Source code for meld.util

# Copyright 2015 by Justin MacCallum, Alberto Perez, Ken Dill
# All rights reserved

Miscellaneous utilities

import contextlib
import logging
import logging.handlers
import os
import shutil
import tempfile
import time
from functools import wraps

from openmm import unit as u  # type: ignore

[docs]def strip_unit(value, unit: u.Unit) -> float: assert isinstance( value, u.Quantity ), f"Expected a Quantity, but {value} has type {type(value)}" return value.value_in_unit(unit)
[docs]@contextlib.contextmanager def in_temp_dir(): """ Context manager to run in temporary directory This is used to run certain operations, e.g. tleap, in a temporary directory. It is also used during the unit tests. """ try: cwd = os.getcwd() tmpdir = tempfile.mkdtemp() os.chdir(tmpdir) yield finally: os.chdir(cwd) shutil.rmtree(tmpdir)
[docs]def log_timing(dest_logger): """ A function decorator to record timing Args: dest_logger: the logger to record timings to """ def wrap(func): @wraps(func) def wrapper(*args, **kwds): t1 = time.time() res = func(*args, **kwds) t2 = time.time() dest_logger.debug("%s took %0.3f ms" % (func.__name__, (t2 - t1) * 1000.0)) return res return wrapper return wrap
[docs]class HostNameContextFilter(logging.Filter): """ Filter class that adds hostid information to logging records. """
[docs] def __init__(self, hostid: str): """ Initialize a HostNameContextFilter Args: hostid: the host id to add to logging output """ logging.Filter.__init__(self) self.hostid = hostid
[docs] def filter(self, record): record.hostid = self.hostid return True