bio-miga/miga

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Avoid comma after the last item of a hash.
Open

    tax_distributions: :tax_dist,
Severity: Minor
Found in lib/miga/cli/base.rb by rubocop

This cop checks for trailing comma in array and hash literals.

Example: EnforcedStyleForMultiline: consistent_comma

# bad
a = [1, 2,]

# good
a = [
  1, 2,
  3,
]

# good
a = [
  1,
  2,
]

Example: EnforcedStyleForMultiline: comma

# bad
a = [1, 2,]

# good
a = [
  1,
  2,
]

Example: EnforcedStyleForMultiline: no_comma (default)

# bad
a = [1, 2,]

# good
a = [
  1,
  2
]

Useless assignment to variable - p.
Open

    p = create_project(:assembly, {}, run_mytaxa_scan: cli[:mytaxa])
Severity: Minor
Found in lib/miga/cli/action/index_wf.rb by rubocop

This cop checks for every useless assignment to local variable in every scope. The basic idea for this cop was from the warning of ruby -cw:

assigned but unused variable - foo

Currently this cop has advanced logic that detects unreferenced reassignments and properly handles varied cases such as branch, loop, rescue, ensure, etc.

Example:

# bad

def some_method
  some_var = 1
  do_something
end

Example:

# good

def some_method
  some_var = 1
  do_something(some_var)
end

Missing top-level class documentation comment.
Open

class MiGA::Cli::Action::IndexWf < MiGA::Cli::Action
Severity: Minor
Found in lib/miga/cli/action/index_wf.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

Unused method argument - d. If it's necessary, use _ or _d as an argument name to indicate that it won't be used.
Open

  def query_probability_distributions(d, cr)
Severity: Minor
Found in lib/miga/cli/action/tax_test.rb by rubocop

This cop checks for unused method arguments.

Example:

# bad

def some_method(used, unused, _unused_but_allowed)
  puts used
end

Example:

# good

def some_method(used, _unused, _unused_but_allowed)
  puts used
end

Prefer Date or Time over DateTime.
Open

      d && DateTime.parse(d.metadata[:updated]) < cli[:updated_before]

This cop checks for uses of DateTime that should be replaced by Date or Time.

Example:

# bad - uses `DateTime` for current time
DateTime.now

# good - uses `Time` for current time
Time.now

# bad - uses `DateTime` for modern date
DateTime.iso8601('2016-06-29')

# good - uses `Date` for modern date
Date.iso8601('2016-06-29')

# good - uses `DateTime` with start argument for historical date
DateTime.iso8601('1751-04-23', Date::ENGLAND)

Prefer single-quoted strings when you don't need string interpolation or special symbols.
Open

      "{{key}}={{value}}"

Checks if uses of quotes match the configured preference.

Example: EnforcedStyle: single_quotes (default)

# bad
"No special symbols"
"No string interpolation"
"Just text"

# good
'No special symbols'
'No string interpolation'
'Just text'
"Wait! What's #{this}!"

Example: EnforcedStyle: double_quotes

# bad
'Just some text'
'No special chars or interpolation'

# good
"Just some text"
"No special chars or interpolation"
"Every string in #{project} uses double_quotes"

Use next to skip iteration.
Open

        unless ok

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

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

Missing top-level class documentation comment.
Open

class MiGA::Cli::Action::New < MiGA::Cli::Action
Severity: Minor
Found in lib/miga/cli/action/new.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

Missing top-level class documentation comment.
Open

class MiGA::Cli::Action::NcbiGet < MiGA::Cli::Action
Severity: Minor
Found in lib/miga/cli/action/ncbi_get.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 comma after the last item of a hash.
Open

    tax_dist:    'Estimate distributions of distance by taxonomy',
Severity: Minor
Found in lib/miga/cli/base.rb by rubocop

This cop checks for trailing comma in array and hash literals.

Example: EnforcedStyleForMultiline: consistent_comma

# bad
a = [1, 2,]

# good
a = [
  1, 2,
  3,
]

# good
a = [
  1,
  2,
]

Example: EnforcedStyleForMultiline: comma

# bad
a = [1, 2,]

# good
a = [
  1,
  2,
]

Example: EnforcedStyleForMultiline: no_comma (default)

# bad
a = [1, 2,]

# good
a = [
  1,
  2
]

Missing magic comment # frozen_string_literal: true.
Open

# @package MiGA
Severity: Minor
Found in lib/miga/cli/action/index_wf.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

Missing top-level class documentation comment.
Open

class MiGA::Cli::Action::GtdbGet < MiGA::Cli::Action
Severity: Minor
Found in lib/miga/cli/action/gtdb_get.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

Missing magic comment # frozen_string_literal: true.
Open

# @package MiGA
Severity: Minor
Found in lib/miga/cli/action/files.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

Use || instead of or.
Open

    if cr.nil? or cr.empty?
Severity: Minor
Found in lib/miga/cli/action/tax_test.rb by rubocop

This cop checks for uses of and and or, and suggests using && and || instead. It can be configured to check only in conditions, or in all contexts.

Example: EnforcedStyle: always (default)

# bad
foo.save and return

# bad
if foo and bar
end

# good
foo.save && return

# good
if foo && bar
end

Example: EnforcedStyle: conditionals

# bad
if foo and bar
end

# good
foo.save && return

# good
foo.save and return

# good
if foo && bar
end

Omit parentheses for ternary conditions.
Open

      (@@TASK_DESC[task] =~ /\(alias: .*\)\./) ?
        @@TASK_DESC[task].sub(/\)\.$/, ", #{nick}).") :
        @@TASK_DESC[task].sub(/\.$/, " (alias: #{nick}).")
Severity: Minor
Found in lib/miga/cli/base.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

Missing top-level class documentation comment.
Open

class MiGA::Cli::Action::Files < MiGA::Cli::Action
Severity: Minor
Found in lib/miga/cli/action/files.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

Missing magic comment # frozen_string_literal: true.
Open

# @package MiGA
Severity: Minor
Found in lib/miga/cli/action/tax_test.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

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

          warn "Impossible to find dataset at line #{$.}: #{dn}. Ignoring..."
Severity: Minor
Found in lib/miga/cli/action/tax_set.rb by rubocop

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
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