CVS commit: pkgsrc/math/py-tables

["Thomas Klausner" <wiz%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   wiz
Date:           Wed Oct 23 22:55:52 UTC 2024

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

Log Message:
py-tables: update to 3.10.1.

3.10.1

Bugfixes

    Fix version constraints for the numpy runtime requirements
    (#1204).
    For a mistake it didn't allow to use PyTables with numpy 2.x.
    Fix compatibility with PyPy (:issue:1205), Thanks to Michał Górny.

Improvements

    Enforce numpy >= 2 as build constraint (see discussion in #1200).
    Use tuple of plain ints for chunk info coordinates.
    Thanks to Ivan Vilata-i-Balaguer.
    Enable faulthandler in tables.tests.test_all. Thanks to Eric Larson.

3.10.0

New features

    New direct chunking API which allows access to raw chunk data skipping the HDF5 filter pipeline (cutting overhead, see "Optimization tips" in User's Guide), as well as querying chunk information 
(#1187). Thanks to Ivan Vilata and Francesc Alted. This development was funded by a NumFOCUS grant.

Improvements

    This release is finally compatible with NumPy 2 with wheels being built against it so that they are still binary-compatible with NumPy 1 installations (#1176, #1183, #1184, #1192, #1195, #1160, 
#1172, #1185). NumPy >= 1.20 is required now. Thanks to Antonio Valentino, Maximilian Linhoff and Eric Larson.
    Fix compatibility with Python 3.13 (#1166), Python >= 3.10 required. Cython 3.0.10 is required for building. Thanks to Antonio Valentino.
    Add type hints to atom.py (#1079). This also narrows some types, only allowing bytes to be stored in VLStringAtom and only str in VLUnicodeAtom. Thanks to Nils Carlson.
    Add type hints to (hopefully) the complete PyTables API (#1119, #1120, #1121, #1123, #1124, #1125, #1125, #1126, #1128, #1129, #1130, #1131, #1132, #1133, #1135, #1136, #1137, #1138, #1139, 
#1140, #1141, #1142, #1143, #1145, #1146, #1147, #1148, #1150, #1151, #1152). Thanks to Ko Stehner.
    Reduce impact of CPU information gathering by caching in local file (#1091, #1118, #1081). Thanks to Antti Mäkinen and Maximilian Linhoff.

Bugfixes

    Fix Windows AMD64 build issues with Bzip2 and C-Blosc2 libraries (#1188). Thanks to Antonio Valentino and Eric Larson.
    Fix typos and may other language errors in docstrings (#1122). Thanks to Ko Stehner.
    Fix Blosc2 filter not setting dparams.schunk on decompression (#1110 and #1109). Thanks to Tom Birch.
    Fix using B2ND optimizations when Blosc2 is not the only enabled filter; move Fletcher32 compression to end of pipeline when enabled (#1191 and #1162). Thanks to Ivan Vilata and Alex Laslavic.
    Fix broken internal passing of createparents argument in Leaf.copy (#1127 and #1125). Thanks to Ko Stehner.
    Re-enable relative paths in ExternalLink class (#1095). Thanks to erikdl-zeiss.
    Fix using prefix in heavy tests methods of test_queries (#1169). Thanks to Miro Hrončok.
    Fix TypeError when computing Blosc2 search paths with missing library (#1188 and #1100). Thanks to martinowitsch, Padraic Calpin and Eric Larson.
    Avoid overflow RuntimeWarning on NumPy expectedrows value (#1010). Thanks to wony-zheng and Ivan Vilata.

Other changes

    Add wheels for macOS ARM64 (Apple Silicon), set MACOSX_DEPLOYMENT_TARGET in Docker (#1050 and #1165). Thanks to Clemens Brunner, Antonio Valentino, Maximilian Linhoff and Eric Larson.
    Avoid illegal hardware instruction under macOS on M1/M2 with Rosetta and AMD64 wheels (#1195 and #1186). Thanks to Antonio Valentino and Jon Peirce.
    Produce nightly wheels (with HDF5 1.14.4), also uploaded to Scientific Python Anaconda repo. Wheels are also produced for PR workflows. Thanks to Antonio Valentino and Eric Larson (#1175).
    Wheels are no longer linked with the LZO library to avoid licensing issues (#1195). Thanks to Antonio Valentino.
    Hash-pin dependencies on wheel workflows to increase build procedure security, with support for Dependabot and Renovatebot updates (#1085 and #1015). Thanks to Joyce Brum and Diogo Teles 
Sant'Anna.
    Hash-pin GitHub action versions in wheels workflow. Thanks to Antonio Valentino.
    Update ReadTheDocs configuration to version 2 (#1092). Thanks to Maximilian Linhoff.
    Assorted fixes to b2nd benchmark, with new results. Thanks to Ivan Vilata.
    Point users to example code to handle "Selection lists cannot have repeated values" exception (#1161 and #1149). Thanks to Joshua Albert.
    Remove unused getLibrary C code. Thanks to Antonio Valentino.
    Update included C-Blosc to 1.21.6 (#1193). Thanks to Ivan Vilata.
    Update included HDF5-Blosc filter to 1.0.1 (#1194). Thanks to Ivan Vilata.


To generate a diff of this commit:
cvs rdiff -u -r1.19 -r1.20 pkgsrc/math/py-tables/Makefile
cvs rdiff -u -r1.5 -r1.6 pkgsrc/math/py-tables/PLIST
cvs rdiff -u -r1.8 -r1.9 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:1.19 pkgsrc/math/py-tables/Makefile:1.20
--- pkgsrc/math/py-tables/Makefile:1.19 Mon Oct 14 06:45:52 2024
+++ pkgsrc/math/py-tables/Makefile      Wed Oct 23 22:55:52 2024
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.19 2024/10/14 06:45:52 wiz Exp $
+# $NetBSD: Makefile,v 1.20 2024/10/23 22:55:52 wiz Exp $
 
-DISTNAME=      tables-3.9.2
+DISTNAME=      tables-3.10.1
 PKGNAME=       ${PYPKGPREFIX}-${DISTNAME}
-PKGREVISION=   1
 CATEGORIES=    math python
 MASTER_SITES=  ${MASTER_SITE_PYPI:=t/tables/}
 
@@ -11,11 +10,13 @@ HOMEPAGE=   https://www.pytables.org/
 COMMENT=       Database package for large amounts of data
 LICENSE=       modified-bsd
 
-TOOL_DEPENDS+= ${PYPKGPREFIX}-cython-[0-9]*:../../devel/py-cython
-TOOL_DEPENDS+= ${PYPKGPREFIX}-setuptools-[0-9]*:../../devel/py-setuptools
+TOOL_DEPENDS+= ${PYPKGPREFIX}-cython>=0.29.32:../../devel/py-cython
+TOOL_DEPENDS+= ${PYPKGPREFIX}-setuptools>=61.0.0:../../devel/py-setuptools
 TOOL_DEPENDS+= ${PYPKGPREFIX}-wheel-[0-9]*:../../devel/py-wheel
+DEPENDS+=      ${PYPKGPREFIX}-cpuinfo-[0-9]*:../../sysutils/py-cpuinfo
 DEPENDS+=      ${PYPKGPREFIX}-packaging-[0-9]*:../../devel/py-packaging
 DEPENDS+=      ${PYPKGPREFIX}-numexpr>=2.6.2:../../math/py-numexpr
+DEPENDS+=      ${PYPKGPREFIX}-typing-extensions>=4.4.0:../../devel/py-typing-extensions
 
 USE_LANGUAGES= c c++
 
@@ -27,9 +28,10 @@ post-install:
        ${MV} pttree pttree-${PYVERSSUFFIX} || ${TRUE}
 
 # needs to be installed first
-# as of 3.9.2:
-# Ran 6799 tests
-# FAILED (errors=2, skipped=58)
+# as of 3.10.1
+# FAILED (errors=314, skipped=59)
+# many with
+# FileNotFoundError: [Errno 2] No such file or directory: '/home/pbulk/.pytables-cpuinfo.json'
 do-test:
        ${PYTHONBIN} -m tables.tests.test_all
 
@@ -39,6 +41,7 @@ do-test:
 .include "../../devel/blosc2/buildlink3.mk"
 .include "../../devel/hdf5/buildlink3.mk"
 .include "../../devel/zlib/buildlink3.mk"
+BUILDLINK_API_DEPENDS.py-numpy+=       ${PYPKGPREFIX}-numpy>=2.0
 .include "../../math/py-numpy/buildlink3.mk"
 .include "../../lang/python/wheel.mk"
 .include "../../mk/bsd.pkg.mk"

Index: pkgsrc/math/py-tables/PLIST
diff -u pkgsrc/math/py-tables/PLIST:1.5 pkgsrc/math/py-tables/PLIST:1.6
--- pkgsrc/math/py-tables/PLIST:1.5     Wed Dec 13 20:18:36 2023
+++ pkgsrc/math/py-tables/PLIST Wed Oct 23 22:55:52 2024
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.5 2023/12/13 20:18:36 wiz Exp $
+@comment $NetBSD: PLIST,v 1.6 2024/10/23 22:55:52 wiz Exp $
 bin/pt2to3-${PYVERSSUFFIX}
 bin/ptdump-${PYVERSSUFFIX}
 bin/ptrepack-${PYVERSSUFFIX}
@@ -219,6 +219,9 @@ ${PYSITELIB}/tables/tests/test_carray.py
 ${PYSITELIB}/tables/tests/test_create.py
 ${PYSITELIB}/tables/tests/test_create.pyc
 ${PYSITELIB}/tables/tests/test_create.pyo
+${PYSITELIB}/tables/tests/test_direct_chunk.py
+${PYSITELIB}/tables/tests/test_direct_chunk.pyc
+${PYSITELIB}/tables/tests/test_direct_chunk.pyo
 ${PYSITELIB}/tables/tests/test_do_undo.py
 ${PYSITELIB}/tables/tests/test_do_undo.pyc
 ${PYSITELIB}/tables/tests/test_do_undo.pyo

Index: pkgsrc/math/py-tables/distinfo
diff -u pkgsrc/math/py-tables/distinfo:1.8 pkgsrc/math/py-tables/distinfo:1.9
--- pkgsrc/math/py-tables/distinfo:1.8  Wed Dec 13 20:18:36 2023
+++ pkgsrc/math/py-tables/distinfo      Wed Oct 23 22:55:52 2024
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.8 2023/12/13 20:18:36 wiz Exp $
+$NetBSD: distinfo,v 1.9 2024/10/23 22:55:52 wiz Exp $
 
-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
+BLAKE2s (tables-3.10.1.tar.gz) = 1150b460680ad8bad06e7fbf137cb576e80de0de2d0d5b1d3175df9ec3a7db2b
+SHA512 (tables-3.10.1.tar.gz) = 7590dccefdd718d170ac288d391173ed540760a911f53fd39e37dd74237dc554f9363c8d9d4d518f067da299d71a1d8cb4a40134b1afaf79daa0a17de248caf5
+Size (tables-3.10.1.tar.gz) = 4762413 bytes