rbbt-util 5.26.32 → 5.26.33

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 9af0c4d82eaf89fe8fa118c8537cca19a799c6aa561d43089d0d6700e9553a71
+  metadata.gz: 6bb743af0b904f9dd8e788c71cb4c4ca14f3134e65645c848763ddd93d6dc219
+  data.tar.gz: 1e197f6519936cf7a1f384d73b7da94c8adce54588f78e84f71271883a1b11e4
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+  metadata.gz: 90799d7fae2157c02d2601f3c3b3eefabcd70818702523851b5008f2107bd458008b9131007d973333a12bce41a02e93ddf7634057f709f8edbfe2013ee8ec55
+  data.tar.gz: ae3655c31d114cfcb692def246116a69113702bb6048b57f5e72ea9f293414f8484ab9830427b228b9860b09d75c221705338e252184cada37908e63b2323765

data/lib/rbbt/hpc.rb

@@ -415,6 +415,7 @@ EOF
       options = IndiferentHash.setup(options.dup)
         
       dry_run          = options.delete :dry_run
+      tail             = options.delete :tail
 
       workflow = job.workflow
       task = job.task_name
@@ -437,6 +438,9 @@ EOF
 
         template = self.template(cmd, options)
         self.issue_template(template, options.merge(:slurm_basedir => slurm_basedir, :dry_run => dry_run))
+
+        return unless tail
+
         t_monitor = Thread.new do
           self.follow_job(slurm_basedir, :STDERR)
         end

data/lib/rbbt/tsv/util.rb

@@ -161,9 +161,9 @@ module TSV
       pos = fields.index field
       return pos if pos
       return identify_field(key_field, fields, field.to_i) if field =~ /^\d+$/
-      raise "Field #{ field } was not found. Options: (#{key_field || "NO_KEY_FIELD"}), #{(fields || ["NO_FIELDS"]) * ", "}" if pos.nil?
+      raise "Field '#{ field }' was not found. Options: (#{key_field || "NO_KEY_FIELD"}), #{(fields || ["NO_FIELDS"]) * ", "}" if pos.nil?
     else
-      raise "Field #{ field } was not found. Options: (#{key_field || "NO_KEY_FIELD"}), #{(fields || ["NO_FIELDS"]) * ", "}"
+      raise "Field '#{ field }' was not found. Options: (#{key_field || "NO_KEY_FIELD"}), #{(fields || ["NO_FIELDS"]) * ", "}"
     end
   end
 

data/lib/rbbt/util/R/plot.rb

@@ -99,7 +99,6 @@ module R
       end
     end
 
-
     def self.ggplotPNG(*args)
       ggplot(*args)
     end

data/lib/rbbt/util/cmd.rb

@@ -13,11 +13,15 @@ module CMD
   end
 
   def self.process_cmd_options(options = {})
+    add_dashes = Misc.process_options options, :add_option_dashes
+
     string = ""
     options.each do |option, value|
       raise "Invalid option key: #{option.inspect}" if option.to_s !~ /^[a-z_0-9\-=]+$/i
       raise "Invalid option value: #{value.inspect}" if value.to_s.include? "'"
 
+      option = "--" << option.to_s if add_dashes and option.to_s[0] != '-'
+
       case 
       when value.nil? || FalseClass === value 
         next

data/lib/rbbt/workflow/step/run.rb

@@ -119,7 +119,7 @@ class Step
     rec_dependencies.
       select{|dependency| ! (defined? WorkflowRESTClient and WorkflowRESTClient::RemoteStep === dependency) }.
       collect{|dependency| Workflow.relocate_dependency self, dependency}.
-      select{|dependency| Open.exists?(dependency.path) || Open.exists?(dependency.info_file) }.
+      select{|dependency| Open.exists?(dependency.path) || (Open.exists?(dependency.info_file) && dependency.status == :cleaned) }.
       select{|dependency| ! Open.remote?(dependency.path) }.
       select{|dependency| dependency.updatable? }.
       select{|dependency| ! dependency.error? }

data/share/rbbt_commands/stat/density

@@ -36,13 +36,13 @@ res = TmpFile.with_file nil, :extension => 'png' do |tmp|
     R.run <<-EOF
 values = #{R.ruby2R values}
 d = density(values)
-rbbt.png_plot(filename = '#{plot || tmp}', 'plot(d, xlim=c(0,#{max})); abline(v=mean(values))')
+rbbt.png_plot(filename = '#{plot || tmp}', 'plot(d, xlim=c(0,#{max})); abline(v=mean(values));rug(jitter(values))')
     EOF
   else
     R.run <<-EOF
 values = #{R.ruby2R values}
 d = density(values)
-rbbt.png_plot(filename = '#{plot || tmp}', 'plot(d); abline(v=mean(values))')
+rbbt.png_plot(filename = '#{plot || tmp}', 'plot(d); abline(v=mean(values));rug(jitter(values))')
     EOF
   end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.26.32
+  version: 5.26.33
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-07-12 00:00:00.000000000 Z
+date: 2019-07-16 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake