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KarrLab/bpforms

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bpforms/alphabet/core.py

Summary

Maintainability
C
1 day
Test Coverage
A
95%

Function parse_pdb_ccd_entry has a Cognitive Complexity of 39 (exceeds 5 allowed). Consider refactoring.
Open

def parse_pdb_ccd_entry(xml_file, valid_types):
    """ Parse an entry of the PDB CCD

    Args:
        xml_file (:obj:`io.BufferedReader`): XML file
Severity: Minor
Found in bpforms/alphabet/core.py - About 5 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 parse_pdb_ccd_entry has 38 lines of code (exceeds 25 allowed). Consider refactoring.
Open

def parse_pdb_ccd_entry(xml_file, valid_types):
    """ Parse an entry of the PDB CCD

    Args:
        xml_file (:obj:`io.BufferedReader`): XML file
Severity: Minor
Found in bpforms/alphabet/core.py - About 1 hr to fix

    Function parse_pdb_ccd has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
    Open

    def parse_pdb_ccd(filename, valid_types, max_monomers):
    """ Parse entries out of the PDB CCD

    Args:
        filename (:obj:`str`): path to tar.gz file for PDB CCD
    Severity: Minor
    Found in bpforms/alphabet/core.py - About 1 hr 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 too many return statements within this function.
    Open

        return (Monomer(id=id, name=name, synonyms=synonyms, identifiers=identifiers),
    Severity: Major
    Found in bpforms/alphabet/core.py - About 30 mins to fix

      Avoid too many return statements within this function.
      Open

              return  # pragma: no cover # element is always present
      Severity: Major
      Found in bpforms/alphabet/core.py - About 30 mins to fix

        Avoid too many return statements within this function.
        Open

                return
        Severity: Major
        Found in bpforms/alphabet/core.py - About 30 mins to fix

          Avoid too many return statements within this function.
          Open

                  return  # pragma: no cover # element is always present
          Severity: Major
          Found in bpforms/alphabet/core.py - About 30 mins to fix

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