bio-miga/miga

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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"

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"

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

Missing top-level class documentation comment.
Open

class MiGA::Cli::Action::QualityWf < MiGA::Cli::Action
Severity: Minor
Found in lib/miga/cli/action/quality_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

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 next to skip iteration.
Open

        if file !~ /\.gz/

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

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

      cli.opt_object(opt, [:project, :project_type_req])
Severity: Minor
Found in lib/miga/cli/action/new.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]

Missing magic comment # frozen_string_literal: true.
Open


module MiGA::Cli::Action::Doctor::Databases

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

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

  def check_dist_eval(cli, p, res)
Severity: Minor
Found in lib/miga/cli/action/doctor/base.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

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

Line is too long. [85/80]
Open

          "  {{variables}}: script, vars, cpus, log, task_name, task_name_simple\n ",

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'

Align the operands of an expression in an assignment spanning multiple lines.
Open

            r.map { |i| "<td>#{i}</td>" }.join(' ') + "</tr>"
Severity: Minor
Found in lib/miga/cli/action/browse.rb by rubocop

This cop checks the indentation of the right hand side operand in binary operations that span more than one line.

Example:

# bad
if a +
b
  something
end

# good
if a +
   b
  something
end

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

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

Useless assignment to variable - md.
Open

      md = p&.metadata

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 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

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.

Line is too long. [85/80]
Open

          "  {{variables}}: script, vars, cpus, log, task_name, task_name_simple\n ",
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