cytosnake package

Subpackages

• cytosnake.cli package
  • Subpackages
    • cytosnake.cli.exec package
      • Submodules
      • cytosnake.cli.exec.workflow_exec module
      • Module contents
  • Submodules
  • cytosnake.cli.args module
    • CliControlPanel
      • CliControlPanel.cli_help
      • CliControlPanel.data_type
      • CliControlPanel.exec_path
      • CliControlPanel.mode
      • CliControlPanel.mode_check
      • CliControlPanel.mode_help
      • CliControlPanel.modes
      • CliControlPanel.param_list
      • CliControlPanel.parse_init_args()
      • CliControlPanel.parse_workflow_args()
      • CliControlPanel.workflow
    • WorkflowSearchPath
    • supported_workflows()
  • cytosnake.cli.cli_checker module
    • Documentation
    • CliProperties
      • CliProperties.modes
      • CliProperties.workflows
      • CliProperties.modes
      • CliProperties.workflows
    • cli_check()
  • cytosnake.cli.cli_docs module
  • cytosnake.cli.cmd module
    • run_cmd()
  • cytosnake.cli.setup_init module
    • init_cp_data()
    • init_dp_data()
  • Module contents
• cytosnake.common package
  • Submodules
  • cytosnake.common.errors module
    • BarcodeMissingError
    • BaseExecutorException
    • BaseFileExistsError
    • BaseFileNotFound
    • BaseValueError
    • BaseWorkflowException
    • ExtensionError
    • InvalidArgumentException
    • InvalidCytosnakeExec
    • InvalidExecutableException
    • InvalidModeException
    • InvalidWorkflowException
    • MultipleModesException
    • MultipleWorkflowsException
    • NoArgumentsException
    • ProjectExistsError
    • WorkflowFailedException
    • WorkflowNotFoundError
    • display_error()
  • Module contents
• cytosnake.guards package
  • Submodules
  • cytosnake.guards.ext_guards module
    • has_parquet_ext()
    • has_sqlite_ext()
  • cytosnake.guards.input_guards module
    • check_init_parameter_inputs()
    • is_barcode_required()
  • cytosnake.guards.path_guards module
    • is_valid_path()
  • Module contents
• cytosnake.utils package
  • Submodules
  • cytosnake.utils.config_utils module
    • load_configs()
    • load_cytosnake_configs()
    • load_data_path_configs()
    • load_general_configs()
    • load_meta_path_configs()
    • load_workflow_path()
    • load_workflow_paths_config()
    • update_config()
  • cytosnake.utils.cyto_paths module
    • get_benchmarks_path()
    • get_config_dir_path()
    • get_config_fpaths()
    • get_cytosnake_config_path()
    • get_cytosnake_package_path()
    • get_meta_path()
    • get_project_dirpaths()
    • get_project_root()
    • get_results_dir_path()
    • get_workflow_fpaths()
    • is_cytosnake_dir()
  • cytosnake.utils.cytosnake_setup module
    • create_cytosnake_dir()
    • generate_meta_path_configs()
    • setup_cytosnake_env()
    • transport_project_files()
  • cytosnake.utils.feature_utils module
    • infer_dp_features()
  • cytosnake.utils.file_utils module
    • file_search()
    • find_project_dir()
  • Module contents

Module contents