rbbt-util 5.26.32 → 5.26.33

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checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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+ data.tar.gz: ae3655c31d114cfcb692def246116a69113702bb6048b57f5e72ea9f293414f8484ab9830427b228b9860b09d75c221705338e252184cada37908e63b2323765
data/lib/rbbt/hpc.rb CHANGED
@@ -415,6 +415,7 @@ EOF
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  options = IndiferentHash.setup(options.dup)
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  dry_run = options.delete :dry_run
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+ tail = options.delete :tail
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  workflow = job.workflow
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  task = job.task_name
@@ -437,6 +438,9 @@ EOF
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  template = self.template(cmd, options)
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  self.issue_template(template, options.merge(:slurm_basedir => slurm_basedir, :dry_run => dry_run))
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+
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+ return unless tail
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+
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  t_monitor = Thread.new do
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  self.follow_job(slurm_basedir, :STDERR)
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  end
data/lib/rbbt/tsv/util.rb CHANGED
@@ -161,9 +161,9 @@ module TSV
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  pos = fields.index field
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  return pos if pos
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  return identify_field(key_field, fields, field.to_i) if field =~ /^\d+$/
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- raise "Field #{ field } was not found. Options: (#{key_field || "NO_KEY_FIELD"}), #{(fields || ["NO_FIELDS"]) * ", "}" if pos.nil?
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+ raise "Field '#{ field }' was not found. Options: (#{key_field || "NO_KEY_FIELD"}), #{(fields || ["NO_FIELDS"]) * ", "}" if pos.nil?
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  else
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- raise "Field #{ field } was not found. Options: (#{key_field || "NO_KEY_FIELD"}), #{(fields || ["NO_FIELDS"]) * ", "}"
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+ raise "Field '#{ field }' was not found. Options: (#{key_field || "NO_KEY_FIELD"}), #{(fields || ["NO_FIELDS"]) * ", "}"
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  end
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  end
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@@ -99,7 +99,6 @@ module R
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  end
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  end
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-
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  def self.ggplotPNG(*args)
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  ggplot(*args)
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  end
data/lib/rbbt/util/cmd.rb CHANGED
@@ -13,11 +13,15 @@ module CMD
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  end
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  def self.process_cmd_options(options = {})
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+ add_dashes = Misc.process_options options, :add_option_dashes
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+
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  string = ""
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  options.each do |option, value|
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  raise "Invalid option key: #{option.inspect}" if option.to_s !~ /^[a-z_0-9\-=]+$/i
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  raise "Invalid option value: #{value.inspect}" if value.to_s.include? "'"
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+ option = "--" << option.to_s if add_dashes and option.to_s[0] != '-'
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+
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  case
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  when value.nil? || FalseClass === value
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  next
@@ -119,7 +119,7 @@ class Step
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  rec_dependencies.
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  select{|dependency| ! (defined? WorkflowRESTClient and WorkflowRESTClient::RemoteStep === dependency) }.
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  collect{|dependency| Workflow.relocate_dependency self, dependency}.
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- select{|dependency| Open.exists?(dependency.path) || Open.exists?(dependency.info_file) }.
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+ select{|dependency| Open.exists?(dependency.path) || (Open.exists?(dependency.info_file) && dependency.status == :cleaned) }.
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  select{|dependency| ! Open.remote?(dependency.path) }.
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  select{|dependency| dependency.updatable? }.
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  select{|dependency| ! dependency.error? }
@@ -36,13 +36,13 @@ res = TmpFile.with_file nil, :extension => 'png' do |tmp|
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  R.run <<-EOF
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  values = #{R.ruby2R values}
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  d = density(values)
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- rbbt.png_plot(filename = '#{plot || tmp}', 'plot(d, xlim=c(0,#{max})); abline(v=mean(values))')
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+ rbbt.png_plot(filename = '#{plot || tmp}', 'plot(d, xlim=c(0,#{max})); abline(v=mean(values));rug(jitter(values))')
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  EOF
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  else
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  R.run <<-EOF
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  values = #{R.ruby2R values}
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  d = density(values)
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- rbbt.png_plot(filename = '#{plot || tmp}', 'plot(d); abline(v=mean(values))')
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+ rbbt.png_plot(filename = '#{plot || tmp}', 'plot(d); abline(v=mean(values));rug(jitter(values))')
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  EOF
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  end
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metadata CHANGED
@@ -1,14 +1,14 @@
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  --- !ruby/object:Gem::Specification
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  name: rbbt-util
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  version: !ruby/object:Gem::Version
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- version: 5.26.32
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+ version: 5.26.33
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  platform: ruby
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  authors:
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  - Miguel Vazquez
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2019-07-12 00:00:00.000000000 Z
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+ date: 2019-07-16 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: rake