Index

B

BarcodeMissingError BaseExecutorException BaseFileExistsError

BaseFileNotFound BaseValueError BaseWorkflowException

C

check_init_parameter_inputs() (in module cytosnake.guards.input_guards) cli_check() (in module cytosnake.cli.cli_checker) cli_help (cytosnake.cli.args.CliControlPanel attribute) CliControlPanel (class in cytosnake.cli.args) CliProperties (class in cytosnake.cli.cli_checker) create_cytosnake_dir() (in module cytosnake.utils.cytosnake_setup) cytosnake module cytosnake.cli module cytosnake.cli.args module cytosnake.cli.cli_checker module cytosnake.cli.cli_docs module cytosnake.cli.cmd module cytosnake.cli.exec module cytosnake.cli.exec.workflow_exec module cytosnake.cli.setup_init module

cytosnake.common module cytosnake.common.errors module cytosnake.guards module cytosnake.guards.ext_guards module cytosnake.guards.input_guards module cytosnake.guards.path_guards module cytosnake.utils module cytosnake.utils.config_utils module cytosnake.utils.cyto_paths module cytosnake.utils.cytosnake_setup module cytosnake.utils.feature_utils module cytosnake.utils.file_utils module

D

data_type (cytosnake.cli.args.CliControlPanel attribute)

display_error() (in module cytosnake.common.errors)

E

exec_path (cytosnake.cli.args.CliControlPanel attribute)

ExtensionError

F

file_search() (in module cytosnake.utils.file_utils)

find_project_dir() (in module cytosnake.utils.file_utils)

G

generate_meta_path_configs() (in module cytosnake.utils.cytosnake_setup) generate_sample_inputs module get_benchmarks_path() (in module cytosnake.utils.cyto_paths) get_config_dir_path() (in module cytosnake.utils.cyto_paths) get_config_fpaths() (in module cytosnake.utils.cyto_paths)

get_cytosnake_config_path() (in module cytosnake.utils.cyto_paths) get_cytosnake_package_path() (in module cytosnake.utils.cyto_paths) get_meta_path() (in module cytosnake.utils.cyto_paths) get_project_dirpaths() (in module cytosnake.utils.cyto_paths) get_project_root() (in module cytosnake.utils.cyto_paths) get_results_dir_path() (in module cytosnake.utils.cyto_paths) get_workflow_fpaths() (in module cytosnake.utils.cyto_paths)

H

has_parquet_ext() (in module cytosnake.guards.ext_guards)

has_sqlite_ext() (in module cytosnake.guards.ext_guards)

I

infer_dp_features() (in module cytosnake.utils.feature_utils) init_cp_data() (in module cytosnake.cli.setup_init) init_dp_data() (in module cytosnake.cli.setup_init) InvalidArgumentException InvalidCytosnakeExec

InvalidExecutableException InvalidModeException InvalidWorkflowException is_barcode_required() (in module cytosnake.guards.input_guards) is_cytosnake_dir() (in module cytosnake.utils.cyto_paths) is_valid_path() (in module cytosnake.guards.path_guards)

L

load_configs() (in module cytosnake.utils.config_utils) load_cytosnake_configs() (in module cytosnake.utils.config_utils) load_data_path_configs() (in module cytosnake.utils.config_utils)

load_general_configs() (in module cytosnake.utils.config_utils) load_meta_path_configs() (in module cytosnake.utils.config_utils) load_workflow_path() (in module cytosnake.utils.config_utils) load_workflow_paths_config() (in module cytosnake.utils.config_utils)

M

mode (cytosnake.cli.args.CliControlPanel attribute) mode_check (cytosnake.cli.args.CliControlPanel attribute) mode_help (cytosnake.cli.args.CliControlPanel attribute) modes (cytosnake.cli.args.CliControlPanel attribute) (cytosnake.cli.cli_checker.CliProperties attribute), [1] module cytosnake cytosnake.cli cytosnake.cli.args cytosnake.cli.cli_checker cytosnake.cli.cli_docs cytosnake.cli.cmd cytosnake.cli.exec cytosnake.cli.exec.workflow_exec cytosnake.cli.setup_init cytosnake.common cytosnake.common.errors cytosnake.guards cytosnake.guards.ext_guards cytosnake.guards.input_guards cytosnake.guards.path_guards cytosnake.utils cytosnake.utils.config_utils cytosnake.utils.cyto_paths cytosnake.utils.cytosnake_setup cytosnake.utils.feature_utils cytosnake.utils.file_utils generate_sample_inputs

MultipleModesException MultipleWorkflowsException

N

NoArgumentsException

P

param_list (cytosnake.cli.args.CliControlPanel attribute) parse_init_args() (cytosnake.cli.args.CliControlPanel method)

parse_workflow_args() (cytosnake.cli.args.CliControlPanel method) ProjectExistsError

R

run_cmd() (in module cytosnake.cli.cmd)

S

setup_cytosnake_env() (in module cytosnake.utils.cytosnake_setup)

supported_workflows() (in module cytosnake.cli.args)

T

transport_project_files() (in module cytosnake.utils.cytosnake_setup)

U

update_config() (in module cytosnake.utils.config_utils)

W

workflow (cytosnake.cli.args.CliControlPanel attribute) workflow_executor() (in module cytosnake.cli.exec.workflow_exec) WorkflowFailedException

WorkflowNotFoundError workflows (cytosnake.cli.cli_checker.CliProperties attribute), [1] WorkflowSearchPath (class in cytosnake.cli.args)