repo stringlengths 2 99 | file stringlengths 13 225 | code stringlengths 0 18.3M | file_length int64 0 18.3M | avg_line_length float64 0 1.36M | max_line_length int64 0 4.26M | extension_type stringclasses 1
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scipy | scipy-main/scipy/sparse/linalg/tests/test_onenormest.py | """Test functions for the sparse.linalg._onenormest module
"""
import numpy as np
from numpy.testing import assert_allclose, assert_equal, assert_
import pytest
import scipy.linalg
import scipy.sparse.linalg
from scipy.sparse.linalg._onenormest import _onenormest_core, _algorithm_2_2
class MatrixProductOperator(scip... | 9,227 | 35.474308 | 88 | py |
scipy | scipy-main/scipy/sparse/linalg/tests/test_propack.py | import os
import pytest
import sys
import numpy as np
from numpy.testing import assert_allclose
from pytest import raises as assert_raises
from scipy.sparse.linalg._svdp import _svdp
from scipy.sparse import csr_matrix, csc_matrix
# dtype_flavour to tolerance
TOLS = {
np.float32: 1e-4,
np.float64: 1e-8,
... | 6,284 | 32.430851 | 84 | py |
scipy | scipy-main/scipy/sparse/linalg/tests/__init__.py | 0 | 0 | 0 | py | |
scipy | scipy-main/scipy/sparse/linalg/tests/test_expm_multiply.py | """Test functions for the sparse.linalg._expm_multiply module."""
from functools import partial
from itertools import product
import numpy as np
import pytest
from numpy.testing import (assert_allclose, assert_, assert_equal,
suppress_warnings)
from scipy.sparse import SparseEfficiencyWarnin... | 13,919 | 39.231214 | 79 | py |
scipy | scipy-main/scipy/sparse/linalg/_isolve/lsqr.py | """Sparse Equations and Least Squares.
The original Fortran code was written by C. C. Paige and M. A. Saunders as
described in
C. C. Paige and M. A. Saunders, LSQR: An algorithm for sparse linear
equations and sparse least squares, TOMS 8(1), 43--71 (1982).
C. C. Paige and M. A. Saunders, Algorithm 583; LSQR: Sparse... | 21,214 | 35.079932 | 84 | py |
scipy | scipy-main/scipy/sparse/linalg/_isolve/setup.py | def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('_isolve', parent_package, top_path)
config.add_data_dir('tests')
return config
if __name__ == '__main__':
from numpy.distutils.core import setup
setup(**configurat... | 347 | 25.769231 | 63 | py |
scipy | scipy-main/scipy/sparse/linalg/_isolve/iterative.py | import warnings
import numpy as np
from scipy.sparse.linalg._interface import LinearOperator
from .utils import make_system
from scipy.linalg import get_lapack_funcs
from scipy._lib.deprecation import _NoValue
__all__ = ['bicg', 'bicgstab', 'cg', 'cgs', 'gmres', 'qmr']
def _get_atol(name, b, tol=_NoValue, atol=0., r... | 34,750 | 31.660714 | 78 | py |
scipy | scipy-main/scipy/sparse/linalg/_isolve/utils.py | __docformat__ = "restructuredtext en"
__all__ = []
from numpy import asanyarray, asarray, array, zeros
from scipy.sparse.linalg._interface import aslinearoperator, LinearOperator, \
IdentityOperator
_coerce_rules = {('f','f'):'f', ('f','d'):'d', ('f','F'):'F',
('f','D'):'D', ('d','f'):'d', ('... | 3,598 | 27.117188 | 79 | py |
scipy | scipy-main/scipy/sparse/linalg/_isolve/minres.py | from numpy import inner, zeros, inf, finfo
from numpy.linalg import norm
from math import sqrt
from .utils import make_system
__all__ = ['minres']
def minres(A, b, x0=None, shift=0.0, tol=1e-5, maxiter=None,
M=None, callback=None, show=False, check=False):
"""
Use MINimum RESidual iteration to so... | 10,878 | 28.16622 | 85 | py |
scipy | scipy-main/scipy/sparse/linalg/_isolve/lgmres.py | # Copyright (C) 2009, Pauli Virtanen <pav@iki.fi>
# Distributed under the same license as SciPy.
import warnings
import numpy as np
from numpy.linalg import LinAlgError
from scipy.linalg import get_blas_funcs
from .utils import make_system
from ._gcrotmk import _fgmres
__all__ = ['lgmres']
def lgmres(A, b, x0=None... | 8,932 | 36.533613 | 85 | py |
scipy | scipy-main/scipy/sparse/linalg/_isolve/__init__.py | "Iterative Solvers for Sparse Linear Systems"
#from info import __doc__
from .iterative import *
from .minres import minres
from .lgmres import lgmres
from .lsqr import lsqr
from .lsmr import lsmr
from ._gcrotmk import gcrotmk
from .tfqmr import tfqmr
__all__ = [
'bicg', 'bicgstab', 'cg', 'cgs', 'gcrotmk', 'gmres... | 479 | 21.857143 | 56 | py |
scipy | scipy-main/scipy/sparse/linalg/_isolve/lsmr.py | """
Copyright (C) 2010 David Fong and Michael Saunders
LSMR uses an iterative method.
07 Jun 2010: Documentation updated
03 Jun 2010: First release version in Python
David Chin-lung Fong clfong@stanford.edu
Institute for Computational and Mathematical Engineering
Stanford University
Michael Saunders ... | 15,657 | 31.151951 | 79 | py |
scipy | scipy-main/scipy/sparse/linalg/_isolve/tfqmr.py | import numpy as np
from .utils import make_system
__all__ = ['tfqmr']
def tfqmr(A, b, x0=None, tol=1e-5, maxiter=None, M=None,
callback=None, atol=None, show=False):
"""
Use Transpose-Free Quasi-Minimal Residual iteration to solve ``Ax = b``.
Parameters
----------
A : {sparse matrix, ... | 6,241 | 32.740541 | 85 | py |
scipy | scipy-main/scipy/sparse/linalg/_isolve/_gcrotmk.py | # Copyright (C) 2015, Pauli Virtanen <pav@iki.fi>
# Distributed under the same license as SciPy.
import warnings
import numpy as np
from numpy.linalg import LinAlgError
from scipy.linalg import (get_blas_funcs, qr, solve, svd, qr_insert, lstsq)
from scipy.sparse.linalg._isolve.utils import make_system
__all__ = ['gc... | 15,984 | 30.343137 | 86 | py |
scipy | scipy-main/scipy/sparse/linalg/_isolve/tests/test_gcrotmk.py | #!/usr/bin/env python
"""Tests for the linalg._isolve.gcrotmk module
"""
from numpy.testing import (assert_, assert_allclose, assert_equal,
suppress_warnings)
import numpy as np
from numpy import zeros, array, allclose
from scipy.linalg import norm
from scipy.sparse import csr_matrix, eye, ... | 5,408 | 31.584337 | 81 | py |
scipy | scipy-main/scipy/sparse/linalg/_isolve/tests/test_lsmr.py | """
Copyright (C) 2010 David Fong and Michael Saunders
Distributed under the same license as SciPy
Testing Code for LSMR.
03 Jun 2010: First version release with lsmr.py
David Chin-lung Fong clfong@stanford.edu
Institute for Computational and Mathematical Engineering
Stanford University
Michael Saunders ... | 6,366 | 33.231183 | 80 | py |
scipy | scipy-main/scipy/sparse/linalg/_isolve/tests/test_lgmres.py | """Tests for the linalg._isolve.lgmres module
"""
from numpy.testing import (assert_, assert_allclose, assert_equal,
suppress_warnings)
import pytest
from platform import python_implementation
import numpy as np
from numpy import zeros, array, allclose
from scipy.linalg import norm
from sc... | 7,060 | 32.306604 | 79 | py |
scipy | scipy-main/scipy/sparse/linalg/_isolve/tests/__init__.py | 0 | 0 | 0 | py | |
scipy | scipy-main/scipy/sparse/linalg/_isolve/tests/test_lsqr.py | import numpy as np
from numpy.testing import assert_allclose, assert_array_equal, assert_equal
import pytest
import scipy.sparse
import scipy.sparse.linalg
from scipy.sparse.linalg import lsqr
# Set up a test problem
n = 35
G = np.eye(n)
normal = np.random.normal
norm = np.linalg.norm
for jj in range(5):
gg = nor... | 3,754 | 30.033058 | 80 | py |
scipy | scipy-main/scipy/sparse/linalg/_isolve/tests/test_iterative.py | """ Test functions for the sparse.linalg._isolve module
"""
import itertools
import platform
import sys
import pytest
import numpy as np
from numpy.testing import assert_array_equal, assert_allclose
from numpy import zeros, arange, array, ones, eye, iscomplexobj
from numpy.linalg import norm
from scipy.sparse import... | 24,865 | 31.126615 | 79 | py |
scipy | scipy-main/scipy/sparse/linalg/_isolve/tests/test_minres.py | import numpy as np
from numpy.testing import assert_equal, assert_allclose, assert_
from scipy.sparse.linalg._isolve import minres
from pytest import raises as assert_raises
from .test_iterative import assert_normclose
def get_sample_problem():
# A random 10 x 10 symmetric matrix
np.random.seed(1234)
mat... | 2,446 | 23.969388 | 69 | py |
scipy | scipy-main/scipy/sparse/linalg/_isolve/tests/test_utils.py | import numpy as np
from pytest import raises as assert_raises
import scipy.sparse.linalg._isolve.utils as utils
def test_make_system_bad_shape():
assert_raises(ValueError, utils.make_system, np.zeros((5,3)), None, np.zeros(4), np.zeros(4))
| 247 | 26.555556 | 97 | py |
scipy | scipy-main/scipy/sparse/linalg/_propack/setup.py | import pathlib
from distutils.sysconfig import get_python_inc
import numpy as np
def _is_32bit():
return np.intp(0).itemsize < 8
def check_propack_submodule():
if not (pathlib.Path(__file__).parent / 'PROPACK/README').exists():
raise RuntimeError("Missing the `PROPACK` submodule! Run "
... | 3,366 | 36.831461 | 81 | py |
scipy | scipy-main/scipy/sparse/linalg/_eigen/_svds.py | import os
import numpy as np
from .arpack import _arpack # type: ignore[attr-defined]
from . import eigsh
from scipy._lib._util import check_random_state
from scipy.sparse.linalg._interface import LinearOperator, aslinearoperator
from scipy.sparse.linalg._eigen.lobpcg import lobpcg # type: ignore[no-redef]
if os.en... | 20,684 | 36.136445 | 79 | py |
scipy | scipy-main/scipy/sparse/linalg/_eigen/setup.py | def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('_eigen',parent_package,top_path)
config.add_subpackage('arpack')
config.add_subpackage('lobpcg')
config.add_data_dir('tests')
return config
if __name__ == '__main... | 417 | 23.588235 | 60 | py |
scipy | scipy-main/scipy/sparse/linalg/_eigen/__init__.py | """
Sparse Eigenvalue Solvers
-------------------------
The submodules of sparse.linalg._eigen:
1. lobpcg: Locally Optimal Block Preconditioned Conjugate Gradient Method
"""
from .arpack import *
from .lobpcg import *
from ._svds import svds
from . import arpack
__all__ = [
'ArpackError', 'ArpackNoConvergen... | 460 | 19.043478 | 77 | py |
scipy | scipy-main/scipy/sparse/linalg/_eigen/_svds_doc.py | def _svds_arpack_doc(A, k=6, ncv=None, tol=0, which='LM', v0=None,
maxiter=None, return_singular_vectors=True,
solver='arpack', random_state=None):
"""
Partial singular value decomposition of a sparse matrix using ARPACK.
Compute the largest or smallest `k` singula... | 15,524 | 38.007538 | 79 | py |
scipy | scipy-main/scipy/sparse/linalg/_eigen/tests/test_svds.py | import os
import re
import copy
import numpy as np
from numpy.testing import assert_allclose, assert_equal, assert_array_equal
import pytest
from scipy.linalg import svd, null_space
from scipy.sparse import csc_matrix, issparse, spdiags, random
from scipy.sparse.linalg import LinearOperator, aslinearoperator
if os.en... | 37,553 | 40.313531 | 79 | py |
scipy | scipy-main/scipy/sparse/linalg/_eigen/tests/__init__.py | 0 | 0 | 0 | py | |
scipy | scipy-main/scipy/sparse/linalg/_eigen/arpack/setup.py | from os.path import join
def configuration(parent_package='',top_path=None):
from numpy.distutils.system_info import get_info
from numpy.distutils.misc_util import Configuration
from scipy._build_utils import (get_g77_abi_wrappers,
gfortran_legacy_flag_hook,
... | 1,842 | 34.442308 | 72 | py |
scipy | scipy-main/scipy/sparse/linalg/_eigen/arpack/__init__.py | """
Eigenvalue solver using iterative methods.
Find k eigenvectors and eigenvalues of a matrix A using the
Arnoldi/Lanczos iterative methods from ARPACK [1]_,[2]_.
These methods are most useful for large sparse matrices.
- eigs(A,k)
- eigsh(A,k)
References
----------
.. [1] ARPACK Software, http://www.caam.rice... | 562 | 25.809524 | 71 | py |
scipy | scipy-main/scipy/sparse/linalg/_eigen/arpack/arpack.py | """
Find a few eigenvectors and eigenvalues of a matrix.
Uses ARPACK: https://github.com/opencollab/arpack-ng
"""
# Wrapper implementation notes
#
# ARPACK Entry Points
# -------------------
# The entry points to ARPACK are
# - (s,d)seupd : single and double precision symmetric matrix
# - (s,d,c,z)neupd: single,doub... | 67,273 | 38.572941 | 89 | py |
scipy | scipy-main/scipy/sparse/linalg/_eigen/arpack/tests/test_arpack.py | __usage__ = """
To run tests locally:
python tests/test_arpack.py [-l<int>] [-v<int>]
"""
import threading
import itertools
import numpy as np
from numpy.testing import assert_allclose, assert_equal, suppress_warnings
from pytest import raises as assert_raises
import pytest
from numpy import dot, conj, random
fr... | 23,750 | 32.03338 | 85 | py |
scipy | scipy-main/scipy/sparse/linalg/_eigen/arpack/tests/__init__.py | 0 | 0 | 0 | py | |
scipy | scipy-main/scipy/sparse/linalg/_eigen/lobpcg/lobpcg.py | """
Locally Optimal Block Preconditioned Conjugate Gradient Method (LOBPCG).
References
----------
.. [1] A. V. Knyazev (2001),
Toward the Optimal Preconditioned Eigensolver: Locally Optimal
Block Preconditioned Conjugate Gradient Method.
SIAM Journal on Scientific Computing 23, no. 2,
pp. ... | 40,882 | 36.784658 | 79 | py |
scipy | scipy-main/scipy/sparse/linalg/_eigen/lobpcg/setup.py | def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('lobpcg',parent_package,top_path)
config.add_data_dir('tests')
return config
if __name__ == '__main__':
from numpy.distutils.core import setup
setup(**configuration(... | 343 | 25.461538 | 60 | py |
scipy | scipy-main/scipy/sparse/linalg/_eigen/lobpcg/__init__.py | """
Locally Optimal Block Preconditioned Conjugate Gradient Method (LOBPCG)
LOBPCG is a preconditioned eigensolver for large symmetric positive definite
(SPD) generalized eigenproblems.
Call the function lobpcg - see help for lobpcg.lobpcg.
"""
from .lobpcg import *
__all__ = [s for s in dir() if not s.startswith('... | 420 | 23.764706 | 76 | py |
scipy | scipy-main/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py | """ Test functions for the sparse.linalg._eigen.lobpcg module
"""
import itertools
import platform
import sys
import pytest
import numpy as np
from numpy import ones, r_, diag
from numpy.testing import (assert_almost_equal, assert_equal,
assert_allclose, assert_array_less)
from scipy import... | 23,518 | 35.691108 | 80 | py |
scipy | scipy-main/scipy/sparse/linalg/_eigen/lobpcg/tests/__init__.py | 0 | 0 | 0 | py | |
scipy | scipy-main/scipy/io/mmio.py | # This file is not meant for public use and will be removed in SciPy v2.0.0.
# Use the `scipy.io` namespace for importing the functions
# included below.
import warnings
from . import _mmio
__all__ = [ # noqa: F822
'mminfo', 'mmread', 'mmwrite', 'MMFile',
'coo_matrix', 'isspmatrix', 'asstr'
]
def __dir__()... | 779 | 25.896552 | 76 | py |
scipy | scipy-main/scipy/io/_netcdf.py | """
NetCDF reader/writer module.
This module is used to read and create NetCDF files. NetCDF files are
accessed through the `netcdf_file` object. Data written to and from NetCDF
files are contained in `netcdf_variable` objects. Attributes are given
as member variables of the `netcdf_file` and `netcdf_variable` objects... | 39,085 | 34.891644 | 107 | py |
scipy | scipy-main/scipy/io/_mmio.py | """
Matrix Market I/O in Python.
See http://math.nist.gov/MatrixMarket/formats.html
for information about the Matrix Market format.
"""
#
# Author: Pearu Peterson <pearu@cens.ioc.ee>
# Created: October, 2004
#
# References:
# http://math.nist.gov/MatrixMarket/
#
import os
import numpy as np
from numpy import (a... | 31,900 | 32.161123 | 81 | py |
scipy | scipy-main/scipy/io/setup.py | def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('io', parent_package, top_path)
config.add_extension('_test_fortran',
sources=['_test_fortran.pyf', '_test_fortran.f'])
config.add_data_dir('tests')
... | 573 | 30.888889 | 74 | py |
scipy | scipy-main/scipy/io/netcdf.py | # This file is not meant for public use and will be removed in SciPy v2.0.0.
# Use the `scipy.io` namespace for importing the functions
# included below.
import warnings
from . import _netcdf
__all__ = [ # noqa: F822
'netcdf_file', 'netcdf_variable',
'array', 'LITTLE_ENDIAN', 'IS_PYPY', 'ABSENT', 'ZERO',
... | 1,080 | 30.794118 | 76 | py |
scipy | scipy-main/scipy/io/harwell_boeing.py | # This file is not meant for public use and will be removed in SciPy v2.0.0.
# Use the `scipy.io` namespace for importing the functions
# included below.
import warnings
from . import _harwell_boeing
__all__ = [ # noqa: F822
'MalformedHeader', 'hb_read', 'hb_write', 'HBInfo',
'HBFile', 'HBMatrixType', 'Fortr... | 898 | 28.966667 | 76 | py |
scipy | scipy-main/scipy/io/_fortran.py | """
Module to read / write Fortran unformatted sequential files.
This is in the spirit of code written by Neil Martinsen-Burrell and Joe Zuntz.
"""
import warnings
import numpy as np
__all__ = ['FortranFile', 'FortranEOFError', 'FortranFormattingError']
class FortranEOFError(TypeError, OSError):
"""Indicates t... | 10,891 | 29.68169 | 93 | py |
scipy | scipy-main/scipy/io/wavfile.py | """
Module to read / write wav files using NumPy arrays
Functions
---------
`read`: Return the sample rate (in samples/sec) and data from a WAV file.
`write`: Write a NumPy array as a WAV file.
"""
import io
import sys
import numpy
import struct
import warnings
from enum import IntEnum
__all__ = [
'WavFileWarn... | 26,642 | 30.680143 | 94 | py |
scipy | scipy-main/scipy/io/idl.py | # This file is not meant for public use and will be removed in SciPy v2.0.0.
# Use the `scipy.io` namespace for importing the functions
# included below.
import warnings
from . import _idl
__all__ = [ # noqa: F822
'readsav', 'DTYPE_DICT', 'RECTYPE_DICT', 'STRUCT_DICT',
'Pointer', 'ObjectPointer', 'AttrDict'... | 794 | 25.5 | 76 | py |
scipy | scipy-main/scipy/io/__init__.py | """
==================================
Input and output (:mod:`scipy.io`)
==================================
.. currentmodule:: scipy.io
SciPy has many modules, classes, and functions available to read data
from and write data to a variety of file formats.
.. seealso:: `NumPy IO routines <https://www.numpy.org/devdo... | 2,719 | 22.247863 | 93 | py |
scipy | scipy-main/scipy/io/_idl.py | # IDLSave - a python module to read IDL 'save' files
# Copyright (c) 2010 Thomas P. Robitaille
# Many thanks to Craig Markwardt for publishing the Unofficial Format
# Specification for IDL .sav files, without which this Python module would not
# exist (http://cow.physics.wisc.edu/~craigm/idl/savefmt).
# This code was... | 26,898 | 28.397814 | 91 | py |
scipy | scipy-main/scipy/io/matlab/mio5_utils.py | # This file is not meant for public use and will be removed in SciPy v2.0.0.
# Use the `scipy.io.matlab` namespace for importing the functions
# included below.
import warnings
from . import _mio5_utils
__all__ = [ # noqa: F822
'VarHeader5', 'VarReader5', 'byteswap_u4', 'chars_to_strings',
'csc_matrix', 'mi... | 899 | 30.034483 | 79 | py |
scipy | scipy-main/scipy/io/matlab/streams.py | # This file is not meant for public use and will be removed in SciPy v2.0.0.
# Use the `scipy.io.matlab` namespace for importing the functions
# included below.
import warnings
from . import _streams
__all__ = [ # noqa: F822
'BLOCK_SIZE', 'GenericStream', 'ZlibInputStream', 'make_stream'
]
def __dir__():
r... | 809 | 27.928571 | 79 | py |
scipy | scipy-main/scipy/io/matlab/_miobase.py | # Authors: Travis Oliphant, Matthew Brett
"""
Base classes for MATLAB file stream reading.
MATLAB is a registered trademark of the Mathworks inc.
"""
import numpy as np
from scipy._lib import doccer
from . import _byteordercodes as boc
__all__ = [
'MatFileReader', 'MatReadError', 'MatReadWarning',
'MatVarR... | 12,875 | 29.084112 | 80 | py |
scipy | scipy-main/scipy/io/matlab/byteordercodes.py | # This file is not meant for public use and will be removed in SciPy v2.0.0.
# Use the `scipy.io.matlab` namespace for importing the functions
# included below.
import warnings
from . import _byteordercodes
__all__ = [ # noqa: F822
'aliases', 'native_code', 'swapped_code',
'sys_is_le', 'to_numpy_code'
]
d... | 849 | 27.333333 | 82 | py |
scipy | scipy-main/scipy/io/matlab/mio5.py | # This file is not meant for public use and will be removed in SciPy v2.0.0.
# Use the `scipy.io.matlab` namespace for importing the functions
# included below.
import warnings
from . import _mio5
__all__ = [ # noqa: F822
'mclass_info', 'mxCHAR_CLASS', 'mxSPARSE_CLASS',
'BytesIO', 'native_code',
'swappe... | 1,435 | 36.789474 | 79 | py |
scipy | scipy-main/scipy/io/matlab/setup.py | def configuration(parent_package='io',top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('matlab', parent_package, top_path)
config.add_extension('_streams', sources=['_streams.c'])
config.add_extension('_mio_utils', sources=['_mio_utils.c'])
config.add_extens... | 538 | 37.5 | 66 | py |
scipy | scipy-main/scipy/io/matlab/_mio4.py | ''' Classes for read / write of matlab (TM) 4 files
'''
import sys
import warnings
import numpy as np
import scipy.sparse
from ._miobase import (MatFileReader, docfiller, matdims, read_dtype,
convert_dtypes, arr_to_chars, arr_dtype_number)
from ._mio_utils import squeeze_element, chars_to_stri... | 20,612 | 32.033654 | 80 | py |
scipy | scipy-main/scipy/io/matlab/mio5_params.py | # This file is not meant for public use and will be removed in SciPy v2.0.0.
# Use the `scipy.io.matlab` namespace for importing the functions
# included below.
import warnings
from . import _mio5_params
__all__ = [ # noqa: F822
'MDTYPES', 'MatlabFunction', 'MatlabObject', 'MatlabOpaque',
'NP_TO_MTYPES', 'N... | 1,526 | 39.184211 | 79 | py |
scipy | scipy-main/scipy/io/matlab/_mio5.py | ''' Classes for read / write of matlab (TM) 5 files
The matfile specification last found here:
https://www.mathworks.com/access/helpdesk/help/pdf_doc/matlab/matfile_format.pdf
(as of December 5 2008)
=================================
Note on functions and mat files
=================================
The document a... | 33,584 | 36.483259 | 84 | py |
scipy | scipy-main/scipy/io/matlab/mio.py | # This file is not meant for public use and will be removed in SciPy v2.0.0.
# Use the `scipy.io.matlab` namespace for importing the functions
# included below.
import warnings
from . import _mio
__all__ = [ # noqa: F822
'mat_reader_factory', 'loadmat', 'savemat', 'whosmat',
'contextmanager', 'docfiller',
... | 894 | 28.833333 | 79 | py |
scipy | scipy-main/scipy/io/matlab/mio4.py | # This file is not meant for public use and will be removed in SciPy v2.0.0.
# Use the `scipy.io.matlab` namespace for importing the functions
# included below.
import warnings
from . import _mio4
__all__ = [ # noqa: F822
'MatFile4Reader', 'MatFile4Writer', 'SYS_LITTLE_ENDIAN',
'VarHeader4', 'VarReader4', '... | 1,201 | 34.352941 | 79 | py |
scipy | scipy-main/scipy/io/matlab/mio_utils.py | # This file is not meant for public use and will be removed in SciPy v2.0.0.
# Use the `scipy.io.matlab` namespace for importing the functions
# included below.
import warnings
from . import _mio_utils
__all__ = ['squeeze_element', 'chars_to_strings'] # noqa: F822
def __dir__():
return __all__
def __getattr... | 786 | 28.148148 | 79 | py |
scipy | scipy-main/scipy/io/matlab/__init__.py | """
MATLAB® file utilies (:mod:`scipy.io.matlab`)
=============================================
.. currentmodule:: scipy.io.matlab
This submodule is meant to provide lower-level file utilies related to reading
and writing MATLAB files.
.. autosummary::
:toctree: generated/
matfile_version - Get the MATLAB fil... | 2,021 | 30.59375 | 78 | py |
scipy | scipy-main/scipy/io/matlab/miobase.py | # This file is not meant for public use and will be removed in SciPy v2.0.0.
# Use the `scipy.io.matlab` namespace for importing the functions
# included below.
import warnings
from . import _miobase
__all__ = [ # noqa: F822
'MatFileReader', 'MatReadError', 'MatReadWarning',
'MatVarReader', 'MatWriteError',... | 988 | 29.90625 | 79 | py |
scipy | scipy-main/scipy/io/matlab/_mio5_params.py | ''' Constants and classes for matlab 5 read and write
See also mio5_utils.pyx where these same constants arise as c enums.
If you make changes in this file, don't forget to change mio5_utils.pyx
'''
import numpy as np
from ._miobase import convert_dtypes
__all__ = [
'MDTYPES', 'MatlabFunction', 'MatlabObject',... | 8,199 | 28.181495 | 98 | py |
scipy | scipy-main/scipy/io/matlab/_byteordercodes.py | ''' Byteorder utilities for system - numpy byteorder encoding
Converts a variety of string codes for little endian, big endian,
native byte order and swapped byte order to explicit NumPy endian
codes - one of '<' (little endian) or '>' (big endian)
'''
import sys
__all__ = [
'aliases', 'native_code', 'swapped_co... | 1,902 | 24.716216 | 74 | py |
scipy | scipy-main/scipy/io/matlab/_mio.py | """
Module for reading and writing matlab (TM) .mat files
"""
# Authors: Travis Oliphant, Matthew Brett
from contextlib import contextmanager
from ._miobase import _get_matfile_version, docfiller
from ._mio4 import MatFile4Reader, MatFile4Writer
from ._mio5 import MatFile5Reader, MatFile5Writer
__all__ = ['mat_reade... | 12,799 | 34.654596 | 90 | py |
scipy | scipy-main/scipy/io/matlab/tests/test_byteordercodes.py | ''' Tests for byteorder module '''
import sys
from numpy.testing import assert_
from pytest import raises as assert_raises
import scipy.io.matlab._byteordercodes as sibc
def test_native():
native_is_le = sys.byteorder == 'little'
assert_(sibc.sys_is_le == native_is_le)
def test_to_numpy():
if sys.byt... | 938 | 30.3 | 68 | py |
scipy | scipy-main/scipy/io/matlab/tests/test_streams.py | """ Testing
"""
import os
import zlib
from io import BytesIO
from tempfile import mkstemp
from contextlib import contextmanager
import numpy as np
from numpy.testing import assert_, assert_equal
from pytest import raises as assert_raises
from scipy.io.matlab._streams import (make_stream,
GenericStream, Zlib... | 7,319 | 30.826087 | 89 | py |
scipy | scipy-main/scipy/io/matlab/tests/test_miobase.py | """ Testing miobase module
"""
import numpy as np
from numpy.testing import assert_equal
from pytest import raises as assert_raises
from scipy.io.matlab._miobase import matdims
def test_matdims():
# Test matdims dimension finder
assert_equal(matdims(np.array(1)), (1, 1)) # NumPy scalar
assert_equal(ma... | 1,464 | 43.393939 | 82 | py |
scipy | scipy-main/scipy/io/matlab/tests/test_mio_funcs.py | ''' Jottings to work out format for __function_workspace__ matrix at end
of mat file.
'''
import os.path
import io
from scipy.io.matlab._mio5 import MatFile5Reader
test_data_path = os.path.join(os.path.dirname(__file__), 'data')
def read_minimat_vars(rdr):
rdr.initialize_read()
mdict = {'__globals__': []}
... | 1,392 | 25.788462 | 72 | py |
scipy | scipy-main/scipy/io/matlab/tests/test_mio_utils.py | """ Testing
"""
import numpy as np
from numpy.testing import assert_array_equal, assert_
from scipy.io.matlab._mio_utils import squeeze_element, chars_to_strings
def test_squeeze_element():
a = np.zeros((1,3))
assert_array_equal(np.squeeze(a), squeeze_element(a))
# 0-D output from squeeze gives scalar... | 1,594 | 33.673913 | 72 | py |
scipy | scipy-main/scipy/io/matlab/tests/test_mio5_utils.py | """ Testing mio5_utils Cython module
"""
import sys
from io import BytesIO
import numpy as np
from numpy.testing import assert_array_equal, assert_equal, assert_
from pytest import raises as assert_raises
import scipy.io.matlab._byteordercodes as boc
import scipy.io.matlab._streams as streams
import scipy.io.matla... | 5,389 | 28.944444 | 75 | py |
scipy | scipy-main/scipy/io/matlab/tests/test_mio.py | ''' Nose test generators
Need function load / save / roundtrip tests
'''
import os
from collections import OrderedDict
from os.path import join as pjoin, dirname
from glob import glob
from io import BytesIO
import re
from tempfile import mkdtemp
import warnings
import shutil
import gzip
from numpy.testing import (a... | 44,564 | 32.532731 | 80 | py |
scipy | scipy-main/scipy/io/matlab/tests/test_pathological.py | """ Test reading of files not conforming to matlab specification
We try and read any file that matlab reads, these files included
"""
from os.path import dirname, join as pjoin
from numpy.testing import assert_
from pytest import raises as assert_raises
from scipy.io.matlab._mio import loadmat
TEST_DATA_PATH = pjoi... | 1,055 | 30.058824 | 73 | py |
scipy | scipy-main/scipy/io/matlab/tests/__init__.py | 0 | 0 | 0 | py | |
scipy | scipy-main/scipy/io/arff/arffread.py | # This file is not meant for public use and will be removed in SciPy v2.0.0.
# Use the `scipy.io.arff` namespace for importing the functions
# included below.
import warnings
from . import _arffread
__all__ = [ # noqa: F822
'MetaData', 'loadarff', 'ArffError', 'ParseArffError',
'r_meta', 'r_comment', 'r_empt... | 1,364 | 35.891892 | 78 | py |
scipy | scipy-main/scipy/io/arff/setup.py | def configuration(parent_package='io',top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('arff', parent_package, top_path)
config.add_data_dir('tests')
return config
if __name__ == '__main__':
from numpy.distutils.core import setup
setup(**configuration(... | 343 | 30.272727 | 60 | py |
scipy | scipy-main/scipy/io/arff/__init__.py | """
Module to read ARFF files
=========================
ARFF is the standard data format for WEKA.
It is a text file format which support numerical, string and data values.
The format can also represent missing data and sparse data.
Notes
-----
The ARFF support in ``scipy.io`` provides file reading functionality only.... | 805 | 26.793103 | 74 | py |
scipy | scipy-main/scipy/io/arff/_arffread.py | # Last Change: Mon Aug 20 08:00 PM 2007 J
import re
import datetime
import numpy as np
import csv
import ctypes
"""A module to read arff files."""
__all__ = ['MetaData', 'loadarff', 'ArffError', 'ParseArffError']
# An Arff file is basically two parts:
# - header
# - data
#
# A header has each of its components... | 26,359 | 28.094923 | 110 | py |
scipy | scipy-main/scipy/io/arff/tests/test_arffread.py | import datetime
import os
import sys
from os.path import join as pjoin
from io import StringIO
import numpy as np
from numpy.testing import (assert_array_almost_equal,
assert_array_equal, assert_equal, assert_)
from pytest import raises as assert_raises
from scipy.io.arff import loadarff
... | 13,084 | 30.303828 | 92 | py |
scipy | scipy-main/scipy/io/arff/tests/__init__.py | 0 | 0 | 0 | py | |
scipy | scipy-main/scipy/io/_harwell_boeing/setup.py | def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('_harwell_boeing',parent_package,top_path)
config.add_data_dir('tests')
return config
if __name__ == '__main__':
from numpy.distutils.core import setup
setup(**config... | 351 | 28.333333 | 69 | py |
scipy | scipy-main/scipy/io/_harwell_boeing/hb.py | """
Implementation of Harwell-Boeing read/write.
At the moment not the full Harwell-Boeing format is supported. Supported
features are:
- assembled, non-symmetric, real matrices
- integer for pointer/indices
- exponential format for float values, and int format
"""
# TODO:
# - Add more support (symmetr... | 19,148 | 32.535902 | 92 | py |
scipy | scipy-main/scipy/io/_harwell_boeing/_fortran_format_parser.py | """
Preliminary module to handle Fortran formats for IO. Does not use this outside
scipy.sparse io for now, until the API is deemed reasonable.
The *Format classes handle conversion between Fortran and Python format, and
FortranFormatParser can create *Format instances from raw Fortran format
strings (e.g. '(3I4)', '(... | 8,916 | 27.764516 | 83 | py |
scipy | scipy-main/scipy/io/_harwell_boeing/__init__.py | from .hb import (MalformedHeader, hb_read, hb_write, HBInfo,
HBFile, HBMatrixType)
from ._fortran_format_parser import (FortranFormatParser, IntFormat,
ExpFormat, BadFortranFormat)
# Deprecated namespaces, to be removed in v2.0.0
from . import hb
__all__ = [
'Ma... | 574 | 30.944444 | 68 | py |
scipy | scipy-main/scipy/io/_harwell_boeing/tests/test_fortran_format.py | import numpy as np
from numpy.testing import assert_equal
from pytest import raises as assert_raises
from scipy.io._harwell_boeing import (
FortranFormatParser, IntFormat, ExpFormat, BadFortranFormat)
class TestFortranFormatParser:
def setup_method(self):
self.parser = FortranFormatParser()
... | 2,360 | 30.48 | 82 | py |
scipy | scipy-main/scipy/io/_harwell_boeing/tests/test_hb.py | from io import StringIO
import tempfile
import numpy as np
from numpy.testing import assert_equal, \
assert_array_almost_equal_nulp
from scipy.sparse import coo_matrix, csc_matrix, rand
from scipy.io import hb_read, hb_write
SIMPLE = """\
No Title ... | 2,284 | 33.621212 | 79 | py |
scipy | scipy-main/scipy/io/_harwell_boeing/tests/__init__.py | 0 | 0 | 0 | py | |
scipy | scipy-main/scipy/io/tests/test_paths.py | """
Ensure that we can use pathlib.Path objects in all relevant IO functions.
"""
from pathlib import Path
import numpy as np
import scipy.io
import scipy.io.wavfile
from scipy._lib._tmpdirs import tempdir
import scipy.sparse
class TestPaths:
data = np.arange(5).astype(np.int64)
def test_savemat(self):
... | 3,178 | 32.819149 | 81 | py |
scipy | scipy-main/scipy/io/tests/test_netcdf.py | ''' Tests for netcdf '''
import os
from os.path import join as pjoin, dirname
import shutil
import tempfile
import warnings
from io import BytesIO
from glob import glob
from contextlib import contextmanager
import numpy as np
from numpy.testing import (assert_, assert_allclose, assert_equal,
... | 19,313 | 34.503676 | 137 | py |
scipy | scipy-main/scipy/io/tests/test_fortran.py | ''' Tests for fortran sequential files '''
import tempfile
import shutil
from os import path
from glob import iglob
import re
from numpy.testing import assert_equal, assert_allclose
import numpy as np
import pytest
from scipy.io import (FortranFile,
_test_fortran,
FortranE... | 7,572 | 30.953586 | 92 | py |
scipy | scipy-main/scipy/io/tests/test_wavfile.py | import os
import sys
from io import BytesIO
import numpy as np
from numpy.testing import (assert_equal, assert_, assert_array_equal,
break_cycles, suppress_warnings, IS_PYPY)
import pytest
from pytest import raises, warns
from scipy.io import wavfile
def datafile(fn):
return os.path.j... | 15,303 | 35.70024 | 78 | py |
scipy | scipy-main/scipy/io/tests/__init__.py | 0 | 0 | 0 | py | |
scipy | scipy-main/scipy/io/tests/test_idl.py | from os import path
import warnings
import numpy as np
from numpy.testing import (assert_equal, assert_array_equal,
assert_, suppress_warnings)
import pytest
from scipy.io import readsav
from scipy.io import _idl
DATA_PATH = path.join(path.dirname(__file__), 'data')
def assert_identical(... | 19,680 | 43.426637 | 105 | py |
scipy | scipy-main/scipy/io/tests/test_mmio.py | from tempfile import mkdtemp
import os
import io
import shutil
import textwrap
import numpy as np
from numpy import array, transpose, pi
from numpy.testing import (assert_equal, assert_allclose,
assert_array_equal, assert_array_almost_equal)
import pytest
from pytest import raises as assert_... | 26,906 | 33.853627 | 86 | py |
scipy | scipy-main/scipy/_build_utils/setup.py | def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('_build_utils', parent_package, top_path)
config.add_data_dir('tests')
return config
if __name__ == '__main__':
from numpy.distutils.core import setup
setup(**configu... | 350 | 30.909091 | 68 | py |
scipy | scipy-main/scipy/_build_utils/tempita.py | import sys
import os
import argparse
from Cython import Tempita as tempita
# XXX: If this import ever fails (does it really?), vendor either
# cython.tempita or numpy/npy_tempita.
def process_tempita(fromfile, outfile=None):
"""Process tempita templated file and write out the result.
The template file is ex... | 1,672 | 29.981481 | 78 | py |
scipy | scipy-main/scipy/_build_utils/_fortran.py | import re
import os
import sys
from distutils.util import get_platform
import numpy as np
from .system_info import combine_dict
__all__ = ['needs_g77_abi_wrapper', 'get_g77_abi_wrappers',
'gfortran_legacy_flag_hook', 'blas_ilp64_pre_build_hook',
'get_f2py_int64_options', 'generic_pre_build_hoo... | 14,937 | 32.493274 | 90 | py |
scipy | scipy-main/scipy/_build_utils/__init__.py | import os
import numpy as np
from ._fortran import *
from .system_info import combine_dict
# Don't use the deprecated NumPy C API. Define this to a fixed version instead of
# NPY_API_VERSION in order not to break compilation for released SciPy versions
# when NumPy introduces a new deprecation. Use in setup.py::
#
#... | 1,084 | 29.138889 | 81 | py |
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