bio-miga/miga

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Use safe navigation (&.) instead of checking if an object exists before calling the method.
Open

    @ftp.close unless @ftp.nil?
Severity: Minor
Found in lib/miga/cli/action/db.rb by rubocop

This cop transforms usages of a method call safeguarded by a non nil check for the variable whose method is being called to safe navigation (&.).

Configuration option: ConvertCodeThatCanStartToReturnNil The default for this is false. When configured to true, this will check for code in the format !foo.nil? && foo.bar. As it is written, the return of this code is limited to false and whatever the return of the method is. If this is converted to safe navigation, foo&.bar can start returning nil as well as what the method returns.

Example:

# bad
foo.bar if foo
foo.bar(param1, param2) if foo
foo.bar { |e| e.something } if foo
foo.bar(param) { |e| e.something } if foo

foo.bar if !foo.nil?
foo.bar unless !foo
foo.bar unless foo.nil?

foo && foo.bar
foo && foo.bar(param1, param2)
foo && foo.bar { |e| e.something }
foo && foo.bar(param) { |e| e.something }

# good
foo&.bar
foo&.bar(param1, param2)
foo&.bar { |e| e.something }
foo&.bar(param) { |e| e.something }

foo.nil? || foo.bar
!foo || foo.bar

# Methods that `nil` will `respond_to?` should not be converted to
# use safe navigation
foo.to_i if foo

Missing magic comment # frozen_string_literal: true.
Open

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

Put empty method definitions on a single line.
Open

  def complete
  end
Severity: Minor
Found in lib/miga/cli/action/generic.rb by rubocop

This cop checks for the formatting of empty method definitions. By default it enforces empty method definitions to go on a single line (compact style), but it can be configured to enforce the end to go on its own line (expanded style).

Note: A method definition is not considered empty if it contains comments.

Example: EnforcedStyle: compact (default)

# bad
def foo(bar)
end

def self.foo(bar)
end

# good
def foo(bar); end

def foo(bar)
  # baz
end

def self.foo(bar); end

Example: EnforcedStyle: expanded

# bad
def foo(bar); end

def self.foo(bar); end

# good
def foo(bar)
end

def self.foo(bar)
end

Use || instead of or.
Open

      next unless cli[:force] or d.done_preprocessing?
Severity: Minor
Found in lib/miga/cli/action/ln.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

Unnecessary splat expansion.
Open

            when *%w[project file verbose help debug]
Severity: Minor
Found in lib/miga/cli/action/get.rb by rubocop

This cop checks for unneeded usages of splat expansion

Example:

# bad

a = *[1, 2, 3]
a = *'a'
a = *1

begin
  foo
rescue *[StandardError, ApplicationError]
  bar
end

case foo
when *[1, 2, 3]
  bar
else
  baz
end

Example:

# good

c = [1, 2, 3]
a = *c
a, b = *c
a, *b = *c
a = *1..10
a = ['a']

begin
  foo
rescue StandardError, ApplicationError
  bar
end

case foo
when *[1, 2, 3]
  bar
else
  baz
end

Shadowing outer local variable - k.
Open

      stats.map { |s| keys.map { |k| s[k].is_a?(Array) ? s[k].first : s[k] } }
Severity: Minor
Found in lib/miga/cli/action/summary.rb by rubocop

This cop looks for use of the same name as outer local variables for block arguments or block local variables. This is a mimic of the warning "shadowing outer local variable - foo" from ruby -cw.

Example:

# bad

def some_method
  foo = 1

  2.times do |foo| # shadowing outer `foo`
    do_something(foo)
  end
end

Example:

# good

def some_method
  foo = 1

  2.times do |bar|
    do_something(bar)
  end
end

Ternary operators must not be nested. Prefer if or else constructs instead.
Open

      stats.map { |s| keys.map { |k| s[k].is_a?(Array) ? s[k].first : s[k] } }
Severity: Minor
Found in lib/miga/cli/action/summary.rb by rubocop

Use == if you meant to do a comparison or wrap the expression in parentheses to indicate you meant to assign in a condition.
Open

    if cli[:result] && r = cli.load_result
Severity: Minor
Found in lib/miga/cli/action/rm.rb by rubocop

This cop checks for assignments in the conditions of if/while/until.

Example:

# bad

if some_var = true
  do_something
end

Example:

# good

if some_var == true
  do_something
end

Missing magic comment # frozen_string_literal: true.
Open

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

Do not use semicolons to terminate expressions.
Open

      ) { |v| puts MiGA::MiGA.LONG_VERSION; exit }
Severity: Minor
Found in lib/miga/cli/action/generic.rb by rubocop

This cop checks for multiple expressions placed on the same line. It also checks for lines terminated with a semicolon.

Example:

# bad
foo = 1; bar = 2;
baz = 3;

# good
foo = 1
bar = 2
baz = 3

Do not use semicolons to terminate expressions.
Open

      ) { |v| puts MiGA::MiGA.CITATION; exit }
Severity: Minor
Found in lib/miga/cli/action/generic.rb by rubocop

This cop checks for multiple expressions placed on the same line. It also checks for lines terminated with a semicolon.

Example:

# bad
foo = 1; bar = 2;
baz = 3;

# good
foo = 1
bar = 2
baz = 3

Avoid using {...} for multi-line blocks.
Open

      stats.map { |s|
Severity: Minor
Found in lib/miga/cli/action/summary.rb by rubocop

Check for uses of braces or do/end around single line or multi-line blocks.

Example: EnforcedStyle: linecountbased (default)

# bad - single line block
items.each do |item| item / 5 end

# good - single line block
items.each { |item| item / 5 }

# bad - multi-line block
things.map { |thing|
  something = thing.some_method
  process(something)
}

# good - multi-line block
things.map do |thing|
  something = thing.some_method
  process(something)
end

Example: EnforcedStyle: semantic

# Prefer `do...end` over `{...}` for procedural blocks.

# return value is used/assigned
# bad
foo = map do |x|
  x
end
puts (map do |x|
  x
end)

# return value is not used out of scope
# good
map do |x|
  x
end

# Prefer `{...}` over `do...end` for functional blocks.

# return value is not used out of scope
# bad
each { |x|
  x
}

# return value is used/assigned
# good
foo = map { |x|
  x
}
map { |x|
  x
}.inspect

Example: EnforcedStyle: bracesforchaining

# bad
words.each do |word|
  word.flip.flop
end.join("-")

# good
words.each { |word|
  word.flip.flop
}.join("-")

Space found before semicolon.
Open

      ) { |v| cli[:activate] = false ; cli[:reason] = v }
Severity: Minor
Found in lib/miga/cli/action/edit.rb by rubocop

Checks for semicolon (;) preceded by space.

Example:

# bad
x = 1 ; y = 2

# good
x = 1; y = 2

Do not use semicolons to terminate expressions.
Open

      ) { puts MiGA::MiGA.FULL_VERSION; exit }
Severity: Minor
Found in lib/miga/cli/action/generic.rb by rubocop

This cop checks for multiple expressions placed on the same line. It also checks for lines terminated with a semicolon.

Example:

# bad
foo = 1; bar = 2;
baz = 3;

# good
foo = 1
bar = 2
baz = 3

Put empty method definitions on a single line.
Open

  def parse_cli
  end
Severity: Minor
Found in lib/miga/cli/action/console.rb by rubocop

This cop checks for the formatting of empty method definitions. By default it enforces empty method definitions to go on a single line (compact style), but it can be configured to enforce the end to go on its own line (expanded style).

Note: A method definition is not considered empty if it contains comments.

Example: EnforcedStyle: compact (default)

# bad
def foo(bar)
end

def self.foo(bar)
end

# good
def foo(bar); end

def foo(bar)
  # baz
end

def self.foo(bar); end

Example: EnforcedStyle: expanded

# bad
def foo(bar); end

def self.foo(bar); end

# good
def foo(bar)
end

def self.foo(bar)
end

Missing magic comment # frozen_string_literal: true.
Open

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

Unnecessary splat expansion.
Open

            when *%w[query ignore-dup get-metadata only-metadata]
Severity: Minor
Found in lib/miga/cli/action/get.rb by rubocop

This cop checks for unneeded usages of splat expansion

Example:

# bad

a = *[1, 2, 3]
a = *'a'
a = *1

begin
  foo
rescue *[StandardError, ApplicationError]
  bar
end

case foo
when *[1, 2, 3]
  bar
else
  baz
end

Example:

# good

c = [1, 2, 3]
a = *c
a, b = *c
a, *b = *c
a = *1..10
a = ['a']

begin
  foo
rescue StandardError, ApplicationError
  bar
end

case foo
when *[1, 2, 3]
  bar
else
  baz
end

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

      cli.opt_object(opt, [:project, :dataset_opt])
Severity: Minor
Found in lib/miga/cli/action/summary.rb by rubocop

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 a guard clause instead of wrapping the code inside a conditional expression.
Open

    unless status&.success?
Severity: Minor
Found in lib/miga/cli/action/cmd.rb by rubocop

Use a guard clause instead of wrapping the code inside a conditional expression

Example:

# bad
def test
  if something
    work
  end
end

# good
def test
  return unless something
  work
end

# also good
def test
  work if something
end

# bad
if something
  raise 'exception'
else
  ok
end

# good
raise 'exception' if something
ok

Do not use semicolons to terminate expressions.
Open

      ) { |v| cli[:activate] = false ; cli[:reason] = v }
Severity: Minor
Found in lib/miga/cli/action/edit.rb by rubocop

This cop checks for multiple expressions placed on the same line. It also checks for lines terminated with a semicolon.

Example:

# bad
foo = 1; bar = 2;
baz = 3;

# good
foo = 1
bar = 2
baz = 3
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