Index

A

add() (pydra.engine.core.Workflow method) (pydra.engine.Workflow method) (pydra.Workflow method) add_edges() (pydra.engine.graph.DiGraph method) add_edges_description() (pydra.engine.graph.DiGraph method) add_exc_note() (in module pydra.utils.misc) add_name_combiner() (in module pydra.engine.helpers_state) add_name_splitter() (in module pydra.engine.helpers_state) add_nodes() (pydra.engine.graph.DiGraph method) ALL (pydra.AuditFlag attribute) (pydra.engine.AuditFlag attribute) (pydra.utils.messenger.AuditFlag attribute) allowed_values_validator() (in module pydra.engine.helpers) annotate() (in module pydra.mark) (in module pydra.mark.functions)

apply_to_instances() (pydra.utils.typing.TypeParser class method) args (pydra.engine.specs.ShellSpec attribute) argstr_formatting() (in module pydra.engine.helpers) attr_fields() (in module pydra.engine.specs) attr_type (pydra.engine.specs.LazyInField attribute) (pydra.engine.specs.LazyOutField attribute) Audit (class in pydra.engine.audit) audit_check() (pydra.engine.audit.Audit method) audit_flags (pydra.engine.core.TaskBase attribute) audit_message() (pydra.engine.audit.Audit method) audit_task() (pydra.engine.audit.Audit method) AuditFlag (class in pydra) (class in pydra.engine) (class in pydra.utils.messenger)

B

bases (pydra.engine.specs.SpecInfo attribute) BaseSpec (class in pydra.engine.specs) bind() (pydra.engine.environments.Container method)

BoshTask (class in pydra.engine.boutiques) bytes_repr_mapping_contents() (in module pydra.utils.hash) bytes_repr_sequence_contents() (in module pydra.utils.hash)

C

Cache (class in pydra.utils.hash) cache_dir (pydra.engine.core.TaskBase property) cache_locations (pydra.engine.core.TaskBase property) calculate_max_paths() (pydra.engine.graph.DiGraph method) can_resume (pydra.engine.core.TaskBase property) cast() (pydra.engine.specs.LazyField method) cast_from (pydra.engine.specs.LazyField attribute) check_coercible() (pydra.utils.typing.TypeParser method) check_fields_input_spec() (pydra.engine.specs.BaseSpec method) check_for_results_files() (pydra.engine.workers.SGEWorker method) check_metadata() (pydra.engine.specs.BaseSpec method) (pydra.engine.specs.FunctionSpec method) (pydra.engine.specs.ShellSpec method) check_type() (pydra.utils.typing.TypeParser method) check_type_coercible() (pydra.utils.typing.TypeParser method) checksum (pydra.engine.core.TaskBase property) (pydra.engine.core.Workflow property) (pydra.engine.Workflow property) (pydra.Workflow property) checksum_states() (pydra.engine.core.TaskBase method) close() (pydra.engine.Submitter method) (pydra.engine.submitter.Submitter method) (pydra.engine.workers.ConcurrentFuturesWorker method) (pydra.engine.workers.DaskWorker method) (pydra.engine.workers.PsijWorker method) (pydra.engine.workers.SerialWorker method) (pydra.engine.workers.Worker method) (pydra.Submitter method) cmdline (pydra.engine.ShellCommandTask property) (pydra.engine.task.ShellCommandTask property) (pydra.ShellCommandTask property) coerce() (pydra.utils.typing.TypeParser method) coercible (pydra.utils.typing.TypeParser attribute) COERCIBLE_DEFAULT (pydra.utils.typing.TypeParser attribute) collect_additional_outputs() (pydra.engine.specs.BaseSpec method) (pydra.engine.specs.ShellOutSpec method)

collect_messages() (in module pydra.utils.messenger) combine() (pydra.engine.core.TaskBase method) combine_final_groups() (in module pydra.engine.helpers_state) combiner (pydra.engine.state.State attribute) (pydra.engine.state.State property) combiner_validation() (pydra.engine.state.State method) command_args() (pydra.engine.ShellCommandTask method) (pydra.engine.task.ShellCommandTask method) (pydra.ShellCommandTask method) ConcurrentFuturesWorker (class in pydra.engine.workers) cont_dim (pydra.engine.core.TaskBase property) Container (class in pydra.engine.environments) container (pydra.engine.specs.RuntimeSpec attribute) contains_type() (pydra.utils.typing.TypeParser class method) converter_groups_to_input() (in module pydra.engine.helpers_state) copy() (pydra.engine.graph.DiGraph method) copy_nested_files() (in module pydra.engine.helpers_file) copyfile_input() (pydra.engine.specs.BaseSpec method) copyfile_workflow() (in module pydra.engine.helpers) cpu_peak_percent (pydra.engine.specs.Runtime attribute) create_checksum() (in module pydra.engine.helpers) create_connections() (pydra.engine.core.Workflow method) (pydra.engine.Workflow method) (pydra.Workflow method) create_dotfile() (pydra.engine.core.Workflow method) (pydra.engine.Workflow method) (pydra.Workflow method) create_dotfile_detailed() (pydra.engine.graph.DiGraph method) create_dotfile_nested() (pydra.engine.graph.DiGraph method) create_dotfile_simple() (pydra.engine.graph.DiGraph method) current_combiner (pydra.engine.state.State property) current_combiner_all (pydra.engine.state.State property) current_splitter (pydra.engine.state.State property) current_splitter_rpn (pydra.engine.state.State property)

D

DaskWorker (class in pydra.engine.workers) DEFAULT_COPY_COLLATION (pydra.engine.core.TaskBase attribute) (pydra.engine.ShellCommandTask attribute) (pydra.engine.task.ShellCommandTask attribute) (pydra.ShellCommandTask attribute)

DiGraph (class in pydra.engine.graph) DistributedWorker (class in pydra.engine.workers) Docker (class in pydra.engine.environments) done (pydra.engine.core.TaskBase property) donothing() (in module pydra.engine.specs)

E

edges (pydra.engine.graph.DiGraph property) edges_names (pydra.engine.graph.DiGraph property) ensure_list() (in module pydra.engine.helpers) (in module pydra.engine.helpers_file) Environment (class in pydra.engine.environments) errored (pydra.engine.core.TaskBase property) (pydra.engine.specs.Result attribute) exc_info_matches() (in module pydra.utils.misc) exec_as_coro() (pydra.engine.workers.ConcurrentFuturesWorker method) exec_dask() (pydra.engine.workers.DaskWorker method) exec_psij() (pydra.engine.workers.PsijWorker method) exec_serial() (pydra.engine.workers.SerialWorker method)

executable (pydra.engine.specs.ShellSpec attribute) execute() (in module pydra.engine.helpers) (pydra.engine.environments.Docker method) (pydra.engine.environments.Environment method) (pydra.engine.environments.Native method) (pydra.engine.environments.Singularity method) expand_runnable() (pydra.engine.Submitter method) (pydra.engine.submitter.Submitter method) (pydra.Submitter method) expand_workflow() (pydra.engine.Submitter method) (pydra.engine.submitter.Submitter method) (pydra.Submitter method) export_graph() (pydra.engine.graph.DiGraph method)

F

fetch_finished() (pydra.engine.workers.DistributedWorker method) (pydra.engine.workers.SerialWorker method) (pydra.engine.workers.Worker method) field (pydra.engine.specs.LazyField attribute) fields (pydra.engine.specs.SpecInfo attribute) FileMessenger (class in pydra.utils.messenger)

final_combined_ind_mapping (pydra.engine.state.State attribute) finalize_audit() (pydra.engine.audit.Audit method) flatten() (in module pydra.engine.helpers_state) fname (pydra.utils.profiler.ResourceMonitor property) from_list_if_single() (in module pydra.engine.helpers) FunctionSpec (class in pydra.engine.specs) FunctionTask (class in pydra.engine.task)

G

gather_runtime_info() (in module pydra.engine.helpers) gen_uuid() (in module pydra.utils.messenger) generate_cifs_table() (pydra.engine.helpers_file.MountIndentifier class method) generated_output_names (pydra.engine.core.TaskBase property) generated_output_names() (pydra.engine.specs.ShellOutSpec method) get_args() (pydra.utils.typing.TypeParser static method) get_available_cpus() (in module pydra.engine.helpers) get_bindings() (pydra.engine.ShellCommandTask method) (pydra.engine.task.ShellCommandTask method) (pydra.ShellCommandTask method) get_input_el() (pydra.engine.core.TaskBase method) get_item_type() (pydra.utils.typing.TypeParser class method) get_max_resources_used() (in module pydra.utils.profiler) get_mount() (pydra.engine.helpers_file.MountIndentifier class method) get_mount_table() (pydra.engine.helpers_file.MountIndentifier class method)

get_open_loop() (in module pydra.engine.helpers) get_origin() (pydra.utils.typing.TypeParser static method) get_output_by_task_pkl() (pydra.engine.workers.SGEWorker method) get_output_field() (pydra.engine.specs.Result method) get_runnable_tasks() (in module pydra.engine.submitter) get_system_total_memory_gb() (in module pydra.utils.profiler) get_tasks_to_run() (pydra.engine.workers.SGEWorker method) get_value() (pydra.engine.specs.LazyInField method) (pydra.engine.specs.LazyOutField method) graph_sorted (pydra.engine.core.Workflow property) (pydra.engine.Workflow property) (pydra.Workflow property) group_for_inputs (pydra.engine.state.State attribute) group_for_inputs_final (pydra.engine.state.State attribute) groups_stack_final (pydra.engine.state.State attribute)

H

hash (pydra.engine.specs.BaseSpec property) hash_changes() (pydra.engine.specs.BaseSpec method) hash_function() (in module pydra.utils.hash)

hash_object() (in module pydra.utils.hash) hash_single() (in module pydra.utils.hash) help() (pydra.engine.core.TaskBase method)

I

inner_inputs (pydra.engine.state.State attribute) (pydra.engine.state.State property) input_shape() (in module pydra.engine.helpers_state) input_spec (pydra.engine.ShellCommandTask attribute) (pydra.engine.task.ShellCommandTask attribute) (pydra.ShellCommandTask attribute) inputs_ind (pydra.engine.state.State attribute) inputs_types_to_dict() (in module pydra.engine.helpers_state)

is_container() (in module pydra.engine.helpers_file) is_instance() (pydra.utils.typing.TypeParser class method) is_lazy() (in module pydra.engine.core) is_local_file() (in module pydra.engine.helpers_file) is_runnable() (in module pydra.engine.submitter) is_subclass() (pydra.utils.typing.TypeParser class method) is_task() (in module pydra.engine.core) is_workflow() (in module pydra.engine.core) iter_splits() (in module pydra.engine.helpers_state)

L

label (pydra.utils.typing.TypeParser attribute) label_str (pydra.utils.typing.TypeParser property) LazyField (class in pydra.engine.specs) LazyIn (class in pydra.engine.specs) LazyInField (class in pydra.engine.specs) LazyInterface (class in pydra.engine.specs) LazyOut (class in pydra.engine.specs) LazyOutField (class in pydra.engine.specs)

load_and_run() (in module pydra.engine.helpers) load_and_run_async() (in module pydra.engine.helpers) load_result() (in module pydra.engine.helpers) load_task() (in module pydra.engine.helpers) log_nodes_cb() (in module pydra.utils.profiler) lzin (pydra.engine.core.Workflow property) (pydra.engine.Workflow property) (pydra.Workflow property) lzout (pydra.engine.core.TaskBase property)

M

make_job() (pydra.engine.workers.PsijWorker method) make_klass() (in module pydra.engine.helpers) make_message() (in module pydra.utils.messenger) make_spec() (pydra.engine.workers.PsijWorker method) map_splits() (in module pydra.engine.helpers_state) match_any_of_union (pydra.utils.typing.TypeParser attribute) matches() (pydra.utils.typing.TypeParser class method) matches_type() (pydra.utils.typing.TypeParser class method) max_jobs (pydra.engine.workers.DistributedWorker attribute) Messenger (class in pydra.utils.messenger) module pydra pydra.engine pydra.engine.audit pydra.engine.boutiques pydra.engine.core pydra.engine.environments pydra.engine.graph pydra.engine.helpers pydra.engine.helpers_file pydra.engine.helpers_state pydra.engine.run_pickled pydra.engine.specs pydra.engine.state pydra.engine.submitter pydra.engine.task pydra.engine.workers pydra.mark pydra.mark.functions pydra.tasks pydra.utils pydra.utils.hash pydra.utils.messenger pydra.utils.misc pydra.utils.profiler pydra.utils.typing

monitor() (pydra.engine.audit.Audit method) MountIndentifier (class in pydra.engine.helpers_file) MultiInputObj (class in pydra.engine.specs) MultiOutputType (class in pydra.engine.specs)

N

name (pydra.engine.specs.LazyField attribute) (pydra.engine.specs.SpecInfo attribute) (pydra.engine.state.State attribute) Native (class in pydra.engine.environments) network (pydra.engine.specs.RuntimeSpec attribute) nodes (pydra.engine.core.Workflow property) (pydra.engine.graph.DiGraph property) (pydra.engine.Workflow property) (pydra.Workflow property)

nodes_details (pydra.engine.graph.DiGraph property) nodes_names_map (pydra.engine.graph.DiGraph property) NONE (pydra.AuditFlag attribute) (pydra.engine.AuditFlag attribute) (pydra.utils.messenger.AuditFlag attribute) not_coercible (pydra.utils.typing.TypeParser attribute) NOT_COERCIBLE_DEFAULT (pydra.utils.typing.TypeParser attribute) now() (in module pydra.utils.messenger)

O

on_cifs() (pydra.engine.helpers_file.MountIndentifier class method) on_same_mount() (pydra.engine.helpers_file.MountIndentifier class method) other_states (pydra.engine.state.State attribute) (pydra.engine.state.State property) outdir (pydra.engine.specs.RuntimeSpec attribute) output (pydra.engine.specs.Result attribute)

output_dir (pydra.engine.core.TaskBase property) output_from_inputfields() (in module pydra.engine.helpers) output_names (pydra.engine.core.TaskBase property) output_spec (pydra.engine.ShellCommandTask attribute) (pydra.engine.task.ShellCommandTask attribute) (pydra.ShellCommandTask attribute)

P

parse_copyfile() (in module pydra.engine.helpers) parse_format_string() (in module pydra.engine.helpers) parse_mount_table() (pydra.engine.helpers_file.MountIndentifier class method) patch_table() (pydra.engine.helpers_file.MountIndentifier class method) path_to_string() (in module pydra.engine.specs) persistent (pydra.utils.hash.Cache attribute) pickle_task() (pydra.engine.core.TaskBase method) plugin_name (pydra.engine.workers.ConcurrentFuturesWorker attribute) (pydra.engine.workers.DaskWorker attribute) (pydra.engine.workers.PsijLocalWorker attribute) (pydra.engine.workers.PsijSlurmWorker attribute) (pydra.engine.workers.SerialWorker attribute) (pydra.engine.workers.SGEWorker attribute) (pydra.engine.workers.SlurmWorker attribute) position_sort() (in module pydra.engine.helpers) post_run (pydra.engine.specs.TaskHook attribute) post_run_task (pydra.engine.specs.TaskHook attribute) pre_run (pydra.engine.specs.TaskHook attribute) pre_run_task (pydra.engine.specs.TaskHook attribute) prepare_inputs() (pydra.engine.state.State method) prepare_runnable_with_state() (in module pydra.engine.submitter) prepare_states() (pydra.engine.state.State method) prepare_states_combined_ind() (pydra.engine.state.State method) prepare_states_ind() (pydra.engine.state.State method) prepare_states_val() (pydra.engine.state.State method) prev_state_combiner (pydra.engine.state.State property) prev_state_combiner_all (pydra.engine.state.State property) prev_state_splitter (pydra.engine.state.State property) prev_state_splitter_rpn (pydra.engine.state.State property) prev_state_splitter_rpn_compact (pydra.engine.state.State property) print_help() (in module pydra.engine.helpers) PrintMessenger (class in pydra.utils.messenger) PROV (pydra.AuditFlag attribute) (pydra.engine.AuditFlag attribute) (pydra.utils.messenger.AuditFlag attribute) PsijLocalWorker (class in pydra.engine.workers) PsijSlurmWorker (class in pydra.engine.workers) PsijWorker (class in pydra.engine.workers) pydra module pydra.engine module pydra.engine.audit module pydra.engine.boutiques module

pydra.engine.core module pydra.engine.environments module pydra.engine.graph module pydra.engine.helpers module pydra.engine.helpers_file module pydra.engine.helpers_state module pydra.engine.run_pickled module pydra.engine.specs module pydra.engine.state module pydra.engine.submitter module pydra.engine.task module pydra.engine.workers module pydra.mark module pydra.mark.functions module pydra.tasks module pydra.utils module pydra.utils.hash module pydra.utils.messenger module pydra.utils.misc module pydra.utils.profiler module pydra.utils.typing module PydraFileLock (class in pydra.engine.helpers) PydraStateError

R

read_and_display() (in module pydra.engine.helpers) read_and_display_async() (in module pydra.engine.helpers) read_stream_and_display() (in module pydra.engine.helpers) record_error() (in module pydra.engine.helpers) register_serializer() (in module pydra.utils.hash) RemoteRESTMessenger (class in pydra.utils.messenger) remove_inp_from_splitter_rpn() (in module pydra.engine.helpers_state) remove_nodes() (pydra.engine.graph.DiGraph method) remove_nodes_connections() (pydra.engine.graph.DiGraph method) remove_previous_connections() (pydra.engine.graph.DiGraph method) remove_successors_nodes() (pydra.engine.graph.DiGraph method) reset() (pydra.engine.specs.TaskHook method) RESOURCE (pydra.AuditFlag attribute) (pydra.engine.AuditFlag attribute) (pydra.utils.messenger.AuditFlag attribute) resource_monitor_post_stop (pydra.utils.messenger.RuntimeHooks attribute) resource_monitor_pre_start (pydra.utils.messenger.RuntimeHooks attribute) ResourceMonitor (class in pydra.utils.profiler) Result (class in pydra.engine.specs)

result() (pydra.engine.core.TaskBase method) retrieve_values() (pydra.engine.specs.BaseSpec method) (pydra.engine.specs.ShellSpec method) return_code (pydra.engine.specs.ShellOutSpec attribute) rpn2splitter() (in module pydra.engine.helpers_state) rss_peak_gb (pydra.engine.specs.Runtime attribute) run() (pydra.utils.profiler.ResourceMonitor method) run_el() (pydra.engine.workers.ConcurrentFuturesWorker method) (pydra.engine.workers.DaskWorker method) (pydra.engine.workers.PsijWorker method) (pydra.engine.workers.SerialWorker method) (pydra.engine.workers.SGEWorker method) (pydra.engine.workers.SlurmWorker method) (pydra.engine.workers.Worker method) run_pickled() (in module pydra.engine.run_pickled) Runtime (class in pydra.engine.specs) runtime (pydra.engine.specs.Result attribute) RuntimeHooks (class in pydra.utils.messenger) RuntimeSpec (class in pydra.engine.specs)

S

sanitize_splitter() (pydra.engine.specs.LazyField class method) save() (in module pydra.engine.helpers) send() (pydra.utils.messenger.FileMessenger method) (pydra.utils.messenger.Messenger method) (pydra.utils.messenger.PrintMessenger method) (pydra.utils.messenger.RemoteRESTMessenger method) send_message() (in module pydra.utils.messenger) SerialWorker (class in pydra.engine.workers) set_input_groups() (pydra.engine.state.State method) set_output() (pydra.engine.core.Workflow method) (pydra.engine.Workflow method) (pydra.Workflow method) set_state() (pydra.engine.core.TaskBase method) setup() (pydra.engine.environments.Environment method) SGEWorker (class in pydra.engine.workers) ShellCommandTask (class in pydra) (class in pydra.engine) (class in pydra.engine.task) ShellOutSpec (class in pydra.engine.specs) ShellSpec (class in pydra.engine.specs) Singularity (class in pydra.engine.environments) SlurmWorker (class in pydra.engine.workers) sorted_nodes (pydra.engine.graph.DiGraph property) sorted_nodes_names (pydra.engine.graph.DiGraph property) sorting() (pydra.engine.graph.DiGraph method) SpecInfo (class in pydra.engine.specs) split() (pydra.engine.core.TaskBase method) (pydra.engine.specs.LazyField method) split_cmd() (in module pydra.engine.task) splits (pydra.engine.specs.LazyField attribute) splits() (pydra.engine.state.State method)

splits_groups() (in module pydra.engine.helpers_state) splitter (pydra.engine.state.State attribute) (pydra.engine.state.State property) splitter2rpn() (in module pydra.engine.helpers_state) splitter_final (pydra.engine.state.State attribute) (pydra.engine.state.State property) splitter_rpn (pydra.engine.state.State attribute) (pydra.engine.state.State property) splitter_rpn_compact (pydra.engine.state.State attribute) (pydra.engine.state.State property) splitter_rpn_final (pydra.engine.state.State property) splitter_validation() (pydra.engine.state.State method) start_audit() (pydra.engine.audit.Audit method) State (class in pydra.engine.state) StateArray (class in pydra.engine.specs) states_ind (pydra.engine.state.State attribute) states_val (pydra.engine.state.State attribute) stderr (pydra.engine.specs.ShellOutSpec attribute) stdout (pydra.engine.specs.ShellOutSpec attribute) stop() (pydra.utils.profiler.ResourceMonitor method) strip_splits() (pydra.utils.typing.TypeParser class method) submit_array_job() (pydra.engine.workers.SGEWorker method) submit_from_call() (pydra.engine.Submitter method) (pydra.engine.submitter.Submitter method) (pydra.Submitter method) Submitter (class in pydra) (class in pydra.engine) (class in pydra.engine.submitter) subtype (pydra.engine.workers.PsijLocalWorker attribute) (pydra.engine.workers.PsijSlurmWorker attribute) superclass_auto_cast (pydra.utils.typing.TypeParser attribute) SUPPORTED_COPY_MODES (pydra.engine.core.TaskBase attribute)

T

task() (in module pydra.mark) (in module pydra.mark.functions) task_execute_post_exit (pydra.utils.messenger.RuntimeHooks attribute) task_execute_pre_entry (pydra.utils.messenger.RuntimeHooks attribute) task_run_entry (pydra.utils.messenger.RuntimeHooks attribute) task_run_exit (pydra.utils.messenger.RuntimeHooks attribute) TaskBase (class in pydra.engine.core)

TaskHook (class in pydra.engine.specs) teardown() (pydra.engine.environments.Environment method) template_update() (in module pydra.engine.helpers_file) (pydra.engine.specs.BaseSpec method) template_update_single() (in module pydra.engine.helpers_file) tp (pydra.utils.typing.TypeParser attribute) type (pydra.engine.specs.LazyField attribute) TypeParser (class in pydra.utils.typing)

U

uid (pydra.engine.core.TaskBase property)

unwrap_splitter() (in module pydra.engine.helpers_state) update_connections() (pydra.engine.state.State method)

V

version (pydra.engine.core.TaskBase property)

vms_peak_gb (pydra.engine.specs.Runtime attribute)

W

Worker (class in pydra.engine.workers) Workflow (class in pydra) (class in pydra.engine) (class in pydra.engine.core)