"""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 # Gael Varoquaux # Fabian Pedregosa # 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