Source code for mdtraj.utils

from __future__ import print_function, division
import time
import warnings
from mdtraj.utils.delay_import import import_
from mdtraj.utils.validation import ensure_type, cast_indices, check_random_state
from mdtraj.utils.unit import in_units_of
from mdtraj.utils.rotation import rotation_matrix_from_quaternion, uniform_quaternion
from mdtraj.utils.unitcell import (lengths_and_angles_to_box_vectors,
                       box_vectors_to_lengths_and_angles)
from mdtraj.utils.contextmanagers import timing, enter_temp_directory

__all__ = ["ensure_type", "import_", "in_units_of",
           "lengths_and_angles_to_box_vectors",
           "box_vectors_to_lengths_and_angles",
           "ilen", "timing", "cast_indices", "check_random_state",
           "rotation_matrix_from_quaternion", "uniform_quaternion",
           "enter_temp_directory", "timing", "deprecated"]


# Make sure that DeprecationWarning get printed
warnings.simplefilter("always", DeprecationWarning)


[docs]def ilen(iterable):
    """Length of an iterator. Note, this consumes the iterator

    Parameters
    ----------
    iterable : iterable
        An iterable, such as a generator, list, etc.

    Returns
    -------
    length  : int
        The number of elements in the iterable
    """
    return sum(1 for _ in iterable)


class deprecated(object):
    """Decorator to mark a function or class as deprecated.

    Issue a warning when the function is called/the class is instantiated and
    adds a warning to the docstring.

    The optional extra argument will be appended to the deprecation message
    and the docstring. Note: to use this with the default value for extra, put
    in an empty of parentheses:

    >>> from sklearn.utils import deprecated
    >>> deprecated() # doctest: +ELLIPSIS
    <sklearn.utils.deprecated object at ...>

    >>> @deprecated()
    ... def some_function(): pass
    """
    # Copied from scikit-learn: sklearn/utils/__init__.py
    # Adapted from http://wiki.python.org/moin/PythonDecoratorLibrary,
    # but with many changes.

    def __init__(self, extra=''):
        """
        Parameters
        ----------
        extra: string
          to be added to the deprecation messages

        """
        self.extra = extra

    def __call__(self, obj):
        if isinstance(obj, type):
            return self._decorate_class(obj)
        else:
            return self._decorate_fun(obj)

    def _decorate_class(self, cls):
        msg = "Class %s is deprecated" % cls.__name__
        if self.extra:
            msg += "; %s" % self.extra

        # FIXME: we should probably reset __new__ for full generality
        init = cls.__init__

        def wrapped(*args, **kwargs):
            warnings.warn(msg, category=DeprecationWarning)
            return init(*args, **kwargs)
        cls.__init__ = wrapped

        wrapped.__name__ = '__init__'
        wrapped.__doc__ = self._update_doc(init.__doc__)
        wrapped.deprecated_original = init

        return cls

    def _decorate_fun(self, fun):
        """Decorate function fun"""

        msg = "Function %s is deprecated" % fun.__name__
        if self.extra:
            msg += "; %s" % self.extra

        def wrapped(*args, **kwargs):
            warnings.warn(msg, category=DeprecationWarning)
            return fun(*args, **kwargs)

        wrapped.__name__ = fun.__name__
        wrapped.__dict__ = fun.__dict__
        wrapped.__doc__ = self._update_doc(fun.__doc__)

        return wrapped

    def _update_doc(self, olddoc):
        newdoc = "DEPRECATED"
        if self.extra:
            newdoc = "%s: %s" % (newdoc, self.extra)
        if olddoc:
            newdoc = "%s\n\n%s" % (newdoc, olddoc)
        return newdoc