rbbt-util 5.31.0 → 5.31.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: cf8f167c63aecfd2f389650ea9c0baeac59c769c9258bdedc973bc58d8a845e4
+  metadata.gz: 61b346a2806a9f5c6f32dd2e972386ad2ebd5d748b4d71ac89fdeabc0250567b
+  data.tar.gz: faa0e2b8eee1eb1271406f16bf8b030ee4ecd3d83e6dfce205a5129e6676e2c9
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+  metadata.gz: 57f76043890f5ad9ecdf7b397f7803d59556bc39fe8110fd719db68192cda82542ccf072899f37f23fd497a03fe79b9d1119146c268e7571843dee9a35eeb506
+  data.tar.gz: 8b4b959e19804a206abb1a080d81866aa73388eee85d1c031021ed79e239df570b055a3f9d007fbe406eb372edd76ade85a556bf9d38dca16011b326efbf8117

data/lib/rbbt/hpc/batch.rb

@@ -11,8 +11,6 @@ module HPC
       env_cmd     = Misc.process_options options, :env_cmd
       development = Misc.process_options options, :development
 
-      job_cmd             = self.rbbt_job_exec_cmd(job, options)
-
       if options[:singularity]
 
         group, user, user_group, scratch_group_dir, projects_group_dir = options.values_at :group, :user, :user_group, :scratch_group_dir, :projects_group_dir

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

@@ -99,7 +99,8 @@ class Step
         if String === value && File.exists?(value)
           Open.ln_s(value, path)
         else
-          Open.write(path + '.yaml', value.to_s.to_yaml)
+          value = "#{value}" if Path === value
+          Open.write(path + '.yaml', value.to_yaml)
         end
       when Array === value
         Open.write(path, value.collect{|v| Step === v ? v.path : v.to_s} * "\n")
@@ -122,15 +123,18 @@ class Step
     workflow = job.workflow
     workflow = Kernel.const_get workflow if String === workflow
     if workflow
-      task_info = workflow.task_info(task_name)
-      input_types = task_info[:input_types]
-      task_inputs = task_info[:inputs]
-      input_defaults = task_info[:input_defaults]
+      task_info = IndiferentHash.setup(workflow.task_info(task_name))
+      input_types = IndiferentHash.setup(task_info[:input_types])
+      task_inputs = IndiferentHash.setup(task_info[:inputs])
+      input_defaults = IndiferentHash.setup(task_info[:input_defaults])
     else
-      task_info = input_types = task_inputs = input_defaults = {}
+      task_info = IndiferentHash.setup({})
+      input_types = IndiferentHash.setup({})
+      task_inputs = IndiferentHash.setup({})
+      input_defaults = IndiferentHash.setup({})
     end
 
-    inputs = {}
+    inputs = IndiferentHash.setup({})
     real_inputs = job.real_inputs || job.info[:real_inputs]
     job.recursive_inputs.zip(job.recursive_inputs.fields).each do |value,name|
       next unless task_inputs.include? name.to_sym

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.31.0
+  version: 5.31.1
 platform: ruby
 authors:
 - Miguel Vazquez