scout-gear 10.0.1 → 10.1.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 5af158e978a724dacd722c9584cb4fd3b7f46fff8a4619272b1d2c2258418600
-  data.tar.gz: 6bd5da8eba38542376f4b5566154fc16105f3742ba0758a37139d0ff9679d06e
+  metadata.gz: ab089af23ec3cb6d23db1190f712d2a981db96e818572aa5b561227a9601b9b8
+  data.tar.gz: d72662def6d6b7207d015d7cea613a1882578efe201ed391f79d37027ab7c70e
 SHA512:
-  metadata.gz: e9f6f4d2a5e223d740332b627c9606907d69536696f477401087b4f72bee09d1b374d060275ecb3fad5e38c27010417d36d661d985c58d71e3cec4bf04bbcbf7
-  data.tar.gz: a7b8e5d1bfd1057bd93cfbd4a2439bccf0e28848f3e08923c81da8bcc2fe1a489ffb2e220587ecb4533ad0cf7edcf506f3c4557955dfa11356d816b87b379968
+  metadata.gz: d5b67fdc030ad2ed3dd4d9da47d7f12068b71f14a1ae390f65c411bc2e835ac2da1648fccb554cbda4a3a56bdf6b16fc63080620453e75481590622cfd883247
+  data.tar.gz: 97fa38ef8db895d3a8aa05d2e4e521bb98d28924b389429994f6e98bceb7bfa7ad74920676c17b8b124bf288700e80078909ea20a84c3c0b24efd0cf7b0632cb

data/.vimproject

@@ -28,81 +28,6 @@ scout-gear=/$PWD filter="*.rb *.yaml" {
   rbbt-scout.rb
   scout.rb
   scout=scout{
-   meta_extension.rb
-   exceptions.rb
-
-   misc.rb
-   misc=misc{
-    format.rb
-    insist.rb
-    digest.rb
-    filesystem.rb
-    monitor.rb
-    system.rb
-   }
-   named_array.rb
-   indiferent_hash.rb
-   indiferent_hash=indiferent_hash{
-    case_insensitive.rb
-    options.rb
-   }
-   log.rb
-   log=log{
-    color.rb
-    color_class.rb
-    fingerprint.rb
-    progress.rb
-    progress=progress{
-     report.rb
-     util.rb
-    }
-    trap.rb
-   }
-   tmpfile.rb
-   simple_opt.rb
-   simple_opt=simple_opt{
-    accessor.rb
-    doc.rb
-    parse.rb
-    get.rb
-    setup.rb
-   }
-   path.rb
-   path=path{
-    find.rb
-    util.rb
-    tmpfile.rb
-   }
-   concurrent_stream.rb
-   cmd.rb
-   open.rb
-   open=open{
-    lock.rb
-    remote.rb
-    stream.rb
-    util.rb
-    lock=lock{
-     lockfile.rb
-    }
-   }
-   resource.rb
-   resource=resource{
-    produce.rb
-    produce=produce{
-     rake.rb
-    }
-    software.rb
-    scout.rb
-    util.rb
-    path.rb
-   }
-   config.rb
-   persist.rb
-   persist=persist{
-    serialize.rb
-    open.rb
-    path.rb
-   }
    workflow.rb
    workflow=workflow{
     definition.rb
@@ -146,6 +71,7 @@ scout-gear=/$PWD filter="*.rb *.yaml" {
      process.rb
      unzip.rb
      reorder.rb
+     sort.rb
     }
     parser.rb
     dumper.rb
@@ -173,9 +99,6 @@ scout-gear=/$PWD filter="*.rb *.yaml" {
     sync.rb
     step.rb
    }
-   hpc=hpc{
-    slurm.rb
-   }
   }
  }
  test=test {

data/Rakefile

@@ -35,6 +35,7 @@ Juwelier::RubygemsDotOrgTasks.new
 
 require 'rake/testtask'
 Rake::TestTask.new(:test) do |test|
+  ENV["SCOUT_LOG"] = "NONE"
   test.libs << 'lib' << 'test'
   test.pattern = 'test/**/test_*.rb'
   test.verbose = true

data/VERSION

@@ -1 +1 @@
-10.0.1
+10.1.0

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

@@ -0,0 +1,74 @@
+module TSV
+  def sort_by(field = nil, just_keys = false, &block)
+    field = :all if field.nil?
+
+    if field == :all
+      elems = collect
+    else
+      elems = []
+      case type
+      when :single
+        through :key, field do |key, field|
+          elems << [key, field]
+        end
+      when :list, :flat
+        through :key, field do |key, fields|
+          elems << [key, fields.first]
+        end
+      when :double
+        through :key, field do |key, fields|
+          elems << [key, fields.first]
+        end
+      end
+    end
+
+    if not block_given?
+      if fields == :all
+        if just_keys
+          keys = elems.sort_by{|key, value| key }.collect{|key, values| key}
+          keys = prepare_entity(keys, key_field, entity_options.merge(:dup_array => true))
+        else
+          elems.sort_by{|key, value| key }
+        end
+      else
+        sorted = elems.sort do |a, b| 
+          a_value = a.last
+          b_value = b.last
+          a_empty = a_value.nil? or (a_value.respond_to?(:empty?) and a_value.empty?)
+          b_empty = b_value.nil? or (b_value.respond_to?(:empty?) and b_value.empty?)
+          case
+          when (a_empty and b_empty)
+            0
+          when a_empty
+            -1
+          when b_empty
+            1
+          when Array === a_value
+            if a_value.length == 1 and b_value.length == 1
+              a_value.first <=> b_value.first
+            else
+              a_value.length <=> b_value.length
+            end
+          else
+            a_value <=> b_value
+          end
+        end
+        if just_keys
+          keys = sorted.collect{|key, value| key}
+          keys = prepare_entity(keys, key_field, entity_options.merge(:dup_array => true)) unless @unnamed
+          keys
+        else
+          sorted.collect{|key, value| [key, self[key]]}
+        end
+      end
+    else
+      if just_keys
+        keys = elems.sort_by(&block).collect{|key, value| key}
+        keys = prepare_entity(keys, key_field, entity_options.merge(:dup_array => true)) unless @unnamed
+        keys
+      else
+        elems.sort_by(&block).collect{|key, value| [key, self[key]]}
+      end
+    end
+  end
+end

data/lib/scout/tsv/util.rb

@@ -6,6 +6,7 @@ require_relative 'util/process'
 require_relative 'util/select'
 require_relative 'util/reorder'
 require_relative 'util/unzip'
+require_relative 'util/sort'
 module TSV
   def self.identify_field(key_field, fields, name, strict: nil)
     return :key if name == :key || (! strict && NamedArray.field_match(key_field, name))

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

@@ -31,6 +31,7 @@ class Step
     Open.rm tmp_path if Open.exist?(tmp_path)
     Open.rm info_file if Open.exist?(info_file)
     Open.rm_rf files_dir if Open.exist?(files_dir)
+    self
   end
 
   def self.clean(file)

data/lib/scout/workflow/step.rb

@@ -124,62 +124,62 @@ class Step
     return @result || self.load if done?
     prepare_dependencies
     run_dependencies
-    @result = 
-      begin
-        Persist.persist(name, type, :path => path, :tee_copies => tee_copies) do
-          clear_info
-          input_names = (task.respond_to?(:inputs) && task.inputs) ? task.inputs.collect{|name,_| name} : []
-          merge_info :status => :start, :start => Time.now,
-            :pid => Process.pid, :pid_hostname => Misc.hostname, 
-            :inputs => MetaExtension.purge(inputs), :input_names => input_names, :type => type,
-            :dependencies => dependencies.collect{|d| d.path }
-
-          @result = exec
-
-          if @result.nil? && File.exist?(self.tmp_path) && ! File.exist?(self.path)
-            Open.mv self.tmp_path, self.path
-          else
-            @result = @result.stream if @result.respond_to?(:stream)
-          end
+    begin
+      @result = Persist.persist(name, type, :path => path, :tee_copies => tee_copies) do
+        clear_info
+        input_names = (task.respond_to?(:inputs) && task.inputs) ? task.inputs.collect{|name,_| name} : []
+        merge_info :status => :start, :start => Time.now,
+          :pid => Process.pid, :pid_hostname => Misc.hostname, 
+          :inputs => MetaExtension.purge(inputs), :input_names => input_names, :type => type,
+          :dependencies => dependencies.collect{|d| d.path }
+
+        @exec_result = exec
+
+        if @exec_result.nil? && File.exist?(self.tmp_path) && ! File.exist?(self.path)
+          Open.mv self.tmp_path, self.path
+        else
+          @exec_result = @exec_result.stream if @exec_result.respond_to?(:stream)
+        end
 
-          @result
+        @exec_result
 
-          if (IO === @result || StringIO === @result) && (ENV["SCOUT_NO_STREAM"] == "true" || ! stream)
-            Open.sensible_write(self.path, @result)
-            @result = nil
-          else
-            @result
-          end
+        if (IO === @exec_result || StringIO === @exec_result) && (ENV["SCOUT_NO_STREAM"] == "true" || ! stream)
+          Open.sensible_write(self.path, @exec_result)
+          @exec_result = nil
+        else
+          @exec_result
         end
-      rescue Exception => e
-        merge_info :status => :error, :exception => e, :end => Time.now
-        abort_dependencies
-        raise e
-      ensure
-        if ! (error? || aborted?)
-          if streaming?
-            ConcurrentStream.setup(@result) do
-              merge_info :status => :done, :end => Time.now
-            end
+      end
+    rescue Exception => e
+      merge_info :status => :error, :exception => e, :end => Time.now
+      abort_dependencies
+      raise e
+    ensure
+      if ! (error? || aborted?)
+        if streaming?
+          ConcurrentStream.setup(@result) do
+            merge_info :status => :done, :end => Time.now
+          end
 
-            @result.abort_callback = proc do |exception|
-              if exception.nil? || Aborted === exception || Interrupt === exception
-                merge_info :status => :aborted, :end => Time.now
-              else
-                begin
-                  merge_info :status => :error, :exception => exception, :end => Time.now
-                rescue Exception
-                  Log.exception $!
-                end
+          @result.abort_callback = proc do |exception|
+            if exception.nil? || Aborted === exception || Interrupt === exception
+              merge_info :status => :aborted, :end => Time.now
+            else
+              begin
+                merge_info :status => :error, :exception => exception, :end => Time.now
+              rescue Exception
+                Log.exception $!
               end
             end
-
-            log :streaming
-          else
-            merge_info :status => :done, :end => Time.now
           end
+
+
+          log :streaming
+        else
+          merge_info :status => :done, :end => Time.now
         end
       end
+    end
   end
 
   def fork

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 10.0.1 ruby lib
+# stub: scout-gear 10.1.0 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "scout-gear".freeze
-  s.version = "10.0.1"
+  s.version = "10.1.0"
 
   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 = "2023-07-04"
+  s.date = "2023-07-07"
   s.description = "Temporary files, logs, path, resources, persistence, workflows, TSV, etc.".freeze
   s.email = "mikisvaz@gmail.com".freeze
   s.executables = ["scout".freeze]
@@ -60,6 +60,7 @@ Gem::Specification.new do |s|
     "lib/scout/tsv/util/process.rb",
     "lib/scout/tsv/util/reorder.rb",
     "lib/scout/tsv/util/select.rb",
+    "lib/scout/tsv/util/sort.rb",
     "lib/scout/tsv/util/unzip.rb",
     "lib/scout/work_queue.rb",
     "lib/scout/work_queue/exceptions.rb",
@@ -132,6 +133,7 @@ Gem::Specification.new do |s|
     "test/scout/tsv/util/test_process.rb",
     "test/scout/tsv/util/test_reorder.rb",
     "test/scout/tsv/util/test_select.rb",
+    "test/scout/tsv/util/test_sort.rb",
     "test/scout/tsv/util/test_unzip.rb",
     "test/scout/work_queue/test_socket.rb",
     "test/scout/work_queue/test_worker.rb",
@@ -155,7 +157,7 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://github.com/mikisvaz/scout-gear".freeze
   s.licenses = ["MIT".freeze]
-  s.rubygems_version = "3.5.0.dev".freeze
+  s.rubygems_version = "3.4.13".freeze
   s.summary = "basic gear for scouts".freeze
 
   s.specification_version = 4

data/scout_commands/workflow/task

@@ -54,10 +54,10 @@ if help
   exit 0
 end
 
+job_inputs = task.get_SOPT
+
 if load_inputs
-  job_inputs = workflow.tasks[task_name].load_inputs(load_inputs)
-else
-  job_inputs = task.get_SOPT
+  job_inputs = job_inputs.merge(workflow.tasks[task_name].load_inputs(load_inputs))
 end
 
 if override_deps

data/test/scout/tsv/test_open.rb

@@ -137,7 +137,7 @@ row2 aa bb cc
     dumper =  TSV::Dumper.new :key_field => "Key", :fields => ["Field"], type: :single
     dumper.init
     assert_raise ScoutException do
-      Log.with_severity 0 do
+      Log.with_severity 7 do
         i = 0
         TSV.traverse lines, :into => dumper, cpus: 3 do |l|
           raise ScoutException if i > 10

data/test/scout/tsv/util/test_sort.rb

@@ -0,0 +1,23 @@
+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/tsv'
+
+class TestClass < Test::Unit::TestCase
+
+  def test_sort_by
+    content =<<-EOF
+#ID ValueA ValueB Comment
+row1 a B c
+row2 A b C
+    EOF
+
+    TmpFile.with_file(content) do |filename|
+      tsv = TSV.open(File.open(filename), :type => :list, :sep => /\s/)
+      assert_equal %w(row2 row1), tsv.sort_by("ValueA").collect{|k,v| k}
+      assert_equal %w(row1 row2), tsv.sort_by("ValueB").collect{|k,v| k}
+    end
+  end
+
+end
+

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: scout-gear
 version: !ruby/object:Gem::Version
-  version: 10.0.1
+  version: 10.1.0
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-07-04 00:00:00.000000000 Z
+date: 2023-07-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: scout-essentials
@@ -172,6 +172,7 @@ files:
 - lib/scout/tsv/util/process.rb
 - lib/scout/tsv/util/reorder.rb
 - lib/scout/tsv/util/select.rb
+- lib/scout/tsv/util/sort.rb
 - lib/scout/tsv/util/unzip.rb
 - lib/scout/work_queue.rb
 - lib/scout/work_queue/exceptions.rb
@@ -244,6 +245,7 @@ files:
 - test/scout/tsv/util/test_process.rb
 - test/scout/tsv/util/test_reorder.rb
 - test/scout/tsv/util/test_select.rb
+- test/scout/tsv/util/test_sort.rb
 - test/scout/tsv/util/test_unzip.rb
 - test/scout/work_queue/test_socket.rb
 - test/scout/work_queue/test_worker.rb
@@ -283,7 +285,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.5.0.dev
+rubygems_version: 3.4.13
 signing_key: 
 specification_version: 4
 summary: basic gear for scouts