nipoppy.workflows.BaseWorkflow

class nipoppy.workflows.BaseWorkflow(name, verbose=False, dry_run=False)

Base workflow class with logging/subprocess/filesystem utilities.

Parameters:
copy(path_source, path_dest, log_level=logging.INFO, **kwargs)

Copy a file or directory.

copytree(path_source, path_dest, log_level=logging.INFO, **kwargs)

Copy directory tree.

Create a symlink to another path.

log_command(command)

Write a command to the log with a special prefix.

Parameters:

command (str)

mkdir(dpath, log_level=logging.INFO, **kwargs)

Create a directory (by default including parents).

Do nothing if the directory already exists.

movetree(path_source, path_dest, kwargs_mkdir=None, kwargs_move=None, log_level=logging.INFO)

Move directory tree.

rm(path, log_level=logging.INFO, **kwargs)

Remove a file or directory.

run()

Run the workflow.

run_cleanup()

Run the cleanup part of the workflow.

run_command(command_or_args, check=True, quiet=False, **kwargs)

Run a command in a subprocess.

The command’s stdout and stderr outputs are written to the log with special prefixes.

If in “dry run” mode, the command is not executed, and the method returns the command string. Otherwise, the subprocess.Popen object is returned unless capture_output is True.

Parameters:

  • command_or_args (Sequence[str] | str) – The command to run.

  • check (bool, optional) – If True, raise an error if the process exits with a non-zero code, by default True

  • quiet (bool, optional) – If True, do not log the command, by default False

  • **kwargs – Passed to subprocess.Popen.

Return type:

subprocess.Popen or str

abstractmethod run_main()

Run the main part of the workflow.

run_setup()

Run the setup part of the workflow.

save_tabular_file(tabular, fpath)

Save a tabular file.

Parameters:
dry_run = False
log_prefix_run = '[RUN]'
log_prefix_run_stderr = '[RUN STDERR]'
log_prefix_run_stdout = '[RUN STDOUT]'
logger
name
return_code = 0
verbose = False