Index

A

add() (pydra.engine.core.Workflow method) (pydra.engine.Workflow method) add_edges() (pydra.engine.graph.DiGraph method) add_edges_description() (pydra.engine.graph.DiGraph method) 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.engine.AuditFlag attribute) (pydra.utils.messenger.AuditFlag attribute) annotate() (in module pydra.mark.functions)

args (pydra.engine.specs.ShellSpec attribute) argstr_formatting() (in module pydra.engine.helpers) attr_fields() (in module pydra.engine.specs) attr_fields_dict() (in module pydra.engine.specs) 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.engine) (class in pydra.utils.messenger)

B

bases (pydra.engine.specs.SpecInfo attribute) BaseSpec (class in pydra.engine.specs)

bind_paths() (pydra.engine.task.ContainerTask method) binds() (pydra.engine.task.ContainerTask method) BoshTask (class in pydra.engine.boutiques)

C

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) check_fields_input_spec() (pydra.engine.specs.BaseSpec method) check_for_results_files() (pydra.engine.workers.SGEWorker method) check_latest_version() (in module pydra) check_metadata() (pydra.engine.specs.BaseSpec method) (pydra.engine.specs.FunctionSpec method) (pydra.engine.specs.ShellSpec method) checksum (pydra.engine.core.TaskBase property) (pydra.engine.core.Workflow property) (pydra.engine.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.SerialWorker method) (pydra.engine.workers.Worker method) cmdline (pydra.engine.ShellCommandTask property) (pydra.engine.task.ShellCommandTask property) 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 property) (pydra.engine.task.ShellCommandTask property) ConcurrentFuturesWorker (class in pydra.engine.workers) cont_dim (pydra.engine.core.TaskBase property)

container (pydra.engine.specs.ContainerSpec attribute) (pydra.engine.specs.DockerSpec attribute) (pydra.engine.specs.RuntimeSpec attribute) (pydra.engine.specs.SingularitySpec attribute) container_args (pydra.engine.DockerTask property) (pydra.engine.task.DockerTask property) (pydra.engine.task.SingularityTask property) container_check() (pydra.engine.task.ContainerTask method) container_xargs (pydra.engine.specs.ContainerSpec attribute) ContainerSpec (class in pydra.engine.specs) ContainerTask (class in pydra.engine.task) converter() (pydra.engine.specs.MultiInputObj class method) (pydra.engine.specs.MultiOutputObj class method) converter_groups_to_input() (in module pydra.engine.helpers_state) copy() (pydra.engine.graph.DiGraph method) copyfile() (in module pydra.engine.helpers_file) copyfile_input() (in module pydra.engine.helpers_file) (pydra.engine.specs.BaseSpec method) copyfile_workflow() (in module pydra.engine.helpers) copyfiles() (in module pydra.engine.helpers_file) 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) create_dotfile() (pydra.engine.core.Workflow method) (pydra.engine.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) custom_validator() (in module pydra.engine.helpers)

D

DaskWorker (class in pydra.engine.workers) DiGraph (class in pydra.engine.graph) Directory (class in pydra.engine.specs) DistributedWorker (class in pydra.engine.workers)

DockerSpec (class in pydra.engine.specs) DockerTask (class in pydra.engine) (class in pydra.engine.task) 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) errored (pydra.engine.core.TaskBase property) (pydra.engine.specs.Result attribute) exec_as_coro() (pydra.engine.workers.ConcurrentFuturesWorker method) exec_dask() (pydra.engine.workers.DaskWorker method)

exec_serial() (pydra.engine.workers.SerialWorker method) executable (pydra.engine.specs.ShellSpec attribute) execute() (in module pydra.engine.helpers) expand_runnable() (pydra.engine.Submitter method) (pydra.engine.submitter.Submitter method) expand_workflow() (pydra.engine.Submitter method) (pydra.engine.submitter.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) fields (pydra.engine.specs.SpecInfo attribute) File (class in pydra.engine.specs) 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) fname_presuffix() (in module pydra.engine.helpers_file) 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) generated_output_names (pydra.engine.core.TaskBase property) generated_output_names() (pydra.engine.specs.ShellOutSpec method) get_available_cpus() (in module pydra.engine.helpers) get_input_el() (pydra.engine.core.TaskBase method) get_max_resources_used() (in module pydra.utils.profiler) get_open_loop() (in module pydra.engine.helpers) get_output_by_task_pkl() (pydra.engine.workers.SGEWorker method) get_output_field() (pydra.engine.specs.Result method)

get_related_files() (in module pydra.engine.helpers_file) 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.LazyField method) graph_sorted (pydra.engine.core.Workflow property) (pydra.engine.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_dir() (in module pydra.engine.helpers_file) hash_file() (in module pydra.engine.helpers_file)

hash_function() (in module pydra.engine.helpers) hash_value() (in module pydra.engine.helpers) help() (pydra.engine.core.TaskBase method)

I

image (pydra.engine.specs.ContainerSpec attribute) init (pydra.engine.DockerTask attribute) (pydra.engine.task.DockerTask attribute) (pydra.engine.task.SingularityTask attribute) 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)

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_existing_file() (in module pydra.engine.helpers_file) is_lazy() (in module pydra.engine.core) is_local_file() (in module pydra.engine.helpers_file) is_runnable() (in module pydra.engine.submitter) is_task() (in module pydra.engine.core) is_workflow() (in module pydra.engine.core) iter_splits() (in module pydra.engine.helpers_state)

L

LazyField (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)

M

make_klass() (in module pydra.engine.helpers) make_message() (in module pydra.utils.messenger) map_splits() (in module pydra.engine.helpers_state) 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.graph pydra.engine.helpers pydra.engine.helpers_file pydra.engine.helpers_state 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.messenger pydra.utils.profiler

monitor() (pydra.engine.audit.Audit method) MultiInputFile (class in pydra.engine.specs) MultiInputObj (class in pydra.engine.specs) MultiOutputFile (class in pydra.engine.specs) MultiOutputObj (class in pydra.engine.specs)

N

name (pydra.engine.specs.SpecInfo attribute) (pydra.engine.state.State attribute) network (pydra.engine.specs.RuntimeSpec attribute) nodes (pydra.engine.core.Workflow property) (pydra.engine.graph.DiGraph property) (pydra.engine.Workflow property)

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

O

on_cifs() (in module pydra.engine.helpers_file) 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)

P

path_to_string() (in module pydra.engine.specs) pickle_task() (pydra.engine.core.TaskBase method) 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.engine.AuditFlag attribute) (pydra.utils.messenger.AuditFlag attribute) pydra module pydra.engine module pydra.engine.audit module pydra.engine.boutiques module pydra.engine.core module

pydra.engine.graph module pydra.engine.helpers module pydra.engine.helpers_file module pydra.engine.helpers_state 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.messenger module pydra.utils.profiler 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) related_filetype_sets (in module pydra.engine.helpers_file) 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.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.SerialWorker method) (pydra.engine.workers.SGEWorker method) (pydra.engine.workers.SlurmWorker method) (pydra.engine.workers.Worker method) 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

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_input_validator() (in module pydra) set_output() (pydra.engine.core.Workflow method) (pydra.engine.Workflow method) set_state() (pydra.engine.core.TaskBase method) SGEWorker (class in pydra.engine.workers) ShellCommandTask (class in pydra.engine) (class in pydra.engine.task) ShellOutSpec (class in pydra.engine.specs) ShellSpec (class in pydra.engine.specs) SingularitySpec (class in pydra.engine.specs) SingularityTask (class in pydra.engine.task) 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) split_cmd() (in module pydra.engine.task)

split_filename() (in module pydra.engine.helpers_file) 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) 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) submit_array_job() (pydra.engine.workers.SGEWorker method) submit_from_call() (pydra.engine.Submitter method) (pydra.engine.submitter.Submitter method) Submitter (class in pydra.engine) (class in pydra.engine.submitter)

T

task() (in module pydra.mark.functions) task_execute_post_exit (pydra.utils.messenger.RuntimeHooks attribute) task_execute_pre_entry (pydra.utils.messenger.RuntimeHooks attribute) task_hash() (in module pydra.engine.helpers) 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) template_update() (in module pydra.engine.helpers_file) (pydra.engine.specs.BaseSpec method) template_update_single() (in module pydra.engine.helpers_file)

U

uid (pydra.engine.core.TaskBase property)

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.engine) (class in pydra.engine.core)