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| Name: python39-h5py | Distribution: openSUSE Tumbleweed |
| Version: 3.9.0 | Vendor: openSUSE |
| Release: 2.1 | Build date: Tue Oct 24 20:24:58 2023 |
| Group: Development/Libraries/Python | Build host: i02-armsrv2 |
| Size: 4417084 | Source RPM: python-h5py-3.9.0-2.1.src.rpm |
| Packager: http://bugs.opensuse.org | |
| Url: https://github.com/h5py/h5py | |
| Summary: Python interface to the Hierarchical Data Format library | |
H5py provides a simple, robust read/write interface to HDF5 data from Python. Existing Python and Numpy concepts are used for the interface; for example, datasets on disk are represented by a proxy class that supports slicing, and has dtype and shape attributes. HDF5 groups are presented using a dictionary metaphor, indexed by name.
BSD-3-Clause
* Mon Oct 23 2023 Nicolas Morey <nicolas.morey@suse.com>
- Drop support for obsolete openmpi[123]
- Prepare support for openmpi5
* Tue Aug 22 2023 Ben Greiner <code@bnavigator.de>
- Update to 3.9.0
* This version of h5py requires Python 3.8 or above.
[#]# New features
* New out argument to read_direct_chunk() to allow passing the
output buffer (PR 2232).
* The objects from Dataset.asstr() and 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 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
h5py.h5p.PropLAID.get_elink_acc_flags() &
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 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 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 modify() instead.
[#]# Building h5py
* When building with Parallel HDF5 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).
* Thu Feb 16 2023 Ben Greiner <code@bnavigator.de>
- Clean up build and runtime requirements
- Drop python-h5py-relax-dependency-versions.patch -- it has become
a noop at the last refresh.
- Only build for supported pythons (>= 3.7)
- PEP517 build
* Wed Feb 08 2023 Arun Persaud <arun@gmx.de>
- specfile:
* update copyright year
* update patch
- update to version 3.8.0:
* New features
+ h5py now has pre-built packages for Python 3.11.
+ h5py is compatible with HDF5 1.14 (:pr:`2187`). Pre-built
packages on PyPI still include HDF5 1.12 for now.
+ :ref:`dataset_fancy` now accepts tuples, or any other sequence
type, rather than only lists and NumPy arrays. This also
includes range objects, but this will normally be less efficient
than the equivalent slice.
+ New property :attr:`.Dataset.is_scale` for checking if the
dataset is a dimension scale (:pr:`2168`).
+ :meth:`.Group.require_dataset` now validates maxshape for
resizable datasets (:pr:`2116`).
+ :class:`.File` now has a meta_block_size argument and
property. This influences how the space for metadata, including
the initial header, is allocated.
+ Chunk cache can be configured per individual HDF5 dataset
(:pr:`2127`). Use :meth:`.Group.create_dataset` for new datasets
or :meth:`.Group.require_dataset` for already existing
datasets. Any combination of the rdcc_nbytes, rdcc_w0, and
rdcc_nslots arguments is allowed. The file defaults apply to
those omitted.
+ HDF5 file names for ros3 driver can now also be s3:// resource
locations (:pr:`2140`). h5py will translate them into AWS
path-style URLs for use by the driver.
+ When using the ros3 driver, AWS authentication will be activated
only if all three driver arguments are provided. Previously AWS
authentication was active if any one of the arguments was set
causing an error from the HDF5 library.
+ :meth:`.Dataset.fields` now implements the __array__() method
(:pr:`2151`). This speeds up accessing fields with functions
that expect this, like np.asarray().
+ Low-level :meth:`h5py.h5d.DatasetID.chunk_iter` method that
invokes a user-supplied callable object on every written chunk
of one dataset (:pr:`2202`). It provides much better performance
when iterating over a large number of chunks.
* Exposing HDF5 functions
+ H5Dchunk_iter as :meth:`h5py.h5d.DatasetID.chunk_iter`.
+ H5Pset_meta_block_size and H5Pget_meta_block_size (:pr:`2106`).
* Bug fixes
+ Fixed getting the default fill value (an empty string) for
variable-length string data (:pr:`2132`).
+ Complex float16 data could cause a TypeError when trying to
coerce to the currently unavailable numpy.dtype('c4'). Now a
compound type is used instead (:pr:`2157`).
+ h5py 3.7 contained a performance regression when using a boolean
mask array to index a 1D dataset, which is now fixed
(:pr:`2193`).
* Building h5py
+ Parallel HDF5 can be built with Microsoft MS-MPI
(:pr:`2147`). See :ref:`build_mpi` for details.
+ Some 'incompatible function pointer type' compile time warnings
were fixed (:pr:`2142`).
+ Fix for finding HDF5 DLL in mingw (:pr:`2105`).
* Sun May 29 2022 Atri Bhattacharya <badshah400@gmail.com>
- Update to version 3.7.0:
* Provide the ability to use the Direct Virtual File Driver
(VFD) from HDF5 (Linux only).
* The :class:`.File` constructor contains two new parameters
alignment_threshold, and alignment_interval controling the
data alignment within the HDF5 file (gh#h5py/h5py#2040).
* :meth:`~.Group.create_dataset` and
:meth:`~.Group.require_dataset` now accept parameters
efile_prefix and virtual_prefix to set a filesystem path
prefix to use to find files for external datasets and for
virtual dataset sources (gh#h5py/h5py#2092). These only affect
the current access; the prefix is not stored in the file.
* Bugs fixed:
- Fix a deadlock which was possible when the same dataset was
accessed from multiple threads (gh#h5py/h5py#2064).
- New attributes are created directly, instead of via a
temporary attribute with subsequent renaming. This fixes
overwriting attributes with track_order=True.
- Fix for building with mpi4py on Python 3.10
(gh#h5py/h5py#2101).
- Fixed fancy indexing with a boolean array for a single
dimension (gh#h5py/h5py#2079).
- Avoid returning unitialised memory when reading from a
chunked dataset with missing chunks and no fill value
(gh#h5py/h5py#2076).
- Enable setting of fillvalue for datasets with variable
length string dtype (gh#h5py/h5py#2044).
- Closing a file or calling get_obj_ids() no longer re-enables
Python garbage collection if it was previously disabled
(gh#h5py/h5py#2020).
- Refresh python-h5py-relax-dependency-versions.patch for updated
version.
* Fri Mar 04 2022 Atri Bhattacharya <badshah400@gmail.com>
- Update to version 3.6.0:
* Using :meth:`.Dataset.astype` as a context manager (with
dset.astype(t):) is deprecated. Slice the object returned by
astype instead (data = dset.astype(t)[:10]).
* Getting the value of h5py.get_config().default_file_mode now
issues a deprecation warning. This has been 'r' by default
from h5py 3.0, and cannot be changed since 3.3.
- Rebase python-h5py-relax-dependency-versions.patch to apply
against updated version.
- Also enforce %requires_eq on hdf5 to force rebuilds when hdf5
gets version updates in Factory (boo#1196682).
- Skip tests marked with 'mpi_skip' when building with openmpi
flavours (see e.g., https://github.com/h5py/h5py/issues/1997).
* Thu Sep 09 2021 Matej Cepl <mcepl@suse.com>
- Correct order of definitions to generate multiple packages for
multiple builds.
* Sun Sep 05 2021 Arun Persaud <arun@gmx.de>
- update to version 3.4.0:
* New features
+ The pre-built wheels now bundle HDF5 1.12.1 (:pr:`1945`).
+ len() now works on dset.astype(), .asstr() and .fields()
wrappers (:pr:`1913`).
* Bug fixes
+ Fix bug introduced in version 3.3 that did not allow the
creation of files using the flag "a" for certain drivers
(e.g. mpiio, core and stdio) (:pr:`1922`).
+ Dataset indexing will now use the optimized fast path, which was
accidentally disabled in a previous version (:pr:`1944`).
+ Fix an error building with Cython 3.0 alpha 8 (cpdef inside
functions) (:pr:`1923`).
* Wed Jun 23 2021 andy great <andythe_great@pm.me>
- Update to version 3.3.0.
* New features
* Compatibility with the upcoming HDF5 1.12.1 and possibly 1.14.
* H5T_BITFIELD types will now be cast to their numpy.uint
equivalent by default (:issue:`1258`). This means that
no knowledge of mixed type compound dataset schemas is
required to read these types, and can simply be read as
follows: arr = dset[:]
Alternatively, 8-bit bitfields can still be cast to booleans
explicitly: arr = dset.astype(numpy.bool_)[:]
* Key types are validated when accessing groups, to give more
helpful errors when a group is indexed like a dataset.
* A new :meth:`.Group.build_virtual_dataset` method acting as
a context manager to assemble virtual datasets.
* If the source and target of a virtual dataset mapping have
different numbers of points, an error should now be thrown
when you make the mapping in the :class:`VirtualLayout`,
rather than later when writing this into the file. This
should make it easier to find the source of such errors.
* Deprecations
* The default_file_mode config option is deprecated, and setting
it to values other than 'r' (for read-only mode) is no longer
allowed. Pass the mode when creating a :class:`.File` object
instead of setting a global default.
* Bug fixes
* Trying to open a file in append mode ('a') should now give
clearer error messages when the file exists but can't be opened.
* Protect :func:`h5py.h5f.get_obj_ids` against garbage collection
invalidating HDF5 IDs while it is retrieving them.
* Make file closing more robust, including when closing files
while the interpreter is shutting down, by using lower-level
code to close HDF5 IDs of objects inside the file.
- Updates for version 3.2.0.
* New features
* Added support to use the HDF5 ROS3 driver to access HDF5 files
on S3.
* Breaking changes & deprecations
* 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.
* Fix reading data with a datatype of variable-length arrays of
fixed length strings.
* Fix :meth:`.Dataset.read_direct` and :meth:`.Dataset.write_direct`
when the source and destination have different shapes.
* Fix selecting data using integer indices in
:meth:`.Dataset.read_direct` and :meth:`.Dataset.write_direct`.
* Fix exception handling in :meth:`.Group.visititems`.
* Issue a warning when File(..., swmr=True) is specified with
any mode other than 'r', as the SWMR option is ignored in
these cases.
* Fix NumPy 1.20 deprecation warnings concerning the use of
None as shape, and the deprecated aliases np.float, np.int
and np.bool.
* 3.2.1 bug fix release
* Fix :attr:`.File.driver` when the read-only S3 driver is
available.
- Rebase python-h5py-relax-dependency-versions.patch
* Thu Feb 18 2021 Ben Greiner <code@bnavigator.de>
- Skip python36 build. NumPy 1.20 in Tumbleweed dropped support for
Python 3.6 (NEP 29)
- Fix sitearch handling between regular and mpi builds suitable for
singlespec with multiple python3 flavors
- Refine requirement versions based on Python version
* Wed Jan 20 2021 John Vandenberg <jayvdb@gmail.com>
- Add runtime dependency cached-property based on Python version
* Fri Dec 11 2020 Atri Bhattacharya <badshah400@gmail.com>
- Replace %__python3 usage by %python_exec.
* Fri Dec 04 2020 Atri Bhattacharya <badshah400@gmail.com>
- Enable parallel hdf5:
* Implement multibuild for different flavors of openmpi.
* Export env variables `HDF5_LIBDIR` and `HDF5_INCLUDEDIR`
pointing to the hdf library and headers location when enabling
openmpi flavored builds.
* Add BuildRequires: python-pytest-mpi for mpi tests.
* Replace python rpm macros with their expansions in most cases
to adapt to mpi paths.
* Thu Nov 26 2020 Atri Bhattacharya <badshah400@gmail.com>
- Update to version 3.1.0:
* See https://docs.h5py.org/en/latest/whatsnew/3.1.html for list
of changes.
- Changes from version 3.0.0: See
https://docs.h5py.org/en/latest/whatsnew/3.0.html
- Drop upstreamed patches:
* remove_unittest2.patch.
* no_include_opt.patch.
- Add python-h5py-relax-dependency-versions.patch to allow building
against more recent versions of numpy than minimally required.
- Python 2 is no longer supported; at least version 3.6 is
required.
- Run all tests except:
* MPI based ones, as we build against the non-mpi version of
hdf5.
* Offset test which overflows on 32-bit.
- Tests require python-cached-property for openSUSE <= 1500.
- Fix `requires_eq` on libhdf5 (oS:F now has libhdf_hl103)
already.
* Mon May 11 2020 Dirk Mueller <dmueller@suse.com>
- ensure rebuild when hdf5 version changes (bsc#1150049)
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