wurmlab/sequenceserver

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lib/sequenceserver/blast/hsp.rb

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:length member overrides Struct#length and it may be unexpected.
Open

                     :gaps, :length, :qcovhsp, :qseq, :sseq, :midline) do
Severity: Minor
Found in lib/sequenceserver/blast/hsp.rb by rubocop

This cop checks unexpected overrides of the Struct built-in methods via Struct.new.

Example:

# bad
Bad = Struct.new(:members, :clone, :count)
b = Bad.new([], true, 1)
b.members #=> [] (overriding `Struct#members`)
b.clone #=> true (overriding `Object#clone`)
b.count #=> 1 (overriding `Enumerable#count`)

# good
Good = Struct.new(:id, :name)
g = Good.new(1, "foo")
g.members #=> [:id, :name]
g.clone #=> #<struct good id="1," name="foo">
g.count #=&gt; 2</struct>

:send member overrides Struct#send and it may be unexpected.
Open

                     :sstart, :send, :qframe, :sframe, :identity, :positives,
Severity: Minor
Found in lib/sequenceserver/blast/hsp.rb by rubocop

This cop checks unexpected overrides of the Struct built-in methods via Struct.new.

Example:

# bad
Bad = Struct.new(:members, :clone, :count)
b = Bad.new([], true, 1)
b.members #=> [] (overriding `Struct#members`)
b.clone #=> true (overriding `Object#clone`)
b.count #=> 1 (overriding `Enumerable#count`)

# good
Good = Struct.new(:id, :name)
g = Good.new(1, "foo")
g.members #=> [:id, :name]
g.clone #=> #<struct good id="1," name="foo">
g.count #=&gt; 2</struct>

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

           gaps length qcovhsp qseq sseq midline].inject({}) { |h, k|
Severity: Minor
Found in lib/sequenceserver/blast/hsp.rb by rubocop

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

Methods that can be either procedural or functional and cannot be categorised from their usage alone is ignored. lambda, proc, and it are their defaults. Additional methods can be added to the IgnoredMethods.

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

# The AllowBracesOnProceduralOneLiners option is ignored unless the
# EnforcedStyle is set to `semantic`. If so:

# If the AllowBracesOnProceduralOneLiners option is unspecified, or
# set to `false` or any other falsey value, then semantic purity is
# maintained, so one-line procedural blocks must use do-end, not
# braces.

# bad
collection.each { |element| puts element }

# good
collection.each do |element| puts element end

# If the AllowBracesOnProceduralOneLiners option is set to `true`, or
# any other truthy value, then one-line procedural blocks may use
# either style. (There is no setting for requiring braces on them.)

# good
collection.each { |element| puts element }

# also good
collection.each do |element| puts element end

Example: EnforcedStyle: bracesforchaining

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

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

Example: EnforcedStyle: always_braces

# bad
words.each do |word|
  word.flip.flop
end

# good
words.each { |word|
  word.flip.flop
}

Example: BracesRequiredMethods: ['sig']

# Methods listed in the BracesRequiredMethods list, such as 'sig'
# in this example, will require `{...}` braces. This option takes
# precedence over all other configurations except IgnoredMethods.

# bad
sig do
  params(
    foo: string,
  ).void
end
def bar(foo)
  puts foo
end

# good
sig {
  params(
    foo: string,
  ).void
}
def bar(foo)
  puts foo
end

Example: IgnoredMethods: ['lambda', 'proc', 'it' ] (default)

# good
foo = lambda do |x|
  puts "Hello, #{x}"
end

foo = lambda do |x|
  x * 100
end

Do not define constants this way within a block.
Open

      INTEGER_ARGS = [1, 3].concat((5..15).to_a).freeze
Severity: Minor
Found in lib/sequenceserver/blast/hsp.rb by rubocop

Do not define constants within a block, since the block's scope does not isolate or namespace the constant in any way.

If you are trying to define that constant once, define it outside of the block instead, or use a variable or method if defining the constant in the outer scope would be problematic.

For meta-programming, use const_set.

Example:

# bad
task :lint do
  FILES_TO_LINT = Dir['lib/*.rb']
end

# bad
describe 'making a request' do
  class TestRequest; end
end

# bad
module M
  extend ActiveSupport::Concern
  included do
    LIST = []
  end
end

# good
task :lint do
  files_to_lint = Dir['lib/*.rb']
end

# good
describe 'making a request' do
  let(:test_request) { Class.new }
  # see also `stub_const` for RSpec
end

# good
module M
  extend ActiveSupport::Concern
  included do
    const_set(:LIST, [])
  end
end

Example: AllowedMethods: ['enums'] (default)

# good

# `enums` for Typed Enums via `T::Enum` in Sorbet.
# https://sorbet.org/docs/tenum
class TestEnum < T::Enum
  enums do
    Foo = new("foo")
  end
end

Do not define constants this way within a block.
Open

      FLOAT_ARGS   = [2, 4].freeze
Severity: Minor
Found in lib/sequenceserver/blast/hsp.rb by rubocop

Do not define constants within a block, since the block's scope does not isolate or namespace the constant in any way.

If you are trying to define that constant once, define it outside of the block instead, or use a variable or method if defining the constant in the outer scope would be problematic.

For meta-programming, use const_set.

Example:

# bad
task :lint do
  FILES_TO_LINT = Dir['lib/*.rb']
end

# bad
describe 'making a request' do
  class TestRequest; end
end

# bad
module M
  extend ActiveSupport::Concern
  included do
    LIST = []
  end
end

# good
task :lint do
  files_to_lint = Dir['lib/*.rb']
end

# good
describe 'making a request' do
  let(:test_request) { Class.new }
  # see also `stub_const` for RSpec
end

# good
module M
  extend ActiveSupport::Concern
  included do
    const_set(:LIST, [])
  end
end

Example: AllowedMethods: ['enums'] (default)

# good

# `enums` for Typed Enums via `T::Enum` in Sorbet.
# https://sorbet.org/docs/tenum
class TestEnum < T::Enum
  enums do
    Foo = new("foo")
  end
end

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