Sign upLogin

epam/miew

View on GitHub
Star
packages/miew/tools/pdbfreq.py

Summary

Maintainability
F
2 wks
Test Coverage

Function process_file has a Cognitive Complexity of 71 (exceeds 5 allowed). Consider refactoring.
Open

def process_file(filename):
  print 'Processing %s...' % filename
  stats = defaultdict(int)
  stats_props = defaultdict(set)
  with open(filename) as f:
Severity: Minor
Found in packages/miew/tools/pdbfreq.py - About 1 day 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 write_csv has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.
Open

def write_csv():
  # create subtotals
  stats_total = defaultdict(int)
  stats_props_total = defaultdict(set)
  for filename, stats, stats_props in files:
Severity: Minor
Found in packages/miew/tools/pdbfreq.py - About 2 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

Avoid deeply nested control flow statements.
Open

          if re.match(r'\s*SMTRY\d ', content):
            stats['REMARK 290 SMTRYn'] += 1
Severity: Major
Found in packages/miew/tools/pdbfreq.py - About 45 mins to fix

    Avoid deeply nested control flow statements.
    Open

              if key == 'resName':
            if tag == 'ATOM':
              if value not in resNames:
                stats_props['%s %s_OTHER' % (tag, key)].add(value)
              elif value in resNamesNucleic:
    Severity: Major
    Found in packages/miew/tools/pdbfreq.py - About 45 mins to fix

      Avoid deeply nested control flow statements.
      Open

                if re.match(r'\s*BIOMT\d ', content):
            stats['REMARK 350 BIOMTn'] += 1
          elif re.match(r'\s*BIOMOLECULE:', content):
            stats['REMARK 350 BIOMOLECULE'] += 1
        if tag == 'REMARK 290':
      Severity: Major
      Found in packages/miew/tools/pdbfreq.py - About 45 mins to fix

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

        Severity: Major
        Found in packages/miew/tools/pdbfreq.py and 1 other location - About 2 wks to fix
        demo/tools/pdbfreq.py on lines 0..152

        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 1641.

        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

        There are no issues that match your filters.

        Category
        Status