bio-miga/miga

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lib/miga/cli/action/doctor/distances.rb

Summary

Maintainability
C
1 day
Test Coverage

Module has too many lines. [111/100]
Open

module MiGA::Cli::Action::Doctor::Distances
  ##
  # Perform databases operation with MiGA::Cli +cli+
  def check_db(cli)
    cli.say 'Checking integrity of databases'

This cop checks if the length a module exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Assignment Branch Condition size for merge_bidir_tmp is too high. [35.52/15]
Open

  def merge_bidir_tmp(tmp)
    dist = { aai: {}, ani: {} }
    cli[:threads].times do |i|
      cli.advance('Merging:', i + 1, cli[:threads], false)
      file = File.join(tmp, "#{i}.json")

This cop checks that the ABC size of methods is not higher than the configured maximum. The ABC size is based on assignments, branches (method calls), and conditions. See http://c2.com/cgi/wiki?AbcMetric

Method has too many lines. [28/10]
Open

  def merge_bidir_tmp(tmp)
    dist = { aai: {}, ani: {} }
    cli[:threads].times do |i|
      cli.advance('Merging:', i + 1, cli[:threads], false)
      file = File.join(tmp, "#{i}.json")

This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Assignment Branch Condition size for partial_bidir_tmp is too high. [33.62/15]
Open

  def partial_bidir_tmp(project, ref_ds)
    n = ref_ds.size

    # Read data first (threaded)
    tmp = File.join(project.path, 'doctor-bidirectional.tmp')

This cop checks that the ABC size of methods is not higher than the configured maximum. The ABC size is based on assignments, branches (method calls), and conditions. See http://c2.com/cgi/wiki?AbcMetric

Method has too many lines. [27/10]
Open

  def check_db(cli)
    cli.say 'Checking integrity of databases'
    p = cli.load_project
    n = p.dataset_names.size
    (0 .. cli[:threads] - 1).map do |i|

This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Method merge_bidir_tmp has a Cognitive Complexity of 24 (exceeds 5 allowed). Consider refactoring.
Open

  def merge_bidir_tmp(tmp)
    dist = { aai: {}, ani: {} }
    cli[:threads].times do |i|
      cli.advance('Merging:', i + 1, cli[:threads], false)
      file = File.join(tmp, "#{i}.json")
Severity: Minor
Found in lib/miga/cli/action/doctor/distances.rb - 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

Method has too many lines. [25/10]
Open

  def partial_bidir_tmp(project, ref_ds)
    n = ref_ds.size

    # Read data first (threaded)
    tmp = File.join(project.path, 'doctor-bidirectional.tmp')

This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Assignment Branch Condition size for check_db is too high. [27.95/15]
Open

  def check_db(cli)
    cli.say 'Checking integrity of databases'
    p = cli.load_project
    n = p.dataset_names.size
    (0 .. cli[:threads] - 1).map do |i|

This cop checks that the ABC size of methods is not higher than the configured maximum. The ABC size is based on assignments, branches (method calls), and conditions. See http://c2.com/cgi/wiki?AbcMetric

Method check_db has a Cognitive Complexity of 19 (exceeds 5 allowed). Consider refactoring.
Open

  def check_db(cli)
    cli.say 'Checking integrity of databases'
    p = cli.load_project
    n = p.dataset_names.size
    (0 .. cli[:threads] - 1).map do |i|
Severity: Minor
Found in lib/miga/cli/action/doctor/distances.rb - 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

Method partial_bidir_tmp has a Cognitive Complexity of 17 (exceeds 5 allowed). Consider refactoring.
Open

  def partial_bidir_tmp(project, ref_ds)
    n = ref_ds.size

    # Read data first (threaded)
    tmp = File.join(project.path, 'doctor-bidirectional.tmp')
Severity: Minor
Found in lib/miga/cli/action/doctor/distances.rb - 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

Method has too many lines. [11/10]
Open

  def check_bidir(cli)
    cli.say 'Checking if reference distances are bidirectional'
    project = cli.load_project
    ref_ds = project.each_dataset.select(&:ref?)

This cop checks if the length of a method exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable.

Perceived complexity for merge_bidir_tmp is too high. [8/7]
Open

  def merge_bidir_tmp(tmp)
    dist = { aai: {}, ani: {} }
    cli[:threads].times do |i|
      cli.advance('Merging:', i + 1, cli[:threads], false)
      file = File.join(tmp, "#{i}.json")

This cop tries to produce a complexity score that's a measure of the complexity the reader experiences when looking at a method. For that reason it considers when nodes as something that doesn't add as much complexity as an if or a &&. Except if it's one of those special case/when constructs where there's no expression after case. Then the cop treats it as an if/elsif/elsif... and lets all the when nodes count. In contrast to the CyclomaticComplexity cop, this cop considers else nodes as adding complexity.

Example:

def my_method                   # 1
  if cond                       # 1
    case var                    # 2 (0.8 + 4 * 0.2, rounded)
    when 1 then func_one
    when 2 then func_two
    when 3 then func_three
    when 4..10 then func_other
    end
  else                          # 1
    do_something until a && b   # 2
  end                           # ===
end                             # 7 complexity points

Assignment Branch Condition size for check_bidir is too high. [15.56/15]
Open

  def check_bidir(cli)
    cli.say 'Checking if reference distances are bidirectional'
    project = cli.load_project
    ref_ds = project.each_dataset.select(&:ref?)

This cop checks that the ABC size of methods is not higher than the configured maximum. The ABC size is based on assignments, branches (method calls), and conditions. See http://c2.com/cgi/wiki?AbcMetric

Method merge_bidir_tmp has 28 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  def merge_bidir_tmp(tmp)
    dist = { aai: {}, ani: {} }
    cli[:threads].times do |i|
      cli.advance('Merging:', i + 1, cli[:threads], false)
      file = File.join(tmp, "#{i}.json")
Severity: Minor
Found in lib/miga/cli/action/doctor/distances.rb - About 1 hr to fix

Method check_db has 27 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  def check_db(cli)
    cli.say 'Checking integrity of databases'
    p = cli.load_project
    n = p.dataset_names.size
    (0 .. cli[:threads] - 1).map do |i|
Severity: Minor
Found in lib/miga/cli/action/doctor/distances.rb - About 1 hr to fix

Prefer $INPUT_LINE_NUMBER or $NR from the stdlib 'English' module (don't forget to require it) over $..
Open

          row or raise "Unexpected format in #{file}:#{$.}"

Use %i or %I for an array of symbols.
Open

      [:aai, :ani].each do |metric|

This cop can check for array literals made up of symbols that are not using the %i() syntax.

Alternatively, it checks for symbol arrays using the %i() syntax on projects which do not want to use that syntax.

Configuration option: MinSize If set, arrays with fewer elements than this value will not trigger the cop. For example, a MinSize of3` will not enforce a style on an array of 2 or fewer elements.

Example: EnforcedStyle: percent (default)

# good
%i[foo bar baz]

# bad
[:foo, :bar, :baz]

Example: EnforcedStyle: brackets

# good
[:foo, :bar, :baz]

# bad
%i[foo bar baz]

Use thr.zero? instead of thr == 0.
Open

      cli.advance('Datasets:', idx + 1, ref_ds.size, false) if thr == 0

This cop checks for usage of comparison operators (==, >, <) to test numbers as zero, positive, or negative. These can be replaced by their respective predicate methods. The cop can also be configured to do the reverse.

The cop disregards #nonzero? as it its value is truthy or falsey, but not true and false, and thus not always interchangeable with != 0.

The cop ignores comparisons to global variables, since they are often populated with objects which can be compared with integers, but are not themselves Interger polymorphic.

Example: EnforcedStyle: predicate (default)

# bad

foo == 0
0 > foo
bar.baz > 0

# good

foo.zero?
foo.negative?
bar.baz.positive?

Example: EnforcedStyle: comparison

# bad

foo.zero?
foo.negative?
bar.baz.positive?

# good

foo == 0
0 > foo
bar.baz > 0

Space inside range literal.
Open

    (0 .. cli[:threads] - 1).map do |i|

Checks for spaces inside range literals.

Example:

# bad
1 .. 3

# good
1..3

# bad
'a' .. 'z'

# good
'a'..'z'

Use next to skip iteration.
Open

          if idx % cli[:threads] == thr

Use next to skip iteration instead of a condition at the end.

Example: EnforcedStyle: skipmodifierifs (default)

# bad
[1, 2].each do |a|
  if a == 1
    puts a
  end
end

# good
[1, 2].each do |a|
  next unless a == 1
  puts a
end

# good
[1, 2].each do |o|
  puts o unless o == 1
end

Example: EnforcedStyle: always

# With `always` all conditions at the end of an iteration needs to be
# replaced by next - with `skip_modifier_ifs` the modifier if like
# this one are ignored: `[1, 2].each { |a| return 'yes' if a == 1 }`

# bad
[1, 2].each do |o|
  puts o unless o == 1
end

# bad
[1, 2].each do |a|
  if a == 1
    puts a
  end
end

# good
[1, 2].each do |a|
  next unless a == 1
  puts a
end

Redundant return detected.
Open

    return tmp

This cop checks for redundant return expressions.

Example:

def test
  return something
end

def test
  one
  two
  three
  return something
end

It should be extended to handle methods whose body is if/else or a case expression with a default branch.

1 trailing blank lines detected.
Open

Missing top-level module documentation comment.
Open

module MiGA::Cli::Action::Doctor::Distances

This cop checks for missing top-level documentation of classes and modules. Classes with no body are exempt from the check and so are namespace modules - modules that have nothing in their bodies except classes, other modules, or constant definitions.

The documentation requirement is annulled if the class or module has a "#:nodoc:" comment next to it. Likewise, "#:nodoc: all" does the same for all its children.

Example:

# bad
class Person
  # ...
end

# good
# Description/Explanation of Person class
class Person
  # ...
end

Use thr.zero? instead of thr == 0.
Open

            cli.advance('Reading:', idx + 1, n, false) if thr == 0

This cop checks for usage of comparison operators (==, >, <) to test numbers as zero, positive, or negative. These can be replaced by their respective predicate methods. The cop can also be configured to do the reverse.

The cop disregards #nonzero? as it its value is truthy or falsey, but not true and false, and thus not always interchangeable with != 0.

The cop ignores comparisons to global variables, since they are often populated with objects which can be compared with integers, but are not themselves Interger polymorphic.

Example: EnforcedStyle: predicate (default)

# bad

foo == 0
0 > foo
bar.baz > 0

# good

foo.zero?
foo.negative?
bar.baz.positive?

Example: EnforcedStyle: comparison

# bad

foo.zero?
foo.negative?
bar.baz.positive?

# good

foo == 0
0 > foo
bar.baz > 0

Missing magic comment # frozen_string_literal: true.
Open


module MiGA::Cli::Action::Doctor::Distances

This cop is designed to help upgrade to Ruby 3.0. It will add the comment # frozen_string_literal: true to the top of files to enable frozen string literals. Frozen string literals may be default in Ruby 3.0. The comment will be added below a shebang and encoding comment. The frozen string literal comment is only valid in Ruby 2.3+.

Example: EnforcedStyle: when_needed (default)

# The `when_needed` style will add the frozen string literal comment
# to files only when the `TargetRubyVersion` is set to 2.3+.
# bad
module Foo
  # ...
end

# good
# frozen_string_literal: true

module Foo
  # ...
end

Example: EnforcedStyle: always

# The `always` style will always add the frozen string literal comment
# to a file, regardless of the Ruby version or if `freeze` or `<<` are
# called on a string literal.
# bad
module Bar
  # ...
end

# good
# frozen_string_literal: true

module Bar
  # ...
end

Example: EnforcedStyle: never

# The `never` will enforce that the frozen string literal comment does
# not exist in a file.
# bad
# frozen_string_literal: true

module Baz
  # ...
end

# good
module Baz
  # ...
end

Use i.zero? instead of i == 0.
Open

          cli.advance('Datasets:', k, n, false) if i == 0

This cop checks for usage of comparison operators (==, >, <) to test numbers as zero, positive, or negative. These can be replaced by their respective predicate methods. The cop can also be configured to do the reverse.

The cop disregards #nonzero? as it its value is truthy or falsey, but not true and false, and thus not always interchangeable with != 0.

The cop ignores comparisons to global variables, since they are often populated with objects which can be compared with integers, but are not themselves Interger polymorphic.

Example: EnforcedStyle: predicate (default)

# bad

foo == 0
0 > foo
bar.baz > 0

# good

foo.zero?
foo.negative?
bar.baz.positive?

Example: EnforcedStyle: comparison

# bad

foo.zero?
foo.negative?
bar.baz.positive?

# good

foo == 0
0 > foo
bar.baz > 0

Redundant return detected.
Open

    return dist

This cop checks for redundant return expressions.

Example:

def test
  return something
end

def test
  one
  two
  three
  return something
end

It should be extended to handle methods whose body is if/else or a case expression with a default branch.

Use thr.zero? instead of thr == 0.
Open

      if thr == 0

This cop checks for usage of comparison operators (==, >, <) to test numbers as zero, positive, or negative. These can be replaced by their respective predicate methods. The cop can also be configured to do the reverse.

The cop disregards #nonzero? as it its value is truthy or falsey, but not true and false, and thus not always interchangeable with != 0.

The cop ignores comparisons to global variables, since they are often populated with objects which can be compared with integers, but are not themselves Interger polymorphic.

Example: EnforcedStyle: predicate (default)

# bad

foo == 0
0 > foo
bar.baz > 0

# good

foo.zero?
foo.negative?
bar.baz.positive?

Example: EnforcedStyle: comparison

# bad

foo.zero?
foo.negative?
bar.baz.positive?

# good

foo == 0
0 > foo
bar.baz > 0

There are no issues that match your filters.

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