hpcflow-new2 0.2.0a190__py3-none-any.whl → 0.2.0a200__py3-none-any.whl

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Files changed (132) hide show
  1. hpcflow/__pyinstaller/hook-hpcflow.py +1 -0
  2. hpcflow/_version.py +1 -1
  3. hpcflow/data/scripts/bad_script.py +2 -0
  4. hpcflow/data/scripts/do_nothing.py +2 -0
  5. hpcflow/data/scripts/env_specifier_test/input_file_generator_pass_env_spec.py +4 -0
  6. hpcflow/data/scripts/env_specifier_test/main_script_test_pass_env_spec.py +8 -0
  7. hpcflow/data/scripts/env_specifier_test/output_file_parser_pass_env_spec.py +4 -0
  8. hpcflow/data/scripts/env_specifier_test/v1/input_file_generator_basic.py +4 -0
  9. hpcflow/data/scripts/env_specifier_test/v1/main_script_test_direct_in_direct_out.py +7 -0
  10. hpcflow/data/scripts/env_specifier_test/v1/output_file_parser_basic.py +4 -0
  11. hpcflow/data/scripts/env_specifier_test/v2/main_script_test_direct_in_direct_out.py +7 -0
  12. hpcflow/data/scripts/input_file_generator_basic.py +3 -0
  13. hpcflow/data/scripts/input_file_generator_basic_FAIL.py +3 -0
  14. hpcflow/data/scripts/input_file_generator_test_stdout_stderr.py +8 -0
  15. hpcflow/data/scripts/main_script_test_direct_in.py +3 -0
  16. hpcflow/data/scripts/main_script_test_direct_in_direct_out_2.py +6 -0
  17. hpcflow/data/scripts/main_script_test_direct_in_direct_out_2_fail_allowed.py +6 -0
  18. hpcflow/data/scripts/main_script_test_direct_in_direct_out_2_fail_allowed_group.py +7 -0
  19. hpcflow/data/scripts/main_script_test_direct_in_direct_out_3.py +6 -0
  20. hpcflow/data/scripts/main_script_test_direct_in_group_direct_out_3.py +6 -0
  21. hpcflow/data/scripts/main_script_test_direct_in_group_one_fail_direct_out_3.py +6 -0
  22. hpcflow/data/scripts/main_script_test_hdf5_in_obj_2.py +12 -0
  23. hpcflow/data/scripts/main_script_test_json_out_FAIL.py +3 -0
  24. hpcflow/data/scripts/main_script_test_shell_env_vars.py +12 -0
  25. hpcflow/data/scripts/main_script_test_std_out_std_err.py +6 -0
  26. hpcflow/data/scripts/output_file_parser_basic.py +3 -0
  27. hpcflow/data/scripts/output_file_parser_basic_FAIL.py +7 -0
  28. hpcflow/data/scripts/output_file_parser_test_stdout_stderr.py +8 -0
  29. hpcflow/data/scripts/script_exit_test.py +5 -0
  30. hpcflow/data/template_components/environments.yaml +1 -1
  31. hpcflow/sdk/__init__.py +5 -0
  32. hpcflow/sdk/app.py +166 -92
  33. hpcflow/sdk/cli.py +263 -84
  34. hpcflow/sdk/cli_common.py +99 -5
  35. hpcflow/sdk/config/callbacks.py +38 -1
  36. hpcflow/sdk/config/config.py +102 -13
  37. hpcflow/sdk/config/errors.py +19 -5
  38. hpcflow/sdk/config/types.py +3 -0
  39. hpcflow/sdk/core/__init__.py +25 -1
  40. hpcflow/sdk/core/actions.py +914 -262
  41. hpcflow/sdk/core/cache.py +76 -34
  42. hpcflow/sdk/core/command_files.py +14 -128
  43. hpcflow/sdk/core/commands.py +35 -6
  44. hpcflow/sdk/core/element.py +122 -50
  45. hpcflow/sdk/core/errors.py +58 -2
  46. hpcflow/sdk/core/execute.py +207 -0
  47. hpcflow/sdk/core/loop.py +408 -50
  48. hpcflow/sdk/core/loop_cache.py +4 -4
  49. hpcflow/sdk/core/parameters.py +382 -37
  50. hpcflow/sdk/core/run_dir_files.py +13 -40
  51. hpcflow/sdk/core/skip_reason.py +7 -0
  52. hpcflow/sdk/core/task.py +119 -30
  53. hpcflow/sdk/core/task_schema.py +68 -0
  54. hpcflow/sdk/core/test_utils.py +66 -27
  55. hpcflow/sdk/core/types.py +54 -1
  56. hpcflow/sdk/core/utils.py +136 -19
  57. hpcflow/sdk/core/workflow.py +1587 -356
  58. hpcflow/sdk/data/workflow_spec_schema.yaml +2 -0
  59. hpcflow/sdk/demo/cli.py +7 -0
  60. hpcflow/sdk/helper/cli.py +1 -0
  61. hpcflow/sdk/log.py +42 -15
  62. hpcflow/sdk/persistence/base.py +405 -53
  63. hpcflow/sdk/persistence/json.py +177 -52
  64. hpcflow/sdk/persistence/pending.py +237 -69
  65. hpcflow/sdk/persistence/store_resource.py +3 -2
  66. hpcflow/sdk/persistence/types.py +15 -4
  67. hpcflow/sdk/persistence/zarr.py +928 -81
  68. hpcflow/sdk/submission/jobscript.py +1408 -489
  69. hpcflow/sdk/submission/schedulers/__init__.py +40 -5
  70. hpcflow/sdk/submission/schedulers/direct.py +33 -19
  71. hpcflow/sdk/submission/schedulers/sge.py +51 -16
  72. hpcflow/sdk/submission/schedulers/slurm.py +44 -16
  73. hpcflow/sdk/submission/schedulers/utils.py +7 -2
  74. hpcflow/sdk/submission/shells/base.py +68 -20
  75. hpcflow/sdk/submission/shells/bash.py +222 -129
  76. hpcflow/sdk/submission/shells/powershell.py +200 -150
  77. hpcflow/sdk/submission/submission.py +852 -119
  78. hpcflow/sdk/submission/types.py +18 -21
  79. hpcflow/sdk/typing.py +24 -5
  80. hpcflow/sdk/utils/arrays.py +71 -0
  81. hpcflow/sdk/utils/deferred_file.py +55 -0
  82. hpcflow/sdk/utils/hashing.py +16 -0
  83. hpcflow/sdk/utils/patches.py +12 -0
  84. hpcflow/sdk/utils/strings.py +33 -0
  85. hpcflow/tests/api/test_api.py +32 -0
  86. hpcflow/tests/conftest.py +19 -0
  87. hpcflow/tests/data/benchmark_script_runner.yaml +26 -0
  88. hpcflow/tests/data/multi_path_sequences.yaml +29 -0
  89. hpcflow/tests/data/workflow_test_run_abort.yaml +34 -35
  90. hpcflow/tests/schedulers/sge/test_sge_submission.py +36 -0
  91. hpcflow/tests/scripts/test_input_file_generators.py +282 -0
  92. hpcflow/tests/scripts/test_main_scripts.py +821 -70
  93. hpcflow/tests/scripts/test_non_snippet_script.py +46 -0
  94. hpcflow/tests/scripts/test_ouput_file_parsers.py +353 -0
  95. hpcflow/tests/shells/wsl/test_wsl_submission.py +6 -0
  96. hpcflow/tests/unit/test_action.py +176 -0
  97. hpcflow/tests/unit/test_app.py +20 -0
  98. hpcflow/tests/unit/test_cache.py +46 -0
  99. hpcflow/tests/unit/test_cli.py +133 -0
  100. hpcflow/tests/unit/test_config.py +122 -1
  101. hpcflow/tests/unit/test_element_iteration.py +47 -0
  102. hpcflow/tests/unit/test_jobscript_unit.py +757 -0
  103. hpcflow/tests/unit/test_loop.py +1332 -27
  104. hpcflow/tests/unit/test_meta_task.py +325 -0
  105. hpcflow/tests/unit/test_multi_path_sequences.py +229 -0
  106. hpcflow/tests/unit/test_parameter.py +13 -0
  107. hpcflow/tests/unit/test_persistence.py +190 -8
  108. hpcflow/tests/unit/test_run.py +109 -3
  109. hpcflow/tests/unit/test_run_directories.py +29 -0
  110. hpcflow/tests/unit/test_shell.py +20 -0
  111. hpcflow/tests/unit/test_submission.py +5 -76
  112. hpcflow/tests/unit/test_workflow_template.py +31 -0
  113. hpcflow/tests/unit/utils/test_arrays.py +40 -0
  114. hpcflow/tests/unit/utils/test_deferred_file_writer.py +34 -0
  115. hpcflow/tests/unit/utils/test_hashing.py +65 -0
  116. hpcflow/tests/unit/utils/test_patches.py +5 -0
  117. hpcflow/tests/unit/utils/test_redirect_std.py +50 -0
  118. hpcflow/tests/workflows/__init__.py +0 -0
  119. hpcflow/tests/workflows/test_directory_structure.py +31 -0
  120. hpcflow/tests/workflows/test_jobscript.py +332 -0
  121. hpcflow/tests/workflows/test_run_status.py +198 -0
  122. hpcflow/tests/workflows/test_skip_downstream.py +696 -0
  123. hpcflow/tests/workflows/test_submission.py +140 -0
  124. hpcflow/tests/workflows/test_workflows.py +142 -2
  125. hpcflow/tests/workflows/test_zip.py +18 -0
  126. hpcflow/viz_demo.ipynb +6587 -3
  127. {hpcflow_new2-0.2.0a190.dist-info → hpcflow_new2-0.2.0a200.dist-info}/METADATA +7 -4
  128. hpcflow_new2-0.2.0a200.dist-info/RECORD +222 -0
  129. hpcflow_new2-0.2.0a190.dist-info/RECORD +0 -165
  130. {hpcflow_new2-0.2.0a190.dist-info → hpcflow_new2-0.2.0a200.dist-info}/LICENSE +0 -0
  131. {hpcflow_new2-0.2.0a190.dist-info → hpcflow_new2-0.2.0a200.dist-info}/WHEEL +0 -0
  132. {hpcflow_new2-0.2.0a190.dist-info → hpcflow_new2-0.2.0a200.dist-info}/entry_points.txt +0 -0

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