rbbt-util 5.38.0 → 5.39.0

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Files changed (44) hide show
  1. checksums.yaml +4 -4
  2. data/lib/rbbt/annotations.rb +2 -0
  3. data/lib/rbbt/persist.rb +2 -2
  4. data/lib/rbbt/resource.rb +12 -3
  5. data/lib/rbbt/tsv/excel.rb +5 -1
  6. data/lib/rbbt/tsv/parser.rb +2 -2
  7. data/lib/rbbt/tsv/util.rb +4 -0
  8. data/lib/rbbt/util/cmd.rb +8 -4
  9. data/lib/rbbt/util/concurrency/processes.rb +1 -1
  10. data/lib/rbbt/util/migrate.rb +1 -2
  11. data/lib/rbbt/util/misc/development.rb +0 -2
  12. data/lib/rbbt/util/misc/format.rb +3 -0
  13. data/lib/rbbt/util/misc/indiferent_hash.rb +9 -6
  14. data/lib/rbbt/util/misc/inspect.rb +23 -8
  15. data/lib/rbbt/util/misc/options.rb +1 -1
  16. data/lib/rbbt/util/misc/pipes.rb +3 -3
  17. data/lib/rbbt/util/open.rb +6 -1
  18. data/lib/rbbt/util/ssh.rb +46 -4
  19. data/lib/rbbt/workflow/remote_workflow/driver/ssh.rb +7 -7
  20. data/lib/rbbt/workflow/remote_workflow/remote_step/ssh.rb +4 -3
  21. data/lib/rbbt/workflow/remote_workflow/remote_step.rb +1 -0
  22. data/lib/rbbt/workflow/step/dependencies.rb +9 -9
  23. data/lib/rbbt/workflow/step/info.rb +1 -1
  24. data/lib/rbbt/workflow/step/save_load_inputs.rb +4 -5
  25. data/lib/rbbt/workflow/step.rb +9 -4
  26. data/lib/rbbt/workflow/usage.rb +1 -1
  27. data/lib/rbbt/workflow/util/trace.rb +2 -1
  28. data/lib/rbbt/workflow.rb +4 -3
  29. data/share/rbbt_commands/resource/claims +57 -0
  30. data/share/rbbt_commands/resource/find +1 -1
  31. data/share/rbbt_commands/resource/glob +1 -1
  32. data/share/rbbt_commands/workflow/task +58 -11
  33. data/test/rbbt/test_resource.rb +7 -2
  34. data/test/rbbt/test_tsv.rb +16 -1
  35. data/test/rbbt/tsv/parallel/test_traverse.rb +2 -2
  36. data/test/rbbt/tsv/test_accessor.rb +21 -4
  37. data/test/rbbt/tsv/test_parser.rb +28 -0
  38. data/test/rbbt/tsv/test_util.rb +14 -0
  39. data/test/rbbt/util/misc/test_indiferent_hash.rb +14 -0
  40. data/test/rbbt/util/test_cmd.rb +7 -1
  41. data/test/rbbt/util/test_migrate.rb +2 -2
  42. data/test/rbbt/util/test_open.rb +3 -3
  43. data/test/rbbt/util/test_ssh.rb +10 -0
  44. metadata +99 -94
metadata CHANGED
@@ -1,14 +1,14 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: rbbt-util
3
3
  version: !ruby/object:Gem::Version
4
- version: 5.38.0
4
+ version: 5.39.0
5
5
  platform: ruby
6
6
  authors:
7
7
  - Miguel Vazquez
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2023-04-11 00:00:00.000000000 Z
11
+ date: 2023-08-02 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: rake
@@ -390,6 +390,7 @@ files:
390
390
  - share/rbbt_commands/migrate
391
391
  - share/rbbt_commands/migrate_job
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392
  - share/rbbt_commands/purge_job
393
+ - share/rbbt_commands/resource/claims
393
394
  - share/rbbt_commands/resource/exists
394
395
  - share/rbbt_commands/resource/find
395
396
  - share/rbbt_commands/resource/get
@@ -530,6 +531,7 @@ files:
530
531
  - test/rbbt/util/misc/test_communication.rb
531
532
  - test/rbbt/util/misc/test_development.rb
532
533
  - test/rbbt/util/misc/test_format.rb
534
+ - test/rbbt/util/misc/test_indiferent_hash.rb
533
535
  - test/rbbt/util/misc/test_lock.rb
534
536
  - test/rbbt/util/misc/test_multipart_payload.rb
535
537
  - test/rbbt/util/misc/test_omics.rb
@@ -556,6 +558,7 @@ files:
556
558
  - test/rbbt/util/test_semaphore.rb
557
559
  - test/rbbt/util/test_simpleDSL.rb
558
560
  - test/rbbt/util/test_simpleopt.rb
561
+ - test/rbbt/util/test_ssh.rb
559
562
  - test/rbbt/util/test_tmpfile.rb
560
563
  - test/rbbt/workflow/step/test_dependencies.rb
561
564
  - test/rbbt/workflow/step/test_save_load_inputs.rb
@@ -587,113 +590,115 @@ required_rubygems_version: !ruby/object:Gem::Requirement
587
590
  - !ruby/object:Gem::Version
588
591
  version: '0'
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  requirements: []
590
- rubygems_version: 3.4.8
593
+ rubygems_version: 3.4.13
591
594
  signing_key:
592
595
  specification_version: 4
593
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  summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
594
597
  test_files:
595
- - test/rbbt/test_entity.rb
596
- - test/rbbt/workflow/test_remote_workflow.rb
597
- - test/rbbt/workflow/util/test_archive.rb
598
- - test/rbbt/workflow/util/test_orchestrator.rb
599
- - test/rbbt/workflow/util/test_data.rb
600
- - test/rbbt/workflow/test_doc.rb
601
- - test/rbbt/workflow/test_schedule.rb
602
- - test/rbbt/workflow/test_step.rb
603
- - test/rbbt/workflow/step/test_dependencies.rb
604
- - test/rbbt/workflow/step/test_save_load_inputs.rb
605
- - test/rbbt/workflow/test_task.rb
606
- - test/rbbt/resource/test_path.rb
607
- - test/rbbt/util/test_colorize.rb
608
- - test/rbbt/util/test_procpath.rb
609
- - test/rbbt/util/python/test_util.rb
610
- - test/rbbt/util/misc/test_development.rb
611
- - test/rbbt/util/misc/test_omics.rb
612
- - test/rbbt/util/misc/test_pipes.rb
613
- - test/rbbt/util/misc/test_serialize.rb
614
- - test/rbbt/util/misc/test_format.rb
615
- - test/rbbt/util/misc/test_communication.rb
616
- - test/rbbt/util/misc/test_lock.rb
617
- - test/rbbt/util/misc/test_multipart_payload.rb
618
- - test/rbbt/util/misc/test_bgzf.rb
619
- - test/rbbt/util/test_concurrency.rb
620
- - test/rbbt/util/test_cmd.rb
621
- - test/rbbt/util/R/test_plot.rb
622
- - test/rbbt/util/R/test_eval.rb
623
- - test/rbbt/util/R/test_model.rb
624
- - test/rbbt/util/test_config.rb
625
- - test/rbbt/util/test_log.rb
626
- - test/rbbt/util/test_simpleDSL.rb
627
- - test/rbbt/util/log/test_progress.rb
628
- - test/rbbt/util/test_tmpfile.rb
629
- - test/rbbt/util/test_R.rb
630
- - test/rbbt/util/test_excel2tsv.rb
631
- - test/rbbt/util/test_misc.rb
632
- - test/rbbt/util/test_open.rb
633
- - test/rbbt/util/test_simpleopt.rb
634
- - test/rbbt/util/simpleopt/test_parse.rb
635
- - test/rbbt/util/simpleopt/test_setup.rb
636
- - test/rbbt/util/simpleopt/test_get.rb
637
- - test/rbbt/util/test_python.rb
638
- - test/rbbt/util/test_filecache.rb
639
- - test/rbbt/util/concurrency/test_processes.rb
640
- - test/rbbt/util/concurrency/test_threads.rb
641
- - test/rbbt/util/concurrency/processes/test_socket.rb
642
- - test/rbbt/util/test_semaphore.rb
643
- - test/rbbt/util/test_chain_methods.rb
644
- - test/rbbt/util/test_migrate.rb
645
- - test/rbbt/test_resource.rb
646
- - test/rbbt/test_packed_index.rb
647
- - test/rbbt/tsv/test_change_id.rb
648
- - test/rbbt/tsv/test_attach.rb
649
- - test/rbbt/tsv/test_filter.rb
650
- - test/rbbt/tsv/test_marshal.rb
651
- - test/rbbt/tsv/test_parser.rb
652
- - test/rbbt/tsv/test_csv.rb
653
- - test/rbbt/tsv/test_accessor.rb
654
- - test/rbbt/tsv/test_matrix.rb
655
- - test/rbbt/tsv/test_field_index.rb
656
- - test/rbbt/tsv/test_util.rb
657
- - test/rbbt/tsv/test_index.rb
658
- - test/rbbt/tsv/test_parallel.rb
659
- - test/rbbt/tsv/test_manipulate.rb
660
- - test/rbbt/tsv/test_excel.rb
661
- - test/rbbt/tsv/parallel/test_through.rb
662
- - test/rbbt/tsv/parallel/test_traverse.rb
663
- - test/rbbt/tsv/test_stream.rb
664
- - test/rbbt/test_association.rb
665
- - test/rbbt/hpc/test_batch.rb
666
- - test/rbbt/hpc/orchestrate/test_chains.rb
667
- - test/rbbt/hpc/orchestrate/test_rules.rb
668
- - test/rbbt/hpc/orchestrate/test_batches.rb
669
- - test/rbbt/hpc/test_slurm.rb
670
- - test/rbbt/hpc/test_orchestrate.rb
598
+ - test/rbbt/annotations/test_util.rb
671
599
  - test/rbbt/association/test_database.rb
600
+ - test/rbbt/association/test_index.rb
672
601
  - test/rbbt/association/test_item.rb
673
602
  - test/rbbt/association/test_open.rb
674
603
  - test/rbbt/association/test_util.rb
675
- - test/rbbt/association/test_index.rb
676
- - test/rbbt/test_knowledge_base.rb
677
- - test/rbbt/persist/tsv/test_kyotocabinet.rb
604
+ - test/rbbt/entity/test_identifiers.rb
605
+ - test/rbbt/hpc/orchestrate/test_batches.rb
606
+ - test/rbbt/hpc/orchestrate/test_chains.rb
607
+ - test/rbbt/hpc/orchestrate/test_rules.rb
608
+ - test/rbbt/hpc/test_batch.rb
609
+ - test/rbbt/hpc/test_orchestrate.rb
610
+ - test/rbbt/hpc/test_slurm.rb
611
+ - test/rbbt/knowledge_base/test_enrichment.rb
612
+ - test/rbbt/knowledge_base/test_entity.rb
613
+ - test/rbbt/knowledge_base/test_query.rb
614
+ - test/rbbt/knowledge_base/test_registry.rb
615
+ - test/rbbt/knowledge_base/test_syndicate.rb
616
+ - test/rbbt/knowledge_base/test_traverse.rb
617
+ - test/rbbt/persist/test_tsv.rb
678
618
  - test/rbbt/persist/tsv/test_cdb.rb
619
+ - test/rbbt/persist/tsv/test_kyotocabinet.rb
620
+ - test/rbbt/persist/tsv/test_leveldb.rb
679
621
  - test/rbbt/persist/tsv/test_lmdb.rb
680
622
  - test/rbbt/persist/tsv/test_sharder.rb
681
- - test/rbbt/persist/tsv/test_leveldb.rb
682
623
  - test/rbbt/persist/tsv/test_tokyocabinet.rb
683
- - test/rbbt/persist/test_tsv.rb
684
- - test/rbbt/test_tsv.rb
624
+ - test/rbbt/resource/test_path.rb
685
625
  - test/rbbt/test_annotations.rb
626
+ - test/rbbt/test_association.rb
627
+ - test/rbbt/test_entity.rb
686
628
  - test/rbbt/test_fix_width_table.rb
687
- - test/rbbt/test_workflow.rb
688
- - test/rbbt/entity/test_identifiers.rb
689
- - test/rbbt/annotations/test_util.rb
690
629
  - test/rbbt/test_hpc.rb
630
+ - test/rbbt/test_knowledge_base.rb
691
631
  - test/rbbt/test_monitor.rb
632
+ - test/rbbt/test_packed_index.rb
692
633
  - test/rbbt/test_persist.rb
693
- - test/rbbt/knowledge_base/test_entity.rb
694
- - test/rbbt/knowledge_base/test_registry.rb
695
- - test/rbbt/knowledge_base/test_syndicate.rb
696
- - test/rbbt/knowledge_base/test_query.rb
697
- - test/rbbt/knowledge_base/test_enrichment.rb
698
- - test/rbbt/knowledge_base/test_traverse.rb
634
+ - test/rbbt/test_resource.rb
635
+ - test/rbbt/test_tsv.rb
636
+ - test/rbbt/test_workflow.rb
637
+ - test/rbbt/tsv/parallel/test_through.rb
638
+ - test/rbbt/tsv/parallel/test_traverse.rb
639
+ - test/rbbt/tsv/test_accessor.rb
640
+ - test/rbbt/tsv/test_attach.rb
641
+ - test/rbbt/tsv/test_change_id.rb
642
+ - test/rbbt/tsv/test_csv.rb
643
+ - test/rbbt/tsv/test_excel.rb
644
+ - test/rbbt/tsv/test_field_index.rb
645
+ - test/rbbt/tsv/test_filter.rb
646
+ - test/rbbt/tsv/test_index.rb
647
+ - test/rbbt/tsv/test_manipulate.rb
648
+ - test/rbbt/tsv/test_marshal.rb
649
+ - test/rbbt/tsv/test_matrix.rb
650
+ - test/rbbt/tsv/test_parallel.rb
651
+ - test/rbbt/tsv/test_parser.rb
652
+ - test/rbbt/tsv/test_stream.rb
653
+ - test/rbbt/tsv/test_util.rb
654
+ - test/rbbt/util/R/test_eval.rb
655
+ - test/rbbt/util/R/test_model.rb
656
+ - test/rbbt/util/R/test_plot.rb
657
+ - test/rbbt/util/concurrency/processes/test_socket.rb
658
+ - test/rbbt/util/concurrency/test_processes.rb
659
+ - test/rbbt/util/concurrency/test_threads.rb
660
+ - test/rbbt/util/log/test_progress.rb
661
+ - test/rbbt/util/misc/test_bgzf.rb
662
+ - test/rbbt/util/misc/test_communication.rb
663
+ - test/rbbt/util/misc/test_development.rb
664
+ - test/rbbt/util/misc/test_format.rb
665
+ - test/rbbt/util/misc/test_indiferent_hash.rb
666
+ - test/rbbt/util/misc/test_lock.rb
667
+ - test/rbbt/util/misc/test_multipart_payload.rb
668
+ - test/rbbt/util/misc/test_omics.rb
669
+ - test/rbbt/util/misc/test_pipes.rb
670
+ - test/rbbt/util/misc/test_serialize.rb
671
+ - test/rbbt/util/python/test_util.rb
672
+ - test/rbbt/util/simpleopt/test_get.rb
673
+ - test/rbbt/util/simpleopt/test_parse.rb
674
+ - test/rbbt/util/simpleopt/test_setup.rb
675
+ - test/rbbt/util/test_R.rb
676
+ - test/rbbt/util/test_chain_methods.rb
677
+ - test/rbbt/util/test_cmd.rb
678
+ - test/rbbt/util/test_colorize.rb
679
+ - test/rbbt/util/test_concurrency.rb
680
+ - test/rbbt/util/test_config.rb
681
+ - test/rbbt/util/test_excel2tsv.rb
682
+ - test/rbbt/util/test_filecache.rb
683
+ - test/rbbt/util/test_log.rb
684
+ - test/rbbt/util/test_migrate.rb
685
+ - test/rbbt/util/test_misc.rb
686
+ - test/rbbt/util/test_open.rb
687
+ - test/rbbt/util/test_procpath.rb
688
+ - test/rbbt/util/test_python.rb
689
+ - test/rbbt/util/test_semaphore.rb
690
+ - test/rbbt/util/test_simpleDSL.rb
691
+ - test/rbbt/util/test_simpleopt.rb
692
+ - test/rbbt/util/test_ssh.rb
693
+ - test/rbbt/util/test_tmpfile.rb
694
+ - test/rbbt/workflow/step/test_dependencies.rb
695
+ - test/rbbt/workflow/step/test_save_load_inputs.rb
696
+ - test/rbbt/workflow/test_doc.rb
697
+ - test/rbbt/workflow/test_remote_workflow.rb
698
+ - test/rbbt/workflow/test_schedule.rb
699
+ - test/rbbt/workflow/test_step.rb
700
+ - test/rbbt/workflow/test_task.rb
701
+ - test/rbbt/workflow/util/test_archive.rb
702
+ - test/rbbt/workflow/util/test_data.rb
703
+ - test/rbbt/workflow/util/test_orchestrator.rb
699
704
  - test/test_helper.rb