module

biopipen.utils.misc

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Functions
  • require_package(package, version, python) — Require a Python package to be installed with optional version check.</>
  • run_command(cmd, fg, wait, print_command, print_command_handler, **kwargs) (subprocess.popen | str) — Run a command.</>
function

biopipen.utils.misc.require_package(package, version=None, python=None)

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Require a Python package to be installed with optional version check.

The version specifier should follow the format used by pip, e.g., '>=1.2.3'. Multiple version specifiers can be separated by commas, e.g., '>=1.2.3,<2.0.0'.

Parameters
  • package (str) — The name of the package to check.
  • version (str | None) — The version specifier string.
  • python (str | None) — The Python interpreter to use.
function

biopipen.utils.misc.run_command(cmd, fg=False, wait=True, print_command=True, print_command_handler=<built-in function print>, **kwargs)

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Run a command.

Parameters
  • cmd (Union) — A string or list of strings representing the command to run.
  • fg (bool, optional) — Whether to run the command in the foreground.Redirects stdout and stderr to the current process.
  • wait (bool, optional) — Whether to wait for the command to finish.The command will be waited for if fg is True.
  • print_command (bool, optional) — Whether to print the command before running it.
  • print_command_handler (Callable, optional) — The function to use to print the command.
  • kwargs — Keyword arguments to pass to subprocess.Popen.
Returns (subprocess.popen | str)

The Popen object, or str when stdout is RETURN or return.