rbbt-util 5.38.1 → 5.39.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 1121593dec25c29d7986047727d555ed0e75df6b158f9f1332764ad4886462c5
-  data.tar.gz: c8e39ef65e23445cf5d0c8817af961a9206016c5e3665d87e042f0fadec2b8df
+  metadata.gz: 12c5401cf3ecb8495ba5c21d0f3d3f35c741c1c335ffa0d3a7d3ee498f6daae8
+  data.tar.gz: 344f30b6651a272f5e9665d3ec6383b4a1d62ba7c64c7889af5cfc573b2285ac
 SHA512:
-  metadata.gz: 22c87766544a52c9c6f0d6da369422a452f553d1a61b82a54674f676a3867a6c1d29028c2efd031563f982cdadbce56d36950c8e100bd34ac2a7e95b39af8a58
-  data.tar.gz: 0a79edc89dad388bca9b94dfeccba1df64c4294e84c4f19743608038e55f8800181911d787980adae3ec1c715a993430ccbf2bc07d6212485b89843ada93de74
+  metadata.gz: 6e8305e1f3e74eeff9e5892592bc66bfc9aac3baa505503942b266c3de996408a9210fcfaa2f6073800fc763bf3cdf5b8f39a50a920696402657d2928a9add8f
+  data.tar.gz: 511c72833b4a8ef747e574376d44a3b4799f96f6a922301d3f405df1cd7aac79a2d2de388075aaab4fc3ef6962ee66ded3de8684227912399f41f7ad00006148

data/lib/rbbt/resource.rb

@@ -354,7 +354,7 @@ url='#{url}'
     path = File.expand_path(path)
     path += "/" if File.directory?(path)
     resource ||= Rbbt
-    locations = (Path::STANDARD_SEARCH + resource.search_order + resource.search_paths.keys)
+    locations = (Path::STANDARD_SEARCH + resource.search_order + resource.search_paths.keys).uniq
     locations -= [:current, "current"]
     locations << :current
     search_paths = IndiferentHash.setup(resource.search_paths)
@@ -374,7 +374,11 @@ url='#{url}'
           if ! m.named_captures.include?("PKGDIR") || m["PKGDIR"] == resource.pkgdir
             unlocated = ([m["TOPLEVEL"],m["SUBPATH"],m["REST"]] * "/")
             unlocated.gsub!(/\/+/,'/')
-            unlocated[self.subdir] = "" if self.subdir
+            if self.subdir && ! self.subdir.empty?
+              subdir = self.subdir
+              subdir += "/" unless subdir.end_with?("/")
+              unlocated[subdir] = ""
+            end
             choices << self.annotate(unlocated)
           end
         end

data/lib/rbbt/tsv/util.rb

@@ -400,5 +400,9 @@ module TSV
     end
     index
   end
+
+  def merge(other)
+    self.annotate(super(other))
+  end
 end
 

data/lib/rbbt/util/cmd.rb

@@ -22,13 +22,17 @@ module CMD
     return tool.to_s unless TOOLS[tool]
 
     @@init_cmd_tool ||= IndiferentHash.setup({})
+
+    claim, test, block, cmd = TOOLS[tool]
+    cmd = tool.to_s if cmd.nil?
+
     if !@@init_cmd_tool[tool]
-      claim, test, block, cmd = TOOLS[tool]
+
       begin
         if test
           CMD.cmd(test + " ")
         else
-          CMD.cmd("#{tool} --help")
+          CMD.cmd("#{cmd} --help")
         end
       rescue
         if claim
@@ -41,7 +45,7 @@ module CMD
       version = nil
       ["--version", "-version", "--help", ""].each do |f|
         begin
-          version_txt += CMD.cmd("#{tool} #{f} 2>&1", :nofail => true).read
+          version_txt += CMD.cmd("#{cmd} #{f} 2>&1", :nofail => true).read
           version = Misc.scan_version_text(version_txt, tool)
           break if version
         rescue
@@ -54,7 +58,7 @@ module CMD
       return cmd if cmd
     end
 
-    tool.to_s
+    cmd
   end
 
   def self.versions

data/lib/rbbt/util/concurrency/processes.rb

@@ -245,7 +245,7 @@ class RbbtProcessQueue
         end
       end if @callback_queue
 
-      @callback_thread.report_on_exception = false
+      @callback_thread.report_on_exception = false if @callback_thread
       
     end
 

data/lib/rbbt/util/migrate.rb

@@ -1,6 +1,5 @@
 module Rbbt 
 
-  prepare_for_execution(job)
   def self.migrate_source_paths(path, resource = Rbbt, source = nil)
     if source
       lpath, *paths = Misc.ssh_run(source, <<-EOF).split("\n")
@@ -60,7 +59,7 @@ puts resource[path].find(search_path)
     test_str = options[:test] ? '-nv' : ''
 
     real_paths.each do |source_path|
-      Log.medium "Migrating #{source_path} #{options[:files].length} files to #{target} - #{Misc.fingerprint(options[:files])}}" if options[:files]
+      Log.low "Migrating #{source_path} #{options[:files].length} files to #{target} - #{Misc.fingerprint(options[:files])}}" if options[:files]
       if File.directory?(source_path) || source_path.end_with?("/")
         source_path += "/" unless source_path.end_with? '/'
         target += "/" unless target.end_with? '/'

data/lib/rbbt/util/misc/inspect.rb

@@ -455,6 +455,7 @@ module Misc
   end
 
   def self.scan_version_text(text, cmd = nil)
+    text = Misc.fixutf8 text
     cmd = "NOCMDGIVE" if cmd.nil? || cmd.empty?
     text.split("\n").each do |line|
       next unless line =~ /\W#{cmd}\W/i

data/lib/rbbt/util/open.rb

@@ -530,16 +530,22 @@ module Open
 
   def self.gzip?(file)
     file = file.find if Path === file
+    file = file.filename if File === file
+    return false unless String === file
     !! (file =~ /\.gz$/)
   end
 
   def self.bgzip?(file)
     file = file.find if Path === file
+    file = file.filename if File === file
+    return false unless String === file
     !! (file =~ /\.bgz$/)
   end
 
   def self.zip?(file)
     file = file.find if Path === file
+    file = file.filename if File === file
+    return false unless String === file
     !! (file =~ /\.zip$/)
   end
 

data/lib/rbbt/util/ssh.rb

@@ -9,7 +9,7 @@ class SSHLine
     @ssh = Net::SSH.start(@host, @user)
 
     @ch = @ssh.open_channel do |ch|
-      ch.exec 'bash'
+      ch.exec 'bash -l'
     end
 
     @ch.on_data do |_,data|

data/lib/rbbt/workflow/remote_workflow/driver/ssh.rb

@@ -253,7 +253,7 @@ job.clean
       Step.wait_for_jobs missing_deps
 
       migrate_dependencies = all_deps.keys.collect{|d| [d] + d.rec_dependencies + d.input_dependencies }.flatten.select{|d| d.done? }.collect{|d| d.path }
-      Log.medium "Migrating #{migrate_dependencies.length} dependencies from #{Misc.fingerprint job_list} to #{ server }" 
+      Log.low "Migrating #{migrate_dependencies.length} dependencies from #{Misc.fingerprint job_list} to #{ server }" 
       Step.migrate(migrate_dependencies, search_path, :target => server) if migrate_dependencies.any?
     end
 

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

@@ -145,9 +145,9 @@ class Step
   end
 
   def input_dependencies
-    @input_dependencies ||= recursive_inputs.flatten.
+    @input_dependencies ||= recursive_inputs(true).flatten.
       select{|i| Step === i || (defined?(RemoteStep) && RemoteStep === i) } + 
-      recursive_inputs.flatten.
+      recursive_inputs(true).flatten.
       select{|dep| Path === dep && Step === dep.resource }.
       #select{|dep| ! dep.resource.started? }. # Ignore input_deps already started
       collect{|dep| dep.resource }
@@ -581,7 +581,6 @@ class Step
   #but dependencies are absent, meanining that the file could have been dropped
   #in
   def rec_dependencies(connected = false, seen = [])
-
     # A step result with no info_file means that it was manually
     # placed. In that case, do not consider its dependencies
     return [] if ! (defined? WorkflowRemoteClient && WorkflowRemoteClient::RemoteStep === self) && ! Open.exists?(self.info_file) && Open.exists?(self.path.to_s) 
@@ -599,7 +598,7 @@ class Step
       #next if self.done? && Open.exists?(info_file) && info[:dependencies] && info[:dependencies].select{|task,name,path| path == step.path }.empty?
       next if archived_deps.include? step.path
       next if seen.include? step
-      next if self.done? && connected && ! updatable?
+      next if step.done? && connected && ! step.updatable?
 
       r = step.rec_dependencies(connected, new_dependencies)
       new_dependencies.concat r

data/lib/rbbt/workflow/step.rb

@@ -90,7 +90,7 @@ class Step
     end
   end
 
-  def recursive_inputs
+  def recursive_inputs(connected = false)
     if NamedArray === inputs
       i = {}
       inputs.zip(inputs.fields).each do |v,f|
@@ -99,7 +99,7 @@ class Step
     else
       i = {}
     end
-    rec_dependencies.each do |dep|
+    rec_dependencies(connected).each do |dep|
       next unless NamedArray === dep.inputs
 
       dep.inputs.zip(dep.inputs.fields).each do |v,f|

data/lib/rbbt/workflow/usage.rb

@@ -20,7 +20,7 @@ module Task
       task_inputs = dep_inputs deps, workflow
       task_inputs.each do |task,new_inputs|
         new_inputs.zip(task.input_types.values_at(*new_inputs)).select do |i,t| 
-          t.to_sym == :select and task.input_options[i][:select_options] 
+          t.to_sym == :select && task.input_options.include?(i) && task.input_options[i][:select_options] 
         end.each do |i,t| 
           selects << [i, task.input_options[i][:select_options]] 
         end

data/lib/rbbt/workflow/util/trace.rb

@@ -81,7 +81,8 @@ module Workflow
 
   def self.plot_trace_job_times(data, plot, width=800, height=800)
     data.R <<-EOF, [:svg]
-rbbt.require('tidyverse')
+rbbt.require('dplyr')
+rbbt.require('tidyr')
 rbbt.require('ggplot2')
 
 names(data) <- make.names(names(data))

data/lib/rbbt/workflow.rb

@@ -23,7 +23,7 @@ module Workflow
 
   #{{{ WORKFLOW MANAGEMENT 
   class << self
-    attr_accessor :workflows, :autoinstall, :workflow_dir
+    attr_accessor :workflows, :autoinstall, :workflow_dir, :main
   end
 
   self.workflows = []
@@ -202,13 +202,14 @@ module Workflow
 
     first = nil
     wf_name.split("+").each do |wf_name|
+      self.main = nil
       require_local_workflow(wf_name) or 
         (Workflow.autoinstall and `rbbt workflow install #{Misc.snake_case(wf_name)} || rbbt workflow install #{wf_name}` and require_local_workflow(wf_name)) or raise("Workflow not found or could not be loaded: #{ wf_name }")
 
       workflow = begin
                    Misc.string2const Misc.camel_case(wf_name)
                  rescue
-                   Workflow.workflows.last || true
+                   self.main || Workflow.workflows.last 
                  end
       workflow.load_documentation
 

data/share/rbbt_commands/resource/claims

@@ -0,0 +1,57 @@
+#!/usr/bin/env ruby
+
+require 'rbbt-util'
+require 'rbbt/resource'
+require 'rbbt/workflow'
+
+options = SOPT.get <<EOF
+-W--workflows* Workflows to use; 'all' for all in Rbbt.etc.workflows:
+-r--requires* Files to require; 'all' for all in Rbbt.etc.requires:
+-f--force Force the production if the file is already present
+-h--help Help
+EOF
+
+if options[:help]
+  puts SOPT.doc 
+  exit
+end
+
+case options[:workflows]
+when nil, false, "false", "none"
+when "all"
+  Rbbt.etc.workflows.list.each do |workflow|
+    Workflow.require_workflow file
+  end if Rbbt.etc.workflows.exists?
+else
+  options[:workflows].split(/[ ,;|]/).each do |workflow|
+    Workflow.require_workflow workflow
+  end
+end
+
+case options[:requires]
+when nil, false, "false", "none"
+when "all"
+  Rbbt.etc.requires.list.each do |file|
+    require file
+  end if Rbbt.etc.requires.exists?
+else
+  options[:requires].split(/[ ,;|]/).each do |file|
+    require file
+  end
+end
+
+resource, path = ARGV
+
+begin
+  resource = Kernel.const_get(resource)
+rescue
+  begin
+    resource = Workflow.require_workflow resource
+  rescue
+    raise "Resource not found: #{ resource }"
+  end
+end
+
+puts resource.claims * "\n"
+ 
+

data/share/rbbt_commands/workflow/task

@@ -220,8 +220,8 @@ The `recursive_clean` cleans all the job dependency steps recursively.
 -rwt--remote_workflow_tasks* Load a yaml file describing remote workflow tasks
 -od--override_deps* Override deps using 'Workflow#task=<path>' array_separated
 -PERF--procpath_performance* Measure performance using procpath
--r--relay* Relay job to SSH server
--sr--slurm_relay* Relay job to SSH SLURM server
+--relay* Relay job to SSH server
+--slurm_relay* Relay job to SSH SLURM server
 -rdep--relay_dependencies* Relay dependencies instead of main job
 -pdr--produce_dependencies_for_relay Prepare dependencies previous to relay jobs
 EOF

data/test/rbbt/test_tsv.rb

@@ -302,7 +302,7 @@ b 2
     EOF
 
     TmpFile.with_file(content) do |filename|
-      tsv = TSV.open(filename, :key_field => "Value", :select => Proc.new{|l| ! l =~ /1/})
+      tsv = TSV.open(filename, :key_field => "Value", :select => Proc.new{|l| l !~ /1/})
       assert(! tsv.include?("3"))
     end
   end
@@ -650,5 +650,20 @@ row3    AA    BB|BBB    Id3|Id2
  
     end
   end
+
+  def test_benchmark
+    num = 10_000
+    txt = num.times.inject(nil) do |acc,i|
+      (acc.nil? ? "" : acc << "\n") << (0..10).collect{|v| v == 0 ? i : [v,v] * "|" } * "\t"
+    end 
+
+    txt = StringIO.new(([txt] * (10))*"\n")
+    #Misc.profile do
+    Misc.benchmark(1) do
+      data = TSV.open(txt, type: :double, bar: true, merge: true)
+      assert_equal num, data.size
+    end
+  end
+
 end
 

data/test/rbbt/tsv/parallel/test_traverse.rb

@@ -50,11 +50,11 @@ class TestTSVParallelThrough < Test::Unit::TestCase
   def test_traverse_stream
     require 'rbbt/sources/organism'
 
-    head = 1000
+    head = 3000
 
     tsv = datafile_test('identifiers').open
     res = {}
-    TSV.traverse tsv, :head => head, :into => res do |k,v|
+    TSV.traverse tsv, :head => head, :into => res, :bar => true do |k,v|
       [k,v]
     end
 

data/test/rbbt/tsv/test_util.rb

@@ -35,4 +35,18 @@ row2    A    B    Id3
       assert_equal %w(aa bb Id2), tsv.unzip_replicates["row1(1)"]
     end
   end
+
+  def test_merge
+   content =<<-EOF
+#Id    ValueA    ValueB    OtherID
+row1    a|aa|aaa    b|bb|bbb    Id1|Id2|Id3
+row2    A    B    Id3
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(filename, :sep => /\s+/)
+      tsv = tsv.merge({"row3" => [["A3"], ["B3"], ["Id4"]]})
+      assert TSV === tsv
+    end
+  end
 end

data/test/rbbt/util/test_migrate.rb

@@ -3,9 +3,9 @@ require 'rbbt-util'
 require 'rbbt/util/migrate'
 
 class TestMigrate < Test::Unit::TestCase
-  def _test_source_locate
+  def test_source_locate
     assert_equal 'var/jobs/', Rbbt.migrate_source_paths(Rbbt.root['var/jobs'].find(:user)).last
-    assert Rbbt.migrate_source_paths(Rbbt.root['var/jobs'].find(:user))[1].include?(File.join(ENV["HOME"], '.rbbt/var/jobs/'))
+    assert_include Rbbt.migrate_source_paths(Rbbt.root['var/jobs'].find(:user))[1], (File.join(ENV["HOME"], '.rbbt/var/jobs'))
   end
 
   def test_migrate

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.38.1
+  version: 5.39.0
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-06-01 00:00:00.000000000 Z
+date: 2023-08-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -390,6 +390,7 @@ files:
 - share/rbbt_commands/migrate
 - share/rbbt_commands/migrate_job
 - share/rbbt_commands/purge_job
+- share/rbbt_commands/resource/claims
 - share/rbbt_commands/resource/exists
 - share/rbbt_commands/resource/find
 - share/rbbt_commands/resource/get
@@ -594,110 +595,110 @@ signing_key:
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
-- test/rbbt/test_entity.rb
-- test/rbbt/workflow/test_remote_workflow.rb
-- test/rbbt/workflow/util/test_archive.rb
-- test/rbbt/workflow/util/test_orchestrator.rb
-- test/rbbt/workflow/util/test_data.rb
-- test/rbbt/workflow/test_doc.rb
-- test/rbbt/workflow/test_schedule.rb
-- test/rbbt/workflow/test_step.rb
-- test/rbbt/workflow/step/test_dependencies.rb
-- test/rbbt/workflow/step/test_save_load_inputs.rb
-- test/rbbt/workflow/test_task.rb
-- test/rbbt/resource/test_path.rb
-- test/rbbt/util/test_colorize.rb
-- test/rbbt/util/test_procpath.rb
-- test/rbbt/util/python/test_util.rb
-- test/rbbt/util/misc/test_development.rb
-- test/rbbt/util/misc/test_indiferent_hash.rb
-- test/rbbt/util/misc/test_omics.rb
-- test/rbbt/util/misc/test_pipes.rb
-- test/rbbt/util/misc/test_serialize.rb
-- test/rbbt/util/misc/test_format.rb
-- test/rbbt/util/misc/test_communication.rb
-- test/rbbt/util/misc/test_lock.rb
-- test/rbbt/util/misc/test_multipart_payload.rb
-- test/rbbt/util/misc/test_bgzf.rb
-- test/rbbt/util/test_concurrency.rb
-- test/rbbt/util/test_cmd.rb
-- test/rbbt/util/R/test_plot.rb
-- test/rbbt/util/R/test_eval.rb
-- test/rbbt/util/R/test_model.rb
-- test/rbbt/util/test_config.rb
-- test/rbbt/util/test_log.rb
-- test/rbbt/util/test_simpleDSL.rb
-- test/rbbt/util/log/test_progress.rb
-- test/rbbt/util/test_tmpfile.rb
-- test/rbbt/util/test_R.rb
-- test/rbbt/util/test_excel2tsv.rb
-- test/rbbt/util/test_misc.rb
-- test/rbbt/util/test_open.rb
-- test/rbbt/util/test_ssh.rb
-- test/rbbt/util/test_simpleopt.rb
-- test/rbbt/util/simpleopt/test_parse.rb
-- test/rbbt/util/simpleopt/test_setup.rb
-- test/rbbt/util/simpleopt/test_get.rb
-- test/rbbt/util/test_python.rb
-- test/rbbt/util/test_filecache.rb
-- test/rbbt/util/concurrency/test_processes.rb
-- test/rbbt/util/concurrency/test_threads.rb
-- test/rbbt/util/concurrency/processes/test_socket.rb
-- test/rbbt/util/test_semaphore.rb
-- test/rbbt/util/test_chain_methods.rb
-- test/rbbt/util/test_migrate.rb
-- test/rbbt/test_resource.rb
-- test/rbbt/test_packed_index.rb
-- test/rbbt/tsv/test_change_id.rb
-- test/rbbt/tsv/test_attach.rb
-- test/rbbt/tsv/test_filter.rb
-- test/rbbt/tsv/test_marshal.rb
-- test/rbbt/tsv/test_parser.rb
-- test/rbbt/tsv/test_csv.rb
-- test/rbbt/tsv/test_accessor.rb
-- test/rbbt/tsv/test_matrix.rb
-- test/rbbt/tsv/test_field_index.rb
-- test/rbbt/tsv/test_util.rb
-- test/rbbt/tsv/test_index.rb
-- test/rbbt/tsv/test_parallel.rb
-- test/rbbt/tsv/test_manipulate.rb
-- test/rbbt/tsv/test_excel.rb
-- test/rbbt/tsv/parallel/test_through.rb
-- test/rbbt/tsv/parallel/test_traverse.rb
-- test/rbbt/tsv/test_stream.rb
-- test/rbbt/test_association.rb
-- test/rbbt/hpc/test_batch.rb
-- test/rbbt/hpc/orchestrate/test_chains.rb
-- test/rbbt/hpc/orchestrate/test_rules.rb
-- test/rbbt/hpc/orchestrate/test_batches.rb
-- test/rbbt/hpc/test_slurm.rb
-- test/rbbt/hpc/test_orchestrate.rb
+- test/rbbt/annotations/test_util.rb
 - test/rbbt/association/test_database.rb
+- test/rbbt/association/test_index.rb
 - test/rbbt/association/test_item.rb
 - test/rbbt/association/test_open.rb
 - test/rbbt/association/test_util.rb
-- test/rbbt/association/test_index.rb
-- test/rbbt/test_knowledge_base.rb
-- test/rbbt/persist/tsv/test_kyotocabinet.rb
+- test/rbbt/entity/test_identifiers.rb
+- test/rbbt/hpc/orchestrate/test_batches.rb
+- test/rbbt/hpc/orchestrate/test_chains.rb
+- test/rbbt/hpc/orchestrate/test_rules.rb
+- test/rbbt/hpc/test_batch.rb
+- test/rbbt/hpc/test_orchestrate.rb
+- test/rbbt/hpc/test_slurm.rb
+- test/rbbt/knowledge_base/test_enrichment.rb
+- test/rbbt/knowledge_base/test_entity.rb
+- test/rbbt/knowledge_base/test_query.rb
+- test/rbbt/knowledge_base/test_registry.rb
+- test/rbbt/knowledge_base/test_syndicate.rb
+- test/rbbt/knowledge_base/test_traverse.rb
+- test/rbbt/persist/test_tsv.rb
 - test/rbbt/persist/tsv/test_cdb.rb
+- test/rbbt/persist/tsv/test_kyotocabinet.rb
+- test/rbbt/persist/tsv/test_leveldb.rb
 - test/rbbt/persist/tsv/test_lmdb.rb
 - test/rbbt/persist/tsv/test_sharder.rb
-- test/rbbt/persist/tsv/test_leveldb.rb
 - test/rbbt/persist/tsv/test_tokyocabinet.rb
-- test/rbbt/persist/test_tsv.rb
-- test/rbbt/test_tsv.rb
+- test/rbbt/resource/test_path.rb
 - test/rbbt/test_annotations.rb
+- test/rbbt/test_association.rb
+- test/rbbt/test_entity.rb
 - test/rbbt/test_fix_width_table.rb
-- test/rbbt/test_workflow.rb
-- test/rbbt/entity/test_identifiers.rb
-- test/rbbt/annotations/test_util.rb
 - test/rbbt/test_hpc.rb
+- test/rbbt/test_knowledge_base.rb
 - test/rbbt/test_monitor.rb
+- test/rbbt/test_packed_index.rb
 - test/rbbt/test_persist.rb
-- test/rbbt/knowledge_base/test_entity.rb
-- test/rbbt/knowledge_base/test_registry.rb
-- test/rbbt/knowledge_base/test_syndicate.rb
-- test/rbbt/knowledge_base/test_query.rb
-- test/rbbt/knowledge_base/test_enrichment.rb
-- test/rbbt/knowledge_base/test_traverse.rb
+- test/rbbt/test_resource.rb
+- test/rbbt/test_tsv.rb
+- test/rbbt/test_workflow.rb
+- test/rbbt/tsv/parallel/test_through.rb
+- test/rbbt/tsv/parallel/test_traverse.rb
+- test/rbbt/tsv/test_accessor.rb
+- test/rbbt/tsv/test_attach.rb
+- test/rbbt/tsv/test_change_id.rb
+- test/rbbt/tsv/test_csv.rb
+- test/rbbt/tsv/test_excel.rb
+- test/rbbt/tsv/test_field_index.rb
+- test/rbbt/tsv/test_filter.rb
+- test/rbbt/tsv/test_index.rb
+- test/rbbt/tsv/test_manipulate.rb
+- test/rbbt/tsv/test_marshal.rb
+- test/rbbt/tsv/test_matrix.rb
+- test/rbbt/tsv/test_parallel.rb
+- test/rbbt/tsv/test_parser.rb
+- test/rbbt/tsv/test_stream.rb
+- test/rbbt/tsv/test_util.rb
+- test/rbbt/util/R/test_eval.rb
+- test/rbbt/util/R/test_model.rb
+- test/rbbt/util/R/test_plot.rb
+- test/rbbt/util/concurrency/processes/test_socket.rb
+- test/rbbt/util/concurrency/test_processes.rb
+- test/rbbt/util/concurrency/test_threads.rb
+- test/rbbt/util/log/test_progress.rb
+- test/rbbt/util/misc/test_bgzf.rb
+- test/rbbt/util/misc/test_communication.rb
+- test/rbbt/util/misc/test_development.rb
+- test/rbbt/util/misc/test_format.rb
+- test/rbbt/util/misc/test_indiferent_hash.rb
+- test/rbbt/util/misc/test_lock.rb
+- test/rbbt/util/misc/test_multipart_payload.rb
+- test/rbbt/util/misc/test_omics.rb
+- test/rbbt/util/misc/test_pipes.rb
+- test/rbbt/util/misc/test_serialize.rb
+- test/rbbt/util/python/test_util.rb
+- test/rbbt/util/simpleopt/test_get.rb
+- test/rbbt/util/simpleopt/test_parse.rb
+- test/rbbt/util/simpleopt/test_setup.rb
+- test/rbbt/util/test_R.rb
+- test/rbbt/util/test_chain_methods.rb
+- test/rbbt/util/test_cmd.rb
+- test/rbbt/util/test_colorize.rb
+- test/rbbt/util/test_concurrency.rb
+- test/rbbt/util/test_config.rb
+- test/rbbt/util/test_excel2tsv.rb
+- test/rbbt/util/test_filecache.rb
+- test/rbbt/util/test_log.rb
+- test/rbbt/util/test_migrate.rb
+- test/rbbt/util/test_misc.rb
+- test/rbbt/util/test_open.rb
+- test/rbbt/util/test_procpath.rb
+- test/rbbt/util/test_python.rb
+- test/rbbt/util/test_semaphore.rb
+- test/rbbt/util/test_simpleDSL.rb
+- test/rbbt/util/test_simpleopt.rb
+- test/rbbt/util/test_ssh.rb
+- test/rbbt/util/test_tmpfile.rb
+- test/rbbt/workflow/step/test_dependencies.rb
+- test/rbbt/workflow/step/test_save_load_inputs.rb
+- test/rbbt/workflow/test_doc.rb
+- test/rbbt/workflow/test_remote_workflow.rb
+- test/rbbt/workflow/test_schedule.rb
+- test/rbbt/workflow/test_step.rb
+- test/rbbt/workflow/test_task.rb
+- test/rbbt/workflow/util/test_archive.rb
+- test/rbbt/workflow/util/test_data.rb
+- test/rbbt/workflow/util/test_orchestrator.rb
 - test/test_helper.rb