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Bump the runtime-dependencies group across 1 directory with 6 updates #1558

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Bumps the runtime-dependencies group with 6 updates in the / directory:

Package From To
asteval 1.0.2 1.0.5
netcdf4 1.7.1.post1 1.7.2
numpy 2.0.1 2.1.3
pandas 2.2.2 2.2.3
pydantic 2.8.2 2.10.1
xarray 2024.7.0 2024.10.0

Updates asteval from 1.0.2 to 1.0.5

Release notes

Sourced from asteval's releases.

1.0.5

bugfix:

  • more work on handling errors, including fixing #133 and adding more comprehensive tests for #129 and #132

1.0.4

bugfix:

  • fix error handling that might result in null exception

1.0.3

bug fixes, a few feature enhancements:

  • functions ("Procedures") defined within asteval have a _signature() method, now use in repr
  • add support for deleting subscript
  • nested symbol tables now have a Group() function
  • update coverage config
  • cleanups of exception handling : errors must now have an exception
  • several related fixes to suppress repeated exceptions: see GH #132 and #129
  • make non-boolean return values from comparison operators behave like Python - not immediately testing as bool
Commits
  • 8d7326d improve error management; shunt .run() with string to .eval()
  • cc1f757 strengthen tests to assure length of errors, testing both .call() and .run()
  • 36dc5f1 more tests and updates for exception handling
  • 84ab7d7 more changes for #133 and exception handling
  • 84ed2f3 improve expection handling with raise_errors=True, fixing GH133
  • 3c55649 add test for GH133
  • fcb2a39 emergency fix for handling errors, exposed by lmfit
  • 1f135fa Procedures: move 'build signature' to _signature() method, use in repr
  • 45beb7b add support for deleting subscript
  • 6a218da add Group() function to nested symbol table
  • Additional commits viewable in compare view

Updates netcdf4 from 1.7.1.post1 to 1.7.2

Changelog

Sourced from netcdf4's changelog.

since version 1.7.2 release

  • support os.PathLike arguments for Dataset.fromcdl and raise a FileNotFoundError if the cdl is missing and a FileExistsError if the nc file already exists (PR #1387)
  • raise more informative error when trying to iterate or perform a membership operation on a Dataset (issue #1383)
  • fix type hint for createEnumType (issue #1378)
  • add python 3.13 to windows wheel builds (PR #1377)

version 1.7.2 (tag v1.7.2rel)

  • add static type hints (PRs #1302, #1349)
  • Expose nc_rc_set, nc_rc_get (via rc_set, rc_get module functions). (PR #1348)
  • Add Variable.get_fill_value and allow fill_value='default' to set _FillValue attribute using default fill values. (issue #1374, PR #1375).
  • Fix NETCDF3 endian error (issue #1373, PR #1355).

version 1.7.1 (tag v1.7.1rel)

  • include nc_complex source code from v0.2.0 tag (instead of using submodule).
  • add aarch64 wheels.

version 1.7.0 (tag v1.7.0rel)

  • add support for complex numbers via auto_complex keyword to Dataset (PR #1295)
  • fix for deprecated Cython DEF and IF statements using compatibility header with shims for unavailable functionality (PR #1277)
  • use szip as the library name on Windows (PR #1304)
  • add support for MS-MPI MPI_Message detection (PR #1305)
  • fix for issue #1306 - surprising result when indexing vlen str with non-contiguous indices.
  • Fix bug in set_collective introduced in PR #1277 (collective mode was always set).

version 1.6.5 (tag v1.6.5rel)

  • fix for issue #1271 (mask ignored if bool MA assigned to uint8 var)
  • include information on specific object when reporting errors from netcdf-c
  • python 3.12 wheels added, support for python 3.7 removed.

version 1.6.4 (tag v1.6.4rel)

  • set path to SSL certificates internally, so https DAP URLs work with wheels (issue #1246, requires nc_rc_set function available starting with netcdf-c 4.9.1, plus bugfix in netcdf-c PR #2690). Added certifi as a dependency.
  • Added isopen method to MFDataset object to check if underlying files are open.

version 1.6.3 (tag v1.6.3rel)

... (truncated)

Commits

Updates numpy from 2.0.1 to 2.1.3

Release notes

Sourced from numpy's releases.

2.1.3 (Nov 2, 2024)

NumPy 2.1.3 Release Notes

NumPy 2.1.3 is a maintenance release that fixes bugs and regressions discovered after the 2.1.2 release. This release also adds support for free threaded Python 3.13 on Windows.

The Python versions supported by this release are 3.10-3.13.

Improvements

  • Fixed a number of issues around promotion for string ufuncs with StringDType arguments. Mixing StringDType and the fixed-width DTypes using the string ufuncs should now generate much more uniform results.

    (gh-27636)

Changes

  • numpy.fix now won't perform casting to a floating data-type for integer and boolean data-type input arrays.

    (gh-26766)

Contributors

A total of 15 people contributed to this release. People with a "+" by their names contributed a patch for the first time.

  • Abhishek Kumar +
  • Austin +
  • Benjamin A. Beasley +
  • Charles Harris
  • Christian Lorentzen
  • Marcel Telka +
  • Matti Picus
  • Michael Davidsaver +
  • Nathan Goldbaum
  • Peter Hawkins
  • Raghuveer Devulapalli
  • Ralf Gommers
  • Sebastian Berg
  • dependabot[bot]
  • kp2pml30 +

Pull requests merged

A total of 21 pull requests were merged for this release.

... (truncated)

Changelog

Sourced from numpy's changelog.

This is a walkthrough of the NumPy 2.1.0 release on Linux, modified for building with GitHub Actions and cibuildwheels and uploading to the anaconda.org staging repository for NumPy <https://anaconda.org/multibuild-wheels-staging/numpy>_. The commands can be copied into the command line, but be sure to replace 2.1.0 by the correct version. This should be read together with the :ref:general release guide <prepare_release>.

Facility preparation

Before beginning to make a release, use the requirements/*_requirements.txt files to ensure that you have the needed software. Most software can be installed with pip, but some will require apt-get, dnf, or whatever your system uses for software. You will also need a GitHub personal access token (PAT) to push the documentation. There are a few ways to streamline things:

  • Git can be set up to use a keyring to store your GitHub personal access token. Search online for the details.
  • You can use the keyring app to store the PyPI password for twine. See the online twine documentation for details.

Prior to release

Add/drop Python versions

When adding or dropping Python versions, three files need to be edited:

  • .github/workflows/wheels.yml # for github cibuildwheel
  • tools/ci/cirrus_wheels.yml # for cibuildwheel aarch64/arm64 builds
  • pyproject.toml # for classifier and minimum version check.

Make these changes in an ordinary PR against main and backport if necessary. Add [wheel build] at the end of the title line of the commit summary so that wheel builds will be run to test the changes. We currently release wheels for new Python versions after the first Python rc once manylinux and cibuildwheel support it. For Python 3.11 we were able to release within a week of the rc1 announcement.

Backport pull requests

Changes that have been marked for this release must be backported to the maintenance/2.1.x branch.

Update 2.1.0 milestones

... (truncated)

Commits
  • 98464cc Merge pull request #27690 from charris/prepare-2.1.3
  • cbda85b REL: Prepare for the NumPy 2.1.3 release [wheel build]
  • daa8699 Merge pull request #27672 from charris/backport-27666
  • 614ca19 Merge pull request #27673 from charris/backport-27636
  • e6b02d7 DOC: add release note
  • 54fd729 BUG: substantially simplify and fix issue with justification promoter
  • a90fe7c BUG: fix more issues with string ufunc promotion
  • a121864 BUG: fixes for StringDType/unicode promoters
  • f055fb9 BUG: Fix a reference count leak in npy_find_descr_for_scalar.
  • 5895c02 Merge pull request #27669 from charris/backport-27663
  • Additional commits viewable in compare view

Updates pandas from 2.2.2 to 2.2.3

Release notes

Sourced from pandas's releases.

Pandas 2.2.3

We are pleased to announce the release of pandas 2.2.3. This release includes some new features, bug fixes, and performance improvements. We recommend that all users upgrade to this version.

See the full whatsnew for a list of all the changes. Pandas 2.2.3 supports Python 3.9 and higher.

The release will be available on the defaults and conda-forge channels:

conda install pandas

Or via PyPI:

python3 -m pip install --upgrade pandas

Please report any issues with the release on the pandas issue tracker.

Thanks to all the contributors who made this release possible.

Commits

Updates pydantic from 2.8.2 to 2.10.1

Release notes

Sourced from pydantic's releases.

v2.10.1 2024-11-21

What's Changed

Packaging

Fixes

Full Changelog: pydantic/pydantic@v2.10.0...v2.10.2

v2.10.0 2024-11-20

The code released in v2.10.0 is practically identical to that of v2.10.0b2. See the v2.10 release blog post for the highlights!

What's Changed

Packaging

New Features

... (truncated)

Changelog

Sourced from pydantic's changelog.

v2.10.1 (2024-11-21)

GitHub release

What's Changed

Packaging

Fixes

New Contributors

v2.10.0 (2024-11-20)

The code released in v2.10.0 is practically identical to that of v2.10.0b2.

GitHub release

See the v2.10 release blog post for the highlights!

What's Changed

Packaging

New Features

... (truncated)

Commits
  • 17e60fa spacing
  • 369b355 remove typo
  • 4c75404 Prepare for v2.10.1 release (#10939)
  • e0fc82f Bump pydantic-core version to v2.27.1 (#10938)
  • 30b31da Fix JSON schema title when specified as '' (#10936)
  • 45bd7a7 Fix URL equality with different validation methods (#10934)
  • 6153054 Fix url constraint application (#10922)
  • 71168ba Use the globals of the function when evaluating the return type of serializ...
  • 4def331 Use the parent configuration during schema generation for stdlib dataclasses ...
  • a2acc52 Fix type checking issue with model_fields and model_computed_fields (#10911)
  • Additional commits viewable in compare view

Updates xarray from 2024.7.0 to 2024.10.0

Release notes

Sourced from xarray's releases.

v2024.10.0

This release brings official support for xarray.DataTree, and compatibility with zarr-python v3!

Aside from these two huge features, it also improves support for vectorised interpolation and fixes various bugs.

Thanks to the 31 contributors to this release: Alfonso Ladino, DWesl, Deepak Cherian, Eni, Etienne Schalk, Holly Mandel, Ilan Gold, Illviljan, Joe Hamman, Justus Magin, Kai Mühlbauer, Karl Krauth, Mark Harfouche, Martey Dodoo, Matt Savoie, Maximilian Roos, Patrick Hoefler, Peter Hill, Renat Sibgatulin, Ryan Abernathey, Spencer Clark, Stephan Hoyer, Tom Augspurger, Tom Nicholas, Vecko, Virgile Andreani, Yvonne Fröhlich, carschandler, joseph nowak, mgunyho and owenlittlejohns

What's Changed

... (truncated)

Commits
  • 165177e v2024.10.0 release summary (#9678)
  • fbe73ef drop the length from numpy's fixed-width string dtypes (#9586)
  • f24cae3 fixing behaviour for group parameter in open_datatree (#9666)
  • 519f05e Use zarr v3 dimension_names (#9669)
  • 5b2e6f1 fix(zarr): use inplace array.resize for zarr 2 and 3 (#9673)
  • 1f5889a implement dask methods on DataTree (#9670)
  • 521b087 support chunks in open_groups and open_datatree (#9660)
  • b133fdc Compatibility for zarr-python 3.x (#9552)
  • 4798707 Update to_dataframe doc to match current behavior (#9662)
  • 5632c8e Reduce graph size through writing indexes directly into graph for ``map_block...
  • Additional commits viewable in compare view

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Summary by Sourcery

Build:

  • Update runtime dependencies in the project, including asteval, netcdf4, numpy, pandas, pydantic, and xarray to their latest versions.

@dependabot
Bump the runtime-dependencies group across 1 directory with 6 updates
9aa51ff 
Bumps the runtime-dependencies group with 6 updates in the / directory:

| Package | From | To |
| --- | --- | --- |
| [asteval](https://github.com/lmfit/asteval) | `1.0.2` | `1.0.5` |
| [netcdf4](https://github.com/Unidata/netcdf4-python) | `1.7.1.post1` | `1.7.2` |
| [numpy](https://github.com/numpy/numpy) | `2.0.1` | `2.1.3` |
| [pandas](https://github.com/pandas-dev/pandas) | `2.2.2` | `2.2.3` |
| [pydantic](https://github.com/pydantic/pydantic) | `2.8.2` | `2.10.1` |
| [xarray](https://github.com/pydata/xarray) | `2024.7.0` | `2024.10.0` |



Updates `asteval` from 1.0.2 to 1.0.5
- [Release notes](https://github.com/lmfit/asteval/releases)
- [Commits](lmfit/asteval@1.0.2...1.0.5)

Updates `netcdf4` from 1.7.1.post1 to 1.7.2
- [Release notes](https://github.com/Unidata/netcdf4-python/releases)
- [Changelog](https://github.com/Unidata/netcdf4-python/blob/master/Changelog)
- [Commits](https://github.com/Unidata/netcdf4-python/commits)

Updates `numpy` from 2.0.1 to 2.1.3
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](numpy/numpy@v2.0.1...v2.1.3)

Updates `pandas` from 2.2.2 to 2.2.3
- [Release notes](https://github.com/pandas-dev/pandas/releases)
- [Commits](pandas-dev/pandas@v2.2.2...v2.2.3)

Updates `pydantic` from 2.8.2 to 2.10.1
- [Release notes](https://github.com/pydantic/pydantic/releases)
- [Changelog](https://github.com/pydantic/pydantic/blob/main/HISTORY.md)
- [Commits](pydantic/pydantic@v2.8.2...v2.10.1)

Updates `xarray` from 2024.7.0 to 2024.10.0
- [Release notes](https://github.com/pydata/xarray/releases)
- [Changelog](https://github.com/pydata/xarray/blob/main/HOW_TO_RELEASE.md)
- [Commits](pydata/xarray@v2024.07.0...v2024.10.0)

---
updated-dependencies:
- dependency-name: asteval
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: runtime-dependencies
- dependency-name: netcdf4
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: runtime-dependencies
- dependency-name: numpy
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: runtime-dependencies
- dependency-name: pandas
  dependency-type: direct:production
  update-type: version-update:semver-patch
  dependency-group: runtime-dependencies
- dependency-name: pydantic
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: runtime-dependencies
- dependency-name: xarray
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: runtime-dependencies
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot bot requested review from a team as code owners November 22, 2024 19:22
@dependabot dependabot bot added dependencies Pull requests that update a dependency file python Pull requests that update Python code labels Nov 22, 2024
@dependabot dependabot bot force-pushed the dependabot/pip/staging/runtime-dependencies-c55036bafb branch from 56d7d92 to 9aa51ff Compare November 22, 2024 19:22
@dependabot dependabot bot requested review from jsnel and s-weigand November 22, 2024 19:22
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sourcery-ai bot commented Nov 22, 2024 •
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Reviewer's Guide by Sourcery

This PR updates several runtime dependencies to their latest versions. The changes primarily consist of version bumps for scientific computing and data analysis libraries, with numpy receiving a notable version constraint update to support versions up to 2.2.

No diagrams generated as the changes look simple and do not need a visual representation.

File-Level Changes

Change Details Files
Update numpy version constraints to support newer versions
  • Modified upper bound constraint from '<2.1' to '<2.2'
  • Maintained minimum version requirement at '>=1.21.2'
 pyproject.toml
requirements_pinned.txt
Update core scientific computing dependencies
  • Upgraded asteval from 1.0.2 to 1.0.5 with improved error handling
  • Upgraded netcdf4 from 1.7.1.post1 to 1.7.2 with new features and bug fixes
  • Upgraded numpy from 2.0.1 to 2.1.3 with performance improvements
  • Upgraded pandas from 2.2.2 to 2.2.3 with bug fixes
 requirements_pinned.txt
Update data validation and analysis libraries
  • Upgraded pydantic from 2.8.2 to 2.10.1 with new features and bug fixes
  • Upgraded xarray from 2024.7.0 to 2024.10.0 with official DataTree support and zarr-python v3 compatibility
 requirements_pinned.txt
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We have skipped reviewing this pull request. It seems to have been created by a bot (hey, dependabot[bot]!). We assume it knows what it's doing!

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Binder 👈 Launch a binder notebook on branch glotaran/pyglotaran/dependabot/pip/staging/runtime-dependencies-c55036bafb

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Quality Gate Passed Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

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dependabot bot commented on behalf of github Nov 29, 2024

Looks like these dependencies are updatable in another way, so this is no longer needed.

@dependabot dependabot bot closed this Nov 29, 2024
@dependabot dependabot bot deleted the dependabot/pip/staging/runtime-dependencies-c55036bafb branch November 29, 2024 19:10
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