Bump tables from 3.8.0 to 3.9.2

[dependabot]

Bumps tables from 3.8.0 to 3.9.2.

Release notes

Sourced from tables's releases.

Release v3.9.2

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 (#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 (#1075 and #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 (#1068). Thanks to Thomas Grainger.
• Relax the reading of Blosc2 NDim to cope with datasets stored with other tools (#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 (#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 (#1066). Thanks to Thomas Grainger.
• Assorted fixes to the b2nd slicing benchmark. Thanks to Ivan Vilata.
• Assorted fixes to b2nd slicing optimization tips (#1069). Thanks to Ivan Vilata.

Thanks

In alphabetical order:

• Antonio Valentino
• Ivan Vilata
• Kiet Pham
• Thomas Grainger

Release 3.9.1

Changes from 3.9.0 to 3.9.1

• [Hot fix] Minimum supported version for Python is 3.9 (see #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 (#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 (#893 and #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).

... (truncated)

Changelog

Sourced from tables's changelog.

Changes from 3.9.2 to 3.9.3

XXX version-specific blurb XXX

Improvements

• Add type hints to atom.py. This also narrows some types, only allowing bytes to be stored in VLStringAtom and only str in VLUnicodeAtom.

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.

... (truncated)

Commits

• ae689fd Merge branch 'releases/v3.9.2'
• f580b56 Update release date in timeline
• d26655d Add notes in announcement
• db32bd3 Update release notes after scanning changes from v3.9.1
• 9d4f6c0 Bump version to v3.9.2 and set release date in timeline
• a0124f5 Fix b2nd slicing benchmark data types
• fc190af Minor fixes to b2nd benchmark
• 71d093d Merge pull request #1080 from avalentino/feature/H5_USE_110_API
• 6e4fa4b Remove compatibility code and clean cdocs/comments for HDF5 1.8.x
• 9430c50 Update comments in setup.py
• Additional commits viewable in compare view

Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

---

Dependabot commands and options

You can trigger Dependabot actions by commenting on this PR:

• @dependabot rebase will rebase this PR
• @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
• @dependabot merge will merge this PR after your CI passes on it
• @dependabot squash and merge will squash and merge this PR after your CI passes on it
• @dependabot cancel merge will cancel a previously requested merge and block automerging
• @dependabot reopen will reopen this PR if it is closed
• @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
• @dependabot show <dependency name> ignore conditions will show all of the ignore conditions of the specified dependency
• @dependabot ignore this major version will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
• @dependabot ignore this minor version will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
• @dependabot ignore this dependency will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)

[dependabot]

Looks like tables is up-to-date now, so this is no longer needed.