Index

Symbols

--add-to-known hpcflow-demo-workflow-go command line option hpcflow-go command line option hpcflow-workflow-WORKFLOW_REF-submit command line option --all hpcflow-config-get command line option hpcflow-demo-data-cache command line option --backup hpcflow-rechunk command line option hpcflow-workflow-WORKFLOW_REF-rechunk command line option hpcflow-workflow-WORKFLOW_REF-rechunk-parameter-base command line option hpcflow-workflow-WORKFLOW_REF-rechunk-runs command line option --cancel hpcflow-demo-workflow-go command line option hpcflow-go command line option hpcflow-workflow-WORKFLOW_REF-submit command line option --chunk-size hpcflow-rechunk command line option hpcflow-workflow-WORKFLOW_REF-rechunk command line option hpcflow-workflow-WORKFLOW_REF-rechunk-parameter-base command line option hpcflow-workflow-WORKFLOW_REF-rechunk-runs command line option --config-dir hpcflow command line option hpcflow-manage-get-config-path command line option hpcflow-manage-reset-config command line option --config-key hpcflow command line option --defaults hpcflow-config-add-scheduler command line option hpcflow-config-add-shell command line option hpcflow-config-add-shell-wsl command line option --doc hpcflow-demo-workflow-copy command line option hpcflow-demo-workflow-show command line option --element hpcflow-workflow-WORKFLOW_REF-abort-run command line option --env-source-file hpcflow-configure-env command line option --exclude-os hpcflow-submission-shell-info command line option --file hpcflow-config-get command line option hpcflow-helper-pid command line option --format hpcflow-demo-workflow-go command line option hpcflow-demo-workflow-make command line option hpcflow-go command line option hpcflow-make command line option --full hpcflow-show command line option --help hpcflow command line option --hostname hpcflow-manage-clear-cache command line option --hpcflow-version hpcflow command line option --include-execute hpcflow-workflow-WORKFLOW_REF-zip command line option hpcflow-zip command line option --include-rechunk-backups hpcflow-workflow-WORKFLOW_REF-zip command line option hpcflow-zip command line option --infile1 hpcflow-demo-software-doSomething command line option --infile2 hpcflow-demo-software-doSomething command line option --jobscripts hpcflow-workflow-WORKFLOW_REF-wait command line option --js-parallelism hpcflow-demo-workflow-go command line option hpcflow-go command line option hpcflow-workflow-WORKFLOW_REF-submit command line option --json hpcflow-config-append command line option hpcflow-config-prepend command line option hpcflow-config-set command line option hpcflow-config-update command line option hpcflow-submission-get-known command line option --legend hpcflow-show command line option --list hpcflow-demo-data command line option hpcflow-demo-workflow command line option --log hpcflow-unzip command line option hpcflow-workflow-WORKFLOW_REF-unzip command line option hpcflow-workflow-WORKFLOW_REF-zip command line option hpcflow-zip command line option --max-recent hpcflow-show command line option --metadata hpcflow-config-get command line option --name hpcflow-demo-workflow-go command line option hpcflow-demo-workflow-make command line option hpcflow-go command line option hpcflow-make command line option hpcflow-open-env-source command line option --new hpcflow-config-import command line option --no-add-to-known hpcflow-demo-workflow-go command line option hpcflow-go command line option hpcflow-workflow-WORKFLOW_REF-submit command line option --no-backup hpcflow-rechunk command line option hpcflow-workflow-WORKFLOW_REF-rechunk command line option hpcflow-workflow-WORKFLOW_REF-rechunk-parameter-base command line option hpcflow-workflow-WORKFLOW_REF-rechunk-runs command line option --no-callback hpcflow-config command line option --no-doc hpcflow-demo-workflow-copy command line option hpcflow-demo-workflow-show command line option --no-rename hpcflow-config-import command line option --no-status hpcflow-demo-workflow-go command line option hpcflow-demo-workflow-make command line option hpcflow-go command line option hpcflow-make command line option hpcflow-rechunk command line option hpcflow-workflow-WORKFLOW_REF-rechunk command line option hpcflow-workflow-WORKFLOW_REF-rechunk-parameter-base command line option hpcflow-workflow-WORKFLOW_REF-rechunk-runs command line option hpcflow-workflow-WORKFLOW_REF-submit command line option --no-syntax hpcflow-demo-workflow-show command line option --no-update hpcflow-show command line option --os-info hpcflow-submission command line option --out hpcflow-demo-software-doSomething command line option --overwrite hpcflow-demo-workflow-go command line option hpcflow-demo-workflow-make command line option hpcflow-go command line option hpcflow-make command line option hpcflow-workflow-WORKFLOW_REF-zip command line option hpcflow-zip command line option

--path hpcflow-config-init command line option hpcflow-config-open command line option hpcflow-demo-workflow-go command line option hpcflow-demo-workflow-make command line option hpcflow-go command line option hpcflow-make command line option hpcflow-open-config command line option hpcflow-open-demo-data-cache-dir command line option hpcflow-open-env-source command line option hpcflow-open-known-subs command line option hpcflow-open-log command line option hpcflow-open-user-cache-dir command line option hpcflow-open-user-cache-hostname-dir command line option hpcflow-open-user-data-dir command line option hpcflow-open-user-data-hostname-dir command line option hpcflow-open-user-runtime-dir command line option hpcflow-open-workflow command line option hpcflow-unzip command line option hpcflow-workflow-WORKFLOW_REF-unzip command line option hpcflow-workflow-WORKFLOW_REF-zip command line option hpcflow-zip command line option --print-idx hpcflow-demo-workflow-go command line option hpcflow-go command line option hpcflow-workflow-WORKFLOW_REF-submit command line option --ref-type hpcflow-cancel command line option hpcflow-open-workflow command line option hpcflow-rechunk command line option hpcflow-workflow command line option hpcflow-zip command line option --rename hpcflow-config-import command line option --run-time-info hpcflow command line option --setup hpcflow-configure-env command line option --status hpcflow-demo-workflow-go command line option hpcflow-demo-workflow-make command line option hpcflow-go command line option hpcflow-make command line option hpcflow-rechunk command line option hpcflow-workflow-WORKFLOW_REF-rechunk command line option hpcflow-workflow-WORKFLOW_REF-rechunk-parameter-base command line option hpcflow-workflow-WORKFLOW_REF-rechunk-runs command line option hpcflow-workflow-WORKFLOW_REF-submit command line option --stderr hpcflow-internal-workflow-PATH-save-parameter command line option --store hpcflow-demo-workflow-go command line option hpcflow-demo-workflow-make command line option hpcflow-go command line option hpcflow-make command line option --string hpcflow-go command line option hpcflow-make command line option --submission hpcflow-workflow-WORKFLOW_REF-abort-run command line option --syntax hpcflow-demo-workflow-show command line option --task hpcflow-workflow-WORKFLOW_REF-abort-run command line option --tasks hpcflow-demo-workflow-go command line option hpcflow-go command line option hpcflow-workflow-WORKFLOW_REF-submit command line option --timeit hpcflow command line option --timeit-file hpcflow command line option --timeout hpcflow-helper-restart command line option hpcflow-helper-run command line option hpcflow-helper-start command line option --timeout-check-interval hpcflow-helper-restart command line option hpcflow-helper-run command line option hpcflow-helper-start command line option --ts-fmt hpcflow-demo-workflow-go command line option hpcflow-demo-workflow-make command line option hpcflow-go command line option hpcflow-make command line option --ts-name-fmt hpcflow-demo-workflow-go command line option hpcflow-demo-workflow-make command line option hpcflow-go command line option hpcflow-make command line option --use-current-env hpcflow-configure-env command line option --value hpcflow-demo-software-doSomething command line option --var hpcflow-demo-workflow-go command line option hpcflow-demo-workflow-make command line option hpcflow-go command line option hpcflow-make command line option --version hpcflow command line option --wait hpcflow-demo-workflow-go command line option hpcflow-go command line option hpcflow-workflow-WORKFLOW_REF-submit command line option --watch-interval hpcflow-helper-restart command line option hpcflow-helper-run command line option hpcflow-helper-start command line option --with-config hpcflow command line option -f hpcflow-helper-pid command line option hpcflow-show command line option -i1 hpcflow-demo-software-doSomething command line option -i2 hpcflow-demo-software-doSomething command line option -j hpcflow-workflow-WORKFLOW_REF-wait command line option -l hpcflow-demo-data command line option hpcflow-demo-workflow command line option -o hpcflow-demo-software-doSomething command line option -r hpcflow-cancel command line option hpcflow-open-workflow command line option hpcflow-rechunk command line option hpcflow-show command line option hpcflow-workflow command line option hpcflow-zip command line option -v hpcflow-demo-software-doSomething command line option hpcflow-demo-workflow-go command line option hpcflow-demo-workflow-make command line option hpcflow-go command line option hpcflow-make command line option

A

a (hpcflow.sdk.core.test_utils.P1_parameter_cls attribute) abort_EARs_file_name (hpcflow.app.Submission property) (hpcflow.sdk.submission.submission.Submission property) abort_EARs_file_path (hpcflow.app.Submission property) (hpcflow.sdk.submission.submission.Submission property) ABORT_EXIT_CODE (in module hpcflow.sdk.core) abort_run() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) abortable (hpcflow.app.Action attribute) (hpcflow.app.InputFileGenerator attribute) (hpcflow.app.OutputFileParser attribute) (hpcflow.sdk.core.actions.Action attribute) (hpcflow.sdk.core.command_files.InputFileGenerator attribute) (hpcflow.sdk.core.command_files.OutputFileParser attribute) aborted (hpcflow.sdk.core.actions.EARStatus attribute) AbstractInputValue (class in hpcflow.sdk.core.parameters) Action (class in hpcflow.app) (class in hpcflow.sdk.core.actions) action (hpcflow.app.ActionRule attribute) (hpcflow.app.ElementAction property) (hpcflow.app.ElementActionRun property) (hpcflow.sdk.core.actions.ActionRule attribute) (hpcflow.sdk.core.actions.ElementAction property) (hpcflow.sdk.core.actions.ElementActionRun property) action_idx (hpcflow.app.ElementAction property) (hpcflow.sdk.core.actions.ElementAction property) (hpcflow.sdk.persistence.base.StoreEAR attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreEAR attribute) action_runs (hpcflow.app.Element property) (hpcflow.app.ElementIteration property) (hpcflow.sdk.core.element.Element property) (hpcflow.sdk.core.element.ElementIteration property) ACTION_SCOPE_ALLOWED_KWARGS (in module hpcflow.sdk.core.actions) ActionEnvironment (class in hpcflow.app) (class in hpcflow.sdk.core.actions) ActionEnvironmentMissingNameError ActionRule (class in hpcflow.app) (class in hpcflow.sdk.core.actions) actions (hpcflow.app.Element property) (hpcflow.app.ElementIteration property) (hpcflow.app.TaskSchema attribute) (hpcflow.sdk.core.element.Element property) (hpcflow.sdk.core.element.ElementIteration property) (hpcflow.sdk.core.task_schema.TaskSchema attribute) ActionScope (class in hpcflow.app) (class in hpcflow.sdk.core.actions) ActionScopeType (class in hpcflow.app) active (hpcflow.sdk.log.TimeIt attribute) add_default_config() (hpcflow.sdk.config.config_file.ConfigFile method) add_EAR() (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) add_EARs (hpcflow.sdk.persistence.pending.PendingChanges attribute) add_elem_IDs (hpcflow.sdk.persistence.pending.PendingChanges attribute) add_elem_iter_EAR_IDs (hpcflow.sdk.persistence.pending.PendingChanges attribute) add_elem_iter_IDs (hpcflow.sdk.persistence.pending.PendingChanges attribute) add_elem_iters (hpcflow.sdk.persistence.pending.PendingChanges attribute) add_element() (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) add_element_iteration() (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) add_element_set() (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) add_element_sets (hpcflow.sdk.persistence.pending.PendingChanges attribute) add_elements (hpcflow.sdk.persistence.pending.PendingChanges attribute) add_elements() (hpcflow.app.WorkflowTask method) (hpcflow.sdk.core.task.WorkflowTask method) add_file() (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) add_file_logger() (hpcflow.sdk.log.AppLog method) add_files (hpcflow.sdk.persistence.pending.PendingChanges attribute) add_group() (hpcflow.app.Task method) (hpcflow.sdk.core.task.Task method) add_iteration() (hpcflow.app.WorkflowLoop method) (hpcflow.sdk.core.loop.WorkflowLoop method) (hpcflow.sdk.core.loop_cache.LoopCache method) add_loop() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) add_loops (hpcflow.sdk.persistence.pending.PendingChanges attribute) add_object() (hpcflow.app.CommandFilesList method) (hpcflow.app.EnvironmentsList method) (hpcflow.app.ExecutablesList method) (hpcflow.app.GroupList method) (hpcflow.app.ParametersList method) (hpcflow.app.ResourceList method) (hpcflow.app.TaskList method) (hpcflow.app.TaskSchemasList method) (hpcflow.app.TaskTemplateList method) (hpcflow.app.WorkflowLoopList method) (hpcflow.app.WorkflowTaskList method) (hpcflow.sdk.core.object_list.AppDataList method) (hpcflow.sdk.core.object_list.CommandFilesList method) (hpcflow.sdk.core.object_list.DotAccessObjectList method) (hpcflow.sdk.core.object_list.EnvironmentsList method) (hpcflow.sdk.core.object_list.ExecutablesList method) (hpcflow.sdk.core.object_list.GroupList method) (hpcflow.sdk.core.object_list.ObjectList method) (hpcflow.sdk.core.object_list.ParametersList method) (hpcflow.sdk.core.object_list.ResourceList method) (hpcflow.sdk.core.object_list.TaskList method) (hpcflow.sdk.core.object_list.TaskSchemasList method) (hpcflow.sdk.core.object_list.TaskTemplateList method) (hpcflow.sdk.core.object_list.WorkflowLoopList method) (hpcflow.sdk.core.object_list.WorkflowTaskList method) add_objects() (hpcflow.app.CommandFilesList method) (hpcflow.app.EnvironmentsList method) (hpcflow.app.ExecutablesList method) (hpcflow.app.GroupList method) (hpcflow.app.ParametersList method) (hpcflow.app.TaskList method) (hpcflow.app.TaskSchemasList method) (hpcflow.app.TaskTemplateList method) (hpcflow.app.WorkflowLoopList method) (hpcflow.app.WorkflowTaskList method) (hpcflow.sdk.core.object_list.AppDataList method) (hpcflow.sdk.core.object_list.CommandFilesList method) (hpcflow.sdk.core.object_list.DotAccessObjectList method) (hpcflow.sdk.core.object_list.EnvironmentsList method) (hpcflow.sdk.core.object_list.ExecutablesList method) (hpcflow.sdk.core.object_list.GroupList method) (hpcflow.sdk.core.object_list.ParametersList method) (hpcflow.sdk.core.object_list.TaskList method) (hpcflow.sdk.core.object_list.TaskSchemasList method) (hpcflow.sdk.core.object_list.TaskTemplateList method) (hpcflow.sdk.core.object_list.WorkflowLoopList method) (hpcflow.sdk.core.object_list.WorkflowTaskList method) add_parameters (hpcflow.sdk.persistence.pending.PendingChanges attribute) add_scheduler() (hpcflow.sdk.config.config.Config method) add_set_parameter() (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) add_shell() (hpcflow.sdk.config.config.Config method) add_shell_WSL() (hpcflow.sdk.config.config.Config method) add_submission() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method)

add_submission_part() (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) add_submission_parts (hpcflow.sdk.persistence.pending.PendingChanges attribute) add_submissions (hpcflow.sdk.persistence.pending.PendingChanges attribute) add_task() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) add_task_after() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) add_task_before() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) add_tasks (hpcflow.sdk.persistence.pending.PendingChanges attribute) add_template_components (hpcflow.sdk.persistence.pending.PendingChanges attribute) add_template_components() (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) add_to_known_opt() (in module hpcflow.sdk.cli_common) add_unset_parameter() (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) additive_factor (hpcflow.app.ValuePerturbation attribute) (hpcflow.sdk.core.parameters.ValuePerturbation attribute) address (hpcflow.app.SubParameter attribute) (hpcflow.sdk.core.parameters.SubParameter attribute) ALL_CREATE_STORE_FORMATS (in module hpcflow.sdk.persistence) all_EAR_IDs (hpcflow.app.Jobscript property) (hpcflow.app.Submission property) (hpcflow.sdk.submission.jobscript.Jobscript property) (hpcflow.sdk.submission.submission.Submission property) all_EARs (hpcflow.app.Jobscript property) (hpcflow.app.Submission property) (hpcflow.sdk.submission.jobscript.Jobscript property) (hpcflow.sdk.submission.submission.Submission property) all_labelled_types (hpcflow.app.SchemaInput property) (hpcflow.sdk.core.parameters.SchemaInput property) all_schema_actions() (hpcflow.app.Task method) (hpcflow.sdk.core.task.Task method) all_schema_input_normalised_paths (hpcflow.app.Task property) (hpcflow.sdk.core.task.Task property) all_schema_input_types (hpcflow.app.Task property) (hpcflow.sdk.core.task.Task property) all_schema_inputs (hpcflow.app.Task property) (hpcflow.sdk.core.task.Task property) all_schema_output_types (hpcflow.app.Task property) (hpcflow.sdk.core.task.Task property) all_schema_outputs (hpcflow.app.Task property) (hpcflow.sdk.core.task.Task property) ALL_SHELLS (in module hpcflow.sdk.submission.shells) all_sourced_normalised_paths (hpcflow.app.Task property) (hpcflow.sdk.core.task.Task property) ALL_STORE_FORMATS (in module hpcflow.sdk.persistence) ALL_TEMPLATE_FORMATS (in module hpcflow.sdk.core) allow_non_coincident_task_sources (hpcflow.app.ElementSet attribute) (hpcflow.sdk.core.task.ElementSet attribute) ALLOWED_PARAMETERS (hpcflow.app.ResourceSpec attribute) (hpcflow.sdk.core.parameters.ResourceSpec attribute) ANY (hpcflow.app.ActionScopeType attribute) (hpcflow.app.TaskSourceType attribute) any() (hpcflow.app.ActionScope class method) (hpcflow.sdk.core.actions.ActionScope class method) API_logger (hpcflow.sdk.app.App property) (hpcflow.sdk.app.BaseApp property) App (class in hpcflow.sdk.app) app (hpcflow.app.Action attribute) (hpcflow.app.ActionEnvironment attribute) (hpcflow.app.ActionRule attribute) (hpcflow.app.ActionScope attribute) (hpcflow.app.Command attribute) (hpcflow.app.DirectPosix attribute) (hpcflow.app.DirectWindows attribute) (hpcflow.app.Element attribute) (hpcflow.app.ElementAction attribute) (hpcflow.app.ElementActionRun attribute) (hpcflow.app.ElementFilter attribute) (hpcflow.app.ElementGroup attribute) (hpcflow.app.ElementIteration attribute) (hpcflow.app.ElementParameter attribute) (hpcflow.app.ElementPropagation attribute) (hpcflow.app.ElementResources attribute) (hpcflow.app.ElementSet attribute) (hpcflow.app.Environment attribute) (hpcflow.app.Executable attribute) (hpcflow.app.ExecutableInstance attribute) (hpcflow.app.FileNameExt attribute) (hpcflow.app.FileNameSpec attribute) (hpcflow.app.FileNameStem attribute) (hpcflow.app.FileSpec attribute) (hpcflow.app.InputFile attribute) (hpcflow.app.InputFileGenerator attribute) (hpcflow.app.InputFileGeneratorSource attribute) (hpcflow.app.InputSource attribute) (hpcflow.app.InputValue attribute) (hpcflow.app.Jobscript attribute) (hpcflow.app.Loop attribute) (hpcflow.app.NumCores attribute) (hpcflow.app.OutputFileParser attribute) (hpcflow.app.OutputFileParserSource attribute) (hpcflow.app.OutputLabel attribute) (hpcflow.app.Parameter attribute) (hpcflow.app.ParameterPath attribute) (hpcflow.app.ResourceSpec attribute) (hpcflow.app.Rule attribute) (hpcflow.app.RunDirAppFiles attribute) (hpcflow.app.SchemaInput attribute) (hpcflow.app.SchemaOutput attribute) (hpcflow.app.SchemaParameter attribute) (hpcflow.app.SGEPosix attribute) (hpcflow.app.SlurmPosix attribute) (hpcflow.app.Submission attribute) (hpcflow.app.Task attribute) (hpcflow.app.TaskObjective attribute) (hpcflow.app.TaskSchema attribute) (hpcflow.app.ValuePerturbation attribute) (hpcflow.app.ValueSequence attribute) (hpcflow.app.Workflow attribute) (hpcflow.app.WorkflowLoop attribute) (hpcflow.app.WorkflowLoopList attribute) (hpcflow.app.WorkflowTask attribute) (hpcflow.app.WorkflowTaskList attribute) (hpcflow.app.WorkflowTemplate attribute) (hpcflow.sdk.log.AppLog attribute) (in module hpcflow.app) AppDataList (class in hpcflow.sdk.core.object_list) append() (hpcflow.sdk.config.config.Config method) append_EAR_IDs() (hpcflow.sdk.persistence.base.StoreElementIter method) (hpcflow.sdk.persistence.zarr.ZarrStoreElementIter method) append_element_IDs() (hpcflow.sdk.persistence.base.StoreTask method) (hpcflow.sdk.persistence.zarr.ZarrStoreTask method) append_items_to_ragged_array() (in module hpcflow.sdk.persistence.zarr) append_iteration_IDs() (hpcflow.sdk.persistence.base.StoreElement method) (hpcflow.sdk.persistence.zarr.ZarrStoreElement method) AppLog (class in hpcflow.sdk.log) args (hpcflow.app.FileNameSpec attribute) (hpcflow.sdk.core.command_files.FileNameSpec attribute) arguments (hpcflow.app.Command attribute) (hpcflow.sdk.core.commands.Command attribute) artifacts_path (hpcflow.app.Workflow property) (hpcflow.sdk.core.workflow.Workflow property) ask_pw_on_auth_exc() (in module hpcflow.sdk.persistence.utils)

B

BaseApp (class in hpcflow.sdk.app) BaseJSONLike (class in hpcflow.sdk.core.json_like) Bash (class in hpcflow.sdk.submission.shells.bash) basic_info (hpcflow.app.TaskSchema property) (hpcflow.sdk.core.task_schema.TaskSchema property) batch_update() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method)

bisect_slice() (in module hpcflow.sdk.core.utils) build() (hpcflow.sdk.core.cache.DependencyCache class method) (hpcflow.sdk.core.loop_cache.LoopCache class method) BuiltinSchemaParameter (class in hpcflow.sdk.core.parameters) bundle_dir (hpcflow.sdk.runtime.RunTimeInfo attribute)

C

cache_all_demo_data_files() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) cache_ctx() (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) cache_demo_data_file() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) cached_load() (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) callback_bool() (in module hpcflow.sdk.config.callbacks) callback_file_paths() (in module hpcflow.sdk.config.callbacks) callback_lowercase() (in module hpcflow.sdk.config.callbacks) callback_scheduler_set_up() (in module hpcflow.sdk.config.callbacks) callback_supported_schedulers() (in module hpcflow.sdk.config.callbacks) callback_supported_shells() (in module hpcflow.sdk.config.callbacks) callback_update_log_console_level() (in module hpcflow.sdk.config.callbacks) callback_vars() (in module hpcflow.sdk.config.callbacks) cancel() (hpcflow.app.Jobscript method) (hpcflow.app.Submission method) (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) (hpcflow.sdk.submission.jobscript.Jobscript method) (hpcflow.sdk.submission.submission.Submission method) (in module hpcflow.app) cancel_jobs() (hpcflow.app.DirectPosix method) (hpcflow.app.DirectWindows method) (hpcflow.app.SGEPosix method) (hpcflow.app.SlurmPosix method) (hpcflow.sdk.submission.schedulers.direct.DirectPosix method) (hpcflow.sdk.submission.schedulers.direct.DirectScheduler method) (hpcflow.sdk.submission.schedulers.direct.DirectWindows method) (hpcflow.sdk.submission.schedulers.sge.SGEPosix method) (hpcflow.sdk.submission.schedulers.slurm.SlurmPosix method) cancel_opt() (in module hpcflow.sdk.cli_common) cancelled (hpcflow.sdk.submission.jobscript_info.JobscriptElementState attribute) capitalise_first_letter() (in module hpcflow.sdk.core.utils) cast (hpcflow.app.Rule attribute) (hpcflow.sdk.core.rule.Rule attribute) check_exists (hpcflow.app.Rule attribute) (hpcflow.sdk.core.rule.Rule attribute) check_exists() (hpcflow.app.ActionRule class method) (hpcflow.sdk.core.actions.ActionRule class method) check_in_object_list() (in module hpcflow.sdk.core.utils) check_load_data_files() (in module hpcflow.sdk.config.callbacks) check_loop_termination() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) check_missing (hpcflow.app.Rule attribute) (hpcflow.sdk.core.rule.Rule attribute) check_missing() (hpcflow.app.ActionRule class method) (hpcflow.sdk.core.actions.ActionRule class method) check_parameters_exist() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) check_valid_py_identifier() (in module hpcflow.sdk.core.utils) ChildObjectSpec (class in hpcflow.sdk.core.json_like) class_name (hpcflow.sdk.core.json_like.ChildObjectSpec attribute) class_obj (hpcflow.sdk.core.json_like.ChildObjectSpec attribute) classproperty (class in hpcflow.sdk.core.utils) clean_up (hpcflow.app.Action attribute) (hpcflow.app.OutputFileParser attribute) (hpcflow.sdk.core.actions.Action attribute) (hpcflow.sdk.core.command_files.OutputFileParser attribute) clear_demo_data_cache_dir() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) clear_helper() (in module hpcflow.sdk.helper.helper) clear_known_submissions_file() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) clear_user_cache_dir() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) clear_user_cache_hostname_dir() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) clear_user_runtime_dir() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) cli (hpcflow.sdk.app.App attribute) (hpcflow.sdk.app.BaseApp attribute) CLI_exception_wrapper_gen() (in module hpcflow.sdk.config.cli) CLI_format() (hpcflow.sdk.core.test_utils.P1_parameter_cls method) (hpcflow.sdk.core.test_utils.P1_sub_parameter_cls method) CLI_format_group() (hpcflow.sdk.core.test_utils.P1_parameter_cls static method) CLI_logger (hpcflow.sdk.app.App property) (hpcflow.sdk.app.BaseApp property) CLI_parse() (hpcflow.sdk.core.test_utils.P1_parameter_cls class method) close() (hpcflow.sdk.persistence.store_resource.JSONFileStoreResource method) (hpcflow.sdk.persistence.store_resource.StoreResource method) (hpcflow.sdk.persistence.store_resource.ZarrAttrsStoreResource method) CMD_IDX hpcflow-internal-workflow-PATH-save-parameter command line option Command (class in hpcflow.app) (class in hpcflow.sdk.core.commands) command (hpcflow.app.ActionRule attribute) (hpcflow.app.Command attribute) (hpcflow.app.ExecutableInstance attribute) (hpcflow.sdk.core.actions.ActionRule attribute) (hpcflow.sdk.core.commands.Command attribute) (hpcflow.sdk.core.environment.ExecutableInstance attribute) command_file_sources (hpcflow.sdk.config.config.Config attribute) command_files (hpcflow.sdk.app.App property) (hpcflow.sdk.app.BaseApp property) CommandFilesList (class in hpcflow.app) (class in hpcflow.sdk.core.object_list) commands (hpcflow.app.Action attribute) (hpcflow.sdk.core.actions.Action attribute) commands_idx (hpcflow.app.ElementActionRun property) (hpcflow.sdk.core.actions.ElementActionRun property) (hpcflow.sdk.persistence.base.StoreEAR attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreEAR attribute) commit_all() (hpcflow.sdk.persistence.pending.PendingChanges method) commit_EAR_ends (hpcflow.sdk.persistence.pending.CommitResourceMap attribute) commit_EAR_ends() (hpcflow.sdk.persistence.pending.PendingChanges method) commit_EAR_skips (hpcflow.sdk.persistence.pending.CommitResourceMap attribute) commit_EAR_skips() (hpcflow.sdk.persistence.pending.PendingChanges method) commit_EAR_starts (hpcflow.sdk.persistence.pending.CommitResourceMap attribute) commit_EAR_starts() (hpcflow.sdk.persistence.pending.PendingChanges method)

commit_EAR_submission_indices (hpcflow.sdk.persistence.pending.CommitResourceMap attribute) commit_EAR_submission_indices() (hpcflow.sdk.persistence.pending.PendingChanges method) commit_EARs (hpcflow.sdk.persistence.pending.CommitResourceMap attribute) commit_EARs() (hpcflow.sdk.persistence.pending.PendingChanges method) commit_EARs_initialised (hpcflow.sdk.persistence.pending.CommitResourceMap attribute) commit_EARs_initialised() (hpcflow.sdk.persistence.pending.PendingChanges method) commit_elem_IDs (hpcflow.sdk.persistence.pending.CommitResourceMap attribute) commit_elem_IDs() (hpcflow.sdk.persistence.pending.PendingChanges method) commit_elem_iter_EAR_IDs (hpcflow.sdk.persistence.pending.CommitResourceMap attribute) commit_elem_iter_EAR_IDs() (hpcflow.sdk.persistence.pending.PendingChanges method) commit_elem_iter_IDs (hpcflow.sdk.persistence.pending.CommitResourceMap attribute) commit_elem_iter_IDs() (hpcflow.sdk.persistence.pending.PendingChanges method) commit_elem_iters (hpcflow.sdk.persistence.pending.CommitResourceMap attribute) commit_elem_iters() (hpcflow.sdk.persistence.pending.PendingChanges method) commit_element_sets (hpcflow.sdk.persistence.pending.CommitResourceMap attribute) commit_element_sets() (hpcflow.sdk.persistence.pending.PendingChanges method) commit_elements (hpcflow.sdk.persistence.pending.CommitResourceMap attribute) commit_elements() (hpcflow.sdk.persistence.pending.PendingChanges method) commit_files (hpcflow.sdk.persistence.pending.CommitResourceMap attribute) commit_files() (hpcflow.sdk.persistence.pending.PendingChanges method) commit_js_metadata (hpcflow.sdk.persistence.pending.CommitResourceMap attribute) commit_js_metadata() (hpcflow.sdk.persistence.pending.PendingChanges method) commit_loop_indices (hpcflow.sdk.persistence.pending.CommitResourceMap attribute) commit_loop_indices() (hpcflow.sdk.persistence.pending.PendingChanges method) commit_loop_num_iters (hpcflow.sdk.persistence.pending.CommitResourceMap attribute) commit_loop_num_iters() (hpcflow.sdk.persistence.pending.PendingChanges method) commit_loop_parents (hpcflow.sdk.persistence.pending.CommitResourceMap attribute) commit_loop_parents() (hpcflow.sdk.persistence.pending.PendingChanges method) commit_loops (hpcflow.sdk.persistence.pending.CommitResourceMap attribute) commit_loops() (hpcflow.sdk.persistence.pending.PendingChanges method) commit_param_sources (hpcflow.sdk.persistence.pending.CommitResourceMap attribute) commit_param_sources() (hpcflow.sdk.persistence.pending.PendingChanges method) commit_parameters (hpcflow.sdk.persistence.pending.CommitResourceMap attribute) commit_parameters() (hpcflow.sdk.persistence.pending.PendingChanges method) commit_submission_parts (hpcflow.sdk.persistence.pending.CommitResourceMap attribute) commit_submission_parts() (hpcflow.sdk.persistence.pending.PendingChanges method) commit_submissions (hpcflow.sdk.persistence.pending.CommitResourceMap attribute) commit_submissions() (hpcflow.sdk.persistence.pending.PendingChanges method) commit_tasks (hpcflow.sdk.persistence.pending.CommitResourceMap attribute) commit_tasks() (hpcflow.sdk.persistence.pending.PendingChanges method) commit_template_components (hpcflow.sdk.persistence.pending.CommitResourceMap attribute) commit_template_components() (hpcflow.sdk.persistence.pending.PendingChanges method) CommitResourceMap (class in hpcflow.sdk.persistence.pending) compose_commands() (hpcflow.app.ElementActionRun method) (hpcflow.sdk.core.actions.ElementActionRun method) compose_jobscript() (hpcflow.app.Jobscript method) (hpcflow.sdk.submission.jobscript.Jobscript method) compose_source() (hpcflow.app.Action method) (hpcflow.app.InputFileGenerator method) (hpcflow.app.OutputFileParser method) (hpcflow.sdk.core.actions.Action method) (hpcflow.sdk.core.command_files.InputFileGenerator method) (hpcflow.sdk.core.command_files.OutputFileParser method) conda_prefix (hpcflow.sdk.runtime.RunTimeInfo attribute) condition (hpcflow.app.Rule attribute) (hpcflow.sdk.core.rule.Rule attribute) Config (class in hpcflow.sdk.config.config) config (hpcflow.sdk.app.App property) (hpcflow.sdk.app.BaseApp property) config_directory (hpcflow.sdk.config.config.Config attribute) config_file_contents (hpcflow.sdk.config.config.Config attribute) config_file_name (hpcflow.sdk.config.config.Config attribute) config_file_path (hpcflow.sdk.config.config.Config attribute) config_key (hpcflow.sdk.config.config.Config attribute) config_logger (hpcflow.sdk.app.App property) (hpcflow.sdk.app.BaseApp property) config_options (hpcflow.sdk.app.App attribute) (hpcflow.sdk.app.BaseApp attribute) config_schemas (hpcflow.sdk.config.config.Config attribute) ConfigChangeFileUpdateError ConfigChangeInvalidError ConfigChangeInvalidJSONError ConfigChangePopIndexError ConfigChangeTypeInvalidError ConfigChangeValidationError ConfigDefaultValidationError ConfigError ConfigFile (class in hpcflow.sdk.config.config_file) ConfigFileInvocationIncompatibleError ConfigFileInvocationUnknownMatchKey ConfigFileValidationError ConfigInvocationKeyNotFoundError ConfigItemAlreadyUnsetError ConfigItemCallbackError ConfigNonConfigurableError ConfigOptions (class in hpcflow.sdk.config.config) ConfigUnknownItemError ConfigUnknownOverrideError configure_env() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) ConfigValidationError console_handler (hpcflow.sdk.log.AppLog attribute) ContainerKeyError contents (hpcflow.app.InputFile property) (hpcflow.app.InputFileGeneratorSource property) (hpcflow.app.OutputFileParserSource property) (hpcflow.sdk.config.config_file.ConfigFile attribute) (hpcflow.sdk.core.command_files.InputFile property) (hpcflow.sdk.core.command_files.InputFileGeneratorSource property) (hpcflow.sdk.core.command_files.OutputFileParserSource property) copy() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) copy_demo_data() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) copy_demo_workflow() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) copy_non_persistent() (hpcflow.app.ResourceSpec method) (hpcflow.sdk.core.parameters.ResourceSpec method) create (hpcflow.sdk.persistence.base.PersistentStoreFeatures attribute) creation_info (hpcflow.app.Workflow property) (hpcflow.sdk.core.workflow.Workflow property) custom_CLI_format() (hpcflow.sdk.core.test_utils.P1_parameter_cls method) custom_CLI_format_prep() (hpcflow.sdk.core.test_utils.P1_parameter_cls method) custom_warning_formatter() (in module hpcflow.sdk.config.cli)

D

d (hpcflow.sdk.core.test_utils.P1_parameter_cls attribute) data (hpcflow.sdk.config.config_file.ConfigFile attribute) (hpcflow.sdk.persistence.base.StoreParameter attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreParameter attribute) data_idx (hpcflow.app.ElementActionRun property) (hpcflow.app.ElementIteration property) (hpcflow.app.ElementParameter property) (hpcflow.sdk.core.actions.ElementActionRun property) (hpcflow.sdk.core.element.ElementIteration property) (hpcflow.sdk.core.element.ElementParameter property) (hpcflow.sdk.core.loop_cache.LoopCache attribute) (hpcflow.sdk.persistence.base.StoreEAR attribute) (hpcflow.sdk.persistence.base.StoreElementIter attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreEAR attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreElementIter attribute) data_idx_is_set (hpcflow.app.ElementParameter property) (hpcflow.sdk.core.element.ElementParameter property) data_rt (hpcflow.sdk.config.config_file.ConfigFile attribute) decode() (hpcflow.sdk.persistence.base.StoreEAR class method) (hpcflow.sdk.persistence.base.StoreElement class method) (hpcflow.sdk.persistence.base.StoreElementIter class method) (hpcflow.sdk.persistence.base.StoreParameter class method) (hpcflow.sdk.persistence.base.StoreTask class method) (hpcflow.sdk.persistence.zarr.ZarrStoreEAR class method) (hpcflow.sdk.persistence.zarr.ZarrStoreElement class method) (hpcflow.sdk.persistence.zarr.ZarrStoreElementIter class method) (hpcflow.sdk.persistence.zarr.ZarrStoreParameter class method) (hpcflow.sdk.persistence.zarr.ZarrStoreTask class method) decorator() (hpcflow.sdk.log.TimeIt class method) DEFAULT (hpcflow.app.InputSourceType attribute) default (hpcflow.app.Parameters attribute) (hpcflow.sdk.core.task.Parameters attribute) default() (hpcflow.app.InputSource class method) (hpcflow.sdk.core.parameters.InputSource class method) DEFAULT_ARRAY_ITEM_VAR (hpcflow.app.SGEPosix attribute) (hpcflow.app.SlurmPosix attribute) (hpcflow.sdk.submission.schedulers.sge.SGEPosix attribute) (hpcflow.sdk.submission.schedulers.slurm.SlurmPosix attribute) DEFAULT_ARRAY_SWITCH (hpcflow.app.SGEPosix attribute) (hpcflow.app.SlurmPosix attribute) (hpcflow.sdk.submission.schedulers.sge.SGEPosix attribute) (hpcflow.sdk.submission.schedulers.slurm.SlurmPosix attribute) default_config (hpcflow.sdk.config.config.ConfigOptions attribute) DEFAULT_CONFIG (in module hpcflow.sdk.config.config) DEFAULT_CWD_SWITCH (hpcflow.app.SGEPosix attribute) (hpcflow.sdk.submission.schedulers.sge.SGEPosix attribute) DEFAULT_DEL_CMD (hpcflow.app.SGEPosix attribute) (hpcflow.app.SlurmPosix attribute) (hpcflow.sdk.submission.schedulers.sge.SGEPosix attribute) (hpcflow.sdk.submission.schedulers.slurm.SlurmPosix attribute) default_directory (hpcflow.sdk.config.config.ConfigOptions attribute) DEFAULT_EXE (hpcflow.sdk.submission.shells.bash.Bash attribute) (hpcflow.sdk.submission.shells.bash.WSLBash attribute) (hpcflow.sdk.submission.shells.powershell.WindowsPowerShell attribute) DEFAULT_JS_CMD (hpcflow.app.SGEPosix attribute) (hpcflow.app.SlurmPosix attribute) (hpcflow.sdk.submission.schedulers.sge.SGEPosix attribute) (hpcflow.sdk.submission.schedulers.slurm.SlurmPosix attribute) default_known_configs_dir (hpcflow.sdk.config.config.ConfigOptions attribute) DEFAULT_LOG_CONSOLE_LEVEL (hpcflow.sdk.log.AppLog attribute) DEFAULT_LOG_FILE_LEVEL (hpcflow.sdk.log.AppLog attribute) DEFAULT_LOGIN_NODE_MATCH (hpcflow.app.SGEPosix attribute) (hpcflow.app.SlurmPosix attribute) (hpcflow.sdk.submission.schedulers.Scheduler attribute) (hpcflow.sdk.submission.schedulers.sge.SGEPosix attribute) (hpcflow.sdk.submission.schedulers.slurm.SlurmPosix attribute) DEFAULT_LOGIN_NODES_CMD (hpcflow.app.SGEPosix attribute) (hpcflow.app.SlurmPosix attribute) (hpcflow.sdk.submission.schedulers.Scheduler attribute) (hpcflow.sdk.submission.schedulers.sge.SGEPosix attribute) (hpcflow.sdk.submission.schedulers.slurm.SlurmPosix attribute) default_scheduler (hpcflow.sdk.config.config.Config attribute) DEFAULT_SHEBANG_ARGS (hpcflow.app.DirectPosix attribute) (hpcflow.app.DirectWindows attribute) (hpcflow.app.SGEPosix attribute) (hpcflow.app.SlurmPosix attribute) (hpcflow.sdk.submission.schedulers.direct.DirectPosix attribute) (hpcflow.sdk.submission.schedulers.direct.DirectScheduler attribute) (hpcflow.sdk.submission.schedulers.direct.DirectWindows attribute) (hpcflow.sdk.submission.schedulers.NullScheduler attribute) (hpcflow.sdk.submission.schedulers.Scheduler attribute) (hpcflow.sdk.submission.schedulers.sge.SGEPosix attribute) (hpcflow.sdk.submission.schedulers.slurm.SlurmPosix attribute) default_shell (hpcflow.sdk.config.config.Config attribute) DEFAULT_SHELL_ARGS (hpcflow.app.DirectPosix attribute) (hpcflow.app.DirectWindows attribute) (hpcflow.app.SGEPosix attribute) (hpcflow.app.SlurmPosix attribute) (hpcflow.sdk.submission.schedulers.direct.DirectPosix attribute) (hpcflow.sdk.submission.schedulers.direct.DirectScheduler attribute) (hpcflow.sdk.submission.schedulers.direct.DirectWindows attribute) (hpcflow.sdk.submission.schedulers.NullScheduler attribute) (hpcflow.sdk.submission.schedulers.Scheduler attribute) (hpcflow.sdk.submission.schedulers.sge.SGEPosix attribute) (hpcflow.sdk.submission.schedulers.slurm.SlurmPosix attribute) DEFAULT_SHELL_EXECUTABLE (hpcflow.app.DirectPosix attribute) (hpcflow.app.DirectWindows attribute) (hpcflow.app.SlurmPosix attribute) (hpcflow.sdk.submission.schedulers.direct.DirectPosix attribute) (hpcflow.sdk.submission.schedulers.direct.DirectWindows attribute) (hpcflow.sdk.submission.schedulers.slurm.SlurmPosix attribute)

DEFAULT_SHELL_NAMES (in module hpcflow.sdk.submission.shells) DEFAULT_SHOW_CMD (hpcflow.app.SGEPosix attribute) (hpcflow.app.SlurmPosix attribute) (hpcflow.sdk.submission.schedulers.sge.SGEPosix attribute) (hpcflow.sdk.submission.schedulers.slurm.SlurmPosix attribute) DEFAULT_STORE_FORMAT (in module hpcflow.sdk.persistence) DEFAULT_SUBMIT_CMD (hpcflow.app.SGEPosix attribute) (hpcflow.app.SlurmPosix attribute) (hpcflow.sdk.submission.schedulers.sge.SGEPosix attribute) (hpcflow.sdk.submission.schedulers.slurm.SlurmPosix attribute) default_value (hpcflow.app.SchemaInput property) (hpcflow.sdk.core.parameters.SchemaInput property) DEFAULT_WSL_EXE (hpcflow.sdk.submission.shells.bash.WSLBash attribute) defined_input_types (hpcflow.app.ElementSet property) (hpcflow.app.Task property) (hpcflow.sdk.core.task.ElementSet property) (hpcflow.sdk.core.task.Task property) delete() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) delete_no_confirm() (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) demo_data_cache_dir (hpcflow.sdk.app.App property) (hpcflow.sdk.app.BaseApp property) demo_data_dir (hpcflow.sdk.app.App attribute) (hpcflow.sdk.app.BaseApp attribute) (hpcflow.sdk.config.config.Config attribute) demo_data_manifest_dir (hpcflow.sdk.app.App attribute) (hpcflow.sdk.app.BaseApp attribute) demo_data_manifest_file (hpcflow.sdk.config.config.Config attribute) dependencies (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property) DependencyCache (class in hpcflow.sdk.core.cache) description (hpcflow.sdk.app.App attribute) (hpcflow.sdk.app.BaseApp attribute) DESTINATION hpcflow-demo-data-copy command line option hpcflow-demo-workflow-copy command line option dict_key_attr (hpcflow.sdk.core.json_like.ChildObjectSpec attribute) dict_val_attr (hpcflow.sdk.core.json_like.ChildObjectSpec attribute) dict_values_process_flat() (in module hpcflow.sdk.core.utils) dir_diff (hpcflow.app.ElementActionRun property) (hpcflow.sdk.core.actions.ElementActionRun property) dir_name (hpcflow.app.Element property) (hpcflow.app.Task property) (hpcflow.app.WorkflowTask property) (hpcflow.sdk.core.element.Element property) (hpcflow.sdk.core.task.Task property) (hpcflow.sdk.core.task.WorkflowTask property) direct_stderr_file_name (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property) direct_stderr_path (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property) direct_stdout_file_name (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property) direct_stdout_path (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property) direct_win_pid_file_name (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property) direct_win_pid_file_path (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property) directory (hpcflow.sdk.config.config_file.ConfigFile attribute) directory_env_var (hpcflow.sdk.config.config.ConfigOptions attribute) DirectPosix (class in hpcflow.app) (class in hpcflow.sdk.submission.schedulers.direct) DirectScheduler (class in hpcflow.sdk.submission.schedulers.direct) DirectWindows (class in hpcflow.app) (class in hpcflow.sdk.submission.schedulers.direct) DISTRIBUTED (hpcflow.sdk.core.parallel.ParallelMode attribute) doc (hpcflow.app.Rule attribute) (hpcflow.app.WorkflowTemplate attribute) (hpcflow.sdk.core.rule.Rule attribute) (hpcflow.sdk.core.workflow.WorkflowTemplate attribute) docs_import_conv (hpcflow.sdk.app.App attribute) (hpcflow.sdk.app.BaseApp attribute) docs_url (hpcflow.sdk.app.App attribute) (hpcflow.sdk.app.BaseApp attribute) DotAccessObjectList (class in hpcflow.sdk.core.object_list) downstream_tasks (hpcflow.app.WorkflowLoop property) (hpcflow.app.WorkflowTask property) (hpcflow.sdk.core.loop.WorkflowLoop property) (hpcflow.sdk.core.task.WorkflowTask property) dump_to_HDF5_group() (hpcflow.app.ParameterValue method) (hpcflow.sdk.core.parameters.ParameterValue method) (hpcflow.sdk.core.test_utils.P1_parameter_cls method) (hpcflow.sdk.core.test_utils.P1_sub_parameter_cls method) (hpcflow.sdk.core.test_utils.P1_sub_parameter_cls_2 method) DuplicateExecutableError

E

e (hpcflow.sdk.core.test_utils.P1_sub_parameter_cls attribute) E_idx_type (in module hpcflow.sdk.typing) EAR_cache (hpcflow.sdk.persistence.base.PersistentStore property) (hpcflow.sdk.persistence.json.JSONPersistentStore property) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore property) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore property) EAR_ID hpcflow-internal-workflow-PATH-check-loop command line option hpcflow-internal-workflow-PATH-get-ear-skipped command line option hpcflow-internal-workflow-PATH-save-parameter command line option hpcflow-internal-workflow-PATH-set-ear-end command line option hpcflow-internal-workflow-PATH-set-ear-skip command line option hpcflow-internal-workflow-PATH-set-ear-start command line option hpcflow-internal-workflow-PATH-write-commands command line option EAR_ID (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property) EAR_ID_file_name (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property) EAR_ID_file_path (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property) EAR_IDs (hpcflow.app.ElementIteration property) (hpcflow.sdk.core.element.ElementIteration property) (hpcflow.sdk.persistence.base.StoreElementIter attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreElementIter attribute) EAR_IDs_flat (hpcflow.app.ElementIteration property) (hpcflow.sdk.core.element.ElementIteration property) EAR_idx_type (in module hpcflow.sdk.typing) EAR_parallelism (hpcflow.sdk.persistence.base.PersistentStoreFeatures attribute) EARs_by_elements (hpcflow.app.Submission property) (hpcflow.sdk.submission.submission.Submission property) EARs_initialised (hpcflow.app.ElementIteration property) (hpcflow.sdk.core.element.ElementIteration property) (hpcflow.sdk.persistence.base.StoreElementIter attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreElementIter attribute) EARStatus (class in hpcflow.sdk.core.actions) edit (hpcflow.sdk.persistence.base.PersistentStoreFeatures attribute) EI_idx_type (in module hpcflow.sdk.typing) elem_elem_dependencies (hpcflow.sdk.core.cache.DependencyCache attribute) elem_elem_dependents (hpcflow.sdk.core.cache.DependencyCache attribute) elem_elem_dependents_rec (hpcflow.sdk.core.cache.DependencyCache attribute) elem_iter_dependencies (hpcflow.sdk.core.cache.DependencyCache attribute) elem_iter_ID (hpcflow.sdk.persistence.base.StoreEAR attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreEAR attribute) elem_iter_IDs (hpcflow.app.ElementSet property) (hpcflow.sdk.core.task.ElementSet property) Element (class in hpcflow.app) (class in hpcflow.sdk.core.element) element (hpcflow.app.ElementAction property) (hpcflow.app.ElementActionRun property) (hpcflow.app.ElementIteration property) (hpcflow.app.ElementParameter attribute) (hpcflow.sdk.core.actions.ElementAction property) (hpcflow.sdk.core.actions.ElementActionRun property) (hpcflow.sdk.core.element.ElementIteration property) (hpcflow.sdk.core.element.ElementParameter attribute) element_action (hpcflow.app.ElementActionRun property) (hpcflow.sdk.core.actions.ElementActionRun property) element_cache (hpcflow.sdk.persistence.base.PersistentStore property) (hpcflow.sdk.persistence.json.JSONPersistentStore property) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore property) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore property) element_dependents (hpcflow.sdk.core.loop_cache.LoopCache attribute) element_ID (hpcflow.sdk.persistence.base.StoreElementIter attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreElementIter attribute) element_IDs (hpcflow.app.WorkflowTask property) (hpcflow.sdk.core.task.WorkflowTask property) (hpcflow.sdk.persistence.base.StoreTask attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreTask attribute) element_iter_cache (hpcflow.sdk.persistence.base.PersistentStore property) (hpcflow.sdk.persistence.json.JSONPersistentStore property) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore property) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore property) element_iteration (hpcflow.app.ElementAction property) (hpcflow.app.ElementActionRun property) (hpcflow.sdk.core.actions.ElementAction property) (hpcflow.sdk.core.actions.ElementActionRun property) element_iterations (hpcflow.app.ElementSet property) (hpcflow.sdk.core.task.ElementSet property) element_iters (hpcflow.app.InputSource attribute) (hpcflow.sdk.core.parameters.InputSource attribute) element_local_idx_range (hpcflow.app.ElementSet property) (hpcflow.sdk.core.task.ElementSet property) element_run_dir_file_name (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property) element_run_dir_file_path (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property) element_set (hpcflow.app.Element property) (hpcflow.app.ElementPropagation property) (hpcflow.app.ResourceList property) (hpcflow.app.ResourceSpec property) (hpcflow.sdk.core.element.Element property) (hpcflow.sdk.core.object_list.ResourceList property) (hpcflow.sdk.core.parameters.ResourceSpec property) (hpcflow.sdk.core.task.ElementPropagation property) element_set_idx (hpcflow.app.Element property) (hpcflow.sdk.core.element.Element property) element_sets (hpcflow.app.Task property) (hpcflow.sdk.core.task.Task property) ElementAction (class in hpcflow.app) (class in hpcflow.sdk.core.actions) ElementActionRun (class in hpcflow.app) (class in hpcflow.sdk.core.actions) ElementFilter (class in hpcflow.app) (class in hpcflow.sdk.core.element) ElementGroup (class in hpcflow.app) (class in hpcflow.sdk.core.element) ElementInputFiles (class in hpcflow.app) (class in hpcflow.sdk.core.element) ElementInputs (class in hpcflow.app) (class in hpcflow.sdk.core.element) ElementIteration (class in hpcflow.app) (class in hpcflow.sdk.core.element) ElementOutputFiles (class in hpcflow.app) (class in hpcflow.sdk.core.element) ElementOutputs (class in hpcflow.app) (class in hpcflow.sdk.core.element) ElementParameter (class in hpcflow.app) (class in hpcflow.sdk.core.element) ElementPropagation (class in hpcflow.app) (class in hpcflow.sdk.core.task) ElementRepeats (class in hpcflow.app) (class in hpcflow.sdk.core.element)

ElementResources (class in hpcflow.app) (class in hpcflow.sdk.core.element) Elements (class in hpcflow.app) (class in hpcflow.sdk.core.task) elements (hpcflow.app.ElementSet property) (hpcflow.app.WorkflowTask property) (hpcflow.sdk.core.cache.DependencyCache attribute) (hpcflow.sdk.core.loop_cache.LoopCache attribute) (hpcflow.sdk.core.task.ElementSet property) (hpcflow.sdk.core.task.WorkflowTask property) elements() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) ElementSet (class in hpcflow.app) (class in hpcflow.sdk.core.task) encode() (hpcflow.sdk.persistence.base.StoreEAR method) (hpcflow.sdk.persistence.base.StoreElement method) (hpcflow.sdk.persistence.base.StoreElementIter method) (hpcflow.sdk.persistence.base.StoreParameter method) (hpcflow.sdk.persistence.base.StoreTask method) (hpcflow.sdk.persistence.zarr.ZarrStoreEAR method) (hpcflow.sdk.persistence.zarr.ZarrStoreElement method) (hpcflow.sdk.persistence.zarr.ZarrStoreElementIter method) 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(hpcflow.sdk.core.actions.ElementActionRun property) Environment (class in hpcflow.app) (class in hpcflow.sdk.core.environment) environment (hpcflow.app.ActionEnvironment attribute) (hpcflow.app.Executable property) (hpcflow.app.ExecutablesList attribute) (hpcflow.app.InputFileGenerator attribute) (hpcflow.app.OutputFileParser attribute) (hpcflow.sdk.core.actions.ActionEnvironment attribute) (hpcflow.sdk.core.command_files.InputFileGenerator attribute) (hpcflow.sdk.core.command_files.OutputFileParser attribute) (hpcflow.sdk.core.environment.Executable property) (hpcflow.sdk.core.object_list.ExecutablesList attribute) environment_presets (hpcflow.app.TaskSchema attribute) (hpcflow.sdk.core.task_schema.TaskSchema attribute) environment_sources (hpcflow.sdk.config.config.Config attribute) EnvironmentPresetUnknownEnvironmentError environments (hpcflow.app.Action attribute) (hpcflow.app.ElementResources attribute) (hpcflow.app.ElementSet attribute) (hpcflow.app.ResourceSpec property) (hpcflow.app.Submission property) (hpcflow.app.WorkflowTemplate attribute) (hpcflow.sdk.core.actions.Action attribute) (hpcflow.sdk.core.element.ElementResources attribute) (hpcflow.sdk.core.parameters.ResourceSpec property) (hpcflow.sdk.core.task.ElementSet attribute) (hpcflow.sdk.core.workflow.WorkflowTemplate attribute) (hpcflow.sdk.submission.submission.Submission property) EnvironmentsList (class in hpcflow.app) (class in hpcflow.sdk.core.object_list) EnvironmentSpecValidationError envs (hpcflow.sdk.app.App property) (hpcflow.sdk.app.BaseApp property) error (hpcflow.sdk.core.actions.EARStatus attribute) errored (hpcflow.sdk.submission.jobscript_info.JobscriptElementState attribute) es_idx (hpcflow.sdk.persistence.base.StoreElement attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreElement attribute) Executable (class in hpcflow.app) (class in hpcflow.sdk.core.environment) executable (hpcflow.app.Command attribute) (hpcflow.sdk.core.commands.Command attribute) (hpcflow.sdk.submission.shells.base.Shell property) (hpcflow.sdk.submission.shells.bash.Bash property) (hpcflow.sdk.submission.shells.bash.WSLBash property) (hpcflow.sdk.submission.shells.powershell.WindowsPowerShell property) executable_name (hpcflow.sdk.runtime.RunTimeInfo property) executable_path (hpcflow.sdk.runtime.RunTimeInfo property) ExecutableInstance (class in hpcflow.app) (class in hpcflow.sdk.core.environment) executables (hpcflow.app.Environment attribute) (hpcflow.sdk.core.environment.Environment attribute) ExecutablesList (class in hpcflow.app) (class in hpcflow.sdk.core.object_list) execution_path (hpcflow.app.Workflow property) (hpcflow.sdk.core.workflow.Workflow property) exists_in_schedulers() (in module hpcflow.sdk.config.callbacks) EXIT_CODE hpcflow-internal-workflow-PATH-set-ear-end command line option exit_code (hpcflow.app.ElementActionRun property) (hpcflow.sdk.core.actions.ElementActionRun property) (hpcflow.sdk.persistence.base.StoreEAR attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreEAR attribute) expand() (hpcflow.app.Action method) (hpcflow.sdk.core.actions.Action method) EXPLICIT (hpcflow.app.ParameterPropagationMode attribute) ext (hpcflow.app.FileNameSpec property) (hpcflow.app.FileSpec property) (hpcflow.sdk.core.command_files.FileNameSpec property) (hpcflow.sdk.core.command_files.FileSpec property) extension (hpcflow.app.InputFile property) (hpcflow.app.InputFileGeneratorSource property) (hpcflow.app.OutputFileParserSource property) (hpcflow.sdk.core.command_files.InputFile property) (hpcflow.sdk.core.command_files.InputFileGeneratorSource property) (hpcflow.sdk.core.command_files.OutputFileParserSource property) extra_schemas (hpcflow.sdk.config.config.ConfigOptions attribute) ExtraInputs

F

f (hpcflow.sdk.core.test_utils.P1_sub_parameter_cls_2 attribute) file (hpcflow.app.InputFile attribute) (hpcflow.sdk.core.command_files.InputFile attribute) (hpcflow.sdk.persistence.base.StoreParameter attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreParameter attribute) FILE_NAME hpcflow-demo-data-cache command line option hpcflow-demo-data-copy command line option file_name (hpcflow.app.FileNameExt attribute) (hpcflow.app.FileNameStem attribute) (hpcflow.sdk.core.command_files.FileNameExt attribute) (hpcflow.sdk.core.command_files.FileNameStem attribute) FILE_PATH hpcflow-config-import command line option file_path (hpcflow.sdk.log.TimeIt attribute) FileNameExt (class in hpcflow.app) (class in hpcflow.sdk.core.command_files) FileNameSpec (class in hpcflow.app) (class in hpcflow.sdk.core.command_files) FileNameStem (class in hpcflow.app) (class in hpcflow.sdk.core.command_files) FileSpec (class in hpcflow.app) (class in hpcflow.sdk.core.command_files) FileSpecValidationError filter() 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(hpcflow.sdk.submission.shells.bash.Bash method) (hpcflow.sdk.submission.shells.bash.WSLBash method) (hpcflow.sdk.submission.shells.powershell.WindowsPowerShell method) format_switch() (hpcflow.app.SGEPosix method) (hpcflow.app.SlurmPosix method) (hpcflow.sdk.submission.schedulers.Scheduler method) (hpcflow.sdk.submission.schedulers.sge.SGEPosix method) (hpcflow.sdk.submission.schedulers.slurm.SlurmPosix method) from_CLI (hpcflow.sdk.runtime.RunTimeInfo attribute) from_data() (hpcflow.sdk.core.test_utils.P1_parameter_cls class method) from_file() (hpcflow.app.ValueSequence class method) (hpcflow.app.Workflow class method) (hpcflow.app.WorkflowTemplate class method) (hpcflow.sdk.core.parameters.ValueSequence class method) (hpcflow.sdk.core.test_utils.P1_parameter_cls class method) (hpcflow.sdk.core.workflow.Workflow class method) (hpcflow.sdk.core.workflow.WorkflowTemplate class method) from_geometric_space() (hpcflow.app.ValueSequence class method) (hpcflow.sdk.core.parameters.ValueSequence class method) from_JSON_file() (hpcflow.app.Workflow class method) (hpcflow.app.WorkflowTemplate class method) (hpcflow.sdk.core.workflow.Workflow class method) (hpcflow.sdk.core.workflow.WorkflowTemplate class method) from_json_like() (hpcflow.app.Action class method) (hpcflow.app.ActionEnvironment class method) (hpcflow.app.ActionRule class method) (hpcflow.app.ActionScope class method) (hpcflow.app.Command class method) (hpcflow.app.CommandFilesList class method) (hpcflow.app.ElementFilter class method) (hpcflow.app.ElementGroup class method) (hpcflow.app.ElementResources class method) (hpcflow.app.ElementSet class method) (hpcflow.app.Environment class method) (hpcflow.app.EnvironmentsList class method) (hpcflow.app.Executable class method) (hpcflow.app.ExecutableInstance class method) (hpcflow.app.ExecutablesList class method) (hpcflow.app.FileNameExt class method) (hpcflow.app.FileNameSpec class method) (hpcflow.app.FileNameStem class method) (hpcflow.app.FileSpec class method) (hpcflow.app.GroupList class method) (hpcflow.app.InputFile class method) (hpcflow.app.InputFileGenerator class method) (hpcflow.app.InputFileGeneratorSource class method) (hpcflow.app.InputSource class method) (hpcflow.app.InputValue class method) (hpcflow.app.Jobscript class method) (hpcflow.app.Loop class method) (hpcflow.app.NumCores class method) (hpcflow.app.OutputFileParser class method) (hpcflow.app.OutputFileParserSource class method) (hpcflow.app.OutputLabel class method) (hpcflow.app.Parameter class method) (hpcflow.app.ParameterPath class method) (hpcflow.app.ParametersList class method) (hpcflow.app.ResourceList class method) (hpcflow.app.ResourceSpec class method) (hpcflow.app.Rule class method) (hpcflow.app.SchemaInput class method) (hpcflow.app.SchemaOutput class method) (hpcflow.app.SchemaParameter class method) (hpcflow.app.Submission class method) (hpcflow.app.Task class method) (hpcflow.app.TaskList class method) 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(hpcflow.sdk.core.object_list.ExecutablesList class method) (hpcflow.sdk.core.object_list.GroupList class method) (hpcflow.sdk.core.object_list.ObjectList class method) (hpcflow.sdk.core.object_list.ParametersList class method) (hpcflow.sdk.core.object_list.ResourceList class method) (hpcflow.sdk.core.object_list.TaskList class method) (hpcflow.sdk.core.object_list.TaskSchemasList class method) (hpcflow.sdk.core.object_list.TaskTemplateList class method) (hpcflow.sdk.core.object_list.WorkflowLoopList class method) (hpcflow.sdk.core.object_list.WorkflowTaskList class method) (hpcflow.sdk.core.parameters.AbstractInputValue class method) (hpcflow.sdk.core.parameters.InputSource class method) (hpcflow.sdk.core.parameters.InputValue class method) (hpcflow.sdk.core.parameters.Parameter class method) (hpcflow.sdk.core.parameters.ParameterPath class method) (hpcflow.sdk.core.parameters.ResourceSpec class method) (hpcflow.sdk.core.parameters.SchemaInput class method) (hpcflow.sdk.core.parameters.SchemaOutput class method) (hpcflow.sdk.core.parameters.SchemaParameter class method) (hpcflow.sdk.core.parameters.ValuePerturbation class method) (hpcflow.sdk.core.parameters.ValueSequence class method) (hpcflow.sdk.core.rule.Rule class method) (hpcflow.sdk.core.task.ElementSet class method) (hpcflow.sdk.core.task.OutputLabel class method) (hpcflow.sdk.core.task.Task class method) (hpcflow.sdk.core.task_schema.TaskObjective class method) (hpcflow.sdk.core.task_schema.TaskSchema class method) (hpcflow.sdk.core.workflow.WorkflowTemplate class method) (hpcflow.sdk.submission.jobscript.Jobscript class method) (hpcflow.sdk.submission.submission.Submission class method)

from_JSON_string() (hpcflow.app.Workflow class method) (hpcflow.app.WorkflowTemplate class method) (hpcflow.sdk.core.workflow.Workflow class method) (hpcflow.sdk.core.workflow.WorkflowTemplate class method) from_linear_space() (hpcflow.app.ValueSequence class method) (hpcflow.sdk.core.parameters.ValueSequence class method) from_log_space() (hpcflow.app.ValueSequence class method) (hpcflow.sdk.core.parameters.ValueSequence class method) from_random_uniform() (hpcflow.app.ValueSequence class method) (hpcflow.sdk.core.parameters.ValueSequence class method) from_range() (hpcflow.app.ValueSequence class method) (hpcflow.sdk.core.parameters.ValueSequence class method) from_rectangle() (hpcflow.app.ValueSequence class method) (hpcflow.sdk.core.parameters.ValueSequence class method) from_spec() (hpcflow.app.ExecutableInstance class method) (hpcflow.app.ValuePerturbation class method) (hpcflow.sdk.core.environment.ExecutableInstance class method) (hpcflow.sdk.core.parameters.ValuePerturbation class method) from_string() (hpcflow.app.InputSource class method) (hpcflow.sdk.core.parameters.InputSource class method) from_template() (hpcflow.app.Workflow class method) (hpcflow.sdk.core.workflow.Workflow class method) from_template_data() (hpcflow.app.Workflow class method) (hpcflow.sdk.core.workflow.Workflow class method) from_YAML_file() (hpcflow.app.Workflow class method) (hpcflow.app.WorkflowTemplate class method) (hpcflow.sdk.core.workflow.Workflow class method) (hpcflow.sdk.core.workflow.WorkflowTemplate class method) from_YAML_string() (hpcflow.app.Workflow class method) (hpcflow.app.WorkflowTemplate class method) (hpcflow.sdk.core.workflow.Workflow class method) (hpcflow.sdk.core.workflow.WorkflowTemplate class method) from_zarr() (hpcflow.sdk.core.zarr_io.ZarrEncodable class method) FromSpecMissingObjectError

G

generate_data_index() (hpcflow.app.Action method) (hpcflow.sdk.core.actions.Action method) generate_EAR_resource_map() (in module hpcflow.sdk.submission.jobscript) generate_new_elements() (hpcflow.app.WorkflowTask method) (hpcflow.sdk.core.task.WorkflowTask method) generator (hpcflow.app.InputFileGeneratorSource attribute) (hpcflow.sdk.core.command_files.InputFileGeneratorSource attribute) get() (hpcflow.app.CommandFilesList method) (hpcflow.app.Element method) (hpcflow.app.ElementAction method) (hpcflow.app.ElementActionRun method) (hpcflow.app.ElementIteration method) (hpcflow.app.EnvironmentsList method) (hpcflow.app.ExecutablesList method) (hpcflow.app.GroupList method) (hpcflow.app.ParametersList method) (hpcflow.app.ResourceList method) (hpcflow.app.TaskList method) (hpcflow.app.TaskSchemasList method) (hpcflow.app.TaskTemplateList method) (hpcflow.app.WorkflowLoopList method) (hpcflow.app.WorkflowTask method) (hpcflow.app.WorkflowTaskList method) (hpcflow.sdk.config.config.Config method) (hpcflow.sdk.core.actions.ElementAction method) (hpcflow.sdk.core.actions.ElementActionRun method) (hpcflow.sdk.core.element.Element method) (hpcflow.sdk.core.element.ElementIteration method) (hpcflow.sdk.core.object_list.AppDataList method) (hpcflow.sdk.core.object_list.CommandFilesList method) (hpcflow.sdk.core.object_list.DotAccessObjectList method) (hpcflow.sdk.core.object_list.EnvironmentsList method) (hpcflow.sdk.core.object_list.ExecutablesList method) (hpcflow.sdk.core.object_list.GroupList method) (hpcflow.sdk.core.object_list.ObjectList method) (hpcflow.sdk.core.object_list.ParametersList method) (hpcflow.sdk.core.object_list.ResourceList method) (hpcflow.sdk.core.object_list.TaskList method) (hpcflow.sdk.core.object_list.TaskSchemasList method) (hpcflow.sdk.core.object_list.TaskTemplateList method) (hpcflow.sdk.core.object_list.WorkflowLoopList method) (hpcflow.sdk.core.object_list.WorkflowTaskList method) (hpcflow.sdk.core.task.WorkflowTask method) get_action_rules() (hpcflow.app.InputFileGenerator method) (hpcflow.app.OutputFileParser method) (hpcflow.sdk.core.command_files.InputFileGenerator method) (hpcflow.sdk.core.command_files.OutputFileParser method) get_activate_env_command() (hpcflow.sdk.runtime.RunTimeInfo method) get_active_jobscripts() (hpcflow.app.Submission method) (hpcflow.sdk.submission.submission.Submission method) get_active_states() (hpcflow.app.Jobscript method) (hpcflow.sdk.submission.jobscript.Jobscript method) get_all() (hpcflow.app.CommandFilesList method) (hpcflow.app.EnvironmentsList method) (hpcflow.app.ExecutablesList method) (hpcflow.app.GroupList method) (hpcflow.app.ParametersList method) (hpcflow.app.ResourceList method) (hpcflow.app.TaskList method) (hpcflow.app.TaskSchemasList method) (hpcflow.app.TaskTemplateList method) (hpcflow.app.WorkflowLoopList method) (hpcflow.app.WorkflowTaskList method) (hpcflow.sdk.config.config.Config method) (hpcflow.sdk.core.object_list.AppDataList method) (hpcflow.sdk.core.object_list.CommandFilesList method) (hpcflow.sdk.core.object_list.DotAccessObjectList method) (hpcflow.sdk.core.object_list.EnvironmentsList method) (hpcflow.sdk.core.object_list.ExecutablesList method) (hpcflow.sdk.core.object_list.GroupList method) (hpcflow.sdk.core.object_list.ObjectList method) (hpcflow.sdk.core.object_list.ParametersList method) (hpcflow.sdk.core.object_list.ResourceList method) (hpcflow.sdk.core.object_list.TaskList method) (hpcflow.sdk.core.object_list.TaskSchemasList method) (hpcflow.sdk.core.object_list.TaskTemplateList method) (hpcflow.sdk.core.object_list.WorkflowLoopList method) (hpcflow.sdk.core.object_list.WorkflowTaskList method) get_all_EARs() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) get_all_element_iterations() (hpcflow.app.Workflow method) (hpcflow.app.WorkflowTask method) (hpcflow.sdk.core.task.WorkflowTask method) (hpcflow.sdk.core.workflow.Workflow method) get_all_elements() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) get_all_parameter_data() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) get_all_parameter_sources() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) get_all_parameters() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) get_all_previous_iteration_runs() (hpcflow.app.ElementActionRun method) (hpcflow.sdk.core.actions.ElementActionRun method) get_all_submission_run_IDs() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) get_app_attribute() (in module hpcflow.sdk.app) get_app_module_all() (in module hpcflow.sdk.app) get_app_module_dir() (in module hpcflow.sdk.app) get_available_task_input_sources() (hpcflow.app.Task method) (hpcflow.sdk.core.task.Task method) get_by_key() (hpcflow.app.TaskSchema class method) (hpcflow.sdk.core.task_schema.TaskSchema class method) get_child_loops() (hpcflow.app.WorkflowLoop method) (hpcflow.sdk.core.loop.WorkflowLoop method) get_command_input_file_labels() (hpcflow.app.Action method) (hpcflow.sdk.core.actions.Action method) get_command_input_types() (hpcflow.app.Action method) (hpcflow.sdk.core.actions.Action method) get_command_line() (hpcflow.app.Command method) (hpcflow.sdk.core.commands.Command method) get_command_output_types() (hpcflow.app.Action method) (hpcflow.sdk.core.actions.Action method) get_commands_action_env() (hpcflow.app.Action method) (hpcflow.sdk.core.actions.Action method) get_commands_file_name() (hpcflow.app.Jobscript method) (hpcflow.app.RunDirAppFiles class method) (hpcflow.sdk.core.run_dir_files.RunDirAppFiles class method) (hpcflow.sdk.submission.jobscript.Jobscript method) get_config_CLI() (in module hpcflow.sdk.config.cli) get_config_file_path() (hpcflow.sdk.config.config_file.ConfigFile static method) get_config_item() (hpcflow.sdk.config.config_file.ConfigFile method) get_config_path() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) get_configurable() (hpcflow.sdk.config.config.Config method) get_creation_info() (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) get_data_idx() (hpcflow.app.Element method) (hpcflow.app.ElementAction method) (hpcflow.app.ElementActionRun method) (hpcflow.app.ElementIteration method) (hpcflow.sdk.core.actions.ElementAction method) (hpcflow.sdk.core.actions.ElementActionRun method) (hpcflow.sdk.core.element.Element method) (hpcflow.sdk.core.element.ElementIteration method) get_deactivate_env_command() (hpcflow.sdk.runtime.RunTimeInfo method) get_default_os_name() (hpcflow.app.ElementResources static method) (hpcflow.sdk.core.element.ElementResources static method) get_default_scheduler() (hpcflow.app.ElementResources class method) (hpcflow.sdk.core.element.ElementResources class method) get_default_shell() (hpcflow.app.ElementResources class method) (hpcflow.sdk.core.element.ElementResources class method) get_defined_parameter_types() (hpcflow.app.ElementSet method) (hpcflow.sdk.core.task.ElementSet method) get_defined_sub_parameter_types() (hpcflow.app.ElementSet method) (hpcflow.sdk.core.task.ElementSet method) get_demo_data_file_path() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) get_demo_data_files_manifest() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) get_demo_software_CLI() (in module hpcflow.sdk.demo.cli) get_demo_workflow_CLI() (in module hpcflow.sdk.demo.cli) get_demo_workflow_template_file() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) get_dependent_EARs() (hpcflow.app.Element method) (hpcflow.app.ElementActionRun method) (hpcflow.app.ElementIteration method) (hpcflow.sdk.core.actions.ElementActionRun method) (hpcflow.sdk.core.element.Element method) (hpcflow.sdk.core.element.ElementIteration method) get_dependent_element_iterations() (hpcflow.app.Element method) (hpcflow.app.ElementIteration method) (hpcflow.sdk.core.element.Element method) (hpcflow.sdk.core.element.ElementIteration method) get_dependent_elements() (hpcflow.app.Element method) (hpcflow.app.ElementIteration method) (hpcflow.app.WorkflowTask method) (hpcflow.sdk.core.element.Element method) (hpcflow.sdk.core.element.ElementIteration method) (hpcflow.sdk.core.task.WorkflowTask method) get_dependent_elements_recursively() (hpcflow.app.Element method) (hpcflow.sdk.core.element.Element method) get_dependent_tasks() (hpcflow.app.Element method) (hpcflow.app.ElementIteration method) (hpcflow.app.WorkflowTask method) (hpcflow.sdk.core.element.Element method) (hpcflow.sdk.core.element.ElementIteration method) (hpcflow.sdk.core.task.WorkflowTask method) get_dir_name() (hpcflow.app.WorkflowTask method) (hpcflow.sdk.core.task.WorkflowTask method) get_direct_submit_command() (hpcflow.sdk.submission.shells.base.Shell method) (hpcflow.sdk.submission.shells.bash.Bash method) (hpcflow.sdk.submission.shells.bash.WSLBash method) (hpcflow.sdk.submission.shells.powershell.WindowsPowerShell method) get_duplicate_items() (in module hpcflow.sdk.core.utils) get_EAR_dependencies() (hpcflow.app.Element method) (hpcflow.app.ElementActionRun method) (hpcflow.app.ElementIteration method) (hpcflow.sdk.core.actions.ElementActionRun method) (hpcflow.sdk.core.element.Element method) (hpcflow.sdk.core.element.ElementIteration method) get_EAR_IDs_of_tasks() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) get_EAR_skipped() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) get_EARs() (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) get_EARs_from_IDs() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) get_EARs_of_tasks() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) get_element_dependencies() (hpcflow.app.Element method) (hpcflow.app.ElementIteration method) (hpcflow.app.WorkflowTask method) (hpcflow.sdk.core.element.Element method) (hpcflow.sdk.core.element.ElementIteration method) (hpcflow.sdk.core.task.WorkflowTask method) get_element_IDs_from_EAR_IDs() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) get_element_iteration_dependencies() (hpcflow.app.Element method) (hpcflow.app.ElementIteration method) (hpcflow.sdk.core.element.Element method) (hpcflow.sdk.core.element.ElementIteration method) get_element_iteration_IDs_from_EAR_IDs() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) get_element_iterations() (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) get_element_iterations_from_IDs() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) get_element_iterations_of_tasks() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) get_elements() (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) get_elements_from_IDs() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) get_end_time() (hpcflow.app.Submission method) (hpcflow.sdk.submission.submission.Submission method) get_enum_by_name_or_val() (in module hpcflow.sdk.core.utils) get_env_instance_filterable_attributes() (hpcflow.app.ElementResources static method) (hpcflow.sdk.core.element.ElementResources static method) get_environment() (hpcflow.app.Action method) (hpcflow.app.ElementActionRun method) (hpcflow.sdk.core.actions.Action method) (hpcflow.sdk.core.actions.ElementActionRun method) get_environment_name() (hpcflow.app.Action method) (hpcflow.sdk.core.actions.Action method) get_environment_spec() (hpcflow.app.Action method) (hpcflow.app.ElementActionRun method) (hpcflow.sdk.core.actions.Action method) (hpcflow.sdk.core.actions.ElementActionRun method) get_helper_CLI() (in module hpcflow.sdk.helper.cli) get_helper_log_path() (in module hpcflow.sdk.helper.helper) get_helper_logger() (in module hpcflow.sdk.helper.helper) get_helper_PID() (in module hpcflow.sdk.helper.helper) get_helper_uptime() (in module hpcflow.sdk.helper.helper) get_helper_watch_list() (in module hpcflow.sdk.helper.helper) get_IFG_input_values() (hpcflow.app.ElementActionRun method) (hpcflow.sdk.core.actions.ElementActionRun method) get_in_container() (in module hpcflow.sdk.core.utils) get_info() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) get_info_html() (hpcflow.app.TaskSchema method) (hpcflow.sdk.core.task_schema.TaskSchema method) get_input_dependencies() (hpcflow.app.Element method) (hpcflow.app.ElementActionRun method) (hpcflow.app.ElementIteration method) (hpcflow.sdk.core.actions.ElementActionRun method) (hpcflow.sdk.core.element.Element method) (hpcflow.sdk.core.element.ElementIteration method) get_input_file_generator_action_env() (hpcflow.app.Action method) (hpcflow.sdk.core.actions.Action method) get_input_file_labels() (hpcflow.app.Action method) (hpcflow.sdk.core.actions.Action method) get_input_statuses() (hpcflow.app.Task method) (hpcflow.sdk.core.task.Task method) get_input_types() (hpcflow.app.Action method) (hpcflow.sdk.core.actions.Action method) get_input_values() (hpcflow.app.ElementActionRun method) (hpcflow.sdk.core.actions.ElementActionRun method) get_input_values_direct() (hpcflow.app.ElementActionRun method) (hpcflow.sdk.core.actions.ElementActionRun method) get_instance() (hpcflow.sdk.app.Singleton method) get_invoc_data() (hpcflow.sdk.config.config_file.ConfigFile method) get_invocation() (hpcflow.sdk.config.config_file.ConfigFile method) get_item_repeat_index() (in module hpcflow.sdk.core.utils) get_iter_IDs() (hpcflow.sdk.core.loop_cache.LoopCache method) get_iter_loop_indices() (hpcflow.sdk.core.loop_cache.LoopCache method) get_iteration_final_run_IDs() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method)

get_iteration_task_pathway() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) get_job_state_info() (hpcflow.app.DirectPosix method) (hpcflow.app.DirectWindows method) (hpcflow.app.SGEPosix method) (hpcflow.app.SlurmPosix method) (hpcflow.sdk.submission.schedulers.direct.DirectPosix method) (hpcflow.sdk.submission.schedulers.direct.DirectScheduler method) (hpcflow.sdk.submission.schedulers.direct.DirectWindows method) (hpcflow.sdk.submission.schedulers.sge.SGEPosix method) (hpcflow.sdk.submission.schedulers.slurm.SlurmPosix method) get_job_statuses() (hpcflow.app.SGEPosix method) (hpcflow.sdk.submission.schedulers.sge.SGEPosix method) get_jobscript_hash() (hpcflow.app.ElementResources method) (hpcflow.sdk.core.element.ElementResources method) get_key() (hpcflow.app.TaskSchema method) (hpcflow.sdk.core.task_schema.TaskSchema method) get_known_submissions() (in module hpcflow.app) get_locally_defined_inputs() (hpcflow.app.ElementSet method) (hpcflow.sdk.core.task.ElementSet method) get_log_file_name() (hpcflow.app.RunDirAppFiles class method) (hpcflow.sdk.core.run_dir_files.RunDirAppFiles class method) get_login_nodes() (hpcflow.app.SGEPosix method) (hpcflow.sdk.submission.schedulers.sge.SGEPosix method) get_loop_map() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) get_loops() (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) get_loops_by_IDs() (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) get_md5_hash() (in module hpcflow.sdk.core.utils) get_name() (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) get_nested_indices() (in module hpcflow.sdk.core.utils) get_non_running_submitted_states() (hpcflow.sdk.core.actions.EARStatus class method) get_OFP_inputs() (hpcflow.app.ElementActionRun method) (hpcflow.sdk.core.actions.ElementActionRun method) get_OFP_output_files() (hpcflow.app.ElementActionRun method) (hpcflow.sdk.core.actions.ElementActionRun method) get_OFP_outputs() (hpcflow.app.ElementActionRun method) (hpcflow.sdk.core.actions.ElementActionRun method) get_OS_info() (in module hpcflow.app) (in module hpcflow.sdk.submission.shells.os_version) get_OS_info_POSIX() (in module hpcflow.sdk.submission.shells.os_version) get_OS_info_windows() (in module hpcflow.sdk.submission.shells.os_version) get_OS_supported_schedulers() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) get_output_file_labels() (hpcflow.app.Action method) (hpcflow.sdk.core.actions.Action method) get_output_file_parser_action_env() (hpcflow.app.Action method) (hpcflow.sdk.core.actions.Action method) get_output_types() (hpcflow.app.Action method) (hpcflow.app.Command method) (hpcflow.sdk.core.actions.Action method) (hpcflow.sdk.core.commands.Command method) get_param_dump_file_path_HDF5() (hpcflow.app.Action method) (hpcflow.sdk.core.actions.Action method) get_param_dump_file_path_JSON() (hpcflow.app.Action method) (hpcflow.sdk.core.actions.Action method) get_param_load_file_path_HDF5() (hpcflow.app.Action method) (hpcflow.sdk.core.actions.Action method) get_param_load_file_path_JSON() (hpcflow.app.Action method) (hpcflow.sdk.core.actions.Action method) get_param_provided_element_sets() (hpcflow.app.Task method) (hpcflow.sdk.core.task.Task method) get_parameter() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) get_parameter_data() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) get_parameter_dependence() (hpcflow.app.Action method) (hpcflow.app.TaskSchema method) (hpcflow.sdk.core.actions.Action method) (hpcflow.sdk.core.task_schema.TaskSchema method) get_parameter_names() (hpcflow.app.Action method) (hpcflow.app.ElementAction method) (hpcflow.app.ElementActionRun method) (hpcflow.app.ElementIteration method) (hpcflow.sdk.core.actions.Action method) (hpcflow.sdk.core.actions.ElementAction method) (hpcflow.sdk.core.actions.ElementActionRun method) (hpcflow.sdk.core.element.ElementIteration method) get_parameter_set_statuses() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) get_parameter_source() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) get_parameter_sources() (hpcflow.app.Element method) (hpcflow.app.ElementAction method) (hpcflow.app.ElementActionRun method) (hpcflow.app.ElementIteration method) (hpcflow.app.Workflow method) (hpcflow.sdk.core.actions.ElementAction method) (hpcflow.sdk.core.actions.ElementActionRun method) (hpcflow.sdk.core.element.Element method) (hpcflow.sdk.core.element.ElementIteration method) (hpcflow.sdk.core.workflow.Workflow method) (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) get_parameter_task_schema_map() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) get_parameters() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) get_parent_loops() (hpcflow.app.WorkflowLoop method) (hpcflow.sdk.core.loop.WorkflowLoop method) get_PID_file_path() (in module hpcflow.sdk.helper.helper) get_possible_scopes() (hpcflow.app.Action method) (hpcflow.sdk.core.actions.Action method) get_precise_scope() (hpcflow.app.Action method) (hpcflow.sdk.core.actions.Action method) get_process_stamp() (in module hpcflow.sdk.core.utils) get_relative_path() (in module hpcflow.sdk.core.utils) get_required_executables() (hpcflow.app.Action method) (hpcflow.app.Command method) (hpcflow.sdk.core.actions.Action method) (hpcflow.sdk.core.commands.Command method) get_resources() (hpcflow.app.ElementActionRun method) (hpcflow.app.ElementIteration method) (hpcflow.sdk.core.actions.ElementActionRun method) (hpcflow.sdk.core.element.ElementIteration method) get_resources_obj() (hpcflow.app.ElementIteration method) (hpcflow.sdk.core.element.ElementIteration method) get_run_file_prefix() (hpcflow.app.RunDirAppFiles static method) (hpcflow.sdk.core.run_dir_files.RunDirAppFiles static method) get_run_param_dump_file_prefix() (hpcflow.app.RunDirAppFiles class method) (hpcflow.sdk.core.run_dir_files.RunDirAppFiles class method) get_run_param_load_file_prefix() (hpcflow.app.RunDirAppFiles class method) (hpcflow.sdk.core.run_dir_files.RunDirAppFiles class method) get_running_elements() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) get_running_runs() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) get_scheduler() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) get_schema() (in module hpcflow.sdk.core.validation) get_schema_action() (hpcflow.app.Task method) (hpcflow.sdk.core.task.Task method) get_scopes() (hpcflow.app.ResourceList method) (hpcflow.sdk.core.object_list.ResourceList method) get_script_name() (hpcflow.app.Action class method) (hpcflow.sdk.core.actions.Action class method) get_SDK_logger() (in module hpcflow.sdk) get_sequence_from_path() (hpcflow.app.ElementSet method) (hpcflow.sdk.core.task.ElementSet method) get_sequence_value() (hpcflow.app.Element method) (hpcflow.sdk.core.element.Element method) get_shell() (in module hpcflow.sdk.submission.shells) get_shell_info() (in module hpcflow.app) get_size() (hpcflow.app.ElementParameter method) (hpcflow.sdk.core.element.ElementParameter method) get_snippet_script_path() (hpcflow.app.Action class method) (hpcflow.sdk.core.actions.Action class method) get_snippet_script_str() (hpcflow.app.Action class method) (hpcflow.sdk.core.actions.Action class method) get_start_time() (hpcflow.app.Submission method) (hpcflow.sdk.submission.submission.Submission method) get_std_file_name() (hpcflow.app.RunDirAppFiles class method) (hpcflow.sdk.core.run_dir_files.RunDirAppFiles class method) get_store_EARs() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) get_store_element_iterations() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) get_store_elements() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) get_store_tasks() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) get_submissions() (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) get_submissions_by_ID() (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) get_submit_command() (hpcflow.app.DirectPosix method) (hpcflow.app.DirectWindows method) (hpcflow.app.SGEPosix method) (hpcflow.app.SlurmPosix method) (hpcflow.sdk.submission.schedulers.direct.DirectPosix method) (hpcflow.sdk.submission.schedulers.direct.DirectScheduler method) (hpcflow.sdk.submission.schedulers.direct.DirectWindows method) (hpcflow.sdk.submission.schedulers.sge.SGEPosix method) (hpcflow.sdk.submission.schedulers.slurm.SlurmPosix method) get_supported_shells() (in module hpcflow.sdk.submission.shells) get_task() (hpcflow.app.InputSource method) (hpcflow.sdk.core.parameters.InputSource method) (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) get_task_dependencies() (hpcflow.app.Element method) (hpcflow.app.ElementIteration method) (hpcflow.app.ElementSet method) (hpcflow.app.WorkflowTask method) (hpcflow.sdk.core.element.Element method) (hpcflow.sdk.core.element.ElementIteration method) (hpcflow.sdk.core.task.ElementSet method) (hpcflow.sdk.core.task.WorkflowTask method) get_task_elements() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) get_task_IDs_from_element_IDs() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) get_task_loop_idx_array() (hpcflow.app.Jobscript method) (hpcflow.sdk.submission.jobscript.Jobscript method) get_task_unique_names() (hpcflow.app.Task static method) (hpcflow.app.Workflow method) (hpcflow.sdk.core.task.Task static method) (hpcflow.sdk.core.workflow.Workflow method) get_tasks() (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) get_tasks_by_IDs() (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) get_template() (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) get_template_components() (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) get_template_resources() (hpcflow.app.ElementIteration method) (hpcflow.sdk.core.element.ElementIteration method) get_time_stamp() (in module hpcflow.sdk.core.utils) get_ts_fmt() (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) get_ts_name_fmt() (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) get_unique_schedulers() (hpcflow.app.Submission method) (hpcflow.sdk.submission.submission.Submission method) get_unique_schedulers_of_jobscripts() (hpcflow.app.Submission static method) (hpcflow.sdk.submission.submission.Submission static method) get_unique_shells() (hpcflow.app.Submission method) (hpcflow.sdk.submission.submission.Submission method) get_version_info() (hpcflow.app.DirectPosix method) (hpcflow.app.DirectWindows method) (hpcflow.app.SGEPosix method) (hpcflow.app.SlurmPosix method) (hpcflow.sdk.submission.schedulers.direct.DirectPosix method) (hpcflow.sdk.submission.schedulers.direct.DirectScheduler method) (hpcflow.sdk.submission.schedulers.direct.DirectWindows method) (hpcflow.sdk.submission.schedulers.NullScheduler method) (hpcflow.sdk.submission.schedulers.Scheduler method) (hpcflow.sdk.submission.schedulers.sge.SGEPosix method) (hpcflow.sdk.submission.schedulers.slurm.SlurmPosix method) (hpcflow.sdk.submission.shells.base.Shell method) (hpcflow.sdk.submission.shells.bash.Bash method) (hpcflow.sdk.submission.shells.bash.WSLBash method) (hpcflow.sdk.submission.shells.powershell.WindowsPowerShell method) get_wait_command() (hpcflow.sdk.submission.shells.base.Shell method) (hpcflow.sdk.submission.shells.bash.Bash method) (hpcflow.sdk.submission.shells.bash.WSLBash method) (hpcflow.sdk.submission.shells.powershell.WindowsPowerShell method) get_watcher_file_path() (in module hpcflow.sdk.helper.helper) gh_org (hpcflow.sdk.app.App attribute) (hpcflow.sdk.app.BaseApp attribute) gh_repo (hpcflow.sdk.app.App attribute) (hpcflow.sdk.app.BaseApp attribute) group_by_dict_key_values() (in module hpcflow.sdk.core.utils) group_by_distinct (hpcflow.app.ElementGroup attribute) (hpcflow.sdk.core.element.ElementGroup attribute) group_resource_map_into_jobscripts() (in module hpcflow.sdk.submission.jobscript) GroupList (class in hpcflow.app) (class in hpcflow.sdk.core.object_list) groups (hpcflow.app.ElementSet attribute) (hpcflow.sdk.core.task.ElementSet attribute) (hpcflow.sdk.persistence.pending.CommitResourceMap attribute)

H

has_default (hpcflow.sdk.core.task.InputStatus attribute) has_pending (hpcflow.sdk.persistence.base.PersistentStore property) (hpcflow.sdk.persistence.json.JSONPersistentStore property) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore property) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore property) helper_timeout() (in module hpcflow.sdk.helper.helper) host_user_id (hpcflow.sdk.config.config.Config attribute) host_user_id_file_path (hpcflow.sdk.config.config.Config attribute) hostname (hpcflow.sdk.runtime.RunTimeInfo attribute) hpcflow command line option --config-dir --config-key --help --hpcflow-version --run-time-info --timeit --timeit-file --version --with-config hpcflow-cancel command line option --ref-type -r WORKFLOW_REF hpcflow-config command line option --no-callback hpcflow-config-add-scheduler command line option --defaults NAME hpcflow-config-add-shell command line option --defaults NAME hpcflow-config-add-shell-wsl command line option --defaults hpcflow-config-append command line option --json NAME VALUE hpcflow-config-get command line option --all --file --metadata NAME hpcflow-config-import command line option --new --no-rename --rename FILE_PATH hpcflow-config-init command line option --path KNOWN_NAME hpcflow-config-open command line option --path hpcflow-config-pop command line option INDEX NAME hpcflow-config-prepend command line option --json NAME VALUE hpcflow-config-set command line option --json NAME VALUE hpcflow-config-set-github-demo-data-dir command line option SHA hpcflow-config-unset command line option NAME hpcflow-config-update command line option --json NAME VALUE hpcflow-configure-env command line option --env-source-file --setup --use-current-env NAME hpcflow-demo-data command line option --list -l hpcflow-demo-data-cache command line option --all FILE_NAME hpcflow-demo-data-copy command line option DESTINATION FILE_NAME hpcflow-demo-software-doSomething command line option --infile1 --infile2 --out --value -i1 -i2 -o -v hpcflow-demo-workflow command line option --list -l hpcflow-demo-workflow-copy command line option --doc --no-doc DESTINATION WORKFLOW_NAME hpcflow-demo-workflow-go command line option --add-to-known --cancel --format --js-parallelism --name --no-add-to-known --no-status --overwrite --path --print-idx --status --store --tasks --ts-fmt --ts-name-fmt --var --wait -v WORKFLOW_NAME hpcflow-demo-workflow-make command line option --format --name --no-status --overwrite --path --status --store --ts-fmt --ts-name-fmt --var -v WORKFLOW_NAME hpcflow-demo-workflow-show command line option --doc --no-doc --no-syntax --syntax WORKFLOW_NAME hpcflow-go command line option --add-to-known --cancel --format --js-parallelism --name --no-add-to-known --no-status --overwrite --path --print-idx --status --store --string --tasks --ts-fmt --ts-name-fmt --var --wait -v TEMPLATE_FILE_OR_STR hpcflow-helper-pid command line option --file -f hpcflow-helper-restart command line option --timeout --timeout-check-interval --watch-interval hpcflow-helper-run command line option --timeout --timeout-check-interval --watch-interval hpcflow-helper-start command line option --timeout --timeout-check-interval --watch-interval hpcflow-internal-workflow command line option PATH hpcflow-internal-workflow-PATH-check-loop command line option EAR_ID LOOP_NAME hpcflow-internal-workflow-PATH-get-ear-skipped command line option EAR_ID hpcflow-internal-workflow-PATH-save-parameter command line option --stderr CMD_IDX EAR_ID NAME VALUE hpcflow-internal-workflow-PATH-set-ear-end command line option EAR_ID EXIT_CODE JS_ACT_IDX JS_IDX hpcflow-internal-workflow-PATH-set-ear-skip command line option EAR_ID hpcflow-internal-workflow-PATH-set-ear-start command line option EAR_ID hpcflow-internal-workflow-PATH-write-commands command line option EAR_ID JOBSCRIPT_IDX JS_ACTION_IDX SUBMISSION_IDX hpcflow-make command line option --format --name --no-status --overwrite --path --status --store --string --ts-fmt --ts-name-fmt --var -v TEMPLATE_FILE_OR_STR hpcflow-manage-clear-cache command line option --hostname hpcflow-manage-get-config-path command line option --config-dir hpcflow-manage-reset-config command line option --config-dir hpcflow-open-config command line option --path hpcflow-open-demo-data-cache-dir command line option --path hpcflow-open-env-source command line option --name --path hpcflow-open-known-subs command line option --path hpcflow-open-log command line option --path hpcflow-open-user-cache-dir command line option --path hpcflow-open-user-cache-hostname-dir command line option --path

hpcflow-open-user-data-dir command line option --path hpcflow-open-user-data-hostname-dir command line option --path hpcflow-open-user-runtime-dir command line option --path hpcflow-open-workflow command line option --path --ref-type -r WORKFLOW_REF hpcflow-rechunk command line option --backup --chunk-size --no-backup --no-status --ref-type --status -r WORKFLOW_REF hpcflow-show command line option --full --legend --max-recent --no-update -f -r hpcflow-submission command line option --os-info hpcflow-submission-get-known command line option --json hpcflow-submission-scheduler command line option SCHEDULER_NAME hpcflow-submission-shell-info command line option --exclude-os SHELL_NAME hpcflow-test command line option PY_TEST_ARGS hpcflow-unzip command line option --log --path WORKFLOW_PATH hpcflow-workflow command line option --ref-type -r WORKFLOW_REF hpcflow-workflow-WORKFLOW_REF-abort-run command line option --element --submission --task hpcflow-workflow-WORKFLOW_REF-get-param command line option INDEX hpcflow-workflow-WORKFLOW_REF-get-param-source command line option INDEX hpcflow-workflow-WORKFLOW_REF-is-param-set command line option INDEX hpcflow-workflow-WORKFLOW_REF-rechunk command line option --backup --chunk-size --no-backup --no-status --status hpcflow-workflow-WORKFLOW_REF-rechunk-parameter-base command line option --backup --chunk-size --no-backup --no-status --status hpcflow-workflow-WORKFLOW_REF-rechunk-runs command line option --backup --chunk-size --no-backup --no-status --status hpcflow-workflow-WORKFLOW_REF-sub command line option SUB_IDX hpcflow-workflow-WORKFLOW_REF-sub-SUB_IDX-js command line option JS_IDX hpcflow-workflow-WORKFLOW_REF-submit command line option --add-to-known --cancel --js-parallelism --no-add-to-known --no-status --print-idx --status --tasks --wait hpcflow-workflow-WORKFLOW_REF-unzip command line option --log --path hpcflow-workflow-WORKFLOW_REF-wait command line option --jobscripts -j hpcflow-workflow-WORKFLOW_REF-zip command line option --include-execute --include-rechunk-backups --log --overwrite --path hpcflow-zip command line option --include-execute --include-rechunk-backups --log --overwrite --path --ref-type -r WORKFLOW_REF hpcflow.app module hpcflow.sdk module hpcflow.sdk.app module hpcflow.sdk.cli module hpcflow.sdk.cli_common module hpcflow.sdk.config module hpcflow.sdk.config.callbacks module hpcflow.sdk.config.cli module hpcflow.sdk.config.config module hpcflow.sdk.config.config_file module hpcflow.sdk.config.errors module hpcflow.sdk.core module hpcflow.sdk.core.actions module hpcflow.sdk.core.cache module hpcflow.sdk.core.command_files module hpcflow.sdk.core.commands module hpcflow.sdk.core.element module hpcflow.sdk.core.environment module hpcflow.sdk.core.errors module hpcflow.sdk.core.json_like module hpcflow.sdk.core.loop module hpcflow.sdk.core.loop_cache module hpcflow.sdk.core.object_list module hpcflow.sdk.core.parallel module hpcflow.sdk.core.parameters module hpcflow.sdk.core.rule module hpcflow.sdk.core.run_dir_files module hpcflow.sdk.core.task module hpcflow.sdk.core.task_schema module hpcflow.sdk.core.test_utils module hpcflow.sdk.core.utils module hpcflow.sdk.core.validation module hpcflow.sdk.core.workflow module hpcflow.sdk.core.zarr_io module hpcflow.sdk.data module hpcflow.sdk.demo module hpcflow.sdk.demo.cli module hpcflow.sdk.helper module hpcflow.sdk.helper.cli module hpcflow.sdk.helper.helper module hpcflow.sdk.helper.watcher module hpcflow.sdk.log module hpcflow.sdk.persistence module hpcflow.sdk.persistence.base module hpcflow.sdk.persistence.json module hpcflow.sdk.persistence.pending module hpcflow.sdk.persistence.store_resource module hpcflow.sdk.persistence.utils module hpcflow.sdk.persistence.zarr module hpcflow.sdk.runtime module hpcflow.sdk.submission module hpcflow.sdk.submission.jobscript module hpcflow.sdk.submission.jobscript_info module hpcflow.sdk.submission.schedulers module hpcflow.sdk.submission.schedulers.direct module hpcflow.sdk.submission.schedulers.sge module hpcflow.sdk.submission.schedulers.slurm module hpcflow.sdk.submission.schedulers.utils module hpcflow.sdk.submission.shells module hpcflow.sdk.submission.shells.base module hpcflow.sdk.submission.shells.bash module hpcflow.sdk.submission.shells.os_version module hpcflow.sdk.submission.shells.powershell module hpcflow.sdk.submission.submission module hpcflow.sdk.typing module HYBRID (hpcflow.sdk.core.parallel.ParallelMode attribute)

I

id_ (hpcflow.app.Element property) (hpcflow.app.ElementActionRun property) (hpcflow.app.ElementIteration property) (hpcflow.app.Workflow property) (hpcflow.sdk.core.actions.ElementActionRun property) (hpcflow.sdk.core.element.Element property) (hpcflow.sdk.core.element.ElementIteration property) (hpcflow.sdk.core.workflow.Workflow property) (hpcflow.sdk.persistence.base.StoreEAR attribute) (hpcflow.sdk.persistence.base.StoreElement attribute) (hpcflow.sdk.persistence.base.StoreElementIter attribute) (hpcflow.sdk.persistence.base.StoreParameter attribute) (hpcflow.sdk.persistence.base.StoreTask attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreEAR attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreElement attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreElementIter attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreParameter attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreTask attribute) ignore_invalid_actions() (hpcflow.app.TaskSchema class method) (hpcflow.sdk.core.task_schema.TaskSchema class method) implementation (hpcflow.app.TaskSchema attribute) (hpcflow.sdk.core.task_schema.TaskSchema attribute) IMPLICIT (hpcflow.app.ParameterPropagationMode attribute) IMPORT (hpcflow.app.InputSourceType attribute) import_() (hpcflow.app.InputSource class method) (hpcflow.sdk.core.parameters.InputSource class method) import_from_file() (hpcflow.sdk.config.config.Config method) import_ref (hpcflow.app.InputSource attribute) (hpcflow.sdk.core.parameters.InputSource attribute) in_ipython (hpcflow.sdk.runtime.RunTimeInfo attribute) in_pytest (hpcflow.sdk.runtime.RunTimeInfo attribute) InapplicableInputSourceElementIters IncompatibleParallelModeError IncompatibleSGEPEError IncompatibleSLURMArgumentsError IncompatibleSLURMPartitionError INDEX hpcflow-config-pop command line option hpcflow-workflow-WORKFLOW_REF-get-param command line option hpcflow-workflow-WORKFLOW_REF-get-param-source command line option hpcflow-workflow-WORKFLOW_REF-is-param-set command line option index (hpcflow.app.Element property) (hpcflow.app.ElementActionRun property) (hpcflow.app.ElementIteration property) (hpcflow.app.ElementSet property) (hpcflow.app.Jobscript property) (hpcflow.app.Submission property) (hpcflow.app.Task property) (hpcflow.app.WorkflowLoop property) (hpcflow.app.WorkflowTask property) (hpcflow.sdk.core.actions.ElementActionRun property) (hpcflow.sdk.core.element.Element property) (hpcflow.sdk.core.element.ElementIteration property) (hpcflow.sdk.core.loop.WorkflowLoop property) (hpcflow.sdk.core.task.ElementSet property) (hpcflow.sdk.core.task.Task property) (hpcflow.sdk.core.task.WorkflowTask property) (hpcflow.sdk.persistence.base.StoreElement attribute) (hpcflow.sdk.persistence.base.StoreTask attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreElement attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreTask attribute) (hpcflow.sdk.submission.jobscript.Jobscript property) (hpcflow.sdk.submission.submission.Submission property) index() (in module hpcflow.sdk.core.object_list) infer_store() (in module hpcflow.sdk.persistence.utils) info (hpcflow.app.TaskSchema property) (hpcflow.sdk.core.task_schema.TaskSchema property) init() (hpcflow.sdk.config.config.Config method) init_loop_index() (hpcflow.app.Element method) (hpcflow.sdk.core.element.Element method) init_schemas() (hpcflow.sdk.config.config.ConfigOptions method) initialise_EARs() (hpcflow.app.WorkflowTask method) (hpcflow.sdk.core.task.WorkflowTask method) inode() (hpcflow.sdk.core.utils.JSONLikeDirSnapShot method) INPUT (hpcflow.app.TaskSourceType attribute) input_file (hpcflow.app.InputFileGenerator attribute) (hpcflow.sdk.core.command_files.InputFileGenerator attribute) INPUT_FILE_GENERATOR (hpcflow.app.ActionScopeType attribute) input_file_generator() (hpcflow.app.ActionScope class method) (hpcflow.sdk.core.actions.ActionScope class method) input_file_generators (hpcflow.app.Action attribute) (hpcflow.sdk.core.actions.Action attribute) input_files (hpcflow.app.Action attribute) (hpcflow.app.Element property) (hpcflow.app.ElementAction property) (hpcflow.app.ElementActionRun property) (hpcflow.app.ElementIteration property) (hpcflow.app.ElementSet attribute) (hpcflow.sdk.core.actions.Action attribute) (hpcflow.sdk.core.actions.ElementAction property) (hpcflow.sdk.core.actions.ElementActionRun property) (hpcflow.sdk.core.element.Element property) (hpcflow.sdk.core.element.ElementIteration property) (hpcflow.sdk.core.task.ElementSet attribute) input_files_path (hpcflow.app.Workflow property) (hpcflow.sdk.core.workflow.Workflow property) input_or_output (hpcflow.app.SchemaInput property) (hpcflow.app.SchemaOutput property) (hpcflow.sdk.core.parameters.SchemaInput property) (hpcflow.sdk.core.parameters.SchemaOutput property) input_path (hpcflow.app.ValueSequence property) (hpcflow.sdk.core.parameters.ValueSequence property) input_source_idx (hpcflow.app.Element property) (hpcflow.sdk.core.element.Element property) input_sources (hpcflow.app.Element property) (hpcflow.app.ElementPropagation attribute) (hpcflow.app.ElementSet attribute) (hpcflow.sdk.core.element.Element property) (hpcflow.sdk.core.task.ElementPropagation attribute) (hpcflow.sdk.core.task.ElementSet attribute) input_type (hpcflow.app.ValueSequence property) (hpcflow.sdk.core.parameters.ValueSequence property) input_types (hpcflow.app.ElementSet property) (hpcflow.app.TaskSchema property) (hpcflow.sdk.core.task.ElementSet property) (hpcflow.sdk.core.task_schema.TaskSchema property) InputFile (class in hpcflow.app) (class in hpcflow.sdk.core.command_files) InputFileGenerator (class in hpcflow.app) (class in hpcflow.sdk.core.command_files) InputFileGeneratorSource (class in hpcflow.app) (class in hpcflow.sdk.core.command_files) inputs (hpcflow.app.Element property) (hpcflow.app.ElementAction property) (hpcflow.app.ElementActionRun property) (hpcflow.app.ElementIteration property) (hpcflow.app.ElementSet attribute) (hpcflow.app.InputFileGenerator attribute) (hpcflow.app.OutputFileParser attribute) (hpcflow.app.TaskSchema attribute) (hpcflow.app.WorkflowTask property) (hpcflow.sdk.core.actions.ElementAction property) (hpcflow.sdk.core.actions.ElementActionRun property) (hpcflow.sdk.core.command_files.InputFileGenerator attribute) (hpcflow.sdk.core.command_files.OutputFileParser attribute) (hpcflow.sdk.core.element.Element property) (hpcflow.sdk.core.element.ElementIteration property) (hpcflow.sdk.core.task.ElementSet attribute) (hpcflow.sdk.core.task.WorkflowTask property) (hpcflow.sdk.core.task_schema.TaskSchema attribute)

InputSource (class in hpcflow.app) (class in hpcflow.sdk.core.parameters) InputSourceType (class in hpcflow.app) InputSourceValidationError InputStatus (class in hpcflow.sdk.core.task) InputValue (class in hpcflow.app) (class in hpcflow.sdk.core.parameters) InputValueDuplicateSequenceAddress insert_ID (hpcflow.app.Task property) (hpcflow.app.WorkflowTask property) (hpcflow.sdk.core.task.Task property) (hpcflow.sdk.core.task.WorkflowTask property) instances (hpcflow.app.Executable attribute) (hpcflow.sdk.core.environment.Executable attribute) InvalidIdentifier InvalidInputSourceTaskReference invocation_command (hpcflow.sdk.runtime.RunTimeInfo property) invoking_user_id (hpcflow.sdk.config.config.Config attribute) is_array (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property) is_conda_venv (hpcflow.sdk.runtime.RunTimeInfo attribute) is_config_loaded (hpcflow.sdk.app.App property) (hpcflow.sdk.app.BaseApp property) is_dict_values (hpcflow.sdk.core.json_like.ChildObjectSpec attribute) is_dict_values_ensure_list (hpcflow.sdk.core.json_like.ChildObjectSpec attribute) is_enum (hpcflow.sdk.core.json_like.ChildObjectSpec attribute) is_extra (hpcflow.sdk.core.task.InputStatus property) is_file (hpcflow.app.Parameter attribute) (hpcflow.sdk.core.parameters.Parameter attribute) is_frozen (hpcflow.sdk.runtime.RunTimeInfo attribute) is_fsspec_url() (in module hpcflow.sdk.core.utils) is_in() (hpcflow.app.InputSource method) (hpcflow.sdk.core.parameters.InputSource method) is_input_type_provided() (hpcflow.app.ElementSet method) (hpcflow.sdk.core.task.ElementSet method) is_input_type_required() (hpcflow.app.Action method) (hpcflow.app.Task method) (hpcflow.sdk.core.actions.Action method) (hpcflow.sdk.core.task.Task method) is_interactive (hpcflow.sdk.runtime.RunTimeInfo attribute) is_item_set() (hpcflow.sdk.config.config_file.ConfigFile method) is_jobscript_active() (hpcflow.app.DirectPosix method) (hpcflow.app.DirectWindows method) (hpcflow.app.SGEPosix method) (hpcflow.app.SlurmPosix method) (hpcflow.sdk.submission.schedulers.direct.DirectPosix method) (hpcflow.sdk.submission.schedulers.direct.DirectScheduler method) (hpcflow.sdk.submission.schedulers.direct.DirectWindows method) (hpcflow.sdk.submission.schedulers.Scheduler method) (hpcflow.sdk.submission.schedulers.sge.SGEPosix method) (hpcflow.sdk.submission.schedulers.slurm.SlurmPosix method) is_multiple (hpcflow.sdk.core.json_like.ChildObjectSpec attribute) is_num_cores_supported() (hpcflow.app.DirectPosix static method) (hpcflow.app.DirectWindows static method) (hpcflow.app.SGEPosix static method) (hpcflow.app.SlurmPosix static method) (hpcflow.sdk.submission.schedulers.direct.DirectPosix static method) (hpcflow.sdk.submission.schedulers.direct.DirectScheduler static method) (hpcflow.sdk.submission.schedulers.direct.DirectWindows static method) (hpcflow.sdk.submission.schedulers.NullScheduler static method) (hpcflow.sdk.submission.schedulers.Scheduler static method) (hpcflow.sdk.submission.schedulers.sge.SGEPosix static method) (hpcflow.sdk.submission.schedulers.slurm.SlurmPosix static method) is_parallel (hpcflow.app.ElementResources property) (hpcflow.sdk.core.element.ElementResources property) is_parameter_set() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) is_pending (hpcflow.app.Element property) (hpcflow.app.ElementActionRun property) (hpcflow.app.ElementIteration property) (hpcflow.sdk.core.actions.ElementActionRun property) (hpcflow.sdk.core.element.Element property) (hpcflow.sdk.core.element.ElementIteration property) (hpcflow.sdk.persistence.base.StoreEAR attribute) (hpcflow.sdk.persistence.base.StoreElement attribute) (hpcflow.sdk.persistence.base.StoreElementIter attribute) (hpcflow.sdk.persistence.base.StoreParameter attribute) (hpcflow.sdk.persistence.base.StoreTask attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreEAR attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreElement attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreElementIter attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreParameter attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreTask attribute) is_provided (hpcflow.sdk.core.task.InputStatus attribute) is_regex (hpcflow.app.FileNameSpec attribute) (hpcflow.sdk.core.command_files.FileNameSpec attribute) is_required (hpcflow.sdk.core.task.InputStatus attribute) is_set (hpcflow.app.ElementParameter property) (hpcflow.sdk.core.element.ElementParameter property) (hpcflow.sdk.persistence.base.StoreParameter attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreParameter attribute) is_single_attribute (hpcflow.sdk.core.json_like.ChildObjectSpec attribute) is_snippet_script() (hpcflow.app.Action static method) (hpcflow.sdk.core.actions.Action static method) is_sub_value (hpcflow.app.InputValue property) (hpcflow.app.ValueSequence property) (hpcflow.sdk.core.parameters.InputValue property) (hpcflow.sdk.core.parameters.ValueSequence property) is_submittable (hpcflow.sdk.persistence.base.PersistentStore property) (hpcflow.sdk.persistence.json.JSONPersistentStore property) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore property) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore property) is_submitted (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property) is_template_components_loaded (hpcflow.sdk.app.App property) (hpcflow.sdk.app.BaseApp property) is_venv (hpcflow.sdk.runtime.RunTimeInfo attribute) isdir() (hpcflow.sdk.core.utils.JSONLikeDirSnapShot method) iter_iter_dependencies (hpcflow.sdk.core.cache.DependencyCache attribute) iter_run_dependencies (hpcflow.sdk.core.cache.DependencyCache attribute) iterable_parameters (hpcflow.app.WorkflowLoop property) (hpcflow.sdk.core.loop.WorkflowLoop property) iteration_IDs (hpcflow.app.Element property) (hpcflow.sdk.core.element.Element property) (hpcflow.sdk.persistence.base.StoreElement attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreElement attribute) iterations (hpcflow.app.Element property) (hpcflow.sdk.core.cache.DependencyCache attribute) (hpcflow.sdk.core.element.Element property) (hpcflow.sdk.core.loop_cache.LoopCache attribute)

J

Jobscript (class in hpcflow.app) (class in hpcflow.sdk.submission.jobscript) JOBSCRIPT_IDX hpcflow-internal-workflow-PATH-write-commands command line option jobscript_indices (hpcflow.app.Submission property) (hpcflow.sdk.submission.submission.Submission property) jobscript_name (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property) jobscript_parallelism (hpcflow.sdk.persistence.base.PersistentStoreFeatures attribute) jobscript_path (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property) JobscriptElementState (class in hpcflow.sdk.submission.jobscript_info) jobscripts (hpcflow.app.Submission property) (hpcflow.sdk.submission.submission.Submission property) jobscripts_to_list() (in module hpcflow.sdk.submission.jobscript) JobscriptSubmissionFailure join() (hpcflow.sdk.helper.watcher.MonitorController method) JS_ACT_IDX hpcflow-internal-workflow-PATH-set-ear-end command line option JS_ACTION_IDX hpcflow-internal-workflow-PATH-write-commands command line option JS_DIRECT_HEADER (hpcflow.sdk.submission.shells.bash.Bash attribute) (hpcflow.sdk.submission.shells.bash.WSLBash attribute) (hpcflow.sdk.submission.shells.powershell.WindowsPowerShell attribute) JS_ELEMENT_ARRAY (hpcflow.sdk.submission.shells.bash.Bash attribute) (hpcflow.sdk.submission.shells.bash.WSLBash attribute) JS_ELEMENT_LOOP (hpcflow.sdk.submission.shells.bash.Bash attribute) (hpcflow.sdk.submission.shells.bash.WSLBash attribute) (hpcflow.sdk.submission.shells.powershell.WindowsPowerShell attribute) JS_ENV_SETUP_INDENT (hpcflow.sdk.submission.shells.bash.Bash attribute) (hpcflow.sdk.submission.shells.bash.WSLBash attribute) (hpcflow.sdk.submission.shells.powershell.WindowsPowerShell attribute)

JS_EXT (hpcflow.sdk.submission.shells.bash.Bash attribute) (hpcflow.sdk.submission.shells.bash.WSLBash attribute) (hpcflow.sdk.submission.shells.powershell.WindowsPowerShell attribute) JS_HEADER (hpcflow.sdk.submission.shells.bash.Bash attribute) (hpcflow.sdk.submission.shells.bash.WSLBash attribute) (hpcflow.sdk.submission.shells.powershell.WindowsPowerShell attribute) JS_IDX hpcflow-internal-workflow-PATH-set-ear-end command line option hpcflow-workflow-WORKFLOW_REF-sub-SUB_IDX-js command line option JS_INDENT (hpcflow.sdk.submission.shells.bash.Bash attribute) (hpcflow.sdk.submission.shells.bash.WSLBash attribute) (hpcflow.sdk.submission.shells.powershell.WindowsPowerShell attribute) JS_MAIN (hpcflow.sdk.submission.shells.bash.Bash attribute) (hpcflow.sdk.submission.shells.bash.WSLBash attribute) (hpcflow.sdk.submission.shells.powershell.WindowsPowerShell attribute) JS_parallelism (hpcflow.app.Submission property) (hpcflow.sdk.submission.submission.Submission property) js_parallelism_option() (in module hpcflow.sdk.cli_common) JS_SCHEDULER_HEADER (hpcflow.sdk.submission.shells.bash.Bash attribute) (hpcflow.sdk.submission.shells.bash.WSLBash attribute) JS_SHEBANG (hpcflow.sdk.submission.shells.bash.Bash attribute) (hpcflow.sdk.submission.shells.bash.WSLBash attribute) (hpcflow.sdk.submission.shells.powershell.WindowsPowerShell attribute) json_like_name (hpcflow.sdk.core.json_like.ChildObjectSpec attribute) JSONFileStoreResource (class in hpcflow.sdk.persistence.store_resource) JSONLike (class in hpcflow.sdk.core.json_like) JSONLikeDirSnapShot (class in hpcflow.sdk.core.utils) JSONPersistentStore (class in hpcflow.sdk.persistence.json)

K

kill_proc_tree() (in module hpcflow.sdk.helper.helper) KNOWN_NAME hpcflow-config-init command line option

known_subs_file_path (hpcflow.sdk.app.App property) (hpcflow.sdk.app.BaseApp property) kwargs (hpcflow.app.ActionScope attribute) (hpcflow.sdk.core.actions.ActionScope attribute)

L

label (hpcflow.app.Executable attribute) (hpcflow.app.FileSpec attribute) (hpcflow.app.InputValue attribute) (hpcflow.app.OutputLabel attribute) (hpcflow.app.ValueSequence attribute) (hpcflow.sdk.core.command_files.FileSpec attribute) (hpcflow.sdk.core.environment.Executable attribute) (hpcflow.sdk.core.parameters.InputValue attribute) (hpcflow.sdk.core.parameters.ValueSequence attribute) (hpcflow.sdk.core.task.OutputLabel attribute) labelled_info() (hpcflow.app.SchemaInput method) (hpcflow.sdk.core.parameters.SchemaInput method) labelled_type (hpcflow.app.InputValue property) (hpcflow.app.ValueSequence property) (hpcflow.sdk.core.parameters.InputValue property) (hpcflow.sdk.core.parameters.ValueSequence property) labels (hpcflow.app.SchemaInput attribute) (hpcflow.sdk.core.parameters.SchemaInput attribute) latest_iteration (hpcflow.app.Element property) (hpcflow.sdk.core.element.Element property) linspace_rect() (in module hpcflow.sdk.core.utils) linux_release_file (hpcflow.sdk.config.config.Config attribute) (hpcflow.sdk.submission.shells.bash.Bash property) (hpcflow.sdk.submission.shells.bash.WSLBash property) list_attrs() (hpcflow.app.CommandFilesList method) (hpcflow.app.EnvironmentsList method) (hpcflow.app.ExecutablesList method) (hpcflow.app.GroupList method) (hpcflow.app.ParametersList method) (hpcflow.app.ResourceList method) (hpcflow.app.TaskList method) (hpcflow.app.TaskSchemasList method) (hpcflow.app.TaskTemplateList method) (hpcflow.app.WorkflowLoopList method) (hpcflow.app.WorkflowTaskList method) (hpcflow.sdk.core.object_list.AppDataList method) (hpcflow.sdk.core.object_list.CommandFilesList method) (hpcflow.sdk.core.object_list.DotAccessObjectList method) (hpcflow.sdk.core.object_list.EnvironmentsList method) (hpcflow.sdk.core.object_list.ExecutablesList method) (hpcflow.sdk.core.object_list.GroupList method) (hpcflow.sdk.core.object_list.ObjectList method) (hpcflow.sdk.core.object_list.ParametersList method) (hpcflow.sdk.core.object_list.ResourceList method) (hpcflow.sdk.core.object_list.TaskList method) (hpcflow.sdk.core.object_list.TaskSchemasList method) (hpcflow.sdk.core.object_list.TaskTemplateList method) (hpcflow.sdk.core.object_list.WorkflowLoopList method) (hpcflow.sdk.core.object_list.WorkflowTaskList method)

list_demo_data_files() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) list_demo_workflows() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) list_to_dict() (in module hpcflow.sdk.core.utils) load_builtin_template_component_data() (hpcflow.sdk.app.App class method) (hpcflow.sdk.app.BaseApp class method) load_config() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) (in module hpcflow.sdk.core.utils) load_demo_workflow() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) load_template_components() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) LOCAL (hpcflow.app.InputSourceType attribute) local() (hpcflow.app.InputSource class method) (hpcflow.sdk.core.parameters.InputSource class method) log (hpcflow.sdk.app.App property) (hpcflow.sdk.app.BaseApp property) log_console_level (hpcflow.sdk.config.config.Config attribute) log_file_level (hpcflow.sdk.config.config.Config attribute) log_file_path (hpcflow.sdk.config.config.Config attribute) logger (hpcflow.sdk.app.App property) (hpcflow.sdk.app.BaseApp property) (hpcflow.sdk.config.config_file.ConfigFile attribute) (hpcflow.sdk.log.AppLog attribute) (hpcflow.sdk.persistence.base.PersistentStore property) (hpcflow.sdk.persistence.json.JSONPersistentStore property) (hpcflow.sdk.persistence.pending.PendingChanges property) (hpcflow.sdk.persistence.store_resource.JSONFileStoreResource property) (hpcflow.sdk.persistence.store_resource.StoreResource property) (hpcflow.sdk.persistence.store_resource.ZarrAttrsStoreResource property) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore property) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore property) (hpcflow.sdk.runtime.RunTimeInfo attribute) Loop (class in hpcflow.app) (class in hpcflow.sdk.core.loop) loop_idx (hpcflow.app.ElementIteration property) (hpcflow.sdk.core.element.ElementIteration property) (hpcflow.sdk.persistence.base.StoreElementIter attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreElementIter attribute) LOOP_NAME hpcflow-internal-workflow-PATH-check-loop command line option LoopAlreadyExistsError LoopCache (class in hpcflow.sdk.core.loop_cache) loops (hpcflow.app.Workflow property) (hpcflow.app.WorkflowTemplate attribute) (hpcflow.sdk.core.workflow.Workflow property) (hpcflow.sdk.core.workflow.WorkflowTemplate attribute) LoopTaskSubsetError

M

machine (hpcflow.sdk.config.config.Config attribute) MAIN (hpcflow.app.ActionScopeType attribute) main() (hpcflow.app.ActionScope class method) (hpcflow.sdk.core.actions.ActionScope class method) make_actions() (in module hpcflow.sdk.core.test_utils) make_and_submit_demo_workflow() (in module hpcflow.app) make_and_submit_workflow() (in module hpcflow.app) make_artifact_dirs() (hpcflow.app.Jobscript method) (hpcflow.sdk.submission.jobscript.Jobscript method) make_cli() (in module hpcflow.sdk.cli) make_demo_workflow() (in module hpcflow.app) make_parameters() (in module hpcflow.sdk.core.test_utils) make_persistent() (hpcflow.app.InputFile method) (hpcflow.app.InputFileGeneratorSource method) (hpcflow.app.InputValue method) (hpcflow.app.OutputFileParserSource method) (hpcflow.app.ResourceSpec method) (hpcflow.app.TaskSchema method) (hpcflow.app.ValuePerturbation method) (hpcflow.app.ValueSequence method) (hpcflow.sdk.core.command_files.InputFile method) (hpcflow.sdk.core.command_files.InputFileGeneratorSource method) (hpcflow.sdk.core.command_files.OutputFileParserSource method) (hpcflow.sdk.core.parameters.AbstractInputValue method) (hpcflow.sdk.core.parameters.InputValue method) (hpcflow.sdk.core.parameters.ResourceSpec method) (hpcflow.sdk.core.parameters.ValuePerturbation method) (hpcflow.sdk.core.parameters.ValueSequence method) (hpcflow.sdk.core.task_schema.TaskSchema method) make_schemas() (in module hpcflow.sdk.core.test_utils) make_status_opt() (in module hpcflow.sdk.cli_common) make_tasks() (in module hpcflow.sdk.core.test_utils) make_test_data_YAML_workflow() (in module hpcflow.sdk.core.test_utils) make_test_data_YAML_workflow_template() (in module hpcflow.sdk.core.test_utils) make_test_store_from_spec() (hpcflow.sdk.persistence.json.JSONPersistentStore class method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore class method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore class method) make_workflow() (in module hpcflow.app) (in module hpcflow.sdk.core.test_utils) make_workflow_id() (in module hpcflow.sdk.core.utils) MalformedNestingOrderPath MalformedParameterPathError MalformedWorkflowError max_array_items (hpcflow.app.ElementResources attribute) (hpcflow.app.ResourceSpec property) (hpcflow.sdk.core.element.ElementResources attribute) (hpcflow.sdk.core.parameters.ResourceSpec property) MayNeedObjectError merge_envs (hpcflow.app.ElementSet attribute) (hpcflow.app.Task attribute) (hpcflow.app.WorkflowTemplate attribute) (hpcflow.sdk.core.task.ElementSet attribute) (hpcflow.sdk.core.task.Task attribute) (hpcflow.sdk.core.workflow.WorkflowTemplate attribute) merge_jobscripts_across_tasks() (in module hpcflow.sdk.submission.jobscript) merge_other() (hpcflow.app.ResourceList method) (hpcflow.sdk.core.object_list.ResourceList method) merge_resources (hpcflow.app.WorkflowTemplate attribute) (hpcflow.sdk.core.workflow.WorkflowTemplate attribute) metadata (hpcflow.app.ElementActionRun property) (hpcflow.sdk.core.actions.ElementActionRun property) (hpcflow.sdk.persistence.base.StoreEAR attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreEAR attribute) method (hpcflow.app.TaskSchema attribute) (hpcflow.sdk.core.task_schema.TaskSchema attribute) MissingActionEnvironment MissingCompatibleActionEnvironment MissingElementGroup MissingEnvironmentError MissingEnvironmentExecutableError MissingEnvironmentExecutableInstanceError MissingEnvironmentFileError MissingInputs MissingParameterData MissingStoreEARError MissingStoreElementError MissingStoreElementIterationError MissingStoreTaskError MissingTaskSchemaFileError

MissingVariableSubstitutionError module hpcflow.app hpcflow.sdk hpcflow.sdk.app hpcflow.sdk.cli hpcflow.sdk.cli_common hpcflow.sdk.config hpcflow.sdk.config.callbacks hpcflow.sdk.config.cli hpcflow.sdk.config.config hpcflow.sdk.config.config_file hpcflow.sdk.config.errors hpcflow.sdk.core hpcflow.sdk.core.actions hpcflow.sdk.core.cache hpcflow.sdk.core.command_files hpcflow.sdk.core.commands hpcflow.sdk.core.element hpcflow.sdk.core.environment hpcflow.sdk.core.errors hpcflow.sdk.core.json_like hpcflow.sdk.core.loop hpcflow.sdk.core.loop_cache hpcflow.sdk.core.object_list hpcflow.sdk.core.parallel hpcflow.sdk.core.parameters hpcflow.sdk.core.rule hpcflow.sdk.core.run_dir_files hpcflow.sdk.core.task hpcflow.sdk.core.task_schema hpcflow.sdk.core.test_utils hpcflow.sdk.core.utils hpcflow.sdk.core.validation hpcflow.sdk.core.workflow hpcflow.sdk.core.zarr_io hpcflow.sdk.data hpcflow.sdk.demo hpcflow.sdk.demo.cli hpcflow.sdk.helper hpcflow.sdk.helper.cli hpcflow.sdk.helper.helper hpcflow.sdk.helper.watcher hpcflow.sdk.log hpcflow.sdk.persistence hpcflow.sdk.persistence.base hpcflow.sdk.persistence.json hpcflow.sdk.persistence.pending hpcflow.sdk.persistence.store_resource hpcflow.sdk.persistence.utils hpcflow.sdk.persistence.zarr hpcflow.sdk.runtime hpcflow.sdk.submission hpcflow.sdk.submission.jobscript hpcflow.sdk.submission.jobscript_info hpcflow.sdk.submission.schedulers hpcflow.sdk.submission.schedulers.direct hpcflow.sdk.submission.schedulers.sge hpcflow.sdk.submission.schedulers.slurm hpcflow.sdk.submission.schedulers.utils hpcflow.sdk.submission.shells hpcflow.sdk.submission.shells.base hpcflow.sdk.submission.shells.bash hpcflow.sdk.submission.shells.os_version hpcflow.sdk.submission.shells.powershell hpcflow.sdk.submission.submission hpcflow.sdk.typing module (hpcflow.sdk.app.App attribute) (hpcflow.sdk.app.BaseApp attribute) MonitorController (class in hpcflow.sdk.helper.watcher) mro() (hpcflow.sdk.app.Singleton method) (hpcflow.sdk.core.utils.Singleton method) mtime() (hpcflow.sdk.core.utils.JSONLikeDirSnapShot method) multi_input_types (hpcflow.app.TaskSchema property) (hpcflow.sdk.core.task_schema.TaskSchema property) multiple (hpcflow.app.SchemaInput attribute) (hpcflow.sdk.core.parameters.SchemaInput attribute) MultipleEnvironmentsError multiplicative_factor (hpcflow.app.ValuePerturbation attribute) (hpcflow.sdk.core.parameters.ValuePerturbation attribute)

N

NAME hpcflow-config-add-scheduler command line option hpcflow-config-add-shell command line option hpcflow-config-append command line option hpcflow-config-get command line option hpcflow-config-pop command line option hpcflow-config-prepend command line option hpcflow-config-set command line option hpcflow-config-unset command line option hpcflow-config-update command line option hpcflow-configure-env command line option hpcflow-internal-workflow-PATH-save-parameter command line option name (hpcflow.app.ElementGroup attribute) (hpcflow.app.Environment attribute) (hpcflow.app.FileNameSpec attribute) (hpcflow.app.FileSpec attribute) (hpcflow.app.Loop property) (hpcflow.app.SchemaInput property) (hpcflow.app.SchemaOutput property) (hpcflow.app.SchemaParameter property) (hpcflow.app.Task property) (hpcflow.app.TaskObjective attribute) (hpcflow.app.TaskSchema property) (hpcflow.app.ValuePerturbation attribute) (hpcflow.app.Workflow property) (hpcflow.app.WorkflowLoop property) (hpcflow.app.WorkflowTask property) (hpcflow.app.WorkflowTemplate attribute) (hpcflow.sdk.app.App attribute) (hpcflow.sdk.app.BaseApp attribute) (hpcflow.sdk.core.command_files.FileNameSpec attribute) (hpcflow.sdk.core.command_files.FileSpec attribute) (hpcflow.sdk.core.element.ElementGroup attribute) (hpcflow.sdk.core.environment.Environment attribute) (hpcflow.sdk.core.json_like.ChildObjectSpec attribute) (hpcflow.sdk.core.loop.Loop property) (hpcflow.sdk.core.loop.WorkflowLoop property) (hpcflow.sdk.core.parameters.SchemaInput property) (hpcflow.sdk.core.parameters.SchemaOutput property) (hpcflow.sdk.core.parameters.SchemaParameter property) (hpcflow.sdk.core.parameters.ValuePerturbation attribute) (hpcflow.sdk.core.task.Task property) (hpcflow.sdk.core.task.WorkflowTask property) (hpcflow.sdk.core.task_schema.TaskObjective attribute) (hpcflow.sdk.core.task_schema.TaskSchema property) (hpcflow.sdk.core.workflow.Workflow property) (hpcflow.sdk.core.workflow.WorkflowTemplate attribute) (hpcflow.sdk.runtime.RunTimeInfo attribute) name_option() (in module hpcflow.sdk.cli_common) needs_submit (hpcflow.app.Submission property) (hpcflow.sdk.submission.submission.Submission property) nesting_order (hpcflow.app.ElementPropagation attribute) (hpcflow.app.ElementSet attribute) (hpcflow.app.ValueSequence attribute) (hpcflow.sdk.core.parameters.ValueSequence attribute) (hpcflow.sdk.core.task.ElementPropagation attribute) (hpcflow.sdk.core.task.ElementSet attribute) NEVER (hpcflow.app.ParameterPropagationMode attribute) new_empty_loop() (hpcflow.app.WorkflowLoop class method) (hpcflow.sdk.core.loop.WorkflowLoop class method) new_empty_task() (hpcflow.app.WorkflowTask class method) (hpcflow.sdk.core.task.WorkflowTask class method) NoAvailableElementSetsError NoCLIFormatMethodError NoCoincidentInputSources NoCompatibleSGEPEError non_iterable_parameters (hpcflow.app.Loop property) (hpcflow.sdk.core.loop.Loop property) non_universal_input_types (hpcflow.app.Task property) (hpcflow.sdk.core.task.Task property) normalise() (hpcflow.app.ResourceList class method) (hpcflow.sdk.core.object_list.ResourceList class method) normalised_files_path (hpcflow.app.InputFile property) (hpcflow.sdk.core.command_files.InputFile property) normalised_inputs_path (hpcflow.app.InputValue property) (hpcflow.app.ValueSequence property) (hpcflow.sdk.core.parameters.InputValue property) (hpcflow.sdk.core.parameters.ValueSequence property) normalised_path (hpcflow.app.InputFile property) (hpcflow.app.InputValue property) (hpcflow.app.ResourceSpec property) (hpcflow.app.ValueSequence property) (hpcflow.sdk.core.command_files.InputFile property) (hpcflow.sdk.core.parameters.InputValue property) (hpcflow.sdk.core.parameters.ResourceSpec property) (hpcflow.sdk.core.parameters.ValueSequence property)

normalised_resources_path (hpcflow.app.ResourceSpec property) (hpcflow.sdk.core.parameters.ResourceSpec property) NotSubmitMachineError nth_key() (in module hpcflow.sdk.core.utils) nth_value() (in module hpcflow.sdk.core.utils) NULL (hpcflow.sdk.core.parameters.NullDefault attribute) NullDefault (class in hpcflow.sdk.core.parameters) NullScheduler (class in hpcflow.sdk.submission.schedulers) num_actions (hpcflow.app.Jobscript property) (hpcflow.app.WorkflowTask property) (hpcflow.sdk.core.task.WorkflowTask property) (hpcflow.sdk.submission.jobscript.Jobscript property) num_added_iterations (hpcflow.app.WorkflowLoop property) (hpcflow.sdk.core.loop.WorkflowLoop property) num_added_tasks (hpcflow.app.Workflow property) (hpcflow.sdk.core.workflow.Workflow property) num_all_schema_actions (hpcflow.app.Task property) (hpcflow.sdk.core.task.Task property) num_cores (hpcflow.app.ElementResources attribute) (hpcflow.app.ExecutableInstance attribute) (hpcflow.app.ResourceSpec property) (hpcflow.sdk.core.element.ElementResources attribute) (hpcflow.sdk.core.environment.ExecutableInstance attribute) (hpcflow.sdk.core.parameters.ResourceSpec property) num_cores_per_node (hpcflow.app.ElementResources attribute) (hpcflow.app.ResourceSpec property) (hpcflow.sdk.core.element.ElementResources attribute) (hpcflow.sdk.core.parameters.ResourceSpec property) num_EARs (hpcflow.app.Workflow property) (hpcflow.sdk.core.workflow.Workflow property) num_EARs_cache (hpcflow.sdk.persistence.base.PersistentStore property) (hpcflow.sdk.persistence.json.JSONPersistentStore property) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore property) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore property) num_element_iterations (hpcflow.app.Workflow property) (hpcflow.sdk.core.workflow.Workflow property) num_element_sets (hpcflow.app.Task property) (hpcflow.app.WorkflowTask property) (hpcflow.sdk.core.task.Task property) (hpcflow.sdk.core.task.WorkflowTask property) num_elements (hpcflow.app.Jobscript property) (hpcflow.app.Workflow property) (hpcflow.app.WorkflowTask property) (hpcflow.sdk.core.task.WorkflowTask property) (hpcflow.sdk.core.workflow.Workflow property) (hpcflow.sdk.submission.jobscript.Jobscript property) num_iterations (hpcflow.app.Loop property) (hpcflow.app.WorkflowLoop property) (hpcflow.sdk.core.loop.Loop property) (hpcflow.sdk.core.loop.WorkflowLoop property) num_loops (hpcflow.app.Workflow property) (hpcflow.sdk.core.workflow.Workflow property) num_nodes (hpcflow.app.ElementResources attribute) (hpcflow.app.ResourceSpec property) (hpcflow.sdk.core.element.ElementResources attribute) (hpcflow.sdk.core.parameters.ResourceSpec property) num_runs (hpcflow.app.ElementAction property) (hpcflow.sdk.core.actions.ElementAction property) num_submissions (hpcflow.app.Workflow property) (hpcflow.sdk.core.workflow.Workflow property) num_tasks (hpcflow.app.Workflow property) (hpcflow.sdk.core.workflow.Workflow property) num_tasks_cache (hpcflow.sdk.persistence.base.PersistentStore property) (hpcflow.sdk.persistence.json.JSONPersistentStore property) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore property) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore property) num_threads (hpcflow.app.ElementResources attribute) (hpcflow.app.ResourceSpec property) (hpcflow.sdk.core.element.ElementResources attribute) (hpcflow.sdk.core.parameters.ResourceSpec property) number (hpcflow.app.ElementRepeats attribute) (hpcflow.sdk.core.element.ElementRepeats attribute) NumCores (class in hpcflow.app) (class in hpcflow.sdk.core.environment)

O

objective (hpcflow.app.Task property) (hpcflow.app.TaskSchema attribute) (hpcflow.sdk.core.task.Task property) (hpcflow.sdk.core.task_schema.TaskSchema attribute) ObjectList (class in hpcflow.sdk.core.object_list) ObjectListMultipleMatchError on_modified() (hpcflow.sdk.helper.watcher.MonitorController method) (hpcflow.sdk.helper.watcher.WorkflowMonitor method) open() (hpcflow.sdk.persistence.store_resource.JSONFileStoreResource method) (hpcflow.sdk.persistence.store_resource.StoreResource method) (hpcflow.sdk.persistence.store_resource.ZarrAttrsStoreResource method) open_file() (in module hpcflow.sdk.core.utils) options (hpcflow.app.OutputFileParser attribute) (hpcflow.sdk.core.command_files.OutputFileParser attribute) os_name (hpcflow.app.ElementResources attribute) (hpcflow.app.Jobscript property) (hpcflow.app.ResourceSpec property) (hpcflow.sdk.core.element.ElementResources attribute) (hpcflow.sdk.core.parameters.ResourceSpec property) (hpcflow.sdk.submission.jobscript.Jobscript property) output (hpcflow.app.OutputFileParser attribute) OUTPUT (hpcflow.app.TaskSourceType attribute) output (hpcflow.sdk.core.command_files.OutputFileParser attribute) OUTPUT_FILE_PARSER (hpcflow.app.ActionScopeType attribute) output_file_parser() (hpcflow.app.ActionScope class method) (hpcflow.sdk.core.actions.ActionScope class method) output_file_parsers (hpcflow.app.Action attribute) (hpcflow.sdk.core.actions.Action attribute) output_files (hpcflow.app.Action attribute) (hpcflow.app.Element property) (hpcflow.app.ElementAction property) (hpcflow.app.ElementActionRun property) (hpcflow.app.ElementIteration property) (hpcflow.app.OutputFileParser attribute) (hpcflow.sdk.core.actions.Action attribute) (hpcflow.sdk.core.actions.ElementAction property) (hpcflow.sdk.core.actions.ElementActionRun property) (hpcflow.sdk.core.command_files.OutputFileParser attribute) (hpcflow.sdk.core.element.Element property) (hpcflow.sdk.core.element.ElementIteration property)

output_labels (hpcflow.app.Task property) (hpcflow.sdk.core.task.Task property) output_types (hpcflow.app.TaskSchema property) (hpcflow.sdk.core.task_schema.TaskSchema property) OutputFileParser (class in hpcflow.app) (class in hpcflow.sdk.core.command_files) OutputFileParserNoOutputError OutputFileParserSource (class in hpcflow.app) (class in hpcflow.sdk.core.command_files) OutputLabel (class in hpcflow.app) (class in hpcflow.sdk.core.task) outputs (hpcflow.app.Element property) (hpcflow.app.ElementAction property) (hpcflow.app.ElementActionRun property) (hpcflow.app.ElementIteration property) (hpcflow.app.OutputFileParser attribute) (hpcflow.app.TaskSchema attribute) (hpcflow.app.WorkflowTask property) (hpcflow.sdk.core.actions.ElementAction property) (hpcflow.sdk.core.actions.ElementActionRun property) (hpcflow.sdk.core.command_files.OutputFileParser attribute) (hpcflow.sdk.core.element.Element property) (hpcflow.sdk.core.element.ElementIteration property) (hpcflow.sdk.core.task.WorkflowTask property) (hpcflow.sdk.core.task_schema.TaskSchema attribute) outstanding_jobscripts (hpcflow.app.Submission property) (hpcflow.sdk.submission.submission.Submission property) overwrite_option() (in module hpcflow.sdk.cli_common)

P

P1_parameter_cls (class in hpcflow.sdk.core.test_utils) P1_sub_parameter_cls (class in hpcflow.sdk.core.test_utils) P1_sub_parameter_cls_2 (class in hpcflow.sdk.core.test_utils) package_name (hpcflow.sdk.app.App attribute) (hpcflow.sdk.app.BaseApp attribute) (hpcflow.sdk.runtime.RunTimeInfo attribute) parallel_mode (hpcflow.app.ElementResources attribute) (hpcflow.app.ExecutableInstance attribute) (hpcflow.app.ResourceSpec property) (hpcflow.sdk.core.element.ElementResources attribute) (hpcflow.sdk.core.environment.ExecutableInstance attribute) (hpcflow.sdk.core.parameters.ResourceSpec property) ParallelMode (class in hpcflow.sdk.core.parallel) param_sources_cache (hpcflow.sdk.persistence.base.PersistentStore property) (hpcflow.sdk.persistence.json.JSONPersistentStore property) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore property) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore property) Parameter (class in hpcflow.app) (class in hpcflow.sdk.core.parameters) parameter (hpcflow.app.InputValue attribute) (hpcflow.app.OutputLabel attribute) (hpcflow.app.SchemaInput attribute) (hpcflow.app.SchemaOutput attribute) (hpcflow.app.SubParameter attribute) (hpcflow.app.ValueSequence property) (hpcflow.sdk.core.parameters.InputValue attribute) (hpcflow.sdk.core.parameters.SchemaInput attribute) (hpcflow.sdk.core.parameters.SchemaOutput attribute) (hpcflow.sdk.core.parameters.SubParameter attribute) (hpcflow.sdk.core.parameters.ValueSequence property) (hpcflow.sdk.core.task.OutputLabel attribute) parameter_cache (hpcflow.sdk.persistence.base.PersistentStore property) (hpcflow.sdk.persistence.json.JSONPersistentStore property) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore property) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore property) parameter_class_modules (hpcflow.app.TaskSchema attribute) (hpcflow.sdk.core.task_schema.TaskSchema attribute) parameter_sources (hpcflow.sdk.config.config.Config attribute) ParameterPath (class in hpcflow.app) (class in hpcflow.sdk.core.parameters) ParameterPropagationMode (class in hpcflow.app) Parameters (class in hpcflow.app) (class in hpcflow.sdk.core.task) parameters (hpcflow.sdk.app.App property) (hpcflow.sdk.app.BaseApp property) ParametersList (class in hpcflow.app) (class in hpcflow.sdk.core.object_list) ParameterSpecValidationError ParameterValue (class in hpcflow.app) (class in hpcflow.sdk.core.parameters) parent (hpcflow.app.ElementParameter attribute) (hpcflow.sdk.core.element.ElementParameter attribute) parent_ref (hpcflow.sdk.core.json_like.ChildObjectSpec attribute) parents (hpcflow.app.WorkflowLoop property) (hpcflow.sdk.core.loop.WorkflowLoop property) parse_jobscript_wait_spec() (in module hpcflow.sdk.cli) parse_submission_output() (hpcflow.app.DirectPosix method) (hpcflow.app.DirectWindows method) (hpcflow.app.SGEPosix method) (hpcflow.app.SlurmPosix method) (hpcflow.sdk.submission.schedulers.direct.DirectPosix method) (hpcflow.sdk.submission.schedulers.direct.DirectScheduler method) (hpcflow.sdk.submission.schedulers.direct.DirectWindows method) (hpcflow.sdk.submission.schedulers.NullScheduler method) (hpcflow.sdk.submission.schedulers.Scheduler method) (hpcflow.sdk.submission.schedulers.sge.SGEPosix method) (hpcflow.sdk.submission.schedulers.slurm.SlurmPosix method) parse_watch_workflows_file() (hpcflow.sdk.helper.watcher.MonitorController static method) parser (hpcflow.app.OutputFileParserSource attribute) (hpcflow.sdk.core.command_files.OutputFileParserSource attribute) PARTIALLY_SUBMITTED (hpcflow.sdk.submission.submission.SubmissionStatus attribute) PATH hpcflow-internal-workflow command line option path (hpcflow.app.ElementParameter attribute) (hpcflow.app.InputFile property) (hpcflow.app.InputFileGeneratorSource property) (hpcflow.app.InputSource attribute) (hpcflow.app.InputValue attribute) (hpcflow.app.OutputFileParserSource property) (hpcflow.app.ParameterPath attribute) (hpcflow.app.Parameters attribute) (hpcflow.app.Rule attribute) (hpcflow.app.Submission property) (hpcflow.app.ValuePerturbation attribute) (hpcflow.app.ValueSequence attribute) (hpcflow.sdk.config.config_file.ConfigFile attribute) (hpcflow.sdk.core.command_files.InputFile property) (hpcflow.sdk.core.command_files.InputFileGeneratorSource property) (hpcflow.sdk.core.command_files.OutputFileParserSource property) (hpcflow.sdk.core.element.ElementParameter attribute) (hpcflow.sdk.core.parameters.InputSource attribute) (hpcflow.sdk.core.parameters.InputValue attribute) (hpcflow.sdk.core.parameters.ParameterPath attribute) (hpcflow.sdk.core.parameters.ValuePerturbation attribute) (hpcflow.sdk.core.parameters.ValueSequence attribute) (hpcflow.sdk.core.rule.Rule attribute) (hpcflow.sdk.core.task.Parameters attribute) (hpcflow.sdk.submission.submission.Submission property) path() (hpcflow.sdk.core.utils.JSONLikeDirSnapShot method) path_option() (in module hpcflow.sdk.cli_common)

path_split (hpcflow.app.ValueSequence property) (hpcflow.sdk.core.parameters.ValueSequence property) path_type (hpcflow.app.ValueSequence property) (hpcflow.sdk.core.parameters.ValueSequence property) PathLike (in module hpcflow.sdk.typing) paths (hpcflow.sdk.core.utils.JSONLikeDirSnapShot property) pending (hpcflow.sdk.core.actions.EARStatus attribute) (hpcflow.sdk.submission.jobscript_info.JobscriptElementState attribute) PENDING (hpcflow.sdk.submission.submission.SubmissionStatus attribute) PendingChanges (class in hpcflow.sdk.persistence.pending) perm_error_retry() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) persistence_logger (hpcflow.sdk.app.App property) (hpcflow.sdk.app.BaseApp property) PersistentStore (class in hpcflow.sdk.persistence.base) PersistentStoreFeatures (class in hpcflow.sdk.persistence.base) pop() (hpcflow.sdk.config.config.Config method) prefixed_names_unlabelled (hpcflow.app.ElementInputFiles property) (hpcflow.app.ElementInputs property) (hpcflow.app.ElementOutputFiles property) (hpcflow.app.ElementOutputs property) (hpcflow.sdk.core.element.ElementInputFiles property) (hpcflow.sdk.core.element.ElementInputs property) (hpcflow.sdk.core.element.ElementOutputFiles property) (hpcflow.sdk.core.element.ElementOutputs property) prefixed_names_unlabelled_str (hpcflow.app.ElementInputFiles property) (hpcflow.app.ElementInputs property) (hpcflow.app.ElementOutputFiles property) (hpcflow.app.ElementOutputs property) (hpcflow.sdk.core.element.ElementInputFiles property) (hpcflow.sdk.core.element.ElementInputs property) (hpcflow.sdk.core.element.ElementOutputFiles property) (hpcflow.sdk.core.element.ElementOutputs property) prepare_element_resolution() (hpcflow.app.Task method) (hpcflow.sdk.core.task.Task method) prepare_element_run_dirs() (hpcflow.sdk.submission.shells.base.Shell method) (hpcflow.sdk.submission.shells.bash.Bash method) (hpcflow.sdk.submission.shells.bash.WSLBash method) (hpcflow.sdk.submission.shells.powershell.WindowsPowerShell method) prepare_JS_path() (hpcflow.sdk.submission.shells.base.Shell method) (hpcflow.sdk.submission.shells.bash.Bash method) (hpcflow.sdk.submission.shells.bash.WSLBash method) (hpcflow.sdk.submission.shells.powershell.WindowsPowerShell method) prepare_JSON_dump() (hpcflow.app.ParameterValue method) (hpcflow.sdk.core.parameters.ParameterValue method) (hpcflow.sdk.core.test_utils.P1_parameter_cls method) (hpcflow.sdk.core.test_utils.P1_sub_parameter_cls method) (hpcflow.sdk.core.test_utils.P1_sub_parameter_cls_2 method) prepare_persistent_copy() (hpcflow.app.ElementSet method) (hpcflow.sdk.core.task.ElementSet method) prepare_test_store_from_spec() (hpcflow.sdk.persistence.base.PersistentStore static method) (hpcflow.sdk.persistence.json.JSONPersistentStore static method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore static method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore static method) prepared (hpcflow.sdk.core.actions.EARStatus attribute) prepend() (hpcflow.sdk.config.config.Config method) PrettyPrinter (class in hpcflow.sdk.core.utils) PRIMITIVES (in module hpcflow.sdk.core.json_like) print_idx_opt() (in module hpcflow.sdk.cli_common) process_app_invoc_executable() (hpcflow.sdk.submission.shells.base.Shell static method) (hpcflow.sdk.submission.shells.bash.Bash static method) (hpcflow.sdk.submission.shells.bash.WSLBash static method) (hpcflow.sdk.submission.shells.powershell.WindowsPowerShell static method) process_ID (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property) process_JS_header_args() (hpcflow.sdk.submission.shells.base.Shell method) (hpcflow.sdk.submission.shells.bash.Bash method) (hpcflow.sdk.submission.shells.bash.WSLBash method) (hpcflow.sdk.submission.shells.powershell.WindowsPowerShell method) process_resources() (hpcflow.app.DirectPosix class method) (hpcflow.app.DirectWindows class method) (hpcflow.app.SGEPosix class method) (hpcflow.app.SlurmPosix class method) (hpcflow.sdk.submission.schedulers.direct.DirectPosix class method) (hpcflow.sdk.submission.schedulers.direct.DirectScheduler class method) (hpcflow.sdk.submission.schedulers.direct.DirectWindows class method) (hpcflow.sdk.submission.schedulers.sge.SGEPosix class method) (hpcflow.sdk.submission.schedulers.slurm.SlurmPosix class method) process_script_data_formats() (hpcflow.app.Action method) (hpcflow.sdk.core.actions.Action method) process_shell_parameter_output() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) process_std_stream() (hpcflow.app.Command method) (hpcflow.sdk.core.commands.Command method) process_string_nodes() (in module hpcflow.sdk.core.utils) PROCESSING (hpcflow.app.ActionScopeType attribute) processing() (hpcflow.app.ActionScope class method) (hpcflow.sdk.core.actions.ActionScope class method) propagation_mode (hpcflow.app.SchemaOutput attribute) (hpcflow.sdk.core.parameters.SchemaOutput attribute) provides_parameters (hpcflow.app.TaskSchema property) (hpcflow.sdk.core.task_schema.TaskSchema property) provides_parameters() (hpcflow.app.Task method) (hpcflow.sdk.core.task.Task method) PY_TEST_ARGS hpcflow-test command line option pytest_args (hpcflow.sdk.app.App attribute) (hpcflow.sdk.app.BaseApp attribute) python_executable_path (hpcflow.sdk.runtime.RunTimeInfo attribute) python_version (hpcflow.sdk.runtime.RunTimeInfo attribute)

R

raise_on_missing (hpcflow.app.Parameters attribute) (hpcflow.sdk.core.task.Parameters attribute) raise_on_unset (hpcflow.app.Parameters attribute) (hpcflow.sdk.core.task.Parameters attribute) rate_limit_safe_url_to_fs() (in module hpcflow.sdk.app) read_contents() (hpcflow.app.InputFile method) (hpcflow.app.InputFileGeneratorSource method) (hpcflow.app.OutputFileParserSource method) (hpcflow.sdk.core.command_files.InputFile method) (hpcflow.sdk.core.command_files.InputFileGeneratorSource method) (hpcflow.sdk.core.command_files.OutputFileParserSource method) read_JSON_file() (in module hpcflow.sdk.core.utils) read_JSON_string() (in module hpcflow.sdk.core.utils) read_known_submissions_file() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) read_YAML_file() (in module hpcflow.sdk.core.utils) read_YAML_str() (in module hpcflow.sdk.core.utils) rechunk() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) rechunk_backup_opt() (in module hpcflow.sdk.cli_common) rechunk_chunk_size_opt() (in module hpcflow.sdk.cli_common) rechunk_parameter_base() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) rechunk_runs() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) rechunk_status_opt() (in module hpcflow.sdk.cli_common) register_config_get_callback() (hpcflow.sdk.config.config.Config method) register_config_set_callback() (hpcflow.sdk.config.config.Config method) reinstate_replaced_dir() (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) reload() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) reload_config() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) reload_template_components() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) remove_ansi_escape_sequences() (in module hpcflow.sdk.core.utils) remove_file_handlers() (hpcflow.sdk.log.AppLog method) remove_path() (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) remove_replaced_dir() (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) rename_config_key() (hpcflow.sdk.config.config_file.ConfigFile method) rename_path() (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) repeats (hpcflow.app.ElementSet attribute) (hpcflow.sdk.core.task.ElementSet attribute) replace_items() (in module hpcflow.sdk.core.utils) reset() (hpcflow.sdk.config.config.Config method) (hpcflow.sdk.persistence.pending.PendingChanges method) reset_config() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) reshape() (in module hpcflow.sdk.core.utils) resolve_element_data_indices() (hpcflow.app.WorkflowTask static method) (hpcflow.sdk.core.task.WorkflowTask static method)

resolve_fsspec() (in module hpcflow.sdk.core.workflow) resolve_jobscript_dependencies() (in module hpcflow.sdk.submission.jobscript) resolve_jobscripts() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) resolved_executable_name (hpcflow.sdk.runtime.RunTimeInfo property) resolved_executable_path (hpcflow.sdk.runtime.RunTimeInfo property) resolved_script_path (hpcflow.sdk.runtime.RunTimeInfo property) resource_scope (hpcflow.app.ValueSequence property) (hpcflow.sdk.core.parameters.ValueSequence property) ResourceList (class in hpcflow.app) (class in hpcflow.sdk.core.object_list) resources (hpcflow.app.ElementActionRun property) (hpcflow.app.ElementSet attribute) (hpcflow.app.Jobscript property) (hpcflow.app.WorkflowTemplate attribute) (hpcflow.sdk.core.actions.ElementActionRun property) (hpcflow.sdk.core.task.ElementSet attribute) (hpcflow.sdk.core.workflow.WorkflowTemplate attribute) (hpcflow.sdk.submission.jobscript.Jobscript property) ResourceSpec (class in hpcflow.app) (class in hpcflow.sdk.core.parameters) ResourceValidationError restart_helper() (in module hpcflow.sdk.helper.helper) return_element_parameters (hpcflow.app.Parameters attribute) (hpcflow.sdk.core.task.Parameters attribute) rich_repr (hpcflow.sdk.core.actions.EARStatus property) (hpcflow.sdk.submission.jobscript_info.JobscriptElementState property) root_path (hpcflow.sdk.core.utils.JSONLikeDirSnapShot attribute) Rule (class in hpcflow.app) (class in hpcflow.sdk.core.rule) rule (hpcflow.app.ActionRule attribute) (hpcflow.sdk.core.actions.ActionRule attribute) rules (hpcflow.app.Action attribute) (hpcflow.app.Command attribute) (hpcflow.app.ElementFilter attribute) (hpcflow.app.InputFileGenerator attribute) (hpcflow.app.OutputFileParser attribute) (hpcflow.sdk.core.actions.Action attribute) (hpcflow.sdk.core.command_files.InputFileGenerator attribute) (hpcflow.sdk.core.command_files.OutputFileParser attribute) (hpcflow.sdk.core.commands.Command attribute) (hpcflow.sdk.core.element.ElementFilter attribute) run_cmd() (in module hpcflow.sdk.submission.schedulers.utils) run_dependencies (hpcflow.sdk.core.cache.DependencyCache attribute) run_dependents (hpcflow.sdk.core.cache.DependencyCache attribute) run_helper() (in module hpcflow.sdk.helper.helper) run_hostname (hpcflow.app.ElementActionRun property) (hpcflow.sdk.core.actions.ElementActionRun property) (hpcflow.sdk.persistence.base.StoreEAR attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreEAR attribute) run_hpcflow_tests() (in module hpcflow.app) run_tests() (in module hpcflow.app) run_time_info (hpcflow.sdk.app.App property) (hpcflow.sdk.app.BaseApp property) RunDirAppFiles (class in hpcflow.app) (class in hpcflow.sdk.core.run_dir_files) running (hpcflow.sdk.core.actions.EARStatus attribute) (hpcflow.sdk.submission.jobscript_info.JobscriptElementState attribute) RunNotAbortableError runs (hpcflow.app.ElementAction property) (hpcflow.sdk.core.actions.ElementAction property) runtime_info_logger (hpcflow.sdk.app.App property) (hpcflow.sdk.app.BaseApp property) RunTimeInfo (class in hpcflow.sdk.runtime)

S

save() (hpcflow.sdk.config.config.Config method) (hpcflow.sdk.config.config_file.ConfigFile method) (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) save_files (hpcflow.app.Action attribute) (hpcflow.app.OutputFileParser attribute) (hpcflow.sdk.core.actions.Action attribute) (hpcflow.sdk.core.command_files.OutputFileParser attribute) save_from_HDF5_group() (hpcflow.app.ParameterValue class method) (hpcflow.sdk.core.parameters.ParameterValue class method) (hpcflow.sdk.core.test_utils.P1_parameter_cls class method) (hpcflow.sdk.core.test_utils.P1_sub_parameter_cls class method) (hpcflow.sdk.core.test_utils.P1_sub_parameter_cls_2 class method) save_from_JSON() (hpcflow.app.ParameterValue class method) (hpcflow.sdk.core.parameters.ParameterValue class method) (hpcflow.sdk.core.test_utils.P1_parameter_cls class method) (hpcflow.sdk.core.test_utils.P1_sub_parameter_cls class method) (hpcflow.sdk.core.test_utils.P1_sub_parameter_cls_2 class method) save_parameter() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) Scheduler (class in hpcflow.sdk.submission.schedulers) scheduler (hpcflow.app.ElementResources attribute) (hpcflow.app.Jobscript property) (hpcflow.app.ResourceSpec property) (hpcflow.sdk.core.element.ElementResources attribute) (hpcflow.sdk.core.parameters.ResourceSpec property) (hpcflow.sdk.submission.jobscript.Jobscript property) scheduler_args (hpcflow.app.ElementResources attribute) (hpcflow.app.ResourceSpec property) (hpcflow.sdk.core.element.ElementResources attribute) (hpcflow.sdk.core.parameters.ResourceSpec property) scheduler_job_ID (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property) scheduler_js_ref (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property) scheduler_lookup (hpcflow.sdk.app.App property) (hpcflow.sdk.app.BaseApp property) SCHEDULER_NAME hpcflow-submission-scheduler command line option scheduler_name (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property) scheduler_ref (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property) schedulers (hpcflow.sdk.config.config.Config attribute) (hpcflow.sdk.persistence.base.PersistentStoreFeatures attribute) SchedulerVersionsFailure schema (hpcflow.app.Task property) (hpcflow.sdk.core.task.Task property) schema_parameters (hpcflow.app.Element property) (hpcflow.app.ElementIteration property) (hpcflow.sdk.core.element.Element property) (hpcflow.sdk.core.element.ElementIteration property) (hpcflow.sdk.persistence.base.StoreElementIter attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreElementIter attribute) SchemaInput (class in hpcflow.app) (class in hpcflow.sdk.core.parameters) SchemaOutput (class in hpcflow.app) (class in hpcflow.sdk.core.parameters) SchemaParameter (class in hpcflow.app) (class in hpcflow.sdk.core.parameters) schemas (hpcflow.app.Task property) (hpcflow.sdk.core.task.Task property) scope (hpcflow.app.ActionEnvironment attribute) (hpcflow.app.ResourceSpec attribute) (hpcflow.sdk.core.actions.ActionEnvironment attribute) (hpcflow.sdk.core.parameters.ResourceSpec attribute) scratch (hpcflow.app.ElementResources attribute) (hpcflow.app.ResourceSpec property) (hpcflow.sdk.core.element.ElementResources attribute) (hpcflow.sdk.core.parameters.ResourceSpec property) script (hpcflow.app.Action attribute) (hpcflow.app.InputFileGenerator attribute) (hpcflow.app.OutputFileParser attribute) (hpcflow.sdk.core.actions.Action attribute) (hpcflow.sdk.core.command_files.InputFileGenerator attribute) (hpcflow.sdk.core.command_files.OutputFileParser attribute) script_data_files_use_opt (hpcflow.app.Action attribute) (hpcflow.sdk.core.actions.Action attribute) script_data_in (hpcflow.app.Action attribute) (hpcflow.sdk.core.actions.Action attribute) script_data_in_grouped (hpcflow.app.Action property) (hpcflow.sdk.core.actions.Action property) script_data_in_has_direct (hpcflow.app.Action property) (hpcflow.sdk.core.actions.Action property) script_data_in_has_files (hpcflow.app.Action property) (hpcflow.sdk.core.actions.Action property) script_data_out (hpcflow.app.Action attribute) (hpcflow.sdk.core.actions.Action attribute) script_data_out_grouped (hpcflow.app.Action property) (hpcflow.sdk.core.actions.Action property) script_data_out_has_direct (hpcflow.app.Action property) (hpcflow.sdk.core.actions.Action property) script_data_out_has_files (hpcflow.app.Action property) (hpcflow.sdk.core.actions.Action property) script_exe (hpcflow.app.Action attribute) (hpcflow.sdk.core.actions.Action attribute) script_is_python (hpcflow.app.Action property) (hpcflow.sdk.core.actions.Action property) script_pass_env_spec (hpcflow.app.Action attribute) (hpcflow.app.InputFileGenerator attribute) (hpcflow.app.OutputFileParser attribute) (hpcflow.sdk.core.actions.Action attribute) (hpcflow.sdk.core.command_files.InputFileGenerator attribute) (hpcflow.sdk.core.command_files.OutputFileParser attribute) script_path (hpcflow.sdk.runtime.RunTimeInfo property) scripts (hpcflow.sdk.app.App property) (hpcflow.sdk.app.BaseApp property) scripts_dir (hpcflow.sdk.app.App attribute) (hpcflow.sdk.app.BaseApp attribute) sdk_classes (in module hpcflow.sdk) sdk_funcs (in module hpcflow.sdk) search_dir_files_by_regex() (in module hpcflow.sdk.core.utils) select_invocation() (hpcflow.sdk.config.config_file.ConfigFile static method) seq_idx (hpcflow.sdk.persistence.base.StoreElement attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreElement attribute) sequence_idx (hpcflow.app.Element property) (hpcflow.sdk.core.element.Element property) sequences (hpcflow.app.ElementSet attribute) (hpcflow.sdk.core.task.ElementSet attribute) set() (hpcflow.sdk.config.config.Config method) set_callback_file_paths() (in module hpcflow.sdk.config.callbacks) set_data() (hpcflow.sdk.persistence.base.StoreParameter method) (hpcflow.sdk.persistence.zarr.ZarrStoreParameter method) set_defaults() (hpcflow.app.ElementResources method) (hpcflow.sdk.core.element.ElementResources method) set_EAR_end() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) set_EAR_ends (hpcflow.sdk.persistence.pending.PendingChanges attribute) set_EAR_skip() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) set_EAR_skips (hpcflow.sdk.persistence.pending.PendingChanges attribute) set_EAR_start() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) set_EAR_starts (hpcflow.sdk.persistence.pending.PendingChanges attribute) set_EAR_submission_index() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) set_EAR_submission_indices (hpcflow.sdk.persistence.pending.PendingChanges attribute) set_EARs_initialised (hpcflow.sdk.persistence.pending.PendingChanges attribute) set_EARs_initialised() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.base.StoreElementIter method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrStoreElementIter method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) set_file() (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.base.StoreParameter method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrStoreParameter method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) set_github_demo_data_dir() (hpcflow.sdk.config.config.Config method) set_in_container() (in module hpcflow.sdk.core.utils) set_jobscript_metadata() (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) set_js_metadata (hpcflow.sdk.persistence.pending.PendingChanges attribute) set_parameter_value() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) set_parameters (hpcflow.sdk.persistence.pending.PendingChanges attribute) set_scheduler_invocation_match() (in module hpcflow.sdk.config.callbacks) set_sequence_parameters() (hpcflow.app.Task method) (hpcflow.sdk.core.task.Task method) setup (hpcflow.app.Environment attribute) (hpcflow.sdk.core.environment.Environment attribute) SGE_parallel_env (hpcflow.app.ElementResources attribute) (hpcflow.app.ResourceSpec property) (hpcflow.sdk.core.element.ElementResources attribute) (hpcflow.sdk.core.parameters.ResourceSpec property) SGEPosix (class in hpcflow.app) (class in hpcflow.sdk.submission.schedulers.sge) SHA hpcflow-config-set-github-demo-data-dir command line option SHARED (hpcflow.sdk.core.parallel.ParallelMode attribute) shared_data_name (hpcflow.sdk.core.json_like.ChildObjectSpec attribute) shared_data_primary_key (hpcflow.sdk.core.json_like.ChildObjectSpec attribute) shebang_executable (hpcflow.sdk.submission.shells.base.Shell property) (hpcflow.sdk.submission.shells.bash.Bash property) (hpcflow.sdk.submission.shells.bash.WSLBash property) (hpcflow.sdk.submission.shells.powershell.WindowsPowerShell property)

Shell (class in hpcflow.sdk.submission.shells.base) shell (hpcflow.app.ElementResources attribute) (hpcflow.app.Jobscript property) (hpcflow.app.ResourceSpec property) (hpcflow.sdk.core.element.ElementResources attribute) (hpcflow.sdk.core.parameters.ResourceSpec property) (hpcflow.sdk.submission.jobscript.Jobscript property) shell_args (hpcflow.app.ElementResources attribute) (hpcflow.app.ResourceSpec property) (hpcflow.sdk.core.element.ElementResources attribute) (hpcflow.sdk.core.parameters.ResourceSpec property) SHELL_NAME hpcflow-submission-shell-info command line option shell_name (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property) shells (hpcflow.sdk.config.config.Config attribute) show() (hpcflow.sdk.runtime.RunTimeInfo method) (in module hpcflow.app) show_all_EAR_statuses() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) show_demo_workflow() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) show_legend() (in module hpcflow.app) single_label (hpcflow.app.SchemaInput property) (hpcflow.sdk.core.parameters.SchemaInput property) single_labelled_data (hpcflow.app.SchemaInput property) (hpcflow.sdk.core.parameters.SchemaInput property) single_labelled_type (hpcflow.app.SchemaInput property) (hpcflow.sdk.core.parameters.SchemaInput property) Singleton (class in hpcflow.sdk.app) (class in hpcflow.sdk.core.utils) size() (hpcflow.sdk.core.utils.JSONLikeDirSnapShot method) skip (hpcflow.app.ElementActionRun property) (hpcflow.sdk.core.actions.ElementActionRun property) (hpcflow.sdk.persistence.base.StoreEAR attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreEAR attribute) skipped (hpcflow.sdk.core.actions.EARStatus attribute) SLURM_is_parallel (hpcflow.app.ElementResources property) (hpcflow.sdk.core.element.ElementResources property) SLURM_num_cpus_per_task (hpcflow.app.ElementResources attribute) (hpcflow.app.ResourceSpec property) (hpcflow.sdk.core.element.ElementResources attribute) (hpcflow.sdk.core.parameters.ResourceSpec property) SLURM_num_nodes (hpcflow.app.ElementResources attribute) (hpcflow.app.ResourceSpec property) (hpcflow.sdk.core.element.ElementResources attribute) (hpcflow.sdk.core.parameters.ResourceSpec property) SLURM_num_tasks (hpcflow.app.ElementResources attribute) (hpcflow.app.ResourceSpec property) (hpcflow.sdk.core.element.ElementResources attribute) (hpcflow.sdk.core.parameters.ResourceSpec property) SLURM_num_tasks_per_node (hpcflow.app.ElementResources attribute) (hpcflow.app.ResourceSpec property) (hpcflow.sdk.core.element.ElementResources attribute) (hpcflow.sdk.core.parameters.ResourceSpec property) SLURM_partition (hpcflow.app.ElementResources attribute) (hpcflow.app.ResourceSpec property) (hpcflow.sdk.core.element.ElementResources attribute) (hpcflow.sdk.core.parameters.ResourceSpec property) SlurmPosix (class in hpcflow.app) (class in hpcflow.sdk.submission.schedulers.slurm) snapshot_end (hpcflow.app.ElementActionRun property) (hpcflow.sdk.core.actions.ElementActionRun property) (hpcflow.sdk.persistence.base.StoreEAR attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreEAR attribute) snapshot_start (hpcflow.app.ElementActionRun property) (hpcflow.sdk.core.actions.ElementActionRun property) (hpcflow.sdk.persistence.base.StoreEAR attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreEAR attribute) source (hpcflow.sdk.persistence.base.StoreParameter attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreParameter attribute) source_file (hpcflow.app.WorkflowTemplate attribute) (hpcflow.sdk.core.workflow.WorkflowTemplate attribute) source_type (hpcflow.app.InputSource attribute) (hpcflow.sdk.core.parameters.InputSource attribute) sourceable_elem_iters (hpcflow.app.ElementSet attribute) (hpcflow.sdk.core.task.ElementSet attribute) specifiers (hpcflow.app.Environment attribute) (hpcflow.sdk.core.environment.Environment attribute) split_param_label() (in module hpcflow.sdk.core.utils) src_idx (hpcflow.sdk.persistence.base.StoreElement attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreElement attribute) start (hpcflow.app.NumCores attribute) (hpcflow.sdk.core.environment.NumCores attribute) start_helper() (in module hpcflow.sdk.helper.helper) start_time (hpcflow.app.ElementActionRun property) (hpcflow.app.Jobscript property) (hpcflow.app.Submission property) (hpcflow.sdk.core.actions.ElementActionRun property) (hpcflow.sdk.persistence.base.StoreEAR attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreEAR attribute) (hpcflow.sdk.submission.jobscript.Jobscript property) (hpcflow.sdk.submission.submission.Submission property) stat_info() (hpcflow.sdk.core.utils.JSONLikeDirSnapShot method) state_lookup (hpcflow.app.SGEPosix attribute) (hpcflow.app.SlurmPosix attribute) (hpcflow.sdk.submission.schedulers.sge.SGEPosix attribute) (hpcflow.sdk.submission.schedulers.slurm.SlurmPosix attribute) status (hpcflow.app.ElementActionRun property) (hpcflow.app.Submission property) (hpcflow.sdk.core.actions.ElementActionRun property) (hpcflow.sdk.submission.submission.Submission property) stderr (hpcflow.app.Command attribute) (hpcflow.sdk.core.commands.Command attribute) stdin (hpcflow.app.Command attribute) (hpcflow.sdk.core.commands.Command attribute) stdout (hpcflow.app.Command attribute) (hpcflow.sdk.core.commands.Command attribute) stem (hpcflow.app.FileNameSpec property) (hpcflow.app.FileSpec property) (hpcflow.sdk.core.command_files.FileNameSpec property) (hpcflow.sdk.core.command_files.FileSpec property) step (hpcflow.app.NumCores attribute) (hpcflow.sdk.core.environment.NumCores attribute) stop (hpcflow.app.NumCores attribute) (hpcflow.sdk.core.environment.NumCores attribute) stop() (hpcflow.sdk.helper.watcher.MonitorController method) (hpcflow.sdk.helper.watcher.WorkflowMonitor method) stop_helper() (in module hpcflow.sdk.helper.helper) store_cls_from_str() (in module hpcflow.sdk.persistence) store_contents (hpcflow.app.InputFile property) (hpcflow.app.InputFileGeneratorSource property) (hpcflow.app.OutputFileParserSource property) (hpcflow.sdk.core.command_files.InputFile property) (hpcflow.sdk.core.command_files.InputFileGeneratorSource property) (hpcflow.sdk.core.command_files.OutputFileParserSource property) store_format (hpcflow.app.Workflow property) (hpcflow.sdk.core.workflow.Workflow property) store_kwargs (hpcflow.app.WorkflowTemplate attribute) (hpcflow.sdk.core.workflow.WorkflowTemplate attribute) store_option() (in module hpcflow.sdk.cli_common) StoreEAR (class in hpcflow.sdk.persistence.base) StoreElement (class in hpcflow.sdk.persistence.base) StoreElementIter (class in hpcflow.sdk.persistence.base) StoreParameter (class in hpcflow.sdk.persistence.base) StoreResource (class in hpcflow.sdk.persistence.store_resource) StoreTask (class in hpcflow.sdk.persistence.base) string_option() (in module hpcflow.sdk.cli) SUB_IDX hpcflow-workflow-WORKFLOW_REF-sub command line option sub_param (hpcflow.sdk.core.test_utils.P1_parameter_cls attribute) sub_param_prop (hpcflow.sdk.core.test_utils.P1_parameter_cls property) sub_parameters (hpcflow.app.Parameter attribute) (hpcflow.sdk.core.parameters.Parameter attribute) sub_tasks_callback() (in module hpcflow.sdk.cli_common) Submission (class in hpcflow.app) (class in hpcflow.sdk.submission.submission) submission (hpcflow.app.Jobscript property) (hpcflow.sdk.persistence.base.PersistentStoreFeatures attribute) (hpcflow.sdk.submission.jobscript.Jobscript property) SUBMISSION_IDX hpcflow-internal-workflow-PATH-write-commands command line option submission_idx (hpcflow.app.ElementActionRun property) (hpcflow.sdk.core.actions.ElementActionRun property) (hpcflow.sdk.persistence.base.StoreEAR attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreEAR attribute) submission_logger (hpcflow.sdk.app.App property) (hpcflow.sdk.app.BaseApp property) submission_parts (hpcflow.app.Submission property) (hpcflow.sdk.submission.submission.Submission property) SubmissionEnvironmentError SubmissionFailure submissions (hpcflow.app.Workflow property) (hpcflow.sdk.core.workflow.Workflow property) submissions_path (hpcflow.app.Workflow property) (hpcflow.sdk.core.workflow.Workflow property) SubmissionStatus (class in hpcflow.sdk.submission.submission) submit() (hpcflow.app.Jobscript method) (hpcflow.app.Submission method) (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) (hpcflow.sdk.submission.jobscript.Jobscript method) (hpcflow.sdk.submission.submission.Submission method) submit_cmdline (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property) submit_hostname (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property) submit_machine (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property) submit_status_opt() (in module hpcflow.sdk.cli_common) submit_time (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property) submit_workflow() (in module hpcflow.app) submitted (hpcflow.sdk.core.actions.EARStatus attribute) SUBMITTED (hpcflow.sdk.submission.submission.SubmissionStatus attribute) submitted_jobscripts (hpcflow.app.Submission property) (hpcflow.sdk.submission.submission.Submission property) SubParameter (class in hpcflow.app) (class in hpcflow.sdk.core.parameters) substitute_string_vars() (in module hpcflow.sdk.core.utils) success (hpcflow.app.ElementActionRun property) (hpcflow.sdk.core.actions.EARStatus attribute) (hpcflow.sdk.core.actions.ElementActionRun property) (hpcflow.sdk.persistence.base.StoreEAR attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreEAR attribute) sum() (hpcflow.sdk.core.test_utils.P1_parameter_cls static method) summarise() (hpcflow.sdk.log.TimeIt class method) summarise_string() (hpcflow.sdk.log.TimeIt class method) swap_nested_dict_keys() (in module hpcflow.sdk.core.utils) sys_base_prefix (hpcflow.sdk.runtime.RunTimeInfo attribute) sys_prefix (hpcflow.sdk.runtime.RunTimeInfo attribute) sys_real_prefix (hpcflow.sdk.runtime.RunTimeInfo attribute)

T

take() (hpcflow.sdk.core.utils.JSONLikeDirSnapShot method) take_snapshot() (hpcflow.app.RunDirAppFiles class method) (hpcflow.sdk.core.run_dir_files.RunDirAppFiles class method) Task (class in hpcflow.app) (class in hpcflow.sdk.core.task) task (hpcflow.app.Element property) (hpcflow.app.ElementAction property) (hpcflow.app.ElementActionRun property) (hpcflow.app.ElementIteration property) (hpcflow.app.ElementParameter attribute) (hpcflow.app.ElementPropagation attribute) (hpcflow.app.Elements property) (hpcflow.app.ElementSet property) TASK (hpcflow.app.InputSourceType attribute) task (hpcflow.app.ParameterPath attribute) (hpcflow.app.Parameters attribute) (hpcflow.app.TaskInputParameters attribute) (hpcflow.app.TaskOutputParameters attribute) (hpcflow.sdk.core.actions.ElementAction property) (hpcflow.sdk.core.actions.ElementActionRun property) (hpcflow.sdk.core.element.Element property) (hpcflow.sdk.core.element.ElementIteration property) (hpcflow.sdk.core.element.ElementParameter attribute) (hpcflow.sdk.core.parameters.ParameterPath attribute) (hpcflow.sdk.core.task.ElementPropagation attribute) (hpcflow.sdk.core.task.Elements property) (hpcflow.sdk.core.task.ElementSet property) (hpcflow.sdk.core.task.Parameters attribute) (hpcflow.sdk.core.task.TaskInputParameters attribute) (hpcflow.sdk.core.task.TaskOutputParameters attribute) task() (hpcflow.app.InputSource class method) (hpcflow.sdk.core.parameters.InputSource class method) task_actions (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property) task_artifacts_path (hpcflow.app.Workflow property) (hpcflow.sdk.core.workflow.Workflow property) task_cache (hpcflow.sdk.persistence.base.PersistentStore property) (hpcflow.sdk.persistence.json.JSONPersistentStore property) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore property) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore property) task_elements (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property) task_ID (hpcflow.sdk.persistence.base.StoreElement attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreElement attribute) task_indices (hpcflow.app.WorkflowLoop property) (hpcflow.sdk.core.loop.WorkflowLoop property) task_insert_IDs (hpcflow.app.Jobscript property) (hpcflow.app.Loop property) (hpcflow.app.WorkflowLoop property) (hpcflow.sdk.core.loop.Loop property) (hpcflow.sdk.core.loop.WorkflowLoop property) (hpcflow.sdk.submission.jobscript.Jobscript property) task_iterations (hpcflow.sdk.core.loop_cache.LoopCache attribute) task_loop_idx (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property) task_objects (hpcflow.app.Loop property) (hpcflow.app.WorkflowLoop property) (hpcflow.sdk.core.loop.Loop property) (hpcflow.sdk.core.loop.WorkflowLoop property) task_ref (hpcflow.app.InputSource attribute) (hpcflow.sdk.core.parameters.InputSource attribute) task_schema (hpcflow.app.Action property) (hpcflow.app.SchemaInput property) (hpcflow.sdk.core.actions.Action property) (hpcflow.sdk.core.parameters.SchemaInput property) task_schema_sources (hpcflow.sdk.config.config.Config attribute) task_schemas (hpcflow.sdk.app.App property) (hpcflow.sdk.app.BaseApp property) task_source_type (hpcflow.app.InputSource attribute) (hpcflow.sdk.core.parameters.InputSource attribute) task_template (hpcflow.app.ElementSet property) (hpcflow.app.TaskSchema property) (hpcflow.sdk.core.task.ElementSet property) (hpcflow.sdk.core.task_schema.TaskSchema property) (hpcflow.sdk.persistence.base.StoreTask attribute) (hpcflow.sdk.persistence.zarr.ZarrStoreTask attribute) TaskInputParameters (class in hpcflow.app) (class in hpcflow.sdk.core.task) TaskList (class in hpcflow.app) (class in hpcflow.sdk.core.object_list) TaskObjective (class in hpcflow.app) (class in hpcflow.sdk.core.task_schema) TaskOutputParameters (class in hpcflow.app) (class in hpcflow.sdk.core.task) tasks (hpcflow.app.Workflow property) (hpcflow.app.WorkflowTemplate attribute) (hpcflow.sdk.core.workflow.Workflow property) (hpcflow.sdk.core.workflow.WorkflowTemplate attribute) tasks_opt() (in module hpcflow.sdk.cli_common) TaskSchema (class in hpcflow.app) (class in hpcflow.sdk.core.task_schema) TaskSchemaMissingParameterError TaskSchemasList (class in hpcflow.app) (class in hpcflow.sdk.core.object_list) TaskSchemaSpecValidationError TaskSourceType (class in hpcflow.app) TaskTemplateInvalidNesting TaskTemplateList (class in hpcflow.app) (class in hpcflow.sdk.core.object_list) TaskTemplateMultipleInputValues TaskTemplateMultipleSchemaObjectives TaskTemplateUnexpectedInput TaskTemplateUnexpectedSequenceInput template (hpcflow.app.Workflow property) (hpcflow.app.WorkflowLoop property) (hpcflow.app.WorkflowTask property) (hpcflow.sdk.core.loop.WorkflowLoop property) (hpcflow.sdk.core.task.WorkflowTask property) (hpcflow.sdk.core.workflow.Workflow property) template_components (hpcflow.app.Workflow property) (hpcflow.sdk.app.App property) (hpcflow.sdk.app.BaseApp property) (hpcflow.sdk.core.workflow.Workflow property) template_components_from_json_like() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) TEMPLATE_FILE_OR_STR hpcflow-go command line option hpcflow-make command line option temporary_rename() (hpcflow.app.Workflow class method) (hpcflow.sdk.core.workflow.Workflow class method) termination (hpcflow.app.Loop property) (hpcflow.sdk.core.loop.Loop property) test() (hpcflow.app.ActionRule method) (hpcflow.app.Rule method) (hpcflow.sdk.core.actions.ActionRule method) (hpcflow.sdk.core.rule.Rule method) test_rules() (hpcflow.app.Action method) (hpcflow.sdk.core.actions.Action method) test_termination() (hpcflow.app.WorkflowLoop method) (hpcflow.sdk.core.loop.WorkflowLoop method) time_limit (hpcflow.app.ElementResources attribute) (hpcflow.app.ResourceSpec property) (hpcflow.sdk.core.element.ElementResources attribute) (hpcflow.sdk.core.parameters.ResourceSpec property) timedelta_format() (in module hpcflow.sdk.submission.submission) timedelta_parse() (in module hpcflow.sdk.submission.submission) TimeIt (class in hpcflow.sdk.log) timeit (hpcflow.sdk.app.App property) (hpcflow.sdk.app.BaseApp property) timeout_check_interval_option() (in module hpcflow.sdk.helper.cli) timeout_option() (in module hpcflow.sdk.helper.cli) timers (hpcflow.sdk.log.TimeIt attribute) to_dict() (hpcflow.app.Action method) (hpcflow.app.ActionEnvironment method) (hpcflow.app.ActionRule method) (hpcflow.app.ActionScope method) (hpcflow.app.Command method) (hpcflow.app.CommandFilesList method) (hpcflow.app.ElementFilter method) (hpcflow.app.ElementGroup method) (hpcflow.app.ElementResources method) (hpcflow.app.ElementSet method) (hpcflow.app.Environment method) (hpcflow.app.EnvironmentsList method) (hpcflow.app.Executable method) (hpcflow.app.ExecutableInstance method) (hpcflow.app.ExecutablesList method) (hpcflow.app.FileNameExt method) (hpcflow.app.FileNameSpec method) (hpcflow.app.FileNameStem method) (hpcflow.app.FileSpec method) (hpcflow.app.GroupList method) (hpcflow.app.InputFile method) (hpcflow.app.InputFileGenerator method) (hpcflow.app.InputFileGeneratorSource method) (hpcflow.app.InputSource method) (hpcflow.app.InputValue method) (hpcflow.app.Jobscript method) (hpcflow.app.Loop method) (hpcflow.app.NumCores method) (hpcflow.app.OutputFileParser method) (hpcflow.app.OutputFileParserSource method) (hpcflow.app.OutputLabel method) (hpcflow.app.Parameter method) (hpcflow.app.ParameterPath method) (hpcflow.app.ParametersList method) (hpcflow.app.ParameterValue method) (hpcflow.app.ResourceList method) (hpcflow.app.ResourceSpec method) (hpcflow.app.Rule method) (hpcflow.app.SchemaInput method) (hpcflow.app.SchemaOutput method) (hpcflow.app.SchemaParameter method) (hpcflow.app.Submission method) (hpcflow.app.Task method) (hpcflow.app.TaskList method) (hpcflow.app.TaskObjective method) (hpcflow.app.TaskSchema method) (hpcflow.app.TaskSchemasList method) (hpcflow.app.TaskTemplateList method) (hpcflow.app.ValuePerturbation method) (hpcflow.app.ValueSequence method) (hpcflow.app.WorkflowLoopList method) (hpcflow.app.WorkflowTaskList method) (hpcflow.app.WorkflowTemplate method) (hpcflow.sdk.core.actions.Action method) (hpcflow.sdk.core.actions.ActionEnvironment method) (hpcflow.sdk.core.actions.ActionRule method) (hpcflow.sdk.core.actions.ActionScope method) (hpcflow.sdk.core.command_files.FileNameExt method) (hpcflow.sdk.core.command_files.FileNameSpec method) (hpcflow.sdk.core.command_files.FileNameStem method) (hpcflow.sdk.core.command_files.FileSpec method) (hpcflow.sdk.core.command_files.InputFile method) (hpcflow.sdk.core.command_files.InputFileGenerator method) (hpcflow.sdk.core.command_files.InputFileGeneratorSource method) (hpcflow.sdk.core.command_files.OutputFileParser method) (hpcflow.sdk.core.command_files.OutputFileParserSource method) (hpcflow.sdk.core.commands.Command method) (hpcflow.sdk.core.element.ElementFilter method) (hpcflow.sdk.core.element.ElementGroup method) (hpcflow.sdk.core.element.ElementResources method) (hpcflow.sdk.core.environment.Environment method) (hpcflow.sdk.core.environment.Executable method) (hpcflow.sdk.core.environment.ExecutableInstance method) (hpcflow.sdk.core.environment.NumCores method) (hpcflow.sdk.core.json_like.BaseJSONLike method) (hpcflow.sdk.core.json_like.JSONLike method) (hpcflow.sdk.core.loop.Loop method) (hpcflow.sdk.core.object_list.AppDataList method) (hpcflow.sdk.core.object_list.CommandFilesList method) (hpcflow.sdk.core.object_list.DotAccessObjectList method) (hpcflow.sdk.core.object_list.EnvironmentsList method) (hpcflow.sdk.core.object_list.ExecutablesList method) (hpcflow.sdk.core.object_list.GroupList method) (hpcflow.sdk.core.object_list.ObjectList method) (hpcflow.sdk.core.object_list.ParametersList method) (hpcflow.sdk.core.object_list.ResourceList method) (hpcflow.sdk.core.object_list.TaskList method) (hpcflow.sdk.core.object_list.TaskSchemasList method) (hpcflow.sdk.core.object_list.TaskTemplateList method) (hpcflow.sdk.core.object_list.WorkflowLoopList method) (hpcflow.sdk.core.object_list.WorkflowTaskList method) (hpcflow.sdk.core.parameters.AbstractInputValue method) (hpcflow.sdk.core.parameters.InputSource method) (hpcflow.sdk.core.parameters.InputValue method) (hpcflow.sdk.core.parameters.Parameter method) (hpcflow.sdk.core.parameters.ParameterPath method) (hpcflow.sdk.core.parameters.ParameterValue method) (hpcflow.sdk.core.parameters.ResourceSpec method) (hpcflow.sdk.core.parameters.SchemaInput method) (hpcflow.sdk.core.parameters.SchemaOutput method) (hpcflow.sdk.core.parameters.SchemaParameter method) (hpcflow.sdk.core.parameters.ValuePerturbation method) (hpcflow.sdk.core.parameters.ValueSequence method) (hpcflow.sdk.core.rule.Rule method) (hpcflow.sdk.core.task.ElementSet method) (hpcflow.sdk.core.task.OutputLabel method) (hpcflow.sdk.core.task.Task method) (hpcflow.sdk.core.task_schema.TaskObjective method) (hpcflow.sdk.core.task_schema.TaskSchema method) (hpcflow.sdk.core.test_utils.P1_parameter_cls method) (hpcflow.sdk.core.test_utils.P1_sub_parameter_cls method) (hpcflow.sdk.core.test_utils.P1_sub_parameter_cls_2 method) (hpcflow.sdk.core.workflow.WorkflowTemplate method) (hpcflow.sdk.core.zarr_io.ZarrEncodable method) (hpcflow.sdk.persistence.base.StoreEAR method) (hpcflow.sdk.persistence.base.StoreElement method) (hpcflow.sdk.persistence.base.StoreElementIter method) (hpcflow.sdk.persistence.zarr.ZarrStoreEAR method) (hpcflow.sdk.persistence.zarr.ZarrStoreElement method) (hpcflow.sdk.persistence.zarr.ZarrStoreElementIter method) (hpcflow.sdk.runtime.RunTimeInfo method) (hpcflow.sdk.submission.jobscript.Jobscript method) (hpcflow.sdk.submission.submission.Submission method)

to_element_set_data() (hpcflow.app.Element method) (hpcflow.sdk.core.element.Element method) to_json_like() (hpcflow.app.Action method) (hpcflow.app.ActionEnvironment method) (hpcflow.app.ActionRule method) (hpcflow.app.ActionScope method) (hpcflow.app.Command method) (hpcflow.app.CommandFilesList method) (hpcflow.app.ElementFilter method) (hpcflow.app.ElementGroup method) (hpcflow.app.ElementResources method) (hpcflow.app.ElementSet method) (hpcflow.app.Environment method) (hpcflow.app.EnvironmentsList method) (hpcflow.app.Executable method) (hpcflow.app.ExecutableInstance method) (hpcflow.app.ExecutablesList method) (hpcflow.app.FileNameExt method) (hpcflow.app.FileNameSpec method) (hpcflow.app.FileNameStem method) (hpcflow.app.FileSpec method) (hpcflow.app.GroupList method) (hpcflow.app.InputFile method) (hpcflow.app.InputFileGenerator method) (hpcflow.app.InputFileGeneratorSource method) (hpcflow.app.InputSource method) (hpcflow.app.InputValue method) (hpcflow.app.Jobscript method) (hpcflow.app.Loop method) (hpcflow.app.NumCores method) (hpcflow.app.OutputFileParser method) (hpcflow.app.OutputFileParserSource method) (hpcflow.app.OutputLabel method) (hpcflow.app.Parameter method) (hpcflow.app.ParameterPath method) (hpcflow.app.ParametersList method) (hpcflow.app.ResourceList method) (hpcflow.app.ResourceSpec method) (hpcflow.app.Rule method) (hpcflow.app.SchemaInput method) (hpcflow.app.SchemaOutput method) (hpcflow.app.SchemaParameter method) (hpcflow.app.Submission method) (hpcflow.app.Task method) (hpcflow.app.TaskList method) (hpcflow.app.TaskObjective method) (hpcflow.app.TaskSchema method) (hpcflow.app.TaskSchemasList method) (hpcflow.app.TaskTemplateList method) (hpcflow.app.ValuePerturbation method) (hpcflow.app.ValueSequence method) (hpcflow.app.WorkflowLoopList method) (hpcflow.app.WorkflowTaskList method) (hpcflow.app.WorkflowTemplate method) (hpcflow.sdk.core.actions.Action method) (hpcflow.sdk.core.actions.ActionEnvironment method) (hpcflow.sdk.core.actions.ActionRule method) (hpcflow.sdk.core.actions.ActionScope method) (hpcflow.sdk.core.command_files.FileNameExt method) (hpcflow.sdk.core.command_files.FileNameSpec method) (hpcflow.sdk.core.command_files.FileNameStem method) (hpcflow.sdk.core.command_files.FileSpec method) (hpcflow.sdk.core.command_files.InputFile method) (hpcflow.sdk.core.command_files.InputFileGenerator method) (hpcflow.sdk.core.command_files.InputFileGeneratorSource method) (hpcflow.sdk.core.command_files.OutputFileParser method) (hpcflow.sdk.core.command_files.OutputFileParserSource method) (hpcflow.sdk.core.commands.Command method) (hpcflow.sdk.core.element.ElementFilter method) (hpcflow.sdk.core.element.ElementGroup method) (hpcflow.sdk.core.element.ElementResources method) (hpcflow.sdk.core.environment.Environment method) (hpcflow.sdk.core.environment.Executable method) (hpcflow.sdk.core.environment.ExecutableInstance method) (hpcflow.sdk.core.environment.NumCores method) (hpcflow.sdk.core.json_like.BaseJSONLike method) (hpcflow.sdk.core.json_like.JSONLike method) (hpcflow.sdk.core.loop.Loop method) (hpcflow.sdk.core.object_list.AppDataList method) (hpcflow.sdk.core.object_list.CommandFilesList method) (hpcflow.sdk.core.object_list.DotAccessObjectList method) (hpcflow.sdk.core.object_list.EnvironmentsList method) (hpcflow.sdk.core.object_list.ExecutablesList method) (hpcflow.sdk.core.object_list.GroupList method) (hpcflow.sdk.core.object_list.ObjectList method) (hpcflow.sdk.core.object_list.ParametersList method) (hpcflow.sdk.core.object_list.ResourceList method) (hpcflow.sdk.core.object_list.TaskList method) (hpcflow.sdk.core.object_list.TaskSchemasList method) (hpcflow.sdk.core.object_list.TaskTemplateList method) (hpcflow.sdk.core.object_list.WorkflowLoopList method) (hpcflow.sdk.core.object_list.WorkflowTaskList method) (hpcflow.sdk.core.parameters.AbstractInputValue method) (hpcflow.sdk.core.parameters.InputSource method) (hpcflow.sdk.core.parameters.InputValue method) (hpcflow.sdk.core.parameters.Parameter method) (hpcflow.sdk.core.parameters.ParameterPath method) (hpcflow.sdk.core.parameters.ResourceSpec method) (hpcflow.sdk.core.parameters.SchemaInput method) (hpcflow.sdk.core.parameters.SchemaOutput method) (hpcflow.sdk.core.parameters.SchemaParameter method) (hpcflow.sdk.core.parameters.ValuePerturbation method) (hpcflow.sdk.core.parameters.ValueSequence method) (hpcflow.sdk.core.rule.Rule method) (hpcflow.sdk.core.task.ElementSet method) (hpcflow.sdk.core.task.OutputLabel method) (hpcflow.sdk.core.task.Task method) (hpcflow.sdk.core.task_schema.TaskObjective method) (hpcflow.sdk.core.task_schema.TaskSchema method) (hpcflow.sdk.core.utils.JSONLikeDirSnapShot method) (hpcflow.sdk.core.workflow.WorkflowTemplate method) (hpcflow.sdk.submission.jobscript.Jobscript method) (hpcflow.sdk.submission.submission.Submission method) (in module hpcflow.sdk.core.json_like) to_persistent() (hpcflow.app.Task method) (hpcflow.sdk.core.task.Task method) to_string() (hpcflow.app.ActionScope method) (hpcflow.app.InputSource method) (hpcflow.sdk.core.actions.ActionScope method) (hpcflow.sdk.core.parameters.InputSource method) to_zarr() (hpcflow.sdk.core.zarr_io.ZarrEncodable method) ToJSONLikeChildReferenceError trace (hpcflow.sdk.log.TimeIt attribute) trace_idx (hpcflow.sdk.log.TimeIt attribute) trace_idx_prev (hpcflow.sdk.log.TimeIt attribute) trace_prev (hpcflow.sdk.log.TimeIt attribute) ts_fmt (hpcflow.app.Workflow property) (hpcflow.sdk.core.workflow.Workflow property) (hpcflow.sdk.persistence.base.PersistentStore property) (hpcflow.sdk.persistence.json.JSONPersistentStore property) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore property) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore property) ts_fmt_option() (in module hpcflow.sdk.cli_common) ts_name_fmt (hpcflow.app.Workflow property) (hpcflow.sdk.core.workflow.Workflow property) ts_name_fmt_option() (in module hpcflow.sdk.cli_common) twice_a (hpcflow.sdk.core.test_utils.P1_parameter_cls property) twice_e (hpcflow.sdk.core.test_utils.P1_sub_parameter_cls property) typ (hpcflow.app.ActionScope attribute) (hpcflow.app.Parameter attribute) (hpcflow.app.SchemaInput property) (hpcflow.app.SchemaOutput property) (hpcflow.app.SchemaParameter property) (hpcflow.sdk.core.actions.ActionScope attribute) (hpcflow.sdk.core.parameters.Parameter attribute) (hpcflow.sdk.core.parameters.SchemaInput property) (hpcflow.sdk.core.parameters.SchemaOutput property) (hpcflow.sdk.core.parameters.SchemaParameter property)

U

UnavailableInputSource undefined_input_types (hpcflow.app.ElementSet property) (hpcflow.app.Task property) (hpcflow.sdk.core.task.ElementSet property) (hpcflow.sdk.core.task.Task property) undefined_inputs (hpcflow.app.Task property) (hpcflow.sdk.core.task.Task property) unique_name (hpcflow.app.WorkflowTask property) (hpcflow.sdk.core.task.WorkflowTask property) unique_properties (hpcflow.app.DirectPosix property) (hpcflow.app.DirectWindows property) (hpcflow.app.SGEPosix property) (hpcflow.app.SlurmPosix property) (hpcflow.sdk.submission.schedulers.direct.DirectPosix property) (hpcflow.sdk.submission.schedulers.direct.DirectScheduler property) (hpcflow.sdk.submission.schedulers.direct.DirectWindows property) (hpcflow.sdk.submission.schedulers.NullScheduler property) (hpcflow.sdk.submission.schedulers.Scheduler property) (hpcflow.sdk.submission.schedulers.sge.SGEPosix property) (hpcflow.sdk.submission.schedulers.slurm.SlurmPosix property) universal_input_types (hpcflow.app.Task property) (hpcflow.sdk.core.task.Task property) UnknownEnvironmentPresetError UnknownResourceSpecItemError UnknownScriptDataKey UnknownScriptDataParameter UnknownSGEPEError UnknownSLURMPartitionError unload_config() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) UnrequiredInputSources unset() (hpcflow.sdk.config.config.Config method) UnsetParameterDataError UnsupportedOSError UnsupportedSchedulerError UnsupportedScriptDataFormat UnsupportedShellError unzip() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) unzip_log_opt() (in module hpcflow.sdk.cli_common) unzip_path_opt() (in module hpcflow.sdk.cli_common) update() (hpcflow.sdk.config.config.Config method) (hpcflow.sdk.persistence.base.StoreEAR method) (hpcflow.sdk.persistence.zarr.ZarrStoreEAR method) update_console_level() (hpcflow.sdk.log.AppLog method) update_invocation() (hpcflow.sdk.config.config_file.ConfigFile method) update_known_subs_file() (hpcflow.sdk.app.App method) (hpcflow.sdk.app.BaseApp method) update_loop_idx() (hpcflow.sdk.persistence.base.StoreElementIter method) (hpcflow.sdk.persistence.zarr.ZarrStoreElementIter method) update_loop_indices (hpcflow.sdk.persistence.pending.PendingChanges attribute)

update_loop_indices() (hpcflow.sdk.core.loop_cache.LoopCache method) update_loop_num_iters (hpcflow.sdk.persistence.pending.PendingChanges attribute) update_loop_num_iters() (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) update_loop_parents (hpcflow.sdk.persistence.pending.PendingChanges attribute) update_loop_parents() (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) update_param_source() (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) update_param_source_dict() (in module hpcflow.sdk.persistence.base) update_param_sources (hpcflow.sdk.persistence.pending.PendingChanges attribute) update_source() (hpcflow.sdk.persistence.base.StoreParameter method) (hpcflow.sdk.persistence.zarr.ZarrStoreParameter method) update_workflow_paths() (hpcflow.sdk.helper.watcher.WorkflowMonitor method) upstream_tasks (hpcflow.app.WorkflowLoop property) (hpcflow.app.WorkflowTask property) (hpcflow.sdk.core.loop.WorkflowLoop property) (hpcflow.sdk.core.task.WorkflowTask property) url (hpcflow.app.Workflow property) (hpcflow.sdk.core.workflow.Workflow property) url_slug (hpcflow.app.Parameter property) (hpcflow.sdk.core.parameters.Parameter property) use_cache (hpcflow.sdk.persistence.base.PersistentStore property) (hpcflow.sdk.persistence.json.JSONPersistentStore property) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore property) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore property) use_job_array (hpcflow.app.ElementResources attribute) (hpcflow.app.ResourceSpec property) (hpcflow.sdk.core.element.ElementResources attribute) (hpcflow.sdk.core.parameters.ResourceSpec property) user_affiliation (hpcflow.sdk.config.config.Config attribute) user_cache_dir (hpcflow.sdk.app.App property) (hpcflow.sdk.app.BaseApp property) user_cache_hostname_dir (hpcflow.sdk.app.App property) (hpcflow.sdk.app.BaseApp property) user_data_dir (hpcflow.sdk.app.App property) (hpcflow.sdk.app.BaseApp property) user_data_hostname_dir (hpcflow.sdk.app.App property) (hpcflow.sdk.app.BaseApp property) user_name (hpcflow.sdk.config.config.Config attribute) user_orcid (hpcflow.sdk.config.config.Config attribute) user_runtime_dir (hpcflow.sdk.app.App property) (hpcflow.sdk.app.BaseApp property) using_resource() (hpcflow.sdk.persistence.base.PersistentStore method) (hpcflow.sdk.persistence.json.JSONPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method)

V

validate() (hpcflow.sdk.config.config.ConfigOptions method) validate_against_machine() (hpcflow.app.ElementResources method) (hpcflow.sdk.core.element.ElementResources method) VALUE hpcflow-config-append command line option hpcflow-config-prepend command line option hpcflow-config-set command line option hpcflow-config-update command line option hpcflow-internal-workflow-PATH-save-parameter command line option value (hpcflow.app.ElementParameter property) (hpcflow.app.InputValue property) (hpcflow.app.ValuePerturbation property) (hpcflow.sdk.core.element.ElementParameter property) (hpcflow.sdk.core.parameters.AbstractInputValue property) (hpcflow.sdk.core.parameters.InputValue property) (hpcflow.sdk.core.parameters.ValuePerturbation property) value() (hpcflow.app.FileNameExt method) (hpcflow.app.FileNameSpec method) (hpcflow.app.FileNameStem method) (hpcflow.app.FileSpec method) (hpcflow.sdk.core.command_files.FileNameExt method) (hpcflow.sdk.core.command_files.FileNameSpec method) (hpcflow.sdk.core.command_files.FileNameStem method) (hpcflow.sdk.core.command_files.FileSpec method)

value_class_method (hpcflow.app.InputValue attribute) (hpcflow.app.ValueSequence attribute) (hpcflow.sdk.core.parameters.InputValue attribute) (hpcflow.sdk.core.parameters.ValueSequence attribute) ValuePerturbation (class in hpcflow.app) (class in hpcflow.sdk.core.parameters) values (hpcflow.app.ValueSequence property) (hpcflow.sdk.core.parameters.ValueSequence property) ValuesAlreadyPersistentError ValueSequence (class in hpcflow.app) (class in hpcflow.sdk.core.parameters) variables (hpcflow.app.Command attribute) (hpcflow.sdk.core.commands.Command attribute) variables_option() (in module hpcflow.sdk.cli_common) venv_path (hpcflow.sdk.runtime.RunTimeInfo attribute) version (hpcflow.app.TaskSchema attribute) (hpcflow.sdk.app.App attribute) (hpcflow.sdk.app.BaseApp attribute) (hpcflow.sdk.core.task_schema.TaskSchema attribute) (hpcflow.sdk.runtime.RunTimeInfo attribute) version_info (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property)

W

wait() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) wait_for_jobscripts() (hpcflow.app.DirectPosix class method) (hpcflow.app.DirectWindows class method) (hpcflow.app.SGEPosix method) (hpcflow.app.SlurmPosix method) (hpcflow.sdk.submission.schedulers.direct.DirectPosix class method) (hpcflow.sdk.submission.schedulers.direct.DirectScheduler class method) (hpcflow.sdk.submission.schedulers.direct.DirectWindows class method) (hpcflow.sdk.submission.schedulers.Scheduler method) (hpcflow.sdk.submission.schedulers.sge.SGEPosix method) (hpcflow.sdk.submission.schedulers.slurm.SlurmPosix method) wait_option() (in module hpcflow.sdk.cli_common) waiting (hpcflow.sdk.submission.jobscript_info.JobscriptElementState attribute) walk() (hpcflow.sdk.core.utils.JSONLikeDirSnapShot method) warning_formatter() (in module hpcflow.sdk.config.cli) watch_interval_option() (in module hpcflow.sdk.helper.cli) web_doc (hpcflow.app.TaskSchema attribute) (hpcflow.sdk.core.task_schema.TaskSchema attribute) where (hpcflow.app.ElementGroup attribute) (hpcflow.app.ElementRepeats attribute) (hpcflow.app.InputSource attribute) (hpcflow.app.OutputLabel attribute) (hpcflow.sdk.core.element.ElementGroup attribute) (hpcflow.sdk.core.element.ElementRepeats attribute) (hpcflow.sdk.core.parameters.InputSource attribute) (hpcflow.sdk.core.task.OutputLabel attribute) where_pending() (hpcflow.sdk.persistence.pending.PendingChanges method) WindowsPowerShell (class in hpcflow.sdk.submission.shells.powershell) Workflow (class in hpcflow.app) (class in hpcflow.sdk.core.workflow) workflow (hpcflow.app.Element property) (hpcflow.app.ElementActionRun property) (hpcflow.app.ElementIteration property) (hpcflow.app.InputFile property) (hpcflow.app.InputFileGeneratorSource property) (hpcflow.app.InputValue property) (hpcflow.app.Jobscript property) (hpcflow.app.OutputFileParserSource property) (hpcflow.app.ResourceSpec property) (hpcflow.app.Submission property) (hpcflow.app.ValuePerturbation property) (hpcflow.app.ValueSequence property) (hpcflow.app.WorkflowLoop property) (hpcflow.app.WorkflowTask property) (hpcflow.app.WorkflowTemplate attribute) (hpcflow.sdk.core.actions.ElementActionRun property) (hpcflow.sdk.core.command_files.InputFile property) (hpcflow.sdk.core.command_files.InputFileGeneratorSource property) (hpcflow.sdk.core.command_files.OutputFileParserSource property) (hpcflow.sdk.core.element.Element property) (hpcflow.sdk.core.element.ElementIteration property) (hpcflow.sdk.core.loop.WorkflowLoop property) (hpcflow.sdk.core.parameters.AbstractInputValue property) (hpcflow.sdk.core.parameters.InputValue property) (hpcflow.sdk.core.parameters.ResourceSpec property) (hpcflow.sdk.core.parameters.ValuePerturbation property) (hpcflow.sdk.core.parameters.ValueSequence property) (hpcflow.sdk.core.task.WorkflowTask property) (hpcflow.sdk.core.workflow.WorkflowTemplate attribute) (hpcflow.sdk.submission.jobscript.Jobscript property) (hpcflow.sdk.submission.submission.Submission property) workflow_app_alias (hpcflow.app.Jobscript property) (hpcflow.sdk.submission.jobscript.Jobscript property) WORKFLOW_NAME hpcflow-demo-workflow-copy command line option hpcflow-demo-workflow-go command line option hpcflow-demo-workflow-make command line option hpcflow-demo-workflow-show command line option

WORKFLOW_PATH hpcflow-unzip command line option WORKFLOW_REF hpcflow-cancel command line option hpcflow-open-workflow command line option hpcflow-rechunk command line option hpcflow-workflow command line option hpcflow-zip command line option workflow_ref_type_opt() (in module hpcflow.sdk.cli) workflow_template (hpcflow.app.Loop property) (hpcflow.app.ResourceList property) (hpcflow.app.ResourceSpec property) (hpcflow.app.Task attribute) (hpcflow.app.WorkflowBlueprint attribute) (hpcflow.sdk.core.loop.Loop property) (hpcflow.sdk.core.object_list.ResourceList property) (hpcflow.sdk.core.parameters.ResourceSpec property) (hpcflow.sdk.core.task.Task attribute) (hpcflow.sdk.core.workflow.WorkflowBlueprint attribute) WorkflowBatchUpdateFailedError WorkflowBlueprint (class in hpcflow.app) (class in hpcflow.sdk.core.workflow) WorkflowLimitsError WorkflowLoop (class in hpcflow.app) (class in hpcflow.sdk.core.loop) WorkflowLoopList (class in hpcflow.app) (class in hpcflow.sdk.core.object_list) WorkflowMonitor (class in hpcflow.sdk.helper.watcher) WorkflowNotFoundError WorkflowParameterMissingError workflows_dir (hpcflow.sdk.app.App attribute) (hpcflow.sdk.app.BaseApp attribute) WorkflowSpecValidationError WorkflowSubmissionFailure WorkflowTask (class in hpcflow.app) (class in hpcflow.sdk.core.task) WorkflowTaskList (class in hpcflow.app) (class in hpcflow.sdk.core.object_list) WorkflowTemplate (class in hpcflow.app) (class in hpcflow.sdk.core.workflow) working_dir (hpcflow.sdk.runtime.RunTimeInfo attribute) wrap_in_subshell() (hpcflow.sdk.submission.shells.bash.Bash method) (hpcflow.sdk.submission.shells.bash.WSLBash method) (hpcflow.sdk.submission.shells.powershell.WindowsPowerShell method) write_commands() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) write_EAR_ID_file() (hpcflow.app.Jobscript method) (hpcflow.sdk.submission.jobscript.Jobscript method) write_element_run_dir_file() (hpcflow.app.Jobscript method) (hpcflow.sdk.submission.jobscript.Jobscript method) write_empty_workflow() (hpcflow.sdk.persistence.json.JSONPersistentStore class method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore class method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore class method) write_jobscript() (hpcflow.app.Jobscript method) (hpcflow.sdk.submission.jobscript.Jobscript method) write_JSON_file() (in module hpcflow.sdk.core.utils) write_source() (hpcflow.app.ElementActionRun method) (hpcflow.app.InputFileGenerator method) (hpcflow.app.OutputFileParser method) (hpcflow.sdk.core.actions.ElementActionRun method) (hpcflow.sdk.core.command_files.InputFileGenerator method) (hpcflow.sdk.core.command_files.OutputFileParser method) write_YAML_file() (in module hpcflow.sdk.core.utils) WSLBash (class in hpcflow.sdk.submission.shells.bash)

Z

zarr_decode() (in module hpcflow.sdk.core.zarr_io) zarr_encode() (in module hpcflow.sdk.core.zarr_io) zarr_store (hpcflow.sdk.persistence.zarr.ZarrPersistentStore property) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore property) ZarrAttrsStoreResource (class in hpcflow.sdk.persistence.store_resource) ZarrEncodable (class in hpcflow.sdk.core.zarr_io) ZarrPersistentStore (class in hpcflow.sdk.persistence.zarr) ZarrStoreEAR (class in hpcflow.sdk.persistence.zarr) ZarrStoreElement (class in hpcflow.sdk.persistence.zarr) ZarrStoreElementIter (class in hpcflow.sdk.persistence.zarr) ZarrStoreParameter (class in hpcflow.sdk.persistence.zarr)

ZarrStoreTask (class in hpcflow.sdk.persistence.zarr) ZarrZipPersistentStore (class in hpcflow.sdk.persistence.zarr) zeroth_iters (hpcflow.sdk.core.loop_cache.LoopCache attribute) zip() (hpcflow.app.Workflow method) (hpcflow.sdk.core.workflow.Workflow method) (hpcflow.sdk.persistence.zarr.ZarrPersistentStore method) (hpcflow.sdk.persistence.zarr.ZarrZipPersistentStore method) zip_include_execute_opt() (in module hpcflow.sdk.cli_common) zip_include_rechunk_backups_opt() (in module hpcflow.sdk.cli_common) zip_log_opt() (in module hpcflow.sdk.cli_common) zip_overwrite_opt() (in module hpcflow.sdk.cli_common) zip_path_opt() (in module hpcflow.sdk.cli_common)