./math/py-tables, Database package for large amounts of data

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Branch: CURRENT, Version: 3.9.2, Package name: py311-tables-3.9.2, Maintainer: pkgsrc-users

PyTables is a hierarchical database package designed to efficiently
manage very large amounts of data. PyTables is built on top of the
HDF5 library and the numarray package. It features an object-oriented
interface that, combined with natural naming and C-code generated from
Pyrex sources, makes it a fast, yet extremely easy-to-use tool for
interactively saving and retrieving very large amounts of data. It also
provides flexible indexed access on disk to anywhere in the data.

Required to run:
[archivers/lzo] [devel/py-setuptools] [devel/hdf5] [math/py-numpy] [devel/py-cython] [math/py-numexpr] [devel/py-mock] [lang/py-six] [devel/blosc]

Required to build:

Master sites:

Filesize: 4573.669 KB

Version history: (Expand)

CVS history: (Expand)

   2023-12-13 21:18:37 by Thomas Klausner | Files touched by this commit (3) | Package updated
Log message:
py-tables: update to 3.9.2.

Changes from 3.9.1 to 3.9.2


- 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.


- 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

Other changes

- Add support for the forthcoming Python 3.12 with binary wheels and automated
- 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
- 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.


- 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
- 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

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


- 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
- 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).
   2023-08-02 01:20:57 by Thomas Klausner | Files touched by this commit (158)
Log message:
*: remove more references to Python 3.7
   2023-07-01 10:37:47 by Thomas Klausner | Files touched by this commit (105) | Package updated
Log message:
*: restrict py-numpy users to 3.9+ in preparation for update
   2022-11-19 10:58:31 by Thomas Klausner | Files touched by this commit (1)
Log message:
py-tables: fix build for python 3.11
   2022-04-15 13:27:41 by Nia Alarie | Files touched by this commit (5)
Log message:
math: Mark some packages incompatible with Python 3.7 due to numpy
   2022-01-05 16:41:32 by Thomas Klausner | Files touched by this commit (289)
Log message:
python: egg.mk: add USE_PKG_RESOURCES flag

This flag should be set for packages that import pkg_resources
and thus need setuptools after the build step.

Set this flag for packages that need it and bump PKGREVISION.
   2022-01-05 08:05:39 by Thomas Klausner | Files touched by this commit (3) | Package updated
Log message:
py-tables: update to 3.7.0.

This is a minor version of PyTables.  The main feature added is that
compatibility with Python 3.10, numpy 1.21 and HDF5 1.12 has been improved,
while support for Python 3.5 has been dropped.

The CI infrastructure has been moved to GitHub Actions.
   2022-01-04 21:55:40 by Thomas Klausner | Files touched by this commit (1595)
Log message:
*: bump PKGREVISION for egg.mk users

They now have a tool dependency on py-setuptools instead of a DEPENDS