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env-llmeval/lib/python3.10/site-packages/scipy/fftpack/tests/fftw_double_ref.npz

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env-llmeval/lib/python3.10/site-packages/scipy/fftpack/tests/fftw_longdouble_ref.npz

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env-llmeval/lib/python3.10/site-packages/scipy/fftpack/tests/fftw_single_ref.npz

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+size 95144

env-llmeval/lib/python3.10/site-packages/scipy/fftpack/tests/test.npz

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+size 11968

env-llmeval/lib/python3.10/site-packages/scipy/io/__init__.py

@@ -0,0 +1,116 @@
+"""
+==================================
+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/devdocs/reference/routines.io.html>`__
+
+MATLAB® files
+=============
+
+.. autosummary::
+   :toctree: generated/
+
+   loadmat - Read a MATLAB style mat file (version 4 through 7.1)
+   savemat - Write a MATLAB style mat file (version 4 through 7.1)
+   whosmat - List contents of a MATLAB style mat file (version 4 through 7.1)
+
+For low-level MATLAB reading and writing utilities, see `scipy.io.matlab`.
+
+IDL® files
+==========
+
+.. autosummary::
+   :toctree: generated/
+
+   readsav - Read an IDL 'save' file
+
+Matrix Market files
+===================
+
+.. autosummary::
+   :toctree: generated/
+
+   mminfo - Query matrix info from Matrix Market formatted file
+   mmread - Read matrix from Matrix Market formatted file
+   mmwrite - Write matrix to Matrix Market formatted file
+
+Unformatted Fortran files
+===============================
+
+.. autosummary::
+   :toctree: generated/
+
+   FortranFile - A file object for unformatted sequential Fortran files
+   FortranEOFError - Exception indicating the end of a well-formed file
+   FortranFormattingError - Exception indicating an inappropriate end
+
+Netcdf
+======
+
+.. autosummary::
+   :toctree: generated/
+
+   netcdf_file - A file object for NetCDF data
+   netcdf_variable - A data object for the netcdf module
+
+Harwell-Boeing files
+====================
+
+.. autosummary::
+   :toctree: generated/
+
+   hb_read   -- read H-B file
+   hb_write  -- write H-B file
+
+Wav sound files (:mod:`scipy.io.wavfile`)
+=========================================
+
+.. module:: scipy.io.wavfile
+
+.. autosummary::
+   :toctree: generated/
+
+   read
+   write
+   WavFileWarning
+
+Arff files (:mod:`scipy.io.arff`)
+=================================
+
+.. module:: scipy.io.arff
+
+.. autosummary::
+   :toctree: generated/
+
+   loadarff
+   MetaData
+   ArffError
+   ParseArffError
+"""
+# matfile read and write
+from .matlab import loadmat, savemat, whosmat
+
+# netCDF file support
+from ._netcdf import netcdf_file, netcdf_variable
+
+# Fortran file support
+from ._fortran import FortranFile, FortranEOFError, FortranFormattingError
+
+from ._fast_matrix_market import mminfo, mmread, mmwrite
+from ._idl import readsav
+from ._harwell_boeing import hb_read, hb_write
+
+# Deprecated namespaces, to be removed in v2.0.0
+from . import arff, harwell_boeing, idl, mmio, netcdf, wavfile
+
+__all__ = [s for s in dir() if not s.startswith('_')]
+
+from scipy._lib._testutils import PytestTester
+test = PytestTester(__name__)
+del PytestTester

env-llmeval/lib/python3.10/site-packages/scipy/io/_fortran.py

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+"""
+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 that the file ended properly.
+
+    This error descends from TypeError because the code used to raise
+    TypeError (and this was the only way to know that the file had
+    ended) so users might have ``except TypeError:``.
+
+    """
+    pass
+
+
+class FortranFormattingError(TypeError, OSError):
+    """Indicates that the file ended mid-record.
+
+    Descends from TypeError for backward compatibility.
+
+    """
+    pass
+
+
+class FortranFile:
+    """
+    A file object for unformatted sequential files from Fortran code.
+
+    Parameters
+    ----------
+    filename : file or str
+        Open file object or filename.
+    mode : {'r', 'w'}, optional
+        Read-write mode, default is 'r'.
+    header_dtype : dtype, optional
+        Data type of the header. Size and endianness must match the input/output file.
+
+    Notes
+    -----
+    These files are broken up into records of unspecified types. The size of
+    each record is given at the start (although the size of this header is not
+    standard) and the data is written onto disk without any formatting. Fortran
+    compilers supporting the BACKSPACE statement will write a second copy of
+    the size to facilitate backwards seeking.
+
+    This class only supports files written with both sizes for the record.
+    It also does not support the subrecords used in Intel and gfortran compilers
+    for records which are greater than 2GB with a 4-byte header.
+
+    An example of an unformatted sequential file in Fortran would be written as::
+
+        OPEN(1, FILE=myfilename, FORM='unformatted')
+
+        WRITE(1) myvariable
+
+    Since this is a non-standard file format, whose contents depend on the
+    compiler and the endianness of the machine, caution is advised. Files from
+    gfortran 4.8.0 and gfortran 4.1.2 on x86_64 are known to work.
+
+    Consider using Fortran direct-access files or files from the newer Stream
+    I/O, which can be easily read by `numpy.fromfile`.
+
+    Examples
+    --------
+    To create an unformatted sequential Fortran file:
+
+    >>> from scipy.io import FortranFile
+    >>> import numpy as np
+    >>> f = FortranFile('test.unf', 'w')
+    >>> f.write_record(np.array([1,2,3,4,5], dtype=np.int32))
+    >>> f.write_record(np.linspace(0,1,20).reshape((5,4)).T)
+    >>> f.close()
+
+    To read this file:
+
+    >>> f = FortranFile('test.unf', 'r')
+    >>> print(f.read_ints(np.int32))
+    [1 2 3 4 5]
+    >>> print(f.read_reals(float).reshape((5,4), order="F"))
+    [[0.         0.05263158 0.10526316 0.15789474]
+     [0.21052632 0.26315789 0.31578947 0.36842105]
+     [0.42105263 0.47368421 0.52631579 0.57894737]
+     [0.63157895 0.68421053 0.73684211 0.78947368]
+     [0.84210526 0.89473684 0.94736842 1.        ]]
+    >>> f.close()
+
+    Or, in Fortran::
+
+        integer :: a(5), i
+        double precision :: b(5,4)
+        open(1, file='test.unf', form='unformatted')
+        read(1) a
+        read(1) b
+        close(1)
+        write(*,*) a
+        do i = 1, 5
+            write(*,*) b(i,:)
+        end do
+
+    """
+    def __init__(self, filename, mode='r', header_dtype=np.uint32):
+        if header_dtype is None:
+            raise ValueError('Must specify dtype')
+
+        header_dtype = np.dtype(header_dtype)
+        if header_dtype.kind != 'u':
+            warnings.warn("Given a dtype which is not unsigned.", stacklevel=2)
+
+        if mode not in 'rw' or len(mode) != 1:
+            raise ValueError('mode must be either r or w')
+
+        if hasattr(filename, 'seek'):
+            self._fp = filename
+        else:
+            self._fp = open(filename, '%sb' % mode)
+
+        self._header_dtype = header_dtype
+
+    def _read_size(self, eof_ok=False):
+        n = self._header_dtype.itemsize
+        b = self._fp.read(n)
+        if (not b) and eof_ok:
+            raise FortranEOFError("End of file occurred at end of record")
+        elif len(b) < n:
+            raise FortranFormattingError(
+                "End of file in the middle of the record size")
+        return int(np.frombuffer(b, dtype=self._header_dtype, count=1)[0])
+
+    def write_record(self, *items):
+        """
+        Write a record (including sizes) to the file.
+
+        Parameters
+        ----------
+        *items : array_like
+            The data arrays to write.
+
+        Notes
+        -----
+        Writes data items to a file::
+
+            write_record(a.T, b.T, c.T, ...)
+
+            write(1) a, b, c, ...
+
+        Note that data in multidimensional arrays is written in
+        row-major order --- to make them read correctly by Fortran
+        programs, you need to transpose the arrays yourself when
+        writing them.
+
+        """
+        items = tuple(np.asarray(item) for item in items)
+        total_size = sum(item.nbytes for item in items)
+
+        nb = np.array([total_size], dtype=self._header_dtype)
+
+        nb.tofile(self._fp)
+        for item in items:
+            item.tofile(self._fp)
+        nb.tofile(self._fp)
+
+    def read_record(self, *dtypes, **kwargs):
+        """
+        Reads a record of a given type from the file.
+
+        Parameters
+        ----------
+        *dtypes : dtypes, optional
+            Data type(s) specifying the size and endianness of the data.
+
+        Returns
+        -------
+        data : ndarray
+            A 1-D array object.
+
+        Raises
+        ------
+        FortranEOFError
+            To signal that no further records are available
+        FortranFormattingError
+            To signal that the end of the file was encountered
+            part-way through a record
+
+        Notes
+        -----
+        If the record contains a multidimensional array, you can specify
+        the size in the dtype. For example::
+
+            INTEGER var(5,4)
+
+        can be read with::
+
+            read_record('(4,5)i4').T
+
+        Note that this function does **not** assume the file data is in Fortran
+        column major order, so you need to (i) swap the order of dimensions
+        when reading and (ii) transpose the resulting array.
+
+        Alternatively, you can read the data as a 1-D array and handle the
+        ordering yourself. For example::
+
+            read_record('i4').reshape(5, 4, order='F')
+
+        For records that contain several variables or mixed types (as opposed
+        to single scalar or array types), give them as separate arguments::
+
+            double precision :: a
+            integer :: b
+            write(1) a, b
+
+            record = f.read_record('<f4', '<i4')
+            a = record[0]  # first number
+            b = record[1]  # second number
+
+        and if any of the variables are arrays, the shape can be specified as
+        the third item in the relevant dtype::
+
+            double precision :: a
+            integer :: b(3,4)
+            write(1) a, b
+
+            record = f.read_record('<f4', np.dtype(('<i4', (4, 3))))
+            a = record[0]
+            b = record[1].T
+
+        NumPy also supports a short syntax for this kind of type::
+
+            record = f.read_record('<f4', '(3,3)<i4')
+
+        See Also
+        --------
+        read_reals
+        read_ints
+
+        """
+        dtype = kwargs.pop('dtype', None)
+        if kwargs:
+            raise ValueError(f"Unknown keyword arguments {tuple(kwargs.keys())}")
+
+        if dtype is not None:
+            dtypes = dtypes + (dtype,)
+        elif not dtypes:
+            raise ValueError('Must specify at least one dtype')
+
+        first_size = self._read_size(eof_ok=True)
+
+        dtypes = tuple(np.dtype(dtype) for dtype in dtypes)
+        block_size = sum(dtype.itemsize for dtype in dtypes)
+
+        num_blocks, remainder = divmod(first_size, block_size)
+        if remainder != 0:
+            raise ValueError(f'Size obtained ({first_size}) is not a multiple of the '
+                             f'dtypes given ({block_size}).')
+
+        if len(dtypes) != 1 and first_size != block_size:
+            # Fortran does not write mixed type array items in interleaved order,
+            # and it's not possible to guess the sizes of the arrays that were written.
+            # The user must specify the exact sizes of each of the arrays.
+            raise ValueError(f'Size obtained ({first_size}) does not match with the '
+                             f'expected size ({block_size}) of multi-item record')
+
+        data = []
+        for dtype in dtypes:
+            r = np.fromfile(self._fp, dtype=dtype, count=num_blocks)
+            if len(r) != num_blocks:
+                raise FortranFormattingError(
+                    "End of file in the middle of a record")
+            if dtype.shape != ():
+                # Squeeze outmost block dimension for array items
+                if num_blocks == 1:
+                    assert r.shape == (1,) + dtype.shape
+                    r = r[0]
+
+            data.append(r)
+
+        second_size = self._read_size()
+        if first_size != second_size:
+            raise ValueError('Sizes do not agree in the header and footer for '
+                             'this record - check header dtype')
+
+        # Unpack result
+        if len(dtypes) == 1:
+            return data[0]
+        else:
+            return tuple(data)
+
+    def read_ints(self, dtype='i4'):
+        """
+        Reads a record of a given type from the file, defaulting to an integer
+        type (``INTEGER*4`` in Fortran).
+
+        Parameters
+        ----------
+        dtype : dtype, optional
+            Data type specifying the size and endianness of the data.
+
+        Returns
+        -------
+        data : ndarray
+            A 1-D array object.
+
+        See Also
+        --------
+        read_reals
+        read_record
+
+        """
+        return self.read_record(dtype)
+
+    def read_reals(self, dtype='f8'):
+        """
+        Reads a record of a given type from the file, defaulting to a floating
+        point number (``real*8`` in Fortran).
+
+        Parameters
+        ----------
+        dtype : dtype, optional
+            Data type specifying the size and endianness of the data.
+
+        Returns
+        -------
+        data : ndarray
+            A 1-D array object.
+
+        See Also
+        --------
+        read_ints
+        read_record
+
+        """
+        return self.read_record(dtype)
+
+    def close(self):
+        """
+        Closes the file. It is unsupported to call any other methods off this
+        object after closing it. Note that this class supports the 'with'
+        statement in modern versions of Python, to call this automatically
+
+        """
+        self._fp.close()
+
+    def __enter__(self):
+        return self
+
+    def __exit__(self, type, value, tb):
+        self.close()

env-llmeval/lib/python3.10/site-packages/scipy/io/_idl.py

@@ -0,0 +1,918 @@
+# 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 developed by with permission from ITT Visual Information
+# Systems. IDL(r) is a registered trademark of ITT Visual Information Systems,
+# Inc. for their Interactive Data Language software.
+
+# Permission is hereby granted, free of charge, to any person obtaining a
+# copy of this software and associated documentation files (the "Software"),
+# to deal in the Software without restriction, including without limitation
+# the rights to use, copy, modify, merge, publish, distribute, sublicense,
+# and/or sell copies of the Software, and to permit persons to whom the
+# Software is furnished to do so, subject to the following conditions:
+
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+# DEALINGS IN THE SOFTWARE.
+
+__all__ = ['readsav']
+
+import struct
+import numpy as np
+import tempfile
+import zlib
+import warnings
+
+# Define the different data types that can be found in an IDL save file
+DTYPE_DICT = {1: '>u1',
+              2: '>i2',
+              3: '>i4',
+              4: '>f4',
+              5: '>f8',
+              6: '>c8',
+              7: '|O',
+              8: '|O',
+              9: '>c16',
+              10: '|O',
+              11: '|O',
+              12: '>u2',
+              13: '>u4',
+              14: '>i8',
+              15: '>u8'}
+
+# Define the different record types that can be found in an IDL save file
+RECTYPE_DICT = {0: "START_MARKER",
+                1: "COMMON_VARIABLE",
+                2: "VARIABLE",
+                3: "SYSTEM_VARIABLE",
+                6: "END_MARKER",
+                10: "TIMESTAMP",
+                12: "COMPILED",
+                13: "IDENTIFICATION",
+                14: "VERSION",
+                15: "HEAP_HEADER",
+                16: "HEAP_DATA",
+                17: "PROMOTE64",
+                19: "NOTICE",
+                20: "DESCRIPTION"}
+
+# Define a dictionary to contain structure definitions
+STRUCT_DICT = {}
+
+
+def _align_32(f):
+    '''Align to the next 32-bit position in a file'''
+
+    pos = f.tell()
+    if pos % 4 != 0:
+        f.seek(pos + 4 - pos % 4)
+    return
+
+
+def _skip_bytes(f, n):
+    '''Skip `n` bytes'''
+    f.read(n)
+    return
+
+
+def _read_bytes(f, n):
+    '''Read the next `n` bytes'''
+    return f.read(n)
+
+
+def _read_byte(f):
+    '''Read a single byte'''
+    return np.uint8(struct.unpack('>B', f.read(4)[:1])[0])
+
+
+def _read_long(f):
+    '''Read a signed 32-bit integer'''
+    return np.int32(struct.unpack('>l', f.read(4))[0])
+
+
+def _read_int16(f):
+    '''Read a signed 16-bit integer'''
+    return np.int16(struct.unpack('>h', f.read(4)[2:4])[0])
+
+
+def _read_int32(f):
+    '''Read a signed 32-bit integer'''
+    return np.int32(struct.unpack('>i', f.read(4))[0])
+
+
+def _read_int64(f):
+    '''Read a signed 64-bit integer'''
+    return np.int64(struct.unpack('>q', f.read(8))[0])
+
+
+def _read_uint16(f):
+    '''Read an unsigned 16-bit integer'''
+    return np.uint16(struct.unpack('>H', f.read(4)[2:4])[0])
+
+
+def _read_uint32(f):
+    '''Read an unsigned 32-bit integer'''
+    return np.uint32(struct.unpack('>I', f.read(4))[0])
+
+
+def _read_uint64(f):
+    '''Read an unsigned 64-bit integer'''
+    return np.uint64(struct.unpack('>Q', f.read(8))[0])
+
+
+def _read_float32(f):
+    '''Read a 32-bit float'''
+    return np.float32(struct.unpack('>f', f.read(4))[0])
+
+
+def _read_float64(f):
+    '''Read a 64-bit float'''
+    return np.float64(struct.unpack('>d', f.read(8))[0])
+
+
+class Pointer:
+    '''Class used to define pointers'''
+
+    def __init__(self, index):
+        self.index = index
+        return
+
+
+class ObjectPointer(Pointer):
+    '''Class used to define object pointers'''
+    pass
+
+
+def _read_string(f):
+    '''Read a string'''
+    length = _read_long(f)
+    if length > 0:
+        chars = _read_bytes(f, length).decode('latin1')
+        _align_32(f)
+    else:
+        chars = ''
+    return chars
+
+
+def _read_string_data(f):
+    '''Read a data string (length is specified twice)'''
+    length = _read_long(f)
+    if length > 0:
+        length = _read_long(f)
+        string_data = _read_bytes(f, length)
+        _align_32(f)
+    else:
+        string_data = ''
+    return string_data
+
+
+def _read_data(f, dtype):
+    '''Read a variable with a specified data type'''
+    if dtype == 1:
+        if _read_int32(f) != 1:
+            raise Exception("Error occurred while reading byte variable")
+        return _read_byte(f)
+    elif dtype == 2:
+        return _read_int16(f)
+    elif dtype == 3:
+        return _read_int32(f)
+    elif dtype == 4:
+        return _read_float32(f)
+    elif dtype == 5:
+        return _read_float64(f)
+    elif dtype == 6:
+        real = _read_float32(f)
+        imag = _read_float32(f)
+        return np.complex64(real + imag * 1j)
+    elif dtype == 7:
+        return _read_string_data(f)
+    elif dtype == 8:
+        raise Exception("Should not be here - please report this")
+    elif dtype == 9:
+        real = _read_float64(f)
+        imag = _read_float64(f)
+        return np.complex128(real + imag * 1j)
+    elif dtype == 10:
+        return Pointer(_read_int32(f))
+    elif dtype == 11:
+        return ObjectPointer(_read_int32(f))
+    elif dtype == 12:
+        return _read_uint16(f)
+    elif dtype == 13:
+        return _read_uint32(f)
+    elif dtype == 14:
+        return _read_int64(f)
+    elif dtype == 15:
+        return _read_uint64(f)
+    else:
+        raise Exception("Unknown IDL type: %i - please report this" % dtype)
+
+
+def _read_structure(f, array_desc, struct_desc):
+    '''
+    Read a structure, with the array and structure descriptors given as
+    `array_desc` and `structure_desc` respectively.
+    '''
+
+    nrows = array_desc['nelements']
+    columns = struct_desc['tagtable']
+
+    dtype = []
+    for col in columns:
+        if col['structure'] or col['array']:
+            dtype.append(((col['name'].lower(), col['name']), np.object_))
+        else:
+            if col['typecode'] in DTYPE_DICT:
+                dtype.append(((col['name'].lower(), col['name']),
+                                    DTYPE_DICT[col['typecode']]))
+            else:
+                raise Exception("Variable type %i not implemented" %
+                                                            col['typecode'])
+
+    structure = np.rec.recarray((nrows, ), dtype=dtype)
+
+    for i in range(nrows):
+        for col in columns:
+            dtype = col['typecode']
+            if col['structure']:
+                structure[col['name']][i] = _read_structure(f,
+                                      struct_desc['arrtable'][col['name']],
+                                      struct_desc['structtable'][col['name']])
+            elif col['array']:
+                structure[col['name']][i] = _read_array(f, dtype,
+                                      struct_desc['arrtable'][col['name']])
+            else:
+                structure[col['name']][i] = _read_data(f, dtype)
+
+    # Reshape structure if needed
+    if array_desc['ndims'] > 1:
+        dims = array_desc['dims'][:int(array_desc['ndims'])]
+        dims.reverse()
+        structure = structure.reshape(dims)
+
+    return structure
+
+
+def _read_array(f, typecode, array_desc):
+    '''
+    Read an array of type `typecode`, with the array descriptor given as
+    `array_desc`.
+    '''
+
+    if typecode in [1, 3, 4, 5, 6, 9, 13, 14, 15]:
+
+        if typecode == 1:
+            nbytes = _read_int32(f)
+            if nbytes != array_desc['nbytes']:
+                warnings.warn("Not able to verify number of bytes from header",
+                              stacklevel=3)
+
+        # Read bytes as numpy array
+        array = np.frombuffer(f.read(array_desc['nbytes']),
+                              dtype=DTYPE_DICT[typecode])
+
+    elif typecode in [2, 12]:
+
+        # These are 2 byte types, need to skip every two as they are not packed
+
+        array = np.frombuffer(f.read(array_desc['nbytes']*2),
+                              dtype=DTYPE_DICT[typecode])[1::2]
+
+    else:
+
+        # Read bytes into list
+        array = []
+        for i in range(array_desc['nelements']):
+            dtype = typecode
+            data = _read_data(f, dtype)
+            array.append(data)
+
+        array = np.array(array, dtype=np.object_)
+
+    # Reshape array if needed
+    if array_desc['ndims'] > 1:
+        dims = array_desc['dims'][:int(array_desc['ndims'])]
+        dims.reverse()
+        array = array.reshape(dims)
+
+    # Go to next alignment position
+    _align_32(f)
+
+    return array
+
+
+def _read_record(f):
+    '''Function to read in a full record'''
+
+    record = {'rectype': _read_long(f)}
+
+    nextrec = _read_uint32(f)
+    nextrec += _read_uint32(f).astype(np.int64) * 2**32
+
+    _skip_bytes(f, 4)
+
+    if record['rectype'] not in RECTYPE_DICT:
+        raise Exception("Unknown RECTYPE: %i" % record['rectype'])
+
+    record['rectype'] = RECTYPE_DICT[record['rectype']]
+
+    if record['rectype'] in ["VARIABLE", "HEAP_DATA"]:
+
+        if record['rectype'] == "VARIABLE":
+            record['varname'] = _read_string(f)
+        else:
+            record['heap_index'] = _read_long(f)
+            _skip_bytes(f, 4)
+
+        rectypedesc = _read_typedesc(f)
+
+        if rectypedesc['typecode'] == 0:
+
+            if nextrec == f.tell():
+                record['data'] = None  # Indicates NULL value
+            else:
+                raise ValueError("Unexpected type code: 0")
+
+        else:
+
+            varstart = _read_long(f)
+            if varstart != 7:
+                raise Exception("VARSTART is not 7")
+
+            if rectypedesc['structure']:
+                record['data'] = _read_structure(f, rectypedesc['array_desc'],
+                                                    rectypedesc['struct_desc'])
+            elif rectypedesc['array']:
+                record['data'] = _read_array(f, rectypedesc['typecode'],
+                                                rectypedesc['array_desc'])
+            else:
+                dtype = rectypedesc['typecode']
+                record['data'] = _read_data(f, dtype)
+
+    elif record['rectype'] == "TIMESTAMP":
+
+        _skip_bytes(f, 4*256)
+        record['date'] = _read_string(f)
+        record['user'] = _read_string(f)
+        record['host'] = _read_string(f)
+
+    elif record['rectype'] == "VERSION":
+
+        record['format'] = _read_long(f)
+        record['arch'] = _read_string(f)
+        record['os'] = _read_string(f)
+        record['release'] = _read_string(f)
+
+    elif record['rectype'] == "IDENTIFICATON":
+
+        record['author'] = _read_string(f)
+        record['title'] = _read_string(f)
+        record['idcode'] = _read_string(f)
+
+    elif record['rectype'] == "NOTICE":
+
+        record['notice'] = _read_string(f)
+
+    elif record['rectype'] == "DESCRIPTION":
+
+        record['description'] = _read_string_data(f)
+
+    elif record['rectype'] == "HEAP_HEADER":
+
+        record['nvalues'] = _read_long(f)
+        record['indices'] = [_read_long(f) for _ in range(record['nvalues'])]
+
+    elif record['rectype'] == "COMMONBLOCK":
+
+        record['nvars'] = _read_long(f)
+        record['name'] = _read_string(f)
+        record['varnames'] = [_read_string(f) for _ in range(record['nvars'])]
+
+    elif record['rectype'] == "END_MARKER":
+
+        record['end'] = True
+
+    elif record['rectype'] == "UNKNOWN":
+
+        warnings.warn("Skipping UNKNOWN record", stacklevel=3)
+
+    elif record['rectype'] == "SYSTEM_VARIABLE":
+
+        warnings.warn("Skipping SYSTEM_VARIABLE record", stacklevel=3)
+
+    else:
+
+        raise Exception(f"record['rectype']={record['rectype']} not implemented")
+
+    f.seek(nextrec)
+
+    return record
+
+
+def _read_typedesc(f):
+    '''Function to read in a type descriptor'''
+
+    typedesc = {'typecode': _read_long(f), 'varflags': _read_long(f)}
+
+    if typedesc['varflags'] & 2 == 2:
+        raise Exception("System variables not implemented")
+
+    typedesc['array'] = typedesc['varflags'] & 4 == 4
+    typedesc['structure'] = typedesc['varflags'] & 32 == 32
+
+    if typedesc['structure']:
+        typedesc['array_desc'] = _read_arraydesc(f)
+        typedesc['struct_desc'] = _read_structdesc(f)
+    elif typedesc['array']:
+        typedesc['array_desc'] = _read_arraydesc(f)
+
+    return typedesc
+
+
+def _read_arraydesc(f):
+    '''Function to read in an array descriptor'''
+
+    arraydesc = {'arrstart': _read_long(f)}
+
+    if arraydesc['arrstart'] == 8:
+
+        _skip_bytes(f, 4)
+
+        arraydesc['nbytes'] = _read_long(f)
+        arraydesc['nelements'] = _read_long(f)
+        arraydesc['ndims'] = _read_long(f)
+
+        _skip_bytes(f, 8)
+
+        arraydesc['nmax'] = _read_long(f)
+
+        arraydesc['dims'] = [_read_long(f) for _ in range(arraydesc['nmax'])]
+
+    elif arraydesc['arrstart'] == 18:
+
+        warnings.warn("Using experimental 64-bit array read", stacklevel=3)
+
+        _skip_bytes(f, 8)
+
+        arraydesc['nbytes'] = _read_uint64(f)
+        arraydesc['nelements'] = _read_uint64(f)
+        arraydesc['ndims'] = _read_long(f)
+
+        _skip_bytes(f, 8)
+
+        arraydesc['nmax'] = 8
+
+        arraydesc['dims'] = []
+        for d in range(arraydesc['nmax']):
+            v = _read_long(f)
+            if v != 0:
+                raise Exception("Expected a zero in ARRAY_DESC")
+            arraydesc['dims'].append(_read_long(f))
+
+    else:
+
+        raise Exception("Unknown ARRSTART: %i" % arraydesc['arrstart'])
+
+    return arraydesc
+
+
+def _read_structdesc(f):
+    '''Function to read in a structure descriptor'''
+
+    structdesc = {}
+
+    structstart = _read_long(f)
+    if structstart != 9:
+        raise Exception("STRUCTSTART should be 9")
+
+    structdesc['name'] = _read_string(f)
+    predef = _read_long(f)
+    structdesc['ntags'] = _read_long(f)
+    structdesc['nbytes'] = _read_long(f)
+
+    structdesc['predef'] = predef & 1
+    structdesc['inherits'] = predef & 2
+    structdesc['is_super'] = predef & 4
+
+    if not structdesc['predef']:
+
+        structdesc['tagtable'] = [_read_tagdesc(f)
+                                  for _ in range(structdesc['ntags'])]
+
+        for tag in structdesc['tagtable']:
+            tag['name'] = _read_string(f)
+
+        structdesc['arrtable'] = {tag['name']: _read_arraydesc(f)
+                                  for tag in structdesc['tagtable']
+                                  if tag['array']}
+
+        structdesc['structtable'] = {tag['name']: _read_structdesc(f)
+                                     for tag in structdesc['tagtable']
+                                     if tag['structure']}
+
+        if structdesc['inherits'] or structdesc['is_super']:
+            structdesc['classname'] = _read_string(f)
+            structdesc['nsupclasses'] = _read_long(f)
+            structdesc['supclassnames'] = [
+                _read_string(f) for _ in range(structdesc['nsupclasses'])]
+            structdesc['supclasstable'] = [
+                _read_structdesc(f) for _ in range(structdesc['nsupclasses'])]
+
+        STRUCT_DICT[structdesc['name']] = structdesc
+
+    else:
+
+        if structdesc['name'] not in STRUCT_DICT:
+            raise Exception("PREDEF=1 but can't find definition")
+
+        structdesc = STRUCT_DICT[structdesc['name']]
+
+    return structdesc
+
+
+def _read_tagdesc(f):
+    '''Function to read in a tag descriptor'''
+
+    tagdesc = {'offset': _read_long(f)}
+
+    if tagdesc['offset'] == -1:
+        tagdesc['offset'] = _read_uint64(f)
+
+    tagdesc['typecode'] = _read_long(f)
+    tagflags = _read_long(f)
+
+    tagdesc['array'] = tagflags & 4 == 4
+    tagdesc['structure'] = tagflags & 32 == 32
+    tagdesc['scalar'] = tagdesc['typecode'] in DTYPE_DICT
+    # Assume '10'x is scalar
+
+    return tagdesc
+
+
+def _replace_heap(variable, heap):
+
+    if isinstance(variable, Pointer):
+
+        while isinstance(variable, Pointer):
+
+            if variable.index == 0:
+                variable = None
+            else:
+                if variable.index in heap:
+                    variable = heap[variable.index]
+                else:
+                    warnings.warn("Variable referenced by pointer not found "
+                                  "in heap: variable will be set to None",
+                                  stacklevel=3)
+                    variable = None
+
+        replace, new = _replace_heap(variable, heap)
+
+        if replace:
+            variable = new
+
+        return True, variable
+
+    elif isinstance(variable, np.rec.recarray):
+
+        # Loop over records
+        for ir, record in enumerate(variable):
+
+            replace, new = _replace_heap(record, heap)
+
+            if replace:
+                variable[ir] = new
+
+        return False, variable
+
+    elif isinstance(variable, np.record):
+
+        # Loop over values
+        for iv, value in enumerate(variable):
+
+            replace, new = _replace_heap(value, heap)
+
+            if replace:
+                variable[iv] = new
+
+        return False, variable
+
+    elif isinstance(variable, np.ndarray):
+
+        # Loop over values if type is np.object_
+        if variable.dtype.type is np.object_:
+
+            for iv in range(variable.size):
+
+                replace, new = _replace_heap(variable.item(iv), heap)
+
+                if replace:
+                    variable.reshape(-1)[iv] = new
+
+        return False, variable
+
+    else:
+
+        return False, variable
+
+
+class AttrDict(dict):
+    '''
+    A case-insensitive dictionary with access via item, attribute, and call
+    notations:
+
+        >>> from scipy.io._idl import AttrDict
+        >>> d = AttrDict()
+        >>> d['Variable'] = 123
+        >>> d['Variable']
+        123
+        >>> d.Variable
+        123
+        >>> d.variable
+        123
+        >>> d('VARIABLE')
+        123
+        >>> d['missing']
+        Traceback (most recent error last):
+        ...
+        KeyError: 'missing'
+        >>> d.missing
+        Traceback (most recent error last):
+        ...
+        AttributeError: 'AttrDict' object has no attribute 'missing'
+    '''
+
+    def __init__(self, init={}):
+        dict.__init__(self, init)
+
+    def __getitem__(self, name):
+        return super().__getitem__(name.lower())
+
+    def __setitem__(self, key, value):
+        return super().__setitem__(key.lower(), value)
+
+    def __getattr__(self, name):
+        try:
+            return self.__getitem__(name)
+        except KeyError:
+            raise AttributeError(
+                f"'{type(self)}' object has no attribute '{name}'") from None
+
+    __setattr__ = __setitem__
+    __call__ = __getitem__
+
+
+def readsav(file_name, idict=None, python_dict=False,
+            uncompressed_file_name=None, verbose=False):
+    """
+    Read an IDL .sav file.
+
+    Parameters
+    ----------
+    file_name : str
+        Name of the IDL save file.
+    idict : dict, optional
+        Dictionary in which to insert .sav file variables.
+    python_dict : bool, optional
+        By default, the object return is not a Python dictionary, but a
+        case-insensitive dictionary with item, attribute, and call access
+        to variables. To get a standard Python dictionary, set this option
+        to True.
+    uncompressed_file_name : str, optional
+        This option only has an effect for .sav files written with the
+        /compress option. If a file name is specified, compressed .sav
+        files are uncompressed to this file. Otherwise, readsav will use
+        the `tempfile` module to determine a temporary filename
+        automatically, and will remove the temporary file upon successfully
+        reading it in.
+    verbose : bool, optional
+        Whether to print out information about the save file, including
+        the records read, and available variables.
+
+    Returns
+    -------
+    idl_dict : AttrDict or dict
+        If `python_dict` is set to False (default), this function returns a
+        case-insensitive dictionary with item, attribute, and call access
+        to variables. If `python_dict` is set to True, this function
+        returns a Python dictionary with all variable names in lowercase.
+        If `idict` was specified, then variables are written to the
+        dictionary specified, and the updated dictionary is returned.
+
+    Examples
+    --------
+    >>> from os.path import dirname, join as pjoin
+    >>> import scipy.io as sio
+    >>> from scipy.io import readsav
+
+    Get the filename for an example .sav file from the tests/data directory.
+
+    >>> data_dir = pjoin(dirname(sio.__file__), 'tests', 'data')
+    >>> sav_fname = pjoin(data_dir, 'array_float32_1d.sav')
+
+    Load the .sav file contents.
+
+    >>> sav_data = readsav(sav_fname)
+
+    Get keys of the .sav file contents.
+
+    >>> print(sav_data.keys())
+    dict_keys(['array1d'])
+
+    Access a content with a key.
+
+    >>> print(sav_data['array1d'])
+    [0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
+     0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
+     0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
+     0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
+     0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
+     0. 0. 0.]
+
+    """
+
+    # Initialize record and variable holders
+    records = []
+    if python_dict or idict:
+        variables = {}
+    else:
+        variables = AttrDict()
+
+    # Open the IDL file
+    f = open(file_name, 'rb')
+
+    # Read the signature, which should be 'SR'
+    signature = _read_bytes(f, 2)
+    if signature != b'SR':
+        raise Exception("Invalid SIGNATURE: %s" % signature)
+
+    # Next, the record format, which is '\x00\x04' for normal .sav
+    # files, and '\x00\x06' for compressed .sav files.
+    recfmt = _read_bytes(f, 2)
+
+    if recfmt == b'\x00\x04':
+        pass
+
+    elif recfmt == b'\x00\x06':
+
+        if verbose:
+            print("IDL Save file is compressed")
+
+        if uncompressed_file_name:
+            fout = open(uncompressed_file_name, 'w+b')
+        else:
+            fout = tempfile.NamedTemporaryFile(suffix='.sav')
+
+        if verbose:
+            print(" -> expanding to %s" % fout.name)
+
+        # Write header
+        fout.write(b'SR\x00\x04')
+
+        # Cycle through records
+        while True:
+
+            # Read record type
+            rectype = _read_long(f)
+            fout.write(struct.pack('>l', int(rectype)))
+
+            # Read position of next record and return as int
+            nextrec = _read_uint32(f)
+            nextrec += _read_uint32(f).astype(np.int64) * 2**32
+
+            # Read the unknown 4 bytes
+            unknown = f.read(4)
+
+            # Check if the end of the file has been reached
+            if RECTYPE_DICT[rectype] == 'END_MARKER':
+                modval = np.int64(2**32)
+                fout.write(struct.pack('>I', int(nextrec) % modval))
+                fout.write(
+                    struct.pack('>I', int((nextrec - (nextrec % modval)) / modval))
+                )
+                fout.write(unknown)
+                break
+
+            # Find current position
+            pos = f.tell()
+
+            # Decompress record
+            rec_string = zlib.decompress(f.read(nextrec-pos))
+
+            # Find new position of next record
+            nextrec = fout.tell() + len(rec_string) + 12
+
+            # Write out record
+            fout.write(struct.pack('>I', int(nextrec % 2**32)))
+            fout.write(struct.pack('>I', int((nextrec - (nextrec % 2**32)) / 2**32)))
+            fout.write(unknown)
+            fout.write(rec_string)
+
+        # Close the original compressed file
+        f.close()
+
+        # Set f to be the decompressed file, and skip the first four bytes
+        f = fout
+        f.seek(4)
+
+    else:
+        raise Exception("Invalid RECFMT: %s" % recfmt)
+
+    # Loop through records, and add them to the list
+    while True:
+        r = _read_record(f)
+        records.append(r)
+        if 'end' in r:
+            if r['end']:
+                break
+
+    # Close the file
+    f.close()
+
+    # Find heap data variables
+    heap = {}
+    for r in records:
+        if r['rectype'] == "HEAP_DATA":
+            heap[r['heap_index']] = r['data']
+
+    # Find all variables
+    for r in records:
+        if r['rectype'] == "VARIABLE":
+            replace, new = _replace_heap(r['data'], heap)
+            if replace:
+                r['data'] = new
+            variables[r['varname'].lower()] = r['data']
+
+    if verbose:
+
+        # Print out timestamp info about the file
+        for record in records:
+            if record['rectype'] == "TIMESTAMP":
+                print("-"*50)
+                print("Date: %s" % record['date'])
+                print("User: %s" % record['user'])
+                print("Host: %s" % record['host'])
+                break
+
+        # Print out version info about the file
+        for record in records:
+            if record['rectype'] == "VERSION":
+                print("-"*50)
+                print("Format: %s" % record['format'])
+                print("Architecture: %s" % record['arch'])
+                print("Operating System: %s" % record['os'])
+                print("IDL Version: %s" % record['release'])
+                break
+
+        # Print out identification info about the file
+        for record in records:
+            if record['rectype'] == "IDENTIFICATON":
+                print("-"*50)
+                print("Author: %s" % record['author'])
+                print("Title: %s" % record['title'])
+                print("ID Code: %s" % record['idcode'])
+                break
+
+        # Print out descriptions saved with the file
+        for record in records:
+            if record['rectype'] == "DESCRIPTION":
+                print("-"*50)
+                print("Description: %s" % record['description'])
+                break
+
+        print("-"*50)
+        print("Successfully read %i records of which:" %
+                                            (len(records)))
+
+        # Create convenience list of record types
+        rectypes = [r['rectype'] for r in records]
+
+        for rt in set(rectypes):
+            if rt != 'END_MARKER':
+                print(" - %i are of type %s" % (rectypes.count(rt), rt))
+        print("-"*50)
+
+        if 'VARIABLE' in rectypes:
+            print("Available variables:")
+            for var in variables:
+                print(f" - {var} [{type(variables[var])}]")
+            print("-"*50)
+
+    if idict:
+        for var in variables:
+            idict[var] = variables[var]
+        return idict
+    else:
+        return variables

env-llmeval/lib/python3.10/site-packages/scipy/io/_mmio.py

@@ -0,0 +1,961 @@
+"""
+  Matrix Market I/O in Python.
+  See http://math.nist.gov/MatrixMarket/formats.html
+  for information about the Matrix Market format.
+"""
+#
+# Author: Pearu Peterson <[email protected]>
+# Created: October, 2004
+#
+# References:
+#  http://math.nist.gov/MatrixMarket/
+#
+import os
+
+import numpy as np
+from numpy import (asarray, real, imag, conj, zeros, ndarray, concatenate,
+                   ones, can_cast)
+
+from scipy.sparse import coo_matrix, issparse
+
+__all__ = ['mminfo', 'mmread', 'mmwrite', 'MMFile']
+
+
+# -----------------------------------------------------------------------------
+def asstr(s):
+    if isinstance(s, bytes):
+        return s.decode('latin1')
+    return str(s)
+
+
+def mminfo(source):
+    """
+    Return size and storage parameters from Matrix Market file-like 'source'.
+
+    Parameters
+    ----------
+    source : str or file-like
+        Matrix Market filename (extension .mtx) or open file-like object
+
+    Returns
+    -------
+    rows : int
+        Number of matrix rows.
+    cols : int
+        Number of matrix columns.
+    entries : int
+        Number of non-zero entries of a sparse matrix
+        or rows*cols for a dense matrix.
+    format : str
+        Either 'coordinate' or 'array'.
+    field : str
+        Either 'real', 'complex', 'pattern', or 'integer'.
+    symmetry : str
+        Either 'general', 'symmetric', 'skew-symmetric', or 'hermitian'.
+
+    Examples
+    --------
+    >>> from io import StringIO
+    >>> from scipy.io import mminfo
+
+    >>> text = '''%%MatrixMarket matrix coordinate real general
+    ...  5 5 7
+    ...  2 3 1.0
+    ...  3 4 2.0
+    ...  3 5 3.0
+    ...  4 1 4.0
+    ...  4 2 5.0
+    ...  4 3 6.0
+    ...  4 4 7.0
+    ... '''
+
+
+    ``mminfo(source)`` returns the number of rows, number of columns,
+    format, field type and symmetry attribute of the source file.
+
+    >>> mminfo(StringIO(text))
+    (5, 5, 7, 'coordinate', 'real', 'general')
+    """
+    return MMFile.info(source)
+
+# -----------------------------------------------------------------------------
+
+
+def mmread(source):
+    """
+    Reads the contents of a Matrix Market file-like 'source' into a matrix.
+
+    Parameters
+    ----------
+    source : str or file-like
+        Matrix Market filename (extensions .mtx, .mtz.gz)
+        or open file-like object.
+
+    Returns
+    -------
+    a : ndarray or coo_matrix
+        Dense or sparse matrix depending on the matrix format in the
+        Matrix Market file.
+
+    Examples
+    --------
+    >>> from io import StringIO
+    >>> from scipy.io import mmread
+
+    >>> text = '''%%MatrixMarket matrix coordinate real general
+    ...  5 5 7
+    ...  2 3 1.0
+    ...  3 4 2.0
+    ...  3 5 3.0
+    ...  4 1 4.0
+    ...  4 2 5.0
+    ...  4 3 6.0
+    ...  4 4 7.0
+    ... '''
+
+    ``mmread(source)`` returns the data as sparse matrix in COO format.
+
+    >>> m = mmread(StringIO(text))
+    >>> m
+    <5x5 sparse matrix of type '<class 'numpy.float64'>'
+    with 7 stored elements in COOrdinate format>
+    >>> m.A
+    array([[0., 0., 0., 0., 0.],
+           [0., 0., 1., 0., 0.],
+           [0., 0., 0., 2., 3.],
+           [4., 5., 6., 7., 0.],
+           [0., 0., 0., 0., 0.]])
+    """
+    return MMFile().read(source)
+
+# -----------------------------------------------------------------------------
+
+
+def mmwrite(target, a, comment='', field=None, precision=None, symmetry=None):
+    r"""
+    Writes the sparse or dense array `a` to Matrix Market file-like `target`.
+
+    Parameters
+    ----------
+    target : str or file-like
+        Matrix Market filename (extension .mtx) or open file-like object.
+    a : array like
+        Sparse or dense 2-D array.
+    comment : str, optional
+        Comments to be prepended to the Matrix Market file.
+    field : None or str, optional
+        Either 'real', 'complex', 'pattern', or 'integer'.
+    precision : None or int, optional
+        Number of digits to display for real or complex values.
+    symmetry : None or str, optional
+        Either 'general', 'symmetric', 'skew-symmetric', or 'hermitian'.
+        If symmetry is None the symmetry type of 'a' is determined by its
+        values.
+
+    Returns
+    -------
+    None
+
+    Examples
+    --------
+    >>> from io import BytesIO
+    >>> import numpy as np
+    >>> from scipy.sparse import coo_matrix
+    >>> from scipy.io import mmwrite
+
+    Write a small NumPy array to a matrix market file.  The file will be
+    written in the ``'array'`` format.
+
+    >>> a = np.array([[1.0, 0, 0, 0], [0, 2.5, 0, 6.25]])
+    >>> target = BytesIO()
+    >>> mmwrite(target, a)
+    >>> print(target.getvalue().decode('latin1'))
+    %%MatrixMarket matrix array real general
+    %
+    2 4
+    1.0000000000000000e+00
+    0.0000000000000000e+00
+    0.0000000000000000e+00
+    2.5000000000000000e+00
+    0.0000000000000000e+00
+    0.0000000000000000e+00
+    0.0000000000000000e+00
+    6.2500000000000000e+00
+
+    Add a comment to the output file, and set the precision to 3.
+
+    >>> target = BytesIO()
+    >>> mmwrite(target, a, comment='\n Some test data.\n', precision=3)
+    >>> print(target.getvalue().decode('latin1'))
+    %%MatrixMarket matrix array real general
+    %
+    % Some test data.
+    %
+    2 4
+    1.000e+00
+    0.000e+00
+    0.000e+00
+    2.500e+00
+    0.000e+00
+    0.000e+00
+    0.000e+00
+    6.250e+00
+
+    Convert to a sparse matrix before calling ``mmwrite``.  This will
+    result in the output format being ``'coordinate'`` rather than
+    ``'array'``.
+
+    >>> target = BytesIO()
+    >>> mmwrite(target, coo_matrix(a), precision=3)
+    >>> print(target.getvalue().decode('latin1'))
+    %%MatrixMarket matrix coordinate real general
+    %
+    2 4 3
+    1 1 1.00e+00
+    2 2 2.50e+00
+    2 4 6.25e+00
+
+    Write a complex Hermitian array to a matrix market file.  Note that
+    only six values are actually written to the file; the other values
+    are implied by the symmetry.
+
+    >>> z = np.array([[3, 1+2j, 4-3j], [1-2j, 1, -5j], [4+3j, 5j, 2.5]])
+    >>> z
+    array([[ 3. +0.j,  1. +2.j,  4. -3.j],
+           [ 1. -2.j,  1. +0.j, -0. -5.j],
+           [ 4. +3.j,  0. +5.j,  2.5+0.j]])
+
+    >>> target = BytesIO()
+    >>> mmwrite(target, z, precision=2)
+    >>> print(target.getvalue().decode('latin1'))
+    %%MatrixMarket matrix array complex hermitian
+    %
+    3 3
+    3.00e+00 0.00e+00
+    1.00e+00 -2.00e+00
+    4.00e+00 3.00e+00
+    1.00e+00 0.00e+00
+    0.00e+00 5.00e+00
+    2.50e+00 0.00e+00
+
+    """
+    MMFile().write(target, a, comment, field, precision, symmetry)
+
+
+###############################################################################
+class MMFile:
+    __slots__ = ('_rows',
+                 '_cols',
+                 '_entries',
+                 '_format',
+                 '_field',
+                 '_symmetry')
+
+    @property
+    def rows(self):
+        return self._rows
+
+    @property
+    def cols(self):
+        return self._cols
+
+    @property
+    def entries(self):
+        return self._entries
+
+    @property
+    def format(self):
+        return self._format
+
+    @property
+    def field(self):
+        return self._field
+
+    @property
+    def symmetry(self):
+        return self._symmetry
+
+    @property
+    def has_symmetry(self):
+        return self._symmetry in (self.SYMMETRY_SYMMETRIC,
+                                  self.SYMMETRY_SKEW_SYMMETRIC,
+                                  self.SYMMETRY_HERMITIAN)
+
+    # format values
+    FORMAT_COORDINATE = 'coordinate'
+    FORMAT_ARRAY = 'array'
+    FORMAT_VALUES = (FORMAT_COORDINATE, FORMAT_ARRAY)
+
+    @classmethod
+    def _validate_format(self, format):
+        if format not in self.FORMAT_VALUES:
+            msg = f'unknown format type {format}, must be one of {self.FORMAT_VALUES}'
+            raise ValueError(msg)
+
+    # field values
+    FIELD_INTEGER = 'integer'
+    FIELD_UNSIGNED = 'unsigned-integer'
+    FIELD_REAL = 'real'
+    FIELD_COMPLEX = 'complex'
+    FIELD_PATTERN = 'pattern'
+    FIELD_VALUES = (FIELD_INTEGER, FIELD_UNSIGNED, FIELD_REAL, FIELD_COMPLEX,
+                    FIELD_PATTERN)
+
+    @classmethod
+    def _validate_field(self, field):
+        if field not in self.FIELD_VALUES:
+            msg = f'unknown field type {field}, must be one of {self.FIELD_VALUES}'
+            raise ValueError(msg)
+
+    # symmetry values
+    SYMMETRY_GENERAL = 'general'
+    SYMMETRY_SYMMETRIC = 'symmetric'
+    SYMMETRY_SKEW_SYMMETRIC = 'skew-symmetric'
+    SYMMETRY_HERMITIAN = 'hermitian'
+    SYMMETRY_VALUES = (SYMMETRY_GENERAL, SYMMETRY_SYMMETRIC,
+                       SYMMETRY_SKEW_SYMMETRIC, SYMMETRY_HERMITIAN)
+
+    @classmethod
+    def _validate_symmetry(self, symmetry):
+        if symmetry not in self.SYMMETRY_VALUES:
+            raise ValueError(f'unknown symmetry type {symmetry}, '
+                             f'must be one of {self.SYMMETRY_VALUES}')
+
+    DTYPES_BY_FIELD = {FIELD_INTEGER: 'intp',
+                       FIELD_UNSIGNED: 'uint64',
+                       FIELD_REAL: 'd',
+                       FIELD_COMPLEX: 'D',
+                       FIELD_PATTERN: 'd'}
+
+    # -------------------------------------------------------------------------
+    @staticmethod
+    def reader():
+        pass
+
+    # -------------------------------------------------------------------------
+    @staticmethod
+    def writer():
+        pass
+
+    # -------------------------------------------------------------------------
+    @classmethod
+    def info(self, source):
+        """
+        Return size, storage parameters from Matrix Market file-like 'source'.
+
+        Parameters
+        ----------
+        source : str or file-like
+            Matrix Market filename (extension .mtx) or open file-like object
+
+        Returns
+        -------
+        rows : int
+            Number of matrix rows.
+        cols : int
+            Number of matrix columns.
+        entries : int
+            Number of non-zero entries of a sparse matrix
+            or rows*cols for a dense matrix.
+        format : str
+            Either 'coordinate' or 'array'.
+        field : str
+            Either 'real', 'complex', 'pattern', or 'integer'.
+        symmetry : str
+            Either 'general', 'symmetric', 'skew-symmetric', or 'hermitian'.
+        """
+
+        stream, close_it = self._open(source)
+
+        try:
+
+            # read and validate header line
+            line = stream.readline()
+            mmid, matrix, format, field, symmetry = \
+                (asstr(part.strip()) for part in line.split())
+            if not mmid.startswith('%%MatrixMarket'):
+                raise ValueError('source is not in Matrix Market format')
+            if not matrix.lower() == 'matrix':
+                raise ValueError("Problem reading file header: " + line)
+
+            # http://math.nist.gov/MatrixMarket/formats.html
+            if format.lower() == 'array':
+                format = self.FORMAT_ARRAY
+            elif format.lower() == 'coordinate':
+                format = self.FORMAT_COORDINATE
+
+            # skip comments
+            # line.startswith('%')
+            while line:
+                if line.lstrip() and line.lstrip()[0] in ['%', 37]:
+                    line = stream.readline()
+                else:
+                    break
+
+            # skip empty lines
+            while not line.strip():
+                line = stream.readline()
+
+            split_line = line.split()
+            if format == self.FORMAT_ARRAY:
+                if not len(split_line) == 2:
+                    raise ValueError("Header line not of length 2: " +
+                                     line.decode('ascii'))
+                rows, cols = map(int, split_line)
+                entries = rows * cols
+            else:
+                if not len(split_line) == 3:
+                    raise ValueError("Header line not of length 3: " +
+                                     line.decode('ascii'))
+                rows, cols, entries = map(int, split_line)
+
+            return (rows, cols, entries, format, field.lower(),
+                    symmetry.lower())
+
+        finally:
+            if close_it:
+                stream.close()
+
+    # -------------------------------------------------------------------------
+    @staticmethod
+    def _open(filespec, mode='rb'):
+        """ Return an open file stream for reading based on source.
+
+        If source is a file name, open it (after trying to find it with mtx and
+        gzipped mtx extensions). Otherwise, just return source.
+
+        Parameters
+        ----------
+        filespec : str or file-like
+            String giving file name or file-like object
+        mode : str, optional
+            Mode with which to open file, if `filespec` is a file name.
+
+        Returns
+        -------
+        fobj : file-like
+            Open file-like object.
+        close_it : bool
+            True if the calling function should close this file when done,
+            false otherwise.
+        """
+        # If 'filespec' is path-like (str, pathlib.Path, os.DirEntry, other class
+        # implementing a '__fspath__' method), try to convert it to str. If this
+        # fails by throwing a 'TypeError', assume it's an open file handle and
+        # return it as-is.
+        try:
+            filespec = os.fspath(filespec)
+        except TypeError:
+            return filespec, False
+
+        # 'filespec' is definitely a str now
+
+        # open for reading
+        if mode[0] == 'r':
+
+            # determine filename plus extension
+            if not os.path.isfile(filespec):
+                if os.path.isfile(filespec+'.mtx'):
+                    filespec = filespec + '.mtx'
+                elif os.path.isfile(filespec+'.mtx.gz'):
+                    filespec = filespec + '.mtx.gz'
+                elif os.path.isfile(filespec+'.mtx.bz2'):
+                    filespec = filespec + '.mtx.bz2'
+            # open filename
+            if filespec.endswith('.gz'):
+                import gzip
+                stream = gzip.open(filespec, mode)
+            elif filespec.endswith('.bz2'):
+                import bz2
+                stream = bz2.BZ2File(filespec, 'rb')
+            else:
+                stream = open(filespec, mode)
+
+        # open for writing
+        else:
+            if filespec[-4:] != '.mtx':
+                filespec = filespec + '.mtx'
+            stream = open(filespec, mode)
+
+        return stream, True
+
+    # -------------------------------------------------------------------------
+    @staticmethod
+    def _get_symmetry(a):
+        m, n = a.shape
+        if m != n:
+            return MMFile.SYMMETRY_GENERAL
+        issymm = True
+        isskew = True
+        isherm = a.dtype.char in 'FD'
+
+        # sparse input
+        if issparse(a):
+            # check if number of nonzero entries of lower and upper triangle
+            # matrix are equal
+            a = a.tocoo()
+            (row, col) = a.nonzero()
+            if (row < col).sum() != (row > col).sum():
+                return MMFile.SYMMETRY_GENERAL
+
+            # define iterator over symmetric pair entries
+            a = a.todok()
+
+            def symm_iterator():
+                for ((i, j), aij) in a.items():
+                    if i > j:
+                        aji = a[j, i]
+                        yield (aij, aji, False)
+                    elif i == j:
+                        yield (aij, aij, True)
+
+        # non-sparse input
+        else:
+            # define iterator over symmetric pair entries
+            def symm_iterator():
+                for j in range(n):
+                    for i in range(j, n):
+                        aij, aji = a[i][j], a[j][i]
+                        yield (aij, aji, i == j)
+
+        # check for symmetry
+        # yields aij, aji, is_diagonal
+        for (aij, aji, is_diagonal) in symm_iterator():
+            if isskew and is_diagonal and aij != 0:
+                isskew = False
+            else:
+                if issymm and aij != aji:
+                    issymm = False
+                with np.errstate(over="ignore"):
+                    # This can give a warning for uint dtypes, so silence that
+                    if isskew and aij != -aji:
+                        isskew = False
+                if isherm and aij != conj(aji):
+                    isherm = False
+            if not (issymm or isskew or isherm):
+                break
+
+        # return symmetry value
+        if issymm:
+            return MMFile.SYMMETRY_SYMMETRIC
+        if isskew:
+            return MMFile.SYMMETRY_SKEW_SYMMETRIC
+        if isherm:
+            return MMFile.SYMMETRY_HERMITIAN
+        return MMFile.SYMMETRY_GENERAL
+
+    # -------------------------------------------------------------------------
+    @staticmethod
+    def _field_template(field, precision):
+        return {MMFile.FIELD_REAL: '%%.%ie\n' % precision,
+                MMFile.FIELD_INTEGER: '%i\n',
+                MMFile.FIELD_UNSIGNED: '%u\n',
+                MMFile.FIELD_COMPLEX: '%%.%ie %%.%ie\n' %
+                    (precision, precision)
+                }.get(field, None)
+
+    # -------------------------------------------------------------------------
+    def __init__(self, **kwargs):
+        self._init_attrs(**kwargs)
+
+    # -------------------------------------------------------------------------
+    def read(self, source):
+        """
+        Reads the contents of a Matrix Market file-like 'source' into a matrix.
+
+        Parameters
+        ----------
+        source : str or file-like
+            Matrix Market filename (extensions .mtx, .mtz.gz)
+            or open file object.
+
+        Returns
+        -------
+        a : ndarray or coo_matrix
+            Dense or sparse matrix depending on the matrix format in the
+            Matrix Market file.
+        """
+        stream, close_it = self._open(source)
+
+        try:
+            self._parse_header(stream)
+            return self._parse_body(stream)
+
+        finally:
+            if close_it:
+                stream.close()
+
+    # -------------------------------------------------------------------------
+    def write(self, target, a, comment='', field=None, precision=None,
+              symmetry=None):
+        """
+        Writes sparse or dense array `a` to Matrix Market file-like `target`.
+
+        Parameters
+        ----------
+        target : str or file-like
+            Matrix Market filename (extension .mtx) or open file-like object.
+        a : array like
+            Sparse or dense 2-D array.
+        comment : str, optional
+            Comments to be prepended to the Matrix Market file.
+        field : None or str, optional
+            Either 'real', 'complex', 'pattern', or 'integer'.
+        precision : None or int, optional
+            Number of digits to display for real or complex values.
+        symmetry : None or str, optional
+            Either 'general', 'symmetric', 'skew-symmetric', or 'hermitian'.
+            If symmetry is None the symmetry type of 'a' is determined by its
+            values.
+        """
+
+        stream, close_it = self._open(target, 'wb')
+
+        try:
+            self._write(stream, a, comment, field, precision, symmetry)
+
+        finally:
+            if close_it:
+                stream.close()
+            else:
+                stream.flush()
+
+    # -------------------------------------------------------------------------
+    def _init_attrs(self, **kwargs):
+        """
+        Initialize each attributes with the corresponding keyword arg value
+        or a default of None
+        """
+
+        attrs = self.__class__.__slots__
+        public_attrs = [attr[1:] for attr in attrs]
+        invalid_keys = set(kwargs.keys()) - set(public_attrs)
+
+        if invalid_keys:
+            raise ValueError('''found {} invalid keyword arguments, please only
+                                use {}'''.format(tuple(invalid_keys),
+                                             public_attrs))
+
+        for attr in attrs:
+            setattr(self, attr, kwargs.get(attr[1:], None))
+
+    # -------------------------------------------------------------------------
+    def _parse_header(self, stream):
+        rows, cols, entries, format, field, symmetry = \
+            self.__class__.info(stream)
+        self._init_attrs(rows=rows, cols=cols, entries=entries, format=format,
+                         field=field, symmetry=symmetry)
+
+    # -------------------------------------------------------------------------
+    def _parse_body(self, stream):
+        rows, cols, entries, format, field, symm = (self.rows, self.cols,
+                                                    self.entries, self.format,
+                                                    self.field, self.symmetry)
+
+        dtype = self.DTYPES_BY_FIELD.get(field, None)
+
+        has_symmetry = self.has_symmetry
+        is_integer = field == self.FIELD_INTEGER
+        is_unsigned_integer = field == self.FIELD_UNSIGNED
+        is_complex = field == self.FIELD_COMPLEX
+        is_skew = symm == self.SYMMETRY_SKEW_SYMMETRIC
+        is_herm = symm == self.SYMMETRY_HERMITIAN
+        is_pattern = field == self.FIELD_PATTERN
+
+        if format == self.FORMAT_ARRAY:
+            a = zeros((rows, cols), dtype=dtype)
+            line = 1
+            i, j = 0, 0
+            if is_skew:
+                a[i, j] = 0
+                if i < rows - 1:
+                    i += 1
+            while line:
+                line = stream.readline()
+                # line.startswith('%')
+                if not line or line[0] in ['%', 37] or not line.strip():
+                    continue
+                if is_integer:
+                    aij = int(line)
+                elif is_unsigned_integer:
+                    aij = int(line)
+                elif is_complex:
+                    aij = complex(*map(float, line.split()))
+                else:
+                    aij = float(line)
+                a[i, j] = aij
+                if has_symmetry and i != j:
+                    if is_skew:
+                        a[j, i] = -aij
+                    elif is_herm:
+                        a[j, i] = conj(aij)
+                    else:
+                        a[j, i] = aij
+                if i < rows-1:
+                    i = i + 1
+                else:
+                    j = j + 1
+                    if not has_symmetry:
+                        i = 0
+                    else:
+                        i = j
+                        if is_skew:
+                            a[i, j] = 0
+                            if i < rows-1:
+                                i += 1
+
+            if is_skew:
+                if not (i in [0, j] and j == cols - 1):
+                    raise ValueError("Parse error, did not read all lines.")
+            else:
+                if not (i in [0, j] and j == cols):
+                    raise ValueError("Parse error, did not read all lines.")
+
+        elif format == self.FORMAT_COORDINATE:
+            # Read sparse COOrdinate format
+
+            if entries == 0:
+                # empty matrix
+                return coo_matrix((rows, cols), dtype=dtype)
+
+            I = zeros(entries, dtype='intc')
+            J = zeros(entries, dtype='intc')
+            if is_pattern:
+                V = ones(entries, dtype='int8')
+            elif is_integer:
+                V = zeros(entries, dtype='intp')
+            elif is_unsigned_integer:
+                V = zeros(entries, dtype='uint64')
+            elif is_complex:
+                V = zeros(entries, dtype='complex')
+            else:
+                V = zeros(entries, dtype='float')
+
+            entry_number = 0
+            for line in stream:
+                # line.startswith('%')
+                if not line or line[0] in ['%', 37] or not line.strip():
+                    continue
+
+                if entry_number+1 > entries:
+                    raise ValueError("'entries' in header is smaller than "
+                                     "number of entries")
+                l = line.split()
+                I[entry_number], J[entry_number] = map(int, l[:2])
+
+                if not is_pattern:
+                    if is_integer:
+                        V[entry_number] = int(l[2])
+                    elif is_unsigned_integer:
+                        V[entry_number] = int(l[2])
+                    elif is_complex:
+                        V[entry_number] = complex(*map(float, l[2:]))
+                    else:
+                        V[entry_number] = float(l[2])
+                entry_number += 1
+            if entry_number < entries:
+                raise ValueError("'entries' in header is larger than "
+                                 "number of entries")
+
+            I -= 1  # adjust indices (base 1 -> base 0)
+            J -= 1
+
+            if has_symmetry:
+                mask = (I != J)       # off diagonal mask
+                od_I = I[mask]
+                od_J = J[mask]
+                od_V = V[mask]
+
+                I = concatenate((I, od_J))
+                J = concatenate((J, od_I))
+
+                if is_skew:
+                    od_V *= -1
+                elif is_herm:
+                    od_V = od_V.conjugate()
+
+                V = concatenate((V, od_V))
+
+            a = coo_matrix((V, (I, J)), shape=(rows, cols), dtype=dtype)
+        else:
+            raise NotImplementedError(format)
+
+        return a
+
+    #  ------------------------------------------------------------------------
+    def _write(self, stream, a, comment='', field=None, precision=None,
+               symmetry=None):
+        if isinstance(a, list) or isinstance(a, ndarray) or \
+           isinstance(a, tuple) or hasattr(a, '__array__'):
+            rep = self.FORMAT_ARRAY
+            a = asarray(a)
+            if len(a.shape) != 2:
+                raise ValueError('Expected 2 dimensional array')
+            rows, cols = a.shape
+
+            if field is not None:
+
+                if field == self.FIELD_INTEGER:
+                    if not can_cast(a.dtype, 'intp'):
+                        raise OverflowError("mmwrite does not support integer "
+                                            "dtypes larger than native 'intp'.")
+                    a = a.astype('intp')
+                elif field == self.FIELD_REAL:
+                    if a.dtype.char not in 'fd':
+                        a = a.astype('d')
+                elif field == self.FIELD_COMPLEX:
+                    if a.dtype.char not in 'FD':
+                        a = a.astype('D')
+
+        else:
+            if not issparse(a):
+                raise ValueError('unknown matrix type: %s' % type(a))
+
+            rep = 'coordinate'
+            rows, cols = a.shape
+
+        typecode = a.dtype.char
+
+        if precision is None:
+            if typecode in 'fF':
+                precision = 8
+            else:
+                precision = 16
+        if field is None:
+            kind = a.dtype.kind
+            if kind == 'i':
+                if not can_cast(a.dtype, 'intp'):
+                    raise OverflowError("mmwrite does not support integer "
+                                        "dtypes larger than native 'intp'.")
+                field = 'integer'
+            elif kind == 'f':
+                field = 'real'
+            elif kind == 'c':
+                field = 'complex'
+            elif kind == 'u':
+                field = 'unsigned-integer'
+            else:
+                raise TypeError('unexpected dtype kind ' + kind)
+
+        if symmetry is None:
+            symmetry = self._get_symmetry(a)
+
+        # validate rep, field, and symmetry
+        self.__class__._validate_format(rep)
+        self.__class__._validate_field(field)
+        self.__class__._validate_symmetry(symmetry)
+
+        # write initial header line
+        data = f'%%MatrixMarket matrix {rep} {field} {symmetry}\n'
+        stream.write(data.encode('latin1'))
+
+        # write comments
+        for line in comment.split('\n'):
+            data = '%%%s\n' % (line)
+            stream.write(data.encode('latin1'))
+
+        template = self._field_template(field, precision)
+        # write dense format
+        if rep == self.FORMAT_ARRAY:
+            # write shape spec
+            data = '%i %i\n' % (rows, cols)
+            stream.write(data.encode('latin1'))
+
+            if field in (self.FIELD_INTEGER, self.FIELD_REAL,
+                         self.FIELD_UNSIGNED):
+                if symmetry == self.SYMMETRY_GENERAL:
+                    for j in range(cols):
+                        for i in range(rows):
+                            data = template % a[i, j]
+                            stream.write(data.encode('latin1'))
+
+                elif symmetry == self.SYMMETRY_SKEW_SYMMETRIC:
+                    for j in range(cols):
+                        for i in range(j + 1, rows):
+                            data = template % a[i, j]
+                            stream.write(data.encode('latin1'))
+
+                else:
+                    for j in range(cols):
+                        for i in range(j, rows):
+                            data = template % a[i, j]
+                            stream.write(data.encode('latin1'))
+
+            elif field == self.FIELD_COMPLEX:
+
+                if symmetry == self.SYMMETRY_GENERAL:
+                    for j in range(cols):
+                        for i in range(rows):
+                            aij = a[i, j]
+                            data = template % (real(aij), imag(aij))
+                            stream.write(data.encode('latin1'))
+                else:
+                    for j in range(cols):
+                        for i in range(j, rows):
+                            aij = a[i, j]
+                            data = template % (real(aij), imag(aij))
+                            stream.write(data.encode('latin1'))
+
+            elif field == self.FIELD_PATTERN:
+                raise ValueError('pattern type inconsisted with dense format')
+
+            else:
+                raise TypeError('Unknown field type %s' % field)
+
+        # write sparse format
+        else:
+            coo = a.tocoo()  # convert to COOrdinate format
+
+            # if symmetry format used, remove values above main diagonal
+            if symmetry != self.SYMMETRY_GENERAL:
+                lower_triangle_mask = coo.row >= coo.col
+                coo = coo_matrix((coo.data[lower_triangle_mask],
+                                 (coo.row[lower_triangle_mask],
+                                  coo.col[lower_triangle_mask])),
+                                 shape=coo.shape)
+
+            # write shape spec
+            data = '%i %i %i\n' % (rows, cols, coo.nnz)
+            stream.write(data.encode('latin1'))
+
+            template = self._field_template(field, precision-1)
+
+            if field == self.FIELD_PATTERN:
+                for r, c in zip(coo.row+1, coo.col+1):
+                    data = "%i %i\n" % (r, c)
+                    stream.write(data.encode('latin1'))
+            elif field in (self.FIELD_INTEGER, self.FIELD_REAL,
+                           self.FIELD_UNSIGNED):
+                for r, c, d in zip(coo.row+1, coo.col+1, coo.data):
+                    data = ("%i %i " % (r, c)) + (template % d)
+                    stream.write(data.encode('latin1'))
+            elif field == self.FIELD_COMPLEX:
+                for r, c, d in zip(coo.row+1, coo.col+1, coo.data):
+                    data = ("%i %i " % (r, c)) + (template % (d.real, d.imag))
+                    stream.write(data.encode('latin1'))
+            else:
+                raise TypeError('Unknown field type %s' % field)
+
+
+def _is_fromfile_compatible(stream):
+    """
+    Check whether `stream` is compatible with numpy.fromfile.
+
+    Passing a gzipped file object to ``fromfile/fromstring`` doesn't work with
+    Python 3.
+    """
+
+    bad_cls = []
+    try:
+        import gzip
+        bad_cls.append(gzip.GzipFile)
+    except ImportError:
+        pass
+    try:
+        import bz2
+        bad_cls.append(bz2.BZ2File)
+    except ImportError:
+        pass
+
+    bad_cls = tuple(bad_cls)
+    return not isinstance(stream, bad_cls)

env-llmeval/lib/python3.10/site-packages/scipy/io/_netcdf.py

@@ -0,0 +1,1095 @@
+"""
+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.
+
+This module implements the Scientific.IO.NetCDF API to read and create
+NetCDF files. The same API is also used in the PyNIO and pynetcdf
+modules, allowing these modules to be used interchangeably when working
+with NetCDF files.
+
+Only NetCDF3 is supported here; for NetCDF4 see
+`netCDF4-python <http://unidata.github.io/netcdf4-python/>`__,
+which has a similar API.
+
+"""
+
+# TODO:
+# * properly implement ``_FillValue``.
+# * fix character variables.
+# * implement PAGESIZE for Python 2.6?
+
+# The Scientific.IO.NetCDF API allows attributes to be added directly to
+# instances of ``netcdf_file`` and ``netcdf_variable``. To differentiate
+# between user-set attributes and instance attributes, user-set attributes
+# are automatically stored in the ``_attributes`` attribute by overloading
+#``__setattr__``. This is the reason why the code sometimes uses
+#``obj.__dict__['key'] = value``, instead of simply ``obj.key = value``;
+# otherwise the key would be inserted into userspace attributes.
+
+
+__all__ = ['netcdf_file', 'netcdf_variable']
+
+
+import warnings
+import weakref
+from operator import mul
+from platform import python_implementation
+
+import mmap as mm
+
+import numpy as np
+from numpy import frombuffer, dtype, empty, array, asarray
+from numpy import little_endian as LITTLE_ENDIAN
+from functools import reduce
+
+
+IS_PYPY = python_implementation() == 'PyPy'
+
+ABSENT = b'\x00\x00\x00\x00\x00\x00\x00\x00'
+ZERO = b'\x00\x00\x00\x00'
+NC_BYTE = b'\x00\x00\x00\x01'
+NC_CHAR = b'\x00\x00\x00\x02'
+NC_SHORT = b'\x00\x00\x00\x03'
+NC_INT = b'\x00\x00\x00\x04'
+NC_FLOAT = b'\x00\x00\x00\x05'
+NC_DOUBLE = b'\x00\x00\x00\x06'
+NC_DIMENSION = b'\x00\x00\x00\n'
+NC_VARIABLE = b'\x00\x00\x00\x0b'
+NC_ATTRIBUTE = b'\x00\x00\x00\x0c'
+FILL_BYTE = b'\x81'
+FILL_CHAR = b'\x00'
+FILL_SHORT = b'\x80\x01'
+FILL_INT = b'\x80\x00\x00\x01'
+FILL_FLOAT = b'\x7C\xF0\x00\x00'
+FILL_DOUBLE = b'\x47\x9E\x00\x00\x00\x00\x00\x00'
+
+TYPEMAP = {NC_BYTE: ('b', 1),
+           NC_CHAR: ('c', 1),
+           NC_SHORT: ('h', 2),
+           NC_INT: ('i', 4),
+           NC_FLOAT: ('f', 4),
+           NC_DOUBLE: ('d', 8)}
+
+FILLMAP = {NC_BYTE: FILL_BYTE,
+           NC_CHAR: FILL_CHAR,
+           NC_SHORT: FILL_SHORT,
+           NC_INT: FILL_INT,
+           NC_FLOAT: FILL_FLOAT,
+           NC_DOUBLE: FILL_DOUBLE}
+
+REVERSE = {('b', 1): NC_BYTE,
+           ('B', 1): NC_CHAR,
+           ('c', 1): NC_CHAR,
+           ('h', 2): NC_SHORT,
+           ('i', 4): NC_INT,
+           ('f', 4): NC_FLOAT,
+           ('d', 8): NC_DOUBLE,
+
+           # these come from asarray(1).dtype.char and asarray('foo').dtype.char,
+           # used when getting the types from generic attributes.
+           ('l', 4): NC_INT,
+           ('S', 1): NC_CHAR}
+
+
+class netcdf_file:
+    """
+    A file object for NetCDF data.
+
+    A `netcdf_file` object has two standard attributes: `dimensions` and
+    `variables`. The values of both are dictionaries, mapping dimension
+    names to their associated lengths and variable names to variables,
+    respectively. Application programs should never modify these
+    dictionaries.
+
+    All other attributes correspond to global attributes defined in the
+    NetCDF file. Global file attributes are created by assigning to an
+    attribute of the `netcdf_file` object.
+
+    Parameters
+    ----------
+    filename : string or file-like
+        string -> filename
+    mode : {'r', 'w', 'a'}, optional
+        read-write-append mode, default is 'r'
+    mmap : None or bool, optional
+        Whether to mmap `filename` when reading.  Default is True
+        when `filename` is a file name, False when `filename` is a
+        file-like object. Note that when mmap is in use, data arrays
+        returned refer directly to the mmapped data on disk, and the
+        file cannot be closed as long as references to it exist.
+    version : {1, 2}, optional
+        version of netcdf to read / write, where 1 means *Classic
+        format* and 2 means *64-bit offset format*.  Default is 1.  See
+        `here <https://docs.unidata.ucar.edu/nug/current/netcdf_introduction.html#select_format>`__
+        for more info.
+    maskandscale : bool, optional
+        Whether to automatically scale and/or mask data based on attributes.
+        Default is False.
+
+    Notes
+    -----
+    The major advantage of this module over other modules is that it doesn't
+    require the code to be linked to the NetCDF libraries. This module is
+    derived from `pupynere <https://bitbucket.org/robertodealmeida/pupynere/>`_.
+
+    NetCDF files are a self-describing binary data format. The file contains
+    metadata that describes the dimensions and variables in the file. More
+    details about NetCDF files can be found `here
+    <https://www.unidata.ucar.edu/software/netcdf/guide_toc.html>`__. There
+    are three main sections to a NetCDF data structure:
+
+    1. Dimensions
+    2. Variables
+    3. Attributes
+
+    The dimensions section records the name and length of each dimension used
+    by the variables. The variables would then indicate which dimensions it
+    uses and any attributes such as data units, along with containing the data
+    values for the variable. It is good practice to include a
+    variable that is the same name as a dimension to provide the values for
+    that axes. Lastly, the attributes section would contain additional
+    information such as the name of the file creator or the instrument used to
+    collect the data.
+
+    When writing data to a NetCDF file, there is often the need to indicate the
+    'record dimension'. A record dimension is the unbounded dimension for a
+    variable. For example, a temperature variable may have dimensions of
+    latitude, longitude and time. If one wants to add more temperature data to
+    the NetCDF file as time progresses, then the temperature variable should
+    have the time dimension flagged as the record dimension.
+
+    In addition, the NetCDF file header contains the position of the data in
+    the file, so access can be done in an efficient manner without loading
+    unnecessary data into memory. It uses the ``mmap`` module to create
+    Numpy arrays mapped to the data on disk, for the same purpose.
+
+    Note that when `netcdf_file` is used to open a file with mmap=True
+    (default for read-only), arrays returned by it refer to data
+    directly on the disk. The file should not be closed, and cannot be cleanly
+    closed when asked, if such arrays are alive. You may want to copy data arrays
+    obtained from mmapped Netcdf file if they are to be processed after the file
+    is closed, see the example below.
+
+    Examples
+    --------
+    To create a NetCDF file:
+
+    >>> from scipy.io import netcdf_file
+    >>> import numpy as np
+    >>> f = netcdf_file('simple.nc', 'w')
+    >>> f.history = 'Created for a test'
+    >>> f.createDimension('time', 10)
+    >>> time = f.createVariable('time', 'i', ('time',))
+    >>> time[:] = np.arange(10)
+    >>> time.units = 'days since 2008-01-01'
+    >>> f.close()
+
+    Note the assignment of ``arange(10)`` to ``time[:]``.  Exposing the slice
+    of the time variable allows for the data to be set in the object, rather
+    than letting ``arange(10)`` overwrite the ``time`` variable.
+
+    To read the NetCDF file we just created:
+
+    >>> from scipy.io import netcdf_file
+    >>> f = netcdf_file('simple.nc', 'r')
+    >>> print(f.history)
+    b'Created for a test'
+    >>> time = f.variables['time']
+    >>> print(time.units)
+    b'days since 2008-01-01'
+    >>> print(time.shape)
+    (10,)
+    >>> print(time[-1])
+    9
+
+    NetCDF files, when opened read-only, return arrays that refer
+    directly to memory-mapped data on disk:
+
+    >>> data = time[:]
+
+    If the data is to be processed after the file is closed, it needs
+    to be copied to main memory:
+
+    >>> data = time[:].copy()
+    >>> del time
+    >>> f.close()
+    >>> data.mean()
+    4.5
+
+    A NetCDF file can also be used as context manager:
+
+    >>> from scipy.io import netcdf_file
+    >>> with netcdf_file('simple.nc', 'r') as f:
+    ...     print(f.history)
+    b'Created for a test'
+
+    """
+    def __init__(self, filename, mode='r', mmap=None, version=1,
+                 maskandscale=False):
+        """Initialize netcdf_file from fileobj (str or file-like)."""
+        if mode not in 'rwa':
+            raise ValueError("Mode must be either 'r', 'w' or 'a'.")
+
+        if hasattr(filename, 'seek'):  # file-like
+            self.fp = filename
+            self.filename = 'None'
+            if mmap is None:
+                mmap = False
+            elif mmap and not hasattr(filename, 'fileno'):
+                raise ValueError('Cannot use file object for mmap')
+        else:  # maybe it's a string
+            self.filename = filename
+            omode = 'r+' if mode == 'a' else mode
+            self.fp = open(self.filename, '%sb' % omode)
+            if mmap is None:
+                # Mmapped files on PyPy cannot be usually closed
+                # before the GC runs, so it's better to use mmap=False
+                # as the default.
+                mmap = (not IS_PYPY)
+
+        if mode != 'r':
+            # Cannot read write-only files
+            mmap = False
+
+        self.use_mmap = mmap
+        self.mode = mode
+        self.version_byte = version
+        self.maskandscale = maskandscale
+
+        self.dimensions = {}
+        self.variables = {}
+
+        self._dims = []
+        self._recs = 0
+        self._recsize = 0
+
+        self._mm = None
+        self._mm_buf = None
+        if self.use_mmap:
+            self._mm = mm.mmap(self.fp.fileno(), 0, access=mm.ACCESS_READ)
+            self._mm_buf = np.frombuffer(self._mm, dtype=np.int8)
+
+        self._attributes = {}
+
+        if mode in 'ra':
+            self._read()
+
+    def __setattr__(self, attr, value):
+        # Store user defined attributes in a separate dict,
+        # so we can save them to file later.
+        try:
+            self._attributes[attr] = value
+        except AttributeError:
+            pass
+        self.__dict__[attr] = value
+
+    def close(self):
+        """Closes the NetCDF file."""
+        if hasattr(self, 'fp') and not self.fp.closed:
+            try:
+                self.flush()
+            finally:
+                self.variables = {}
+                if self._mm_buf is not None:
+                    ref = weakref.ref(self._mm_buf)
+                    self._mm_buf = None
+                    if ref() is None:
+                        # self._mm_buf is gc'd, and we can close the mmap
+                        self._mm.close()
+                    else:
+                        # we cannot close self._mm, since self._mm_buf is
+                        # alive and there may still be arrays referring to it
+                        warnings.warn(
+                            "Cannot close a netcdf_file opened with mmap=True, when "
+                            "netcdf_variables or arrays referring to its data still "
+                            "exist. All data arrays obtained from such files refer "
+                            "directly to data on disk, and must be copied before the "
+                            "file can be cleanly closed. "
+                            "(See netcdf_file docstring for more information on mmap.)",
+                            category=RuntimeWarning, stacklevel=2,
+                        )
+                self._mm = None
+                self.fp.close()
+    __del__ = close
+
+    def __enter__(self):
+        return self
+
+    def __exit__(self, type, value, traceback):
+        self.close()
+
+    def createDimension(self, name, length):
+        """
+        Adds a dimension to the Dimension section of the NetCDF data structure.
+
+        Note that this function merely adds a new dimension that the variables can
+        reference. The values for the dimension, if desired, should be added as
+        a variable using `createVariable`, referring to this dimension.
+
+        Parameters
+        ----------
+        name : str
+            Name of the dimension (Eg, 'lat' or 'time').
+        length : int
+            Length of the dimension.
+
+        See Also
+        --------
+        createVariable
+
+        """
+        if length is None and self._dims:
+            raise ValueError("Only first dimension may be unlimited!")
+
+        self.dimensions[name] = length
+        self._dims.append(name)
+
+    def createVariable(self, name, type, dimensions):
+        """
+        Create an empty variable for the `netcdf_file` object, specifying its data
+        type and the dimensions it uses.
+
+        Parameters
+        ----------
+        name : str
+            Name of the new variable.
+        type : dtype or str
+            Data type of the variable.
+        dimensions : sequence of str
+            List of the dimension names used by the variable, in the desired order.
+
+        Returns
+        -------
+        variable : netcdf_variable
+            The newly created ``netcdf_variable`` object.
+            This object has also been added to the `netcdf_file` object as well.
+
+        See Also
+        --------
+        createDimension
+
+        Notes
+        -----
+        Any dimensions to be used by the variable should already exist in the
+        NetCDF data structure or should be created by `createDimension` prior to
+        creating the NetCDF variable.
+
+        """
+        shape = tuple([self.dimensions[dim] for dim in dimensions])
+        shape_ = tuple([dim or 0 for dim in shape])  # replace None with 0 for NumPy
+
+        type = dtype(type)
+        typecode, size = type.char, type.itemsize
+        if (typecode, size) not in REVERSE:
+            raise ValueError("NetCDF 3 does not support type %s" % type)
+
+        # convert to big endian always for NetCDF 3
+        data = empty(shape_, dtype=type.newbyteorder("B"))
+        self.variables[name] = netcdf_variable(
+                data, typecode, size, shape, dimensions,
+                maskandscale=self.maskandscale)
+        return self.variables[name]
+
+    def flush(self):
+        """
+        Perform a sync-to-disk flush if the `netcdf_file` object is in write mode.
+
+        See Also
+        --------
+        sync : Identical function
+
+        """
+        if hasattr(self, 'mode') and self.mode in 'wa':
+            self._write()
+    sync = flush
+
+    def _write(self):
+        self.fp.seek(0)
+        self.fp.write(b'CDF')
+        self.fp.write(array(self.version_byte, '>b').tobytes())
+
+        # Write headers and data.
+        self._write_numrecs()
+        self._write_dim_array()
+        self._write_gatt_array()
+        self._write_var_array()
+
+    def _write_numrecs(self):
+        # Get highest record count from all record variables.
+        for var in self.variables.values():
+            if var.isrec and len(var.data) > self._recs:
+                self.__dict__['_recs'] = len(var.data)
+        self._pack_int(self._recs)
+
+    def _write_dim_array(self):
+        if self.dimensions:
+            self.fp.write(NC_DIMENSION)
+            self._pack_int(len(self.dimensions))
+            for name in self._dims:
+                self._pack_string(name)
+                length = self.dimensions[name]
+                self._pack_int(length or 0)  # replace None with 0 for record dimension
+        else:
+            self.fp.write(ABSENT)
+
+    def _write_gatt_array(self):
+        self._write_att_array(self._attributes)
+
+    def _write_att_array(self, attributes):
+        if attributes:
+            self.fp.write(NC_ATTRIBUTE)
+            self._pack_int(len(attributes))
+            for name, values in attributes.items():
+                self._pack_string(name)
+                self._write_att_values(values)
+        else:
+            self.fp.write(ABSENT)
+
+    def _write_var_array(self):
+        if self.variables:
+            self.fp.write(NC_VARIABLE)
+            self._pack_int(len(self.variables))
+
+            # Sort variable names non-recs first, then recs.
+            def sortkey(n):
+                v = self.variables[n]
+                if v.isrec:
+                    return (-1,)
+                return v._shape
+            variables = sorted(self.variables, key=sortkey, reverse=True)
+
+            # Set the metadata for all variables.
+            for name in variables:
+                self._write_var_metadata(name)
+            # Now that we have the metadata, we know the vsize of
+            # each record variable, so we can calculate recsize.
+            self.__dict__['_recsize'] = sum([
+                    var._vsize for var in self.variables.values()
+                    if var.isrec])
+            # Set the data for all variables.
+            for name in variables:
+                self._write_var_data(name)
+        else:
+            self.fp.write(ABSENT)
+
+    def _write_var_metadata(self, name):
+        var = self.variables[name]
+
+        self._pack_string(name)
+        self._pack_int(len(var.dimensions))
+        for dimname in var.dimensions:
+            dimid = self._dims.index(dimname)
+            self._pack_int(dimid)
+
+        self._write_att_array(var._attributes)
+
+        nc_type = REVERSE[var.typecode(), var.itemsize()]
+        self.fp.write(nc_type)
+
+        if not var.isrec:
+            vsize = var.data.size * var.data.itemsize
+            vsize += -vsize % 4
+        else:  # record variable
+            try:
+                vsize = var.data[0].size * var.data.itemsize
+            except IndexError:
+                vsize = 0
+            rec_vars = len([v for v in self.variables.values()
+                            if v.isrec])
+            if rec_vars > 1:
+                vsize += -vsize % 4
+        self.variables[name].__dict__['_vsize'] = vsize
+        self._pack_int(vsize)
+
+        # Pack a bogus begin, and set the real value later.
+        self.variables[name].__dict__['_begin'] = self.fp.tell()
+        self._pack_begin(0)
+
+    def _write_var_data(self, name):
+        var = self.variables[name]
+
+        # Set begin in file header.
+        the_beguine = self.fp.tell()
+        self.fp.seek(var._begin)
+        self._pack_begin(the_beguine)
+        self.fp.seek(the_beguine)
+
+        # Write data.
+        if not var.isrec:
+            self.fp.write(var.data.tobytes())
+            count = var.data.size * var.data.itemsize
+            self._write_var_padding(var, var._vsize - count)
+        else:  # record variable
+            # Handle rec vars with shape[0] < nrecs.
+            if self._recs > len(var.data):
+                shape = (self._recs,) + var.data.shape[1:]
+                # Resize in-place does not always work since
+                # the array might not be single-segment
+                try:
+                    var.data.resize(shape)
+                except ValueError:
+                    dtype = var.data.dtype
+                    var.__dict__['data'] = np.resize(var.data, shape).astype(dtype)
+
+            pos0 = pos = self.fp.tell()
+            for rec in var.data:
+                # Apparently scalars cannot be converted to big endian. If we
+                # try to convert a ``=i4`` scalar to, say, '>i4' the dtype
+                # will remain as ``=i4``.
+                if not rec.shape and (rec.dtype.byteorder == '<' or
+                        (rec.dtype.byteorder == '=' and LITTLE_ENDIAN)):
+                    rec = rec.byteswap()
+                self.fp.write(rec.tobytes())
+                # Padding
+                count = rec.size * rec.itemsize
+                self._write_var_padding(var, var._vsize - count)
+                pos += self._recsize
+                self.fp.seek(pos)
+            self.fp.seek(pos0 + var._vsize)
+
+    def _write_var_padding(self, var, size):
+        encoded_fill_value = var._get_encoded_fill_value()
+        num_fills = size // len(encoded_fill_value)
+        self.fp.write(encoded_fill_value * num_fills)
+
+    def _write_att_values(self, values):
+        if hasattr(values, 'dtype'):
+            nc_type = REVERSE[values.dtype.char, values.dtype.itemsize]
+        else:
+            types = [(int, NC_INT), (float, NC_FLOAT), (str, NC_CHAR)]
+
+            # bytes index into scalars in py3k. Check for "string" types
+            if isinstance(values, (str, bytes)):
+                sample = values
+            else:
+                try:
+                    sample = values[0]  # subscriptable?
+                except TypeError:
+                    sample = values     # scalar
+
+            for class_, nc_type in types:
+                if isinstance(sample, class_):
+                    break
+
+        typecode, size = TYPEMAP[nc_type]
+        dtype_ = '>%s' % typecode
+        # asarray() dies with bytes and '>c' in py3k. Change to 'S'
+        dtype_ = 'S' if dtype_ == '>c' else dtype_
+
+        values = asarray(values, dtype=dtype_)
+
+        self.fp.write(nc_type)
+
+        if values.dtype.char == 'S':
+            nelems = values.itemsize
+        else:
+            nelems = values.size
+        self._pack_int(nelems)
+
+        if not values.shape and (values.dtype.byteorder == '<' or
+                (values.dtype.byteorder == '=' and LITTLE_ENDIAN)):
+            values = values.byteswap()
+        self.fp.write(values.tobytes())
+        count = values.size * values.itemsize
+        self.fp.write(b'\x00' * (-count % 4))  # pad
+
+    def _read(self):
+        # Check magic bytes and version
+        magic = self.fp.read(3)
+        if not magic == b'CDF':
+            raise TypeError("Error: %s is not a valid NetCDF 3 file" %
+                            self.filename)
+        self.__dict__['version_byte'] = frombuffer(self.fp.read(1), '>b')[0]
+
+        # Read file headers and set data.
+        self._read_numrecs()
+        self._read_dim_array()
+        self._read_gatt_array()
+        self._read_var_array()
+
+    def _read_numrecs(self):
+        self.__dict__['_recs'] = self._unpack_int()
+
+    def _read_dim_array(self):
+        header = self.fp.read(4)
+        if header not in [ZERO, NC_DIMENSION]:
+            raise ValueError("Unexpected header.")
+        count = self._unpack_int()
+
+        for dim in range(count):
+            name = self._unpack_string().decode('latin1')
+            length = self._unpack_int() or None  # None for record dimension
+            self.dimensions[name] = length
+            self._dims.append(name)  # preserve order
+
+    def _read_gatt_array(self):
+        for k, v in self._read_att_array().items():
+            self.__setattr__(k, v)
+
+    def _read_att_array(self):
+        header = self.fp.read(4)
+        if header not in [ZERO, NC_ATTRIBUTE]:
+            raise ValueError("Unexpected header.")
+        count = self._unpack_int()
+
+        attributes = {}
+        for attr in range(count):
+            name = self._unpack_string().decode('latin1')
+            attributes[name] = self._read_att_values()
+        return attributes
+
+    def _read_var_array(self):
+        header = self.fp.read(4)
+        if header not in [ZERO, NC_VARIABLE]:
+            raise ValueError("Unexpected header.")
+
+        begin = 0
+        dtypes = {'names': [], 'formats': []}
+        rec_vars = []
+        count = self._unpack_int()
+        for var in range(count):
+            (name, dimensions, shape, attributes,
+             typecode, size, dtype_, begin_, vsize) = self._read_var()
+            # https://www.unidata.ucar.edu/software/netcdf/guide_toc.html
+            # Note that vsize is the product of the dimension lengths
+            # (omitting the record dimension) and the number of bytes
+            # per value (determined from the type), increased to the
+            # next multiple of 4, for each variable. If a record
+            # variable, this is the amount of space per record. The
+            # netCDF "record size" is calculated as the sum of the
+            # vsize's of all the record variables.
+            #
+            # The vsize field is actually redundant, because its value
+            # may be computed from other information in the header. The
+            # 32-bit vsize field is not large enough to contain the size
+            # of variables that require more than 2^32 - 4 bytes, so
+            # 2^32 - 1 is used in the vsize field for such variables.
+            if shape and shape[0] is None:  # record variable
+                rec_vars.append(name)
+                # The netCDF "record size" is calculated as the sum of
+                # the vsize's of all the record variables.
+                self.__dict__['_recsize'] += vsize
+                if begin == 0:
+                    begin = begin_
+                dtypes['names'].append(name)
+                dtypes['formats'].append(str(shape[1:]) + dtype_)
+
+                # Handle padding with a virtual variable.
+                if typecode in 'bch':
+                    actual_size = reduce(mul, (1,) + shape[1:]) * size
+                    padding = -actual_size % 4
+                    if padding:
+                        dtypes['names'].append('_padding_%d' % var)
+                        dtypes['formats'].append('(%d,)>b' % padding)
+
+                # Data will be set later.
+                data = None
+            else:  # not a record variable
+                # Calculate size to avoid problems with vsize (above)
+                a_size = reduce(mul, shape, 1) * size
+                if self.use_mmap:
+                    data = self._mm_buf[begin_:begin_+a_size].view(dtype=dtype_)
+                    data.shape = shape
+                else:
+                    pos = self.fp.tell()
+                    self.fp.seek(begin_)
+                    data = frombuffer(self.fp.read(a_size), dtype=dtype_
+                                      ).copy()
+                    data.shape = shape
+                    self.fp.seek(pos)
+
+            # Add variable.
+            self.variables[name] = netcdf_variable(
+                    data, typecode, size, shape, dimensions, attributes,
+                    maskandscale=self.maskandscale)
+
+        if rec_vars:
+            # Remove padding when only one record variable.
+            if len(rec_vars) == 1:
+                dtypes['names'] = dtypes['names'][:1]
+                dtypes['formats'] = dtypes['formats'][:1]
+
+            # Build rec array.
+            if self.use_mmap:
+                buf = self._mm_buf[begin:begin+self._recs*self._recsize]
+                rec_array = buf.view(dtype=dtypes)
+                rec_array.shape = (self._recs,)
+            else:
+                pos = self.fp.tell()
+                self.fp.seek(begin)
+                rec_array = frombuffer(self.fp.read(self._recs*self._recsize),
+                                       dtype=dtypes).copy()
+                rec_array.shape = (self._recs,)
+                self.fp.seek(pos)
+
+            for var in rec_vars:
+                self.variables[var].__dict__['data'] = rec_array[var]
+
+    def _read_var(self):
+        name = self._unpack_string().decode('latin1')
+        dimensions = []
+        shape = []
+        dims = self._unpack_int()
+
+        for i in range(dims):
+            dimid = self._unpack_int()
+            dimname = self._dims[dimid]
+            dimensions.append(dimname)
+            dim = self.dimensions[dimname]
+            shape.append(dim)
+        dimensions = tuple(dimensions)
+        shape = tuple(shape)
+
+        attributes = self._read_att_array()
+        nc_type = self.fp.read(4)
+        vsize = self._unpack_int()
+        begin = [self._unpack_int, self._unpack_int64][self.version_byte-1]()
+
+        typecode, size = TYPEMAP[nc_type]
+        dtype_ = '>%s' % typecode
+
+        return name, dimensions, shape, attributes, typecode, size, dtype_, begin, vsize
+
+    def _read_att_values(self):
+        nc_type = self.fp.read(4)
+        n = self._unpack_int()
+
+        typecode, size = TYPEMAP[nc_type]
+
+        count = n*size
+        values = self.fp.read(int(count))
+        self.fp.read(-count % 4)  # read padding
+
+        if typecode != 'c':
+            values = frombuffer(values, dtype='>%s' % typecode).copy()
+            if values.shape == (1,):
+                values = values[0]
+        else:
+            values = values.rstrip(b'\x00')
+        return values
+
+    def _pack_begin(self, begin):
+        if self.version_byte == 1:
+            self._pack_int(begin)
+        elif self.version_byte == 2:
+            self._pack_int64(begin)
+
+    def _pack_int(self, value):
+        self.fp.write(array(value, '>i').tobytes())
+    _pack_int32 = _pack_int
+
+    def _unpack_int(self):
+        return int(frombuffer(self.fp.read(4), '>i')[0])
+    _unpack_int32 = _unpack_int
+
+    def _pack_int64(self, value):
+        self.fp.write(array(value, '>q').tobytes())
+
+    def _unpack_int64(self):
+        return frombuffer(self.fp.read(8), '>q')[0]
+
+    def _pack_string(self, s):
+        count = len(s)
+        self._pack_int(count)
+        self.fp.write(s.encode('latin1'))
+        self.fp.write(b'\x00' * (-count % 4))  # pad
+
+    def _unpack_string(self):
+        count = self._unpack_int()
+        s = self.fp.read(count).rstrip(b'\x00')
+        self.fp.read(-count % 4)  # read padding
+        return s
+
+
+class netcdf_variable:
+    """
+    A data object for netcdf files.
+
+    `netcdf_variable` objects are constructed by calling the method
+    `netcdf_file.createVariable` on the `netcdf_file` object. `netcdf_variable`
+    objects behave much like array objects defined in numpy, except that their
+    data resides in a file. Data is read by indexing and written by assigning
+    to an indexed subset; the entire array can be accessed by the index ``[:]``
+    or (for scalars) by using the methods `getValue` and `assignValue`.
+    `netcdf_variable` objects also have attribute `shape` with the same meaning
+    as for arrays, but the shape cannot be modified. There is another read-only
+    attribute `dimensions`, whose value is the tuple of dimension names.
+
+    All other attributes correspond to variable attributes defined in
+    the NetCDF file. Variable attributes are created by assigning to an
+    attribute of the `netcdf_variable` object.
+
+    Parameters
+    ----------
+    data : array_like
+        The data array that holds the values for the variable.
+        Typically, this is initialized as empty, but with the proper shape.
+    typecode : dtype character code
+        Desired data-type for the data array.
+    size : int
+        Desired element size for the data array.
+    shape : sequence of ints
+        The shape of the array. This should match the lengths of the
+        variable's dimensions.
+    dimensions : sequence of strings
+        The names of the dimensions used by the variable. Must be in the
+        same order of the dimension lengths given by `shape`.
+    attributes : dict, optional
+        Attribute values (any type) keyed by string names. These attributes
+        become attributes for the netcdf_variable object.
+    maskandscale : bool, optional
+        Whether to automatically scale and/or mask data based on attributes.
+        Default is False.
+
+
+    Attributes
+    ----------
+    dimensions : list of str
+        List of names of dimensions used by the variable object.
+    isrec, shape
+        Properties
+
+    See also
+    --------
+    isrec, shape
+
+    """
+    def __init__(self, data, typecode, size, shape, dimensions,
+                 attributes=None,
+                 maskandscale=False):
+        self.data = data
+        self._typecode = typecode
+        self._size = size
+        self._shape = shape
+        self.dimensions = dimensions
+        self.maskandscale = maskandscale
+
+        self._attributes = attributes or {}
+        for k, v in self._attributes.items():
+            self.__dict__[k] = v
+
+    def __setattr__(self, attr, value):
+        # Store user defined attributes in a separate dict,
+        # so we can save them to file later.
+        try:
+            self._attributes[attr] = value
+        except AttributeError:
+            pass
+        self.__dict__[attr] = value
+
+    def isrec(self):
+        """Returns whether the variable has a record dimension or not.
+
+        A record dimension is a dimension along which additional data could be
+        easily appended in the netcdf data structure without much rewriting of
+        the data file. This attribute is a read-only property of the
+        `netcdf_variable`.
+
+        """
+        return bool(self.data.shape) and not self._shape[0]
+    isrec = property(isrec)
+
+    def shape(self):
+        """Returns the shape tuple of the data variable.
+
+        This is a read-only attribute and can not be modified in the
+        same manner of other numpy arrays.
+        """
+        return self.data.shape
+    shape = property(shape)
+
+    def getValue(self):
+        """
+        Retrieve a scalar value from a `netcdf_variable` of length one.
+
+        Raises
+        ------
+        ValueError
+            If the netcdf variable is an array of length greater than one,
+            this exception will be raised.
+
+        """
+        return self.data.item()
+
+    def assignValue(self, value):
+        """
+        Assign a scalar value to a `netcdf_variable` of length one.
+
+        Parameters
+        ----------
+        value : scalar
+            Scalar value (of compatible type) to assign to a length-one netcdf
+            variable. This value will be written to file.
+
+        Raises
+        ------
+        ValueError
+            If the input is not a scalar, or if the destination is not a length-one
+            netcdf variable.
+
+        """
+        if not self.data.flags.writeable:
+            # Work-around for a bug in NumPy.  Calling itemset() on a read-only
+            # memory-mapped array causes a seg. fault.
+            # See NumPy ticket #1622, and SciPy ticket #1202.
+            # This check for `writeable` can be removed when the oldest version
+            # of NumPy still supported by scipy contains the fix for #1622.
+            raise RuntimeError("variable is not writeable")
+
+        self.data[:] = value
+
+    def typecode(self):
+        """
+        Return the typecode of the variable.
+
+        Returns
+        -------
+        typecode : char
+            The character typecode of the variable (e.g., 'i' for int).
+
+        """
+        return self._typecode
+
+    def itemsize(self):
+        """
+        Return the itemsize of the variable.
+
+        Returns
+        -------
+        itemsize : int
+            The element size of the variable (e.g., 8 for float64).
+
+        """
+        return self._size
+
+    def __getitem__(self, index):
+        if not self.maskandscale:
+            return self.data[index]
+
+        data = self.data[index].copy()
+        missing_value = self._get_missing_value()
+        data = self._apply_missing_value(data, missing_value)
+        scale_factor = self._attributes.get('scale_factor')
+        add_offset = self._attributes.get('add_offset')
+        if add_offset is not None or scale_factor is not None:
+            data = data.astype(np.float64)
+        if scale_factor is not None:
+            data = data * scale_factor
+        if add_offset is not None:
+            data += add_offset
+
+        return data
+
+    def __setitem__(self, index, data):
+        if self.maskandscale:
+            missing_value = (
+                    self._get_missing_value() or
+                    getattr(data, 'fill_value', 999999))
+            self._attributes.setdefault('missing_value', missing_value)
+            self._attributes.setdefault('_FillValue', missing_value)
+            data = ((data - self._attributes.get('add_offset', 0.0)) /
+                    self._attributes.get('scale_factor', 1.0))
+            data = np.ma.asarray(data).filled(missing_value)
+            if self._typecode not in 'fd' and data.dtype.kind == 'f':
+                data = np.round(data)
+
+        # Expand data for record vars?
+        if self.isrec:
+            if isinstance(index, tuple):
+                rec_index = index[0]
+            else:
+                rec_index = index
+            if isinstance(rec_index, slice):
+                recs = (rec_index.start or 0) + len(data)
+            else:
+                recs = rec_index + 1
+            if recs > len(self.data):
+                shape = (recs,) + self._shape[1:]
+                # Resize in-place does not always work since
+                # the array might not be single-segment
+                try:
+                    self.data.resize(shape)
+                except ValueError:
+                    dtype = self.data.dtype
+                    self.__dict__['data'] = np.resize(self.data, shape).astype(dtype)
+        self.data[index] = data
+
+    def _default_encoded_fill_value(self):
+        """
+        The default encoded fill-value for this Variable's data type.
+        """
+        nc_type = REVERSE[self.typecode(), self.itemsize()]
+        return FILLMAP[nc_type]
+
+    def _get_encoded_fill_value(self):
+        """
+        Returns the encoded fill value for this variable as bytes.
+
+        This is taken from either the _FillValue attribute, or the default fill
+        value for this variable's data type.
+        """
+        if '_FillValue' in self._attributes:
+            fill_value = np.array(self._attributes['_FillValue'],
+                                  dtype=self.data.dtype).tobytes()
+            if len(fill_value) == self.itemsize():
+                return fill_value
+            else:
+                return self._default_encoded_fill_value()
+        else:
+            return self._default_encoded_fill_value()
+
+    def _get_missing_value(self):
+        """
+        Returns the value denoting "no data" for this variable.
+
+        If this variable does not have a missing/fill value, returns None.
+
+        If both _FillValue and missing_value are given, give precedence to
+        _FillValue. The netCDF standard gives special meaning to _FillValue;
+        missing_value is  just used for compatibility with old datasets.
+        """
+
+        if '_FillValue' in self._attributes:
+            missing_value = self._attributes['_FillValue']
+        elif 'missing_value' in self._attributes:
+            missing_value = self._attributes['missing_value']
+        else:
+            missing_value = None
+
+        return missing_value
+
+    @staticmethod
+    def _apply_missing_value(data, missing_value):
+        """
+        Applies the given missing value to the data array.
+
+        Returns a numpy.ma array, with any value equal to missing_value masked
+        out (unless missing_value is None, in which case the original array is
+        returned).
+        """
+
+        if missing_value is None:
+            newdata = data
+        else:
+            try:
+                missing_value_isnan = np.isnan(missing_value)
+            except (TypeError, NotImplementedError):
+                # some data types (e.g., characters) cannot be tested for NaN
+                missing_value_isnan = False
+
+            if missing_value_isnan:
+                mymask = np.isnan(data)
+            else:
+                mymask = (data == missing_value)
+
+            newdata = np.ma.masked_where(mymask, data)
+
+        return newdata
+
+
+NetCDFFile = netcdf_file
+NetCDFVariable = netcdf_variable

env-llmeval/lib/python3.10/site-packages/scipy/io/harwell_boeing.py

@@ -0,0 +1,21 @@
+# 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.
+
+from scipy._lib.deprecation import _sub_module_deprecation
+
+__all__ = [  # noqa: F822
+    'MalformedHeader', 'hb_read', 'hb_write', 'HBInfo',
+    'HBFile', 'HBMatrixType', 'FortranFormatParser', 'IntFormat',
+    'ExpFormat', 'BadFortranFormat', 'hb'
+]
+
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    return _sub_module_deprecation(sub_package="io", module="harwell_boeing",
+                                   private_modules=["_harwell_boeing"], all=__all__,
+                                   attribute=name)

env-llmeval/lib/python3.10/site-packages/scipy/io/idl.py

@@ -0,0 +1,20 @@
+# 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.
+
+from scipy._lib.deprecation import _sub_module_deprecation
+
+__all__ = [  # noqa: F822
+    'readsav', 'DTYPE_DICT', 'RECTYPE_DICT', 'STRUCT_DICT',
+    'Pointer', 'ObjectPointer', 'AttrDict'
+]
+
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    return _sub_module_deprecation(sub_package="io", module="idl",
+                                   private_modules=["_idl"], all=__all__,
+                                   attribute=name)

env-llmeval/lib/python3.10/site-packages/scipy/io/matlab/byteordercodes.py

@@ -0,0 +1,20 @@
+# 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.
+
+from scipy._lib.deprecation import _sub_module_deprecation
+
+__all__ = [  # noqa: F822
+    'aliases', 'native_code', 'swapped_code',
+    'sys_is_le', 'to_numpy_code'
+]
+
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    return _sub_module_deprecation(sub_package="io.matlab", module="byteordercodes",
+                                   private_modules=["_byteordercodes"], all=__all__,
+                                   attribute=name)

env-llmeval/lib/python3.10/site-packages/scipy/io/matlab/mio5_params.py

@@ -0,0 +1,28 @@
+# 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.
+
+from scipy._lib.deprecation import _sub_module_deprecation
+
+__all__ = [  # noqa: F822
+    'MDTYPES', 'MatlabFunction', 'MatlabObject', 'MatlabOpaque',
+    'NP_TO_MTYPES', 'NP_TO_MXTYPES', 'OPAQUE_DTYPE', 'codecs_template',
+    'mat_struct', 'mclass_dtypes_template', 'mclass_info', 'mdtypes_template',
+    'miCOMPRESSED', 'miDOUBLE', 'miINT16', 'miINT32', 'miINT64', 'miINT8',
+    'miMATRIX', 'miSINGLE', 'miUINT16', 'miUINT32', 'miUINT64', 'miUINT8',
+    'miUTF16', 'miUTF32', 'miUTF8', 'mxCELL_CLASS', 'mxCHAR_CLASS',
+    'mxDOUBLE_CLASS', 'mxFUNCTION_CLASS', 'mxINT16_CLASS', 'mxINT32_CLASS',
+    'mxINT64_CLASS', 'mxINT8_CLASS', 'mxOBJECT_CLASS',
+    'mxOBJECT_CLASS_FROM_MATRIX_H', 'mxOPAQUE_CLASS', 'mxSINGLE_CLASS',
+    'mxSPARSE_CLASS', 'mxSTRUCT_CLASS', 'mxUINT16_CLASS', 'mxUINT32_CLASS',
+    'mxUINT64_CLASS', 'mxUINT8_CLASS', 'convert_dtypes'
+]
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    return _sub_module_deprecation(sub_package="io.matlab", module="mio5_params",
+                                   private_modules=["_mio5_params"], all=__all__,
+                                   attribute=name)

env-llmeval/lib/python3.10/site-packages/scipy/io/matlab/streams.py

@@ -0,0 +1,18 @@
+# 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.
+
+from scipy._lib.deprecation import _sub_module_deprecation
+
+__all__ = [  # noqa: F822
+    'BLOCK_SIZE', 'GenericStream', 'ZlibInputStream', 'make_stream'
+]
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    return _sub_module_deprecation(sub_package="io.matlab", module="streams",
+                                   private_modules=["_streams"], all=__all__,
+                                   attribute=name)

env-llmeval/lib/python3.10/site-packages/scipy/io/netcdf.py

@@ -0,0 +1,25 @@
+# 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.
+
+from scipy._lib.deprecation import _sub_module_deprecation
+
+__all__ = [  # noqa: F822
+    'netcdf_file', 'netcdf_variable',
+    'array', 'LITTLE_ENDIAN', 'IS_PYPY', 'ABSENT', 'ZERO',
+    'NC_BYTE', 'NC_CHAR', 'NC_SHORT', 'NC_INT', 'NC_FLOAT',
+    'NC_DOUBLE', 'NC_DIMENSION', 'NC_VARIABLE', 'NC_ATTRIBUTE',
+    'FILL_BYTE', 'FILL_CHAR', 'FILL_SHORT', 'FILL_INT', 'FILL_FLOAT',
+    'FILL_DOUBLE', 'TYPEMAP', 'FILLMAP', 'REVERSE', 'NetCDFFile',
+    'NetCDFVariable'
+]
+
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    return _sub_module_deprecation(sub_package="io", module="netcdf",
+                                   private_modules=["_netcdf"], all=__all__,
+                                   attribute=name)