miga-base 1.2.0.0 → 1.2.0.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: a39c566d1d00000ae288bd2fd08017236af5537cbde7f2d39e91168aa7561748
+  metadata.gz: 27068ded9d2ff63c3575a5aafd3fa68374f4bcf8aef924354e0c9cbde7dc1f6d
+  data.tar.gz: ef438e828180d304a9e3449d49551ace933a5e5a46128970b3c8bc385c836d58
 SHA512:
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+  data.tar.gz: 8bea4585b36855195f3a2d76005a6ff664133c1df639a677402907c88fd8f6b0a25fb34cc4bd0e9e38bc7666dbe3a382644137dcf5cddd4005c93256d2c75c05

data/lib/miga/cli/opt_helper.rb

@@ -1,6 +1,7 @@
-# @package MiGA
-# @license Artistic-2.0
+# frozen_string_literal: true
 
+##
+# Helper module including functions for CLI options
 module MiGA::Cli::OptHelper
   ##
   # Send MiGA's banner to OptionParser +opt+
@@ -65,7 +66,7 @@ module MiGA::Cli::OptHelper
   # - :result_project To require a type of project result
   # The options :result, :result_opt, :result_dataset, and :result_project
   # are mutually exclusive
-  def opt_object(opt, what = [:project, :dataset])
+  def opt_object(opt, what = %i[project dataset])
     what.each do |w|
       case w
       when :project
@@ -90,7 +91,7 @@ module MiGA::Cli::OptHelper
       when :result, :result_opt
         opt.on(
           '-r', '--result STRING',
-          "#{"(Mandatory) " if w == :result}Name of the result",
+          "#{'(Mandatory) ' if w == :result}Name of the result",
           'Recognized names for dataset-specific results include:',
           *MiGA::Dataset.RESULT_DIRS.keys.map { |n| " ~ #{n}" },
           'Recognized names for project-wide results include:',
@@ -122,7 +123,7 @@ module MiGA::Cli::OptHelper
   # - :active To filter by active (--active) or inactive (--no-active)
   # - :taxonomy To filter by taxonomy (--taxonomy)
   # The "k-th" filter (--dataset-k) is always included
-  def opt_filter_datasets(opt, what = [:ref, :multi, :active, :taxonomy])
+  def opt_filter_datasets(opt, what = %i[ref multi active taxonomy])
     what.each do |w|
       case w
       when :ref
@@ -165,6 +166,6 @@ module MiGA::Cli::OptHelper
   # If +sym+ is nil, +flag+ is used as Symbol
   def opt_flag(opt, flag, description, sym = nil)
     sym = flag.to_sym if sym.nil?
-    opt.on("--#{flag.to_s.gsub('_', '-')}", description) { |v| self[sym] = v }
+    opt.on("--#{flag.to_s.tr('_', '-')}", description) { |v| self[sym] = v }
   end
 end

data/lib/miga/version.rb

@@ -12,7 +12,7 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.2, 0, 0].freeze
+  VERSION = [1.2, 0, 1].freeze
 
   ##
   # Nickname for the current major.minor version.

data/utils/find-medoid.R

@@ -26,7 +26,6 @@ find_medoids <- function (ani.df, out, clades) {
   medoids <- c()
   for(i in cl){
     lab <- strsplit(i, ",")[[1]]
-    cat("Clade of:", lab[1], "\n")
     if(length(lab) == 1) {
       lab.s <- lab
     } else {

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.2.0.0
+  version: 1.2.0.1
 platform: ruby
 authors:
 - Luis M. Rodriguez-R