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KarrLab/bpforms

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examples/modomics.py

Summary

Maintainability
F
6 days
Test Coverage

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

def run_trna(session, modomics_short_code_to_monomer, monomer_codes, out_filename):
    response = session.get(URL, params={
        'RNA_type': 'tRNA',
        'RNA_subtype': 'all',
        'organism': 'all species',
Severity: Minor
Found in examples/modomics.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

Function run_rrna has a Cognitive Complexity of 31 (exceeds 5 allowed). Consider refactoring.
Open

def run_rrna(session, modomics_short_code_to_monomer, monomer_codes, out_filename):
    response = session.get(URL, params={
        'RNA_type': 'rRNA',
        'RNA_subtype': 'all',
        'organism': 'all species',
Severity: Minor
Found in examples/modomics.py - About 4 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

File modomics.py has 325 lines of code (exceeds 250 allowed). Consider refactoring.
Open

""" Generate BpForms for all of the tRNA in MODOMICS, verify
them, and calculate their properties

:Author: Jonathan Karr <karr@mssm.edu>
:Date: 2019-06-20
Severity: Minor
Found in examples/modomics.py - About 3 hrs to fix

    Function run has 42 lines of code (exceeds 25 allowed). Consider refactoring.
    Open

    def run():
    # create dict of MODOMICS single character monomer codes
    modomics_short_code_to_monomer = {}
    for monomer in bpforms.rna_alphabet.monomers.values():
        for identifier in monomer.identifiers:
    Severity: Minor
    Found in examples/modomics.py - About 1 hr to fix

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

      def plot_codes(code_freq, monomer_codes, axis, ignore_canonical=False, use_rel=True,
      Severity: Major
      Found in examples/modomics.py - About 1 hr to fix

        Function plot_codes has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
        Open

        def plot_codes(code_freq, monomer_codes, axis, ignore_canonical=False, use_rel=True,
               title=None, x_axis_label=None, y_axis_label='Frequency (%)',
               axis_font_size=10, tick_font_size=6, font_family='Raleway',
               x_label_pad=None):
    monomer_ids = {}
        Severity: Minor
        Found in examples/modomics.py - About 55 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

        Avoid deeply nested control flow statements.
        Open

                            if monomer is None:
                        unsupported_codes.add(code)
                        monomer = bpforms.Monomer(id=code)
                    else:
                        monomer_codes[code] = monomer
        Severity: Major
        Found in examples/modomics.py - About 45 mins to fix

          Avoid deeply nested control flow statements.
          Open

                              if code not in code_freq:
                        code_freq[code] = 0
                    code_freq[code] += 1
          Severity: Major
          Found in examples/modomics.py - About 45 mins to fix

            Avoid deeply nested control flow statements.
            Open

                                if monomer is None:
                        unsupported_codes.add(code)
                        monomer = bpforms.Monomer(id=code)
                    else:
                        monomer_codes[code] = monomer
            Severity: Major
            Found in examples/modomics.py - About 45 mins to fix

              Function run has a Cognitive Complexity of 6 (exceeds 5 allowed). Consider refactoring.
              Open

              def run():
    # create dict of MODOMICS single character monomer codes
    modomics_short_code_to_monomer = {}
    for monomer in bpforms.rna_alphabet.monomers.values():
        for identifier in monomer.identifiers:
              Severity: Minor
              Found in examples/modomics.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

                                  if monomer is None:
                        unsupported_codes.add(code)
                        monomer = bpforms.Monomer(id=code)
                    else:
                        monomer_codes[code] = monomer
              Severity: Major
              Found in examples/modomics.py and 1 other location - About 4 hrs to fix
              examples/modomics.py on lines 194..201

              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 78.

              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 monomer is None:
                    unsupported_codes.add(code)
                    monomer = bpforms.Monomer(id=code)
                else:
                    monomer_codes[code] = monomer
              Severity: Major
              Found in examples/modomics.py and 1 other location - About 4 hrs to fix
              examples/modomics.py on lines 182..189

              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 78.

              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

                  with open(os.path.join('examples', 'modomics.trna.canonical-code-freq.tsv'), 'w') as file:
        writer = csv.DictWriter(file, fieldnames=['Code', 'Frequency'], dialect='excel-tab')
        writer.writeheader()
        for code, freq in canonical_code_freq.items():
            writer.writerow({'Code': code, 'Frequency': freq})
              Severity: Major
              Found in examples/modomics.py and 1 other location - About 4 hrs to fix
              examples/modomics.py on lines 237..241

              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 76.

              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

                  with open(os.path.join('examples', 'modomics.trna.code-freq.tsv'), 'w') as file:
        writer = csv.DictWriter(file, fieldnames=['Code', 'Frequency'], dialect='excel-tab')
        writer.writeheader()
        for code, freq in code_freq.items():
            writer.writerow({'Code': code, 'Frequency': freq})
              Severity: Major
              Found in examples/modomics.py and 1 other location - About 4 hrs to fix
              examples/modomics.py on lines 231..235

              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 76.

              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 4 locations. Consider refactoring.
              Open

                      canonical_code_freq['U'] += \
            rna_forms[-1]['Sequence (IUPAC)'].count('U') \
            - rna_form.seq.count(bpforms.rna_alphabet.monomers.U)
              Severity: Major
              Found in examples/modomics.py and 3 other locations - About 2 hrs to fix
              examples/modomics.py on lines 215..217
              examples/modomics.py on lines 218..220
              examples/modomics.py on lines 221..223

              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 51.

              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 4 locations. Consider refactoring.
              Open

                      canonical_code_freq['C'] += \
            rna_forms[-1]['Sequence (IUPAC)'].count('C') \
            - rna_form.seq.count(bpforms.rna_alphabet.monomers.C)
              Severity: Major
              Found in examples/modomics.py and 3 other locations - About 2 hrs to fix
              examples/modomics.py on lines 215..217
              examples/modomics.py on lines 221..223
              examples/modomics.py on lines 224..226

              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 51.

              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 4 locations. Consider refactoring.
              Open

                      canonical_code_freq['G'] += \
            rna_forms[-1]['Sequence (IUPAC)'].count('G') \
            - rna_form.seq.count(bpforms.rna_alphabet.monomers.G)
              Severity: Major
              Found in examples/modomics.py and 3 other locations - About 2 hrs to fix
              examples/modomics.py on lines 215..217
              examples/modomics.py on lines 218..220
              examples/modomics.py on lines 224..226

              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 51.

              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 4 locations. Consider refactoring.
              Open

                      canonical_code_freq['A'] += \
            rna_forms[-1]['Sequence (IUPAC)'].count('A') \
            - rna_form.seq.count(bpforms.rna_alphabet.monomers.A)
              Severity: Major
              Found in examples/modomics.py and 3 other locations - About 2 hrs to fix
              examples/modomics.py on lines 218..220
              examples/modomics.py on lines 221..223
              examples/modomics.py on lines 224..226

              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 51.

              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 monomer is None:
                    unsupported_codes.add(code)
                    monomer = bpforms.Monomer(id=code)
                else:
                    monomer_codes[code] = monomer
              Severity: Major
              Found in examples/modomics.py and 1 other location - About 1 hr to fix
              examples/modomics.py on lines 118..122

              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 44.

              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 monomer is None:
                        unsupported_codes.add(code)
                        monomer = bpforms.Monomer(id=code)
                    else:
                        monomer_codes[code] = monomer
              Severity: Major
              Found in examples/modomics.py and 1 other location - About 1 hr to fix
              examples/modomics.py on lines 127..131

              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 44.

              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 4 locations. Consider refactoring.
              Open

                  results_dict['Number of modified A'] = canonical_seq.count('A') - rna_form.seq.count(bpforms.rna_alphabet.monomers.A)
              Severity: Major
              Found in examples/modomics.py and 3 other locations - About 55 mins to fix
              examples/modomics.py on lines 257..257
              examples/modomics.py on lines 258..258
              examples/modomics.py on lines 259..259

              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 37.

              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 4 locations. Consider refactoring.
              Open

                  results_dict['Number of modified U'] = canonical_seq.count('U') - rna_form.seq.count(bpforms.rna_alphabet.monomers.U)
              Severity: Major
              Found in examples/modomics.py and 3 other locations - About 55 mins to fix
              examples/modomics.py on lines 256..256
              examples/modomics.py on lines 257..257
              examples/modomics.py on lines 258..258

              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 37.

              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 4 locations. Consider refactoring.
              Open

                  results_dict['Number of modified C'] = canonical_seq.count('C') - rna_form.seq.count(bpforms.rna_alphabet.monomers.C)
              Severity: Major
              Found in examples/modomics.py and 3 other locations - About 55 mins to fix
              examples/modomics.py on lines 256..256
              examples/modomics.py on lines 258..258
              examples/modomics.py on lines 259..259

              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 37.

              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 4 locations. Consider refactoring.
              Open

                  results_dict['Number of modified G'] = canonical_seq.count('G') - rna_form.seq.count(bpforms.rna_alphabet.monomers.G)
              Severity: Major
              Found in examples/modomics.py and 3 other locations - About 55 mins to fix
              examples/modomics.py on lines 256..256
              examples/modomics.py on lines 257..257
              examples/modomics.py on lines 259..259

              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 37.

              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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