CVS commit: pkgsrc/devel/py-h5py

To: pkgsrc-changes%NetBSD.org@localhost
Subject: CVS commit: pkgsrc/devel/py-h5py
From: "Thomas Klausner" <wiz%netbsd.org@localhost>
Date: Mon, 7 Jul 2025 06:54:28 +0000

Module Name:    pkgsrc
Committed By:   wiz
Date:           Mon Jul  7 06:54:28 UTC 2025

Modified Files:
        pkgsrc/devel/py-h5py: Makefile PLIST distinfo

Log Message:
py-h5py: update to 3.14.0.

What's new in h5py 3.14
=======================

New features
------------

* On NumPy 2.x, it is now possible to read and write native `NumPy variable-width
  strings <https://numpy.org/doc/stable/user/basics.strings.html#variable-width-strings>`_,
  a.k.a. ``StringDType()`` or ``dtype='T'``, which are more efficient
  than arrays of Python string objects (:pr:`2557`). Variable length string data
  is still read as string objects by default, for consistency with previous
  versions of h5py and to work with NumPy 1.x; use ``dset.astype('T')`` to read
  in the new format. See :ref:`npystrings`.

Exposing HDF5 functions
-----------------------

* :meth:`h5py.h5d.DatasetID.write_direct_chunk` now wraps ``H5Dwrite_chunk``
  instead of ``H5DOwrite_chunk``. This should not change its behaviour (:pr:`2586`).

Bug fixes
---------

* Fixed a problem with `phil` Lock handling in forked processes when h5py is
  also used from other threads (:pr:`2585`).
* Fixed an error using :meth:`.Dataset.read_direct` with a zero-size selection
  (:pr:`2577`).
* Creating a virtual dataset containing 0 mappings from the high-level API now
  works, making a dataset with virtual layout (:pr:`2562`).

Building h5py
-------------

* setuptools 77 or above is now required, due to changes in the license metadata
  in ``pyproject.toml`` (:pr:`2580`).
* Numpy variable-width string support does not alter the build process: you need
  NumPy 2.x to build (as before), but the built packages remain backwards
  compatible with NumPy 1.x.

What's new in h5py 3.13
=======================

New features
------------

* New :meth:`.File.in_memory` constructor to conveniently build an HDF5 file
  structure in memory (:pr:`2517`).
* :class:`.Dataset` views returned by :meth:`~.Dataset.astype`,
  :meth:`~.Dataset.asstr` and :meth:`~.Dataset.fields` have gained the
  ``.dtype``, ``.ndim``, ``.shape``, and ``.size`` attributes (:pr:`2550`).
* The bundled HDF5 library in the pre-built packages was updated to 1.14.6
  (:pr:`2554`).
* Opening an existing dataset in a file is faster since it now only loads the
  "dataset creation property list" when required (:pr:`2552`).

Exposing HDF5 functions
-----------------------

* ``H5Sselect_shape_same`` exposed as :meth:`h5py.h5s.SpaceID.select_shape_same`
  (:pr:`2529`).

Bug fixes
---------

* Fix various bugs when applying ``np.array`` or ``np.asarray`` to a
  :class:`.Dataset` view returned by :meth:`~.Dataset.astype`,
  :meth:`~.Dataset.asstr`, or :meth:`~.Dataset.fields`.

Building h5py
-------------

* Fixed building h5py with Numpy 2.3 (:pr:`2556`).
* Bump the specified mpi4py version to fix building with MPI support on
  Python 3.13 (:pr:`2524`).
* Fix for running ``api_gen.py`` directly (:pr:`2534`).

What's new in h5py 3.12
=======================

New features
------------

* h5py now has pre-built packages for Python 3.13.

  * However, h5py is not yet compatible with the new free-threading mode;
    we're tracking work on that in issue :issue:`2475`.

Breaking changes
----------------

* Support for Python 3.8 was dropped (:pr:`2471`). Python 3.9 or newer is
  required to build or install h5py 3.12.
* The minimum supported version of HDF5 was increased to 1.10.6 (:pr:`2486`).
  If you need h5py on HDF5 1.10.4 or .5, please use h5py 3.11.
* The fill time for chunked storage was previously set to ``h5d.FILL_TIME_ALLOC``.
  Now this the default comes from HDF5, which uses ``h5d.FILL_TIME_IFSET``
  (equivalent to ``fill_time='ifset'``) (:pr:`2463`). Please use
  ``fill_time='alloc'`` if the change is a problem for you.

Exposing HDF5 functions
-----------------------

* Expose fill time option in dataset creation property list via the
  ``fill_time`` parameter in :meth:`~.Group.create_dataset` (:pr:`2463`).

Bug fixes
---------

* Fix an error where native float16 support is not available (:pr:`2422`).
* Fixed values of ``H5F_close_degree_t`` enum (:pr:`2433`).
* External links are now accessed with libhdf5's default access properties
  (:pr:`2433`).
* Fix the iteration order for the root group in a file with creation order
  tracked (:pr:`2410`).
* Fixed some deprecation warnings from NumPy (:pr:`2416`).

Building h5py
-------------

* Require a newer version of mpi4py for Python 3.12 (:pr:`2418`).
* The test suite is now configured to fail on unexpected warnings (:pr:`2428`).
* The generated Cython wrapper code (``defs.*`` & ``_hdf5.pxd``) is now specific
  to the version of HDF5 it's building for. If the version of HDF5 has changed,
  ``api_gen.py`` should be run automatically to recreate this (:pr:`2479`,
  :pr:`2480`).
* Various PRs modernising & cleaning up old Cython code, see the `3.12 milestone
  on Github <https://github.com/h5py/h5py/milestone/31?closed=1>`_ for details.

3.12.1 bug fix release
----------------------

* Fix bundling HDF5 DLLs in pre-built packages for Windows (:pr:`2507`).


To generate a diff of this commit:
cvs rdiff -u -r1.23 -r1.24 pkgsrc/devel/py-h5py/Makefile
cvs rdiff -u -r1.10 -r1.11 pkgsrc/devel/py-h5py/PLIST
cvs rdiff -u -r1.13 -r1.14 pkgsrc/devel/py-h5py/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/devel/py-h5py/Makefile
diff -u pkgsrc/devel/py-h5py/Makefile:1.23 pkgsrc/devel/py-h5py/Makefile:1.24
--- pkgsrc/devel/py-h5py/Makefile:1.23  Thu Jul  3 19:18:03 2025
+++ pkgsrc/devel/py-h5py/Makefile       Mon Jul  7 06:54:27 2025
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.23 2025/07/03 19:18:03 wiz Exp $
+# $NetBSD: Makefile,v 1.24 2025/07/07 06:54:27 wiz Exp $
 
-DISTNAME=      h5py-3.11.0
+DISTNAME=      h5py-3.14.0
 PKGNAME=       ${PYPKGPREFIX}-${DISTNAME}
-PKGREVISION=   1
 CATEGORIES=    devel python
 MASTER_SITES=  ${MASTER_SITE_PYPI:=h/h5py/}
 

Index: pkgsrc/devel/py-h5py/PLIST
diff -u pkgsrc/devel/py-h5py/PLIST:1.10 pkgsrc/devel/py-h5py/PLIST:1.11
--- pkgsrc/devel/py-h5py/PLIST:1.10     Sat Apr 12 11:08:23 2025
+++ pkgsrc/devel/py-h5py/PLIST  Mon Jul  7 06:54:27 2025
@@ -1,8 +1,14 @@
-@comment $NetBSD: PLIST,v 1.10 2025/04/12 11:08:23 adam Exp $
+@comment $NetBSD: PLIST,v 1.11 2025/07/07 06:54:27 wiz Exp $
 ${PYSITELIB}/${WHEEL_INFODIR}/METADATA
 ${PYSITELIB}/${WHEEL_INFODIR}/RECORD
 ${PYSITELIB}/${WHEEL_INFODIR}/WHEEL
 ${PYSITELIB}/${WHEEL_INFODIR}/licenses/LICENSE
+${PYSITELIB}/${WHEEL_INFODIR}/licenses/licenses/hdf5.txt
+${PYSITELIB}/${WHEEL_INFODIR}/licenses/licenses/license.txt
+${PYSITELIB}/${WHEEL_INFODIR}/licenses/licenses/pytables.txt
+${PYSITELIB}/${WHEEL_INFODIR}/licenses/licenses/python.txt
+${PYSITELIB}/${WHEEL_INFODIR}/licenses/licenses/stdint.txt
+${PYSITELIB}/${WHEEL_INFODIR}/licenses/lzf/LICENSE.txt
 ${PYSITELIB}/${WHEEL_INFODIR}/top_level.txt
 ${PYSITELIB}/h5py/__init__.py
 ${PYSITELIB}/h5py/__init__.pyc
@@ -48,6 +54,7 @@ ${PYSITELIB}/h5py/_hl/selections2.pyo
 ${PYSITELIB}/h5py/_hl/vds.py
 ${PYSITELIB}/h5py/_hl/vds.pyc
 ${PYSITELIB}/h5py/_hl/vds.pyo
+${PYSITELIB}/h5py/_npystrings.so
 ${PYSITELIB}/h5py/_objects.so
 ${PYSITELIB}/h5py/_proxy.so
 ${PYSITELIB}/h5py/_selector.so
@@ -168,12 +175,18 @@ ${PYSITELIB}/h5py/tests/test_h5p.pyo
 ${PYSITELIB}/h5py/tests/test_h5pl.py
 ${PYSITELIB}/h5py/tests/test_h5pl.pyc
 ${PYSITELIB}/h5py/tests/test_h5pl.pyo
+${PYSITELIB}/h5py/tests/test_h5s.py
+${PYSITELIB}/h5py/tests/test_h5s.pyc
+${PYSITELIB}/h5py/tests/test_h5s.pyo
 ${PYSITELIB}/h5py/tests/test_h5t.py
 ${PYSITELIB}/h5py/tests/test_h5t.pyc
 ${PYSITELIB}/h5py/tests/test_h5t.pyo
 ${PYSITELIB}/h5py/tests/test_h5z.py
 ${PYSITELIB}/h5py/tests/test_h5z.pyc
 ${PYSITELIB}/h5py/tests/test_h5z.pyo
+${PYSITELIB}/h5py/tests/test_npystrings.py
+${PYSITELIB}/h5py/tests/test_npystrings.pyc
+${PYSITELIB}/h5py/tests/test_npystrings.pyo
 ${PYSITELIB}/h5py/tests/test_objects.py
 ${PYSITELIB}/h5py/tests/test_objects.pyc
 ${PYSITELIB}/h5py/tests/test_objects.pyo

Index: pkgsrc/devel/py-h5py/distinfo
diff -u pkgsrc/devel/py-h5py/distinfo:1.13 pkgsrc/devel/py-h5py/distinfo:1.14
--- pkgsrc/devel/py-h5py/distinfo:1.13  Tue Jun 18 10:42:30 2024
+++ pkgsrc/devel/py-h5py/distinfo       Mon Jul  7 06:54:27 2025
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.13 2024/06/18 10:42:30 markd Exp $
+$NetBSD: distinfo,v 1.14 2025/07/07 06:54:27 wiz Exp $
 
-BLAKE2s (h5py-3.11.0.tar.gz) = caf409a47070af4357348633f37f298e5f380affbb7af05f19f9444704329aa2
-SHA512 (h5py-3.11.0.tar.gz) = 05d99093d5e7c280779b4167bd3594488dfc348b800da95c2275ddc8d77b4208fd1353942bf8863c4859d0208e8aa8bf84e628b3c5942eb947ecdcf0a7d19e88
-Size (h5py-3.11.0.tar.gz) = 406519 bytes
+BLAKE2s (h5py-3.14.0.tar.gz) = ab5706cec26b12ddd26f455c135d55cef3e021315356f73567a0a17f329638ba
+SHA512 (h5py-3.14.0.tar.gz) = 54e0054a542c8b62da90e15c110a153cc0cadc6cba1914074d35a6380f8b270ba051de860feb7e31c2ee3d4f09903e456c94e9faa3570764af0e36c480e1c44e
+Size (h5py-3.14.0.tar.gz) = 424323 bytes

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