scout-gear 10.8.0 → 10.8.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 7a3b309720cd9c3116460e682e1da0810a8601a406de1a86bb2e63c2dc1b2e7e
-  data.tar.gz: 03ee884261ff3393b2d9e52c1361260bd2c55d3038c244251dc75b357891eb93
+  metadata.gz: a469436e6ab560158eead4f0fae044ebddebe65d611a97a69837ab7884cad3e4
+  data.tar.gz: a60763c026694b77083f23cf14784e4e6575bd34886980c4af28ead001f8590e
 SHA512:
-  metadata.gz: 66b6d4780304a2f50f6a7aa384c86df78909851d1c9176d71ebaa67c7bb43b334b10b092fb4d636d1dbeada466db19d17af12d28f181de27ec0fd54450a1367c
-  data.tar.gz: 4efa2ebbc04db80cae4592887ab7f825cdc4783ffd381c1073c5d1e762f034b9c0c0a6e581948bfca96195653d88500c07525e922d7229c81306893a13e41809
+  metadata.gz: 5620d8f89b1c5b7bff57c21c2fb28bac8c31168220a7fd8b9804179e9381b75603e9844440e233f07c0d80ebc7de8f684235a34297263ca927679a4f08aa348c
+  data.tar.gz: b91fb51fec1e97b351a2d7a91b07186498b49d2b8bdf4561bb806b7b38cf45c2c2239642830bc1bfb9909b2f5ed7f173b3ce3707ca2f9fd799fd89d246217fa3

data/VERSION

@@ -1 +1 @@
-10.8.0
+10.8.2

data/bin/scout

@@ -66,7 +66,7 @@ require 'scout/simple_opt'
 require 'scout/log'
 
 options = SOPT.setup <<EOF
-Ruby bioinformatics toolkit
+Scout
 
 $ #{$0} <command> <subcommand> ... -a --arg1 --arg2='value' --arg3 'another-value'
 
@@ -75,7 +75,7 @@ $ #{$0} <command> <subcommand> ... -a --arg1 --arg2='value' --arg3 'another-valu
 --dev*                  #{Log.color :yellow, "Find development libraries in the directory specified"}
 --nocolor               #{Log.color :yellow, "Disable colored output"}
 --nobar                 #{Log.color :yellow, "Disable progress report"}
---locate_file           #{Log.color :yellow, "Report the location of the script instead of executing it"}
+--locate_file           #{Log.color :yellow, "Report the location of the script but do not execute it"}
 -ck--config_keys*       #{Log.color :yellow, "Override some config keys"}
 EOF
 

data/lib/scout/knowledge_base/traverse.rb

@@ -106,7 +106,7 @@ class KnowledgeBase
         new_paths = _fp(rest, clean_matches, new_assignments)
         next unless new_paths
         paths[match] = new_paths
-      end
+      end if matches
 
       return false if paths.empty?
 

data/lib/scout/workflow/entity.rb

@@ -2,11 +2,21 @@ require 'scout/entity'
 require 'scout/workflow'
 
 module EntityWorkflow
+  attr_accessor :entity_name
+
+  def entity_name=(name)
+    @entity_name = name
+    helper name do
+      entity
+    end
+  end
 
   def self.extended(base)
     base.extend Workflow
     base.extend Entity
 
+    base.entity_name ||= 'entity'
+
     base.instance_variable_set(:@annotation_inputs, IndiferentHash.setup({})) unless base.instance_variables.include?(:@annotation_inputs)
     class << base
       def annotation_input(name, type=nil, desc=nil, default=nil, options = {})
@@ -20,7 +30,7 @@ module EntityWorkflow
       base.setup(clean_name.dup, inputs.to_hash)
     end
 
-    base.helper :entity_list do 
+    base.helper :entity_list do
       list = inputs.last
       list = list.load if Step === list
       base.setup(list, inputs.to_hash)
@@ -46,12 +56,13 @@ module EntityWorkflow
         input annotation
       end
     end
+
     case property_type
     when :single, :single2array
-      input :entity, :string, "#{self.to_s} identifier", nil, jobname: true
+      input entity_name, :string, "#{self.to_s} identifier", nil, jobname: true
       task(task_name => result_type, &block)
     when :both
-      input :entity, :string, "#{self.to_s} identifier", nil, jobname: true
+      input entity_name, :string, "#{self.to_s} identifier", nil, jobname: true
       input :list, :array, "#{self.to_s} identifier list"
       task(task_name => result_type, &block)
     else
@@ -59,7 +70,8 @@ module EntityWorkflow
       task(task_name => result_type, &block)
     end
 
-    property task_name => property_type do |*args|
+    property_name = task_name.to_s.sub(/^(#{entity_name}_list|#{entity_name}|list)_/, '')
+    property property_name => property_type do |*args|
       job = job(task_name, *args)
       Array === job ? job.collect(&:run) : job.run
     end

data/lib/scout/workflow/task.rb

@@ -83,11 +83,12 @@ module Task
 
       id = DEFAULT_NAME if id.nil?
 
+      sanitized_id = Path.sanitize_filename(id, 150)
       if non_default_inputs.any? && !(non_default_inputs == [jobname_input] && provided_inputs[jobname_input] == id)
         hash = Misc.digest(:inputs => input_digest_str, :dependencies => dependencies)
-        name = [id, hash] * "_"
+        name = [sanitized_id, hash] * "_"
       else
-        name = id
+        name = sanitized_id
       end
 
       extension = self.extension

data/lib/scout/workflow/usage.rb

@@ -139,14 +139,16 @@ module Workflow
     dep_tree = {}
     task = self.tasks[task_name]
     raise TaskNotFound, "Task #{task_name} in #{self.to_s}" if task.nil?
-    task.deps.each do |workflow, task, options|
-      next if seen.include? dep
-      seen << [workflow, task, options.merge(seen_options)]
-      next if task.nil?
 
-      key = [workflow, task]
+    task.deps.each do |workflow, dep_task, options|
+      dep = [workflow, dep_task, options.merge(seen_options)]
+      #next if seen.include? dep
+      seen << dep
+      next if dep_task.nil?
 
-      dep_tree[key] = workflow.dep_tree(task, seen, options.merge(seen_options))
+      dep_key = [workflow, dep_task]
+
+      dep_tree[dep_key] = workflow.dep_tree(dep_task, seen, options.merge(seen_options))
     end if task.deps
 
     @dep_tree[key] = dep_tree if save
@@ -163,6 +165,7 @@ module Workflow
   def _prov_tasks(tree)
     tasks = [] 
     heap = tree.values
+    heap = [tree]
     while heap.any?
       t = heap.pop
       t.each do |k,v|
@@ -188,10 +191,8 @@ module Workflow
       first = last.nil?
       last = _prov_tasks(workflow.dep_tree(task_name))
 
-      break if child
-
       if child
-        description << "->" << task_name.to_s
+        #·description << "->" << task_name.to_s
       elsif first
         description << "" << task_name.to_s
       else
@@ -204,7 +205,6 @@ module Workflow
   end
 
   def prov_tree(tree, offset = 0, seen = [])
-
     return "" if tree.empty?
 
     lines = []

data/scout-gear.gemspec

@@ -2,16 +2,16 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: scout-gear 10.8.0 ruby lib
+# stub: scout-gear 10.8.2 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "scout-gear".freeze
-  s.version = "10.8.0".freeze
+  s.version = "10.8.2".freeze
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib".freeze]
   s.authors = ["Miguel Vazquez".freeze]
-  s.date = "2025-06-05"
+  s.date = "2025-06-13"
   s.description = "Scout gear: workflow, TSVs, persistence, entities, associations, and knowledge_bases.".freeze
   s.email = "mikisvaz@gmail.com".freeze
   s.executables = ["scout".freeze]

data/scout_commands/glob

@@ -0,0 +1,90 @@
+#!/usr/bin/env ruby
+
+require 'scout-gear'
+
+$0 = "scout #{$previous_commands.any? ? $previous_commands*" " + " " : "" }#{ File.basename(__FILE__) }" if $previous_commands
+
+options = SOPT.setup <<EOF
+
+Find files with glob
+
+$ #{$0} [<options>] (<resource> <path>|<path>)
+
+-h--help Print this help
+-r--requires* Files to require; 'all' for all in Scout.etc.requires
+-lw--load_workflow* Files to require; 'all' for all in Scout.etc.requires
+-w--where* Where to look for the path
+EOF
+if options[:help]
+  if defined? scout_usage
+    scout_usage
+  else
+    puts SOPT.doc
+  end
+  exit 0
+end
+
+resource, path = ARGV
+path, resource = resource, nil if path.nil?
+
+raise MissingParameterException.new(:path) if path.nil?
+
+case options[:workflows]
+when nil, false, "false", "none"
+when "all"
+  Scout.etc.workflows.list.each do |workflow|
+    Workflow.require_workflow file
+  end if Scout.etc.workflows.exists?
+else
+  options[:workflows].split(/[ ,;|]/).each do |workflow|
+    Workflow.require_workflow workflow
+  end
+end
+
+case options[:requires]
+when nil, false, "false", "none"
+when "all"
+  Scout.etc.requires.list.each do |file|
+    require file
+  end if Scout.etc.requires.exists?
+else
+  options[:requires].split(/[ ,;|]/).each do |file|
+    require file
+  end
+end
+
+location = nil
+where = options[:where]
+all = options[:all]
+
+begin
+  resource = Workflow.require_workflow resource
+rescue
+  begin
+    resource = Kernel.const_get(resource)
+  rescue
+    raise "Resource not found: #{ resource }"
+  end
+end if resource
+
+path = (resource || Scout)[path.dup]
+
+if where.nil? || where == 'all' || path.path_maps.include?(where.to_sym)
+  case where
+  when nil
+    location = path.glob
+  when 'all'
+    location = path.glob_all
+  else
+    location = path.find(where).glob
+  end
+
+  if Array === location
+    puts location * "\n"
+  else
+    location = nil if ! Open.exists?(location)
+    puts location
+  end
+else
+  raise ParameterException, "Where '#{where}' not identified. Try scout-camp if looking for a remote file"
+end

data/scout_commands/workflow/task

@@ -18,7 +18,7 @@ $ #{$0} [<options>] <workflow> <task>
 -h--help Print this help
 --nostream Disable job streaming
 --update Update jobs with newer dependencies
---deploy* Deploy mode: serial, local, or SLURM (default 'serial')
+--deploy* Deploy mode: serial, local, queue, or SLURM (default 'serial')
 --fork Fork and return path
 --load_inputs* Directory or file with inputs files to load
 --save_inputs* Directory or tar.gz file path to store inputs
@@ -115,7 +115,8 @@ else
   when "serial"
     job.run(true) 
   when "local"
-    orchestrator = Workflow::Orchestrator.new 3, "cpus" => Misc.processors
+    refresh = Scout::Config.get :refresh, :deploy, :local, :orchestrator, default: 3
+    orchestrator = Workflow::Orchestrator.new refresh.to_f, "cpus" => Misc.processors
     orchestrator.process({}, job)
   when "slurm"
     require 'rbbt-scout'

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification
 name: scout-gear
 version: !ruby/object:Gem::Version
-  version: 10.8.0
+  version: 10.8.2
 platform: ruby
 authors:
 - Miguel Vazquez
 bindir: bin
 cert_chain: []
-date: 2025-06-05 00:00:00.000000000 Z
+date: 2025-06-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: scout-essentials