rbbt-util 5.32.11 → 5.32.12

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: fab4cf5fb60bb998eeed28a4e07758efd68f1103de0eff61a5b5c1d4a9fd2583
-  data.tar.gz: 47c9a2bdc555645ebc833c2a3b92a3452df259546c1dbf200d77dcee04b8969f
+  metadata.gz: 355cf2694fc6b449600580f6c09f2a0a6055013285b5c53ada6ad2f920d7f63c
+  data.tar.gz: 26e430d330e39371b8fb59f3508b3e1eb215bf042bf2faa5262040fd19369e24
 SHA512:
-  metadata.gz: 92121d5df854b036a37413c27d2244cef0325874c018433abce1a93887c93efc650474e059c13b84c0be9a708d6fdc735daba6f861e1d05a670950fea3d32916
-  data.tar.gz: 0d24d99a64101fd33f2ac5774c30267f238c81d6479a754445fc02424384ba716e4c672b8a7c0d1c6f22b9f16c2ac1e1104ba9d35f7697bf4a9631e3a776bb02
+  metadata.gz: ecec79da1a0b8ecdbcec6e600965d6cc8a336f6d33a4dd3ada4a75e2c6ae8d98300a210bc17eec7bb16639c4d73b4a6efe7bceb043037fa0aeaf76d3da20b172
+  data.tar.gz: 3af9d791b8423f99c67c473541fcc6b685c2cb4ca454423ff0b69d686442b40574d337df749dcf811369b81d68c648ff733dcf3c4e2e655953aba0f4569b85b1

data/lib/rbbt/util/cmd.rb

@@ -202,8 +202,7 @@ module CMD
           serr.close
         end
       else
-        Misc.consume_stream(serr, true)
-        err_thread = nil
+        err_thread = Misc.consume_stream(serr, true)
       end
 
       sout.threads = [in_thread, err_thread, wait_thr].compact

data/lib/rbbt/util/log/progress/report.rb

@@ -12,32 +12,35 @@ module Log
     attr_accessor :history, :mean_max, :max_history
     def thr_msg
       if @history.nil?
-        @history ||= [[@ticks, Time.now] ]
+        @history ||= [[0, @start], [@ticks, Time.now] ]
       elsif @last_ticks != @ticks
         @history << [@ticks, Time.now]
-        max_history ||= case 
-                      when @ticks > 20
-                        count = @ticks - @last_count
-                        count = 1 if count == 0
-                        if @max
-                          times = @max / count
-                          num = times / 20
-                          num = 2 if num < 2
-                        else
-                          num = 10
+        max_history ||= begin
+                          max_history = case 
+                                        when @ticks > 20
+                                          count = @ticks - @last_count
+                                          count = 1 if count == 0
+                                          if @max
+                                            times = @max / count
+                                            num = times / 20
+                                            num = 2 if num < 2
+                                          else
+                                            num = 10
+                                          end
+                                          count * num
+                                        else
+                                          20
+                                        end
+                          max_history = 30 if max_history > 30
+                          max_history
                         end
-                        count * num
-                      else
-                        20
-                      end
-        max_history = 30 if max_history > 30
         @history.shift if @history.length > max_history
       end
 
       @last_ticks = @ticks
 
       @mean_max ||= 0
-      if @history.length > 2
+      if @history.length > 3
 
         sticks, stime = @history.first
         ssticks, sstime = @history[-3]

data/lib/rbbt/workflow/accessor.rb

@@ -302,7 +302,7 @@ module Workflow
         workflow, task = m.values_at 1, 2
         workflow = self.to_s if workflow.empty?
         override_dependencies[workflow] ||= IndiferentHash.setup({})
-        override_dependencies[workflow][task] = value.dup
+        override_dependencies[workflow][task] = value
       end
     end
     override_dependencies

data/lib/rbbt/workflow/step.rb

@@ -161,7 +161,7 @@ class Step
 
     archived_info = {}
     dependencies.each do |dep|
-      if Symbol === dep.overriden
+      if Symbol === dep.overriden && ! Open.exists?(dep.info_file)
         archived_info[dep.path] = dep.overriden
       else
         archived_info[dep.path] = dep.info

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

@@ -188,6 +188,7 @@ rbbt.png_plot('#{plot}', 'plot(timeline)', width=#{width}, height=#{height}, poi
     seed_jobs.each do |step|
       jobs += step.rec_dependencies + [step]
       step.info[:archived_info].each do |path,ainfo|
+        next unless Hash === ainfo
         archived_step = Step.new path
 
         archived_step.define_singleton_method :info do
@@ -205,7 +206,7 @@ rbbt.png_plot('#{plot}', 'plot(timeline)', width=#{width}, height=#{height}, poi
 
     end
 
-    jobs = jobs.uniq.sort_by{|job| t = job.info[:started] || Open.mtime(job.path) || Time.now; Time === t ? t : Time.parse(t) }
+    jobs = jobs.uniq.sort_by{|job| [job, job.info]; t = job.info[:started] || Open.mtime(job.path) || Time.now; Time === t ? t : Time.parse(t) }
 
     data = trace_job_times(jobs, options[:fix_gap])
 

data/share/rbbt_commands/hpc/list

@@ -173,7 +173,7 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
    select = true if queued && deps && (running_jobs & deps).any? || queued && is_running && nodes.empty?
    select = true if running && nodes.any? && (exit_status.nil? && running_jobs.include?(id)) && (!deps || (running_jobs & deps).empty?)
    select = true if jobid && jobid.split(",").include?(id)
-   select = select && cmd.match(/#{search}/) if search
+   select = select && step_path.match(/#{search}/) if search
    next unless select 
  elsif search
    select = false
@@ -292,13 +292,17 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
      step_path = step_line.split(": ").last.strip
      step = Step.new step_path
      step.load_dependencies_from_info
+     has_bar = false
      (step.rec_dependencies + [step]).reverse.each do |j|
        next if j.done? 
-       next unless j.file(:progress).exists?
-       bar = Log::ProgressBar.new 
-       bar.load(j.file(:progress).yaml)
-       puts Log.color(:magenta, "Progress: ") + bar.report_msg + " " + Log.color(:yellow, j.task_signature)
+       if j.file(:progress).exists?
+         bar = Log::ProgressBar.new 
+         bar.load(j.file(:progress).yaml)
+         puts Log.color(:magenta, "Progress: ") + bar.report_msg + " " + Log.color(:yellow, j.task_signature)
+         has_bar = true
+       end
      end
+     puts Log.color(:magenta, "Progress: ") + Log.color(:yellow, step.task_signature) + " #{step.status}" unless has_bar
    end
  end
 

data/share/rbbt_commands/lsf/list

@@ -173,7 +173,7 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
    select = true if queued && deps && (running_jobs & deps).any? || queued && is_running && nodes.empty?
    select = true if running && nodes.any? && (exit_status.nil? && running_jobs.include?(id)) && (!deps || (running_jobs & deps).empty?)
    select = true if jobid && jobid.split(",").include?(id)
-   select = select && cmd.match(/#{search}/) if search
+   select = select && step_path.match(/#{search}/) if search
    next unless select 
  elsif search
    select = false
@@ -292,13 +292,17 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
      step_path = step_line.split(": ").last.strip
      step = Step.new step_path
      step.load_dependencies_from_info
+     has_bar = false
      (step.rec_dependencies + [step]).reverse.each do |j|
        next if j.done? 
-       next unless j.file(:progress).exists?
-       bar = Log::ProgressBar.new 
-       bar.load(j.file(:progress).yaml)
-       puts Log.color(:magenta, "Progress: ") + bar.report_msg + " " + Log.color(:yellow, j.task_signature)
+       if j.file(:progress).exists?
+         bar = Log::ProgressBar.new 
+         bar.load(j.file(:progress).yaml)
+         puts Log.color(:magenta, "Progress: ") + bar.report_msg + " " + Log.color(:yellow, j.task_signature)
+         has_bar = true
+       end
      end
+     puts Log.color(:magenta, "Progress: ") + Log.color(:yellow, step.task_signature) + " #{step.status}" unless has_bar
    end
  end
 

data/share/rbbt_commands/slurm/list

@@ -173,7 +173,7 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
    select = true if queued && deps && (running_jobs & deps).any? || queued && is_running && nodes.empty?
    select = true if running && nodes.any? && (exit_status.nil? && running_jobs.include?(id)) && (!deps || (running_jobs & deps).empty?)
    select = true if jobid && jobid.split(",").include?(id)
-   select = select && cmd.match(/#{search}/) if search
+   select = select && step_path.match(/#{search}/) if search
    next unless select 
  elsif search
    select = false
@@ -292,13 +292,17 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
      step_path = step_line.split(": ").last.strip
      step = Step.new step_path
      step.load_dependencies_from_info
+     has_bar = false
      (step.rec_dependencies + [step]).reverse.each do |j|
        next if j.done? 
-       next unless j.file(:progress).exists?
-       bar = Log::ProgressBar.new 
-       bar.load(j.file(:progress).yaml)
-       puts Log.color(:magenta, "Progress: ") + bar.report_msg + " " + Log.color(:yellow, j.task_signature)
+       if j.file(:progress).exists?
+         bar = Log::ProgressBar.new 
+         bar.load(j.file(:progress).yaml)
+         puts Log.color(:magenta, "Progress: ") + bar.report_msg + " " + Log.color(:yellow, j.task_signature)
+         has_bar = true
+       end
      end
+     puts Log.color(:magenta, "Progress: ") + Log.color(:yellow, step.task_signature) + " #{step.status}" unless has_bar
    end
  end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.32.11
+  version: 5.32.12
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-05-17 00:00:00.000000000 Z
+date: 2021-05-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake