Index

_

_abc_impl (_EditJsonLikeParams attribute) (_FunctionDefinition attribute) (AbstractJobConfig attribute) (AddVariables attribute) (CaseMatrixCreator attribute) (CaseMatrixExpansionParams attribute) (CaseMatrixRunSetup attribute) (ColumnarOperationParameters attribute) (CompiledJob attribute) (CompileResponse attribute) (CompleteReturn attribute) (ConditionalExecution attribute) (ContainerConfig attribute) (ContinuousRange attribute) (CopyParams attribute), [1] (CreateFileParams attribute) (DeleteParams attribute) (DiscreteRange attribute) (DispatchParams attribute) (EditExternalParams attribute) (EditJsonParams attribute) (EditYamlParams attribute) (ExistsParams attribute) (ExternalAnalysisParams attribute) (ExternalExtractParams attribute) (ExternalSimpleParams attribute) (FileContentsParams attribute) (FromCsvToParquetParameters attribute) (FromExcelToCsvParameters attribute) (GetJobResponse attribute) (GetJobReturn attribute) (GetJsonSchemaResponse attribute) (HostParams attribute) (IfElseParams attribute) (InitialConfig attribute) (JobConfig attribute) (JobInfo attribute) (JobReturn attribute) (JobsReport attribute) (JobState attribute) (JobStatusReport attribute) (JobWithContext attribute) (JoinParquetParams attribute) (LocalConfig attribute) (LocalForLoopParams attribute) (LocalPipelineParameters attribute) (LocalRunnerConfig attribute) (Mkdirparams attribute) (MoveParams attribute), [1] (PendingReturn attribute) (QueueInterface attribute) (RemoteConfig attribute) (RsyncParams attribute) (RunLogResponse attribute) (RunResponse attribute) (Settings attribute) (SetVariables attribute) (SlurmRunnerConfig attribute) (SqliteQueue attribute) (SshConfig attribute) (StartRunResponse attribute) (SubmitParams attribute) (TemporaryDirectoryParams attribute) (TouchFileParameters attribute) (ValidateResponse attribute) (VariableContextParams attribute) (VariableDefinition attribute) (VirtualJobConfig attribute) (VirtualParamModel attribute) _add_dependency() (in module pyantz.infrastructure.runner.slurm.slurm_runner) _add_dependency_to_sbatch() (in module pyantz.infrastructure.runner.slurm.slurm_runner) _asdict() (JobResult method) _build_parser() (in module pyantz.__main__) _build_remote_command() (in module pyantz.infrastructure.runner._remotes.ssh) _check_dependencies_exist() (InitialConfig method) _check_empty_type() (SqliteQueue static method) _check_for_deadlock() (in module pyantz.infrastructure.runner.local.local_runner) _check_import_allowed() (in module pyantz.infrastructure.config.fn_utils) _check_params() (in module pyantz.infrastructure.config.parameters.compile_check) _check_step_is_positive() (ContinuousRange method) _check_unique_ids() (in module pyantz.infrastructure.virtual.compile) _classify_job_annotation() (in module pyantz.infrastructure.virtual.compile) _compare() (in module pyantz.jobs.branching.if_else) _compare_text() (in module pyantz.jobs.branching.if_else) _compile_parameters() (in module pyantz.infrastructure.virtual.compile) _compile_parameters_singular() (in module pyantz.infrastructure.virtual.compile) _compile_singular() (in module pyantz.infrastructure.virtual.compile) _connect() (in module pyantz.infrastructure.runner._remotes.ssh) _create_engine() (SqliteQueue method)

_create_job_submitter() (in module pyantz.infrastructure.runner.slurm.slurm_runner) _create_sbatch() (in module pyantz.infrastructure.runner.slurm.slurm_runner) _current_user() (in module pyantz.infrastructure.config.host_config) _describe() (in module pyantz.__main__) _edit_jsonlike() (in module pyantz.jobs.files.edit) _EditJsonLikeParams (class in pyantz.jobs.files.edit) _engine (SqliteQueue attribute) _ensure_image() (in module pyantz.infrastructure.runner._remotes.container) _exclude_unneeded() (in module pyantz.infrastructure.runner._remotes._transfers) _extract_output() (in module pyantz.infrastructure.runner._remotes.container) _ExtraField (in module pyantz.jobs.files.edit) _field_defaults (JobResult attribute) _fields (JobResult attribute) _fill_queue() (in module pyantz.infrastructure.runner.local.local_runner) _find_joblike_parameters_with_model() (in module pyantz.infrastructure.virtual.compile) _FunctionDefinition (class in pyantz.jobs.files.edit) _generate_jobs_report() (SqliteQueue static method) _get_dependent_jobs() (in module pyantz.infrastructure.runner.slurm.slurm_runner) _get_job_config() (SqliteQueue static method) _get_slurm_env_variables() (in module pyantz.infrastructure.runner.slurm.slurm_runner) _has_time_limit() (in module pyantz.infrastructure.runner.slurm.slurm_runner) _host_key_policy() (in module pyantz.infrastructure.runner._remotes.ssh) _initial_submit() (in module pyantz.infrastructure.runner.slurm.slurm_runner) _insert_job() (SqliteQueue method) _is_non_empty_iterable() (in module pyantz.infrastructure.virtual.compile) _is_protocol (QueueInterface attribute) (SqliteQueue attribute) (VirtualParamModel attribute) _is_runtime_protocol (VirtualParamModel attribute) _is_virtual() (in module pyantz.infrastructure.config.virtual) _json_editor_factory() (in module pyantz.jobs.files.edit) _load_config_data() (in module pyantz.__main__) _load_job_config() (in module pyantz.infrastructure.runner.slurm.slurm_runner) _log_failures() (in module pyantz.infrastructure.runner.local.local_runner) _log_progress() (in module pyantz.infrastructure.runner.local.local_runner) _make() (JobResult class method) _make_client() (in module pyantz.infrastructure.runner._remotes.container) _make_pipeline() (in module pyantz.infrastructure.config.pipeline) _make_remote_dir() (in module pyantz.infrastructure.runner._remotes.ssh) _make_submit_fn() (in module pyantz.infrastructure.runner.local.local_runner) _name_matches() (in module pyantz.infrastructure.config.parameters.decorators) _nested_jobs() (in module pyantz.jobs.branching.case_matrix) _PathMismatchError _pipeline_factory_factory() (in module pyantz.jobs.branching.case_matrix) _POOL_CONTEXT (in module pyantz.infrastructure.runner.local.local_runner) _prepare_working_dir() (in module pyantz.infrastructure.runner._remotes.ssh) _problems() (in module pyantz.api.endpoints.pipelines.endpoints) _PROCESSES (in module pyantz.api.endpoints.pipelines.endpoints) _rebuild() (in module pyantz.infrastructure.config.variables) _record_result() (in module pyantz.infrastructure.runner.local.local_runner) _regenerate_nested_ids() (in module pyantz.jobs.branching.case_matrix) _remove() (in module pyantz.jobs.files.moving) _remove_repeats() (DiscreteRange class method) _remove_stale_queue() (in module pyantz.infrastructure.runner.local.local_runner) _replace() (JobResult method) _resolve_var_str() (in module pyantz.infrastructure.config.variables) _rewrite_ids() (in module pyantz.jobs.branching.case_matrix) _run_checked() (in module pyantz.infrastructure.runner._remotes.ssh) _run_dir() (in module pyantz.api.endpoints.pipelines.endpoints) _run_in_child() (in module pyantz.infrastructure.runner.local.local_runner) _run_job_no_parent_wrapper_with_details() (in module pyantz.infrastructure.runner.job_manager) _run_jobs_temp_dir_local() (in module pyantz.jobs.wrappers.variables) _run_jobs_temp_dir_remote() (in module pyantz.jobs.wrappers.variables) _run_on_connection() (in module pyantz.infrastructure.runner._remotes.ssh) _run_on_node() (in module pyantz.infrastructure.runner.slurm.slurm_runner) _run_with_timeout() (in module pyantz.infrastructure.runner.local.local_runner) _run_within_same_proc() (in module pyantz.infrastructure.runner.local.local_runner) _sa_class_manager (DependencyTable attribute) (JobConfigTable attribute) (JobQueue attribute) (StatusTable attribute) _sa_registry (Base attribute) _save_output() (in module pyantz.jobs.subproc.dispatch) _save_slurm_config() (in module pyantz.infrastructure.runner.slurm.slurm_runner) _SEQUENCE_AND_SET_TYPES (in module pyantz.infrastructure.config.variables) _setup_logging() (in module pyantz.__main__) _sigterm_as_keyboard_interrupt() (in module pyantz.infrastructure.runner.local.local_runner) _start_pool() (in module pyantz.infrastructure.runner.local.local_runner) _stop_workers() (in module pyantz.infrastructure.runner.local.local_runner) _sync_output() (in module pyantz.infrastructure.runner._remotes.ssh) _to_number() (in module pyantz.jobs.branching.if_else) _try_dequeue() (SqliteQueue method) _try_to_validate_job() (in module pyantz.infrastructure.virtual.compile) _update_ids_in_hyper_parameters() (JobWithContext class method) _update_job_statuses() (SqliteQueue method) _wait_for_workers() (in module pyantz.infrastructure.runner.local.local_runner) _worker() (in module pyantz.infrastructure.runner.local.local_runner) _worker_process() (in module pyantz.infrastructure.runner.local.local_runner) _write_atomically() (in module pyantz.jobs.files.edit)

A

abs_tol (ConditionalExecution attribute) (IfElseParams attribute) AbstractJobConfig (class in pyantz.infrastructure.config.abstract_job) add_job() (QueueInterface method) (SqliteQueue method) add_parameters() (in module pyantz.infrastructure.config.parameters.decorators) add_to_tar_file() (in module pyantz.infrastructure.runner._remotes._transfers)

AddVariables (class in pyantz.virtual.add_variables) all_succeeded (JobsReport property) ALLOWED_MODULES_VARIABLE (in module pyantz.infrastructure.config.fn_utils) AnyRunner (in module pyantz.infrastructure.config.initial) API_TOKEN_VARIABLE (in module pyantz.api.settings) app (in module pyantz.api.backend) args (_FunctionDefinition attribute)

B

Base (class in pyantz.infrastructure.distributed_queue.sql.orm)

BUSY_TIMEOUT_SECONDS (in module pyantz.infrastructure.distributed_queue.sql.sql_queue)

C

case_matrix_parquet (CaseMatrixExpansionParams attribute) CaseMatrixCreator (class in pyantz.jobs.branching.case_matrix) CaseMatrixExpansionParams (class in pyantz.jobs.branching.case_matrix) CaseMatrixRunSetup (class in pyantz.jobs.branching.case_matrix) change_config_in_place() (QueueInterface method) (SqliteQueue method) check_config() (in module pyantz.infrastructure.config.parameters.compile_check) check_file_paths() (JoinParquetParams method) check_safe_to_bind() (in module pyantz.api.settings) check_syncs() (SshConfig method) CHUNKSIZE (in module pyantz.infrastructure.distributed_queue.sql.orm) cmd (DispatchParams attribute) coerce (ConditionalExecution attribute) (IfElseParams attribute) Coercion (in module pyantz.jobs.branching.if_else) cols_to_exclude (CaseMatrixExpansionParams attribute) columnar_operation() (in module pyantz.jobs.analysis.simple) ColumnarOperationParameters (class in pyantz.jobs.analysis.simple) comparator (ConditionalExecution attribute) (IfElseParams attribute) compile_config() (in module pyantz.api.endpoints.pipelines.endpoints) compile_virtual() (AddVariables method) (in module pyantz.infrastructure.virtual.compile) (VirtualJobConfig method) (VirtualParamModel method) compiled_params (VirtualJobConfig property)

CompiledJob (class in pyantz.api.endpoints.pipelines.models) CompileResponse (class in pyantz.api.endpoints.pipelines.models) CompleteReturn (class in pyantz.infrastructure.distributed_queue.common.return_types) ConditionalExecution (class in pyantz.jobs.branching.if_else) conditionally_execute() (in module pyantz.jobs.branching.if_else) CONFIG_FILE_ENVIRON_VAR_NAME (in module pyantz.infrastructure.runner.slurm.slurm_runner) ConfigBody (in module pyantz.api.endpoints.pipelines.endpoints) CONFLICT (in module pyantz.infrastructure.runner._remotes.container) connect_timeout (SshConfig attribute) container_service (ContainerConfig attribute) ContainerConfig (class in pyantz.infrastructure.config.host_config) contents (CreateFileParams attribute) ContinuousRange (class in pyantz.jobs.branching.case_matrix) copy() (in module pyantz.jobs.files.moving) (in module pyantz.jobs.files.simple) copy_project_dir (RemoteConfig attribute) CopyParams (class in pyantz.jobs.files.moving) (class in pyantz.jobs.files.simple) CORS_ORIGINS_VARIABLE (in module pyantz.api.settings) create() (in module pyantz.jobs.files.simple) create_app() (in module pyantz.api.backend) create_case_matrix() (in module pyantz.jobs.branching.case_matrix) CreateFileParams (class in pyantz.jobs.files.simple) csv_file (FromCsvToParquetParameters attribute) (FromExcelToCsvParameters attribute) csv_to_parquet() (in module pyantz.jobs.files.reformat) cwd (DispatchParams attribute)

D

database_file (SqliteQueue attribute) DEADLOCK_POLLS (in module pyantz.infrastructure.runner.local.local_runner) DEATH_CHECK_SECONDS (in module pyantz.infrastructure.runner.local.local_runner) DEFAULT_CONTAINER_WORKING_DIR (in module pyantz.infrastructure.runner._remotes._transfers) DEFAULT_HOST (in module pyantz.api.settings) DEFAULT_JOB_TIMEOUT (in module pyantz.infrastructure.config.runners.slurm_runner) DEFAULT_LOG_BYTES (in module pyantz.api.endpoints.pipelines.endpoints) DEFAULT_PORT (in module pyantz.api.settings) DEFAULT_REL_TOL (in module pyantz.jobs.branching.if_else) delete() (in module pyantz.jobs.files.simple) DeleteParams (class in pyantz.jobs.files.simple) dependency_type (JobConfig attribute) DependencyTable (class in pyantz.infrastructure.distributed_queue.sql.orm) depends_on (AbstractJobConfig attribute) (CompiledJob attribute) (DependencyTable attribute)

describe_job() (in module pyantz.api.endpoints.get_jobs.endpoint) describe_run() (in module pyantz.status) description (JobInfo attribute) destination (CopyParams attribute) (MoveParams attribute) (RsyncParams attribute) details (JobResult attribute) (JobState attribute) (StatusTable attribute) dir_path (Mkdirparams attribute) DiscreteRange (class in pyantz.jobs.branching.case_matrix) dispatch() (in module pyantz.jobs.subproc.dispatch) DispatchParams (class in pyantz.jobs.subproc.dispatch) do_nothing() (in module pyantz.jobs.testing.nop) dst (CopyParams attribute) (MoveParams attribute) dump_schemas() (in module pyantz.api.dump_schemas)

E

edges (CompileResponse attribute) edit_external_method() (in module pyantz.jobs.files.edit) edit_json() (in module pyantz.jobs.files.edit) edit_yaml() (in module pyantz.jobs.files.edit) EditExternalParams (class in pyantz.jobs.files.edit) EditJsonParams (class in pyantz.jobs.files.edit) EditYamlParams (class in pyantz.jobs.files.edit) ENTRY_BASH_FILE_PATH (in module pyantz.infrastructure.runner.slurm.slurm_runner) ENTRY_MODULE_NAME (in module pyantz.infrastructure.runner.slurm.slurm_runner) env (DispatchParams attribute) environment_variables (RemoteConfig attribute) environment_variables_file (RemoteConfig attribute) error (JobsReport attribute) ERROR (JobStatus attribute) errors (ValidateResponse attribute) excel_file (FromExcelToCsvParameters attribute)

excel_to_csv() (in module pyantz.jobs.files.reformat) EXCLUDED_DIRECTORIES (in module pyantz.infrastructure.runner._remotes._transfers) EXCLUDED_SUFFIXES (in module pyantz.infrastructure.runner._remotes._transfers) exist_ok (TouchFileParameters attribute) ExistsParams (class in pyantz.jobs.files.check) external_analysis() (in module pyantz.jobs.analysis.external) external_function (ExternalAnalysisParams attribute) (ExternalExtractParams attribute) (ExternalSimpleParams attribute) external_simple() (in module pyantz.jobs.analysis.external) ExternalAnalysisParams (class in pyantz.jobs.analysis.external) ExternalExtractParams (class in pyantz.jobs.analysis.external) ExternalSimpleParams (class in pyantz.jobs.analysis.external) extra_field (_EditJsonLikeParams attribute) (EditExternalParams attribute) extract_function (EditExternalParams attribute)

F

fail_deadlocked_jobs() (QueueInterface method) (SqliteQueue method) fail_jobs_of_worker() (QueueInterface method) (SqliteQueue method) file (_EditJsonLikeParams attribute) (ExistsParams attribute) (FileContentsParams attribute) file_contains() (in module pyantz.jobs.files.check) file_exists() (in module pyantz.jobs.files.check) FileContentsParams (class in pyantz.jobs.files.check) find_graph_problems() (in module pyantz.infrastructure.config.graph_validation) find_project_root() (in module pyantz.infrastructure.runner._remotes._transfers) FLOAT_DECIMALS (in module pyantz.jobs.branching.case_matrix) fn_path (GetJsonSchemaResponse attribute)

from_config() (JobWithContext class method) FromCsvToParquetParameters (class in pyantz.jobs.files.reformat) FromExcelToCsvParameters (class in pyantz.jobs.files.reformat) FRONTEND_DIR_VARIABLE (in module pyantz.api.settings) func (_FunctionDefinition attribute) function (CompiledJob attribute) (JobConfig attribute) (VirtualJobConfig attribute) function_args (ExternalAnalysisParams attribute) (ExternalExtractParams attribute) (ExternalSimpleParams attribute) function_kwargs (ExternalAnalysisParams attribute) (ExternalExtractParams attribute) (ExternalSimpleParams attribute)

G

get_api_token() (in module pyantz.api.settings) get_bundled_frontend_dir() (in module pyantz.api.frontend_server) get_cmd() (in module pyantz.infrastructure.runner._remotes._transfers) get_cors_origins() (in module pyantz.api.settings) get_environment() (in module pyantz.infrastructure.runner._remotes._transfers) get_failed_jobs() (QueueInterface method) (SqliteQueue method) get_frontend_dir() (in module pyantz.api.settings) get_job() (QueueInterface method) (SqliteQueue method) get_job_ids_with_status() (SqliteQueue method) get_job_schema() (in module pyantz.api.endpoints.get_parameters.endpoints) get_job_status() (QueueInterface method) (SqliteQueue method) get_jobs() (in module pyantz.api.endpoints.get_jobs.endpoint)

get_jobs_report() (QueueInterface method) (SqliteQueue method) get_parameters() (in module pyantz.infrastructure.config.parameters.decorators) get_params() (in module pyantz.infrastructure.config.parameters.compile_check) get_project_dir() (in module pyantz.infrastructure.runner._remotes._transfers) get_registered_functions() (in module pyantz.infrastructure.config.parameters.decorators) get_run() (in module pyantz.api.endpoints.pipelines.endpoints) get_run_log() (in module pyantz.api.endpoints.pipelines.endpoints) get_runs_dir() (in module pyantz.api.settings) get_settings() (in module pyantz.api.settings) get_setup_tar() (in module pyantz.infrastructure.runner._remotes._transfers) get_values() (ContinuousRange method) (DiscreteRange method) GetJobResponse (class in pyantz.api.endpoints.get_jobs.models) GetJobReturn (class in pyantz.infrastructure.distributed_queue.common.return_types) GetJsonSchemaResponse (class in pyantz.api.endpoints.get_parameters.models)

H

host (InitialConfig attribute) (Settings attribute) host_config (HostParams attribute)

HOST_VARIABLE (in module pyantz.api.settings) HostConfig (in module pyantz.infrastructure.config.host_config) HostParams (class in pyantz.jobs.wrappers.submit) how (JoinParquetParams attribute)

I

if_else() (in module pyantz.jobs.branching.if_else) if_false (IfElseParams attribute) if_true (ConditionalExecution attribute) (IfElseParams attribute) IfElseParams (class in pyantz.jobs.branching.if_else) image (ContainerConfig attribute) import_function_by_name() (in module pyantz.infrastructure.config.fn_utils) import_module_item_by_name() (in module pyantz.infrastructure.config.fn_utils)

ImportedCallable (in module pyantz.infrastructure.config.fn_utils) index_variable (LocalForLoopParams attribute) inherit_context() (JobWithContext method) inherit_dependencies (SlurmRunnerConfig attribute) InitialConfig (class in pyantz.infrastructure.config.initial) input_stream (DispatchParams attribute) inter_job_named_pipes (LocalPipelineParameters attribute) is_virtual() (in module pyantz.infrastructure.config.parameters.decorators)

J

job (JobReturn attribute) job_config_content (JobConfigTable attribute) job_id (AbstractJobConfig attribute) (CompiledJob attribute) (DependencyTable attribute) (JobConfigTable attribute) (JobQueue attribute) (JobState attribute) (JobStatusReport attribute) (StatusTable attribute) job_status (StatusTable attribute) job_subindex (JobConfigTable attribute) JobConfig (class in pyantz.infrastructure.config.job) JobConfigTable (class in pyantz.infrastructure.distributed_queue.sql.orm) JobFunctionType (in module pyantz.infrastructure.config.job) JobInfo (class in pyantz.api.endpoints.get_jobs.models) JobPipeline (in module pyantz.infrastructure.config.pipeline) JobQueue (class in pyantz.infrastructure.distributed_queue.sql.orm) JobResult (class in pyantz.infrastructure.runner.job_manager) JobReturn (class in pyantz.infrastructure.distributed_queue.common.return_types) jobs (CompileResponse attribute) (GetJobResponse attribute) (HostParams attribute) (InitialConfig attribute) (LocalForLoopParams attribute) (LocalPipelineParameters attribute) (RunResponse attribute) (SetVariables attribute) (SubmitParams attribute) (TemporaryDirectoryParams attribute) (VariableContextParams attribute)

jobs_report (CompleteReturn attribute) (PendingReturn attribute) JobsReport (class in pyantz.infrastructure.distributed_queue.common.return_types) JobState (class in pyantz.api.endpoints.pipelines.models) JobStatus (class in pyantz.infrastructure.distributed_queue.common.return_types) JobStatusReport (class in pyantz.infrastructure.distributed_queue.common.return_types) JobVariables (in module pyantz.infrastructure.runner.job_manager) JobWithContext (class in pyantz.infrastructure.config.job) join_parquets() (in module pyantz.jobs.analysis.simple) JoinParquetParams (class in pyantz.jobs.analysis.simple) JSON_INDENT (in module pyantz.jobs.files.edit) json_schema (GetJsonSchemaResponse attribute)

K

key_filename (SshConfig attribute)

known_hosts_policy (SshConfig attribute) kwargs (_FunctionDefinition attribute)

L

lazy_or_eager (ExternalAnalysisParams attribute) left_col (ColumnarOperationParameters attribute) left_parquet (JoinParquetParams attribute) left_side (ConditionalExecution attribute) (IfElseParams attribute) local_for_loop() (in module pyantz.jobs.wrappers.loops)

LOCAL_HOSTS (in module pyantz.api.settings) LocalConfig (class in pyantz.infrastructure.config.host_config) LocalForLoopParams (class in pyantz.jobs.wrappers.loops) LocalPipelineParameters (class in pyantz.jobs.wrappers.local) LocalRunnerConfig (class in pyantz.infrastructure.config.runners.local_runner) log (RunLogResponse attribute) LOG_LEVELS (in module pyantz.__main__)

M

main() (in module pyantz.__main__) (in module pyantz.api.dump_schemas) (in module pyantz.status) make_and_compile() (in module pyantz.infrastructure.config.initial) make_job() (in module pyantz.infrastructure.config.job) mark_virtual() (in module pyantz.infrastructure.config.parameters.decorators) max_job_time_seconds (SlurmRunnerConfig attribute) MAX_LOG_BYTES (in module pyantz.api.endpoints.pipelines.endpoints) MAX_PORT (in module pyantz.api.settings) MAX_RESOLUTION_DEPTH (in module pyantz.infrastructure.config.variables) max_retries (JobConfig attribute) max_value (ContinuousRange attribute) min_value (ContinuousRange attribute) missing_ok (DeleteParams attribute) mkdir() (in module pyantz.jobs.files.simple) Mkdirparams (class in pyantz.jobs.files.simple) model_validate() (VirtualParamModel class method) module pyantz pyantz.__main__ pyantz.api pyantz.api.auth pyantz.api.backend pyantz.api.dev_server pyantz.api.dump_schemas pyantz.api.endpoints pyantz.api.endpoints.get_jobs pyantz.api.endpoints.get_jobs.endpoint pyantz.api.endpoints.get_jobs.models pyantz.api.endpoints.get_parameters pyantz.api.endpoints.get_parameters.endpoints pyantz.api.endpoints.get_parameters.models pyantz.api.endpoints.pipelines pyantz.api.endpoints.pipelines.endpoints pyantz.api.endpoints.pipelines.models pyantz.api.frontend_server pyantz.api.settings pyantz.infrastructure pyantz.infrastructure.config pyantz.infrastructure.config.abstract_job pyantz.infrastructure.config.abtrast_job pyantz.infrastructure.config.fn_utils pyantz.infrastructure.config.graph_validation pyantz.infrastructure.config.host_config pyantz.infrastructure.config.initial pyantz.infrastructure.config.job pyantz.infrastructure.config.parameters pyantz.infrastructure.config.parameters.compile_check pyantz.infrastructure.config.parameters.decorators pyantz.infrastructure.config.pipeline pyantz.infrastructure.config.runners pyantz.infrastructure.config.runners.local_runner pyantz.infrastructure.config.runners.slurm_runner pyantz.infrastructure.config.variables pyantz.infrastructure.config.virtual pyantz.infrastructure.distributed_queue pyantz.infrastructure.distributed_queue.common pyantz.infrastructure.distributed_queue.common.interface pyantz.infrastructure.distributed_queue.common.return_types pyantz.infrastructure.distributed_queue.sql pyantz.infrastructure.distributed_queue.sql.orm pyantz.infrastructure.distributed_queue.sql.sql_queue pyantz.infrastructure.runner pyantz.infrastructure.runner._remotes pyantz.infrastructure.runner._remotes._transfers pyantz.infrastructure.runner._remotes.container pyantz.infrastructure.runner._remotes.ssh pyantz.infrastructure.runner.job_manager pyantz.infrastructure.runner.local pyantz.infrastructure.runner.local.local_runner pyantz.infrastructure.runner.slurm pyantz.infrastructure.runner.slurm.slurm_runner pyantz.infrastructure.runner.starter pyantz.infrastructure.virtual pyantz.infrastructure.virtual.compile pyantz.jobs pyantz.jobs.analysis pyantz.jobs.analysis.external pyantz.jobs.analysis.simple pyantz.jobs.branching pyantz.jobs.branching.case_matrix pyantz.jobs.branching.if_else pyantz.jobs.files pyantz.jobs.files.check pyantz.jobs.files.edit pyantz.jobs.files.moving pyantz.jobs.files.reformat pyantz.jobs.files.simple pyantz.jobs.subproc pyantz.jobs.subproc.dispatch pyantz.jobs.testing pyantz.jobs.testing.nop pyantz.jobs.testing.touch_file pyantz.jobs.wrappers pyantz.jobs.wrappers.local pyantz.jobs.wrappers.loops pyantz.jobs.wrappers.submit pyantz.jobs.wrappers.variables pyantz.status pyantz.virtual pyantz.virtual.add_variables

move() (in module pyantz.jobs.files.moving) (in module pyantz.jobs.files.simple) MoveParams (class in pyantz.jobs.files.moving) (class in pyantz.jobs.files.simple)

N

name (CompiledJob attribute) (ContainerConfig attribute) (JobConfig attribute) (JobInfo attribute) (VirtualJobConfig attribute) new_host() (in module pyantz.jobs.wrappers.submit)

NO_DESCRIPTION (in module pyantz.api.endpoints.get_jobs.endpoint) no_submit_fn() (in module pyantz.infrastructure.config.parameters.decorators) NOT_INSTALLED (in module pyantz.api.frontend_server) num_attempted_runs (JobConfig attribute) num_iterations (LocalForLoopParams attribute) number_processes (LocalRunnerConfig attribute)

O

on_ (JoinParquetParams attribute) OP_MAPPING (in module pyantz.jobs.analysis.simple) op_mapping (in module pyantz.jobs.branching.if_else) operation (ColumnarOperationParameters attribute) output_dir (CaseMatrixRunSetup attribute) (RemoteConfig attribute)

output_parquet (JoinParquetParams attribute) overwrite (CopyParams attribute) (CreateFileParams attribute) (MoveParams attribute)

P

parameters (AbstractJobConfig attribute) ParametersType (in module pyantz.infrastructure.config.job) parquet_file (FromCsvToParquetParameters attribute) path (CreateFileParams attribute) (DeleteParams attribute) (TouchFileParameters attribute) payload (GetJobReturn attribute) pending (JobsReport attribute) PENDING (JobStatus attribute) PendingReturn (class in pyantz.infrastructure.distributed_queue.common.return_types) pipeline_expansion() (in module pyantz.jobs.branching.case_matrix) pipeline_expansion_with_output_dir() (in module pyantz.jobs.branching.case_matrix) pipeline_template (CaseMatrixExpansionParams attribute) PipelineSubmitter (in module pyantz.jobs.branching.case_matrix) poll_timeout (LocalRunnerConfig attribute) port (Settings attribute) PORT_VARIABLE (in module pyantz.api.settings) possible_values (DiscreteRange attribute) progress_interval (LocalRunnerConfig attribute) pyantz module pyantz.__main__ module pyantz.api module pyantz.api.auth module pyantz.api.backend module pyantz.api.dev_server module pyantz.api.dump_schemas module pyantz.api.endpoints module pyantz.api.endpoints.get_jobs module pyantz.api.endpoints.get_jobs.endpoint module pyantz.api.endpoints.get_jobs.models module pyantz.api.endpoints.get_parameters module pyantz.api.endpoints.get_parameters.endpoints module pyantz.api.endpoints.get_parameters.models module pyantz.api.endpoints.pipelines module pyantz.api.endpoints.pipelines.endpoints module pyantz.api.endpoints.pipelines.models module pyantz.api.frontend_server module pyantz.api.settings module pyantz.infrastructure module pyantz.infrastructure.config module pyantz.infrastructure.config.abstract_job module pyantz.infrastructure.config.abtrast_job module pyantz.infrastructure.config.fn_utils module pyantz.infrastructure.config.graph_validation module pyantz.infrastructure.config.host_config module pyantz.infrastructure.config.initial module pyantz.infrastructure.config.job module pyantz.infrastructure.config.parameters module pyantz.infrastructure.config.parameters.compile_check module pyantz.infrastructure.config.parameters.decorators module pyantz.infrastructure.config.pipeline module pyantz.infrastructure.config.runners module pyantz.infrastructure.config.runners.local_runner module pyantz.infrastructure.config.runners.slurm_runner module pyantz.infrastructure.config.variables module pyantz.infrastructure.config.virtual module

pyantz.infrastructure.distributed_queue module pyantz.infrastructure.distributed_queue.common module pyantz.infrastructure.distributed_queue.common.interface module pyantz.infrastructure.distributed_queue.common.return_types module pyantz.infrastructure.distributed_queue.sql module pyantz.infrastructure.distributed_queue.sql.orm module pyantz.infrastructure.distributed_queue.sql.sql_queue module pyantz.infrastructure.runner module pyantz.infrastructure.runner._remotes module pyantz.infrastructure.runner._remotes._transfers module pyantz.infrastructure.runner._remotes.container module pyantz.infrastructure.runner._remotes.ssh module pyantz.infrastructure.runner.job_manager module pyantz.infrastructure.runner.local module pyantz.infrastructure.runner.local.local_runner module pyantz.infrastructure.runner.slurm module pyantz.infrastructure.runner.slurm.slurm_runner module pyantz.infrastructure.runner.starter module pyantz.infrastructure.virtual module pyantz.infrastructure.virtual.compile module pyantz.jobs module pyantz.jobs.analysis module pyantz.jobs.analysis.external module pyantz.jobs.analysis.simple module pyantz.jobs.branching module pyantz.jobs.branching.case_matrix module pyantz.jobs.branching.if_else module pyantz.jobs.files module pyantz.jobs.files.check module pyantz.jobs.files.edit module pyantz.jobs.files.moving module pyantz.jobs.files.reformat module pyantz.jobs.files.simple module pyantz.jobs.subproc module pyantz.jobs.subproc.dispatch module pyantz.jobs.testing module pyantz.jobs.testing.nop module pyantz.jobs.testing.touch_file module pyantz.jobs.wrappers module pyantz.jobs.wrappers.local module pyantz.jobs.wrappers.loops module pyantz.jobs.wrappers.submit module pyantz.jobs.wrappers.variables module pyantz.status module pyantz.virtual module pyantz.virtual.add_variables module PYANTZ_REGISTERED_FUNCTION (in module pyantz.infrastructure.config.parameters.decorators)

Q

q_index (JobQueue attribute)

QUEUE_FILE_NAME (in module pyantz.status) QueueInterface (class in pyantz.infrastructure.distributed_queue.common.interface)

R

range (VariableDefinition attribute) ready (JobsReport attribute) READY (JobStatus attribute) recursive (DeleteParams attribute) rel_tol (ConditionalExecution attribute) (IfElseParams attribute) remote_host (SshConfig attribute) REMOTE_LOG_FILE (in module pyantz.infrastructure.runner._remotes.ssh) remote_port (SshConfig attribute) remote_user (SshConfig attribute) RemoteConfig (class in pyantz.infrastructure.config.host_config) report (RunResponse attribute) require_token() (in module pyantz.api.auth) requirements (RemoteConfig attribute) resolve_parameters() (in module pyantz.infrastructure.config.variables) resolve_var_any() (in module pyantz.infrastructure.config.variables) result_col (ColumnarOperationParameters attribute) result_parquet_file (ColumnarOperationParameters attribute) result_parquet_location (ExternalExtractParams attribute) right_col (ColumnarOperationParameters attribute) right_parquet (JoinParquetParams attribute) right_side (ConditionalExecution attribute) (IfElseParams attribute) router (in module pyantz.api.endpoints) (in module pyantz.api.endpoints.get_jobs.endpoint) (in module pyantz.api.endpoints.get_parameters.endpoints) (in module pyantz.api.endpoints.pipelines.endpoints)

rsync() (in module pyantz.jobs.files.moving) RsyncParams (class in pyantz.jobs.files.moving) run_async (SshConfig attribute) run_container() (in module pyantz.infrastructure.runner._remotes.container) run_id (RunLogResponse attribute) (RunResponse attribute) (StartRunResponse attribute) RUN_ID_PATTERN (in module pyantz.api.endpoints.pipelines.endpoints) run_job() (in module pyantz.infrastructure.runner.job_manager) run_job_no_parent_wrapper() (in module pyantz.infrastructure.runner.job_manager) run_job_with_details() (in module pyantz.infrastructure.runner.job_manager) run_jobs_in_context() (in module pyantz.jobs.wrappers.variables) run_jobs_with_temp_dir() (in module pyantz.jobs.wrappers.variables) run_local() (in module pyantz.infrastructure.runner.starter) run_pipeline() (in module pyantz.jobs.wrappers.local) run_ssh() (in module pyantz.infrastructure.runner._remotes.ssh) RunLogResponse (class in pyantz.api.endpoints.pipelines.models) runner_config (SubmitParams attribute) running (JobsReport attribute) RUNNING (JobStatus attribute) RunResponse (class in pyantz.api.endpoints.pipelines.models) RUNS_DIR_VARIABLE (in module pyantz.api.settings) runs_router (in module pyantz.api.endpoints.pipelines.endpoints)

S

save_file (CaseMatrixCreator attribute) save_from_external_extraction() (in module pyantz.jobs.analysis.external) save_function (EditExternalParams attribute) SECONDS_PER_MINUTE (in module pyantz.infrastructure.runner.slurm.slurm_runner) serialize_function() (in module pyantz.infrastructure.config.fn_utils) serialize_job_function() (JobConfig method) set_job_kwargs (SetVariables attribute) set_job_worker() (QueueInterface method) (SqliteQueue method) set_variables() (in module pyantz.jobs.wrappers.variables) setter_job (SetVariables attribute) Settings (class in pyantz.api.settings) SetVariables (class in pyantz.jobs.wrappers.variables) shared_variables (VariableContextParams attribute) shared_working_dir (TemporaryDirectoryParams attribute) sheet_name (FromExcelToCsvParameters attribute) slurm_args (SlurmRunnerConfig attribute) SlurmRunnerConfig (class in pyantz.infrastructure.config.runners.slurm_runner) source (CopyParams attribute) (MoveParams attribute) (RsyncParams attribute) source_parquet_file (ColumnarOperationParameters attribute) SqliteQueue (class in pyantz.infrastructure.distributed_queue.sql.sql_queue) src (CopyParams attribute) (MoveParams attribute) SshConfig (class in pyantz.infrastructure.config.host_config) start() (in module pyantz.infrastructure.runner.local.local_runner) (in module pyantz.infrastructure.runner.slurm.slurm_runner) (in module pyantz.infrastructure.runner.starter) start_dev_server() (in module pyantz.api.dev_server) start_frontend_server() (in module pyantz.api.frontend_server)

start_prod_server() (in module pyantz.api.backend) start_run() (in module pyantz.api.endpoints.pipelines.endpoints) StartRunResponse (class in pyantz.api.endpoints.pipelines.models) STARTUP_WAIT_SECONDS (in module pyantz.infrastructure.runner.local.local_runner) state (RunResponse attribute) status (JobState attribute) (JobStatusReport attribute) status_details (JobStatusReport attribute) StatusTable (class in pyantz.infrastructure.distributed_queue.sql.orm) stderr_file (DispatchParams attribute) STDERR_HEADER (in module pyantz.jobs.subproc.dispatch) stdout_file (DispatchParams attribute) step (ContinuousRange attribute) stop_on_failure (LocalForLoopParams attribute) STOP_WAIT_SECONDS (in module pyantz.infrastructure.runner.local.local_runner) str_uuid4() (in module pyantz.infrastructure.config.abstract_job) strict (AbstractJobConfig attribute) strip_format() (in module pyantz.api.endpoints.get_parameters.endpoints) SubmissionFnType (in module pyantz.infrastructure.config.job) SubmissionFnWithParentType (in module pyantz.infrastructure.runner.job_manager) submit() (in module pyantz.jobs.wrappers.submit) submit_config (HostParams attribute) submit_type (TemporaryDirectoryParams attribute) SubmitParams (class in pyantz.jobs.wrappers.submit) submitter (InitialConfig attribute) subsequent_host (RemoteConfig attribute) substring (FileContentsParams attribute) success (JobResult attribute) (JobsReport attribute) SUCCESS (JobStatus attribute) sync_data_at_end (SshConfig attribute)

T

TemporaryDirectoryParams (class in pyantz.jobs.wrappers.variables) timeout (DispatchParams attribute) (LocalRunnerConfig attribute) timeout_seconds (JobConfig attribute) total (JobsReport attribute) touch_file() (in module pyantz.jobs.testing.touch_file) TouchFileParameters (class in pyantz.jobs.testing.touch_file) trace_fn() (in module pyantz.infrastructure.config.parameters.decorators)

truncated (RunLogResponse attribute) type_ (CompleteReturn attribute) (ContainerConfig attribute) (JobReturn attribute) (LocalConfig attribute) (LocalRunnerConfig attribute) (PendingReturn attribute) (SlurmRunnerConfig attribute) (SshConfig attribute)

U

update_deps() (in module pyantz.infrastructure.config.parameters.decorators) update_job_status() (QueueInterface method) (SqliteQueue method)

updates (_EditJsonLikeParams attribute) (EditExternalParams attribute) use_same_proc (LocalRunnerConfig attribute)

V

valid (ValidateResponse attribute) validate_config() (in module pyantz.api.endpoints.pipelines.endpoints) validate_fn() (JobConfig method) validate_submit_and_dir() (TemporaryDirectoryParams method) ValidateResponse (class in pyantz.api.endpoints.pipelines.models) ValidOperators (in module pyantz.jobs.branching.if_else) variable_name (TemporaryDirectoryParams attribute) variable_names_to_parquets (ExternalAnalysisParams attribute) VARIABLE_REGEX (in module pyantz.infrastructure.config.variables) VariableContextParams (class in pyantz.jobs.wrappers.variables)

VariableDefinition (class in pyantz.jobs.branching.case_matrix) variables (AddVariables attribute) (CaseMatrixCreator attribute) (InitialConfig attribute) (JobWithContext attribute) virtual (JobConfig attribute) (VirtualJobConfig attribute) VIRTUAL_MARKER (in module pyantz.infrastructure.config.parameters.decorators) VirtualJobConfig (class in pyantz.infrastructure.config.virtual) VirtualParamModel (class in pyantz.infrastructure.config.virtual)

W

with_new_host() (InitialConfig method) worker_id (StatusTable attribute) WORKER_STOP_TIMEOUT (in module pyantz.infrastructure.runner.local.local_runner)

WorkerTerminatedError working_dir (RemoteConfig attribute) (SlurmRunnerConfig attribute) working_directory (LocalRunnerConfig attribute)

Y

YAML_SUFFIXES (in module pyantz.__main__)