins to fix
examples/graupnerbrunelstdp/stdputil.py on lines 47..60

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

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