#!/usr/bin/env python3
"""
Clean the output of an HADDOCK3 run directory.
The clean process performs file archiving and file compressing
operations.
All `.inp` and `.out` files are deleted except for the first one, which
is compressed to `.gz`. On the other hand, all `.seed` and `.con` files
are compressed and archived to `.tgz` files. Finally, `.pdb` and `.psf`
files are compressed to `.gz`.
The <run_directory> can either be a whole HADDOCK3 run folder or a
specific folder of the workflow step. <ncores> defines the number of
threads to use; by default uses a single core.
Usage::
haddock3-clean -h
haddock3-clean <run_directory>
haddock3-clean run1
haddock3-clean run1/1_rigidbody
haddock3-clean run1 -n # uses all cores
haddock3-clean run1 -n 2 # uses 2 cores
"""
import argparse
import sys
from haddock.core.typing import (
ArgumentParser,
Callable,
FilePath,
Namespace,
Optional,
)
from haddock.libs import libcli
# Command line interface parser
ap = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.RawDescriptionHelpFormatter,
)
libcli.add_rundir_arg(ap)
libcli.add_ncores_arg(ap)
libcli.add_version_arg(ap)
def _ap() -> ArgumentParser:
return ap
[docs]def load_args(ap: ArgumentParser) -> Namespace:
"""Load argument parser args."""
return ap.parse_args()
[docs]def cli(ap: ArgumentParser, main: Callable[..., None]) -> None:
"""Command-line interface entry point."""
cmd = load_args(ap)
main(**vars(cmd))
[docs]def maincli() -> None:
"""Execute main client."""
cli(ap, main)
[docs]def main(run_dir: FilePath, ncores: Optional[int] = 1) -> None:
"""
Clean a HADDOCK3 directory.
Usually, this concerns compressing and archiving files (see below).
Parameters
----------
run_dir : str or :external:py:class:`pathlib.Path`.
The path to the run directory or to a folder of a specific step
of the workflow.
ncores : int, or None
The number of cores to use. If ``None``, use all possible threads.
Defaults to 1.
See Also
--------
`haddock.gear.clean_steps`
"""
# anti-pattern to speed up CLI initiation
from pathlib import Path
from haddock import log
from haddock.gear.clean_steps import clean_output
from haddock.libs.libtimer import log_time
from haddock.libs.libutil import parse_ncores
from haddock.modules import get_module_steps_folders, is_step_folder
log.info(f"Compressing {str(run_dir)!r} folder")
ncores = parse_ncores(ncores)
if is_step_folder(run_dir):
with log_time("compressing took"):
clean_output(run_dir, ncores)
else:
step_folders = get_module_steps_folders(run_dir)
for folder in step_folders:
with log_time("compressing took"):
clean_output(Path(run_dir, folder), ncores)
return
if __name__ == "__main__":
sys.exit(maincli()) # type: ignore