scout-gear 10.7.3 → 10.7.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 469b6e128a39e5612de5698005de8f4859c015bf3d65a5490a58f2f9f0312a39
-  data.tar.gz: 0a76edd86052c35af31f6de227c0bc43c71bb6b64fdc757e1179bf88a4ce8701
+  metadata.gz: 92262edf62404f5935bf749d3ab71d2ce39ffc7292a1b3d860fd5dc712501fcb
+  data.tar.gz: 47f69a80c0a135d3a9b3b42558e7b91e766b7781ff2360cd8344ef9c0f7ac8b9
 SHA512:
-  metadata.gz: c8753c031fda58c461afdefa3412a0d7996c6d5139a30653b1e6fcfaeba7fdf31b4d300bb2cb07060e7eb12d63891fc7a157cec3964c59d5cc68584ffc8823c8
-  data.tar.gz: 05cbb772edf0384f2889ad1be2cc597425d071da8c488364a8c72b23e6b7098aea0089247c180da09165f3eb7d899de494dca9ce2a00f285dcfaa564c8dc3e68
+  metadata.gz: 3d532c6a4ac2bd3d0b5584761531b0364f381c317a9864b85b22c7a23bd61dbf2b31d1655f5fc7085c893c843f1b3f36a1b23fffae4c4b9dc2253352f3f5febf
+  data.tar.gz: 50e36c694239f0d74528b9156435b8769d16ae172dd87029ee741c0002b8ef3606f5088fc2c8f881d413b78f1f00f66134f06fc14129da3015648546130809c6

data/.vimproject

@@ -31,6 +31,7 @@ scout-gear=/$PWD filter="*.rb *.yaml" {
     task=task{
      dependencies.rb
      inputs.rb
+     info.rb
     }
     deployment.rb
     deployment=deployment{

data/VERSION

@@ -1 +1 @@
-10.7.3
+10.7.4

data/bin/scout

@@ -52,6 +52,16 @@ if dev_dir
   end
 end
 
+requires = nil
+if _i = ARGV.index("--require")
+  requires = ARGV[_i+1].split(",")
+  ARGV.delete_at _i + 1
+  ARGV.delete_at _i
+  requires.each do |p|
+    require p
+  end
+end
+
 require 'scout-gear'
 
 require 'scout/simple_opt'
@@ -97,8 +107,11 @@ if config_keys = options.delete(:config_keys)
   end
 end
 
-$scout_command_dir = Scout.bin.scout
-$scout_command_dir.path_maps[:scout_commands] = File.join(File.dirname(__dir__), "{PATH/bin\\/scout/scout_commands}")
+#$scout_command_dir = Scout.bin.scout
+#$scout_command_dir.path_maps[:scout_commands] = File.join(File.dirname(__dir__), "{PATH/bin\\/scout/scout_commands}")
+
+$scout_command_dir = Scout.scout_commands
+#$scout_command_dir.path_maps[:scout_commands] = File.join(File.dirname(__dir__), "{PATH/bin\\/scout/scout_commands}")
 
 SOPT.description =<<EOF
 This command controls many aspects of the Scout framework, from configuration tasks to running applications. 

data/lib/scout/association.rb

@@ -11,7 +11,9 @@ module Association
     target = kwargs.delete :target if kwargs.include?(:target)
 
     if Path.is_filename?(obj)
-      options = TSV.parse_options(obj).merge(kwargs)
+      tsv_header_options = TSV.parse_options(obj)
+      tsv_header_options = tsv_header_options.slice(TSV.acceptable_parser_options)
+      options = tsv_header_options.merge(kwargs)
     else
       options = kwargs.dup
     end
@@ -116,11 +118,12 @@ module Association
     persist_options = IndiferentHash.pull_keys kwargs, :persist
 
     database_persist_options = IndiferentHash.add_defaults persist_options.dup, persist: true, 
-      prefix: "Association::Index", serializer: :list,
+      prefix: "Association::Index", serializer: :double,
       other_options: kwargs  
 
     Persist.tsv(file, kwargs, engine: "BDB", persist_options: database_persist_options) do |data|
       tsv = open(file, *args, **kwargs)
+      data.serializer =  TSVAdapter.serializer_module(tsv.type) if data.respond_to?(:serializer)
       if TSV::Transformer === tsv 
         tsv.tsv(merge: true, data: data) 
       elsif data.respond_to?(:persistence_path)

data/lib/scout/entity/property.rb

@@ -62,7 +62,6 @@ module Entity
 
       properties.push name
 
-
       entity_class = self
       if type == :multiple
         self.define_method(real_method) do |*args,**kwargs|
@@ -89,7 +88,7 @@ module Entity
 
             new_responses = missing.instance_exec(*args, **kwargs, &block)
 
-            missing.each do |item,i|
+            missing.each do |item|
               responses[item] = Entity::Property.persist(name, item, type, options) do
                 Array === new_responses ? new_responses[item.container_index] : new_responses[item]
               end

data/lib/scout/knowledge_base/entity.rb

@@ -63,7 +63,7 @@ class KnowledgeBase
     entities.collect{|entity| Entity.formats[entity] }.uniq
   end
 
-  def identifier_files(name)
+  def database_identifier_files(name)
     get_database(name).identifier_files.dup + self.identifier_files
   end
 
@@ -73,7 +73,11 @@ class KnowledgeBase
 
   def source_index(name)
     Persist.memory("Source index #{name}: KB directory #{dir}") do
-      identifier_files = identifier_files(name)
+      if @identifier_files && @identifier_files.any?
+        identifier_files = @identifier_files
+      else
+        identifier_files = database_identifier_files(name)
+      end
       identifier_files.concat Entity.identifier_files(source(name)) if defined? Entity
       identifier_files.uniq!
       identifier_files.collect!{|f| f.annotate(f.gsub(/\bNAMESPACE\b/, namespace))} if namespace
@@ -97,7 +101,12 @@ class KnowledgeBase
 
   def identify_source(name, entity)
     return :all if entity == :all
-    index = begin source_index(name) rescue nil end
+    index = begin 
+              source_index(name) 
+            rescue 
+              Log.exception $!
+              nil
+            end
     return entity if index.nil?
     if Array === entity
       entity.collect{|e| index[e] || e }

data/lib/scout/knowledge_base/registry.rb

@@ -43,9 +43,11 @@ class KnowledgeBase
   end
 
   def undirected(name)
-    description(name)[2]
+    description(name).length == 3
   end
 
+  alias undirected? undirected
+
   def get_index(name, options = {})
     name = name.to_s
     options[:namespace] ||= self.namespace unless self.namespace.nil?

data/lib/scout/persist/engine/tokyocabinet.rb

@@ -1,105 +1,112 @@
-require 'tokyocabinet'
-
-module ScoutCabinet
-  attr_accessor :persistence_path, :persistence_class
-
-  def self.open(path, write = true, tokyocabinet_class = TokyoCabinet::HDB)
-    path = path.find if Path === path
-    if String === tokyocabinet_class && tokyocabinet_class.include?(":big")
-      big = true
-      tokyocabinet_class = tokyocabinet_class.split(":").first
-    else
-      big = false
-    end
+begin
+  require 'tokyocabinet'
+  continue = true
+rescue Exception
+  Log.warn "The Tokyocabinet gem could not be loaded: TSV persistence may not work"
+  continue = false
+end
 
-    dir = File.dirname(File.expand_path(path))
-    Open.mkdir(dir) unless File.exist?(dir)
+if continue
+  module ScoutCabinet
+    attr_accessor :persistence_path, :persistence_class
 
-    tokyocabinet_class = tokyocabinet_class.to_s if Symbol === tokyocabinet_class
-    tokyocabinet_class = TokyoCabinet::HDB if tokyocabinet_class == "HDB" or tokyocabinet_class.nil?
-    tokyocabinet_class = TokyoCabinet::BDB if tokyocabinet_class == "BDB"
+    def self.open(path, write = true, tokyocabinet_class = TokyoCabinet::HDB)
+      path = path.find if Path === path
+      if String === tokyocabinet_class && tokyocabinet_class.include?(":big")
+        big = true
+        tokyocabinet_class = tokyocabinet_class.split(":").first
+      else
+        big = false
+      end
 
-    # Hack - Ignore warning: undefining the allocator of T_DATA class
-    # TokyoCabinet::HDB_data
-    database = Log.ignore_stderr do Persist::CONNECTIONS[path] ||= tokyocabinet_class.new end
+      dir = File.dirname(File.expand_path(path))
+      Open.mkdir(dir) unless File.exist?(dir)
 
-    if big and not Open.exists?(path)
-      database.tune(nil, nil, nil, tokyocabinet_class::TLARGE | tokyocabinet_class::TDEFLATE) 
-    end
+      tokyocabinet_class = tokyocabinet_class.to_s if Symbol === tokyocabinet_class
+      tokyocabinet_class = TokyoCabinet::HDB if tokyocabinet_class == "HDB" or tokyocabinet_class.nil?
+      tokyocabinet_class = TokyoCabinet::BDB if tokyocabinet_class == "BDB"
 
-    flags = (write ? tokyocabinet_class::OWRITER | tokyocabinet_class::OCREAT : tokyocabinet_class::OREADER)
-    database.close 
+      # Hack - Ignore warning: undefining the allocator of T_DATA class
+      # TokyoCabinet::HDB_data
+      database = Log.ignore_stderr do Persist::CONNECTIONS[path] ||= tokyocabinet_class.new end
 
-    if !database.open(path, flags)
-      ecode = database.ecode
-      raise "Open error: #{database.errmsg(ecode)}. Trying to open file #{path}"
-    end
+      if big and not Open.exists?(path)
+        database.tune(nil, nil, nil, tokyocabinet_class::TLARGE | tokyocabinet_class::TDEFLATE) 
+      end
 
-    database.extend ScoutCabinet
-    database.persistence_path ||= path
-    database.persistence_class = tokyocabinet_class
+      flags = (write ? tokyocabinet_class::OWRITER | tokyocabinet_class::OCREAT : tokyocabinet_class::OREADER)
+      database.close 
 
-    database.open(path, tokyocabinet_class::OREADER)
+      if !database.open(path, flags)
+        ecode = database.ecode
+        raise "Open error: #{database.errmsg(ecode)}. Trying to open file #{path}"
+      end
 
-    database.define_singleton_method(:fingerprint){ "#{self.persistence_class}:#{self.persistence_path}" }
+      database.extend ScoutCabinet
+      database.persistence_path ||= path
+      database.persistence_class = tokyocabinet_class
 
-    Persist::CONNECTIONS[path] = database
+      database.open(path, tokyocabinet_class::OREADER)
 
-    database
-  end
+      database.define_singleton_method(:fingerprint){ "#{self.persistence_class}:#{self.persistence_path}" }
 
-  def close
-    @closed = true
-    @writable = false
-    super
-  end
+      Persist::CONNECTIONS[path] = database
 
-  def read(force = false)
-    return if ! @writable && ! @closed && ! force
-    self.close
-    if !self.open(@persistence_path, persistence_class::OREADER)
-      ecode = self.ecode
-      raise "Open error: #{self.errmsg(ecode)}. Trying to open file #{@persistence_path}"
+      database
     end
 
-    @writable = false
-    @closed = false
-
-    self
-  end
+    def close
+      @closed = true
+      @writable = false
+      super
+    end
 
-  def write?
-    @writable
-  end
+    def read(force = false)
+      return if ! @writable && ! @closed && ! force
+      self.close
+      if !self.open(@persistence_path, persistence_class::OREADER)
+        ecode = self.ecode
+        raise "Open error: #{self.errmsg(ecode)}. Trying to open file #{@persistence_path}"
+      end
 
-  def closed?
-    @closed
-  end
+      @writable = false
+      @closed = false
 
+      self
+    end
 
-  def write(force = true)
-    return if write? && ! closed? && ! force
-    self.close
+    def write?
+      @writable
+    end
 
-    if !self.open(@persistence_path, persistence_class::OWRITER)
-      ecode = self.ecode
-      raise "Open error: #{self.errmsg(ecode)}. Trying to open file #{@persistence_path}"
+    def closed?
+      @closed
     end
 
-    @writable = true
-    @closed = false
 
-    self
-  end
+    def write(force = true)
+      return if write? && ! closed? && ! force
+      self.close
 
-  def write_and_read
-    begin
-      write
-      yield
-    ensure
-      read
+      if !self.open(@persistence_path, persistence_class::OWRITER)
+        ecode = self.ecode
+        raise "Open error: #{self.errmsg(ecode)}. Trying to open file #{@persistence_path}"
+      end
+
+      @writable = true
+      @closed = false
+
+      self
+    end
+
+    def write_and_read
+      begin
+        write
+        yield
+      ensure
+        read
+      end
     end
-  end
 
   def write_and_close
     begin
@@ -139,4 +146,5 @@ module ScoutCabinet
   end
 
   alias load_stream importtsv
+  end
 end

data/lib/scout/persist/tsv/adapter/base.rb

@@ -23,6 +23,7 @@ module TSVAdapter
   end
 
   def save_annotation_hash
+    self.close
     self.with_write do
       self.orig_set(ANNOTATION_ATTR_HASH_KEY, ANNOTATION_ATTR_HASH_SERIALIZER.dump(self.annotation_hash))
     end
@@ -165,15 +166,6 @@ module TSVAdapter
     end
   end
 
-  def with_write(*args, &block)
-    if @write
-      yield
-    elsif @closed
-      write_and_close &block
-    else
-      write_and_read &block
-    end
-  end
 
   def close(*args)
     begin
@@ -250,12 +242,11 @@ module TSVAdapter
 
     lock do
       write(true) if closed? || ! write?
-      res = begin
-              yield
-            ensure
-              close
-            end
-      res
+      begin
+        yield
+      ensure
+        close
+      end
     end
   end
 
@@ -272,18 +263,13 @@ module TSVAdapter
       return yield
     else
       if self.read?
-        self.write_and_read do
-          return yield
-        end
+        self.write_and_read(&block)
       else
-        self.write_and_close do
-          return yield
-        end
+        self.write_and_close(&block)
       end
     end
   end
 
-
   def read_and_close
     if read? || write?
       begin

data/lib/scout/tsv/parser.rb

@@ -1,5 +1,15 @@
 require 'scout/named_array'
 module TSV
+  def self.acceptable_parser_options(func = nil)
+    if func.nil?
+      TSV.method(:parse_line).parameters.collect{|a| a.last } +
+        TSV.method(:parse_stream).parameters.collect{|a| a.last } +
+        TSV.method(:parse).parameters.collect{|a| a.last } - [:line, :block]
+    else
+      TSV.method(func).parameters.collect{|a| a.last }
+    end.uniq
+  end
+
   def self.cast_value(value, cast)
     if Array === value
       value.collect{|e| cast_value(e, cast) }

data/lib/scout/tsv/transformer.rb

@@ -175,5 +175,17 @@ module TSV
     end
     res
   end
+
+  def head(max=10)
+    res = self.annotate({})
+    transformer = Transformer.new self, res
+    i = 0
+    transformer.traverse do |k,v|
+      i += 1
+      break if i > max
+      [k, v]
+    end
+    res
+  end
 end
 

data/lib/scout/tsv/util/process.rb

@@ -30,9 +30,9 @@ module TSV
       when type == :flat
         self[key] = new_values
       else
-        if ! values[field_pos].frozen? && ((String === values[field_pos] && String === new_values) ||
+        if ! values[field_pos].frozen? && ! NamedArray === values && ((String === values[field_pos] && String === new_values) ||
           (Array === values[field_pos] && Array === new_values))
-           values[field_pos].replace new_values
+          values[field_pos].replace new_values
         else
           values[field_pos] = new_values
         end

data/lib/scout/workflow/definition.rb

@@ -13,8 +13,12 @@ module Workflow
 
   end
 
+  def to_s
+    @name || super
+  end
+
   def name
-    @name ||= self.to_s
+    @name || to_s
   end
 
   def helpers
@@ -192,7 +196,7 @@ module Workflow
           when 'true'
             dep.clean
           when 'recursive'
-            (dep.dependencies + dep.rec_dependencies).uniq.each do |d|
+            (dep.dependencies.to_a + dep.rec_dependencies.to_a).uniq.each do |d|
               next if d.overriden
               d.clean unless Scout::Config.get(:remove_dep, "task:#{d.task_signature}", "task:#{d.task_name}", "workflow:#{d.workflow.name}", :default => true).to_s == 'false'
             end

data/lib/scout/workflow/deployment/trace.rb

@@ -164,7 +164,7 @@ module Workflow
   def self.trace(seed_jobs, options = {})
     jobs = []
     seed_jobs.each do |step|
-      jobs += step.rec_dependencies + [step]
+      jobs += step.rec_dependencies.to_a + [step]
       step.info[:archived_info].each do |path,ainfo|
         next unless Hash === ainfo
         archived_step = Step.new path

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

@@ -1,5 +1,5 @@
 class Step
-  def rec_dependencies(connected = false, seen = [])
+  def rec_dependencies(connected = false, seen = Set.new)
     @rec_dependencies = {}
     @rec_dependencies[connected] ||= begin
                             direct_deps = []
@@ -8,11 +8,8 @@ class Step
                               next if connected && dep.done? && dep.updated?
                               direct_deps << dep
                             end if dependencies
-                            seen.concat direct_deps.collect{|d| d.path }
-                            seen.uniq!
-                            direct_deps.inject(direct_deps){|acc,d| acc.concat(d.rec_dependencies(connected, seen)); acc }
-                            direct_deps.uniq!
-                            direct_deps
+                            seen += direct_deps.collect{|d| d.path }
+                            direct_deps.inject(Set.new(direct_deps)){|acc,d| acc += d.rec_dependencies(connected, seen) }
                           end
   end
 

data/lib/scout/workflow/step/info.rb

@@ -1,5 +1,6 @@
+require 'scout/config'
 class Step
-  SERIALIZER = :marshal
+  SERIALIZER = Scout::Config.get(:serializer, :step_info, :info, :step, env: "SCOUT_SERIALIZER", default: :json)
   def info_file
     return nil if @path.nil?
     @info_file ||= begin
@@ -13,7 +14,11 @@ class Step
     info = begin
              Persist.load(info_file, SERIALIZER) || {}
            rescue
-             {status: :noinfo}
+             begin
+               Persist.load(info_file, :marshal) || {}
+             rescue
+               {status: :noinfo}
+             end
            end
     IndiferentHash.setup(info)
   end

data/lib/scout/workflow/task/info.rb

@@ -0,0 +1,99 @@
+require_relative 'inputs'
+module Workflow
+
+  def rec_inputs(task_name)
+    tasks[task_name].recursive_inputs.collect{|name, _| name }
+  end
+
+  def rec_input_types(task_name)
+    tasks[task_name].recursive_inputs.inject({}) do |acc,l|
+      name, type, desc, default, options = l
+      acc.merge!(name => type) unless acc.include?(name)
+      acc
+    end
+  end
+
+
+  def rec_input_descriptions(task_name)
+    tasks[task_name].recursive_inputs.inject({}) do |acc,l|
+      name, type, desc, default, options = l
+      acc.merge!(name => desc)  unless desc.nil? || acc.include?(name)
+      acc
+    end
+  end
+
+  def rec_input_defaults(task_name)
+    tasks[task_name].recursive_inputs.inject({}) do |acc,l|
+      name, type, desc, default, options = l
+      acc.merge!(name => default)  unless default.nil? || acc.include?(name)
+      acc
+    end
+  end
+
+  def rec_input_options(task_name)
+    tasks[task_name].recursive_inputs.inject({}) do |acc,l|
+      name, type, desc, default, options = l
+      acc.merge!(name => options) unless options.nil? unless acc.include?(name)
+      acc
+    end
+  end
+
+
+  def rec_input_use(task_name)
+    input_use = {}
+    task = self.tasks[task_name]
+    task.inputs.each do |name,_| 
+      input_use[name] ||= {} 
+      input_use[name][self] ||= []
+      input_use[name][self] << task_name
+    end
+
+    task.deps.inject(input_use) do |acc,p|
+      workflow, task_name = p
+      next if task_name.nil?
+      workflow.rec_input_use(task_name).each do |name,uses|
+        acc[name] ||= {}
+        uses.each do |workflow, task_names|
+          acc[name][workflow] ||= []
+          acc[name][workflow].concat(task_names)
+        end
+      end
+      acc
+    end if task.deps
+
+    input_use
+  end
+  def task_info(name)
+    name = name.to_sym
+    task = tasks[name]
+    raise "No '#{name}' task in '#{self.name}' Workflow" if task.nil?
+    id = File.join(self.name, name.to_s)
+    @task_info ||= {}
+    @task_info[id] ||= begin 
+                         description = task.description
+                         returns = task.returns
+
+                         inputs = rec_inputs(name).uniq
+                         input_types = rec_input_types(name)
+                         input_descriptions = rec_input_descriptions(name)
+                         input_use = rec_input_use(name)
+                         input_defaults = rec_input_defaults(name)
+                         input_options = rec_input_options(name)
+                         extension = task.extension
+
+                         dependencies = tasks[name].deps
+                         { :id => id,
+                           :description => description,
+                           :inputs => inputs,
+                           :input_types => input_types,
+                           :input_descriptions => input_descriptions,
+                           :input_defaults => input_defaults,
+                           :input_options => input_options,
+                           :input_use => input_use,
+                           :returns => returns,
+                           :dependencies => dependencies,
+                           :extension => extension
+                         }
+                       end
+  end
+end

data/lib/scout/workflow/task.rb

@@ -3,6 +3,7 @@ require 'scout/named_array'
 require_relative 'step'
 require_relative 'task/inputs'
 require_relative 'task/dependencies'
+require_relative 'task/info'
 
 module Task
   extend Annotation

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 10.7.3 ruby lib
+# stub: scout-gear 10.7.4 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "scout-gear".freeze
-  s.version = "10.7.3".freeze
+  s.version = "10.7.4".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 = "2025-01-17"
+  s.date = "2025-03-10"
   s.description = "Temporary files, logs, path, resources, persistence, workflows, TSV, etc.".freeze
   s.email = "mikisvaz@gmail.com".freeze
   s.executables = ["scout".freeze]
@@ -121,6 +121,7 @@ Gem::Specification.new do |s|
     "lib/scout/workflow/step/status.rb",
     "lib/scout/workflow/task.rb",
     "lib/scout/workflow/task/dependencies.rb",
+    "lib/scout/workflow/task/info.rb",
     "lib/scout/workflow/task/inputs.rb",
     "lib/scout/workflow/usage.rb",
     "lib/scout/workflow/util.rb",
@@ -235,6 +236,7 @@ Gem::Specification.new do |s|
     "test/scout/workflow/step/test_provenance.rb",
     "test/scout/workflow/step/test_status.rb",
     "test/scout/workflow/task/test_dependencies.rb",
+    "test/scout/workflow/task/test_info.rb",
     "test/scout/workflow/task/test_inputs.rb",
     "test/scout/workflow/test_definition.rb",
     "test/scout/workflow/test_documentation.rb",
@@ -249,7 +251,7 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://github.com/mikisvaz/scout-gear".freeze
   s.licenses = ["MIT".freeze]
-  s.rubygems_version = "3.5.23".freeze
+  s.rubygems_version = "3.6.5".freeze
   s.summary = "basic gear for scouts".freeze
 
   s.specification_version = 4

data/scout_commands/doc

@@ -26,12 +26,12 @@ end
 
 module_name = ARGV.first
 if module_name.nil?
-  puts Rbbt.doc.lib.scout.glob("**/*.md").collect{|f| File.basename(f.unset_extension) } * "\n"
+  puts Scout.doc.lib.scout.glob("**/*.md").collect{|f| File.basename(f.unset_extension) } * "\n"
 else
   begin
-    puts Rbbt.doc.lib.scout[module_name].find_with_extension('md', :lib).read
+    puts Scout.doc.lib.scout[module_name].find_with_extension('md', :lib).read
   rescue
-    puts Rbbt.doc.lib.scout.glob("**/*.md").select{|f| File.basename(f.unset_extension) == module_name }.first.read
+    puts Scout.doc.lib.scout.glob("**/*.md").select{|f| File.basename(f.unset_extension) == module_name }.first.read
   end
 end
 

data/scout_commands/workflow/task

@@ -19,6 +19,7 @@ $ #{$0} [<options>] <workflow> <task>
 --nostream Disable job streaming
 --update Update jobs with newer dependencies
 --deploy* Deploy mode: serial, local, or SLURM (default 'serial')
+--fork Fork and return path
 -jn--jobname* Name to use as job identifier
 -li--load_inputs* Directory with inputs files to load
 -pf--printpath Print the file path
@@ -39,8 +40,8 @@ task = workflow.tasks[task_name.to_sym] if task_name
 
 options[:help] = true if task.nil?
 
-help, provenance, clean, recursive_clean, clean_task, load_inputs, jobname, printpath, deploy, override_deps = IndiferentHash.process_options options, 
-  :help, :provenance, :clean, :recursive_clean, :clean_task, :load_inputs, :jobname, :printpath, :deploy, :override_deps,
+help, provenance, clean, recursive_clean, clean_task, load_inputs, jobname, printpath, deploy, override_deps, do_fork = IndiferentHash.process_options options, 
+  :help, :provenance, :clean, :recursive_clean, :clean_task, :load_inputs, :jobname, :printpath, :deploy, :override_deps, :fork,
   :deploy => 'serial'
 
 if help
@@ -92,6 +93,10 @@ end
 
 if provenance
   puts Step.prov_report(job)
+elsif do_fork
+  job.fork
+  puts job.path
+  exit 0
 else
   case deploy
   when "serial"

data/test/scout/knowledge_base/test_list.rb

@@ -14,10 +14,10 @@ class TestKnowledgeBaseQuery < Test::Unit::TestCase
       kb.save_list("bro_and_sis", list)
       assert_equal list, kb.load_list("bro_and_sis")
 
-      assert_include kb.list_files["Person"], "bro_and_sis"
+      assert_include kb.lists["Person"], "bro_and_sis"
       kb.delete_list("bro_and_sis")
 
-      refute kb.list_files["simple"]
+      refute kb.lists["simple"]
     end
   end
 
@@ -30,11 +30,11 @@ class TestKnowledgeBaseQuery < Test::Unit::TestCase
 
       assert_equal list, kb.load_list("bro_and_sis")
 
-      assert_include kb.list_files["simple"], "bro_and_sis"
+      assert_include kb.lists["simple"], "bro_and_sis"
 
       kb.delete_list("bro_and_sis")
 
-      refute kb.list_files["simple"]
+      refute kb.lists["simple"].any?
     end
   end
 end

data/test/scout/knowledge_base/test_registry.rb

@@ -12,5 +12,24 @@ class TestKnowlegeBase < Test::Unit::TestCase
       assert_include kb.all_databases, :brothers
     end
   end
+
+  def test_registry_identifiers
+    identifier =<<-EOF
+#Alias,Initials
+Clei,CC
+Miki,MV
+Guille,GC
+Isa,IV
+    EOF
+    TmpFile.with_dir do |dir|
+      TmpFile.with_file(identifier) do |identifier_file|
+        identifiers = TSV.open(identifier_file, sep: ",", type: :single)
+        brothers = datafile_test(:person).brothers
+        kb = KnowledgeBase.new dir
+        kb.register :brothers, brothers, identifiers: identifiers
+        assert_include kb.get_index(:brothers, source: "=>Initials"), "CC~Guille"
+      end
+    end
+  end
 end
 

data/test/scout/persist/test_tsv.rb

@@ -74,6 +74,7 @@ row2    a    a    id3
     assert_include tsv.keys, 'row1'
     assert_include tsv.keys, 'row2'
 
+    tsv.close
     assert_nothing_raised do
       tsv = Persist.persist("TEST Persist TSV", :HDB) do 
         raise

data/test/scout/test_association.rb

@@ -61,5 +61,20 @@ class TestAssociation < Test::Unit::TestCase
     database = Association.database(datadir_test.person.brothers, source: "Older=~Older (Alias)=>Name", persist: true)
     assert database.respond_to?(:persistence_path)
   end
+
+  def test_extra_options
+    file=<<-EOF
+#: :extra_option=:test
+#Key,Value
+k,v
+    EOF
+
+    TmpFile.with_path(file.gsub(',', "\t")) do |f|
+      assert_nothing_raised do
+        Association.open(f, target: "Value", source: "Key")
+      end
+    end
+
+  end
 end
 

data/test/scout/test_tsv.rb

@@ -427,4 +427,19 @@ row2    A    B    Id3
       assert_equal %w(a aa aaa), tsv["row1"]
     end
   end
+
+  def test_number_key
+    content =<<-EOF
+#Id    ValueA    ValueB    OtherID
+1    a|aa|aaa    b    Id1|Id2
+2    A    B    Id3
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(filename, :sep => /\s+/, field: "ValueB")
+      assert_equal "b", tsv["1"]
+    end
+
+
+  end
 end

data/test/scout/tsv/test_parser.rb

@@ -317,4 +317,8 @@ k4    a|A    b|B
       assert Open.read(tmp_logfile).include?("directly into")
     end
   end
+
+  def test_acceptable_parser_options
+    assert_include TSV.acceptable_parser_options, :namespace
+  end
 end

data/test/scout/tsv/test_transformer.rb

@@ -153,4 +153,17 @@ row2    A2    B2
     tsv = TSV.open(content)
     assert_equal %w(A1), tsv.to_double["row1"]["ValueA"]
   end
+
+  def test_head
+    content =<<-EOF
+#: :sep=" "
+#ID    ValueA    ValueB
+row1    A1    B1
+row2    A2    B2
+row3    A3    B3
+    EOF
+
+    tsv = TSV.open(content)
+    assert_equal ["row1", "row2"], tsv.head(2).keys
+  end
 end

data/test/scout/workflow/step/test_info.rb

@@ -3,6 +3,17 @@ require File.expand_path(__FILE__).sub(%r(.*/test/), '').sub(/test_(.*)\.rb/,'\1
 require 'scout/workflow'
 
 class TestStepInfo < Test::Unit::TestCase
+  def test_benchmark
+    i = {a:1, b: [1,2], c: "String"}
+    times = 100000
+    Misc.benchmark(times) do
+      Marshal.dump(i)
+    end
+    Misc.benchmark(times) do
+      i.to_json
+    end
+  end
+
   def test_dependency
     TmpFile.with_file do |tmpdir|
       Path.setup(tmpdir)

data/test/scout/workflow/task/test_info.rb

@@ -0,0 +1,22 @@
+require File.expand_path(__FILE__).sub(%r(/test/.*), '/test/test_helper.rb')
+require File.expand_path(__FILE__).sub(%r(.*/test/), '').sub(/test_(.*)\.rb/,'\1')
+
+require 'scout/workflow'
+class TestWorkflowInfo < Test::Unit::TestCase
+  def test_task_info
+    m = Module.new do
+      extend Workflow
+      self.name = "TestWF"
+
+      input :option1
+      task :step1 do end
+
+      dep :step1
+      input :option2
+      task :step2 do end
+    end
+    info = m.task_info :step2
+    assert_equal "TestWF/step2", info[:id]
+  end
+end
+

metadata

@@ -1,14 +1,13 @@
 --- !ruby/object:Gem::Specification
 name: scout-gear
 version: !ruby/object:Gem::Version
-  version: 10.7.3
+  version: 10.7.4
 platform: ruby
 authors:
 - Miguel Vazquez
-autorequire: 
 bindir: bin
 cert_chain: []
-date: 2025-01-17 00:00:00.000000000 Z
+date: 2025-03-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: scout-essentials
@@ -233,6 +232,7 @@ files:
 - lib/scout/workflow/step/status.rb
 - lib/scout/workflow/task.rb
 - lib/scout/workflow/task/dependencies.rb
+- lib/scout/workflow/task/info.rb
 - lib/scout/workflow/task/inputs.rb
 - lib/scout/workflow/usage.rb
 - lib/scout/workflow/util.rb
@@ -347,6 +347,7 @@ files:
 - test/scout/workflow/step/test_provenance.rb
 - test/scout/workflow/step/test_status.rb
 - test/scout/workflow/task/test_dependencies.rb
+- test/scout/workflow/task/test_info.rb
 - test/scout/workflow/task/test_inputs.rb
 - test/scout/workflow/test_definition.rb
 - test/scout/workflow/test_documentation.rb
@@ -362,7 +363,6 @@ homepage: http://github.com/mikisvaz/scout-gear
 licenses:
 - MIT
 metadata: {}
-post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
@@ -377,8 +377,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.5.23
-signing_key: 
+rubygems_version: 3.6.5
 specification_version: 4
 summary: basic gear for scouts
 test_files: []