rbbt-util 5.34.24 → 5.34.25

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 0a030eb0b6f9648a60c11abaac383fe33b24845c288ddd7a28eb8e9aa8d8ac1c
+  metadata.gz: f1a0dc0772864a83c7c6b159d53dc1c5d95e7f58619c4e4b0c630e8240a621aa
+  data.tar.gz: c8a029debfd1ee7c820185aa1dead29575ecd173a1868692751c6a01dc7be01a
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+  metadata.gz: b151561ce56b42af19160eff58a8f45be7fedd6226d960987111e8b9d1147802eb612f96b85a47ad849476b7d4520df457ed70e91e9528d67e9e03a6959f78c4
+  data.tar.gz: 60b1a486a88bd2c65a4c003130c7c81de42ce72446420797132d1047be2446fce74f7cb35c80a652a1f56dcc630ba6e32d7c991a524efeab85a05325aaae1024

data/lib/rbbt/hpc/batch.rb

@@ -101,6 +101,11 @@ module HPC
 
       task = Symbol === job.overriden ? job.overriden : job.task_name
 
+      #override_deps = job.overriden_deps.collect do |dep| 
+      #  name = [dep.workflow.to_s, dep.task_name] * "#"
+      #  [name, dep.path] * "="  
+      #end.uniq * ","
+
       if job.overriden?
         #override_deps = job.rec_dependencies.
         #  select{|dep| Symbol === dep.overriden }.
@@ -568,7 +573,7 @@ env > #{batch_options[:fenv]}
         Misc.add_defaults options, 
           :batch_dir => batch_dir, 
           :inputs_dir => File.join(batch_dir, "inputs_dir"),
-          :workflows => workflows_to_load.uniq * ","
+          :workflows => workflows_to_load.any? ? workflows_to_load.uniq * "," : nil
 
         options[:procpath_performance] ||= File.join(batch_dir, "procpath##{procpath.gsub(',', '#')}") if procpath
 

data/lib/rbbt/workflow/dependencies.rb

@@ -73,8 +73,10 @@ module Workflow
     return [] if dep == :skip || dep == 'skip'
 
     if not Step === dep
-      located = Open.exists?(dep)
+      located = Open.exists?(dep) || Open.exists?(dep + '.info')
       dep = Workflow.load_step(dep)
+    else
+      located = true
     end
 
     dep.original_workflow ||= dep.workflow if dep.workflow

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

@@ -527,7 +527,7 @@ class Step
 
   def overriden?
     return true if @overriden
-    return true if dependencies && dependencies.select{|dep| dep.overriden? }.any?
+    return true if dependencies && dependencies.select{|dep| TrueClass === dep.overriden }.any?
     info[:archived_info].each do |f,i|
       next if Symbol === i
       return true if i[:overriden] || i["overriden"]

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

@@ -31,6 +31,8 @@ module Workflow
 
         type = :step_array if file.split(".").last == 'as_step_array'
 
+        type = :number_array if file.split(".").last == 'as_number_array'
+
         type = :step_file if file.split(".").last == 'as_step_file'
 
         type = :step_file_array if file.split(".").last == 'as_step_file_array'
@@ -57,6 +59,9 @@ module Workflow
         when :step_array
           steps = Open.read(file).strip.split("\n").collect{|path| Workflow.load_step(path) }
           inputs[input.to_sym] = steps
+        when :number_array
+          numbers = Open.read(file).strip.split("\n").collect{|num| num.to_f }
+          inputs[input.to_sym] = numbers
         when :step
           steps = Open.read(file).strip.split("\n").collect{|path| Workflow.load_step(path) }
           inputs[input.to_sym] = steps.first
@@ -176,6 +181,8 @@ class Step
       when Step
         path = path + '.as_step_array'
         value = value.collect{|s| s.path }
+      when Numeric
+        path = path + '.as_number_array'
       end
 
       value = value * "\n"

data/lib/rbbt/workflow.rb

@@ -437,8 +437,8 @@ module Workflow
       jobname_input = nil 
     end
 
-    if jobname_input && jobname && inputs[jobname_input].nil?
-      inputs[jobname_input] = jobname
+    if jobname_input && inputs[jobname_input].nil?
+      inputs[jobname_input] = jobname || DEFAULT_NAME
     end
 
     real_inputs = {}
@@ -503,7 +503,7 @@ module Workflow
     when :not_overriden_dep
       job.overriden = true if has_overriden_inputs || true_overriden_deps.any?
     else
-      job.overriden = true if has_overriden_inputs || overriden_deps.any?
+      job.overriden = true if has_overriden_inputs || true_overriden_deps.any?
     end
 
     job.real_inputs = real_inputs.keys

data/share/rbbt_commands/hpc/orchestrate

@@ -61,7 +61,8 @@ class Step
     else
       begin
         Log.debug "Issuing SLURM job for #{self.path}"
-        @batch_job_id, @batch_job_dir = HPC::BATCH_MODULE.orchestrate_job(self, SOPT::GOT_OPTIONS.merge($slurm_options)) 
+        #@batch_job_id, @batch_job_dir = HPC::BATCH_MODULE.orchestrate_job(self, SOPT::GOT_OPTIONS.merge($slurm_options)) 
+        @batch_job_id, @batch_job_dir = HPC::BATCH_MODULE.orchestrate_job(self, $slurm_options) 
         if no_load
           self
         else

data/share/rbbt_commands/lsf/orchestrate

@@ -61,7 +61,8 @@ class Step
     else
       begin
         Log.debug "Issuing SLURM job for #{self.path}"
-        @batch_job_id, @batch_job_dir = HPC::BATCH_MODULE.orchestrate_job(self, SOPT::GOT_OPTIONS.merge($slurm_options)) 
+        #@batch_job_id, @batch_job_dir = HPC::BATCH_MODULE.orchestrate_job(self, SOPT::GOT_OPTIONS.merge($slurm_options)) 
+        @batch_job_id, @batch_job_dir = HPC::BATCH_MODULE.orchestrate_job(self, $slurm_options) 
         if no_load
           self
         else

data/share/rbbt_commands/slurm/orchestrate

@@ -61,7 +61,8 @@ class Step
     else
       begin
         Log.debug "Issuing SLURM job for #{self.path}"
-        @batch_job_id, @batch_job_dir = HPC::BATCH_MODULE.orchestrate_job(self, SOPT::GOT_OPTIONS.merge($slurm_options)) 
+        #@batch_job_id, @batch_job_dir = HPC::BATCH_MODULE.orchestrate_job(self, SOPT::GOT_OPTIONS.merge($slurm_options)) 
+        @batch_job_id, @batch_job_dir = HPC::BATCH_MODULE.orchestrate_job(self, $slurm_options) 
         if no_load
           self
         else

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.34.24
+  version: 5.34.25
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-12-09 00:00:00.000000000 Z
+date: 2022-12-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake