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bluepyopt/ephys/models.py

Summary

Maintainability
F
2 wks
Test Coverage

File models.py has 685 lines of code (exceeds 250 allowed). Consider refactoring.
Open

"""Cell template class"""

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

    Function _create_sim_desc has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring.
    Open

        def _create_sim_desc(self, param_values,
                         ignored_globals=(), template=None,
                         disable_banner=False,
                         template_dir=None,
                         extra_params=None,
    Severity: Minor
    Found in bluepyopt/ephys/models.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

    Function __init__ has 10 arguments (exceeds 4 allowed). Consider refactoring.
    Open

        def __init__(
    Severity: Major
    Found in bluepyopt/ephys/models.py - About 1 hr to fix

      Function create_acc has 8 arguments (exceeds 4 allowed). Consider refactoring.
      Open

          def create_acc(self, param_values,
      Severity: Major
      Found in bluepyopt/ephys/models.py - About 1 hr to fix

        Function _create_sim_desc has 7 arguments (exceeds 4 allowed). Consider refactoring.
        Open

            def _create_sim_desc(self, param_values,
        Severity: Major
        Found in bluepyopt/ephys/models.py - About 50 mins to fix

          Function __init__ has 7 arguments (exceeds 4 allowed). Consider refactoring.
          Open

              def __init__(
          Severity: Major
          Found in bluepyopt/ephys/models.py - About 50 mins to fix

            Function write_acc has 6 arguments (exceeds 4 allowed). Consider refactoring.
            Open

                def write_acc(self, output_dir, param_values,
            Severity: Minor
            Found in bluepyopt/ephys/models.py - About 45 mins to fix

              Function instantiate has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.
              Open

                  def instantiate(self, sim=None):
        """Instantiate model in simulator"""
        from LFPy import Cell
        from lfpykit import RecExtElectrode
              Severity: Minor
              Found in bluepyopt/ephys/models.py - About 45 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_hoc has 5 arguments (exceeds 4 allowed). Consider refactoring.
              Open

                  def create_hoc(
              Severity: Minor
              Found in bluepyopt/ephys/models.py - About 35 mins to fix

                Function create_hoc has 5 arguments (exceeds 4 allowed). Consider refactoring.
                Open

                    def create_hoc(self, param_values,
                Severity: Minor
                Found in bluepyopt/ephys/models.py - About 35 mins to fix

                  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 __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

                  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 __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 instantiate has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
                  Open

                      def instantiate(self, sim=None):
        """Instantiate model in simulator"""

        self.instantiate_morphology(sim)
                  Severity: Minor
                  Found in bluepyopt/ephys/models.py - About 25 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

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

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

        content = "%s:\n" % self.name
                  Severity: Major
                  Found in bluepyopt/ephys/models.py and 1 other location - About 1 day to fix
                  bluepyopt/ephys/models.py on lines 430..450

                  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 147.

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

        content = '%s:\n' % self.name
                  Severity: Major
                  Found in bluepyopt/ephys/models.py and 1 other location - About 1 day to fix
                  bluepyopt/ephys/models.py on lines 871..891

                  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 147.

                  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 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 124..142

                  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

                  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

                  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

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

                          if not hasattr(sim.neuron.h, self.name):
            self.icell = self.create_empty_cell(
                self.name,
                sim=sim,
                seclist_names=self.seclist_names,
                  Severity: Major
                  Found in bluepyopt/ephys/models.py and 1 other location - About 3 hrs to fix
                  bluepyopt/ephys/models.py on lines 230..237

                  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 69.

                  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

                          if not hasattr(sim.neuron.h, self.name):
            self.icell = self.create_empty_cell(
                self.name,
                sim=sim,
                seclist_names=self.seclist_names,
                  Severity: Major
                  Found in bluepyopt/ephys/models.py and 1 other location - About 3 hrs to fix
                  bluepyopt/ephys/models.py on lines 764..772

                  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 69.

                  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_cell(
            name,
            sim,
            seclist_names=None,
                  Severity: Major
                  Found in bluepyopt/ephys/models.py and 1 other location - About 2 hrs to fix
                  bluepyopt/ephys/models.py on lines 743..756

                  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 60.

                  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_cell(name, sim, seclist_names=None, secarray_names=None):
        """Create an empty cell in Neuron"""

        # TODO minize hardcoded definition
                  Severity: Major
                  Found in bluepyopt/ephys/models.py and 1 other location - About 2 hrs to fix
                  bluepyopt/ephys/models.py on lines 206..224

                  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 60.

                  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

                          for param in self.params.values():
            if not param.frozen:
                param.freeze(param_values[param.name])
                to_unfreeze.append(param.name)
                  Severity: Major
                  Found in bluepyopt/ephys/models.py and 1 other location - About 2 hrs to fix
                  bluepyopt/ephys/models.py on lines 843..846

                  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 50.

                  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

                          for param in self.params.values():
            if not param.frozen:
                param.freeze(param_values[param.name])
                to_unfreeze.append(param.name)
                  Severity: Major
                  Found in bluepyopt/ephys/models.py and 1 other location - About 2 hrs to fix
                  bluepyopt/ephys/models.py on lines 309..312

                  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 50.

                  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 check_nonfrozen_params(self, param_names):  # pylint: disable=W0613
        """Check if all nonfrozen params are set"""

        for param_name, param in self.params.items():
            if not param.frozen:
                  Severity: Major
                  Found in bluepyopt/ephys/models.py and 1 other location - About 1 hr to fix
                  bluepyopt/ephys/models.py on lines 822..828

                  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 48.

                  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 check_nonfrozen_params(self, param_names):  # pylint: disable=W0613
        """Check if all nonfrozen params are set"""

        for param_name, param in self.params.items():
            if not param.frozen:
                  Severity: Major
                  Found in bluepyopt/ephys/models.py and 1 other location - About 1 hr to fix
                  bluepyopt/ephys/models.py on lines 290..296

                  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 48.

                  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

                          if self.params is not None:
            for param in self.params.values():
                param.instantiate(sim=sim, icell=self.icell,
                                  params=self.params)
                  Severity: Major
                  Found in bluepyopt/ephys/models.py and 1 other location - About 1 hr to fix
                  bluepyopt/ephys/models.py on lines 795..798

                  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 45.

                  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

                          if self.params is not None:
            for param in self.params.values():
                param.instantiate(sim=sim, icell=self.icell,
                                  params=self.params)
                  Severity: Major
                  Found in bluepyopt/ephys/models.py and 1 other location - About 1 hr to fix
                  bluepyopt/ephys/models.py on lines 262..265

                  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 45.

                  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

                          if self.mechanisms is not None:
            for mechanism in self.mechanisms:
                mechanism.instantiate(sim=sim, icell=self.icell)
                  Severity: Minor
                  Found in bluepyopt/ephys/models.py and 1 other location - About 50 mins to fix
                  bluepyopt/ephys/models.py on lines 258..260

                  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 36.

                  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

                          ret = sim_desc_creator(mechs=self.mechanisms,
                               parameters=self.params.values(),
                  Severity: Minor
                  Found in bluepyopt/ephys/models.py and 1 other location - About 50 mins to fix
                  bluepyopt/ephys/models.py on lines 855..857

                  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 36.

                  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

                          ret = create_hoc.create_hoc(
            mechs=self.mechanisms,
            parameters=self.params.values(),
                  Severity: Minor
                  Found in bluepyopt/ephys/models.py and 1 other location - About 50 mins to fix
                  bluepyopt/ephys/models.py on lines 356..357

                  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 36.

                  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

                          if self.mechanisms is not None:
            for mechanism in self.mechanisms:
                mechanism.instantiate(sim=sim, icell=self.icell)
                  Severity: Minor
                  Found in bluepyopt/ephys/models.py and 1 other location - About 50 mins to fix
                  bluepyopt/ephys/models.py on lines 791..793

                  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 36.

                  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

                          if seclist_names is None:
            self.seclist_names = [
                "all",
                "somatic",
                "basal",
                  Severity: Minor
                  Found in bluepyopt/ephys/models.py and 1 other location - About 30 mins to fix
                  bluepyopt/ephys/models.py on lines 110..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 32.

                  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

                          if seclist_names is None:
            self.seclist_names = [
                'all', 'somatic', 'basal', 'apical', 'axonal', 'myelinated'
            ]
        else:
                  Severity: Minor
                  Found in bluepyopt/ephys/models.py and 1 other location - About 30 mins to fix
                  bluepyopt/ephys/models.py on lines 637..647

                  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 32.

                  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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