rbbt-util 5.31.0 → 5.31.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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+  metadata.gz: 4a455f72e89c6996a19cea23673b6c49f99ffd891bf04b6d0d239fbf79a1897a
+  data.tar.gz: d8dd575e2869c014508eaeebe52ef20cc29b6baed79a6d3e7559c9fdd1d8da19
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+  metadata.gz: 8613bbffa085f4899e64a5cb71071a061d20f08b479f95d8bc95e9c5abfd5735539a87ee4dddb6ed4822f3acc65d4bac787704e98213b99e4c7922d6ca8a0645
+  data.tar.gz: 231dc925d3ae454cadacd5f60f0d7f40d3646df2f7dc00949a7ae5f3e7480f372df06c4c59a3a85d36151d898511eee4c604315aaa2cbae92cf36ffbb1378e7d

data/lib/rbbt/hpc/batch.rb

@@ -11,7 +11,11 @@ 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 contain = options[:contain]
+        contain = File.expand_path(contain)
+        env_cmd ||= ""
+        env_cmd << " TMPDIR='#{contain}/.rbbt/tmp' "
+      end
 
       if options[:singularity]
 
@@ -19,24 +23,23 @@ module HPC
 
         singularity_img, singularity_opt_dir, singularity_ruby_inline = options.values_at :singularity_img, :singularity_opt_dir, :singularity_ruby_inline
 
-        singularity_cmd = %(singularity exec -e -B #{singularity_opt_dir}:/singularity_opt/ -B /apps/) 
+        singularity_cmd = %(singularity exec -e -B #{singularity_opt_dir}:/singularity_opt/ -B "#{singularity_ruby_inline}":"/.singularity_ruby_inline":rw ) 
 
-        if contain = options[:contain]
-          contain = File.expand_path(contain)
+        if contain && options[:hardened]
           singularity_cmd << %( -C -H "#{contain}" \
+-B "/.singularity_ruby_inline":"#{contain}/.singularity_ruby_inline":rw 
 -B "#{options[:batch_dir]}" \
 -B /scratch/tmp \
 #{ group != user_group ? "-B /gpfs/projects/#{user_group}" : "" } \
 -B #{scratch_group_dir} \
 -B #{projects_group_dir} \
--B "#{singularity_ruby_inline}":"#{contain}/.ruby_inline":rw  \
+-B /apps/ \
 -B ~/git:"#{contain}/git":ro \
 #{Open.exists?('~/.rbbt/software/opt/')? '-B ~/.rbbt/software/opt/:"/opt/":ro' : '' } \
 -B ~/.rbbt:"#{contain}/home/":ro)
-          singularity_cmd << " #{singularity_img} "
         end
-        env_cmd ||= ""
-        env_cmd << " TMPDIR='#{contain}/.rbbt/tmp' "
+
+        singularity_cmd << " #{singularity_img} "
       end
 
       if env_cmd
@@ -172,7 +175,7 @@ EOF
         batch_options[:wipe_container] ||= 'post'
       end
 
-      if batch_options[:contain] && ! batch_options[:singularity]
+      if batch_options[:contain] && ! batch_options[:hardened]
         options[:workdir_all] = batch_options[:contain]
       end
 
@@ -306,7 +309,7 @@ module load singularity
 mkdir -p "#{singularity_opt_dir}"
         EOF
 
-        if contain
+        if contain && options[:hardened]
 
           prepare_environment +=<<-EOF
 # Prepare container for singularity

data/lib/rbbt/hpc/lsf.rb

@@ -7,7 +7,8 @@ module HPC
 
     def self.batch_system_variables
       <<-EOF
-MAX_MEMORY=$LSB_MAX_MEM_RUSAGE || let MAX_MEMORY="$(grep MemTotal /proc/meminfo|grep -o "[[:digit:]]*") / 1024"
+[[ -z $LSB_MAX_MEM_RUSAGE ]] || MAX_MEMORY=$LSB_MAX_MEM_RUSAGE 
+[[ -z $MAX_MEMORY ]] && let MAX_MEMORY="$(grep MemTotal /proc/meminfo|grep -o "[[:digit:]]*") / 1024"
 BATCH_JOB_ID=$LSF_JOBID
 BATCH_SYSTEM=LSF
       EOF

data/lib/rbbt/workflow/integration/ansible.rb

@@ -2,7 +2,7 @@ require_relative 'ansible/workflow'
 require 'rbbt/workflow/usage'
 
 module Ansible
-  def self.play(playbook, inventory = nil)
+  def self.play(playbook, inventory = nil, verbose = false)
     inventory = Rbbt.etc.ansible_inventory.find
     Log.with_severity 0 do
       TmpFile.with_file do |tmp|
@@ -10,7 +10,11 @@ module Ansible
           Open.write(tmp, [playbook].to_yaml)
           playbook = tmp
         end
-        CMD.cmd_log("ansible-playbook -i #{inventory} #{playbook}")
+        if verbose
+          CMD.cmd_log("ansible-playbook -i #{inventory} -v #{playbook}")
+        else
+          CMD.cmd_log("ansible-playbook -i #{inventory} #{playbook}")
+        end
       end
     end
   end
@@ -46,7 +50,7 @@ module Ansible
   def self.playbook(file, task = nil, options = {})
     task = 'default' if task.nil?
 
-    workflow = Workflow.require_workflow file
+    workflow = Workflow === file ? file : Workflow.require_workflow(file)
     task = workflow.tasks.keys.last if workflow.tasks[task].nil?
     workflow2playbook workflow, task, options
   end

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

@@ -99,7 +99,9 @@ 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.collect{|v| v = "#{v}" if Path === v; v }if Array === value
+          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 +124,18 @@ 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
@@ -545,7 +550,7 @@ class Step
 
   def aborted?
     status = self.status
-    status == :aborted || ((status != :cleaned && status != :noinfo && status != :setup && status != :noinfo) && nopid?)
+    status == :aborted || ((status != :dependencies && status != :cleaned && status != :noinfo && status != :setup && status != :noinfo) && nopid?)
   end
 
   # {{{ INFO

data/share/install/software/lib/install_helpers

@@ -147,6 +147,8 @@ get_git(){
           git pull origin master
           git rebase master
           git stash apply
+          git submodule init
+          git submodule update
         fi
     else
       if [ $version == 'none' ];then
@@ -154,6 +156,10 @@ get_git(){
       else
         git clone --recursive "$url" "$name" -b $version
       fi
+
+      cd "$name" 
+      git submodule init
+      git submodule update
     fi
 
     clean_build

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.31.0
+  version: 5.31.5
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-03-24 00:00:00.000000000 Z
+date: 2021-03-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake