rbbt-util 5.32.0 → 5.32.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: '087009c9ac6b4fee6d9fa7bceb003e050a0cc1e73f96987ec792c07388760633'
+  metadata.gz: 4491182540571f16f4059ec742f210152862e77bda8c31355285c81daf8bfd8e
+  data.tar.gz: 313a4e9252f8b443fef52b4267e94b177f9cacd36a89d6db63010b4ae7fb275f
 SHA512:
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-  data.tar.gz: eb43875132a5f4ddc7ff9ae5dcaed7677c6bff84a4d61454cad9a83361d2a3dd63432cd5b28c656cd9e7bb589b8517bbdd3b57c0fa370527724d3ae55810b0cb
+  metadata.gz: 81b4b06eac8a44027a0c0f97510c75a2b0f3daf6594da4cd977c5d197318ee7e22db35e0c12f68dced5ab5aa0c1f0c152be77ed7bafe8c5588f2d274292b2035
+  data.tar.gz: 5ea83c058de9bde5bbae17b1c08308a7311c5c48d1c589f236300c3f437b667bd7012ad48a2c4890ab0c924168916809569367155b3a9300723a9c6596837d52

data/lib/rbbt/tsv/csv.rb

@@ -8,6 +8,7 @@ module TSV
     noheaders = ! headers
 
     type = options.delete :type
+    cast = options.delete :cast
     merge = options.delete :merge
     key_field = options.delete :key_field
     fields = options.delete :fields
@@ -46,6 +47,10 @@ module TSV
       else
         key, *values = row
       end
+      
+      if cast
+        values = values.collect{|v| v.send cast }
+      end
 
       case type
       when :double, :flat

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

@@ -97,6 +97,7 @@ class Step
         Open.ln_s(value.path, path)
       when type.to_s == "file"
         if String === value && File.exists?(value)
+          value = File.expand_path(value)
           Open.ln_s(value, path)
         else
           value = value.collect{|v| v = "#{v}" if Path === v; v }if Array === value

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

@@ -1,6 +1,6 @@
 class Step
 
-  MAIN_RSYNC_ARGS="-avztAXHP"
+  MAIN_RSYNC_ARGS="-avztAXHP --copy-links"
   
   def self.link_job(path, target_dir, task = nil, workflow = nil)
     Path.setup(target_dir)

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

@@ -70,8 +70,8 @@ module Workflow
 
     start = data.column("Start.second").values.flatten.collect{|v| v.to_f}.min
     eend = data.column("End.second").values.flatten.collect{|v| v.to_f}.max
-    total = eend - start
-    Log.info "Total time elapsed: #{total} seconds"
+    total = eend - start unless eend.nil? || start.nil?
+    Log.info "Total time elapsed: #{total} seconds" if total
 
     data
   end
@@ -178,7 +178,6 @@ rbbt.png_plot('#{plot}', 'plot(timeline)', width=#{width}, height=#{height}, poi
     jobs = []
     seed_jobs.each do |step|
       jobs += step.rec_dependencies + [step]
-
       step.info[:archived_info].each do |path,ainfo|
         archived_step = Step.new path
         class << archived_step
@@ -188,9 +187,10 @@ rbbt.png_plot('#{plot}', 'plot(timeline)', width=#{width}, height=#{height}, poi
         end
         jobs << archived_step
       end if step.info[:archived_info]
+
     end
 
-    jobs = jobs.uniq.sort_by{|job| t = job.info[:done]; t || Open.mtime(job.path) || 0 }
+    jobs = jobs.uniq.sort_by{|job| t = job.info[:started]; t || Open.mtime(job.path) || Time.now }
 
     data = trace_job_times(jobs, options[:fix_gap])
 
@@ -200,10 +200,10 @@ rbbt.png_plot('#{plot}', 'plot(timeline)', width=#{width}, height=#{height}, poi
 
     raise "No jobs to process" if data.size == 0
 
-    plot, size, width, height = options.values_at :plot, :width, :height
+    plot, size, width, height = options.values_at :plot, :size, :width, :height
 
     size = 800 if size.nil?
-    width = size * 2 if width.nil?
+    width = size.to_i * 2 if width.nil?
     height = size  if height.nil?
 
     plot_trace_job_times(data, plot, width, height) if plot

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.32.0
+  version: 5.32.1
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-04-15 00:00:00.000000000 Z
+date: 2021-04-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake