File: fixes.py

package info (click to toggle)
scikit-learn 0.20.2%2Bdfsg-6
  • links: PTS, VCS
  • area: main
  • in suites: buster
  • size: 51,036 kB
  • sloc: python: 108,171; ansic: 8,722; cpp: 5,651; makefile: 192; sh: 40
file content (379 lines) | stat: -rw-r--r-- 12,379 bytes parent folder | download
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
"""Compatibility fixes for older version of python, numpy and scipy

If you add content to this file, please give the version of the package
at which the fixe is no longer needed.
"""
# Authors: Emmanuelle Gouillart <emmanuelle.gouillart@normalesup.org>
#          Gael Varoquaux <gael.varoquaux@normalesup.org>
#          Fabian Pedregosa <fpedregosa@acm.org>
#          Lars Buitinck
#
# License: BSD 3 clause

import os
import errno
import sys

from distutils.version import LooseVersion

import numpy as np
import scipy.sparse as sp
import scipy

try:
    from inspect import signature
except ImportError:
    from ..externals.funcsigs import signature


def _parse_version(version_string):
    version = []
    for x in version_string.split('.'):
        try:
            version.append(int(x))
        except ValueError:
            # x may be of the form dev-1ea1592
            version.append(x)
    return tuple(version)


euler_gamma = getattr(np, 'euler_gamma',
                      0.577215664901532860606512090082402431)

np_version = _parse_version(np.__version__)
sp_version = _parse_version(scipy.__version__)
PY3_OR_LATER = sys.version_info[0] >= 3


# Remove when minimum required NumPy >= 1.10
try:
    if (not np.allclose(np.divide(.4, 1, casting="unsafe"),
                        np.divide(.4, 1, casting="unsafe", dtype=np.float64))
            or not np.allclose(np.divide(.4, 1), .4)):
        raise TypeError('Divide not working with dtype: '
                        'https://github.com/numpy/numpy/issues/3484')
    divide = np.divide

except TypeError:
    # Compat for old versions of np.divide that do not provide support for
    # the dtype args
    def divide(x1, x2, out=None, dtype=None):
        out_orig = out
        if out is None:
            out = np.asarray(x1, dtype=dtype)
            if out is x1:
                out = x1.copy()
        else:
            if out is not x1:
                out[:] = x1
        if dtype is not None and out.dtype != dtype:
            out = out.astype(dtype)
        out /= x2
        if out_orig is None and np.isscalar(x1):
            out = np.asscalar(out)
        return out


# boxcox ignore NaN in scipy.special.boxcox after 0.14
if sp_version < (0, 14):
    from scipy import stats

    def boxcox(x, lmbda):
        with np.errstate(invalid='ignore'):
            return stats.boxcox(x, lmbda)
else:
    from scipy.special import boxcox  # noqa


if sp_version < (0, 15):
    # Backport fix for scikit-learn/scikit-learn#2986 / scipy/scipy#4142
    from ._scipy_sparse_lsqr_backport import lsqr as sparse_lsqr
else:
    from scipy.sparse.linalg import lsqr as sparse_lsqr  # noqa


try:  # SciPy >= 0.19
    from scipy.special import comb, logsumexp
except ImportError:
    from scipy.misc import comb, logsumexp  # noqa


if sp_version >= (0, 19):
    def _argmax(arr_or_spmatrix, axis=None):
        return arr_or_spmatrix.argmax(axis=axis)
else:
    # Backport of argmax functionality from scipy 0.19.1, can be removed
    # once support for scipy 0.18 and below is dropped

    def _find_missing_index(ind, n):
        for k, a in enumerate(ind):
            if k != a:
                return k

        k += 1
        if k < n:
            return k
        else:
            return -1

    def _arg_min_or_max_axis(self, axis, op, compare):
        if self.shape[axis] == 0:
            raise ValueError("Can't apply the operation along a zero-sized "
                             "dimension.")

        if axis < 0:
            axis += 2

        zero = self.dtype.type(0)

        mat = self.tocsc() if axis == 0 else self.tocsr()
        mat.sum_duplicates()

        ret_size, line_size = mat._swap(mat.shape)
        ret = np.zeros(ret_size, dtype=int)

        nz_lines, = np.nonzero(np.diff(mat.indptr))
        for i in nz_lines:
            p, q = mat.indptr[i:i + 2]
            data = mat.data[p:q]
            indices = mat.indices[p:q]
            am = op(data)
            m = data[am]
            if compare(m, zero) or q - p == line_size:
                ret[i] = indices[am]
            else:
                zero_ind = _find_missing_index(indices, line_size)
                if m == zero:
                    ret[i] = min(am, zero_ind)
                else:
                    ret[i] = zero_ind

        if axis == 1:
            ret = ret.reshape(-1, 1)

        return np.asmatrix(ret)

    def _arg_min_or_max(self, axis, out, op, compare):
        if out is not None:
            raise ValueError("Sparse matrices do not support "
                             "an 'out' parameter.")

        # validateaxis(axis)

        if axis is None:
            if 0 in self.shape:
                raise ValueError("Can't apply the operation to "
                                 "an empty matrix.")

            if self.nnz == 0:
                return 0
            else:
                zero = self.dtype.type(0)
                mat = self.tocoo()
                mat.sum_duplicates()
                am = op(mat.data)
                m = mat.data[am]

                if compare(m, zero):
                    return mat.row[am] * mat.shape[1] + mat.col[am]
                else:
                    size = np.product(mat.shape)
                    if size == mat.nnz:
                        return am
                    else:
                        ind = mat.row * mat.shape[1] + mat.col
                        zero_ind = _find_missing_index(ind, size)
                        if m == zero:
                            return min(zero_ind, am)
                        else:
                            return zero_ind

        return _arg_min_or_max_axis(self, axis, op, compare)

    def _sparse_argmax(self, axis=None, out=None):
        return _arg_min_or_max(self, axis, out, np.argmax, np.greater)

    def _argmax(arr_or_matrix, axis=None):
        if sp.issparse(arr_or_matrix):
            return _sparse_argmax(arr_or_matrix, axis=axis)
        else:
            return arr_or_matrix.argmax(axis=axis)


def parallel_helper(obj, methodname, *args, **kwargs):
    """Workaround for Python 2 limitations of pickling instance methods

    Parameters
    ----------
    obj
    methodname
    *args
    **kwargs

    """
    return getattr(obj, methodname)(*args, **kwargs)


if 'exist_ok' in signature(os.makedirs).parameters:
    makedirs = os.makedirs
else:
    def makedirs(name, mode=0o777, exist_ok=False):
        """makedirs(name [, mode=0o777][, exist_ok=False])

        Super-mkdir; create a leaf directory and all intermediate ones.  Works
        like mkdir, except that any intermediate path segment (not just the
        rightmost) will be created if it does not exist. If the target
        directory already exists, raise an OSError if exist_ok is False.
        Otherwise no exception is raised.  This is recursive.

        """

        try:
            os.makedirs(name, mode=mode)
        except OSError as e:
            if (not exist_ok or e.errno != errno.EEXIST
                    or not os.path.isdir(name)):
                raise


if np_version < (1, 12):
    class MaskedArray(np.ma.MaskedArray):
        # Before numpy 1.12, np.ma.MaskedArray object is not picklable
        # This fix is needed to make our model_selection.GridSearchCV
        # picklable as the ``cv_results_`` param uses MaskedArray
        def __getstate__(self):
            """Return the internal state of the masked array, for pickling
            purposes.

            """
            cf = 'CF'[self.flags.fnc]
            data_state = super(np.ma.MaskedArray, self).__reduce__()[2]
            return data_state + (np.ma.getmaskarray(self).tostring(cf),
                                 self._fill_value)
else:
    from numpy.ma import MaskedArray    # noqa


if np_version < (1, 11):
    def nanpercentile(a, q):
        """
        Compute the qth percentile of the data along the specified axis,
        while ignoring nan values.

        Returns the qth percentile(s) of the array elements.

        Parameters
        ----------
        a : array_like
            Input array or object that can be converted to an array.
        q : float in range of [0,100] (or sequence of floats)
            Percentile to compute, which must be between 0 and 100
            inclusive.

        Returns
        -------
        percentile : scalar or ndarray
            If `q` is a single percentile and `axis=None`, then the result
            is a scalar. If multiple percentiles are given, first axis of
            the result corresponds to the percentiles. The other axes are
            the axes that remain after the reduction of `a`. If the input
            contains integers or floats smaller than ``float64``, the output
            data-type is ``float64``. Otherwise, the output data-type is the
            same as that of the input. If `out` is specified, that array is
            returned instead.

        """
        data = np.compress(~np.isnan(a), a)
        if data.size:
            return np.percentile(data, q)
        else:
            size_q = 1 if np.isscalar(q) else len(q)
            return np.array([np.nan] * size_q)
else:
    from numpy import nanpercentile  # noqa


if np_version < (1, 9):
    def nanmedian(a, axis=None):
        if axis is None:
            data = a.reshape(-1)
            return np.median(np.compress(~np.isnan(data), data))
        else:
            data = a.T if not axis else a
            return np.array([np.median(np.compress(~np.isnan(row), row))
                             for row in data])
else:
    from numpy import nanmedian  # noqa


# Fix for behavior inconsistency on numpy.equal for object dtypes.
# For numpy versions < 1.13, numpy.equal tests element-wise identity of objects
# instead of equality. This fix returns the mask of NaNs in an array of
# numerical or object values for all numpy versions.
if np_version < (1, 13):
    def _object_dtype_isnan(X):
        return np.frompyfunc(lambda x: x != x, 1, 1)(X).astype(bool)
else:
    def _object_dtype_isnan(X):
        return X != X


# To be removed once this fix is included in six
try:
    from collections.abc import Sequence as _Sequence  # noqa
    from collections.abc import Iterable as _Iterable  # noqa
    from collections.abc import Mapping as _Mapping  # noqa
    from collections.abc import Sized as _Sized  # noqa
except ImportError:  # python <3.3
    from collections import Sequence as _Sequence  # noqa
    from collections import Iterable as _Iterable  # noqa
    from collections import Mapping as _Mapping  # noqa
    from collections import Sized as _Sized  # noqa


def _joblib_parallel_args(**kwargs):
    """Set joblib.Parallel arguments in a compatible way for 0.11 and 0.12+

    For joblib 0.11 this maps both ``prefer`` and ``require`` parameters to
    a specific ``backend``.

    Parameters
    ----------

    prefer : str in {'processes', 'threads'} or None
        Soft hint to choose the default backend if no specific backend
        was selected with the parallel_backend context manager.

    require : 'sharedmem' or None
        Hard condstraint to select the backend. If set to 'sharedmem',
        the selected backend will be single-host and thread-based even
        if the user asked for a non-thread based backend with
        parallel_backend.

    See joblib.Parallel documentation for more details
    """
    from . import _joblib

    if _joblib.__version__ >= LooseVersion('0.12'):
        return kwargs

    extra_args = set(kwargs.keys()).difference({'prefer', 'require'})
    if extra_args:
        raise NotImplementedError('unhandled arguments %s with joblib %s'
                                  % (list(extra_args), _joblib.__version__))
    args = {}
    if 'prefer' in kwargs:
        prefer = kwargs['prefer']
        if prefer not in ['threads', 'processes', None]:
            raise ValueError('prefer=%s is not supported' % prefer)
        args['backend'] = {'threads': 'threading',
                           'processes': 'multiprocessing',
                           None: None}[prefer]

    if 'require' in kwargs:
        require = kwargs['require']
        if require not in [None, 'sharedmem']:
            raise ValueError('require=%s is not supported' % require)
        if require == 'sharedmem':
            args['backend'] = 'threading'
    return args