Bump the python-packages group with 6 updates

[dependabot]

Bumps the python-packages group with 6 updates:

Package	From	To
numpy	1.26.4	2.1.0
pyyaml	6.0.1	6.0.2
scipy	1.13.1	1.14.1
shapely	2.0.5	2.0.6
sql-metadata	2.12.0	2.13.0
sqlalchemy	2.0.30	2.0.32

Updates numpy from 1.26.4 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 pyyaml from 6.0.1 to 6.0.2

Release notes

Sourced from pyyaml's releases.

6.0.2

What's Changed

• Support for Cython 3.x and Python 3.13.

Full Changelog: yaml/pyyaml@6.0.1...6.0.2

6.0.2rc1

• Support for extension build with Cython 3.x
• Support for Python 3.13
• Added PyPI wheels for musllinux on aarch64

Changelog

Sourced from pyyaml's changelog.

6.0.2 (2024-08-06)

• yaml/pyyaml#808 -- Support for Cython 3.x and Python 3.13

Commits

• 41309b0 Release 6.0.2 (#819)
• dd9f0e1 6.0.2rc1 (#809)
• f5527a2 disable CI trigger on PR edits
• b4d80a7 Python 3.12 + musllinux_1_1_x86_64 wheel support
• See full diff in compare view

Updates scipy from 1.13.1 to 1.14.1

Release notes

Sourced from scipy's releases.

SciPy 1.14.1 Release Notes

SciPy 1.14.1 adds support for Python 3.13, including binary wheels on PyPI. Apart from that, it is a bug-fix release with no new features compared to 1.14.0.

Authors

• Name (commits)
• h-vetinari (1)
• Evgeni Burovski (1)
• CJ Carey (2)
• Lucas Colley (3)
• Ralf Gommers (3)
• Melissa Weber Mendonça (1)
• Andrew Nelson (3)
• Nick ODell (1)
• Tyler Reddy (36)
• Daniel Schmitz (1)
• Dan Schult (4)
• Albert Steppi (2)
• Ewout ter Hoeven (1)
• Tibor Völcker (2) +
• Adam Turner (1) +
• Warren Weckesser (2)
• ਗਗਨਦੀਪ ਸਿੰਘ (Gagandeep Singh) (1)

A total of 17 people contributed to this release. People with a "+" by their names contributed a patch for the first time. This list of names is automatically generated, and may not be fully complete.

SciPy 1.14.0 Release Notes

SciPy 1.14.0 is the culmination of 3 months of hard work. It contains many new features, numerous bug-fixes, improved test coverage and better documentation. There have been a number of deprecations and API changes in this release, which are documented below. All users are encouraged to upgrade to this release, as there are a large number of bug-fixes and optimizations. Before upgrading, we recommend that users check that their own code does not use deprecated SciPy functionality (to do so, run your code with python -Wd and check for DeprecationWarning s). Our development attention will now shift to bug-fix releases on the 1.14.x branch, and on adding new features on the main branch.

This release requires Python 3.10+ and NumPy 1.23.5 or greater.

... (truncated)

Commits

• 92d2a85 REL: 1.14.1 rel commit [wheel build]
• 85623a1 Merge pull request #21362 from tylerjereddy/treddy_1.14.1_backports
• d924005 MAINT: PR 21362 revisions [wheel build]
• b901a4e MAINT, CI: PR 21362 revisions [wheel build]
• 2a7ec60 MAINT, BLD: PR 21362 revisions [wheel build]
• f4f084d MAINT, CI: PR 21362 revisions [wheel build]
• b712fc6 DOC: update 1.14.1 relnotes [wheel build]
• cdd5aca MAINT: special: Accommodate changed integer handling in NumPy 2.0. (#21401)
• 0f91838 BLD: cp313 wheels on manylinux_aarch64 (#21409)
• 6dd0b00 MAINT, CI: wheel build changes [wheel build]
• Additional commits viewable in compare view

Updates shapely from 2.0.5 to 2.0.6

Release notes

Sourced from shapely's releases.

2.0.6

Wheels are available for Python 3.13 (and still include GEOS 3.11.4).

Bug fixes:

• Fix compatibility with NumPy 2.1.0 (#2099).

For a full changelog, see https://shapely.readthedocs.io/en/latest/release/2.x.html#version-2-0-6

Changelog

Sourced from shapely's changelog.

2.0.6 (2024-08-19)

Bug fixes:

• Fix compatibility with NumPy 2.1.0 (#2099).

Wheels are available for Python 3.13 (and still include GEOS 3.11.4).

Commits

• 5a4207d RLS: 2.0.6
• c65fa42 Bump pypa/cibuildwheel from 2.19.2 to 2.20.0 (build Python 3.13 wheels) (#2103)
• 2f411ee DOC/RLS: starts changelog for 2.0.6 (#2113)
• 225445c BLD: suppress 'incompatible-function-pointer-types' error for clang>=16 (#2114)
• 3ab8fbc TST/CI: enable testing Python 3.13, NumPy 2.1, GEOS 3.13 (#2105)
• 2a83905 Fix compatibility with numpy 2.1 dev to cast GeometryType to int as ufunc inp...
• See full diff in compare view

Updates sql-metadata from 2.12.0 to 2.13.0

Release notes

Sourced from sql-metadata's releases.

Support the TRUNCATE TABLE query

Fixes and improvements

• Support for the TRUNCATE TABLE query parsing by @​T-Santos in macbre/sql-metadata#521
• fix is_alias_without_as logical error by @​MiuNice in macbre/sql-metadata#523

Dependencies

• Bump urllib3 from 1.26.18 to 1.26.19 by @​dependabot in macbre/sql-metadata#501
• Bump pylint from 3.2.3 to 3.2.4 by @​dependabot in macbre/sql-metadata#503
• Bump pylint from 3.2.4 to 3.2.5 by @​dependabot in macbre/sql-metadata#504
• Bump dependabot/fetch-metadata from 2.1.0 to 2.2.0 by @​dependabot in macbre/sql-metadata#505
• Bump certifi from 2023.7.22 to 2024.7.4 by @​dependabot in macbre/sql-metadata#508
• Bump sqlparse from 0.5.0 to 0.5.1 by @​dependabot in macbre/sql-metadata#511
• Bump pytest from 8.2.2 to 8.3.1 by @​dependabot in macbre/sql-metadata#512
• Bump pylint from 3.2.5 to 3.2.6 by @​dependabot in macbre/sql-metadata#513
• Bump pytest from 8.3.1 to 8.3.2 by @​dependabot in macbre/sql-metadata#515
• Bump snok/install-poetry from 1.3.4 to 1.4.0 by @​dependabot in macbre/sql-metadata#516
• Bump black from 24.4.2 to 24.8.0 by @​dependabot in macbre/sql-metadata#517
• Bump snok/install-poetry from 1.4.0 to 1.4.1 by @​dependabot in macbre/sql-metadata#518

New Contributors

• @​T-Santos made their first contribution in macbre/sql-metadata#521, hi 👋🏻

Full Changelog: macbre/sql-metadata@v2.12.0...v2.13.0

Commits

• 3e47e9a v2.13.0
• 3713f14 Feature/support for truncate table query parsing (#1) (#521)
• 9a78fbc fix is_alias_without_as logical error (#523)
• 504f6aa Bump snok/install-poetry from 1.4.0 to 1.4.1 (#518)
• 7508158 Bump black from 24.4.2 to 24.8.0 (#517)
• 8c83c99 Bump snok/install-poetry from 1.3.4 to 1.4.0 (#516)
• 7fd2c00 Bump pytest from 8.3.1 to 8.3.2 (#515)
• b519740 Bump pylint from 3.2.5 to 3.2.6 (#513)
• 90cbcdb Bump pytest from 8.2.2 to 8.3.1 (#512)
• 4ae53f8 Bump sqlparse from 0.5.0 to 0.5.1 (#511)
• Additional commits viewable in compare view

Updates sqlalchemy from 2.0.30 to 2.0.32

Release notes

Sourced from sqlalchemy's releases.

2.0.32

Released: August 5, 2024

general

• [general] [bug] [regression] Restored legacy class names removed from sqlalalchemy.orm.collections.*, including _orm.MappedCollection, _orm.mapped_collection(), _orm.column_mapped_collection(), _orm.attribute_mapped_collection(). Pull request courtesy Takashi Kajinami.

  References: #11435

orm

• [orm] [usecase] The _orm.aliased.name parameter to _orm.aliased() may now be combined with the _orm.aliased.flat parameter, producing per-table names based on a name-prefixed naming convention. Pull request courtesy Eric Atkin.

  References: #11575

• [orm] [bug] [regression] Fixed regression going back to 1.4 where accessing a collection using the "dynamic" strategy on a transient object and attempting to query would raise an internal error rather than the expected NoResultFound that occurred in 1.3.

  This change is also backported to: 1.4.53

  References: #11562

• [orm] [bug] Fixed issue where using the _orm.Query.enable_eagerloads() and _orm.Query.yield_per() methods at the same time, in order to disable eager loading that's configured on the mapper directly, would be silently ignored, leading to errors or unexpected eager population of attributes.

  References: #10834

• [orm] [bug] [regression] Fixed regression appearing in 2.0.21 caused by #10279 where using a _sql.delete() or _sql.update() against an ORM class that is the base of an inheritance hierarchy, while also specifying that subclasses should be loaded polymorphically, would leak the polymorphic joins into the UPDATE or DELETE statement as well creating incorrect SQL.

  References: #11625

• [orm] [bug] [regression] Fixed regression from version 1.4 in

... (truncated)

Commits

• See full diff 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 <dependency name> major version will close this group update PR and stop Dependabot creating any more for the specific dependency's major version (unless you unignore this specific dependency's major version or upgrade to it yourself)
• @dependabot ignore <dependency name> minor version will close this group update PR and stop Dependabot creating any more for the specific dependency's minor version (unless you unignore this specific dependency's minor version or upgrade to it yourself)
• @dependabot ignore <dependency name> will close this group update PR and stop Dependabot creating any more for the specific dependency (unless you unignore this specific dependency or upgrade to it yourself)
• @dependabot unignore <dependency name> will remove all of the ignore conditions of the specified dependency
• @dependabot unignore <dependency name> <ignore condition> will remove the ignore condition of the specified dependency and ignore conditions

[gherka]

Merging after fixing Numpy 2.x migration errors related to np.NaN.