CVS commit: pkgsrc/math/py-tables

To: pkgsrc-changes%NetBSD.org@localhost
Subject: CVS commit: pkgsrc/math/py-tables
From: "Thomas Klausner" <wiz%netbsd.org@localhost>
Date: Wed, 13 Dec 2023 20:18:37 +0000

Module Name:    pkgsrc
Committed By:   wiz
Date:           Wed Dec 13 20:18:37 UTC 2023

Modified Files:
        pkgsrc/math/py-tables: Makefile PLIST distinfo

Log Message:
py-tables: update to 3.9.2.

Changes from 3.9.1 to 3.9.2
===========================

Bugfixes
--------

- Fix the assembly of returned slice data in Blosc2 NDim optimized slice reads
  by using Blosc2's `b2nd_copy_buffer` (:PR:`1078`).  The bug only showed up
  when the chunk did not fully cover the innermost dimension.  Add unit tests
  to ckeck for regressions, along with foreign-generated files, and enable and
  fix Blosc2 NDim tests which were not being run.  Thanks to Ivan Vilata.

Improvements
------------

- PyTables wheels now use a threadsafe build of the HDF5 library
  (:issue:`1075` and :PR:`1077`).  Concurrent reads should be possible with no
  need for additional locking or monkey-patching of the file open function.
  Thanks to Kiet Pham.
- Partial support for the future NumPy 2, with some tests still failing
  (:PR:`1068`).  Thanks to Thomas Grainger.
- Relax the reading of Blosc2 NDim to cope with datasets stored with other
  tools (:PR:`1072`), e.g. missing chunk rank/shape in filter values, having
  HDF5 chunks where the Blosc2 super-chunk contains more than one inner chunk,
  or chunks with data not padded to the full chunk size (example script and
  tests included).  Also enhance checks, comments and logged messages.  Thanks
  to Ivan Vilata.

Other changes
-------------

- Drop compatibility with the obsolete HDF5 1.8 API.  PyTables now requires at
  least the 1.10 API (:PR:`1080`).  Thanks to Antonio Valentino.
- Require python-blosc2 >= 2.3.0 or c-blosc2 >= 2.11.0 (which adds support for
  the `b2nd_copy_buffer` function).
- Use the main Conda Forge channel for Python 3.12 (:PR:`1066`).  Thanks to
  Thomas Grainger.
- Assorted fixes to the b2nd slicing benchmark.  Thanks to Ivan Vilata.
- Assorted fixes to b2nd slicing optimization tips (:PR:`1069`).  Thanks to
  Ivan Vilata.

Changes from 3.9.0 to 3.9.1
===========================

- Minimum supported version for Python is 3.9 (see :issue:`1062`).

Changes from 3.8.0 to 3.9.0
===========================

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

- Apply optimized slice read to Blosc2-compressed `CArray` and `EArray`, with
  Blosc2 NDim 2-level partitioning for multidimensional arrays (:PR:`1056`).
  See "Multidimensional slicing and chunk/block sizes" in the User's Guide.
  Thanks to Marta Iborra and Ivan Vilata.  This development was funded by a
  NumFOCUS grant.
- Add basic API for column-level attributes as `Col._v_col_attrs` (:PR:`893`
  and :issue:`821`).  Thanks to Jonathan Wheeler, Thorben Menne, Ezequiel
  Cimadevilla Alvarez, odidev, Sander Roet, Antonio Valentino, Munehiro
  Nishida, Zbigniew Jędrzejewski-Szmek, Laurent Repiton, xmatthias, Logan
  Kilpatrick.

Other changes
-------------

- Add support for the forthcoming Python 3.12 with binary wheels and automated
  testing.
- Drop wheels and automated testing for Python 3.8; users or distributions may
  still build and test with Python 3.8 on their own (see :commit:`ae1e60e` and
  :commit:`47f5946`).
- New benchmark for ERA5 climate data.  Thanks to Óscar Guiñón.
- New "100 trillion baby" benchmark.  Thanks to Francesc Alted.
- New benchmark for querying meteorologic data.  Thanks to Francesc Alted.

Improvements
------------

- Use `H5Dchunk_iter` (when available) to speed up walking over many chunks in
  a very large table, as well as with random reads (:issue:`991`, :PR:`997`,
  :PR:`999`).  Thanks to Francesc Alted and Mark Kittisopikul.
- Improve `setup.py` (now using `pyproject.toml` as per PEP 518) and `blosc2`
  discovery mechanism.  Blosc2 may be used both via python-blosc2 or system
  c-blosc2 (:PR:`987`, :PR:`1000`, :issue:`998`, :PR:`1017`,
  :PR:`1045`). Thanks to Antonio Valentino, Ben Greiner, Iwo-KX, nega.
- Enable compatibility with Cython 3 (:PR:`1008` and :issue:`1003`).  Thanks
  to Matus Valo and Michał Górny.
- Set GitHub workflow permissions to least privileges (:PR:`1007`).  Thanks to
  Joyce Brum.
- Add `SECURITY.md` with security policy (:PR:`1012` and :issue:`1011`).
  Thanks to Joyce Brum.
- Handle py-cpuinfo missing in some platforms (:PR:`1013`).  Thanks to Sam
  James.
- Avoid NumPy >= 1.25 deprecations, use `numpy.all`, `numpy.any`,
  etc. instead.  Thanks to Antonio Valentino.
- Avoid C-related build warnings.  Thanks to Antonio Valentino.
- Streamline CI wheel building & testing with `cibuildwheel`, more clear
  distinctions between build and runtime dependencies.
- Update included c-blosc to v1.21.5 (fixes SSE2/AVX build issue).
- Require python-blosc2 >= 2.2.8 or c-blosc2 >= 2.10.4 (Python 3.12 support
  and assorted fixes).
- Update external libraries for CI-based wheel builds (:PR:`1018` and
  :issue:`967`):

  * hdf5 v1.14.2
  * lz4 v1.9.4
  * zlib v1.2.13

Bugfixes
--------

- Fix crash in Blosc2 optimized path with large tables (:issue:`995` and
  :PR:`996`).  Thanks to Francesc Alted.
- Fix compatibility with NumExpr v2.8.5 (:PR:`1046`).  Thanks to Antonio
  Valentino.
- Fix build errors on Windows ARM64 (:PR:`989`).  Thanks to Cristoph Gohlke.
- Fix `ptrepack` failures with external links (:issue:`938` and :PR:`990`).
  Thanks to Adrian Altenhoff.
- Replace stderr messages with Python warnings (:issue:`992` and :PR:`993`).
  Thanks to Maximilian Linhoff.
- Fixes to CI workflow and wheel building (:PR:`1009`, :PR:`1047`).  Thanks to
  Antonio Valentino.
- Fix garbled rendering of `File.get_node` docstring (:PR:`1021`).  Thanks to
  Steffen Rehberg.
- Fix open `extern "C"` block (:PR:`1026`).  Thanks to Ivan Vilata.
- Fix Cython slice indexing under Python 3.12 (:PR:`1033`).  Thanks to
  Zbigniew Jędrzejewski-Szmek.
- Fix unsafe temporary file creation in benchmark (:PR:`1053`).  Thanks to Al
  Arafat Tanin (Project Alpha-Omega).


To generate a diff of this commit:
cvs rdiff -u -r1.16 -r1.17 pkgsrc/math/py-tables/Makefile
cvs rdiff -u -r1.4 -r1.5 pkgsrc/math/py-tables/PLIST
cvs rdiff -u -r1.7 -r1.8 pkgsrc/math/py-tables/distinfo

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

Modified files:

Index: pkgsrc/math/py-tables/Makefile
diff -u pkgsrc/math/py-tables/Makefile:1.16 pkgsrc/math/py-tables/Makefile:1.17
--- pkgsrc/math/py-tables/Makefile:1.16 Tue Aug  1 23:20:49 2023
+++ pkgsrc/math/py-tables/Makefile      Wed Dec 13 20:18:36 2023
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.16 2023/08/01 23:20:49 wiz Exp $
+# $NetBSD: Makefile,v 1.17 2023/12/13 20:18:36 wiz Exp $
 
-DISTNAME=      tables-3.7.0
+DISTNAME=      tables-3.9.2
 PKGNAME=       ${PYPKGPREFIX}-${DISTNAME}
-PKGREVISION=   2
 CATEGORIES=    math python
 MASTER_SITES=  ${MASTER_SITE_PYPI:=t/tables/}
 
@@ -11,14 +10,9 @@ HOMEPAGE=    https://www.pytables.org/
 COMMENT=       Database package for large amounts of data
 LICENSE=       modified-bsd
 
-PYSETUPBUILDARGS+=     --blosc=${BUILDLINK_PREFIX.blosc}
-PYSETUPBUILDARGS+=     --bzip2=${BUILDLINK_PREFIX.bzip2}
-PYSETUPBUILDARGS+=     --hdf5=${BUILDLINK_PREFIX.hdf5}
-PYSETUPBUILDARGS+=     --lzo=${BUILDLINK_PREFIX.lzo}
-
-# check if cython dependency and post-extract target are still
-# needed when updating > 3.7.0
 TOOL_DEPENDS+= ${PYPKGPREFIX}-cython-[0-9]*:../../devel/py-cython
+TOOL_DEPENDS+= ${PYPKGPREFIX}-setuptools-[0-9]*:../../devel/py-setuptools
+TOOL_DEPENDS+= ${PYPKGPREFIX}-wheel-[0-9]*:../../devel/py-wheel
 DEPENDS+=      ${PYPKGPREFIX}-packaging-[0-9]*:../../devel/py-packaging
 DEPENDS+=      ${PYPKGPREFIX}-numexpr>=2.6.2:../../math/py-numexpr
 
@@ -26,12 +20,6 @@ USE_LANGUAGES=       c c++
 
 PYTHON_VERSIONS_INCOMPATIBLE=  27 38
 
-USE_PKG_RESOURCES=     yes
-
-post-extract:
-       cd ${WRKSRC}/tables && ${RM} _comp_*.c *extension.c
-       cythonize-${PYVERSSUFFIX} -3 ${WRKSRC}/tables/*.pxd
-
 post-install:
        cd ${DESTDIR}${PREFIX}/bin && \
        ${MV} pt2to3 pt2to3-${PYVERSSUFFIX} && \
@@ -40,16 +28,17 @@ post-install:
        ${MV} pttree pttree-${PYVERSSUFFIX} || ${TRUE}
 
 # needs to be installed first
-# as of 3.7.0:
-# FAILED (errors=2, skipped=55)
+# as of 3.9.2:
+# Ran 6799 tests
+# FAILED (errors=2, skipped=58)
 do-test:
        ${PYTHONBIN} -m tables.tests.test_all
 
 .include "../../archivers/bzip2/buildlink3.mk"
 .include "../../archivers/lzo/buildlink3.mk"
-.include "../../devel/blosc/buildlink3.mk"
+.include "../../devel/blosc2/buildlink3.mk"
 .include "../../devel/hdf5/buildlink3.mk"
 .include "../../devel/zlib/buildlink3.mk"
 .include "../../math/py-numpy/buildlink3.mk"
-.include "../../lang/python/egg.mk"
+.include "../../lang/python/wheel.mk"
 .include "../../mk/bsd.pkg.mk"

Index: pkgsrc/math/py-tables/PLIST
diff -u pkgsrc/math/py-tables/PLIST:1.4 pkgsrc/math/py-tables/PLIST:1.5
--- pkgsrc/math/py-tables/PLIST:1.4     Wed Jan  5 07:05:39 2022
+++ pkgsrc/math/py-tables/PLIST Wed Dec 13 20:18:36 2023
@@ -1,24 +1,24 @@
-@comment $NetBSD: PLIST,v 1.4 2022/01/05 07:05:39 wiz Exp $
+@comment $NetBSD: PLIST,v 1.5 2023/12/13 20:18:36 wiz Exp $
 bin/pt2to3-${PYVERSSUFFIX}
 bin/ptdump-${PYVERSSUFFIX}
 bin/ptrepack-${PYVERSSUFFIX}
 bin/pttree-${PYVERSSUFFIX}
-${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
-${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
-${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
-${PYSITELIB}/${EGG_INFODIR}/entry_points.txt
-${PYSITELIB}/${EGG_INFODIR}/not-zip-safe
-${PYSITELIB}/${EGG_INFODIR}/requires.txt
-${PYSITELIB}/${EGG_INFODIR}/top_level.txt
+${PYSITELIB}/${WHEEL_INFODIR}/LICENSE.txt
+${PYSITELIB}/${WHEEL_INFODIR}/METADATA
+${PYSITELIB}/${WHEEL_INFODIR}/RECORD
+${PYSITELIB}/${WHEEL_INFODIR}/WHEEL
+${PYSITELIB}/${WHEEL_INFODIR}/entry_points.txt
+${PYSITELIB}/${WHEEL_INFODIR}/top_level.txt
 ${PYSITELIB}/tables/__init__.py
 ${PYSITELIB}/tables/__init__.pyc
 ${PYSITELIB}/tables/__init__.pyo
-${PYSITELIB}/tables/_comp_bzip2.c
 ${PYSITELIB}/tables/_comp_bzip2.pyx
 ${PYSITELIB}/tables/_comp_bzip2.so
-${PYSITELIB}/tables/_comp_lzo.c
 ${PYSITELIB}/tables/_comp_lzo.pyx
 ${PYSITELIB}/tables/_comp_lzo.so
+${PYSITELIB}/tables/_version.py
+${PYSITELIB}/tables/_version.pyc
+${PYSITELIB}/tables/_version.pyo
 ${PYSITELIB}/tables/array.py
 ${PYSITELIB}/tables/array.pyc
 ${PYSITELIB}/tables/array.pyo
@@ -59,7 +59,6 @@ ${PYSITELIB}/tables/flavor.pyo
 ${PYSITELIB}/tables/group.py
 ${PYSITELIB}/tables/group.pyc
 ${PYSITELIB}/tables/group.pyo
-${PYSITELIB}/tables/hdf5extension.c
 ${PYSITELIB}/tables/hdf5extension.pxd
 ${PYSITELIB}/tables/hdf5extension.pyx
 ${PYSITELIB}/tables/hdf5extension.so
@@ -72,7 +71,6 @@ ${PYSITELIB}/tables/index.pyo
 ${PYSITELIB}/tables/indexes.py
 ${PYSITELIB}/tables/indexes.pyc
 ${PYSITELIB}/tables/indexes.pyo
-${PYSITELIB}/tables/indexesextension.c
 ${PYSITELIB}/tables/indexesextension.pyx
 ${PYSITELIB}/tables/indexesextension.so
 ${PYSITELIB}/tables/leaf.py
@@ -81,10 +79,8 @@ ${PYSITELIB}/tables/leaf.pyo
 ${PYSITELIB}/tables/link.py
 ${PYSITELIB}/tables/link.pyc
 ${PYSITELIB}/tables/link.pyo
-${PYSITELIB}/tables/linkextension.c
 ${PYSITELIB}/tables/linkextension.pyx
 ${PYSITELIB}/tables/linkextension.so
-${PYSITELIB}/tables/lrucacheextension.c
 ${PYSITELIB}/tables/lrucacheextension.pxd
 ${PYSITELIB}/tables/lrucacheextension.pyx
 ${PYSITELIB}/tables/lrucacheextension.so
@@ -145,7 +141,6 @@ ${PYSITELIB}/tables/scripts/pttree.pyo
 ${PYSITELIB}/tables/table.py
 ${PYSITELIB}/tables/table.pyc
 ${PYSITELIB}/tables/table.pyo
-${PYSITELIB}/tables/tableextension.c
 ${PYSITELIB}/tables/tableextension.pyx
 ${PYSITELIB}/tables/tableextension.so
 ${PYSITELIB}/tables/tests/Table2_1_lzo_nrv2e_shuffle.h5
@@ -158,6 +153,7 @@ ${PYSITELIB}/tables/tests/__init__.pyc
 ${PYSITELIB}/tables/tests/__init__.pyo
 ${PYSITELIB}/tables/tests/array_mdatom.h5
 ${PYSITELIB}/tables/tests/attr-u16.h5
+${PYSITELIB}/tables/tests/b2nd-no-chunkshape.h5
 ${PYSITELIB}/tables/tests/blosc_bigendian.h5
 ${PYSITELIB}/tables/tests/bug-idx.h5
 ${PYSITELIB}/tables/tests/check_leaks.py
@@ -166,7 +162,6 @@ ${PYSITELIB}/tables/tests/check_leaks.py
 ${PYSITELIB}/tables/tests/common.py
 ${PYSITELIB}/tables/tests/common.pyc
 ${PYSITELIB}/tables/tests/common.pyo
-${PYSITELIB}/tables/tests/create-nested-type.c
 ${PYSITELIB}/tables/tests/create_backcompat_indexes.py
 ${PYSITELIB}/tables/tests/create_backcompat_indexes.pyc
 ${PYSITELIB}/tables/tests/create_backcompat_indexes.pyo
@@ -251,6 +246,9 @@ ${PYSITELIB}/tables/tests/test_indexes.p
 ${PYSITELIB}/tables/tests/test_indexvalues.py
 ${PYSITELIB}/tables/tests/test_indexvalues.pyc
 ${PYSITELIB}/tables/tests/test_indexvalues.pyo
+${PYSITELIB}/tables/tests/test_large_tables.py
+${PYSITELIB}/tables/tests/test_large_tables.pyc
+${PYSITELIB}/tables/tests/test_large_tables.pyo
 ${PYSITELIB}/tables/tests/test_links.py
 ${PYSITELIB}/tables/tests/test_links.pyc
 ${PYSITELIB}/tables/tests/test_links.pyo
@@ -311,7 +309,6 @@ ${PYSITELIB}/tables/unimplemented.pyo
 ${PYSITELIB}/tables/utils.py
 ${PYSITELIB}/tables/utils.pyc
 ${PYSITELIB}/tables/utils.pyo
-${PYSITELIB}/tables/utilsextension.c
 ${PYSITELIB}/tables/utilsextension.pxd
 ${PYSITELIB}/tables/utilsextension.pyx
 ${PYSITELIB}/tables/utilsextension.so

Index: pkgsrc/math/py-tables/distinfo
diff -u pkgsrc/math/py-tables/distinfo:1.7 pkgsrc/math/py-tables/distinfo:1.8
--- pkgsrc/math/py-tables/distinfo:1.7  Wed Jan  5 07:05:39 2022
+++ pkgsrc/math/py-tables/distinfo      Wed Dec 13 20:18:36 2023
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.7 2022/01/05 07:05:39 wiz Exp $
+$NetBSD: distinfo,v 1.8 2023/12/13 20:18:36 wiz Exp $
 
-BLAKE2s (tables-3.7.0.tar.gz) = a49638994427991e7285e80cee2746ddf81078fb123ca6291325951b0e41c684
-SHA512 (tables-3.7.0.tar.gz) = eaa368d063b5fad87e6d0f9ab6f02da0b2a3542740a52fe8c2bb58e41121495d07b6d2710ad402a28891294aa61a11238c6a7e2cf2933a1bb11391b79cf4fd13
-Size (tables-3.7.0.tar.gz) = 8227955 bytes
+BLAKE2s (tables-3.9.2.tar.gz) = 5d1782c32c1aa358baaa79c6425cb242f96ebe1c7995d18c86cf57c3523182a1
+SHA512 (tables-3.9.2.tar.gz) = 9b416222304b7798585a20d4d7d61934023f151d4262a58a4f0ee969aa365264270c12a734461a194d2c857a13a8e09fb7a1386042267113f601560c041cecd9
+Size (tables-3.9.2.tar.gz) = 4683437 bytes

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