[python-hdf5storage] annotated tag 0.1.10 created (now 9b3dc60)

Ghislain Vaillant ghisvail-guest at moszumanska.debian.org
Mon Feb 29 08:24:56 UTC 2016


This is an automated email from the git hooks/post-receive script.

ghisvail-guest pushed a change to annotated tag 0.1.10
in repository python-hdf5storage.

        at  9b3dc60   (tag)
   tagging  1f0c24bf7c1c9bc9e96aea1aa2d04b2bb66da955 (commit)
  replaces  0.1.9
 tagged by  Freja Nordsiek
        on  Sun Dec 27 15:34:15 2015 +0100

- Log -----------------------------------------------------------------
Added functions for reading and writing more than one data object at a time and improved the performance of loadmat and savemat.

Freja Nordsiek (5):
      Added functions for reading and writing more than one data item at a time (writes and reads) and made write and read into wrappers around them.
      Added tests for reading and writing more than one data item at a time.
      Made savemat and loadmat use writes and reads instead of write and read to improve performance.
      Updated documentation for version 0.1.10 which added the ability to write and read more than one piece of data at once.
      Incremented version to 0.1.10

-----------------------------------------------------------------------

This annotated tag includes the following new commits:

       new  8167dd7   Initial commit
       new  3e70816   Added some needed files including license.
       new  e6d9c0c   Initial set of python codes to write only (still need polishing)
       new  d22803c   Changed line endings to be native.
       new  73450df   Added missing import.
       new  8fd3b65   Fixed method call typo.
       new  2ffa814   Fixed error in detection of whether an overwrite is needed based on shape and type information.
       new  bbb0482   Fixed bug in writting MATLAB_int_decode attribute for strings.
       new  94eb039   Fleshed out core.Options (properties and docstrings) and added core module docstring.
       new  e042e6f   Fleshed out the rest of Marshallers.TypeMarshaller to support reading.
       new  e779992   Added docstrings to Marshallers.TypeMarshaller.
       new  69f745a   Added minimal docstring for Marshallers module.
       new  6ba7878   Small, mostly docstring fixes in core.Options.
       new  177f9e6   More docstring work and adding a method in the core module.
       new  d3a5afa   API changes in preparation for read support, especially in regard to MATLAB types.
       new  00d15ff   Added a function to get an Attribute.
       new  7ebe9aa   Added low level, somewhat buggy for strings, read support for Numpy types.
       new  33124c8   Added utility function to encode complex types to be written to HDF5 file with the right complex field names.
       new  254420b   Changed writing of complex types to set complex field names manually.
       new  7631790   Fixed but in complex type encoding where type was not kept constant.
       new  3f75a8d   Made utilities.decode_complex more general (can set one or both field names manually).
       new  7b8c734   Added read support for Python scaler types and None.
       new  649b3d8   Changed the way marshallers for container objects recursively write their elements.
       new  6b008c4   Removed partial code for the currently impossible to set MATLAB_fields attribute.
       new  d507cd7   Added read support for dicts.
       new  2089de7   Added utility to convert strings to str, and changed other string conversion utilities to use it.
       new  553f044   Added Python string read support and changed it so bytearrays are written as numpy.string_ instead of numpy.uint8.
       new  f04e283   Added high level read function.
       new  1a72e51   Fixed reading bugs.
       new  844b751   Fixed bugs with reading/writing scalar types and reading complex types.
       new  71a2c88   Fixed bug on writing empty datasets so that Matlab can read them.
       new  3b2e602   Fixed bugs in writing boolean types in a Matlab compatible way.
       new  e497e0f   Changed reading to have the Matlab compatiblity option set to False by default.
       new  1dd5482   Removed quad support as h5py doesn't support them.
       new  54e13e8   Added package installer (distutils) and wrote Readme.
       new  ef8501e   Escaped underscores in README.rst.
       new  e3e2889   Added what Python types are converted to in numpy in README.rst
       new  a43da17   Changed the way that None is written.
       new  d997d00   Added and fixed documentation.
       new  b401071   Added initial Sphinx based documentation.
       new  9209376   Added ability to pass an Options object to the high level functions directly.
       new  a7aa29d   Changed default names to read and write data to in the high level functions.
       new  374e62f   Gathered all options keywords in high level read/write functions into a **keywords.
       new  9e75476   Fixed error in README.rst about package functionality.
       new  4d24528   Changed calling arguments for core.read and core.write and added their doc strings.
       new  7b12ec5   Added Sphixnx API documentation structure for Marshallers.
       new  28ed1f0   Fixed documentation and changed references to the aliases np.string_ and np.unicode to their targets np.bytes_ and np.str_.
       new  d2f0a32   Changed manifest to include documentation.
       new  1284b76   Moved items in core module to main module (__init__.py), added examples, and fixed Sphinx based documentation.
       new  56cdd73   Added initial tests.
       new  cee850c   Added more tests for write and readback when not writing MATLAB metadata.
       new  2c8716e   Added tests to the manifest.
       new  0a8db47   Fixed bugs with writing and reading empty strings, in addition to a small file closing bug.
       new  1083c70   Added read/write support for numpy.object_ types (become HDF5 references).
       new  bc9c847   Added read/write support for lists.
       new  9d8a8e9   Added read/write support for tuple, set, frozenset, and collections.deque.
       new  5bc85e0   Dropped the C in all the CPython parts of attribute names.
       new  bb8b912   Added write readback tests for the numerical numpy types (not strings).
       new  927e5b2   Fixed issue in test where NaN's were causing equality tests to fail.
       new  0923f91   Fixed bug of scalar numpy complex types being turned into arrays when doing write readback.
       new  25682d3   Changed option name from MATLAB_comaptible to matlab_compatible.
       new  9e4bc8c   Fixed name of the PyTables package and group.
       new  62b39fd   Added file truncation options for writing.
       new  452ba79   Fixed bugs in numpy bools not being converted back to book from uint8 correctly.
       new  3246897   Added numpy bool read writeback tests.
       new  54d2b0f   Fixed a file clean up bug on error.
       new  38dd35d   Changed tests over to nose.
       new  d726cab   Fixed and rearranged tests.
       new  988b052   Added tests for numpy bytes_ and str_ types.
       new  6b2dbc3   Fixed bugs in preserving the shape when reading back arrays of strings (all kinds).
       new  5c9b649   Switched from distutils to setuptools for packaging so unit tests could be run from setup.py.
       new  b078faa   Changes to setup.py for using setuptools (forgot to add in the last commit).
       new  f261dbf   Added write readback tests for numpy.object_ type.
       new  a0a9730   Fixed a bug with deleting the H5PATH attribute on numpy.object_ arrays when not doint matlab compatibility.
       new  7fc2be1   Split previously 2d array write readback test into 1d, 2d, and 3d cases.
       new  1b3f53e   Fixed bug in decoding 3d and higher dimensionality arrays of numpy string types when encoded as uints.
       new  9e7b15a   Added write readback unit tests for list, tuple, set, frozenset, and collection.deque.
       new  6d5a8e7   Consolidated the assertion functions for python and numpy types together.
       new  bbb8638   Rearranged write readback test code and added some comments.
       new  cadb9eb   Fixed string encoding and decoding bugs.
       new  d46aae8   Added write readback tests to file with no python type information stored (either no information or just matlab information).
       new  126e8e4   Added tests for bug where a complex number with one field as NaN but the other not is read back as NaN in both fields.
       new  470bd87   Parameterized the sizes of the random datasets used in the tests.
       new  349b676   Renamed the convert_strings_to_utf16 option to convert_numpy_bytes_to_utf16.
       new  ec11484   Added an option to optionally convert numpy.str_ to np.uint16 in UTF-16 format and changed it so that str is converted to numpy.str_ instead of numpy.bytes_.
       new  7526cdc   Renamed decoders for numpy bytes_ and str_ in utilities.
       new  192f430   Updated documentation on the utilities module.
       new  bf3702e   Added custom assert functions for the tests into their own module.
       new  048e24a   Moved the none format (not type or matlab information) and the matlab format assertion functions to tests/asserts.py as well as consolidating the assertions for different types together and adding in assertial code for dictionaries.
       new  3cb8514   Added write readback tests for dicts.
       new  73c79d1   Adjuste appearance of the first table in the README.
       new  4c75ef1   Added oned_as option to control whether 1D arrays become row or column vectors when converted to 2D.
       new  e7ca164   Renamed the convert_scalars_to_arrays option to make_atleast_2d.
       new  bc4f382   Added a savemat function modelled after scipy.io.savemat.
       new  47f2cf4   Added a loadmat function modelled after scipy.io.loadmat.
       new  a6472a2   Added existing file truncation options to savemat.
       new  b5a0169   Added main information page to documentation (replicate of README.rst) and adjusted titles.
       new  bb295d3   Created a skeleton introduction in the documentation and then moved the examples from __init__.py to it and updated them.
       new  444dc47   Fixed error in README where the other numpy integer types were not in the table of supported types.
       new  76ab931   Reorganized table in README.
       new  3fe9b62   Renamed name arguments in read and write functions to path.
       new  12a6eec   Finished rest of introduction.rst in the documentation.
       new  1b70ac1   Added documentation on the storage format.
       new  cd4309a   Fixed bugs where the name keyword argument was not updated to path in savemat and loadmat.
       new  5bd9cfe   Renamed the store_type_information option to store_python_metadata.
       new  6924018   Added more documentation regarding the matlab_compatible option and how types are read back from MAT files.
       new  a0f1a5b   Added licence header to test files.
       new  85cd471   Added more information to setup.py
       new  9b5c74c   Added numpy.chararray support.
       new  bc4bab8   Added numpy.void support.
       new  742f1eb   Added ability to discard or throw an error when writing a matlab incompatible type when doing matlab compatibility.
       new  10067f0   Fixed bugs in tests resulting from the changes in how matlab incompatible types are written.
       new  82774db   Fixed bugs in documentation.
       new  760d2e7   Documentation and docstring updates and fixes.
       new  f381b8d   Added write support for numpy.ndarrays that have fields in their dtype as Groups/matlab structures.
       new  de1364b   Added the use of the canonical empty inside the group for references.
       new  3b355b6   Updated documentation.
       new  9194e81   Fixed missing information about exceptions in docstrings.
       new  40c4b68   Moved the code to read an h5py.Reference array and make a numpy.object_ array from it to a function.
       new  84dc2ff   Added read support for structured numpy.ndarrays as they are, as opposed to reading them as dicts.
       new  9608d03   Removed commented out code.
       new  05aac0c   Made it so that structured numpy.ndarrays with one element have their fields written as is as opposed to packing them into HDF5 Reference arrays, and made it so they can be read back correctly.
       new  7e261a8   Changed the default marshaller for HDF5 Groups to be NumpyScalarArrayMarshaller as opposed to PythonDictMarshaller.
       new  39a97c7   Renamed the fielded_numpy_ndarray_as_struct option to structured_numpy_ndarray_as_struct.
       new  917d99b   Fixed tests to work with how dicts are read back as structured np.ndarrays if python metadata isn't stored.
       new  cf753c7   Updated documentation with regards to reading/writing structured numpy.ndarrays and fixed errors.
       new  8df8175   Changed the setting of string array attributes to use str instead of np.bytes_ (unicode instead of ASCII).
       new  18210e6   Renamed the Attribute Python.numpy.Fields to Python.Fields and made it so that if it wasn't given, fields are sorted when making a structured ndarray.
       new  03c0586   Updated documentation.
       new  7cebd72   Added read/write numpy.recarray support.
       new  2c059a0   Fixed a bug where a dict with no members was marked with metadata as a zero sized struct, instead of one with no fields.
       new  b585cc0   Added/changed code to handle empty structured ndarrays.
       new  e3fa8a1   Renamed all the different string converters in utilities from starting with decode_to to convert_to
       new  7c4d561   Added license info in README.rst
       new  8145a42   Added a development information page in the documentation.
       new  6b71a13   Moved from using list.copy to copy.deepcopy(list) for Python 2 compatibility.
       new  f64d310   Added Python 2.7 support.
       new  1e6a69e   Replaced dictionary comprehensions to make code Python 2.6 compatible.
       new  3166122   Changed all sets to be constructed through set([...]) instead of {...}
       new  f5b59b5   Fixed bug on Python 2.6 where sys.version_info is just a tuple unlike in later Python versions.
       new  7aa9e8a   Fixed bug on Python 2.6 where byterray.fromhex was given a non-unicode argument.
       new  c0eaddf   Fixed bug on Python 2.6 where the encoding to bytes.decode needs to be given as the first positional argument as opposed to as a keyword argument.
       new  90b4296   Formally added Python 2.6 support in the README.rst and the installer.
       new  20b5798   Fixed bug where loadmat was not returning a dict of the variables and not putting it in mdict if it was given.
       new  b338a43   Added tests for reading data written by MATLAB.
       new  9418e50   Fixed bugs in installer.
       new  0c5e8c6   Added additional tests to take the data read from MATLAB, send it back, read it back, and compare.
       new  77b9800   Renamed MATLAB compatibility tests.
       new  0a74e01   Fixed bug where subprocess.check_output is not available on Python 2.6.
       new  c9f675f   Modified MATLAB test code to reduce output.
       new  95fa1ea   Last changes to README.rst before releasing package.
       new  8fe2b6c   Changed description.
       new  c62b3c3   Fixed bug where str was converted to numpy.bytes_ instead of numpy.str_ before writing.
       new  dc3657b   Changed tests to work after fixing bug where str was written like numpy.bytes_ instead of like numpy.str_ and added test for writing and reading back unicode characters.
       new  0189bcd   Fixed bug when reading complex numbers where one part is NaN but the other is not.
       new  4fd8430   Modified tests to work with real/complex numbers that have NaN part/s.
       new  1762f64   Fixed string conversion bug in Python 2.
       new  946f513   Fixed bug where MATLAB structures could not be read back correctly in Python 2.
       new  3037724   Fixed bug in Python2 where str.decode does not use a keyword for the encoding.
       new  756f869   Removed replace keyword in str.decode for Python 2.6
       new  94f10e2   Changed a reference to numpy.str_ to numpy.unicode_ so that they will be written as numpy.uin16 if possible on Python 2.
       new  031d234   Fixed bug in tests.
       new  286d6ea   Incremented version to 0.1.1
       new  e2ef6f3   Fixed version in documentation.
       new  9a271e8   Made it so that MATLAB compatible userblock is put in HDF5 file before data is written as opposed to after (fixes bug where the file becomes not MATLAB compatible if an exception occurs).
       new  5a1bf8a   Added MATLAB_fields Attribute support to the dict marshaller.
       new  29fcef7   Added MATLAB_fields Attribute write support to the NumpyScalarArrayMarshaller.
       new  72d97a1   Fixed bug where Attribute MATLAB_fields is not deleted for non-structured ndarrays.
       new  9118a9a   Added MATLAB_fields Attribute read support for empty structure arrays to the NumpyScalarArrayMarshaller.
       new  6e31b58   Fixed bug in MATLAB_fields Attribute generation for NumpyScalarArrayMarshaller.
       new  1973e2b   Fixed bug in MATLAB_fields Attribute generation for NumpyScalarArrayMarshaller.
       new  713276d   Fixed bug in reading empty MATLAB structures.
       new  5ff55a5   Fixed bug in reading empty MATLAB structures.
       new  1a1f2d7   Fixed bug in reading empty MATLAB structures.
       new  99d573c   Fixed writing of empty matlab structs to use a Dataset with the appropriate fields attributes set and several reading errors with the new format.
       new  41731cf   Made it so that the MATLAB_fields Attribute is properly used on structures to order the fields in the right order.
       new  d6c1a7d   Fixed bug where structured numpy.ndarrays with a field having an 'object' type is written as an HDF5 COMPOUND when the structured_numpy_ndarray_as_struct option is disabled. Is now written as a GROUP instead as if the option was set.
       new  cc763ff   Added check for non-unicode keys in PythonDictMarshaller right to the beginning of the writing process so that nothing is changed if there is a non-unicode key.
       new  392909a   Removed numpy.float16 support for when the h5py version is less than 2.2 since that was when support for it was introduced.
       new  a15966c   Updated documentation to reflect code changes and new version.
       new  017d36c   Incremented package version to 0.1.2
       new  03f0a58   Made it so that ez_setup.py is for sure included in the manifest.
       new  1e9af3c   Added structured numpy ndarray tests (both filled and empty).
       new  f2ac363   Added workaround for bug when allocating numpy.ndarray when its dtype.itemsize is zero.
       new  bd060b3   Fixed bugs in reading and writing structured numpy.ndarrays, especially empty ones.
       new  506fbf7   Fixed bugs in tests where structured numpy.ndarrays which were read right were found to be inequal.
       new  b1c9976   Fixed bug in tests where the partial squeezing of singleton arrays was not detected when no metadata was written.
       new  7e96e8e   Fixed set syntax error for python 2.6 introduced into the tests.
       new  6a49781   Added text to the documentation about this package not using pickling at all and why.
       new  0db8e61   Incremented version to 0.1.3 and added text in the README.rst explaining why.
       new  30a0d05   Updated version in package source.
       new  afb1208   MP-77: Fix bug in hdf5storage
       new  603aa1a   Fix h5py version detection on old h5py
       new  db003be   Merge pull request #15 from mrdomino/master
       new  b161b78   Added comment to the h5py.__version__ grab and set to 2.0 if not available to explain its presence.
       new  1345ca5   Made the h5py version variable private.
       new  0196745   Updated README.rst with the bugfix information.
       new  249114e   Fixed README.rst bugfix line that didn't look good when in html.
       new  53c17fb   Incremented the version to 0.1.4
       new  8ff4dfb   Updated copyright years.
       new  f6aca67   Fixed bug where too big a number can be read into an int in Python 2.x. Gets read into a long if this is the case.
       new  006539d   Updated documentation to reflect the too large int bug fix.
       new  bc7c5e6   Incremented version to 0.1.5
       new  a33f0dd   Added code to throw exception for longs that are too big to fit into a numpy.int64.
       new  dd04627   Fixed bug where python 2.x longs could not be written.
       new  8ecd25c   Fixed bug in Python 3.x where having a structured numpy.ndarray with a field with a non-ascii character threw UnicodeEncodeError instead of the UnicodeDecodeError that was originally expected.
       new  eef4ded   Fixed bug from isinstance(True, int) being True in Python 3.x
       new  18fdf88   Fixed bug where structured ndarrays with non-ascii characters in fields couldn't be read in Python 2.x
       new  feb6f02   Code cleanup and comment updating in Marshallers.
       new  be360ae   Fixed bug where structured ndarrays with UTF-8 encoded fields couldn't be written in Python 2.x
       new  9e811a7   Added tests for write-readback of longs and an error being raised when trying to write an int or long too big for a numpy.int64.
       new  88caa63   Added tests for write-readback of bytes encoded in UTF-8 and structured numpy.ndarray with non-ascii or UTF-8 encoded fields.
       new  76cfc04   Fixes for the string conversions to read and write UTF-8 encoded fields of structured numpy.ndarrays on Python 2.x.
       new  1addbf5   Added to the tests a check for preservaation of the ordering of the fields for structured numpy.ndarrays.
       new  24e17a8   Writing non-ASCII numpy.bytes_ when using MATLAB formatting now throws an exception.
       new  97364e7   Updated documentation for the 0.1.5 release.
       new  8b2f9ae   Fixed bug on 32-bit Python 2.x with determining the maximum int size.
       new  fa08faa   Incremented version to 0.1.6 and added entry to Changelong in README.rst.
       new  c4b0c58   Incremented version in __init__.py to 0.1.6
       new  8b6e6e3   Separated out all the random variable making methods in tests/test_write_readback.py from the master branch into their own test module (tests/make_randoms.py) and made the tests use them.
       new  e49b3ef   Removed unused imports in test_write_readback
       new  cd7f908   Added a test for reading data for any set of HDF5 filters.
       new  c19a430   Fixed issue where a local variable having the same name as a global was confusting.
       new  95f9727   Added workaround for reading MAT files with variables larger than 2 GB when the variables to read aren't given explicitly.
       new  baffeb1   Made it so that Options would take additional keyword arguments even though it will ignore them to be more compatible with future versions of the package.
       new  3dc2ac0   Updated README.rst for the 0.1.7 release.
       new  7ed464c   Incremented package version to 0.1.7.
       new  ab15800   Fixed bug where the 'MATLAB_class' Attribute is not set when writing dicts.
       new  4324217   Fixed bug where dicts could be written with null characters and / in their keys
       new  c9233ec   Fixed bug where structured numpy.ndarrays could be written with null characters and, depending on the case, / in their field names (not valid characters).
       new  d91c5fb   Updated documentation for version 0.1.8
       new  28f2f69   Incremented package version to 0.1.8
       new  509ac37   Added compression to Options and the Numpy marshaller. (cherry picked from commit b63e610bea6cc66eeaa350ca1a9f127f07cb6631)
       new  b8e4ac6   Added HDF5 filter tests for writing compressed and uncompressed data. (cherry picked from commit bdd216c3b71e9ff22ccd87bf196053ba09f7f166)
       new  15cdeba   Made it so that Options would take additional keyword arguments even though it will ignore them to be more compatible with future versions of the package. (cherry picked from commit baffeb1896977e3870aa415c046fce6ce275c9f7)
       new  55992e2   Added documentation page for compression. (cherry picked from commit e8b33a0bf1b4c0897fc7ae7491143ed2000d4325)
       new  0395073   Added compression information to the introduction in the documentation. (cherry picked from commit 95bcf291dbd280c03e3693d0ff2a488e792db7e7)
       new  8d35b8e   Updated documentation to reflect compression being backported to the 0.1.x branch. (cherry picked from commit 56139ce1c3fedc1a0605805bef35a3a1ac4541d9)
       new  63da84e   Updated README for the 0.1.9 release.
       new  c5af0aa   Incremented the package version to 0.1.9.
       new  7892490   Documentation updates for compression.
       new  bc0e960   Updated examples in the documentation to write and read data to /a instead of /
       new  987c893   Fixed bug where a structured ndarray with a field having the name 'O' was always written as an HDF5 Group.
       new  2bb70bb   Added functions for reading and writing more than one data item at a time (writes and reads) and made write and read into wrappers around them.
       new  4d997ed   Added tests for reading and writing more than one data item at a time.
       new  f020ad0   Made savemat and loadmat use writes and reads instead of write and read to improve performance.
       new  ce832b6   Updated documentation for version 0.1.10 which added the ability to write and read more than one piece of data at once.
       new  1f0c24b   Incremented version to 0.1.10

The 248 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


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