scout-gear 9.0.0 → 10.0.1

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 9.0.0 ruby lib
+# stub: scout-gear 10.0.1 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "scout-gear".freeze
-  s.version = "9.0.0"
+  s.version = "10.0.1"
 
   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 = "2023-06-27"
+  s.date = "2023-07-04"
   s.description = "Temporary files, logs, path, resources, persistence, workflows, TSV, etc.".freeze
   s.email = "mikisvaz@gmail.com".freeze
   s.executables = ["scout".freeze]
@@ -33,65 +33,12 @@ Gem::Specification.new do |s|
     "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",
-    "lib/scout/indiferent_hash/options.rb",
-    "lib/scout/log.rb",
-    "lib/scout/log/color.rb",
-    "lib/scout/log/color_class.rb",
-    "lib/scout/log/fingerprint.rb",
-    "lib/scout/log/progress.rb",
-    "lib/scout/log/progress/report.rb",
-    "lib/scout/log/progress/util.rb",
-    "lib/scout/log/trap.rb",
-    "lib/scout/meta_extension.rb",
-    "lib/scout/misc.rb",
-    "lib/scout/misc/digest.rb",
-    "lib/scout/misc/filesystem.rb",
-    "lib/scout/misc/format.rb",
-    "lib/scout/misc/helper.rb",
-    "lib/scout/misc/insist.rb",
-    "lib/scout/misc/monitor.rb",
-    "lib/scout/misc/system.rb",
-    "lib/scout/named_array.rb",
     "lib/scout/offsite.rb",
+    "lib/scout/offsite/exceptions.rb",
     "lib/scout/offsite/ssh.rb",
     "lib/scout/offsite/step.rb",
     "lib/scout/offsite/sync.rb",
-    "lib/scout/open.rb",
-    "lib/scout/open/lock.rb",
-    "lib/scout/open/lock/lockfile.rb",
-    "lib/scout/open/remote.rb",
-    "lib/scout/open/stream.rb",
-    "lib/scout/open/util.rb",
-    "lib/scout/path.rb",
-    "lib/scout/path/find.rb",
-    "lib/scout/path/tmpfile.rb",
-    "lib/scout/path/util.rb",
-    "lib/scout/persist.rb",
-    "lib/scout/persist/open.rb",
-    "lib/scout/persist/path.rb",
-    "lib/scout/persist/serialize.rb",
-    "lib/scout/resource.rb",
-    "lib/scout/resource/open.rb",
-    "lib/scout/resource/path.rb",
-    "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",
-    "lib/scout/simple_opt/accessor.rb",
-    "lib/scout/simple_opt/doc.rb",
-    "lib/scout/simple_opt/get.rb",
-    "lib/scout/simple_opt/parse.rb",
-    "lib/scout/simple_opt/setup.rb",
-    "lib/scout/tmpfile.rb",
     "lib/scout/tsv.rb",
     "lib/scout/tsv/attach.rb",
     "lib/scout/tsv/change_id.rb",
@@ -115,6 +62,7 @@ Gem::Specification.new do |s|
     "lib/scout/tsv/util/select.rb",
     "lib/scout/tsv/util/unzip.rb",
     "lib/scout/work_queue.rb",
+    "lib/scout/work_queue/exceptions.rb",
     "lib/scout/work_queue/socket.rb",
     "lib/scout/work_queue/worker.rb",
     "lib/scout/workflow.rb",
@@ -157,49 +105,12 @@ Gem::Specification.new do |s|
     "share/software/install_helpers",
     "share/templates/command",
     "share/templates/workflow.rb",
-    "test/scout/indiferent_hash/test_case_insensitive.rb",
-    "test/scout/indiferent_hash/test_options.rb",
-    "test/scout/log/test_color.rb",
-    "test/scout/log/test_progress.rb",
-    "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/offsite/test_ssh.rb",
     "test/scout/offsite/test_step.rb",
     "test/scout/offsite/test_sync.rb",
     "test/scout/offsite/test_task.rb",
-    "test/scout/open/test_lock.rb",
-    "test/scout/open/test_remote.rb",
-    "test/scout/open/test_stream.rb",
-    "test/scout/open/test_util.rb",
-    "test/scout/path/test_find.rb",
-    "test/scout/path/test_util.rb",
-    "test/scout/persist/test_open.rb",
-    "test/scout/persist/test_path.rb",
-    "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",
-    "test/scout/simple_opt/test_parse.rb",
-    "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_offsite.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",
@@ -244,15 +155,14 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://github.com/mikisvaz/scout-gear".freeze
   s.licenses = ["MIT".freeze]
-  s.rubygems_version = "3.4.13".freeze
+  s.rubygems_version = "3.5.0.dev".freeze
   s.summary = "basic gear for scouts".freeze
 
   s.specification_version = 4
 
-  s.add_runtime_dependency(%q<term-ansicolor>.freeze, [">= 0"])
+  s.add_runtime_dependency(%q<scout-essentials>.freeze, [">= 0"])
   s.add_runtime_dependency(%q<net-ssh>.freeze, [">= 0"])
   s.add_runtime_dependency(%q<matrix>.freeze, [">= 0"])
-  s.add_runtime_dependency(%q<sys-proctable>.freeze, [">= 0"])
   s.add_runtime_dependency(%q<RubyInline>.freeze, [">= 0"])
   s.add_development_dependency(%q<rdoc>.freeze, ["~> 3.12"])
   s.add_development_dependency(%q<bundler>.freeze, ["~> 1.0"])

data/scout_commands/workflow/task

@@ -18,6 +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')
 -jn--jobname* Name to use as job identifier
 -li--load_inputs* Directory with inputs files to load
 -pf--print_filepath Print the file path
@@ -25,7 +26,6 @@ $ #{$0} [<options>] <workflow> <task>
 -cl--clean Clean the last step
 -rcl--recursive_clean Clean all steps
 -ct--clean_task* Clean a particular task
--d--deploy* Deploy mode: serial, local, or SLURM (default 'serial')
 -od--override_deps* Override deps using 'Workflow#task=<path>' array_separated
 EOF
 
@@ -86,8 +86,7 @@ if clean_task
       dep.set_info :status, :cleaned
     end
 
-    job.clean if job.task_name.to_s == clean_task.to_s
-    job.clean unless job.updated?
+    job.clean if (job.task_name.to_s == clean_task.to_s) || ! job.updated?
   end
 end
 

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

@@ -3,7 +3,7 @@ require File.expand_path(__FILE__).sub(%r(.*/test/), '').sub(/test_(.*)\.rb/,'\1
 
 require 'scout/workflow'
 class TestStepProvenance < Test::Unit::TestCase
-  def test_true
+  def test_prov_report
     tmpfile = tmpdir.test_step
     step1 = Step.new tmpfile.step1, ["12"] do |s|
       s.length
@@ -21,5 +21,28 @@ class TestStepProvenance < Test::Unit::TestCase
     assert_include Step.prov_report(step2), 'step1'
     assert_include Step.prov_report(step2), 'step2'
   end
+
+  def __test_input_dependencies
+    wf = Workflow.annonymous_workflow "TaskInputDepProv" do
+      input :value1, :integer
+      task :number1 => :integer do |i| i end
+
+      input :value2, :integer
+      task :number2 => :integer do |i| i end
+
+      input :number1, :integer
+      input :number2, :integer
+      task :sum => :integer do |i1,i2| i1 + i2 end
+
+      dep :number1, :value1 => 1
+      dep :number2, :value1 => 2
+      dep_task :my_sum, self, :sum, :number1 => :number1, :number2 => :number2
+
+    end
+    job = wf.job(:my_sum)
+
+    ppp Step.prov_report(job)
+
+  end
 end
 

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

@@ -219,14 +219,10 @@ class TestTaskInput < Test::Unit::TestCase
       original_digest =  task.process_inputs(inputs).last
 
       TmpFile.with_file do |save_directory|
-        iii inputs
         task.save_inputs(save_directory, inputs)
         Open.rm(file1)
         new_inputs = task.load_inputs(save_directory)
-        iii new_inputs
         new_digest =  task.process_inputs(new_inputs).last
-        iii new_digest
-        iii original_digest
         assert_equal original_digest, new_digest
       end
     end

metadata

@@ -1,17 +1,17 @@
 --- !ruby/object:Gem::Specification
 name: scout-gear
 version: !ruby/object:Gem::Version
-  version: 9.0.0
+  version: 10.0.1
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-06-27 00:00:00.000000000 Z
+date: 2023-07-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: term-ansicolor
+  name: scout-essentials
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -52,20 +52,6 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
-- !ruby/object:Gem::Dependency
-  name: sys-proctable
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
 - !ruby/object:Gem::Dependency
   name: RubyInline
   requirement: !ruby/object:Gem::Requirement
@@ -159,65 +145,12 @@ files:
 - 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
-- lib/scout/indiferent_hash/options.rb
-- lib/scout/log.rb
-- lib/scout/log/color.rb
-- lib/scout/log/color_class.rb
-- lib/scout/log/fingerprint.rb
-- lib/scout/log/progress.rb
-- lib/scout/log/progress/report.rb
-- lib/scout/log/progress/util.rb
-- lib/scout/log/trap.rb
-- lib/scout/meta_extension.rb
-- lib/scout/misc.rb
-- lib/scout/misc/digest.rb
-- lib/scout/misc/filesystem.rb
-- lib/scout/misc/format.rb
-- lib/scout/misc/helper.rb
-- lib/scout/misc/insist.rb
-- lib/scout/misc/monitor.rb
-- lib/scout/misc/system.rb
-- lib/scout/named_array.rb
 - lib/scout/offsite.rb
+- lib/scout/offsite/exceptions.rb
 - lib/scout/offsite/ssh.rb
 - lib/scout/offsite/step.rb
 - lib/scout/offsite/sync.rb
-- lib/scout/open.rb
-- lib/scout/open/lock.rb
-- lib/scout/open/lock/lockfile.rb
-- lib/scout/open/remote.rb
-- lib/scout/open/stream.rb
-- lib/scout/open/util.rb
-- lib/scout/path.rb
-- lib/scout/path/find.rb
-- lib/scout/path/tmpfile.rb
-- lib/scout/path/util.rb
-- lib/scout/persist.rb
-- lib/scout/persist/open.rb
-- lib/scout/persist/path.rb
-- lib/scout/persist/serialize.rb
-- lib/scout/resource.rb
-- lib/scout/resource/open.rb
-- lib/scout/resource/path.rb
-- 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
-- lib/scout/simple_opt/accessor.rb
-- lib/scout/simple_opt/doc.rb
-- lib/scout/simple_opt/get.rb
-- lib/scout/simple_opt/parse.rb
-- lib/scout/simple_opt/setup.rb
-- lib/scout/tmpfile.rb
 - lib/scout/tsv.rb
 - lib/scout/tsv/attach.rb
 - lib/scout/tsv/change_id.rb
@@ -241,6 +174,7 @@ files:
 - lib/scout/tsv/util/select.rb
 - lib/scout/tsv/util/unzip.rb
 - lib/scout/work_queue.rb
+- lib/scout/work_queue/exceptions.rb
 - lib/scout/work_queue/socket.rb
 - lib/scout/work_queue/worker.rb
 - lib/scout/workflow.rb
@@ -283,49 +217,12 @@ files:
 - share/software/install_helpers
 - share/templates/command
 - share/templates/workflow.rb
-- test/scout/indiferent_hash/test_case_insensitive.rb
-- test/scout/indiferent_hash/test_options.rb
-- test/scout/log/test_color.rb
-- test/scout/log/test_progress.rb
-- 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/offsite/test_ssh.rb
 - test/scout/offsite/test_step.rb
 - test/scout/offsite/test_sync.rb
 - test/scout/offsite/test_task.rb
-- test/scout/open/test_lock.rb
-- test/scout/open/test_remote.rb
-- test/scout/open/test_stream.rb
-- test/scout/open/test_util.rb
-- test/scout/path/test_find.rb
-- test/scout/path/test_util.rb
-- test/scout/persist/test_open.rb
-- test/scout/persist/test_path.rb
-- 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
-- test/scout/simple_opt/test_parse.rb
-- 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_offsite.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
@@ -386,7 +283,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.4.13
+rubygems_version: 3.5.0.dev
 signing_key: 
 specification_version: 4
 summary: basic gear for scouts