Source code for pharmpy.utils

import os
import shutil
import time
import warnings
import weakref
from pathlib import Path
from tempfile import mkdtemp

import sympy
import sympy.physics.units as units


class TemporaryDirectoryChanger:
    def __init__(self, path):
        self.path = path
        self.old_path = Path.cwd()

    def __enter__(self):
        os.chdir(self.path)
        return self

    def __exit__(self, *args):
        os.chdir(self.old_path)


# This is copied and modified from the python 3.9 implementation
# The aim is to be able to handle Permission issues in Windows
class TemporaryDirectory:
    """Create and return a temporary directory.  This has the same
    behavior as mkdtemp but can be used as a context manager.  For
    example:

        with TemporaryDirectory() as tmpdir:
            ...

    Upon exiting the context, the directory and everything contained
    in it are removed.
    """

    def __init__(self, suffix=None, prefix=None, dir=None):
        self.name = mkdtemp(suffix, prefix, dir)
        self._finalizer = weakref.finalize(
            self, self._cleanup, self.name, warn_message="Implicitly cleaning up {!r}".format(self)
        )

    @classmethod
    def _rmtree(cls, name):
        def onerror(func, path, exc_info):
            if issubclass(exc_info[0], PermissionError):

                def resetperms(path):
                    try:
                        os.chflags(path, 0)
                    except AttributeError:
                        pass
                    os.chmod(path, 0o700)

                try:
                    if path != name:
                        resetperms(os.path.dirname(path))
                    resetperms(path)

                    try:
                        os.unlink(path)
                    # PermissionError is raised on FreeBSD for directories
                    except (IsADirectoryError, PermissionError):
                        time.sleep(0.1)
                        cls._rmtree(path)
                except FileNotFoundError:
                    pass
            elif issubclass(exc_info[0], FileNotFoundError):
                pass
            else:
                raise

        shutil.rmtree(name, onerror=onerror)

    @classmethod
    def _cleanup(cls, name, warn_message):
        cls._rmtree(name)
        warnings.warn(warn_message, ResourceWarning)

    def __repr__(self):
        return "<{} {!r}>".format(self.__class__.__name__, self.name)

    def __enter__(self):
        return self.name

    def __exit__(self, exc, value, tb):
        self.cleanup()

    def cleanup(self):
        if self._finalizer.detach():
            self._rmtree(self.name)


if os.name != 'nt':
    # Only use the custom implementation for Windows.
    from tempfile import TemporaryDirectory  # noqa


unit_subs = {}
for k, v in units.__dict__.items():
    if isinstance(v, sympy.Expr) and v.has(units.Unit):
        unit_subs[sympy.Symbol(k)] = v


def parse_units(s):
    if not isinstance(s, str):
        return s
    return sympy.sympify(s).subs(unit_subs)