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Bump the runtime-dependencies group across 1 directory with 6 updates #1563

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@dependabot dependabot bot commented on behalf of github Dec 13, 2024

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

Package From To
asteval 1.0.3 1.0.5
netcdf4 1.7.1.post2 1.7.2
numpy 2.0.2 2.2.0
pandas 2.2.2 2.2.3
sdtfile 2024.5.24 2024.12.6
xarray 2024.9.0 2024.11.0

Updates asteval from 1.0.3 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
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
  • See full diff in compare view

Updates netcdf4 from 1.7.1.post2 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 2.0.2 to 2.2.0

Release notes

Sourced from numpy's releases.

2.2.0 (Dec 8, 2024)

NumPy 2.2.0 Release Notes

The NumPy 2.2.0 release is quick release that brings us back into sync with the usual twice yearly release cycle. There have been an number of small cleanups, as well as work bringing the new StringDType to completion and improving support for free threaded Python. Highlights are:

  • New functions matvec and vecmat, see below.
  • Many improved annotations.
  • Improved support for the new StringDType.
  • Improved support for free threaded Python
  • Fixes for f2py

This release supports Python versions 3.10-3.13.

Deprecations

  • _add_newdoc_ufunc is now deprecated. ufunc.__doc__ = newdoc should be used instead.

    (gh-27735)

Expired deprecations

  • bool(np.array([])) and other empty arrays will now raise an error. Use arr.size > 0 instead to check whether an array has no elements.

    (gh-27160)

Compatibility notes

  • numpy.cov now properly transposes single-row (2d array) design matrices when rowvar=False. Previously, single-row design matrices would return a scalar in this scenario, which is not correct, so this is a behavior change and an array of the appropriate shape will now be returned.

    (gh-27661)

New Features

  • New functions for matrix-vector and vector-matrix products

    Two new generalized ufuncs were defined:

    • numpy.matvec - matrix-vector product, treating the arguments as stacks of matrices and column vectors,

... (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
  • e7a123b Merge pull request #27928 from charris/prepare-2.2.0
  • d97d071 MAINT: Try fixing MacOS cirrus build failures. [wheel build]
  • 1ed7b67 REL: Prepare for the NumPy 2.2.0 release [wheel build]
  • fd9e7ef Merge pull request #27916 from charris/backport-27915
  • 2e0941f MAINT: Bump actions/cache from 4.1.2 to 4.2.0
  • 013656d Merge pull request #27912 from charris/backport-27877
  • 7895ba6 Merge pull request #27913 from charris/backport-27896
  • ee8d1cd PERF: improve multithreaded ufunc scaling (#27896)
  • 77fff6b ENH: Refactor __qualname__ across API (#27877)
  • b30a338 Merge pull request #27911 from charris/backport-27891
  • 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 sdtfile from 2024.5.24 to 2024.12.6

Release notes

Sourced from sdtfile's releases.

v2024.12.6

Read Becker & Hickl SDT files

Sdtfile is a Python library to read SDT files produced by Becker & Hickl SPCM software. SDT files contain time correlated single photon counting instrumentation parameters and measurement data. Currently only the "Setup & Data", "DLL Data", and "FCS Data" formats are supported.

Changes

  • Fix read MeasureInfo fields as scalars (breaking).
  • Update some structure field names with BH reference (breaking).
  • Parse some SetupBlock binary structures (#7).
  • Include more information in str(SdtFile).
  • Add subtype to FileRevision.

v2024.11.24

Read Becker & Hickl SDT files

Sdtfile is a Python library to read SDT files produced by Becker & Hickl SPCM software. SDT files contain time correlated single photon counting instrumentation parameters and measurement data. Currently only the "Setup & Data", "DLL Data", and "FCS Data" formats are supported.

Changelog

Sourced from sdtfile's changelog.

2024.12.6

  • Fix read MeasureInfo fields as scalars (breaking).
  • Update some structure field names with BH reference (breaking).
  • Parse some SetupBlock binary structures (#7).
  • Include more information in str(SdtFile).
  • Add subtype to FileRevision.

2024.11.24

  • Update MEASURE_INFO_EXT struct to SPCM v.9.9 (breaking).
Commits

Updates xarray from 2024.9.0 to 2024.11.0

Release notes

Sourced from xarray's releases.

v2024.11.0

What's Changed

... (truncated)

Commits

Most Recent Ignore Conditions Applied to This Pull Request
Dependency Name Ignore Conditions
numpy [>= 1.25.a, < 1.26]

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Summary by Sourcery

Build:

  • Update runtime dependencies: asteval to 1.0.5, netcdf4 to 1.7.2, numpy to 2.2.0, pandas to 2.2.3, sdtfile to 2024.12.6, and xarray to 2024.11.0.

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

| Package | From | To |
| --- | --- | --- |
| [asteval](https://github.com/lmfit/asteval) | `1.0.3` | `1.0.5` |
| [netcdf4](https://github.com/Unidata/netcdf4-python) | `1.7.1.post2` | `1.7.2` |
| [numpy](https://github.com/numpy/numpy) | `2.0.2` | `2.2.0` |
| [pandas](https://github.com/pandas-dev/pandas) | `2.2.2` | `2.2.3` |
| [sdtfile](https://github.com/cgohlke/sdtfile) | `2024.5.24` | `2024.12.6` |
| [xarray](https://github.com/pydata/xarray) | `2024.9.0` | `2024.11.0` |



Updates `asteval` from 1.0.3 to 1.0.5
- [Release notes](https://github.com/lmfit/asteval/releases)
- [Commits](lmfit/asteval@1.0.3...1.0.5)

Updates `netcdf4` from 1.7.1.post2 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 2.0.2 to 2.2.0
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](numpy/numpy@v2.0.2...v2.2.0)

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 `sdtfile` from 2024.5.24 to 2024.12.6
- [Release notes](https://github.com/cgohlke/sdtfile/releases)
- [Changelog](https://github.com/cgohlke/sdtfile/blob/master/CHANGES.rst)
- [Commits](cgohlke/sdtfile@v2024.5.24...v2024.12.6)

Updates `xarray` from 2024.9.0 to 2024.11.0
- [Release notes](https://github.com/pydata/xarray/releases)
- [Changelog](https://github.com/pydata/xarray/blob/main/HOW_TO_RELEASE.md)
- [Commits](pydata/xarray@v2024.09.0...v2024.11.0)

---
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: sdtfile
  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] <[email protected]>
@dependabot dependabot bot requested review from a team as code owners December 13, 2024 19:14
@dependabot dependabot bot added dependencies Pull requests that update a dependency file python Pull requests that update Python code labels Dec 13, 2024
@dependabot dependabot bot requested review from jsnel and s-weigand December 13, 2024 19:14
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sourcery-ai bot commented Dec 13, 2024

Reviewer's Guide by Sourcery

This pull request updates several runtime dependencies to their latest versions. The main changes involve updating version constraints in setup.cfg and requirements_dev.txt to accommodate newer versions of numpy (from <2.1 to <2.3) along with version bumps for other packages including asteval, netcdf4, pandas, sdtfile, and xarray.

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

File-Level Changes

Change Details Files
Update numpy version constraint to support newer releases
  • Modified upper bound from <2.1 to <2.3 to allow newer numpy versions
  • Maintains backward compatibility with minimum version requirement of >=1.21.2
setup.cfg
Update asteval package with improved error handling
  • Added more comprehensive error handling tests
  • Fixed error handling that could result in null exceptions
requirements_dev.txt
Update netcdf4 with new features and improvements
  • Added support for os.PathLike arguments for Dataset.fromcdl
  • Added Variable.get_fill_value functionality
  • Added static type hints
requirements_dev.txt
Update pandas with maintenance release changes
  • Includes bug fixes and performance improvements
  • Maintains Python 3.9+ support
requirements_dev.txt
Update sdtfile with structural improvements
  • Fixed reading MeasureInfo fields as scalars
  • Updated structure field names with BH reference
  • Added parsing for some SetupBlock binary structures
requirements_dev.txt
Update xarray with new features and optimizations
  • Added support for GroupBy with chunked arrays
  • Improved performance for rolling reductions with Dask
  • Added new interpolation methods from scipy
  • Fixed writing of DataTree subgroups to zarr or netCDF
requirements_dev.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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dependabot bot commented on behalf of github Dec 29, 2024

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

@dependabot dependabot bot closed this Dec 29, 2024
@dependabot dependabot bot deleted the dependabot/pip/runtime-dependencies-6f68ce9b2a branch December 29, 2024 18:53
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