import errno
import functools
import io
import os
import pickle
import re
import string
import sys
import time
import warnings
from contextlib import ExitStack, contextmanager
from importlib import import_module
from math import atan2, cos, degrees, gcd, radians, sin
from pathlib import Path, PurePath
from typing import Callable, Dict, List, Type, Union
import numpy as np
from ase.formula import formula_hill, formula_metal
__all__ = ['basestring', 'import_module', 'seterr', 'plural',
'devnull', 'gcd', 'convert_string_to_fd', 'Lock',
'opencew', 'OpenLock', 'rotate', 'irotate', 'pbc2pbc', 'givens',
'hsv2rgb', 'hsv', 'pickleload', 'reader',
'formula_hill', 'formula_metal', 'PurePath', 'xwopen',
'tokenize_version', 'get_python_package_path_description']
def tokenize_version(version_string: str):
"""Parse version string into a tuple for version comparisons.
Usage: tokenize_version('3.8') < tokenize_version('3.8.1').
"""
tokens = []
for component in version_string.split('.'):
match = re.match(r'(\d*)(.*)', component)
assert match is not None, f'Cannot parse component {component}'
number_str, tail = match.group(1, 2)
try:
number = int(number_str)
except ValueError:
number = -1
tokens += [number, tail]
return tuple(tokens)
# Python 2+3 compatibility stuff (let's try to remove these things):
basestring = str
pickleload = functools.partial(pickle.load, encoding='bytes')
def deprecated(
message: Union[str, Warning],
category: Type[Warning] = FutureWarning,
callback: Callable[[List, Dict], bool] = lambda args, kwargs: True
):
"""Return a decorator deprecating a function.
Parameters
----------
message : str or Warning
The message to be emitted. If ``message`` is a Warning, then
``category`` is ignored and ``message.__class__`` will be used.
category : Type[Warning], default=FutureWarning
The type of warning to be emitted. If ``message`` is a ``Warning``
instance, then ``category`` will be ignored and ``message.__class__``
will be used.
callback : Callable[[List, Dict], bool], default=lambda args, kwargs: True
A callable that determines if the warning should be emitted and handles
any processing prior to calling the deprecated function. The callable
will receive two arguments, a list and a dictionary. The list will
contain the positional arguments that the deprecated function was
called with at runtime while the dictionary will contain the keyword
arguments. The callable *must* return ``True`` if the warning is to be
emitted and ``False`` otherwise. The list and dictionary will be
unpacked into the positional and keyword arguments, respectively, used
to call the deprecated function.
Returns
-------
deprecated_decorator : Callable
A decorator for deprecated functions that can be used to conditionally
emit deprecation warnings and/or pre-process the arguments of a
deprecated function.
Example
-------
>>> # Inspect & replace a keyword parameter passed to a deprecated function
>>> from typing import Any, Callable, Dict, List
>>> import warnings
>>> from ase.utils import deprecated
>>> def alias_callback_factory(kwarg: str, alias: str) -> Callable:
... def _replace_arg(_: List, kwargs: Dict[str, Any]) -> bool:
... kwargs[kwarg] = kwargs[alias]
... del kwargs[alias]
... return True
... return _replace_arg
>>> MESSAGE = ("Calling this function with `atoms` is deprecated. "
... "Use `optimizable` instead.")
>>> @deprecated(
... MESSAGE,
... category=DeprecationWarning,
... callback=alias_callback_factory("optimizable", "atoms")
... )
... def function(*, atoms=None, optimizable=None):
... '''
... .. deprecated:: 3.23.0
... Calling this function with ``atoms`` is deprecated.
... Use ``optimizable`` instead.
... '''
... print(f"atoms: {atoms}")
... print(f"optimizable: {optimizable}")
>>> with warnings.catch_warnings(record=True) as w:
... warnings.simplefilter("always")
... function(atoms="atoms")
atoms: None
optimizable: atoms
>>> w[-1].category == DeprecationWarning
True
"""
def deprecated_decorator(func):
@functools.wraps(func)
def deprecated_function(*args, **kwargs):
_args = list(args)
if callback(_args, kwargs):
warnings.warn(message, category=category, stacklevel=2)
return func(*_args, **kwargs)
return deprecated_function
return deprecated_decorator
[docs]@contextmanager
def seterr(**kwargs):
"""Set how floating-point errors are handled.
See np.seterr() for more details.
"""
old = np.seterr(**kwargs)
try:
yield
finally:
np.seterr(**old)
[docs]def plural(n, word):
"""Use plural for n!=1.
>>> from ase.utils import plural
>>> plural(0, 'egg'), plural(1, 'egg'), plural(2, 'egg')
('0 eggs', '1 egg', '2 eggs')
"""
if n == 1:
return '1 ' + word
return '%d %ss' % (n, word)
class DevNull:
encoding = 'UTF-8'
closed = False
_use_os_devnull = deprecated('use open(os.devnull) instead',
DeprecationWarning)
# Deprecated for ase-3.21.0. Change to futurewarning later on.
@_use_os_devnull
def write(self, string):
pass
@_use_os_devnull
def flush(self):
pass
@_use_os_devnull
def seek(self, offset, whence=0):
return 0
@_use_os_devnull
def tell(self):
return 0
@_use_os_devnull
def close(self):
pass
@_use_os_devnull
def isatty(self):
return False
@_use_os_devnull
def read(self, n=-1):
return ''
devnull = DevNull()
[docs]@deprecated('convert_string_to_fd does not facilitate proper resource '
'management. '
'Please use e.g. ase.utils.IOContext class instead.')
def convert_string_to_fd(name, world=None):
"""Create a file-descriptor for text output.
Will open a file for writing with given name. Use None for no output and
'-' for sys.stdout.
.. deprecated:: 3.22.1
Please use e.g. :class:`ase.utils.IOContext` class instead.
"""
if world is None:
from ase.parallel import world
if name is None or world.rank != 0:
return open(os.devnull, 'w')
if name == '-':
return sys.stdout
if isinstance(name, (str, PurePath)):
return open(str(name), 'w') # str for py3.5 pathlib
return name # we assume name is already a file-descriptor
# Only Windows has O_BINARY:
CEW_FLAGS = os.O_CREAT | os.O_EXCL | os.O_WRONLY | getattr(os, 'O_BINARY', 0)
@contextmanager
def xwopen(filename, world=None):
"""Create and open filename exclusively for writing.
If master cpu gets exclusive write access to filename, a file
descriptor is returned (a dummy file descriptor is returned on the
slaves). If the master cpu does not get write access, None is
returned on all processors."""
fd = opencew(filename, world)
try:
yield fd
finally:
if fd is not None:
fd.close()
# @deprecated('use "with xwopen(...) as fd: ..." to prevent resource leak')
[docs]def opencew(filename, world=None):
return _opencew(filename, world)
def _opencew(filename, world=None):
import ase.parallel as parallel
if world is None:
world = parallel.world
closelater = []
def opener(file, flags):
return os.open(file, flags | CEW_FLAGS)
try:
error = 0
if world.rank == 0:
try:
fd = open(filename, 'wb', opener=opener)
except OSError as ex:
error = ex.errno
else:
closelater.append(fd)
else:
fd = open(os.devnull, 'wb')
closelater.append(fd)
# Synchronize:
error = world.sum_scalar(error)
if error == errno.EEXIST:
return None
if error:
raise OSError(error, 'Error', filename)
return fd
except BaseException:
for fd in closelater:
fd.close()
raise
def opencew_text(*args, **kwargs):
fd = opencew(*args, **kwargs)
if fd is None:
return None
return io.TextIOWrapper(fd)
class Lock:
def __init__(self, name='lock', world=None, timeout=float('inf')):
self.name = str(name)
self.timeout = timeout
if world is None:
from ase.parallel import world
self.world = world
def acquire(self):
dt = 0.2
t1 = time.time()
while True:
fd = opencew(self.name, self.world)
if fd is not None:
self.fd = fd
break
time_left = self.timeout - (time.time() - t1)
if time_left <= 0:
raise TimeoutError
time.sleep(min(dt, time_left))
dt *= 2
def release(self):
self.world.barrier()
# Important to close fd before deleting file on windows
# as a WinError would otherwise be raised.
self.fd.close()
if self.world.rank == 0:
os.remove(self.name)
self.world.barrier()
def __enter__(self):
self.acquire()
def __exit__(self, type, value, tb):
self.release()
class OpenLock:
def acquire(self):
pass
def release(self):
pass
def __enter__(self):
pass
def __exit__(self, type, value, tb):
pass
def search_current_git_hash(arg, world=None):
"""Search for .git directory and current git commit hash.
Parameters:
arg: str (directory path) or python module
.git directory is searched from the parent directory of
the given directory or module.
"""
if world is None:
from ase.parallel import world
if world.rank != 0:
return None
# Check argument
if isinstance(arg, str):
# Directory path
dpath = arg
else:
# Assume arg is module
dpath = os.path.dirname(arg.__file__)
# dpath = os.path.abspath(dpath)
# in case this is just symlinked into $PYTHONPATH
dpath = os.path.realpath(dpath)
dpath = os.path.dirname(dpath) # Go to the parent directory
git_dpath = os.path.join(dpath, '.git')
if not os.path.isdir(git_dpath):
# Replace this 'if' with a loop if you want to check
# further parent directories
return None
HEAD_file = os.path.join(git_dpath, 'HEAD')
if not os.path.isfile(HEAD_file):
return None
with open(HEAD_file) as fd:
line = fd.readline().strip()
if line.startswith('ref: '):
ref = line[5:]
ref_file = os.path.join(git_dpath, ref)
else:
# Assuming detached HEAD state
ref_file = HEAD_file
if not os.path.isfile(ref_file):
return None
with open(ref_file) as fd:
line = fd.readline().strip()
if all(c in string.hexdigits for c in line):
return line
return None
def rotate(rotations, rotation=np.identity(3)):
"""Convert string of format '50x,-10y,120z' to a rotation matrix.
Note that the order of rotation matters, i.e. '50x,40z' is different
from '40z,50x'.
"""
if rotations == '':
return rotation.copy()
for i, a in [('xyz'.index(s[-1]), radians(float(s[:-1])))
for s in rotations.split(',')]:
s = sin(a)
c = cos(a)
if i == 0:
rotation = np.dot(rotation, [(1, 0, 0),
(0, c, s),
(0, -s, c)])
elif i == 1:
rotation = np.dot(rotation, [(c, 0, -s),
(0, 1, 0),
(s, 0, c)])
else:
rotation = np.dot(rotation, [(c, s, 0),
(-s, c, 0),
(0, 0, 1)])
return rotation
def givens(a, b):
"""Solve the equation system::
[ c s] [a] [r]
[ ] . [ ] = [ ]
[-s c] [b] [0]
"""
sgn = np.sign
if b == 0:
c = sgn(a)
s = 0
r = abs(a)
elif abs(b) >= abs(a):
cot = a / b
u = sgn(b) * (1 + cot**2)**0.5
s = 1. / u
c = s * cot
r = b * u
else:
tan = b / a
u = sgn(a) * (1 + tan**2)**0.5
c = 1. / u
s = c * tan
r = a * u
return c, s, r
def irotate(rotation, initial=np.identity(3)):
"""Determine x, y, z rotation angles from rotation matrix."""
a = np.dot(initial, rotation)
cx, sx, rx = givens(a[2, 2], a[1, 2])
cy, sy, ry = givens(rx, a[0, 2])
cz, sz, rz = givens(cx * a[1, 1] - sx * a[2, 1],
cy * a[0, 1] - sy * (sx * a[1, 1] + cx * a[2, 1]))
x = degrees(atan2(sx, cx))
y = degrees(atan2(-sy, cy))
z = degrees(atan2(sz, cz))
return x, y, z
def pbc2pbc(pbc):
newpbc = np.empty(3, bool)
newpbc[:] = pbc
return newpbc
def string2index(stridx: str) -> Union[int, slice, str]:
"""Convert index string to either int or slice"""
if ':' not in stridx:
# may contain database accessor
try:
return int(stridx)
except ValueError:
return stridx
i = [None if s == '' else int(s) for s in stridx.split(':')]
return slice(*i)
def hsv2rgb(h, s, v):
"""http://en.wikipedia.org/wiki/HSL_and_HSV
h (hue) in [0, 360[
s (saturation) in [0, 1]
v (value) in [0, 1]
return rgb in range [0, 1]
"""
if v == 0:
return 0, 0, 0
if s == 0:
return v, v, v
i, f = divmod(h / 60., 1)
p = v * (1 - s)
q = v * (1 - s * f)
t = v * (1 - s * (1 - f))
if i == 0:
return v, t, p
elif i == 1:
return q, v, p
elif i == 2:
return p, v, t
elif i == 3:
return p, q, v
elif i == 4:
return t, p, v
elif i == 5:
return v, p, q
else:
raise RuntimeError('h must be in [0, 360]')
def hsv(array, s=.9, v=.9):
array = (array + array.min()) * 359. / (array.max() - array.min())
result = np.empty((len(array.flat), 3))
for rgb, h in zip(result, array.flat):
rgb[:] = hsv2rgb(h, s, v)
return np.reshape(result, array.shape + (3,))
# This code does the same, but requires pylab
# def cmap(array, name='hsv'):
# import pylab
# a = (array + array.min()) / array.ptp()
# rgba = getattr(pylab.cm, name)(a)
# return rgba[:-1] # return rgb only (not alpha)
def longsum(x):
"""128-bit floating point sum."""
return float(np.asarray(x, dtype=np.longdouble).sum())
[docs]@contextmanager
def workdir(path, mkdir=False):
"""Temporarily change, and optionally create, working directory."""
path = Path(path)
if mkdir:
path.mkdir(parents=True, exist_ok=True)
olddir = os.getcwd()
os.chdir(path)
try:
yield # Yield the Path or dirname maybe?
finally:
os.chdir(olddir)
class iofunction:
"""Decorate func so it accepts either str or file.
(Won't work on functions that return a generator.)"""
def __init__(self, mode):
self.mode = mode
def __call__(self, func):
@functools.wraps(func)
def iofunc(file, *args, **kwargs):
openandclose = isinstance(file, (str, PurePath))
fd = None
try:
if openandclose:
fd = open(str(file), self.mode)
else:
fd = file
obj = func(fd, *args, **kwargs)
return obj
finally:
if openandclose and fd is not None:
# fd may be None if open() failed
fd.close()
return iofunc
def writer(func):
return iofunction('w')(func)
def reader(func):
return iofunction('r')(func)
# The next two functions are for hotplugging into a JSONable class
# using the jsonable decorator. We are supposed to have this kind of stuff
# in ase.io.jsonio, but we'd rather import them from a 'basic' module
# like ase/utils than one which triggers a lot of extra (cyclic) imports.
def write_json(self, fd):
"""Write to JSON file."""
from ase.io.jsonio import write_json as _write_json
_write_json(fd, self)
@classmethod # type: ignore[misc]
def read_json(cls, fd):
"""Read new instance from JSON file."""
from ase.io.jsonio import read_json as _read_json
obj = _read_json(fd)
assert isinstance(obj, cls)
return obj
def jsonable(name):
"""Decorator for facilitating JSON I/O with a class.
Pokes JSON-based read and write functions into the class.
In order to write an object to JSON, it needs to be a known simple type
(such as ndarray, float, ...) or implement todict(). If the class
defines a string called ase_objtype, the decoder will want to convert
the object back into its original type when reading."""
def jsonableclass(cls):
cls.ase_objtype = name
if not hasattr(cls, 'todict'):
raise TypeError('Class must implement todict()')
# We may want the write and read to be optional.
# E.g. a calculator might want to be JSONable, but not
# that .write() produces a JSON file.
#
# This is mostly for 'lightweight' object IO.
cls.write = write_json
cls.read = read_json
return cls
return jsonableclass
class ExperimentalFeatureWarning(Warning):
pass
def experimental(func):
"""Decorator for functions not ready for production use."""
@functools.wraps(func)
def expfunc(*args, **kwargs):
warnings.warn('This function may change or misbehave: {}()'
.format(func.__qualname__),
ExperimentalFeatureWarning)
return func(*args, **kwargs)
return expfunc
def lazymethod(meth):
"""Decorator for lazy evaluation and caching of data.
Example::
class MyClass:
@lazymethod
def thing(self):
return expensive_calculation()
The method body is only executed first time thing() is called, and
its return value is stored. Subsequent calls return the cached
value."""
name = meth.__name__
@functools.wraps(meth)
def getter(self):
try:
cache = self._lazy_cache
except AttributeError:
cache = self._lazy_cache = {}
if name not in cache:
cache[name] = meth(self)
return cache[name]
return getter
def atoms_to_spglib_cell(atoms):
"""Convert atoms into data suitable for calling spglib."""
return (atoms.get_cell(),
atoms.get_scaled_positions(),
atoms.get_atomic_numbers())
def warn_legacy(feature_name):
warnings.warn(
f'The {feature_name} feature is untested and ASE developers do not '
'know whether it works or how to use it. Please rehabilitate it '
'(by writing unittests) or it may be removed.',
FutureWarning)
def lazyproperty(meth):
"""Decorator like lazymethod, but making item available as a property."""
return property(lazymethod(meth))
class IOContext:
@lazyproperty
def _exitstack(self):
return ExitStack()
def __enter__(self):
return self
def __exit__(self, *args):
self.close()
def closelater(self, fd):
return self._exitstack.enter_context(fd)
def close(self):
self._exitstack.close()
def openfile(self, file, comm, mode='w'):
if hasattr(file, 'close'):
return file # File already opened, not for us to close.
encoding = None if mode.endswith('b') else 'utf-8'
if file is None or comm.rank != 0:
return self.closelater(open(os.devnull, mode=mode,
encoding=encoding))
if file == '-':
return sys.stdout
return self.closelater(open(file, mode=mode, encoding=encoding))
def get_python_package_path_description(
package, default='module has no path') -> str:
"""Helper to get path description of a python package/module
If path has multiple elements, the first one is returned.
If it is empty, the default is returned.
Exceptions are returned as strings default+(exception).
Always returns a string.
"""
try:
p = list(package.__path__)
if p:
return str(p[0])
else:
return default
except Exception as ex:
return f"{default} ({ex})"