Index

_

__add__() (BatchSet method) (CaseInsensitiveEnum method) (COMMANDS method) (ConfigType method) (HardwareOption method) (Q_COLUMNS method) (QOSOption method) (StatusField method) (StatusOption method)

__mul__() (BatchSet method) (CaseInsensitiveEnum method) (COMMANDS method) (ConfigType method) (HardwareOption method) (Q_COLUMNS method) (QOSOption method) (StatusField method) (StatusOption method)

A

AbstractBaseCLICommandConfiguration (class in gaps.cli.command) add_dataset() (Collector class method) add_handlers() (in module gaps.log) add_job() (Status class method)

arg_combo (BatchSet attribute) as_click_command() (in module gaps.cli.cli) as_df() (Status method), [1] as_script_str() (in module gaps.cli.config) AWSPC (HardwareOption attribute)

B

batch_command() (in module gaps.cli.batch) BatchJob (class in gaps.batch) (class in gaps.legacy)

BatchSet (class in gaps.batch)

C

CANCEL (COMMANDS attribute) cancel() (BatchJob method), [1] (HpcJobManager method) (PBS method) (SLURM method) cancel_all() (BatchJob class method) (Pipeline class method), [1] capitalize() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) casefold() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) CaseInsensitiveEnum (class in gaps.utilities) center() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) charge_factor (HardwareOption property) check_status_using_job_id() (HardwareOption method) (HpcJobManager method) (PBS method) (SLURM method) check_status_using_job_name() (HpcJobManager method) (PBS method) (SLURM method)

clear() (Status method), [1] CLICommandConfiguration() (in module gaps.cli.command) CLICommandFromClass (class in gaps.cli.command) CLICommandFromFunction (class in gaps.cli.command) CMD_BASE (Pipeline property) collect() (Collector method) (in module gaps.cli.collect) collect_dataset() (DatasetCollector class method) Collector (class in gaps.collection) COLUMN_HEADERS (HpcJobManager property) combine_meta() (Collector method) combine_time_index() (Collector method) command (PipelineStep property) command_help() (CommandDocumentation method) CommandDocumentation (class in gaps.cli.documentation) COMMANDS (class in gaps.hpc) (HpcJobManager property) (Pipeline property) config_as_str_for_docstring() (in module gaps.config) config_help() (CommandDocumentation method) ConfigType (class in gaps.config) count() (BatchSet method) (CaseInsensitiveEnum method) (COMMANDS method) (ConfigType method) (HardwareOption method) (Q_COLUMNS method) (QOSOption method) (StatusField method) (StatusOption method)

D

DatasetCollector (class in gaps.collection) default_exec_values (CommandDocumentation property) DEFAULT_STDOUT_PATH (in module gaps.hpc) delete() (BatchJob method), [1] delete_all() (BatchJob class method) df (ProjectPoints property) documentation (AbstractBaseCLICommandConfiguration property) (CLICommandFromClass property) (CLICommandFromFunction property) dump() (Handler class method) (JSON5Handler class method) (JSONHandler class method) (Status method), [1] (TOMLHandler class method) (YAMLHandler class method)

dumps() (Handler class method) (JSON5Handler class method) (JSONHandler class method) (TOMLHandler class method) (YAMLHandler class method) duplicate_gids (DatasetCollector property)

E

EAGLE (HardwareOption attribute) encode() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) endswith() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method)

exec_control_doc (CommandDocumentation property) expandtabs() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) extended_summary (CommandDocumentation property)

F

FILE_EXTENSION (Handler property) file_set (BatchSet attribute) find() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) find_h5_files() (in module gaps.collection) FORMAT (in module gaps.log) format() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method)

format_env() (in module gaps.hpc) format_map() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) format_walltime() (in module gaps.hpc) from_config() (in module gaps.cli.config) from_range() (ProjectPoints class method)

G

gaps module gaps.batch module gaps.cli module gaps.cli.batch module gaps.cli.cli module gaps.cli.collect module gaps.cli.command module gaps.cli.config module gaps.cli.documentation module gaps.cli.execution module gaps.cli.pipeline module gaps.cli.preprocessing module gaps.cli.reset module gaps.cli.script module gaps.cli.status module gaps.cli.templates module gaps.collection module gaps.config module gaps.exceptions module

gaps.hpc module gaps.legacy module gaps.log module gaps.pipeline module gaps.project_points module gaps.status module gaps.utilities module gaps.version module gaps.warnings module gapsCollectionWarning gapsConfigError gapsDeprecationWarning gapsError gapsExecutionError gapsFileNotFoundError gapsHPCError gapsHPCWarning gapsIndexError gapsIOError gapsKeyError gapsRuntimeError gapsTypeError gapsValueError gapsWarning get() (Status method), [1] get_dataset_shape() (Collector method) get_sites_from_key() (ProjectPoints method) gids (Collector property) (DatasetCollector property) (ProjectPoints property)

H

h5_files (Collector property) Handler (class in gaps.config) HardwareOption (class in gaps.status) HardwareStatusRetriever (class in gaps.legacy) (class in gaps.status)

HIGH (QOSOption attribute) hpc_parameter_help (CommandDocumentation property) HpcJobManager (class in gaps.hpc)

I

ID (Q_COLUMNS attribute) index() (BatchSet method) (CaseInsensitiveEnum method) (COMMANDS method) (ConfigType method) (HardwareOption method) (ProjectPoints method) (Q_COLUMNS method) (QOSOption method) (StatusField method) (StatusOption method) init_logger() (in module gaps.log) init_logging_from_config_file() (in module gaps.config) is_hpc (HardwareOption property) is_split_spatially (AbstractBaseCLICommandConfiguration property) (CLICommandFromClass property) (CLICommandFromFunction property) isalnum() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) isalpha() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) isascii() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) isdecimal() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) isdigit() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method)

isidentifier() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) islower() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) isnumeric() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) isprintable() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) isspace() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) istitle() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) isupper() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) items() (Status method), [1]

J

job_exists() (Status class method), [1] job_hardware (Status property), [1] job_ids (Status property), [1] job_table (BatchJob property), [1] join() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method)

join_df() (ProjectPoints method) JSON5Handler (class in gaps.config) JSONHandler (class in gaps.config)

K

KESTREL (HardwareOption attribute)

keys() (Status method), [1] kickoff_job() (in module gaps.cli.execution)

L

ljust() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) load() (Handler class method) (JSON5Handler class method) (JSONHandler class method) (TOMLHandler class method) (YAMLHandler class method) load_config() (in module gaps.config) loads() (Handler class method) (JSON5Handler class method) (JSONHandler class method) (TOMLHandler class method) (YAMLHandler class method)

LOCAL (HardwareOption attribute) log_mem() (in module gaps.log) log_versions() (in module gaps.log) lower() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) lstrip() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method)

M

main_monitor() (in module gaps.cli.status) make_cli() (in module gaps.cli.cli) make_handler() (in module gaps.log) make_job_file() (Status static method) make_log_file_handler() (in module gaps.log) make_log_stream_handler() (in module gaps.log) make_script_str() (HpcJobManager method) (PBS method) (SLURM method) make_sh() (in module gaps.hpc) make_single_job_file() (Status class method), [1] maketrans() (CaseInsensitiveEnum static method) (ConfigType static method) (HardwareOption static method) (QOSOption static method) (StatusField static method) (StatusOption static method) mark_job_as_submitted() (Status class method), [1] members_as_str() (CaseInsensitiveEnum class method) (ConfigType class method) (HardwareOption class method) (QOSOption class method) (StatusField class method) (StatusOption class method) module gaps gaps.batch gaps.cli gaps.cli.batch gaps.cli.cli gaps.cli.collect gaps.cli.command gaps.cli.config gaps.cli.documentation gaps.cli.execution gaps.cli.pipeline gaps.cli.preprocessing gaps.cli.reset gaps.cli.script gaps.cli.status gaps.cli.templates gaps.collection gaps.config gaps.exceptions gaps.hpc gaps.legacy gaps.log gaps.pipeline gaps.project_points gaps.status gaps.utilities gaps.version gaps.warnings

move_chunks() (Collector method)

N

name (Pipeline property), [1] NAME (Q_COLUMNS attribute)

node_kwargs() (in module gaps.cli.config) NORMAL (QOSOption attribute)

P

param_required() (CommandDocumentation method) parameter_help (CommandDocumentation property) parse_gids_from_files() (in module gaps.collection) parse_meta() (in module gaps.collection) parse_previous_status() (in module gaps.pipeline) parse_project_points() (in module gaps.collection) parse_queue_str() (HpcJobManager class method) (PBS class method) (SLURM class method) parse_step_status() (Status class method), [1] partition() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) PBS (class in gaps.hpc)

PEREGRINE (HardwareOption attribute) Pipeline (class in gaps.legacy) (class in gaps.pipeline) pipeline() (in module gaps.cli.pipeline) PIPELINE_BACKGROUND_METHOD (BatchJob property) PIPELINE_CLASS (BatchJob property) pipeline_command() (in module gaps.cli.pipeline) PipelineError PipelineStep (class in gaps.pipeline) pop() (Status method), [1] popitem() (Status method), [1] preprocess_collect_config() (in module gaps.cli.preprocessing) preprocess_script_config() (in module gaps.cli.preprocessing) print_logging_info() (in module gaps.log) print_logging_info_all_libraries() (in module gaps.log) project_points_from_container_or_slice() (in module gaps.utilities) ProjectPoints (class in gaps.project_points) purge_chunks() (Collector method)

Q

Q_COLUMNS (class in gaps.hpc) Q_SUBMITTED_STATUS (HpcJobManager property) QOSOption (class in gaps.status) query_queue() (HpcJobManager method) (PBS method) (SLURM method)

queue (HpcJobManager property) (PBS property) (SLURM property)

R

record_monitor_pid() (Status class method), [1] recursively_update_dict() (in module gaps.utilities) reload() (Status method), [1] removeprefix() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) removesuffix() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) replace() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) required_args (CommandDocumentation property) reset_after() (Status method), [1] reset_all_cached_queries() (HardwareOption class method) reset_command() (in module gaps.cli.reset) reset_query_cache() (HpcJobManager method) (PBS method) (SLURM method) resolve_all_paths() (in module gaps.config) resolve_path() (in module gaps.utilities) retrieve_job_status() (Status class method), [1] rfind() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method)

rindex() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) rjust() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) rpartition() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) rsplit() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) rstrip() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) run() (BatchJob class method) (BatchJob method) (Pipeline class method), [1] run_with_status_updates() (in module gaps.cli.config)

S

script() (in module gaps.cli.script) setdefault() (Status method), [1] sites_as_slice (ProjectPoints property) SLURM (class in gaps.hpc) (HardwareOption attribute) split() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (ProjectPoints method) (QOSOption method) (StatusField method) (StatusOption method) split_project_points_into_ranges() (in module gaps.cli.preprocessing) splitlines() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) STANDBY (QOSOption attribute) startswith() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) Status (class in gaps.legacy) (class in gaps.status)

status (Pipeline property), [1] STATUS (Q_COLUMNS attribute) status_command() (in module gaps.cli.status) StatusField (class in gaps.status) StatusOption (class in gaps.status) StatusUpdates (class in gaps.status) step_index() (Status method), [1] strip() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method) sub_dirs (BatchJob property), [1] SUBMIT (COMMANDS attribute) submit() (HpcJobManager method) (in module gaps.hpc) (PBS method) (SLURM method) supports_categorical_qos (HardwareOption property) swapcase() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method)

T

tag (BatchSet attribute) template_command() (in module gaps.cli.templates) template_config (CommandDocumentation property) template_pipeline_config() (in module gaps.cli.pipeline) title() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method)

TOMLHandler (class in gaps.config) translate() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method)

U

UNSPECIFIED (QOSOption attribute) update() (Status method), [1] update_from_all_job_files() (Status method), [1] update_job_status() (Status method), [1] upper() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method)

V

values() (Status method), [1]

W

write() (Handler class method) (JSON5Handler class method) (JSONHandler class method) (TOMLHandler class method) (YAMLHandler class method)

Y

YAMLHandler (class in gaps.config)

Z

zfill() (CaseInsensitiveEnum method) (ConfigType method) (HardwareOption method) (QOSOption method) (StatusField method) (StatusOption method)