Overview ========
    This Python package provides high level utilities to read/write a
    variety of Python types to/from HDF5 (Heirarchal Data Format) formatted
    files. This package also provides support for MATLAB MAT v7.3 formatted
    files, which are just HDF5 files with a different extension and some
    extra meta-data.

    All of this is done without pickling data. Pickling is bad for security
    because it allows arbitrary code to be executed in the interpreter. One
    wants to be able to read possibly HDF5 and MAT files from untrusted
    sources, so pickling is avoided in this package.

    The package's documetation is found at
    http://pythonhosted.org/hdf5storage/

    The package's source code is found at
    https://github.com/frejanordsiek/hdf5storage

    The package is licensed under a 2-clause BSD license
    (https://github.com/frejanordsiek/hdf5storage/blob/master/COPYING.txt).

    Installation
    ============

    This package only supports Python >= 2.6.

    This package requires the numpy and h5py (>= 2.1) packages. An optional
    dependency is the scipy package.

    To install hdf5storage, download the package and run the command on
    Python 3 ::

        python3 setup.py install

    or the command on Python 2 ::

        python setup.py install

    Python 2
    ========

    This package was designed and written for Python 3, with Python 2.7 and
    2.6 support added later. This does mean that a few things are a little
    clunky in Python 2. Examples include requiring ``unicode`` keys for
    dictionaries, the ``int`` and ``long`` types both being mapped to the
    Python 3 ``int`` type, etc. The storage format's metadata looks more
    familiar from a Python 3 standpoint as well.

    The documentation is written in terms of Python 3 syntax and types
    primarily. Important Python 2 information beyond direct translations of
    syntax and types will be pointed out.

    Hierarchal Data Format 5 (HDF5)
    ===============================

    HDF5 files (see http://www.hdfgroup.org/HDF5/) are a commonly used file
    format for exchange of numerical data. It has built in support for a
    large variety of number formats (un/signed integers, floating point
    numbers, strings, etc.) as scalars and arrays, enums and compound types.
    It also handles differences in data representation on different hardware
    platforms (endianness, different floating point formats, etc.). As can
    be imagined from the name, data is represented in an HDF5 file in a
    hierarchal form modelling a Unix filesystem (Datasets are equivalent to
    files, Groups are equivalent to directories, and links are supported).

    This package interfaces HDF5 files using the h5py package
    (http://www.h5py.org/) as opposed to the PyTables package
    (http://www.pytables.org/).

    MATLAB MAT v7.3 file support
    ============================

    MATLAB (http://www.mathworks.com/) MAT files version 7.3 and later are
    HDF5 files with a different file extension (``.mat``) and a very
    specific set of meta-data and storage conventions. This package provides
    read and write support for a limited set of Python and MATLAB types.

    SciPy (http://scipy.org/) has functions to read and write the older MAT
    file formats. This package has functions modeled after the
    ``scipy.io.savemat`` and ``scipy.io.loadmat`` functions, that have the
    same names and similar arguments. The dispatch to the SciPy versions if
    the MAT file format is not an HDF5 based one.

    Supported Types
    ===============

    The supported Python and MATLAB types are given in the tables below.
    The tables assume that one has imported collections and numpy as::

        import collections as cl
        import numpy as np

    The table gives which Python types can be read and written, the first
    version of this package to support it, the numpy type it gets
    converted to for storage (if type information is not written, that
    will be what it is read back as) the MATLAB class it becomes if
    targetting a MAT file, and the first version of this package to
    support writing it so MATlAB can read it.

    ===============  =======  ==========================  ===========  ==============
    Python                                                MATLAB
    ----------------------------------------------------  ---------------------------
    Type             Version  Converted to                Class        Version
    ===============  =======  ==========================  ===========  ==============
    bool             0.1      np.bool\_ or np.uint8       logical      0.1 [1]_
    None             0.1      ``np.float64([])``          ``[]``       0.1
    int [2]_ [3]_    0.1      np.int64 [2]_               int64        0.1
    long [3]_ [4]_   0.1      np.int64                    int64        0.1
    float            0.1      np.float64                  double       0.1
    complex          0.1      np.complex128               double       0.1
    str              0.1      np.uint32/16                char         0.1 [5]_
    bytes            0.1      np.bytes\_ or np.uint16     char         0.1 [6]_
    bytearray        0.1      np.bytes\_ or np.uint16     char         0.1 [6]_
    list             0.1      np.object\_                 cell         0.1
    tuple            0.1      np.object\_                 cell         0.1
    set              0.1      np.object\_                 cell         0.1
    frozenset        0.1      np.object\_                 cell         0.1
    cl.deque         0.1      np.object\_                 cell         0.1
    dict             0.1                                  struct       0.1 [7]_
    np.bool\_        0.1                                  logical      0.1
    np.void          0.1
    np.uint8         0.1                                  uint8        0.1
    np.uint16        0.1                                  uint16       0.1
    np.uint32        0.1                                  uint32       0.1
    np.uint64        0.1                                  uint64       0.1
    np.uint8         0.1                                  int8         0.1
    np.int16         0.1                                  int16        0.1
    np.int32         0.1                                  int32        0.1
    np.int64         0.1                                  int64        0.1
    np.float16 [8]_  0.1
    np.float32       0.1                                  single       0.1
    np.float64       0.1                                  double       0.1
    np.complex64     0.1                                  single       0.1
    np.complex128    0.1                                  double       0.1
    np.str\_         0.1      np.uint32/16                char/uint32  0.1 [5]_
    np.bytes\_       0.1      np.bytes\_ or np.uint16     char         0.1 [6]_
    np.object\_      0.1                                  cell         0.1
    np.ndarray       0.1      [9]_ [10]_                  [9]_ [10]_   0.1 [9]_ [11]_
    np.matrix        0.1      [9]_                        [9]_         0.1 [9]_
    np.chararray     0.1      [9]_                        [9]_         0.1 [9]_
    np.recarray      0.1      structured np.ndarray       [9]_ [10]_   0.1 [9]_
    ===============  =======  ==========================  ===========  ==============

    .. [1] Depends on the selected options. Always ``np.uint8`` when doing
           MATLAB compatiblity, or if the option is explicitly set.
    .. [2] In Python 2.x, it may be read back as a ``long`` if it can't fit
           in the size of an ``int``.
    .. [3] Must be small enough to fit into an ``np.int64``.
    .. [4] Type found only in Python 2.x. Python 2.x's ``long`` and ``int``
           are unified into a single ``int`` type in Python 3.x. Read as an
           ``int`` in Python 3.x.
    .. [5] Depends on the selected options and whether it can be converted
           to UTF-16 without using doublets. If the option is explicity set
           (or implicitly when doing MATLAB compatibility) and it can be
           converted to UTF-16 without losing any characters that can't be
           represented in UTF-16 or using UTF-16 doublets (MATLAB doesn't
           support them), then it is written as ``np.uint16`` in UTF-16
           encoding. Otherwise, it is stored at ``np.uint32`` in UTF-32
           encoding.
    .. [6] Depends on the selected options. If the option is explicitly set
           (or implicitly when doing MATLAB compatibility), it will be
           stored as ``np.uint16`` in UTF-16 encoding unless it has
           non-ASCII characters in which case a ``NotImplementedError`` is
           thrown). Otherwise, it is just written as ``np.bytes_``.
    .. [7] All keys must be ``str`` in Python 3 or ``unicode`` in Python 2.
           They cannot have null characters (``'\x00'``) or forward slashes
           (``'/'``) in them.
    .. [8] ``np.float16`` are not supported for h5py versions before
           ``2.2``.
    .. [9] Container types are only supported if their underlying dtype is
           supported. Data conversions are done based on its dtype.
    .. [10] Structured ``np.ndarray`` s (have fields in their dtypes) can be
            written as an HDF5 COMPOUND type or as an HDF5 Group with
            Datasets holding its fields (either the values directly, or as
            an HDF5 Reference array to the values for the different elements
            of the data). Can only be written as an HDF5 COMPOUND type if
            none of its field are of dtype ``'object'``. Field names cannot
            have null characters (``'\x00'``) and, when writing as an HDF5
            GROUP, forward slashes (``'/'``) in them.
    .. [11] Structured ``np.ndarray`` s with no elements, when written like a
            structure, will not be read back with the right dtypes for their
            fields (will all become 'object').

    This table gives the MATLAB classes that can be read from a MAT file,
    the first version of this package that can read them, and the Python
    type they are read as.

    ===============  =======  =================================
    MATLAB Class     Version  Python Type
    ===============  =======  =================================
    logical          0.1      np.bool\_
    single           0.1      np.float32 or np.complex64 [12]_
    double           0.1      np.float64 or np.complex128 [12]_
    uint8            0.1      np.uint8
    uint16           0.1      np.uint16
    uint32           0.1      np.uint32
    uint64           0.1      np.uint64
    int8             0.1      np.int8
    int16            0.1      np.int16
    int32            0.1      np.int32
    int64            0.1      np.int64
    char             0.1      np.str\_
    struct           0.1      structured np.ndarray
    cell             0.1      np.object\_
    canonical empty  0.1      ``np.float64([])``
    ===============  =======  =================================

    .. [12] Depends on whether there is a complex part or not.


    Versions
    ========

    0.1.11. Bugfix release fixing the following.
            * Issue #30. Fixed ``loadmat`` not opening files in read mode.

    0.1.10. Minor feature/performance fix release doing the following.
            * Issue #29. Added ``writes`` and ``reads`` functions to write
              and read more than one piece of data at a time and made
              ``savemat`` and ``loadmat`` use them to increase performance.
              Previously, the HDF5 file was being opened and closed for
              each piece of data, which impacted performance, especially
          for large files.

    0.1.9. Bugfix and minor feature release doing the following.
           * Issue #23. Fixed bug where a structured ``np.ndarray`` with
             a field name of ``'O'`` could never be written as an
             HDF5 COMPOUND Dataset (falsely thought a field's dtype was
             object).
           * Issue #6. Added optional data compression and the storage of
             data checksums. Controlled by several new options.

    0.1.8. Bugfix release fixing the following two bugs.
           * Issue #21. Fixed bug where the ``'MATLAB_class'`` Attribute is
             not set when writing ``dict`` types when writing MATLAB
             metadata.
           * Issue #22. Fixed bug where null characters (``'\x00'``) and
             forward slashes (``'/'``) were allowed in ``dict`` keys and the
             field names of structured ``np.ndarray`` (except that forward
             slashes are allowed when the
             ``structured_numpy_ndarray_as_struct`` is not set as is the
             case when the ``matlab_compatible`` option is set). These
             cause problems for the ``h5py`` package and the HDF5 library.
             ``NotImplementedError`` is now thrown in these cases.

    0.1.7. Bugfix release with an added compatibility option and some added test code. Did the following.
           * Fixed an issue reading variables larger than 2 GB in MATLAB
             MAT v7.3 files when no explicit variable names to read are
             given to ``hdf5storage.loadmat``. Fix also reduces memory
             consumption and processing time a little bit by removing an
             unneeded memory copy.
           * ``Options`` now will accept any additional keyword arguments it
             doesn't support, ignoring them, to be API compatible with future
             package versions with added options.
           * Added tests for reading data that has been compressed or had
             other HDF5 filters applied.

    0.1.6. Bugfix release fixing a bug with determining the maximum size of a Python 2.x ``int`` on a 32-bit system.

    0.1.5. Bugfix release fixing the following bug.
           * Fixed bug where an ``int`` could be stored that is too big to
             fit into an ``int`` when read back in Python 2.x. When it is
             too big, it is converted to a ``long``.
           * Fixed a bug where an ``int`` or ``long`` that is too big to
         big to fit into an ``np.int64`` raised the wrong exception.
           * Fixed bug where fields names for structured ``np.ndarray`` with
             non-ASCII characters (assumed to be UTF-8 encoded in
             Python 2.x) can't be read or written properly.
           * Fixed bug where ``np.bytes_`` with non-ASCII characters can
             were converted incorrectly to UTF-16 when that option is set
             (set implicitly when doing MATLAB compatibility). Now, it throws
             a ``NotImplementedError``.

    0.1.4. Bugfix release fixing the following bugs. Thanks goes to `mrdomino <https://github.com/mrdomino>`_ for writing the bug fixes.
           * Fixed bug where ``dtype`` is used as a keyword parameter of
             ``np.ndarray.astype`` when it is a positional argument.
           * Fixed error caused by ``h5py.__version__`` being absent on
             Ubuntu 12.04.

    0.1.3. Bugfix release fixing the following bug.
           * Fixed broken ability to correctly read and write empty
             structured ``np.ndarray`` (has fields).

    0.1.2. Bugfix release fixing the following bugs.
           * Removed mistaken support for ``np.float16`` for h5py versions
             before ``2.2`` since that was when support for it was
             introduced.
           * Structured ``np.ndarray`` where one or more fields is of the
             ``'object'`` dtype can now be written without an error when
             the ``structured_numpy_ndarray_as_struct`` option is not set.
             They are written as an HDF5 Group, as if the option was set.
           * Support for the ``'MATLAB_fields'`` Attribute for data types
             that are structures in MATLAB has been added for when the
             version of the h5py package being used is ``2.3`` or greater.
             Support is still missing for earlier versions (this package
             requires a minimum version of ``2.1``).
           * The check for non-unicode string keys (``str`` in Python 3 and
             ``unicode`` in Python 2) in the type ``dict`` is done right
             before any changes are made to the HDF5 file instead of in the
             middle so that no changes are applied if an invalid key is
             present.
           * HDF5 userblock set with the proper metadata for MATLAB support
             right at the beginning of when data is being written to an HDF5
             file instead of at the end, meaning the writing can crash and
             the file will still be a valid MATLAB file.

    0.1.1. Bugfix release fixing the following bugs.
           * ``str`` is now written like ``numpy.str_`` instead of
             ``numpy.bytes_``.
           * Complex numbers where the real or imaginary part are ``nan``
             but the other part are not are now read correctly as opposed
             to setting both parts to ``nan``.
           * Fixed bugs in string conversions on Python 2 resulting from
             ``str.decode()`` and ``unicode.encode()`` not taking the same
             keyword arguments as in Python 3.
           * MATLAB structure arrays can now be read without producing an
             error on Python 2.
           * ``numpy.str_`` now written as ``numpy.uint16`` on Python 2 if
             the ``convert_numpy_str_to_utf16`` option is set and the
             conversion can be done without using UTF-16 doublets, instead
             of always writing them as ``numpy.uint32``.

    0.1. Initial version.
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