scout-gear 6.0.0 → 7.2.0

data/lib/scout/workflow/task.rb

@@ -4,7 +4,7 @@ require_relative 'task/inputs'
 
 module Task
   extend MetaExtension
-  extension_attr :name, :type, :inputs, :deps, :directory, :description
+  extension_attr :name, :type, :inputs, :deps, :directory, :description, :returns, :extension, :workflow
 
   DEFAULT_NAME = "Default"
 
@@ -54,7 +54,7 @@ module Task
       resolved_inputs = {}
       inputs.each do |k,v|
         if Symbol === v
-          input_dep = dependencies.select{|d| d.task_name == v}.first
+          input_dep = dependencies.select{|d| d.task_name == v }.first
           resolved_inputs[k] = input_dep || inputs[v] || k
         else
           resolved_inputs[k] = v
@@ -143,13 +143,14 @@ module Task
     non_default_inputs.concat provided_inputs.keys.select{|k| String === k && k.include?("#") } if Hash === provided_inputs
 
     if non_default_inputs.any?
-      hash = Misc.digest(:inputs => input_hash, :non_default_inputs => non_default_inputs, :dependencies => dependencies)
-      Log.debug "Hash #{name} - #{hash}: #{Misc.digest_str(:inputs => inputs, :dependencies => dependencies)}"
+      hash = Misc.digest(:inputs => input_hash, :dependencies => dependencies)
+      Log.debug "Hash #{name} - #{hash}: #{Misc.digest_str(:inputs => inputs, :non_default_inputs => non_default_inputs, :dependencies => dependencies)}"
       id = [id, hash] * "_"
     end
 
     path = directory[id]
 
+    NamedArray.setup(inputs, @inputs.collect{|i| i[0] }) if @inputs
     Step.new path.find, inputs, dependencies, &self
   end
 end

data/lib/scout/workflow/usage.rb

@@ -34,7 +34,6 @@ module Task
         str.puts Log.color :yellow, dep + ":"
         str.puts
         str.puts SOPT.input_array_doc(inputs)
-        str.puts
       end
 
       #task_inputs = dep_inputs deps, workflow
@@ -72,6 +71,7 @@ module Task
       str.puts
     end
 
+    str.puts
     str.puts Log.color(:magenta, "Returns: ") << Log.color(:blue, type.to_s) << "\n"
     str.puts
 

data/lib/scout/workflow.rb

@@ -24,17 +24,25 @@ module Workflow
     base.libdir = Path.setup(libdir).tap{|p| p.resource = base}
   end
 
-  def self.require_workflow(workflow)
-    workflow = Path.setup('workflows')[workflow]["workflow.rb"] unless Open.exists?(workflow)
+  def self.require_workflow(workflow_name)
+    workflow = workflow_name 
+    workflow = Path.setup('workflows')[workflow_name]["workflow.rb"] unless Open.exists?(workflow)
+    workflow = Path.setup('workflows')[Misc.snake_case(workflow_name)]["workflow.rb"] unless Open.exists?(workflow)
+    workflow = Path.setup('workflows')[Misc.camel_case(workflow_name)]["workflow.rb"] unless Open.exists?(workflow)
     if Open.exists?(workflow)
       workflow = workflow.find if Path === workflow
+      $LOAD_PATH.unshift(File.join(File.dirname(workflow), 'lib'))
       load workflow
+    else
+      raise "Workflow #{workflow_name} not found"
     end
     workflows.last
   end
 
   def job(name, *args)
     task = tasks[name]
-    task.job(*args)
+    step = task.job(*args)
+    step.extend step_module
+    step
   end
 end

data/lib/scout-gear.rb

@@ -7,3 +7,4 @@ require_relative 'scout/simple_opt'
 require_relative 'scout/resource'
 require_relative 'scout/resource/scout'
 require_relative 'scout/persist'
+require_relative 'scout/tsv'

data/lib/scout.rb

@@ -1 +1,2 @@
 require 'workflow-scout'
+require 'rbbt-scout'

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 6.0.0 ruby lib
+# stub: scout-gear 7.2.0 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "scout-gear".freeze
-  s.version = "6.0.0"
+  s.version = "7.2.0"
 
   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 = "2023-04-29"
+  s.date = "2023-05-09"
   s.description = "Temporary files, logs, etc.".freeze
   s.email = "mikisvaz@gmail.com".freeze
   s.executables = ["scout".freeze]
@@ -28,10 +28,12 @@ Gem::Specification.new do |s|
     "Rakefile",
     "VERSION",
     "bin/scout",
+    "lib/rbbt-scout.rb",
     "lib/scout-gear.rb",
     "lib/scout.rb",
     "lib/scout/cmd.rb",
     "lib/scout/concurrent_stream.rb",
+    "lib/scout/config.rb",
     "lib/scout/exceptions.rb",
     "lib/scout/indiferent_hash.rb",
     "lib/scout/indiferent_hash/case_insensitive.rb",
@@ -50,6 +52,8 @@ Gem::Specification.new do |s|
     "lib/scout/misc/format.rb",
     "lib/scout/misc/insist.rb",
     "lib/scout/misc/monitor.rb",
+    "lib/scout/misc/system.rb",
+    "lib/scout/named_array.rb",
     "lib/scout/open.rb",
     "lib/scout/open/lock.rb",
     "lib/scout/open/remote.rb",
@@ -68,6 +72,7 @@ Gem::Specification.new do |s|
     "lib/scout/resource/produce.rb",
     "lib/scout/resource/produce/rake.rb",
     "lib/scout/resource/scout.rb",
+    "lib/scout/resource/software.rb",
     "lib/scout/resource/util.rb",
     "lib/scout/semaphore.rb",
     "lib/scout/simple_opt.rb",
@@ -77,6 +82,16 @@ Gem::Specification.new do |s|
     "lib/scout/simple_opt/parse.rb",
     "lib/scout/simple_opt/setup.rb",
     "lib/scout/tmpfile.rb",
+    "lib/scout/tsv.rb",
+    "lib/scout/tsv/dumper.rb",
+    "lib/scout/tsv/index.rb",
+    "lib/scout/tsv/parser.rb",
+    "lib/scout/tsv/path.rb",
+    "lib/scout/tsv/persist.rb",
+    "lib/scout/tsv/persist/adapter.rb",
+    "lib/scout/tsv/persist/tokyocabinet.rb",
+    "lib/scout/tsv/traverse.rb",
+    "lib/scout/tsv/util.rb",
     "lib/scout/work_queue.rb",
     "lib/scout/work_queue/socket.rb",
     "lib/scout/work_queue/worker.rb",
@@ -84,8 +99,12 @@ Gem::Specification.new do |s|
     "lib/scout/workflow/definition.rb",
     "lib/scout/workflow/documentation.rb",
     "lib/scout/workflow/step.rb",
+    "lib/scout/workflow/step/config.rb",
+    "lib/scout/workflow/step/dependencies.rb",
+    "lib/scout/workflow/step/file.rb",
     "lib/scout/workflow/step/info.rb",
     "lib/scout/workflow/step/load.rb",
+    "lib/scout/workflow/step/provenance.rb",
     "lib/scout/workflow/task.rb",
     "lib/scout/workflow/task/inputs.rb",
     "lib/scout/workflow/usage.rb",
@@ -102,6 +121,7 @@ Gem::Specification.new do |s|
     "scout_commands/workflow/task_old",
     "share/color/color_names",
     "share/color/diverging_colors.hex",
+    "share/software/install_helpers",
     "test/scout/indiferent_hash/test_case_insensitive.rb",
     "test/scout/indiferent_hash/test_options.rb",
     "test/scout/log/test_color.rb",
@@ -109,6 +129,7 @@ Gem::Specification.new do |s|
     "test/scout/misc/test_digest.rb",
     "test/scout/misc/test_filesystem.rb",
     "test/scout/misc/test_insist.rb",
+    "test/scout/misc/test_system.rb",
     "test/scout/open/test_lock.rb",
     "test/scout/open/test_remote.rb",
     "test/scout/open/test_stream.rb",
@@ -120,6 +141,7 @@ Gem::Specification.new do |s|
     "test/scout/persist/test_serialize.rb",
     "test/scout/resource/test_path.rb",
     "test/scout/resource/test_produce.rb",
+    "test/scout/resource/test_software.rb",
     "test/scout/resource/test_util.rb",
     "test/scout/simple_opt/test_doc.rb",
     "test/scout/simple_opt/test_get.rb",
@@ -127,22 +149,35 @@ Gem::Specification.new do |s|
     "test/scout/simple_opt/test_setup.rb",
     "test/scout/test_cmd.rb",
     "test/scout/test_concurrent_stream.rb",
+    "test/scout/test_config.rb",
     "test/scout/test_indiferent_hash.rb",
     "test/scout/test_log.rb",
     "test/scout/test_meta_extension.rb",
     "test/scout/test_misc.rb",
+    "test/scout/test_named_array.rb",
     "test/scout/test_open.rb",
     "test/scout/test_path.rb",
     "test/scout/test_persist.rb",
     "test/scout/test_resource.rb",
     "test/scout/test_semaphore.rb",
     "test/scout/test_tmpfile.rb",
+    "test/scout/test_tsv.rb",
     "test/scout/test_work_queue.rb",
     "test/scout/test_workflow.rb",
+    "test/scout/tsv/persist/test_adapter.rb",
+    "test/scout/tsv/persist/test_tokyocabinet.rb",
+    "test/scout/tsv/test_dumper.rb",
+    "test/scout/tsv/test_index.rb",
+    "test/scout/tsv/test_parser.rb",
+    "test/scout/tsv/test_persist.rb",
+    "test/scout/tsv/test_traverse.rb",
+    "test/scout/tsv/test_util.rb",
     "test/scout/work_queue/test_socket.rb",
     "test/scout/work_queue/test_worker.rb",
+    "test/scout/workflow/step/test_dependencies.rb",
     "test/scout/workflow/step/test_info.rb",
     "test/scout/workflow/step/test_load.rb",
+    "test/scout/workflow/step/test_provenance.rb",
     "test/scout/workflow/task/test_inputs.rb",
     "test/scout/workflow/test_definition.rb",
     "test/scout/workflow/test_documentation.rb",

data/scout_commands/find

@@ -69,7 +69,7 @@ end if resource
 
 path = (resource || Scout)[path.dup]
 
-if where.nil? || where == 'all' || path.search_paths.include?(where.to_sym)
+if where.nil? || where == 'all' || path.path_maps.include?(where.to_sym)
   location = path.find(where)
 
   if Array === location

data/scout_commands/workflow/task

@@ -13,6 +13,7 @@ $ #{$0} [<options>] <workflow> <task>
 -h--help Print this help
 -jn--job_name* Name to use as job identifier
 -pf--print_filepath Print the file path
+-prov--provenance Print the step provenance
 -cl--clean Clean the last step
 -rcl--recursive_clean Clean all steps
 EOF
@@ -22,7 +23,8 @@ workflow_name, task_name = ARGV
 raise MissingParameterException.new :workflow if workflow_name.nil?
 
 workflow = Workflow.require_workflow workflow_name
-task = workflow.tasks[task_name.to_sym] if task_name
+task_name = task_name.to_sym if task_name
+task = workflow.tasks[task_name.to_sym] 
 
 options[:help] = true if task.nil?
 
@@ -38,20 +40,24 @@ if options[:help]
 end
 
 job_options = task.get_SOPT(task)
-job = task.job(options[:job_name], job_options)
+job = workflow.job(task_name, options[:job_name], job_options)
 
 job.recursive_clean if options[:recursive_clean]
 job.clean if options[:clean]
 
-job.run
-
-if options[:print_filepath]
-  path = job.path
-  path = path.find if Path === path
-  puts path
+if options[:provenance]
+  puts Step.prov_report(job)
 else
-  if ! Open.consume_stream(job.stream, false, STDOUT, false).end_with? "\n"
-    puts
+  job.run unless job.done?
+
+  if options[:print_filepath]
+    path = job.path
+    path = path.find if Path === path
+    puts path
+  else
+    if ! ((c = Open.consume_stream(job.get_stream, false, STDOUT, false)) && c.end_with?("\n"))
+      puts
+    end
   end
 end