nipoppy.workflows.BaseWorkflow¶

class nipoppy.workflows.BaseWorkflow(dpath_root, name, fpath_layout=None, logger=None, dry_run=False)¶

Base class with logging/subprocess utilities.

Parameters:

dpath_root (nipoppy.env.StrOrPathLike)
name (str)
fpath_layout (Optional[nipoppy.env.StrOrPathLike])
logger (Optional[logging.Logger])

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_symlink(path_source, path_dest, log_level=logging.INFO, **kwargs)¶: Create a symlink to another path.

generate_fpath_log(dnames_parent=None, fname_stem=None)¶

Generate a log file path.

Parameters:

dnames_parent (Optional[str | list[str]])
fname_stem (Optional[str])

Return type:

pathlib.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.

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, **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
**kwargs – Passed to subprocess.Popen.

Return type: