bio-miga/miga

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lib/miga/cli/action/tax_dist.rb

Summary

Maintainability
B
5 hrs
Test Coverage

Class has too many lines. [103/100]
Open

class MiGA::Cli::Action::TaxDist < MiGA::Cli::Action
  def parse_cli
    cli.parse do |opt|
      cli.opt_object(opt, [:project])
      cli.opt_filter_datasets(opt)
Severity: Minor
Found in lib/miga/cli/action/tax_dist.rb by rubocop

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

Assignment Branch Condition size for read_distances is too high. [42.4/15]
Open

  def read_distances
    p = cli.load_project
    cli[:metric] ||= p.clade? ? 'ani' : 'aai'
    res_n = "#{cli[:metric]}_distances"
    cli.say "Reading distances: 1-#{cli[:metric].upcase}"
Severity: Minor
Found in lib/miga/cli/action/tax_dist.rb by rubocop

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. [32/10]
Open

  def traverse_taxonomy(tab, dist)
    cli.say 'Traversing taxonomy'
    rank_i = 0
    Taxonomy.KNOWN_RANKS.each do |rank|
      next if rank == :ns
Severity: Minor
Found in lib/miga/cli/action/tax_dist.rb by rubocop

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 traverse_taxonomy is too high. [31.67/15]
Open

  def traverse_taxonomy(tab, dist)
    cli.say 'Traversing taxonomy'
    rank_i = 0
    Taxonomy.KNOWN_RANKS.each do |rank|
      next if rank == :ns
Severity: Minor
Found in lib/miga/cli/action/tax_dist.rb by rubocop

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 traverse_taxonomy has a Cognitive Complexity of 23 (exceeds 5 allowed). Consider refactoring.
Open

  def traverse_taxonomy(tab, dist)
    cli.say 'Traversing taxonomy'
    rank_i = 0
    Taxonomy.KNOWN_RANKS.each do |rank|
      next if rank == :ns
Severity: Minor
Found in lib/miga/cli/action/tax_dist.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. [20/10]
Open

  def read_distances
    p = cli.load_project
    cli[:metric] ||= p.clade? ? 'ani' : 'aai'
    res_n = "#{cli[:metric]}_distances"
    cli.say "Reading distances: 1-#{cli[:metric].upcase}"
Severity: Minor
Found in lib/miga/cli/action/tax_dist.rb by rubocop

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 perform is too high. [22.56/15]
Open

  def perform
    dist = read_distances
    Dir.mktmpdir do |dir|
      tab = get_tab_index(dir)
      dist = traverse_taxonomy(tab, dist)
Severity: Minor
Found in lib/miga/cli/action/tax_dist.rb by rubocop

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

Assignment Branch Condition size for get_tab_index is too high. [21.4/15]
Open

  def get_tab_index(dir)
    if cli[:index].nil?
      ds = cli.load_and_filter_datasets
      ds.keep_if { |d| !d.metadata[:tax].nil? }

Severity: Minor
Found in lib/miga/cli/action/tax_dist.rb by rubocop

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. [14/10]
Open

  def parse_cli
    cli.parse do |opt|
      cli.opt_object(opt, [:project])
      cli.opt_filter_datasets(opt)
      opt.on(
Severity: Minor
Found in lib/miga/cli/action/tax_dist.rb by rubocop

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 traverse_taxonomy is too high. [9/7]
Open

  def traverse_taxonomy(tab, dist)
    cli.say 'Traversing taxonomy'
    rank_i = 0
    Taxonomy.KNOWN_RANKS.each do |rank|
      next if rank == :ns
Severity: Minor
Found in lib/miga/cli/action/tax_dist.rb by rubocop

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

Cyclomatic complexity for traverse_taxonomy is too high. [8/6]
Open

  def traverse_taxonomy(tab, dist)
    cli.say 'Traversing taxonomy'
    rank_i = 0
    Taxonomy.KNOWN_RANKS.each do |rank|
      next if rank == :ns
Severity: Minor
Found in lib/miga/cli/action/tax_dist.rb by rubocop

This cop checks that the cyclomatic complexity of methods is not higher than the configured maximum. The cyclomatic complexity is the number of linearly independent paths through a method. The algorithm counts decision points and adds one.

An if statement (or unless or ?:) increases the complexity by one. An else branch does not, since it doesn't add a decision point. The && operator (or keyword and) can be converted to a nested if statement, and ||/or is shorthand for a sequence of ifs, so they also add one. Loops can be said to have an exit condition, so they add one.

Method has too many lines. [12/10]
Open

  def get_tab_index(dir)
    if cli[:index].nil?
      ds = cli.load_and_filter_datasets
      ds.keep_if { |d| !d.metadata[:tax].nil? }

Severity: Minor
Found in lib/miga/cli/action/tax_dist.rb by rubocop

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 has too many lines. [11/10]
Open

  def perform
    dist = read_distances
    Dir.mktmpdir do |dir|
      tab = get_tab_index(dir)
      dist = traverse_taxonomy(tab, dist)
Severity: Minor
Found in lib/miga/cli/action/tax_dist.rb by rubocop

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.

Cyclomatic complexity for read_distances is too high. [7/6]
Open

  def read_distances
    p = cli.load_project
    cli[:metric] ||= p.clade? ? 'ani' : 'aai'
    res_n = "#{cli[:metric]}_distances"
    cli.say "Reading distances: 1-#{cli[:metric].upcase}"
Severity: Minor
Found in lib/miga/cli/action/tax_dist.rb by rubocop

This cop checks that the cyclomatic complexity of methods is not higher than the configured maximum. The cyclomatic complexity is the number of linearly independent paths through a method. The algorithm counts decision points and adds one.

An if statement (or unless or ?:) increases the complexity by one. An else branch does not, since it doesn't add a decision point. The && operator (or keyword and) can be converted to a nested if statement, and ||/or is shorthand for a sequence of ifs, so they also add one. Loops can be said to have an exit condition, so they add one.

Method traverse_taxonomy has 32 lines of code (exceeds 25 allowed). Consider refactoring.
Open

  def traverse_taxonomy(tab, dist)
    cli.say 'Traversing taxonomy'
    rank_i = 0
    Taxonomy.KNOWN_RANKS.each do |rank|
      next if rank == :ns
Severity: Minor
Found in lib/miga/cli/action/tax_dist.rb - About 1 hr to fix

Method read_distances has a Cognitive Complexity of 10 (exceeds 5 allowed). Consider refactoring.
Open

  def read_distances
    p = cli.load_project
    cli[:metric] ||= p.clade? ? 'ani' : 'aai'
    res_n = "#{cli[:metric]}_distances"
    cli.say "Reading distances: 1-#{cli[:metric].upcase}"
Severity: Minor
Found in lib/miga/cli/action/tax_dist.rb - 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

Block has too many lines. [27/25]
Open

    Taxonomy.KNOWN_RANKS.each do |rank|
      next if rank == :ns

      rank_n = 0
      rank_i += 1
Severity: Minor
Found in lib/miga/cli/action/tax_dist.rb by rubocop

This cop checks if the length of a block exceeds some maximum value. Comment lines can optionally be ignored. The maximum allowed length is configurable. The cop can be configured to ignore blocks passed to certain methods.

Use each_key instead of keys.each.
Open

    dist.keys.each do |k|
Severity: Minor
Found in lib/miga/cli/action/tax_dist.rb by rubocop

This cop checks for uses of each_key and each_value Hash methods.

Note: If you have an array of two-element arrays, you can put parentheses around the block arguments to indicate that you're not working with a hash, and suppress RuboCop offenses.

Example:

# bad
hash.keys.each { |k| p k }
hash.values.each { |v| p v }
hash.each { |k, _v| p k }
hash.each { |_k, v| p v }

# good
hash.each_key { |k| p k }
hash.each_value { |v| p v }

Missing top-level class documentation comment.
Open

class MiGA::Cli::Action::TaxDist < MiGA::Cli::Action
Severity: Minor
Found in lib/miga/cli/action/tax_dist.rb by rubocop

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

Avoid multi-line ternary operators, use if or unless instead.
Open

    mfh = (matrix =~ /\.gz$/) ?
      Zlib::GzipReader.open(matrix) : File.open(matrix, 'r')
Severity: Minor
Found in lib/miga/cli/action/tax_dist.rb by rubocop

This cop checks for multi-line ternary op expressions.

Example:

# bad
a = cond ?
  b : c
a = cond ? b :
    c
a = cond ?
    b :
    c

# good
a = cond ? b : c
a =
  if cond
    b
  else
    c
  end

Avoid the use of Perl-style backrefs.
Open

            ds_i = $1
Severity: Minor
Found in lib/miga/cli/action/tax_dist.rb by rubocop

This cop looks for uses of Perl-style regexp match backreferences like $1, $2, etc.

Example:

# bad
puts $1

# good
puts Regexp.last_match(1)

(...) interpreted as grouped expression.
Open

      puts (k.split('-') + dist[k]).join("\t")
Severity: Minor
Found in lib/miga/cli/action/tax_dist.rb by rubocop

Checks for space between the name of a called method and a left parenthesis.

Example:

# bad

puts (x + y)

Example:

# good

puts(x + y)

Missing magic comment # frozen_string_literal: true.
Open

# @package MiGA
Severity: Minor
Found in lib/miga/cli/action/tax_dist.rb by rubocop

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

Avoid the use of Perl-style backrefs.
Open

            in_rank = $2 == '?' ? nil : $1
Severity: Minor
Found in lib/miga/cli/action/tax_dist.rb by rubocop

This cop looks for uses of Perl-style regexp match backreferences like $1, $2, etc.

Example:

# bad
puts $1

# good
puts Regexp.last_match(1)

Use (mfh.lineno % 1_000).zero? instead of (mfh.lineno % 1_000) == 0.
Open

      cli.advance('Lines:', mfh.lineno, nil, false) if (mfh.lineno % 1_000) == 0
Severity: Minor
Found in lib/miga/cli/action/tax_dist.rb by rubocop

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

Avoid the use of Perl-style backrefs.
Open

            in_rank = $2 == '?' ? nil : $1
Severity: Minor
Found in lib/miga/cli/action/tax_dist.rb by rubocop

This cop looks for uses of Perl-style regexp match backreferences like $1, $2, etc.

Example:

# bad
puts $1

# good
puts Regexp.last_match(1)

Omit parentheses for ternary conditions.
Open

    mfh = (matrix =~ /\.gz$/) ?
      Zlib::GzipReader.open(matrix) : File.open(matrix, 'r')
Severity: Minor
Found in lib/miga/cli/action/tax_dist.rb by rubocop

This cop checks for the presence of parentheses around ternary conditions. It is configurable to enforce inclusion or omission of parentheses using EnforcedStyle. Omission is only enforced when removing the parentheses won't cause a different behavior.

Example: EnforcedStyle: requirenoparentheses (default)

# bad
foo = (bar?) ? a : b
foo = (bar.baz?) ? a : b
foo = (bar && baz) ? a : b

# good
foo = bar? ? a : b
foo = bar.baz? ? a : b
foo = bar && baz ? a : b

Example: EnforcedStyle: require_parentheses

# bad
foo = bar? ? a : b
foo = bar.baz? ? a : b
foo = bar && baz ? a : b

# good
foo = (bar?) ? a : b
foo = (bar.baz?) ? a : b
foo = (bar && baz) ? a : b

Example: EnforcedStyle: requireparentheseswhen_complex

# bad
foo = (bar?) ? a : b
foo = (bar.baz?) ? a : b
foo = bar && baz ? a : b

# good
foo = bar? ? a : b
foo = bar.baz? ? a : b
foo = (bar && baz) ? a : b

There are no issues that match your filters.

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