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

    def check_name(self):
        """Check if name complies with requirements"""

        allowed_chars = string.ascii_letters + string.digits + '_'
Severity: Major
Found in bluepyopt/ephys/models.py and 1 other location - About 1 day to fix
bluepyopt/ephys/models.py on lines 654..674

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 143.

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

        class cmd_build_exe(_build_exe):
            def run(self):
                root = get_root()
                cfg = get_config_from_root(root)
                versions = get_versions()
Severity: Major
Found in versioneer.py and 1 other location - About 1 day to fix
versioneer.py on lines 1699..1719

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 140.

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

        class cmd_py2exe(_py2exe):
            def run(self):
                root = get_root()
                cfg = get_config_from_root(root)
                versions = get_versions()
Severity: Major
Found in versioneer.py and 1 other location - About 1 day to fix
versioneer.py on lines 1666..1686

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 140.

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

    @staticmethod
    def create_empty_template(
        template_name, seclist_names=None, secarray_names=None
    ):
        """create an hoc template named template_name for an empty cell"""
Severity: Major
Found in bluepyopt/ephys/models.py and 1 other location - About 1 day to fix
bluepyopt/ephys/models.py on lines 161..204

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 139.

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

    @staticmethod
    def create_empty_template(
            template_name,
            seclist_names=None,
            secarray_names=None):
Severity: Major
Found in bluepyopt/ephys/models.py and 1 other location - About 1 day to fix
bluepyopt/ephys/models.py on lines 694..741

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 139.

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 protocols.py has 525 lines of code (exceeds 250 allowed). Consider refactoring.
Open

"""Protocol classes"""
from .recordings import LFPRecording
from .simulators import LFPySimulator
from .stimuli import LFPStimulus
Severity: Major
Found in bluepyopt/ephys/protocols.py - About 1 day to fix

    File efeatures.py has 525 lines of code (exceeds 250 allowed). Consider refactoring.
    Open

    """eFeature classes"""

"""
Copyright (c) 2016-2020, EPFL/Blue Brain Project
    Severity: Major
    Found in bluepyopt/ephys/efeatures.py - About 1 day to fix

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

      def render_pep440_old(pieces):
    """TAG[.postDISTANCE[.dev0]] .

    The ".dev0" means dirty.
      Severity: Major
      Found in bluepyopt/_version.py and 1 other location - About 1 day to fix
      versioneer.py on lines 1383..1402

      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 125.

      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 render_pep440_old(pieces):
    """TAG[.postDISTANCE[.dev0]] .

    The ".dev0" means dirty.
      Severity: Major
      Found in versioneer.py and 1 other location - About 1 day to fix
      bluepyopt/_version.py on lines 400..419

      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 125.

      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 biophys.py has 503 lines of code (exceeds 250 allowed). Consider refactoring.
      Open

      """Functions to create neuroml biophysiology"""

"""
Copyright (c) 2016-2022, EPFL/Blue Brain Project
 This file is part of BluePyOpt <https://github.com/BlueBrain/BluePyOpt>
      Severity: Major
      Found in bluepyopt/neuroml/biophys.py - About 1 day to fix

        File l5pc_analysis.py has 477 lines of code (exceeds 250 allowed). Consider refactoring.
        Open

        """Run simple cell optimisation"""

"""
Copyright (c) 2016-2020, EPFL/Blue Brain Project
        Severity: Minor
        Found in examples/l5pc/l5pc_analysis.py - About 7 hrs to fix

          File locations.py has 475 lines of code (exceeds 250 allowed). Consider refactoring.
          Open

          """Location classes"""

"""
Copyright (c) 2016-2020, EPFL/Blue Brain Project
          Severity: Minor
          Found in bluepyopt/ephys/locations.py - About 7 hrs to fix

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

                erf_arg = -((param['rho_star'] - rho_bar +
                 (rho_bar - rho_0) * np.exp(-n / (tau_eff * f))) /
                (np.sqrt(sigma_rho_sq * (1.0 -
                                         np.exp(-2.0 * n / (tau_eff * f))))))
            Severity: Major
            Found in examples/graupnerbrunelstdp/stdputil.py and 1 other location - About 6 hrs to fix
            examples/graupnerbrunelstdp/stdputil.py on lines 381..384

            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 109.

            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

                erf_arg = -((param['rho_star'] - rho_bar +
                 (rho_bar - rho_0) * np.exp(-n / (tau_eff * f))) /
                (np.sqrt(sigma_rho_sq * (1.0 -
                                         np.exp(-2.0 * n / (tau_eff * f))))))
            Severity: Major
            Found in examples/graupnerbrunelstdp/stdputil.py and 1 other location - About 6 hrs to fix
            examples/graupnerbrunelstdp/stdputil.py on lines 389..392

            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 109.

            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 define_fitness_calculator has a Cognitive Complexity of 44 (exceeds 5 allowed). Consider refactoring.
            Open

            def define_fitness_calculator(main_protocol, features_filename, prefix=""):
    """Define fitness calculator"""

    with open(os.path.join(os.path.dirname(__file__), '..', features_filename)) as protocol_file:
        feature_definitions = json.load(protocol_file)
            Severity: Minor
            Found in examples/thalamocortical-cell/CellEvalSetup/evaluator.py - About 6 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

                def __init__(
            self,
            name,
            value=None,
            frozen=False,
            Severity: Major
            Found in bluepyopt/ephys/parameters.py and 1 other location - About 6 hrs to fix
            bluepyopt/ephys/parameters.py on lines 176..217

            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 107.

            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 __init__(
            self,
            name,
            value=None,
            frozen=False,
            Severity: Major
            Found in bluepyopt/ephys/parameters.py and 1 other location - About 6 hrs to fix
            bluepyopt/ephys/parameters.py on lines 325..365

            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 107.

            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 _translate_mech has a Cognitive Complexity of 41 (exceeds 5 allowed). Consider refactoring.
            Open

                def _translate_mech(cls, mech_name, mech_params, arb_cats):
        """Translate NMODL mechanism to Arbor ACC format

        Args:
            mech_name (): NMODL mechanism name (suffix)
            Severity: Minor
            Found in bluepyopt/ephys/create_acc.py - About 6 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

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

            def render_git_describe(pieces):
    """TAG[-DISTANCE-gHEX][-dirty].

    Like 'git describe --tags --dirty --always'.
            Severity: Major
            Found in bluepyopt/_version.py and 1 other location - About 6 hrs to fix
            versioneer.py on lines 1405..1422

            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 100.

            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 render_git_describe(pieces):
    """TAG[-DISTANCE-gHEX][-dirty].

    Like 'git describe --tags --dirty --always'.
            Severity: Major
            Found in versioneer.py and 1 other location - About 6 hrs to fix
            bluepyopt/_version.py on lines 422..439

            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 100.

            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

            Severity
            Category
            Status
            Source
            Language