rbbt-util 5.26.32 → 5.26.33
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/lib/rbbt/hpc.rb +4 -0
- data/lib/rbbt/tsv/util.rb +2 -2
- data/lib/rbbt/util/R/plot.rb +0 -1
- data/lib/rbbt/util/cmd.rb +4 -0
- data/lib/rbbt/workflow/step/run.rb +1 -1
- data/share/rbbt_commands/stat/density +2 -2
- metadata +2 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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SHA256:
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-
metadata.gz:
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data.tar.gz:
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metadata.gz: 6bb743af0b904f9dd8e788c71cb4c4ca14f3134e65645c848763ddd93d6dc219
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4
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data.tar.gz: 1e197f6519936cf7a1f384d73b7da94c8adce54588f78e84f71271883a1b11e4
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 90799d7fae2157c02d2601f3c3b3eefabcd70818702523851b5008f2107bd458008b9131007d973333a12bce41a02e93ddf7634057f709f8edbfe2013ee8ec55
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7
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data.tar.gz: ae3655c31d114cfcb692def246116a69113702bb6048b57f5e72ea9f293414f8484ab9830427b228b9860b09d75c221705338e252184cada37908e63b2323765
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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
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@@ -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
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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+$/
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-
raise "Field #{ field } was not found. Options: (#{key_field || "NO_KEY_FIELD"}), #{(fields || ["NO_FIELDS"]) * ", "}" if pos.nil?
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raise "Field '#{ field }' was not found. Options: (#{key_field || "NO_KEY_FIELD"}), #{(fields || ["NO_FIELDS"]) * ", "}" if pos.nil?
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else
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-
raise "Field #{ field } was not found. Options: (#{key_field || "NO_KEY_FIELD"}), #{(fields || ["NO_FIELDS"]) * ", "}"
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raise "Field '#{ field }' was not found. Options: (#{key_field || "NO_KEY_FIELD"}), #{(fields || ["NO_FIELDS"]) * ", "}"
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end
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end
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data/lib/rbbt/util/R/plot.rb
CHANGED
data/lib/rbbt/util/cmd.rb
CHANGED
@@ -13,11 +13,15 @@ module CMD
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end
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def self.process_cmd_options(options = {})
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add_dashes = Misc.process_options options, :add_option_dashes
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string = ""
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options.each do |option, value|
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raise "Invalid option key: #{option.inspect}" if option.to_s !~ /^[a-z_0-9\-=]+$/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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case
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when value.nil? || FalseClass === value
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next
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@@ -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? }
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@@ -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.
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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-
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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
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