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Revision 1.11 / (download) - annotate - [select for diffs], Thu Aug 31 11:58:40 2023 UTC (3 weeks, 5 days ago) by adam
Branch: MAIN
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py-h5py: updated to 3.9.0
What's new in h5py 3.9
======================
This version of h5py requires Python 3.8 or above.
New features
------------
* New ``out`` argument to :meth:`~h5py.h5d.DatasetID.read_direct_chunk` to allow passing
the output buffer (:pr:`2232`).
* The objects from :meth:`.Dataset.asstr` and :meth:`.Dataset.astype` now
implement the ``__array__()`` method (:pr:`2269`).
This speeds up access for functions that support it, such as ``np.asarray()``.
* Validate key types when creating groups and attributes, giving better error
messages when invalid types are used (:pr:`2266`).
Deprecations & removals
-----------------------
* Using :meth:`.Dataset.astype` as a context manager has been removed, after
being deprecated in h5py 3.6. Read data by slicing the returned object instead:
``dset.astype('f4')[:]``.
Exposing HDF5 functions
-----------------------
* ``H5Pget_elink_acc_flags`` & ``H5Pset_elink_acc_flags`` as
:meth:`h5py.h5p.PropLAID.get_elink_acc_flags` & :meth:`h5py.h5p.PropLAID.set_elink_acc_flags`:
access the external link file access traversal flags in a link access property
list (:pr:`2244`).
* ``H5Zregister`` as :func:`h5py.h5z.register_filter`: register an HDF5 filter
(:pr:`2229`).
Bug fixes
---------
* ``Group.__contains__`` and ``Group.get`` now use the default link access
property list systematically (:pr:`2244`).
* Removed various calls to the deprecated ``numpy.product`` function (:pr:`2242`
& :pr:`2273`).
* Fix the IPython tab-completion integration in IPython 8.12 (:pr:2256`).
* Replacing attributes with :meth:`.AttributeManager.create` now deletes the old
attributes before creating the new one, rather than using a temporary name
and renaming the new attribute (:pr:`2274`). This should avoid some confusing
bugs affecting attributes. However, failures creating an attribute are less
likely to leave an existing attribute of the same name in place. To change an
attribute value without changing its shape or dtype, use
:meth:`~.AttributeManager.modify` instead.
Building h5py
-------------
* When building with :ref:`parallel` support, the version of mpi4py used on
various Python versions is increased to 3.1.1, fixing building with a newer
setuptools (:pr:`2225`).
* Some fixes towards compatibility with the upcoming Cython 3 (:pr:`2247`).
Revision 1.10 / (download) - annotate - [select for diffs], Tue Oct 26 10:18:32 2021 UTC (23 months ago) by nia
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archivers: Replace RMD160 checksums with BLAKE2s checksums All checksums have been double-checked against existing RMD160 and SHA512 hashes Could not be committed due to merge conflict: devel/py-traitlets/distinfo The following distfiles were unfetchable (note: some may be only fetched conditionally): ./devel/pvs/distinfo pvs-3.2-solaris.tgz ./devel/eclipse/distinfo eclipse-sourceBuild-srcIncluded-3.0.1.zip
Revision 1.9 / (download) - annotate - [select for diffs], Thu Oct 7 13:43:14 2021 UTC (23 months, 2 weeks ago) by nia
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Revision 1.8 / (download) - annotate - [select for diffs], Fri Jun 18 12:15:22 2021 UTC (2 years, 3 months ago) by nia
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py-h5py: Fix numpy requirement in setup.py for pkgsrc-friendliness
Revision 1.7 / (download) - annotate - [select for diffs], Mon Jun 7 11:57:50 2021 UTC (2 years, 3 months ago) by adam
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py-h5py: updated to 3.2.1
What's new in h5py 3.2
======================
New features
------------
* Added support to use the HDF5 ROS3 driver to access HDF5 files on S3
(:pr:`1755`). This is not enabled in the pre-built packages on PyPI. To use
it, ensure HDF5 is built with read-only S3 support enabled, and then
:ref:`build h5py from source <source_install>` using that HDF5 library.
Breaking changes & deprecations
-------------------------------
* Python 3.7 is now the minimum supported version. It may still be possible to
use this release with Python 3.6, but it isn't tested and wheels are not
provided for Python 3.6.
* Setting the config option ``default_file_mode`` to values other than ``'r'``
is deprecated. Pass the desired mode when opening a :class:`~.File` instead.
Exposing HDF5 functions
-----------------------
* ``H5Pset_fapl_ros3`` & ``H5Pget_fapl_ros3`` (where HDF5 is built with
read-only S3 support).
Bug fixes
---------
* :exc:`OSError` exceptions raised by h5py should now have a useful ``.errno``
attribute, where HDF5 provides this information. Subclasses such as
:exc:`FileNotFoundError` should also be raised where appropriate (:pr:`1815`).
* Fix reading data with a datatype of variable-length arrays of fixed length
strings (:issue:`1817`).
* Fix :meth:`.Dataset.read_direct` and :meth:`.Dataset.write_direct` when the
source and destination have different shapes (:pr:`1796`).
* Fix selecting data using integer indices in :meth:`.Dataset.read_direct`
and :meth:`.Dataset.write_direct` (:pr:`1818`).
* Fix exception handling in :meth:`.Group.visititems` (:issue:`1740`).
* Issue a warning when ``File(..., swmr=True)`` is specified with any mode other
than ``'r'``, as the SWMR option is ignored in these cases (:pr:`1812`).
* Fix NumPy 1.20 deprecation warnings concerning the use of None as shape, and
the deprecated aliases np.float, np.int and np.bool (:pr:`1780`).
3.2.1 bug fix release
---------------------
* Fix :attr:`.File.driver` when the read-only S3 driver is available (:pr:`1844`).
What's new in h5py 3.1
======================
Bug fixes
---------
* Fix reading numeric data which is not in the native endianness,
e.g. big-endian data on a little-endian system (:issue:`1729`).
* Fix using bytes as names for :meth:`.Group.create_dataset` and
:meth:`.Group.create_virtual_dataset` (:issue:`1732`).
* Fix writing data as a list to a dataset with a sub-array data type
(:issue:`1735`).
Building h5py
-------------
* Allow building against system lzf library by setting ``H5PY_SYSTEM_LZF=1``.
See :ref:`custom_install`.
Development
-----------
* If pytest is missing `pytest-mpi <https://pytest-mpi.readthedocs.io/en/latest/>`_
it will now fail with a clear error.
* Fix a test which was failing on big-endian systems.
What's new in h5py 3.0
======================
New features
------------
* The interface for storing & reading strings has changed - see :doc:`/strings`.
The new rules are hopefully more consistent, but may well require some changes
in coding using h5py.
* Reading & writing data now releases the GIL, so another Python thread can
continue while HDF5 accesses data. Where HDF5 can call back into Python, such
as for data conversion, h5py re-acquires the GIL. However, HDF5 has its own
global lock, so this won't speed up parallel data access using multithreading.
* Numpy datetime and timedelta arrays can now be stored and read as HDF5
opaque data (:issue:`1339`), though other tools will not understand them.
See :ref:`opaque_dtypes` for more information.
* New :meth:`.Dataset.iter_chunks` method, to iterate over chunks within the
given selection.
* Compatibility with HDF5 1.12.
* Methods which accept a shape tuple, e.g. to create a dataset, now also allow
an integer for a 1D shape (:pr:`1340`).
* Casting data to a specified type on reading (:meth:`.Dataset.astype`) can now
be done without a with statement, like this::
data = dset.astype(np.int32)[:]
* A new :meth:`.Dataset.fields` method lets you read only selected fields from
a dataset with a compound datatype.
* Reading data has less overhead, as selection has been implemented in Cython.
Making many small reads from the same dataset can be as much as 10 times
faster, but there are many factors that can affect performance.
* A new NumPy-style :attr:`.Dataset.nbytes` attribute to get the size of the
dataset's data in bytes. This differs from the :attr:`~.Dataset.size`
attribute, which gives the number of elements.
* The ``external`` argument of :meth:`.Group.create_dataset`, which
specifies any external storage for the dataset, accepts more types
(:issue:`1260`), as follows:
* The top-level container may be any iterable, not only a list.
* The names of external files may be not only ``str`` but also ``bytes`` or
``os.PathLike`` objects.
* The offsets and sizes may be NumPy integers as well as Python integers.
See also the deprecation related to the ``external`` argument.
* Support for setting file space strategy at file creation. Includes option to
persist empty space tracking between sessions. See :class:`.File` for details.
* More efficient writing when assiging a scalar to a chunked dataset, when the
number of elements to write is no more than the size of one chunk.
* Introduced support for the split :ref:`file driver <file_driver>`
(:pr:`1468`).
* Allow making virtual datasets which can grow as the source data is resized
- see :doc:`/vds`.
* New `allow_unknown_filter` option to :meth:`.Group.create_dataset`. This should
only be used if you will compress the data before writing it with the
low-level :meth:`~h5py.h5d.DatasetID.write_direct_chunk` method.
* The low-level chunk query API provides information about dataset chunks in an
HDF5 file: :meth:`~h5py.h5d.DatasetID.get_num_chunks`,
:meth:`~h5py.h5d.DatasetID.get_chunk_info` and
:meth:`~h5py.h5d.DatasetID.get_chunk_info_by_coord`.
* The low-level :meth:`h5py.h5f.FileID.get_vfd_handle` method now works for any
file driver that supports it, not only the sec2 driver.
Breaking changes & deprecations
-------------------------------
* h5py now requires Python 3.6 or above; it is no longer compatible with Python
2.7.
* The default mode for opening files is now 'r' (read-only).
See :ref:`file_open` for other possible modes if you need to write to a file.
* In previous versions, creating a dataset from a list of bytes objects would
choose a fixed length string datatype to fit the biggest item. It will now
use a variable length string datatype. To store fixed length strings, use a
suitable dtype from :func:`h5py.string_dtype`.
* Variable-length UTF-8 strings in datasets are now read as ``bytes`` objects
instead of ``str`` by default, for consistency with other kinds of strings.
See :doc:`/strings` for more details.
* When making a virtual dataset, a dtype must be specified in
:class:`.VirtualLayout`. There is no longer a default dtype, as this was
surprising in some cases.
* The ``external`` argument of :meth:`Group.create_dataset` no longer accepts
the following forms (:issue:`1260`):
* a list containing *name*, [*offset*, [*size*]];
* a list containing *name1*, *name2*, ãà and
* a list containing tuples such as ``(name,)`` and ``(name, offset)`` that
lack the offset or size.
Furthermore, each *name*offset*ãàsize* triplet now must be a tuple rather
than an arbitrary iterable. See also the new feature related to the
``external`` argument.
* The MPI mode no longer supports mpi4py 1.x.
* The deprecated ``h5py.h5t.available_ftypes`` dictionary was removed.
* The deprecated ``Dataset.value`` property was removed.
Use ``ds[()]`` to read all data from any dataset.
* The deprecated functions ``new_vlen``, ``new_enum``, ``get_vlen`` and
``get_enum`` have been removed. See :doc:`/special` for the newer APIs.
* Removed deprecated File.fid attribute. Use :attr:`.File.id` instead.
* Remove the deprecated ``h5py.highlevel`` module.
The high-level API is available directly in the ``h5py`` module.
* The third argument of ``h5py._hl.selections.select()`` is now an optional
high-level :class:`.Dataset` object, rather than a ``DatasetID``.
This is not really a public API - it has to be imported through the private
``_hl`` module - but probably some people are using it anyway.
Exposing HDF5 functions
-----------------------
* H5Dget_num_chunks
* H5Dget_chunk_info
* H5Dget_chunk_info_by_coord
* H5Oget_info1
* H5Oget_info_by_name1
* H5Oget_info_by_idx1
* H5Ovisit1
* H5Ovisit_by_name1
* H5Pset_attr_phase_change
* H5Pset_fapl_split
* H5Pget_file_space_strategy
* H5Pset_file_space_strategy
* H5Sencode1
* H5Tget_create_plist
Bug fixes
---------
* Fix segmentation fault when accessing vlen of strings (:issue:`1336`).
* Fix the storage of non-contiguous arrays, such as numpy slices, as HDF5 vlen
data (:issue:`1649`).
* Fix pathologically slow reading/writing in certain conditions with integer
indexing (:issue:`492`).
* Fix bug when :meth:`.Group.copy` source is a high-level object and destination
is a Group (:issue:`1005`).
* Fix reading data for region references pointing to an empty selection.
* Unregister converter functions at exit, preventing segfaults on exit in some
situations with threads (:pr:`1440`).
* As HDF5 1.10.6 and later support UTF-8 paths on Windows, h5py built against
HDF5 1.10.6 will use UTF-8 for file names, allowing all filenames.
* Fixed :meth:`h5py.h5d.DatasetID.get_storage_size` to report storage size of
zero bytes without raising an exception (:issue:`1475`).
* Attribute Managers (``obj.attrs``) can now work on HDF5 stored
datatypes (:issue:`1476`).
* Remove broken inherited ``ds.dims.values()`` and ``ds.dims.items()`` methods.
The dimensions interface behaves as a sequence, not a mapping (:issue:`744`).
* Fix creating attribute with :class:`.Empty` by converting its dtype to a numpy
dtype object.
* Fix getting :attr:`~.Dataset.maxshape` on empty/null datasets.
* The :attr:`.File.swmr_mode` property is always available (:issue:`1580`).
* The :attr:`.File.mode` property handles SWMR access modes in addition to plain
RDONLY/RDWR modes
* Importing an MPI build of h5py no longer initialises MPI immediately,
which will hopefully avoid various strange behaviours.
* Avoid launching a subprocess by using ``platform.machine()`` at import time.
This could trigger a warning in MPI.
* Removed an equality comparison with an empty array, which will cause problems
with future versions of numpy.
* Better error message if you try to use the mpio driver and h5py was not built
with MPI support.
* Improved error messages when requesting chunked storage for an empty dataset.
* Data conversion functions should fail more gracefully if no memory is
available.
* Fix some errors for internal functions that were raising "TypeError:
expected bytes, str found" instead of the correct error.
* Use relative path for virtual data sources if the source dataset is in the
same file as the virtual dataset.
* Generic exception types used in tests' assertRaise (exception types changed in
new HDF5 version)
* Use ``dtype=object`` in tests with ragged arrays
Building h5py
-------------
* The ``setup.py configure`` command was removed. Configuration for the build
can be specified with environment variables instead. See :ref:`custom_install`
for details.
* It is now possible to specify separate include and library directories for
HDF5 via environment variables. See :ref:`custom_install` for more details.
* The pkg-config name to use when looking up the HDF5 library can now be
configured, this can assist with selecting the correct HDF5 library when using
MPI. See :ref:`custom_install` for more details.
* Using bare ``char*`` instead of ``array.array`` in h5d.read_direct_chunk since
``array.array`` is a private CPython C-API interface
* Define ``NPY_NO_DEPRECATED_API`` to silence a warning.
* Make the lzf filter build with HDF5 1.10 (:issue:`1219`).
* If HDF5 is not loaded, an additional message is displayed to check HDF5
installation
* Rely much more on the C-interface provided by Cython to call Python and NumPy.
* Removed an old workaround which tried to run Cython in a subprocess if
cythonize() didn't work. This shouldn't be necessary for any recent version
of setuptools.
* Migrate all Cython code base to Cython3 syntax
* The only noticeable change is in exception raising from cython which use bytes
* Massively use local imports everywhere as expected from Python3
* Explicitly mark several Cython functions as non-binding
Development
-----------
* Unregistering converter functions on exit (:pr:`1440`) should allow profiling
and code coverage tools to work on Cython code.
Revision 1.6 / (download) - annotate - [select for diffs], Sun Jun 16 14:11:49 2019 UTC (4 years, 3 months ago) by adam
Branch: MAIN
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Changes since 1.5: +5 -5
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py-h5py: updated to 2.9.0 What's new in h5py 2.9 New features * A convenient high-level API for creating virtual datasets, HDF5 objects which act as a view over one or more real datasets. See :ref:vds for details. * :class:File can now be constructed with a Python file-like object, making it easy to create an HDF5 file in memory using :class:io.BytesIO See :ref:file_fileobj for details. * :class:File now accepts parameters to control the chunk cache. See :ref:file_cache for details. * New options to record the order of insertion for attributes and group entries. Iterating over these collections now follows insertion order if it was recorded, or name order if not. * A new method :meth:Group.create_dataset_like to create a new dataset with similar properties to an existing one. * Datasets can now be created with storage backed by external non-HDF5 files * Lists or tuples of unicode strings can now be stored as HDF5 attributes * Inspecting the view returned by .keys() now shows the key names, for convenient interactive use. Exposing HDF5 functions * H5LTopen_file_image as :func:h5py.h5f.open_file_image. * External dataset storage functions H5Pset_external, H5Pget_external and H5Pget_external_count as methods on :class:h5py.h5p.PropDCID Bugfixes * Fix reading/writing of float128 data. * Converting data to float16 when creating a dataset. Support for old Python Support for Python 3.3 has been dropped. Support for Python 2.6 has been dropped.
Revision 1.5 / (download) - annotate - [select for diffs], Tue Nov 20 05:39:28 2018 UTC (4 years, 10 months ago) by markd
Branch: MAIN
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Changes since 1.4: +5 -5
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py-h5py: update to 2.8.0 Features - allow registration of new drivers - add option to track object creation order Bug fixes - allow slices with stop < start as empty - improve building with custom hdf5 installation - ensure libver defaults to LIBVER_EARLIEST - improve handling of float types - support non-ascii external paths on py2 - avoid crashing IPython auto-completer API changes - deprecate ``h5t.available_ftypes``. This is no longer used internally and will be removed in the future. There is no replacement public API. - Do not sort fields in compound types. This is account for changes in numpy 1.14. - Minimum version of cython is now 0.23
Revision 1.4 / (download) - annotate - [select for diffs], Thu Nov 16 22:36:04 2017 UTC (5 years, 10 months ago) by minskim
Branch: MAIN
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devel/py-h5py: Update to 2.7.1 Notable changes since 2.5.0: - Support for HDF5 Virtual Dataset API - Add MPI Collective I/O Support
Revision 1.3 / (download) - annotate - [select for diffs], Tue Nov 3 03:29:08 2015 UTC (7 years, 10 months ago) by agc
Branch: MAIN
CVS Tags: pkgsrc-2017Q3-base,
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pkgsrc-2016Q4-base,
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pkgsrc-2016Q1-base,
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Add SHA512 digests for distfiles for devel category Issues found with existing distfiles: distfiles/eclipse-sourceBuild-srcIncluded-3.0.1.zip distfiles/fortran-utils-1.1.tar.gz distfiles/ivykis-0.39.tar.gz distfiles/enum-1.11.tar.gz distfiles/pvs-3.2-libraries.tgz distfiles/pvs-3.2-linux.tgz distfiles/pvs-3.2-solaris.tgz distfiles/pvs-3.2-system.tgz No changes made to these distinfo files. Otherwise, existing SHA1 digests verified and found to be the same on the machine holding the existing distfiles (morden). All existing SHA1 digests retained for now as an audit trail.
Revision 1.2 / (download) - annotate - [select for diffs], Wed Sep 23 12:11:47 2015 UTC (8 years ago) by joerg
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Update py-h5py to 2.5.0 to sync with the API changes in devel/hdf. cython is now unconditional and the package is installed as egg.
Revision 1.1 / (download) - annotate - [select for diffs], Thu Feb 6 14:22:51 2014 UTC (9 years, 7 months ago) by drochner
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add py-h5py-2.2.1, Python bindings to hdf5, from Kamel Derouiche per pkgsrc-wip