pype.misc

pype.misc.import_module(module_name, module_path)

Import a module from a specific path.

Parameters:

• module_name (str) – Name to give to the imported module

• module_path (str) – Path to the module file

Returns:

Imported module object

Raises:

ImportError – If module cannot be loaded

Return type:

ModuleType

pype.misc.generate_uid(n=4, timestamp=True)

Generate a unique identifier with timestamp and random chars.

Parameters:

• n (int)

• timestamp (bool)

Return type:

str

pype.misc.package_modules(package)

Get all Python modules in a package directory.

Parameters:

package (ModuleType)

Return type:

Set[str]

pype.misc.package_files(package, extension)

Get all files with specific extension in a package directory.

Parameters:

• package (ModuleType)

• extension (str)

Return type:

Set[str]

pype.misc.try_import(path, module_name)

Import a module, creating __init__.py if needed.

Parameters:

• path (str) – Directory path where the module should be located/created

• module_name (str) – Name of the module to import

Returns:

Imported module object

Raises:

ImportError – If module cannot be created or loaded

Return type:

ModuleType

pype.misc.get_modules(parent, subparsers, progs)

Get all modules and their parsers.

Parameters:

• parent (ModuleType)

• subparsers (Any)

• progs (Dict)

Return type:

Dict

pype.misc.get_modules_names(parent)

Get names of all valid modules in parent.

Parameters:

parent (ModuleType)

Return type:

List[str]

pype.misc.get_module_method(parent, module, method)

Get a specific method from a module.

Parameters:

• parent (ModuleType) – Parent module package

• module (str) – Name of submodule within parent

• method (str) – Name of method/function to retrieve

Returns:

The method/function if found, None otherwise

Return type:

Any | None

pype.misc.xopen(filename, mode='r')

Smart file opener that handles gzip and stdin/stdout.

Parameters:

• filename (str)

• mode (str)

Return type:

Any

pype.misc.check_exit_code(process, sting, results_dict, log)

pype.misc.human_format(num, base=1000)

Format numbers with human readable units.

Parameters:

• num (int | float)

• base (int)

Return type:

str

pype.misc.bases_format(string_unit, base=1000)

Convert string with units to number of bases.

Parameters:

• string_unit (str)

• base (int)

Return type:

int

pype.misc.basename_no_extension(file_name)

Get basename without extension.

Parameters:

file_name (str)

Return type:

str

class pype.misc.Tee(f1, f2)

Bases: object

File-like object that writes to two output streams simultaneously.

Parameters:

• f1 (TextIO)

• f2 (TextIO)

__init__(f1, f2)

Initialize Tee with two output streams.

Parameters:

• f1 (TextIO) – First output stream

• f2 (TextIO) – Second output stream

Return type:

None

write(msg)

Write message to both streams.

Parameters:

msg (str) – Message string to write

Returns:

Number of characters written (from first stream)

Return type:

int

class pype.misc.SubcommandHelpFormatter(prog, indent_increment=2, max_help_position=24, width=None)

Bases: RawDescriptionHelpFormatter

Custom formatter that groups subcommands by category.

CATEGORIES = {'API Integration': ['compute_bio'], 'Diagnostics': ['validate'], 'Manage': ['profiles', 'registry'], 'Run': ['pipelines', 'snippets', 'resume'], 'Simplified': ['run']}

class pype.misc.DefaultHelpParser(prog=None, usage=None, description=None, epilog=None, parents=[], formatter_class=<class 'pype.argparse.HelpFormatter'>, prefix_chars='-', fromfile_prefix_chars=None, argument_default=None, conflict_handler='error', add_help=True, allow_abbrev=True, exit_on_error=True)

Bases: ArgumentParser

ArgumentParser that prints help before exiting on errors.

error(message)

Handle parse errors by printing help and exiting.

Parameters:

message (str) – Error message to display

Raises:

SystemExit – Always exits with code 2

Return type:

None

pype.misc.responsive_sleep(stop_event, duration)

Sleep with immediate exit capability via stop_event.

Sleeps for the specified duration in 1-second intervals, checking for stop event between each interval. Allows responsive shutdown in threading scenarios without waiting for the full duration.

Parameters:

• stop_event – threading.Event that when set causes immediate return

• duration (int) – Number of seconds to sleep

Return type:

None

pype.misc.create_minimal_profile(name='minimal')

Create a minimal profile object for use with PypeLogger.

Used when a real profile object isn’t available (e.g., in listener daemon or resume mode). Provides __name__ and __path__ attributes that PypeLogger expects.

Parameters:

name (str) – Name for the profile (default: “minimal”)

Returns:

Module-like object with __name__ and __path__ attributes

Return type:

ModuleType