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vanheeringen-lab/ANANSE

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ananse/benchmark.py

Summary

Maintainability
A
2 hrs
Test Coverage
F
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Function prepare_reference_network has a Cognitive Complexity of 18 (exceeds 15 allowed). Consider refactoring.
Open

def prepare_reference_network(network, filter_tfs=True):
    """Generate reference network.

    This network contains all possible edges, based on the TFs
    and the target genes in the input. TFs are optionally filtered
Severity: Minor
Found in ananse/benchmark.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

Avoid too many return statements within this function.
Open

        return prepare_reference_network(_read_msigdb_reference(fname))
Severity: Major
Found in ananse/benchmark.py - About 30 mins to fix

    Avoid too many return statements within this function.
    Open

            return prepare_reference_network(_read_regnet_reference(fname))
    Severity: Major
    Found in ananse/benchmark.py - About 30 mins to fix

      Avoid too many return statements within this function.
      Open

              return prepare_reference_network(fname)
      Severity: Major
      Found in ananse/benchmark.py - About 30 mins to fix

        Function _read_enrichr_perturbation_reference has a Cognitive Complexity of 16 (exceeds 15 allowed). Consider refactoring.
        Open

        def _read_enrichr_perturbation_reference(fname=None):
    """Uses the TF perturbations from Enrichr[1,2] to create reference edges.

    Targets are defined by up- or down-regulated gened from the following sets:
    Up: INDUCTION, ACTIVATION, OE.
        Severity: Minor
        Found in ananse/benchmark.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

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