protenix/openfold_local/data/tools/utils.py

# Copyright 2021 AlQuraishi Laboratory
# Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#      http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

"""Common utilities for data pipeline tools."""
import contextlib
import datetime
import logging
import shutil
import tempfile
import time
from typing import Optional


@contextlib.contextmanager
def tmpdir_manager(base_dir: Optional[str] = None):
    """Context manager that deletes a temporary directory on exit."""
    tmpdir = tempfile.mkdtemp(dir=base_dir)
    try:
        yield tmpdir
    finally:
        shutil.rmtree(tmpdir, ignore_errors=True)


@contextlib.contextmanager
def timing(msg: str):
    logging.info("Started %s", msg)
    tic = time.perf_counter()
    yield
    toc = time.perf_counter()
    logging.info("Finished %s in %.3f seconds", msg, toc - tic)


def to_date(s: str):
    return datetime.datetime(year=int(s[:4]), month=int(s[5:7]), day=int(s[8:10]))