Bump the pip-version group with 3 updates

[dependabot]

Bumps the pip-version group with 3 updates: coverage, numpy and tables.

Updates coverage from 7.6.0 to 7.6.1

Changelog

Sourced from coverage's changelog.

Version 7.6.1 — 2024-08-04

• Fix: coverage used to fail when measuring code using :func:runpy.run_path <python:runpy.run_path> with a :class:Path <python:pathlib.Path> argument. This is now fixed, thanks to Ask Hjorth Larsen <pull 1819_>_.

• Fix: backslashes preceding a multi-line backslashed string could confuse the HTML report. This is now fixed, thanks to LiuYinCarl <pull 1828_>_.

• Now we publish wheels for Python 3.13, both regular and free-threaded.

.. _pull 1819: nedbat/coveragepy#1819 .. _pull 1828: nedbat/coveragepy#1828

.. _changes_7-6-0:

Commits

• 29f5898 docs: sample HTML for 7.6.1
• 9b829f1 docs: prep for 7.6.1
• ebbb6a2 build: wheels for 3.13rc1
• 3872525 chore: make upgrade
• 7a27f40 test: fix a test on free-threading, use abiflags to get site-packages path co...
• 2b53664 build: include gil/nogil in the version banner
• da1682f docs: changelog and contributor for #1828
• dc819ff test: two tests for #1828
• 9aaa404 fix: properly handle backslash before multi-line string (#1828)
• 9c50270 chore: make upgrade
• Additional commits viewable in compare view

Updates numpy from 2.0.1 to 2.1.0

Release notes

Sourced from numpy's releases.

2.1.0 (Aug 18, 2024)

NumPy 2.1.0 Release Notes

NumPy 2.1.0 provides support for the upcoming Python 3.13 release and drops support for Python 3.9. In addition to the usual bug fixes and updated Python support, it helps get us back into our usual release cycle after the extended development of 2.0. The highlights for this release are:

• Support for the array-api 2023.12 standard.
• Support for Python 3.13.
• Preliminary support for free threaded Python 3.13.

Python versions 3.10-3.13 are supported in this release.

New functions

New function numpy.unstack

A new function np.unstack(array, axis=...) was added, which splits an array into a tuple of arrays along an axis. It serves as the inverse of [numpy.stack]{.title-ref}.

(gh-26579)

Deprecations

• The fix_imports keyword argument in numpy.save is deprecated. Since NumPy 1.17, numpy.save uses a pickle protocol that no longer supports Python 2, and ignored fix_imports keyword. This keyword is kept only for backward compatibility. It is now deprecated.

  (gh-26452)

• Passing non-integer inputs as the first argument of [bincount]{.title-ref} is now deprecated, because such inputs are silently cast to integers with no warning about loss of precision.

  (gh-27076)

Expired deprecations

• Scalars and 0D arrays are disallowed for numpy.nonzero and numpy.ndarray.nonzero.

  (gh-26268)

• set_string_function internal function was removed and PyArray_SetStringFunction was stubbed out.

... (truncated)

Commits

• 2f7fe64 Merge pull request #27236 from charris/prepare-2.1.0
• b6f434f REL: Prepare for the NumPy 2.1.0 release [wheel build]
• 3cf9394 Merge pull request #27234 from charris/backport-25984
• 7443dcc Merge pull request #27233 from charris/backport-27223
• 85b1cab BUG: Allow fitting of degree zero polynomials with Polynomial.fit
• 395a81d DOC: reword discussion about shared arrays to hopefully be clearer
• 5af2e96 Move NUMUSERTYPES thread safety discussion to legacy DType API docs
• d902c24 DOC: add docs on thread safety in NumPy
• c080180 Merge pull request #27229 from charris/backport-27226
• 44ce7e8 BUG: Fix PyArray_ZeroContiguousBuffer (resize) with struct dtypes
• Additional commits viewable in compare view

Updates tables from 3.9.2 to 3.10.1

Release notes

Sourced from tables's releases.

Release v3.10.1

Changes from 3.10.1 to 3.10.0

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.

Release v3.10.0

Changes from 3.10.0 to 3.9.2

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).

... (truncated)

Changelog

Sourced from tables's changelog.

Changes from 3.10.2 to 3.10.1

XXX version-specific blurb XXX

Changes from 3.10.1 to 3.10.0

Bugfixes

• Fix version constraints for the numpy runtime requirements (:issue: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 :issue: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.

Commits

• 13410b6 Update release date
• 8dabc8c Typo
• 26706af Update announcement template
• 6a8e92b Update release notes
• 3a8a2ed Update the version number
• 65e5ff7 Merge pull request #1204 from avalentino/bugfix/fix-dependency-constraints
• b94b4d5 Update pyproject.toml
• 2f86a74 Update pyproject.toml
• 2e8e2d9 Enforce the use of numpy 2 at build time
• 85bfe57 PyTables is now comaptible with numpy 2 (Closes #1200)
• Additional commits viewable in compare view

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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 86.09%. Comparing base (930abc7) to head (8d823a4).
Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1004      +/-   ##
==========================================
+ Coverage   86.01%   86.09%   +0.08%     
==========================================
  Files          20       20              
  Lines        3503     3503              
  Branches      770      770              
==========================================
+ Hits         3013     3016       +3     
+ Misses        333      330       -3     
  Partials      157      157              

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[cbkerr]

Numpy 2.1.0 does not support 3.9, so the ubuntu-latest, 3.9 was failing to install numpy. Rather than remove the test for Python 3.9, I bumped it to the oldest requirements. To fix that, I had to bump the 1.19.0 to 1.19.3, which has binary wheels available for all platforms.

I based this on the list of compatible versions contained in the deprecated oldest-supported-numpy project

Now, it looks like something about Cython requirement is causing it to try to find numpy 1.14.5, which fails

      Collecting Cython>=0.29.13
        Downloading Cython-3.0.11-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.2 kB)
      Collecting numpy==1.14.5
        Downloading numpy-1.14.5.zip (4.9 MB)

[bdice]

Fixing this probably requires a bump of pandas, too. That's pinned to an old NumPy/Cython in its build dependencies and is trying to build from a tarball.

Collecting pandas==1.0.0 (from -r .github/workflows/ci-oldest-reqs.txt (line 9))
  Downloading pandas-1.0.0.tar.gz (4.8 MB)

I have been requiring that our "oldest" dependencies must have wheels available. Pandas 1.2.0 is the first minor version with wheels for Python 3.9, so I'll use that.

edit: similar issue for h5py, too.

[bdice]

I'm not sure why this is not auto-merging. I'm going to bypass branch protections to merge this since CI passed and it has an approval. cc: @joaander @cbkerr