rbbt-util 5.34.15 → 5.34.17

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 279844e3cda015f07db9429faf3e9941f12080be28b21bafa2f8472d784969b8
+  metadata.gz: db0f07cbefa25d669572e39d0740ae5eab280bfd314629377f1a526d998944de
+  data.tar.gz: 60845114700c0dc2ce3c016fd4264f2de5aa01a18f90f13a7d534c6379a575c8
 SHA512:
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-  data.tar.gz: 227c22590c7d08d4e47121c1f814af71d11b9afa7f5fd71aabed014a8e857b6ebd7424b70ed669b8bc3aa993461339209ca1a67a15c3ab9cf81ac9fd85a83cbe
+  metadata.gz: ba349615e02ea9ae7b96943824b69ece55449e0a79a0bb8564de3d2dffd7f693c695d0f7feef1916f181554559482d3d9784548f7cda469369f4dde2d4b1ac6a
+  data.tar.gz: 2201fb56e611a703dbd3b4508195270743894b2b7dd3292b08b688bb8df49c91bc495b3e777b6ea2ddea76a6fe2c5f26b500151966cf4e7c886fc2f5c1f84071

data/lib/rbbt/hpc/slurm.rb

@@ -10,7 +10,9 @@ module HPC
       <<-EOF
 let TOTAL_PROCESORS="$(cat /proc/cpuinfo|grep ^processor |wc -l)"
 let MAX_MEMORY_DEFAULT="$(grep MemTotal /proc/meminfo|grep -o "[[:digit:]]*") / ( (1024 * $TOTAL_PROCESORS) / $SLURM_CPUS_PER_TASK )"
-[ ! -z $SLURM_MEM_PER_CPU ] && let MAX_MEMORY="$SLURM_MEM_PER_CPU * $SLURM_CPUS_PER_TASK" || MAX_MEMORY="$MAX_MEMORY_DEFAULT"
+MAX_MEMORY="$MAX_MEMORY_DEFAULT"
+[ ! -z $SLURM_MEM_PER_CPU ] && let MAX_MEMORY="$SLURM_MEM_PER_CPU * $SLURM_CPUS_PER_TASK" 
+[ ! -z $SLURM_MEM_PER_NODE ] && MAX_MEMORY="$SLURM_MEM_PER_NODE"
 export MAX_MEMORY_DEFAULT
 export MAX_MEMORY
 export BATCH_JOB_ID=$SLURM_JOB_ID

data/lib/rbbt/persist.rb

@@ -84,6 +84,8 @@ module Persist
       perfile = prefix.to_s + ":" + file.to_s.gsub(/\//, '>') 
     end
 
+    perfile.sub!(/\.b?gz$/,'')
+
     if options.include? :filters
       options[:filters].each do |match,value|
         perfile = perfile + "&F[#{match}=#{Misc.digest(value.inspect)}]"

data/lib/rbbt/tsv/parser.rb

@@ -135,7 +135,7 @@ module TSV
                  []
                else
                  parts.values_at *field_positions
-               end.collect{|value| (value.empty? || value.nil?) ? [nil] : value.split(@sep2, -1) }
+               end.collect{|value| (value.nil? || value.empty?) ? [] : value.split(@sep2, -1) }
       [keys, values]
     end
 

data/lib/rbbt/tsv/util.rb

@@ -377,7 +377,7 @@ module TSV
         return self
       when :list
         through do |k,v|
-          new[k] = v.first
+          new[k] = v.nil? ? nil : v.first
         end
       end
     end

data/lib/rbbt/tsv.rb

@@ -137,12 +137,12 @@ module TSV
     case
     when Path === stream 
       stream.open do |f|
-        f.no_fail = false if ConcurrentStream === f
+        f.no_fail = true if ConcurrentStream === f
         Parser.new f, options
       end
     when (String === stream and stream.length < 300 and (Open.exists? stream or Open.remote? stream))
       Open.open(stream) do |f|
-        f.no_fail = false if ConcurrentStream === f
+        f.no_fail = true if ConcurrentStream === f
         Parser.new f, options
       end
     else

data/lib/rbbt/util/cmd.rb

@@ -163,6 +163,7 @@ module CMD
 
     if in_content.respond_to?(:read)
       in_thread = Thread.new(Thread.current) do |parent|
+        Thread.current.report_on_exception = false if no_fail
         begin
           begin
             while c = in_content.readpartial(Misc::BLOCK_SIZE)
@@ -177,7 +178,7 @@ module CMD
             in_content.join if in_content.respond_to? :join 
           end
         rescue
-          Log.error "Error in CMD  [#{pid}] #{cmd}: #{$!.message}"
+          Log.error "Error in CMD  [#{pid}] #{cmd}: #{$!.message}" unless no_fail
           raise $!
         end
       end

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

@@ -35,21 +35,21 @@ module Misc
     v_range = v_max - v_min
     range = max.to_f - min.to_f
 
-    v.collect{|e| min + range * (e.to_f - v_min) / v_range } 
+    v.collect{|e| (e.nil? || e.nan?) ? e : min + range * (e.to_f - v_min) / v_range } 
   end
 
   def self.sum(list)
-    list.compact.inject(0.0){|acc,e| acc += e}
+    list.compact.inject(0.0){|acc,e| acc += e }
   end
 
   def self.mean(list)
-    sum(list).to_f / list.compact.length
+    sum(list.compact.collect{|v| v.to_f } ) / list.compact.length
   end
 
   def self.median(array)
     sorted = array.sort
     len = sorted.length
-    (sorted[(len - 1) / 2] + sorted[len / 2]) / 2.0
+    (sorted[(len - 1) / 2] + sorted[len / 2]).to_f / 2
   end
 
   def self.variance(list)

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

@@ -493,7 +493,7 @@ class Step
       begin Exception
         execute_and_dup(step, dep_step) 
       rescue 
-        raise $! unless canfail_paths.include? step.path
+        raise $! unless canfail_paths.include?(step.path)
       end
     end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.34.15
+  version: 5.34.17
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-10-03 00:00:00.000000000 Z
+date: 2022-10-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake