hpcflow-new2 0.2.0a189__py3-none-any.whl → 0.2.0a199__py3-none-any.whl

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Files changed (176) hide show
  1. hpcflow/__pyinstaller/hook-hpcflow.py +9 -6
  2. hpcflow/_version.py +1 -1
  3. hpcflow/app.py +1 -0
  4. hpcflow/data/scripts/bad_script.py +2 -0
  5. hpcflow/data/scripts/do_nothing.py +2 -0
  6. hpcflow/data/scripts/env_specifier_test/input_file_generator_pass_env_spec.py +4 -0
  7. hpcflow/data/scripts/env_specifier_test/main_script_test_pass_env_spec.py +8 -0
  8. hpcflow/data/scripts/env_specifier_test/output_file_parser_pass_env_spec.py +4 -0
  9. hpcflow/data/scripts/env_specifier_test/v1/input_file_generator_basic.py +4 -0
  10. hpcflow/data/scripts/env_specifier_test/v1/main_script_test_direct_in_direct_out.py +7 -0
  11. hpcflow/data/scripts/env_specifier_test/v1/output_file_parser_basic.py +4 -0
  12. hpcflow/data/scripts/env_specifier_test/v2/main_script_test_direct_in_direct_out.py +7 -0
  13. hpcflow/data/scripts/input_file_generator_basic.py +3 -0
  14. hpcflow/data/scripts/input_file_generator_basic_FAIL.py +3 -0
  15. hpcflow/data/scripts/input_file_generator_test_stdout_stderr.py +8 -0
  16. hpcflow/data/scripts/main_script_test_direct_in.py +3 -0
  17. hpcflow/data/scripts/main_script_test_direct_in_direct_out_2.py +6 -0
  18. hpcflow/data/scripts/main_script_test_direct_in_direct_out_2_fail_allowed.py +6 -0
  19. hpcflow/data/scripts/main_script_test_direct_in_direct_out_2_fail_allowed_group.py +7 -0
  20. hpcflow/data/scripts/main_script_test_direct_in_direct_out_3.py +6 -0
  21. hpcflow/data/scripts/main_script_test_direct_in_group_direct_out_3.py +6 -0
  22. hpcflow/data/scripts/main_script_test_direct_in_group_one_fail_direct_out_3.py +6 -0
  23. hpcflow/data/scripts/main_script_test_hdf5_in_obj.py +1 -1
  24. hpcflow/data/scripts/main_script_test_hdf5_in_obj_2.py +12 -0
  25. hpcflow/data/scripts/main_script_test_hdf5_out_obj.py +1 -1
  26. hpcflow/data/scripts/main_script_test_json_out_FAIL.py +3 -0
  27. hpcflow/data/scripts/main_script_test_shell_env_vars.py +12 -0
  28. hpcflow/data/scripts/main_script_test_std_out_std_err.py +6 -0
  29. hpcflow/data/scripts/output_file_parser_basic.py +3 -0
  30. hpcflow/data/scripts/output_file_parser_basic_FAIL.py +7 -0
  31. hpcflow/data/scripts/output_file_parser_test_stdout_stderr.py +8 -0
  32. hpcflow/data/scripts/script_exit_test.py +5 -0
  33. hpcflow/data/template_components/environments.yaml +1 -1
  34. hpcflow/sdk/__init__.py +26 -15
  35. hpcflow/sdk/app.py +2192 -768
  36. hpcflow/sdk/cli.py +506 -296
  37. hpcflow/sdk/cli_common.py +105 -7
  38. hpcflow/sdk/config/__init__.py +1 -1
  39. hpcflow/sdk/config/callbacks.py +115 -43
  40. hpcflow/sdk/config/cli.py +126 -103
  41. hpcflow/sdk/config/config.py +674 -318
  42. hpcflow/sdk/config/config_file.py +131 -95
  43. hpcflow/sdk/config/errors.py +125 -84
  44. hpcflow/sdk/config/types.py +148 -0
  45. hpcflow/sdk/core/__init__.py +25 -1
  46. hpcflow/sdk/core/actions.py +1771 -1059
  47. hpcflow/sdk/core/app_aware.py +24 -0
  48. hpcflow/sdk/core/cache.py +139 -79
  49. hpcflow/sdk/core/command_files.py +263 -287
  50. hpcflow/sdk/core/commands.py +145 -112
  51. hpcflow/sdk/core/element.py +828 -535
  52. hpcflow/sdk/core/enums.py +192 -0
  53. hpcflow/sdk/core/environment.py +74 -93
  54. hpcflow/sdk/core/errors.py +455 -52
  55. hpcflow/sdk/core/execute.py +207 -0
  56. hpcflow/sdk/core/json_like.py +540 -272
  57. hpcflow/sdk/core/loop.py +751 -347
  58. hpcflow/sdk/core/loop_cache.py +164 -47
  59. hpcflow/sdk/core/object_list.py +370 -207
  60. hpcflow/sdk/core/parameters.py +1100 -627
  61. hpcflow/sdk/core/rule.py +59 -41
  62. hpcflow/sdk/core/run_dir_files.py +21 -37
  63. hpcflow/sdk/core/skip_reason.py +7 -0
  64. hpcflow/sdk/core/task.py +1649 -1339
  65. hpcflow/sdk/core/task_schema.py +308 -196
  66. hpcflow/sdk/core/test_utils.py +191 -114
  67. hpcflow/sdk/core/types.py +440 -0
  68. hpcflow/sdk/core/utils.py +485 -309
  69. hpcflow/sdk/core/validation.py +82 -9
  70. hpcflow/sdk/core/workflow.py +2544 -1178
  71. hpcflow/sdk/core/zarr_io.py +98 -137
  72. hpcflow/sdk/data/workflow_spec_schema.yaml +2 -0
  73. hpcflow/sdk/demo/cli.py +53 -33
  74. hpcflow/sdk/helper/cli.py +18 -15
  75. hpcflow/sdk/helper/helper.py +75 -63
  76. hpcflow/sdk/helper/watcher.py +61 -28
  77. hpcflow/sdk/log.py +122 -71
  78. hpcflow/sdk/persistence/__init__.py +8 -31
  79. hpcflow/sdk/persistence/base.py +1360 -606
  80. hpcflow/sdk/persistence/defaults.py +6 -0
  81. hpcflow/sdk/persistence/discovery.py +38 -0
  82. hpcflow/sdk/persistence/json.py +568 -188
  83. hpcflow/sdk/persistence/pending.py +382 -179
  84. hpcflow/sdk/persistence/store_resource.py +39 -23
  85. hpcflow/sdk/persistence/types.py +318 -0
  86. hpcflow/sdk/persistence/utils.py +14 -11
  87. hpcflow/sdk/persistence/zarr.py +1337 -433
  88. hpcflow/sdk/runtime.py +44 -41
  89. hpcflow/sdk/submission/{jobscript_info.py → enums.py} +39 -12
  90. hpcflow/sdk/submission/jobscript.py +1651 -692
  91. hpcflow/sdk/submission/schedulers/__init__.py +167 -39
  92. hpcflow/sdk/submission/schedulers/direct.py +121 -81
  93. hpcflow/sdk/submission/schedulers/sge.py +170 -129
  94. hpcflow/sdk/submission/schedulers/slurm.py +291 -268
  95. hpcflow/sdk/submission/schedulers/utils.py +12 -2
  96. hpcflow/sdk/submission/shells/__init__.py +14 -15
  97. hpcflow/sdk/submission/shells/base.py +150 -29
  98. hpcflow/sdk/submission/shells/bash.py +283 -173
  99. hpcflow/sdk/submission/shells/os_version.py +31 -30
  100. hpcflow/sdk/submission/shells/powershell.py +228 -170
  101. hpcflow/sdk/submission/submission.py +1014 -335
  102. hpcflow/sdk/submission/types.py +140 -0
  103. hpcflow/sdk/typing.py +182 -12
  104. hpcflow/sdk/utils/arrays.py +71 -0
  105. hpcflow/sdk/utils/deferred_file.py +55 -0
  106. hpcflow/sdk/utils/hashing.py +16 -0
  107. hpcflow/sdk/utils/patches.py +12 -0
  108. hpcflow/sdk/utils/strings.py +33 -0
  109. hpcflow/tests/api/test_api.py +32 -0
  110. hpcflow/tests/conftest.py +27 -6
  111. hpcflow/tests/data/multi_path_sequences.yaml +29 -0
  112. hpcflow/tests/data/workflow_test_run_abort.yaml +34 -35
  113. hpcflow/tests/schedulers/sge/test_sge_submission.py +36 -0
  114. hpcflow/tests/schedulers/slurm/test_slurm_submission.py +5 -2
  115. hpcflow/tests/scripts/test_input_file_generators.py +282 -0
  116. hpcflow/tests/scripts/test_main_scripts.py +866 -85
  117. hpcflow/tests/scripts/test_non_snippet_script.py +46 -0
  118. hpcflow/tests/scripts/test_ouput_file_parsers.py +353 -0
  119. hpcflow/tests/shells/wsl/test_wsl_submission.py +12 -4
  120. hpcflow/tests/unit/test_action.py +262 -75
  121. hpcflow/tests/unit/test_action_rule.py +9 -4
  122. hpcflow/tests/unit/test_app.py +33 -6
  123. hpcflow/tests/unit/test_cache.py +46 -0
  124. hpcflow/tests/unit/test_cli.py +134 -1
  125. hpcflow/tests/unit/test_command.py +71 -54
  126. hpcflow/tests/unit/test_config.py +142 -16
  127. hpcflow/tests/unit/test_config_file.py +21 -18
  128. hpcflow/tests/unit/test_element.py +58 -62
  129. hpcflow/tests/unit/test_element_iteration.py +50 -1
  130. hpcflow/tests/unit/test_element_set.py +29 -19
  131. hpcflow/tests/unit/test_group.py +4 -2
  132. hpcflow/tests/unit/test_input_source.py +116 -93
  133. hpcflow/tests/unit/test_input_value.py +29 -24
  134. hpcflow/tests/unit/test_jobscript_unit.py +757 -0
  135. hpcflow/tests/unit/test_json_like.py +44 -35
  136. hpcflow/tests/unit/test_loop.py +1396 -84
  137. hpcflow/tests/unit/test_meta_task.py +325 -0
  138. hpcflow/tests/unit/test_multi_path_sequences.py +229 -0
  139. hpcflow/tests/unit/test_object_list.py +17 -12
  140. hpcflow/tests/unit/test_parameter.py +29 -7
  141. hpcflow/tests/unit/test_persistence.py +237 -42
  142. hpcflow/tests/unit/test_resources.py +20 -18
  143. hpcflow/tests/unit/test_run.py +117 -6
  144. hpcflow/tests/unit/test_run_directories.py +29 -0
  145. hpcflow/tests/unit/test_runtime.py +2 -1
  146. hpcflow/tests/unit/test_schema_input.py +23 -15
  147. hpcflow/tests/unit/test_shell.py +23 -2
  148. hpcflow/tests/unit/test_slurm.py +8 -7
  149. hpcflow/tests/unit/test_submission.py +38 -89
  150. hpcflow/tests/unit/test_task.py +352 -247
  151. hpcflow/tests/unit/test_task_schema.py +33 -20
  152. hpcflow/tests/unit/test_utils.py +9 -11
  153. hpcflow/tests/unit/test_value_sequence.py +15 -12
  154. hpcflow/tests/unit/test_workflow.py +114 -83
  155. hpcflow/tests/unit/test_workflow_template.py +0 -1
  156. hpcflow/tests/unit/utils/test_arrays.py +40 -0
  157. hpcflow/tests/unit/utils/test_deferred_file_writer.py +34 -0
  158. hpcflow/tests/unit/utils/test_hashing.py +65 -0
  159. hpcflow/tests/unit/utils/test_patches.py +5 -0
  160. hpcflow/tests/unit/utils/test_redirect_std.py +50 -0
  161. hpcflow/tests/workflows/__init__.py +0 -0
  162. hpcflow/tests/workflows/test_directory_structure.py +31 -0
  163. hpcflow/tests/workflows/test_jobscript.py +334 -1
  164. hpcflow/tests/workflows/test_run_status.py +198 -0
  165. hpcflow/tests/workflows/test_skip_downstream.py +696 -0
  166. hpcflow/tests/workflows/test_submission.py +140 -0
  167. hpcflow/tests/workflows/test_workflows.py +160 -15
  168. hpcflow/tests/workflows/test_zip.py +18 -0
  169. hpcflow/viz_demo.ipynb +6587 -3
  170. {hpcflow_new2-0.2.0a189.dist-info → hpcflow_new2-0.2.0a199.dist-info}/METADATA +8 -4
  171. hpcflow_new2-0.2.0a199.dist-info/RECORD +221 -0
  172. hpcflow/sdk/core/parallel.py +0 -21
  173. hpcflow_new2-0.2.0a189.dist-info/RECORD +0 -158
  174. {hpcflow_new2-0.2.0a189.dist-info → hpcflow_new2-0.2.0a199.dist-info}/LICENSE +0 -0
  175. {hpcflow_new2-0.2.0a189.dist-info → hpcflow_new2-0.2.0a199.dist-info}/WHEEL +0 -0
  176. {hpcflow_new2-0.2.0a189.dist-info → hpcflow_new2-0.2.0a199.dist-info}/entry_points.txt +0 -0

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