Utilities: msmbuilder.utils

class msmbuilder.utils.Counter

Mapping where default values are zero

msmbuilder.utils.check_assignment_array_input(assignments, check_ndarray=True, check_integer=True, ndim=2)

Check if input is an appropriate data type for assignments.

Parameters:

assignments : ndarray

Assignment data whose format will be checked.

check_ndarray : bool, optional

Default True; set False to skip checking for ndarray type

check_integer : bool, optional

Default True; set False to skip checking for integer dtype

ndim : int, optional

Default is 2, which is the correct value for an assignment array.

Notes

Checks if type is Numpy array, if dtype is int-like, and if ndim is ndim (2 by default).

msmbuilder.utils.deprecated(replacement=None, removal_version=None)

A decorator which can be used to mark functions as deprecated. replacement is a callable that will be called with the same args as the decorated function.

Code adapted from http://code.activestate.com/recipes/577819-deprecated-decorator/, MIT license

>>> @deprecated()
... def foo(x):
...     return x
...
>>> ret = foo(1)
DeprecationWarning: foo is deprecated
>>> ret
1
>>>
>>>
>>> def newfun(x):
...     return 0
...
>>> @deprecated(newfun)
... def foo(x):
...     return x
...
>>> ret = foo(1)
DeprecationWarning: foo is deprecated; use newfun instead
>>> ret
0
>>>

msmbuilder.utils.format_block(block)

Format the given block of text, trimming leading/trailing empty lines and any leading whitespace that is common to all lines. The purpose is to let us list a code block as a multiline, triple-quoted Python string, taking care of indentation concerns.

msmbuilder.utils.future_warning(func)

This is a decorator which can be used to mark functions as to-be deprecated. It will result in a warning being emitted when the function is used.

msmbuilder.utils.highlight(text, color='Red', bold=False)

Return a highlighted string using color or bold.

@param[in] text The string that the printout is based upon. This function will return the highlighted string.

@param[in] color String or number corresponding to the color. 1 red

2 green

3 yellow

4 blue

5 magenta

6 cyan

7 white

@param[in] bold Whether to use bold print

msmbuilder.utils.keynat(string)

A natural sort helper function for sort() and sorted() without using regular expression.

>>> items = ('Z', 'a', '10', '1', '9')
>>> sorted(items)
['1', '10', '9', 'Z', 'a']
>>> sorted(items, key=keynat)
['1', '9', '10', 'Z', 'a']

msmbuilder.utils.lru_cache(maxsize=100)

Least-recently-used cache decorator.

Arguments to the cached function must be hashable. Cache performance statistics stored in f.hits and f.misses. Clear the cache with f.clear(). http://en.wikipedia.org/wiki/Cache_algorithms#Least_Recently_Used

msmbuilder.utils.make_methods_pickable()

Run this at the top of a script to register pickable methods

msmbuilder.utils.uneven_zip(*args)

Zip the arguments together like the builtin function, except that when one argument runs out (because its shorter), you keep filling it in with its last value

i.e.

uneven_zip([1,2,3], ‘a’, [10,11]) = [[1, ‘a’, 10], [2, ‘a’, 11], [3, ‘a’, 11]]